WO2020219668A1 - Compositions and methods for treating ras-mutant cancers - Google Patents

Compositions and methods for treating ras-mutant cancers Download PDF

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WO2020219668A1
WO2020219668A1 PCT/US2020/029513 US2020029513W WO2020219668A1 WO 2020219668 A1 WO2020219668 A1 WO 2020219668A1 US 2020029513 W US2020029513 W US 2020029513W WO 2020219668 A1 WO2020219668 A1 WO 2020219668A1
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txnrd1
seq
subject
inhibitor
cancer
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PCT/US2020/029513
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French (fr)
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Chun-Hao Huang
Spencer Charles Knight
Scott Lowe
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Memorial Sloan Kettering Cancer Center
Algen Biotechnologies, Inc.
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Priority to US17/604,864 priority Critical patent/US20220193109A1/en
Priority to JP2021562908A priority patent/JP2022529824A/en
Priority to EP20794527.0A priority patent/EP3959199A4/en
Priority to CN202080045296.2A priority patent/CN114025772A/en
Publication of WO2020219668A1 publication Critical patent/WO2020219668A1/en

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    • A61K31/336—Heterocyclic compounds having oxygen as the only ring hetero atom, e.g. fungichromin having three-membered rings, e.g. oxirane, fumagillin
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    • A61K31/35—Heterocyclic compounds having oxygen as the only ring hetero atom, e.g. fungichromin having six-membered rings with one oxygen as the only ring hetero atom
    • A61K31/352—Heterocyclic compounds having oxygen as the only ring hetero atom, e.g. fungichromin having six-membered rings with one oxygen as the only ring hetero atom condensed with carbocyclic rings, e.g. methantheline 
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    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
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    • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
    • A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
    • A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
    • A61K31/7068—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid
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    • C07D303/02—Compounds containing oxirane rings
    • C07D303/38—Compounds containing oxirane rings with hydrocarbon radicals, substituted by carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals
    • C07D303/46—Compounds containing oxirane rings with hydrocarbon radicals, substituted by carbon atoms having three bonds to hetero atoms with at the most one bond to halogen, e.g. ester or nitrile radicals by amide or nitrile radicals
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    • C07D311/02—Heterocyclic compounds containing six-membered rings having one oxygen atom as the only hetero atom, condensed with other rings ortho- or peri-condensed with carbocyclic rings or ring systems
    • C07D311/04—Benzo[b]pyrans, not hydrogenated in the carbocyclic ring
    • C07D311/22—Benzo[b]pyrans, not hydrogenated in the carbocyclic ring with oxygen or sulfur atoms directly attached in position 4
    • C07D311/26—Benzo[b]pyrans, not hydrogenated in the carbocyclic ring with oxygen or sulfur atoms directly attached in position 4 with aromatic rings attached in position 2 or 3
    • C07D311/28—Benzo[b]pyrans, not hydrogenated in the carbocyclic ring with oxygen or sulfur atoms directly attached in position 4 with aromatic rings attached in position 2 or 3 with aromatic rings attached in position 2 only
    • C07D311/30—Benzo[b]pyrans, not hydrogenated in the carbocyclic ring with oxygen or sulfur atoms directly attached in position 4 with aromatic rings attached in position 2 or 3 with aromatic rings attached in position 2 only not hydrogenated in the hetero ring, e.g. flavones
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    • C07D487/22—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00 in which the condensed system contains four or more hetero rings
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    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1137—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against enzymes
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    • C12Y108/01—Oxidoreductases acting on sulfur groups as donors (1.8) with NAD+ or NADP+ as acceptor (1.8.1)
    • C12Y108/01009—Thioredoxin-disulfide reductase (1.8.1.9), i.e. thioredoxin-reductase
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    • C40B40/04—Libraries containing only organic compounds
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
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Definitions

  • the present technology relates generally to compositions and methods for treating, preventing, and/or ameliorating a RAS-mutant cancer in a subject in need thereof.
  • the present technology relates to methods for treating, preventing, and/or ameliorating RAS-mutant pancreatic cancer by administration of a therapeutically effective amount of a TXNRD1 inhibitor.
  • pancreatic ductal adenocarcinoma (PD AC)
  • PD AC pancreatic ductal adenocarcinoma
  • genes that are frequently mutated in PD AC include KRAS, TP53 , CDKN2A , SMAD4 , MLL3 , TGFBR2 , ARID 1 A and SF3B1, EPC1 and ARID 2, ATM , ZIM2, MAP2K4 , NALCN, SLC16A4 , MAGEA6 , ROB02 , KDM6A , PREX2, ERBB2 , MET ; FGFR1, CDK6 , PIK3R3, PIK3CA , BRCA1, BRCA2 , /M/.//2, efc.
  • KRAS is mutated in 95% of PD AC cases. See, e.g., Biankin et al., Nature 491(7424): 399-405 (2012); Waddell et al. , Nature 518(7540):495-501 (2015); and Jones et al., Science 321(5897): 1801-1806 (2008).
  • KRAS protein is a GTPase that plays an important role in cellular signal transduction pathways.
  • KRAS protein is considered to act as a binary ON-OFF switch, cycling between an active guanosine triphosphate (GTP)-bound and inactive guanosine diphosphate (GDP)- bound state.
  • GTP active guanosine triphosphate
  • GDP inactive guanosine diphosphate
  • KRAS is mostly found in the GDP-bound inactive state.
  • Cell-surface receptors transiently promote formation of the active KRAS-GTP, in response to extracellular stimuli.
  • the KRAS mutations in PD AC and other types of cancer are typically missense mutations that render KRAS protein constitutively GTP -bound, resulting in overstimulation of signaling pathways that drive cancer growth.
  • the oncogenic mutant KRAS protein drives tumor progression in multiple cancer types.
  • the mutant KRAS proteins regulate reprogramming of pancreatic acinar cell to ductal cell intraepithelial neoplasia.
  • KRAS is also required in the growth and maintenance of PDAC and other cancers. See, e.g., Ying et al., Cell 149(3):656-70 (2012). Indeed, PDAC is considered to be one of the most“KRAS-addicted” types of cancer.
  • KRAS is considered an important therapeutic target against PDAC and other KRAS mutant cancers. See, e.g., Waters and Der, Cold Spring Harb PerspectMed. 8(9): a031435 (2016).
  • the present disclosure provides methods for treating a RAS-mutant cancer in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a TXNRDl inhibitor selected from the group consisting of auranofm, Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, protoporphyrin IX, an anti-TXNRDl antibody, and any derivatives thereof.
  • a TXNRDl inhibitor selected from the group consisting of auranofm, Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, protoporphyrin IX, an anti-TXNRDl antibody, and any derivatives thereof.
  • the inhibitory nucleic acid comprises a sequence selected from the group consisting of TCTAATATCATTAACACCATGG (SEQ ID NO: 1; human shTXNRDl),
  • TTAATAATAACTTATGATATTA SEQ ID NO: 3; human shTXNRDl
  • TTTAAATGAAAATCCTTCACAT SEQ ID NO: 5; human shTXNRDl
  • TTTTCATTTATCTTCACCCCTA SEQ ID NO: 8; human shTXNRDl
  • the RAS-mutant cancer may be lung cancer (e.g., lung cancer).
  • the RAS-mutant cancer comprises a KRAS, NRAS, or HRAS mutation selected from the group consisting of G12C, G12D, G12V, G12A, G12S, G12R, G13D, G13C, G13S, G13R, G13A, G13V, Q61H, Q61L, Q61R, Q61K, Q61P, and Q61E. Additionally or alternatively, in some embodiments, the KRAS, NRAS, or HRAS mutation is detected via DNA sequencing.
  • the subject displays elevated expression levels of RAS protein (e.g., KRAS, HRAS, NRAS) in cancer cells prior to treatment.
  • RAS protein e.g., KRAS, HRAS, NRAS
  • the subject exhibits one or more signs or symptoms selected from among pain in the upper abdomen that radiates towards the back, loss of appetite or unintended weight loss, depression, new-onset diabetes, blood clots, fatigue, yellowing of skin and the whites of eyes (jaundice), bloating, nausea, and vomiting.
  • the subject harbors one or more point mutations in TP53, CDKN2A, SMAD4, MLL3,
  • TGFBR2 TGFBR2, ARID 1 A, SF3B1, EPC1, ARID2, ATM, ZIM2, MAP2K4, NALCN, SLC16A4, MAGEA6, ROB02, KDM6A, PREX2, ERBB2, MET, FGFR1, CDK6, PIK3R3, PIK3CA, BRCA1, BRCA2, or PALB2.
  • the subject is human.
  • the TXNRDl inhibitor or the inhibitory nucleic acid that inhibits TXNRDl expression may be administered orally, topically, intranasally, systemically, intravenously, subcutaneously, intraperitoneally, intradermally, intraocularly, iontophoretically, transmucosally, or intramuscularly.
  • the TXNRDl inhibitor or the inhibitory nucleic acid is administered daily for 6 weeks or more. In other embodiments, the TXNRDl inhibitor or the inhibitory nucleic acid is administered daily for 12 weeks or more.
  • the methods further comprise separately, sequentially or simultaneously administering one or more additional therapeutic agents to the subject.
  • additional therapeutic agents include, but are not limited to, paclitaxel, gemcitabine, AMG 510, 5-FU (fluorouracil), and irinotecan.
  • the present disclosure provides a method for monitoring the therapeutic efficacy of a TXNRD1 inhibitor in a subject diagnosed with a RAS-mutant cancer comprising: (a) detecting TXNRD1 protein levels in a test sample obtained from the subject after the subject has been administered the TXNRD1 inhibitor; and (b) determining that the TXNRD1 inhibitor is effective when the TXNRD1 protein levels in the test sample are reduced compared to that observed in a control sample obtained from the subject prior to administration of the TXNRD1 inhibitor.
  • TXNRD1 inhibitors include auranofm, Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, protoporphyrin IX, an anti-TXNRDl antibody, an inhibitory nucleic acid that inhibits TXNRD1 expression, or any derivatives thereof.
  • the inhibitory RNA is a shRNA, an antisense oligonucleotide, or a sgRNA.
  • the present disclosure provides a method for inhibiting RAS-mutant cell proliferation in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of at least one TXNRD1 inhibitor, wherein the at least one TXNRD1 inhibitor is selected from the group consisting of auranofm, Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, protoporphyrin IX, an anti-TXNRDl antibody, an inhibitory nucleic acid that inhibits TXNRDl expression, and any derivatives thereof, and wherein the subject suffers from a disease or condition characterized by elevated expression levels and/or increased activity of RAS (e.g ., KRAS, HRAS, NRAS) and/or TXNRDl .
  • the inhibitory nucleic acid comprises a nucle
  • shTXNRDl T A A AT A A A AC T GA AT AT GGT C A (SEQ ID NO: 2; human shTXNRDl), TTAATAATAACTTATGATATTA (SEQ ID NO: 3; human shTXNRDl),
  • TTTAAATGAAAATCCTTCACAT SEQ ID NO: 5; human shTXNRDl
  • TTTTCATTTATCTTCACCCCTA (SEQ ID NO: 8; human shTXNRDl), T T AG A A AG A AT AG AT AC C C A A (SEQ ID NO: 9; human shTXNRDl),
  • TTCGTCACTGACAACGTTGTGA (SEQ ID NO: 12; murine shTxnrdl).
  • TXNRD1 and/or RAS e.g ., KRAS, HRAS, NRAS expression levels are detected via RNA-seq, northern blotting, microarrays, dot or slot blots, fluorescent in situ hybridization, Reverse transcription polymerase chain reaction (RT-PCR), ribonuclease protection assay (RPA), real-time quantitative RT-PCR, high-performance liquid chromatography (HPLC), liquid
  • the method further comprises administering to the subject a therapeutically effective amount of gemcitabine.
  • the method further comprises administering to the subject a therapeutically effective amount of a KRAS g12C inhibitor, optionally wherein the KRAS G12C inhibitor is AMG 510.
  • FIG. 1A shows a schematic diagram illustrating the pipeline used in the present disclosure for discovery of therapeutic targets in KRAS-mutant pancreatic cancer.
  • the pipeline included low multiplicity-of-infection (MOI) transduction of KRAS-mutant pancreatic cancer cells with a clustered regularly interspaced short palindromic repeats based interference (CRISPRi) library (See, e.g., Gilbert et al., Cell 154: 442-451 (2013)), single-cell RNA sequencing (scRNA-seq), genomic alignments and generation of count matrix (See, e.g., Tang et al., Nature Methods 6: 377-382 (2009)), supervised dimensionality reduction, and machine learning algorithms to identify novel targets in which suppression maximally and selectively target cancer cells.
  • MOI low multiplicity-of-infection
  • CRISPRi clustered regularly interspaced short palindromic repeats based interference
  • FIG. IB shows a scatter plot of z-transformed therapeutic scores for several CRISPR target candidates. The therapeutic index was scored across two negative guide RNAs based on a machine learning algorithm, which collectively established negative control benchmarks for identifying therapeutic targets.
  • FIG. 2B shows a heat map illustrating z-transformed therapeutic scores for the top 20 candidate targets.
  • the candidate targets are displayed in descending order based on average rank across the four indicated decision functions from a machine learning algorithm. As shown, TXNRD1 exhibited the highest average rank.
  • FIG. 2C shows a graph depicting weight-averaged decision function scores for therapeutic index across a panel of candidate targets. TXNRD1 emerged as the highest- ranking target.
  • FIG. 3A shows the results of cross-analysis of shRNA-mediated pooled negative selection screening. shRNA-mediated pooled negative selection screening was performed in
  • FIG. 3B shows a bar graph demonstrating validation of candidate genes obtained from FIG. 3A.
  • Competitive proliferation assays were performed in mPDAC cells, mHCC cells, and nontransformed immortalized mouse embryonic fibroblasts (iMEF). These cells were transduced with a Venus + virus carrying an inducible shRNA.
  • the following controls shRNAs were used: Ren.713 (a non-targeting shRNA serving as a negative control),
  • FIG. 3C shows immunoblots illustrating TXNRD1 knockdown in mPDAC, mHCC and iMEF cells.
  • FIG. 3D shows the effect of pharmacological inhibition of TXNRD1 in pancreatic cancer cells.
  • mPDAC cells were treated with increasing doses of auranofm for 72 hours.
  • Relative proliferation was calculated by measuring viable cell numbers, and normalizing to the viable cell numbers of DMSO-treated cells, which were set to 1. Relative proliferation was then plotted as a function of auranofm concentration and fit to an exponential curve.
  • FIG. 3E shows the effect of pharmacological inhibition of TXNRD1 in human pancreatic cancer cells, as measured by the change in viable cell numbers after 72 hours in culture with increasing doses of auranofm.
  • Relative proliferation was calculated by measuring viable cell numbers, and normalizing to the viable cell numbers of DMSO-treated cells, which were set to 1. Relative proliferation was then plotted as a function of auranofm concentration and fit to an exponential curve.
  • L3.3, Colo357, and BXPC3 have wild-type KRAS , and rest of the cell lines harbor a KRAS mutation.
  • FIG. 4D shows the effect of pharmacological inhibition of TXNRD1 as measured by treatment of pancreatic cancer cells with piperlongumine (another TXNRD1 inhibitor) for 72 hours.
  • Cancer cells harboring different KRAS mutations (G12C, G12D, G12V) or wild-type allele were assayed.
  • Relative proliferation was calculated by measuring viable cell numbers, and normalizing to the viable cell numbers of DMSO-treated cells, which were set to 1. Relative proliferation was then plotted as a function of auranofm concentration and fit to an exponential curve.
  • FIGs. 4F-4H show evaluation of changes in the gene signatures upon TXNRDl knockdown in mPDAC cells.
  • Gene set enrichment analysis GSEA was used to evaluate changes in the gene signatures of KRAS dependency (FIG. 4F), pancreatic cancer (FIG.
  • FIG. 5A shows a schematic representation of conditional RNAi experiments.
  • Tet-On competent murine PD AC cells were transduced with TRMPV-Neo-miR-E shRNAs and a luciferase-hygro vector.
  • the transduced cells were selected for G418 and hygromycin resistance, and transplanted into the pancreas of recipient mice.
  • shRNA expression was induced in a subset of mice by doxycycline (dox) supplementation in drinking water and chow.
  • dox doxycycline
  • FIG. 5C shows bioluminescent imaging of representative mice orthotopically transplanted with mPDAC cells harboring the indicated TRMPV-Neo-miR-E shRNAs with and without dox treatment for 7 days. Dox was administered upon disease onset.
  • FIG. 5D shows a bar graph illustrating in vivo tumor weigh reduction caused by auranofm treatment.
  • FIG. 5E shows a bar graph illustrating in vivo effects of auranofm treatment on human pancreatic cancer cell line tumor weights.
  • MIAPaCa-2 KRAS mutant
  • Colo357 KRAS wild-type organoids
  • FIGs. 6A-6B show heat maps illustrating the survival dependency of the indicated cell lines on listed genes. Each column represents a cell line that exhibited the highest average rank and each row represents a gene. Gene dependency score was calculated by taking the average of log2FC (abundance fold change relative to non-diseased tissue) of all corresponding sgRNAs (FIG. 6A) or shRNAs (FIG. 6B). Zero represents no change, negative number represents depletion, and positive number represents an enrichment of indicated cell lines. Un-supervised clustering was used to cluster genes with similar phenotypes. As shown, knocking out or knocking down replication genes RAP1 or PCNA resulted in general lethality to almost all cell lines. In contrast, TXNRD1 is conditionally required for certain cell lines which exhibit similar dependency for KRAS, HRAS, and NRAS.
  • FIGs. 7A-7D show the antiproliferative effects of TXNRD1 inhibitor Auranofm in KRAS-mutant pancreatic cancer cells and potential synergistic inhibitory effects when combined with Gemcitabine.
  • FIG. 7 A shows dose-dependent effects of Auranofm
  • FIG. 7C shows Combination Index (Cl) plots for MIAPaCa-2 (KRAS G12C ) and PSN1 (KRAS g12R ) cells treated with Auranofm in combination with Gemcitabine. According to FIG. 7C, Cl values of ⁇ 1 indicated synergism between Auranofm and Gemcitabine.
  • FIG. 7D shows
  • Each Cl score represents data from at least three independent experiments.
  • FIGs. 8A-8D show the antiproliferative effects of TXNRD1 inhibitor Auranofm in KRAS-mutant pancreatic cancer cells and potential synergistic inhibitory effects when combined with KRAS G12C inhibitor AMG 510.
  • FIG. 8A shows dose-dependent effects of Auranofm, AMG 510, and their combination on MIAPaCa-2 (KRAS G12C ) and PSN1 (KRAS g12R ) pancreatic cancer cell lines.
  • FIG. 8B shows percent growth inhibition at each concentration of Auranofm and AMG 510 in MIAPaCa-2 (KRAS G12C ) and PSN1
  • FIG. 8C shows Cl plots presenting Cl values of ⁇ 1 indicated synergism between Auranofm and AMG 510.
  • FIG. 8D shows Combination Index (Cl) scores for MIAPaCa-2 (KRAS g12C ) and PSN1 (KRAS G12R ) cells treated with Auranofm in combination with AMG 510 at the indicated concentrations. Each Cl score represents data from at least three independent experiments.
  • FIG. 9 shows overall survival in patients with pancreatic adenocarcinoma who have TXNRD1 mRNA upregulation.
  • the present disclosure is based, in part, on the discovery that TXNRDl is a therapeutic target for treating RAS-mutant pancreatic cancer, and that pharmacological inhibition of TXNRD1 in pancreatic cancer cells was effective in treating RAS mutant pancreatic cancer.
  • the term“about” in reference to a number is generally taken to include numbers that fall within a range of 1%, 5%, or 10% in either direction (greater than or less than) of the number unless otherwise stated or otherwise evident from the context (except where such number would be less than 0% or exceed 100% of a possible value).
  • the“administration” of an agent or drug to a subject includes any route of introducing or delivering to a subject a compound to perform its intended function. Administration can be carried out by any suitable route, including orally, intranasally, parenterally (intravenously, intramuscularly, intraperitoneally, or subcutaneously), or topically. Administration includes self-administration and the administration by another.
  • the term“antibody” collectively refers to immunoglobulins or immunoglobulin-like molecules including by way of example and without limitation, IgA, IgD, IgE, IgG and IgM, combinations thereof, and similar molecules produced during an immune response in any vertebrate, for example, in mammals such as humans, goats, rabbits and mice, as well as non-mammalian species, such as shark immunoglobulins.
  • “antibodies” includes intact immunoglobulins) and“antigen binding fragments” specifically bind to a molecule of interest (or a group of highly similar molecules of interest) to the substantial exclusion of binding to other molecules (for example, antibodies and antibody fragments that have a binding constant for the molecule of interest that is at least 10 3 M 1 greater, at least 10 4 M 1 greater or at least 10 5 M 1 greater than a binding constant for other molecules in a biological sample).
  • the term“antibody” also includes genetically engineered forms such as chimeric antibodies (for example, humanized murine antibodies), heteroconjugate antibodies (such as, bispecific antibodies). See also, Pierce Catalog and Handbook, 1994-1995 (Pierce Chemical Co., Rockford, Ill.); Kuby, J., Immunology , 3 rd Ed., W.H. Freeman & Co., New York, 1997.
  • antibody refers to a polypeptide ligand comprising at least a light chain immunoglobulin variable region or heavy chain immunoglobulin variable region which specifically recognizes and binds an epitope of an antigen.
  • Antibodies are composed of a heavy and a light chain, each of which has a variable region, termed the variable heavy (VH) region and the variable light (VL) region. Together, the VH region and the VL region are responsible for binding the antigen recognized by the antibody.
  • VH variable heavy
  • VL variable light
  • immunoglobulin has heavy (H) chains and light (L) chains interconnected by disulfide bonds. There are two types of light chain, lambda (l) and kappa (K). There are five main heavy chain classes (or isotypes) which determine the functional activity of an antibody molecule: IgM, IgD, IgG, IgA and IgE. Each heavy and light chain contains a constant region and a variable region, (the regions are also known as“domains”). In combination, the heavy and the light chain variable regions specifically bind the antigen. Light and heavy chain variable regions contain a“framework” region interrupted by three hypervariable regions, also called “complementarity-determining regions” or“CDRs”.
  • framework region and CDRs have been defined (see, Rabat et al., Sequences of Proteins of Immunological Interest , U.S. Department of Health and Human Services, 1991, which is hereby incorporated by reference).
  • the Rabat database is now maintained online.
  • the sequences of the framework regions of different light or heavy chains are relatively conserved within a species.
  • the framework region of an antibody that is the combined framework regions of the constituent light and heavy chains, largely adopt a b-sheet conformation and the CDRs form loops which connect, and in some cases form part of, the b-sheet structure.
  • framework regions act to form a scaffold that provides for positioning the CDRs in correct orientation by inter chain, non-covalent interactions.
  • the CDRs are primarily responsible for binding to an epitope of an antigen.
  • the CDRs of each chain are typically referred to as CDR1, CDR2, and CDR3, numbered sequentially starting from the N-terminus, and are also typically identified by the chain in which the particular CDR is located.
  • a VH CDR3 is located in the variable domain of the heavy chain of the antibody in which it is found
  • a VL CDRl is the CDR1 from the variable domain of the light chain of the antibody in which it is found.
  • An antibody that binds TXNRD1 protein will have a specific VH region and the VL region sequence, and thus specific CDR sequences.
  • Antibodies with different specificities i.e.
  • immunoglobulin-related compositions refers to antibodies (including monoclonal antibodies, polyclonal antibodies, humanized antibodies, chimeric antibodies, recombinant antibodies, multi-specific antibodies, bispecific antibodies, etc.,) as well as antibody fragments. An antibody or antigen binding fragment thereof specifically binds to an antigen.
  • antibody-related polypeptide means antigen-binding antibody fragments, including single-chain antibodies, that can comprise the variable region(s) alone, or in combination, with all or part of the following polypeptide elements: hinge region, CHi, CFh, and CFE domains of an antibody molecule. Also included in the technology are any combinations of variable region(s) and hinge region, CHi, CFh, and CFE domains.
  • Antibody-related molecules useful in the present methods e.g ., but are not limited to, Fab, Fab' and F(ab')2, Fd, single-chain Fvs (scFv), single-chain antibodies, disulfide- linked Fvs (sdFv) and fragments comprising either a VL or VH domain.
  • Examples include: (i) a Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CHi domains; (ii) a F(ab')2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the VH and CHi domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al. , Nature 341 : 544-546, 1989), which consists of a VH domain; and (vi) an isolated complementarity determining region (CDR).
  • CDR complementarity determining region
  • antibody fragments or “antigen binding fragments” can comprise a portion of a full length antibody, generally the antigen binding or variable region thereof.
  • antibody fragments or antigen binding fragments include Fab, Fab 1 , F(ab')2, and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules; and multi-specific antibodies formed from antibody fragments.
  • antigen binding fragment refers to a fragment of the whole immunoglobulin structure which possesses a part of a polypeptide responsible for binding to antigen.
  • antigen binding fragment useful in the present technology include scFv, (SCFV)2, SCFVFC, Fab, Fab' and F(ab')2, but are not limited thereto.
  • the term“diabodies” refers to small antibody fragments with two antigen-binding sites, which fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) in the same polypeptide chain (VH VL).
  • VH heavy-chain variable domain
  • VL light-chain variable domain
  • VH VL polypeptide chain
  • the terms“single-chain antibodies” or“single-chain Fv (scFv)” refer to an antibody fusion molecule of the two domains of the Fv fragment, VL and VH.
  • Single-chain antibody molecules may comprise a polymer with a number of individual molecules, for example, dimer, trimer or other polymers.
  • the two domains of the F v fragment, VL and VH are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single-chain F v (scF v )).
  • Such single-chain antibodies can be prepared by recombinant techniques or enzymatic or chemical cleavage of intact antibodies.
  • any of the above-noted antibody fragments are obtained using conventional techniques known to those of skill in the art, and the fragments are screened for binding specificity and neutralization activity in the same manner as are intact antibodies.
  • nucleic acid sequence refers to an oligonucleotide which, when aligned with the nucleic acid sequence such that the 5' end of one sequence is paired with the 3' end of the other, is in“antiparallel association.”
  • sequence“5'-A-G-T-3'” is complementary to the sequence “3'-T-C-A-5”
  • bases not commonly found in naturally-occurring nucleic acids may be included in the nucleic acids described herein. These include, for example, inosine, 7- deazaguanine, Locked Nucleic Acids (LNA), and Peptide Nucleic Acids (PNA).
  • duplex stability need not be perfect; stable duplexes may contain mismatched base pairs, degenerative, or unmatched bases.
  • Those skilled in the art of nucleic acid technology can determine duplex stability empirically considering a number of variables including, for example, the length of the oligonucleotide, base composition and sequence of the
  • a complementary sequence can also be an RNA sequence complementary to the DNA sequence or its complementary sequence, and can also be a cDNA.
  • the term“consensus FR” means a framework (FR) antibody region in a consensus immunoglobulin sequence. The FR regions of an antibody do not contact the antigen.
  • control is an alternative sample used in an experiment for comparison purpose.
  • a control can be "positive” or “negative.”
  • a positive control a compound or composition known to exhibit the desired therapeutic effect
  • a negative control a subject or a sample that does not receive the therapy or receives a placebo
  • the term“effective amount” refers to a quantity sufficient to achieve a desired therapeutic and/or prophylactic effect, e.g ., an amount which results in the prevention of, or a decrease in a disease or condition described herein or one or more signs or symptoms associated with a disease or condition described herein.
  • the amount of a composition administered to the subject will vary depending on the composition, the degree, type, and severity of the disease and on the characteristics of the individual, such as general health, age, sex, body weight and tolerance to drugs. The skilled artisan will be able to determine appropriate dosages depending on these and other factors.
  • the compositions can also be administered in combination with one or more additional therapeutic compounds.
  • the therapeutic compositions may be administered to a subject having one or more signs or symptoms of a RAS-mutant cancer.
  • a“therapeutically effective amount” of a composition refers to composition levels in which the physiological effects of a disease or condition are ameliorated or eliminated.
  • a therapeutically effective amount can be given in one or more administrations.
  • “expression” includes one or more of the following: transcription of the gene into precursor mRNA; splicing and other processing of the precursor mRNA to produce mature mRNA; mRNA stability; translation of the mature mRNA into protein (including codon usage and tRNA availability); and glycosylation and/or other modifications of the translation product, if required for proper expression and function.
  • the term“gene” means a segment of DNA that contains all the information for the regulated biosynthesis of an RNA product, including promoters, exons, introns, and other untranslated regions that control expression.
  • Homology or“identity” or“similarity” refers to sequence similarity between two peptides or between two nucleic acid molecules. Homology can be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same nucleobase or amino acid, then the molecules are homologous at that position. A degree of homology between sequences is a function of the number of matching or homologous positions shared by the sequences.
  • a polynucleotide or polynucleotide region has a certain percentage (for example, at least 60%, 65%, 70%, 75%, 80%, 85%,
  • “sequence identity” to another sequence means that, when aligned, that percentage of bases (or amino acids) are the same in comparing the two sequences.
  • This alignment and the percent homology or sequence identity can be determined using software programs known in the art.
  • default parameters are used for alignment.
  • One alignment program is BLAST, using default parameters.
  • Bioly equivalent polynucleotides are those having the specified percent homology and encoding a polypeptide having the same or similar biological activity. Two sequences are deemed“unrelated” or“non-homologous” if they share less than 40% identity, or less than 25% identity, with each other.
  • hypervariable region refers to the amino acid residues of an antibody which are responsible for antigen-binding.
  • the hypervariable region generally comprises amino acid residues from a“complementarity determining region” or“CDR” (e.g, around about residues 24-34 (LI), 50-56 (L2) and 89-97 (L3) in the VL, and around about 31- 35B (HI), 50-65 (H2) and 95-102 (H3) in the VH (Kabat et al. , Sequences of Proteins of Immunological Interest , 5th Ed. Public Health Service, National Institutes of Health,
  • CDR complementarity determining region
  • residues from a“hypervariable loop” e.g, residues 26- 32 (LI), 50-52 (L2) and 91-96 (L3) in the VL, and 26-32 (HI), 52A-55 (H2) and 96-101 (H3) in the VH (Chothia and Lesk J Mol. Biol. 196:901-917 (1987)).
  • hybridize refers to a process where two substantially complementary nucleic acid strands (at least about 65% complementary over a stretch of at least 14 to 25 nucleotides, at least about 75%, or at least about 90% complementary) anneal to each other under appropriately stringent conditions to form a duplex or heteroduplex through formation of hydrogen bonds between complementary base pairs.
  • Nucleic acid hybridization techniques are well known in the art. See , e.g, Sambrook, et al., 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Press, Plainview, N.Y.
  • Hybridization and the strength of hybridization is influenced by such factors as the degree of complementarity between the nucleic acids, stringency of the conditions involved, and the thermal melting point (T m ) of the formed hybrid.
  • T m thermal melting point
  • specific hybridization occurs under stringent hybridization conditions.
  • An oligonucleotide or polynucleotide e.g ., a probe or a primer
  • a probe or a primer that is specific for a target nucleic acid will “hybridize” to the target nucleic acid under suitable conditions.
  • oligonucleotide refers to a molecule that has a sequence of nucleic acid bases on a backbone comprised mainly of identical monomer units at defined intervals. The bases are arranged on the backbone in such a way that they can bind with a nucleic acid having a sequence of bases that are complementary to the bases of the oligonucleotide.
  • the most common oligonucleotides have a backbone of sugar phosphate units. A distinction may be made between oligodeoxyribonucleotides that do not have a hydroxyl group at the 2' position and oligoribonucleotides that have a hydroxyl group at the 2' position.
  • Oligonucleotides may also include derivatives, in which the hydrogen of the hydroxyl group is replaced with organic groups, e.g., an allyl group.
  • oligonucleotide may also be modified to include a phosphorothioate bond (e.g, one of the two oxygen atoms in the phosphate backbone which is not involved in the internucleotide bridge, is replaced by a sulfur atom) to increase resistance to nuclease degradation.
  • a phosphorothioate bond e.g, one of the two oxygen atoms in the phosphate backbone which is not involved in the internucleotide bridge, is replaced by a sulfur atom
  • the exact size of the oligonucleotide will depend on many factors, which in turn depend on the ultimate function or use of the oligonucleotide.
  • the oligonucleotide may be generated in any manner, including, for example, chemical synthesis, DNA replication, restriction endonuclease digestion of plasmids or phage DNA, reverse transcription, PCR, or a combination thereof.
  • the oligonucleotide may be modified e.
  • the term“pharmaceutically-acceptable carrier” is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal compounds, isotonic and absorption delaying compounds, and the like, compatible with pharmaceutical administration.
  • Pharmaceutically-acceptable carriers and their formulations are known to one skilled in the art and are described, for example, in Remington's
  • polynucleotide or“nucleic acid” means any RNA or DNA, which may be unmodified or modified RNA or DNA.
  • Polynucleotides include, without limitation, single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, RNA that is mixture of single- and double-stranded regions, and hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double- stranded regions.
  • polynucleotide refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA.
  • the term polynucleotide also includes DNAs or RNAs containing one or more modified bases and DNAs or RNAs with backbones modified for stability or for other reasons.
  • “prevention,”“prevent,” or“preventing” of a disorder or condition refers to one or more compounds that, in a statistical sample, reduces the occurrence of the disorder or condition in the treated sample relative to an untreated control sample, or delays the onset of one or more symptoms of the disorder or condition relative to the untreated control sample.
  • preventing a RAS-mutant cancer includes preventing or delaying the initiation of symptoms of a RAS-mutant cancer.
  • prevention of a RAS-mutant cancer also includes preventing a recurrence of one or more signs or symptoms of a RAS-mutant cancer.
  • sample refers to clinical samples obtained from a subject.
  • Biological samples may include tissues, cells, protein or membrane extracts of cells, mucus, sputum, bone marrow, bronchial alveolar lavage (BAL), bronchial wash (BW), and biological fluids (e.g ., ascites fluid or cerebrospinal fluid (CSF)) isolated from a subject, as well as tissues, cells and fluids (blood, plasma, saliva, urine, serum etc.) present within a subject.
  • BAL bronchial alveolar lavage
  • BW bronchial wash
  • biological fluids e.g ., ascites fluid or cerebrospinal fluid (CSF)
  • the term“separate” therapeutic use refers to an administration of at least two active ingredients at the same time or at substantially the same time by different routes.
  • the term“sequential” therapeutic use refers to administration of at least two active ingredients at different times, the administration route being identical or different. More particularly, sequential use refers to the whole administration of one of the active ingredients before administration of the other or others commences. It is thus possible to administer one of the active ingredients over several minutes, hours, or days before administering the other active ingredient or ingredients. There is no simultaneous treatment in this case.
  • the term“simultaneous” therapeutic use refers to the administration of at least two active ingredients by the same route and at the same time or at substantially the same time.
  • the individual, patient or subject is a human.
  • target sequence and“target nucleic acid sequence” refer to a specific nucleic acid sequence to be modulated ( e.g ., inhibited or downregulated).
  • TXNRD1 inhibitor refers to an agent that inhibits gene expression or biological activity of TXNRD1.
  • TXNRD1 biological activity include, but are not limited to, enzymatic activity, substrate binding activity, homo- or hetero dimerization activity, and binding to a cellular structure.
  • thioredoxin reductase 1 Several different isoforms of thioredoxin reductase 1 exist.
  • the TXNRD1 inhibitors of the present disclosure inhibit at least one biological activity of at least one isoform.
  • TXNRD1 inhibitors include, but are not limited to, auranofm, Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, protoporphyrin IX, shRNAs or siRNAs against TXNRD1, anti-sense oligonucleotides against TXNRD1, anti- TXNRD1 antibodies, or any derivatives thereof.
  • Treating”,“treat”, or“treatment” covers the treatment of a disease or disorder described herein, in a subject, such as a human, and includes: (i) inhibiting a disease or disorder, i.e., arresting its development; (ii) relieving a disease or disorder, i.e., causing regression of the disorder; (iii) slowing progression of the disorder; and/or (iv) inhibiting, relieving, or slowing progression of one or more symptoms of the disease or disorder.
  • treatment means that the symptoms associated with the disease are, e.g., alleviated, reduced, cured, or placed in a state of remission.
  • the various modes of treatment or prevention of medical diseases and conditions as described are intended to mean“substantial,” which includes total but also less than total treatment or prevention, and wherein some biologically or medically relevant result is achieved.
  • the treatment may be a continuous prolonged treatment for a chronic disease or a single, or few time administrations for the treatment of an acute condition.
  • TXNRD1 protein (also known as, thioredoxin reductase 1, GRIM-12, TR, TR1, TRXRl, or TXNR) is a member of the pyridine nucleotide oxidoreductase family, and is a component of the thioredoxin (Trx) system.
  • TXNRDl is a flavoenzyme, which reduces thioredoxins, as well as other substrates, and plays a key role in redox homoeostasis and selenium metabolism.
  • TXNRDl protein functions as a homodimer containing FAD, and has a selenocysteine (Sec) at the active site.
  • the present disclosure provides compositions for treating a RAS-mutant cancer.
  • the TXNRDl inhibitor reduces gene expression and/or activity levels of TXNRDl.
  • the TXNRDl inhibitor reduces a TXNRDl activity selected from the group consisting of enzymatic activity, substrate binding activity, homo- or hetero-dimerization activity, and binding to a cellular structure.
  • the present disclosure provides pharmacological inhibitors including, but not limited to, auranofm, Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, and protoporphyrin IX.
  • pharmacological inhibitors including, but not limited to, auranofm, Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, and protoporphyrin IX.
  • Anti- TXNRDl antibodies or any derivatives thereof, may also be used in the methods disclosed herein.
  • the present disclosure provides inhibitory RNAs (e.g., sgRNAs, antisense RNAs or shRNAs) that inhibit TXNRDl expression and/or activity levels.
  • inhibitory RNAs e.g., sgRNAs, antisense RNAs or shRNAs
  • inhibitory RNAs include those with sequences comprising
  • TTAATAATAACTTATGATATTA SEQ ID NO: 3; human shTXNRDl
  • TTTAAATGAAAATCCTTCACAT SEQ ID NO: 5; human shTXNRDl
  • TTTTCATTTATCTTCACCCCTA SEQ ID NO: 8; human shTXNRDl
  • TTT AGTC AC AGGGT AATTCGT C (SEQ ID NO: 11; murine shTxnrdl), and TTCGTCACTGACAACGTTGTGA (SEQ ID NO: 12; murine shTxnrdl), or any complement thereof.
  • the present disclosure provides an antisense nucleic acid comprising a nucleic acid sequence that is complementary to and specifically hybridizes with a portion of any one of
  • NM_182729.2 Homo sapiens thioredoxin reductase 1 (TXNRD1), transcript variant 1, mRNA (SEQ ID NO: 13)
  • NM_182742.2 Homo sapiens thioredoxin reductase 1 (TXNRD1), transcript variant 2, mRNA (SEQ ID NO: 14)
  • TXNRD1 Homo sapiens thioredoxin reductase 1 (TXNRD1), transcript variant 3, mRNA
  • TXNRD1 thioredoxin reductase 1
  • transcript variant 4 mRNA NCBI Reference Sequence: NM_003330.3 (SEQ ID NO: 16)
  • TXNRD1 Homo sapiens thioredoxin reductase 1 (TXNRD1), transcript variant 5, mRNA
  • TXNRD1 Homo sapiens thioredoxin reductase 1 (TXNRD1), transcript variant 6, mRNA
  • TXNRD1 thioredoxin reductase 1
  • NCBI Reference Sequence NM 001042523.1 (SEQ ID NO: 23)
  • the antisense nucleic acid may be antisense RNA, or antisense DNA.
  • Antisense nucleic acids based on the known TXNRD1 gene sequence can be readily designed and engineered using methods known in the art.
  • the antisense nucleic acid comprises the nucleic acid sequence of any one of SEQ ID NOs: 1-12, or a complement thereof.
  • Antisense nucleic acids are molecules which are complementary to a sense nucleic acid strand, e.g ., complementary to the coding strand of a double-stranded DNA molecule (or cDNA) or complementary to an mRNA sequence. Accordingly, an antisense nucleic acid can form hydrogen bonds with a sense nucleic acid.
  • the antisense nucleic acid can be
  • the antisense nucleic acid is an oligonucleotide which is complementary to only a portion of the coding region of TXNRD1 mRNA.
  • an antisense nucleic acid molecule can be complementary to a noncoding region of the TXNRD1 coding strand.
  • the noncoding region refers to the 5' and 3' untranslated regions that flank the coding region and are not translated into amino acids.
  • the antisense is not translated into amino acids.
  • oligonucleotide can be complementary to the region surrounding the translation start site of TXNRD1.
  • An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length.
  • an antisense nucleic acid can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art.
  • an antisense nucleic acid e.g, an antisense oligonucleotide
  • an antisense nucleic acid can be chemically synthesized using naturally occurring nucleotides or modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids, e.g, phosphorothioate derivatives and acridine substituted nucleotides.
  • modified nucleotides which can be used to generate the antisense nucleic acid include 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-hodouracil,
  • hypoxanthine xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl)uracil, 5- carboxymethylaminomethyl-2-thouridine, 5-carboxymethylaminometh-yluracil,
  • dihydrouracil beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-metnylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5- methoxyaminom ethyl-2 -thiouracil, beta-D-mannosylqueosine, 5'- methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopenten-yladenine, uracil- 5-oxyacetic acid (v), wybutosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2- thiouracil, 2-thlouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid
  • the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e ., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest).
  • the antisense nucleic acid molecules may be administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding the protein of interest to thereby inhibit expression of the protein, e.g. , by inhibiting transcription and/or translation.
  • the hybridization can occur via Watson-Crick base pairing to form a stable duplex, or in the case of an antisense nucleic acid molecule which binds to DNA duplexes, through specific interactions in the major groove of the double helix.
  • the antisense nucleic acid molecules are modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecules to peptides or antibodies which bind to cell surface receptors or antigens.
  • the antisense nucleic acid molecule is an alpha-anomeric nucleic acid molecule.
  • An alpha-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual b- units, the strands run parallel to each other (Gaultier et al., Nucleic Acids. Res. 15:6625- 6641(1987)).
  • the antisense nucleic acid molecule can also comprise a 2'-0 - methylribonucleotide (Inoue et al., Nucleic Acids Res. 15:6131-6148 (1987)) or a chimeric RNA-DNA analogue (Inoue et al., FEBS Lett. 215:327-330 (1987)).
  • the present disclosure also provides a short hairpin RNA (shRNA) or small interfering RNA (siRNA) comprising a nucleic acid sequence that is complementary to and specifically hybridizes with a portion of any one of SEQ ID NOs: 13-23 (TXNRDl mRNA isoforms), thereby reducing or inhibiting TXNRDl expression.
  • shRNA or siRNA is about 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29 base pairs in length.
  • Double-stranded RNA (dsRNA) can induce sequence-specific post-transcriptional gene silencing (e.g., RNA interference (RNAi)) in many organisms such as C. elegans,
  • RNAi is a process that interferes with or significantly reduces the number of protein copies made by an mRNA.
  • a double-stranded siRNA or shRNA molecule is engineered to complement and hybridize to a mRNA of a target gene. Following intracellular delivery, the siRNA or shRNA molecule associates with an RNA-induced silencing complex (RISC), which then binds and degrades a complementary target mRNA (such as TXNRD1 mRNA).
  • RISC RNA-induced silencing complex
  • the shRNA or siRNA comprises the nucleic acid sequence of any one of SEQ ID NOs: 1-12.
  • the present disclosure also provides a ribozyme comprising a nucleic acid sequence that is complementary to and specifically hybridizes with a portion of any one of SEQ ID NOs: 13-23 (TXNRDl mRNA isoforms), thereby reducing or inhibiting TXNRD1 expression.
  • Ribozymes are catalytic RNA molecules with ribonuclease activity which are capable of cleaving a complementary single-stranded nucleic acid, such as an mRNA.
  • ribozymes e.g ., hammerhead ribozymes (described in Haselhoff and Gerlach, Nature 334:585-591 (1988))
  • ribozymes can be used to catalytically cleave TXNRDl transcripts, thereby inhibiting translation of TXNRDl.
  • a ribozyme having specificity for a TXNRDl-e ncoding nucleic acid can be designed based upon a TXNRDl nucleic acid sequence disclosed herein.
  • a derivative of a Tetrahymena L-19 IV S RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in a TXNRDl -mcodlmg mRNA. See, e.g., U.S. Pat. No. 4,987,071 and U.S. Pat. No. 5,116,742.
  • TXNRDl mRNA can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel and Szostak (1993) Science 261 : 1411-1418, incorporated herein by reference.
  • the present disclosure also provides a synthetic guide RNA (sgRNA) comprising a nucleic acid sequence that is complementary to and specifically hybridizes with a portion of any one of SEQ ID NOs: 13-23 (TXNRDl mRNA isoforms).
  • Guide RNAs for use in CRISPR-Cas systems are typically generated as a single guide RNA comprising a crRNA segment and a tracrRNA segment.
  • the crRNA segment and a tracrRNA segment can also be generated as separate RNA molecules.
  • the crRNA segment comprises the targeting sequence that binds to a portion of any one of SEQ ID NOs: 13-23 (TXNRDl mRNA isoforms), and a stem portion that hybridizes to a tracrRNA.
  • the tracrRNA segment comprises a nucleotide sequence that is partially or completely complementary to the stem sequence of the crRNA and a nucleotide sequence that binds to the CRISPR enzyme.
  • the crRNA segment and the tracrRNA segment are provided as a single guide RNA.
  • the crRNA segment and the tracrRNA segment are provided as separate RNAs.
  • the combination of the CRISPR enzyme with the crRNA and tracrRNA make up a functional CRISPR-Cas system. Exemplary CRISPR-Cas systems for targeting nucleic acids, are described, for example, in WO2015/089465.
  • a synthetic guide RNA is a single RNA represented as comprising the following elements:
  • XI and X2 represent the crRNA segment, where XI is the targeting sequence that binds to a portion of any one of SEQ ID NOs: 13-23, X2 is a stem sequence the hybridizes to a tracrRNA, Z represents a tracrRNA segment comprising a nucleotide sequence that is partially or completely complementary to X2, and Y represents a linker sequence.
  • the linker sequence comprises two or more nucleotides and links the crRNA and tracrRNA segments. In some embodiments, the linker sequence comprises 2, 3, 4, 5, 6,
  • the linker is the loop of the hairpin structure formed when the stem sequence hybridized with the tracrRNA.
  • a synthetic guide RNA is provided as two separate RNAs where one RNA represents a crRNA segment: 5'-Xl-X2-3' where XI is the targeting sequence that binds to a portion of any one of SEQ ID NOs: 13-23, X2 is a stem sequence the hybridizes to a tracrRNA, and one RNA represents a tracrRNA segment, Z, that is a separate RNA from the crRNA segment and comprises a nucleotide sequence that is partially or completely complementary to X2 of the crRNA.
  • a stem sequence includes any sequence that has sufficient complementarity with a complementary sequence in the tracrRNA to promote formation of a CRISPR complex at a target sequence, wherein the CRISPR complex comprises the stem sequence hybridized to the tracrRNA.
  • degree of complementarity is with reference to the optimal alignment of the stem and complementary sequence in the tracrRNA, along the length of the shorter of the two sequences. Optimal alignment may be determined by any suitable alignment algorithm, and may further account for secondary structures, such as self-complementarity within either the stem sequence or the complementary sequence in the tracrRNA.
  • the degree of complementarity between the stem sequence and the complementary sequence in the tracrRNA along the length of the shorter of the two when optimally aligned is about or more than about 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97.5%, 99%, or higher.
  • the stem sequence is about or more than about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, or more nucleotides in length.
  • the stem sequence and complementary sequence in the tracrRNA are contained within a single RNA, such that hybridization between the two produces a transcript having a secondary structure, such as a hairpin.
  • the tracrRNA has additional complementary sequences that form hairpins. In some embodiments, the tracrRNA has at least two or more hairpins. In some embodiments, the tracrRNA has two, three, four or five hairpins. In some embodiments, the tracrRNA has at most five hairpins.
  • the portion of the sequence 5' of the final“N” and upstream of the loop corresponds to the crRNA stem sequence
  • the portion of the sequence 3' of the loop corresponds to the tracrRNA sequence.
  • single polynucleotides comprising a guide sequence, a stem sequence, and a tracr sequence are as follows (listed 5' to 3'), where“N” represents a base of a guide sequence ( e.g . a modified oligonucleotide provided herein), the first block of lower case letters represent stem sequence, and the second block of lower case letters represent the tracrRNA sequence, and the final poly-T sequence represents the transcription terminator: (a)
  • oligonucleotides for use in as a targeting sequence in a CRISPR Cas system depends on several factors including the particular CRISPR enzyme to be used and the presence of corresponding proto-spacer adjacent motifs (PAMs) downstream of the target sequence in the target nucleic acid.
  • PAMs proto-spacer adjacent motifs
  • a suitable PAM is 5'- NRG or 5'-NNGRR (where N is any Nucleotide) for SpCas9 or SaCas9 enzymes (or derived enzymes), respectively.
  • the PAM sequences should be present between about 1 to about 10 nucleotides of the target sequence to generate efficient cleavage of the target nucleic acid.
  • the guide RNA forms a complex with the CRISPR enzyme, the complex locates the target and PAM sequence, unwinds the DNA duplex, and the guide RNA anneals to the complementary sequence on the opposite strand. This enables the Cas9 nuclease to create a double-strand break.
  • the sgRNA comprises the nucleic acid sequence of any one of SEQ ID NOs: 1-12.
  • CRISPR enzymes are available for use in conjunction with the disclosed guide RNAs of the present disclosure.
  • the CRISPR enzyme is a Type II CRISPR enzyme.
  • the CRISPR enzyme catalyzes DNA cleavage.
  • the CRISPR enzyme catalyzes RNA cleavage.
  • the CRISPR enzyme is any Cas9 protein, for instance any naturally-occurring bacterial Cas9 as well as any chimeras, mutants, homologs or orthologs.
  • Cas proteins include Casl, CaslB, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csnl and Csxl2), CaslO, Csyl, Csy2, Csy3, Csel, Cse2, Cscl, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3, Csxl, Csxl5, Csfl, Csf2, Csf3, Csf4, homologues thereof, or modified variants thereof.
  • the CRISPR enzyme cleaves both strands of the target nucleic acid at the Protospacer
  • the CRISPR enzyme is a nickase, which cleaves only one strand of the target nucleic acid.
  • the CRISPR enzyme is a dCas9 tagged with additional enzyme activities, which suppress or activate the expression of genes of interest.
  • compositions comprising a TXNRD1 inhibitor.
  • the pharmaceutical compositions of the present disclosure may be prepared by any of the methods known in the pharmaceutical arts.
  • the amount of active ingredient that can be combined with a carrier material to produce a single dosage form will vary depending upon the host being treated and the particular mode of administration.
  • the amount of active ingredient that can be combined with a carrier material to produce a single dosage form will generally be that amount of the compound that produces a therapeutic effect.
  • the amount of active compound will be in the range of about 0.1 to 99 percent, more typically, about 5 to 70 percent, and more typically, about 10 to 30 percent.
  • compositions of the present technology may contain one or more pharmaceutically-acceptable carriers, which as used herein, generally refers to a pharmaceutically-acceptable composition, such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g ., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, useful for introducing the active agent into the body.
  • a pharmaceutically-acceptable carriers such as a liquid or solid filler, diluent, excipient, manufacturing aid (e.g ., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, useful for introducing the active agent into the body.
  • aqueous and non-aqueous carriers examples include, for example, water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), vegetable oils (such as olive oil), and injectable organic esters (such as ethyl oleate), and suitable mixtures thereof.
  • polyols such as glycerol, propylene glycol, polyethylene glycol, and the like
  • vegetable oils such as olive oil
  • injectable organic esters such as ethyl oleate
  • the formulations may include one or more of sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients, such as cocoa butter and suppository waxes; oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, com oil and soybean oil; glycols, such as propylene glycol; polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; esters, such as ethyl oleate and ethyl laurate; agar; alginic acid; buffering agents, such as magnesium hydroxide and aluminum hydroxide; pyrogen-free water; isotonic sa
  • sugars such as lacto
  • auxiliary agents such as wetting agents, emulsifiers, lubricants (e.g ., sodium lauryl sulfate and magnesium stearate), coloring agents, release agents, coating agents, sweetening agents, flavoring agents, preservative agents, and antioxidants can also be included in the pharmaceutical composition of the present technology.
  • antioxidants include: water soluble antioxidants, such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabi sulfite, sodium sulfite, and the like; oil-soluble antioxidants, such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propyl gallate, alpha-tocopherol, and the like; and metal chelating agents, such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like.
  • water soluble antioxidants such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabi sulfite, sodium sulfite, and the like
  • oil-soluble antioxidants such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT
  • pharmaceutical formulation includes an excipient selected from, for example, celluloses, liposomes, lipid nanoparticles, micelle-forming agents (e.g., bile acids), and polymeric carriers, e.g., polyesters and polyanhydrides.
  • Suspensions in addition to the active compounds, may contain suspending agents, such as, for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.
  • antibacterial and antifungal agents such as, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. It may also be desirable to include isotonic agents, such as sugars, sodium chloride, and the like into the compositions.
  • isotonic agents such as sugars, sodium chloride, and the like into the compositions.
  • prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents that delay absorption, such as aluminum monostearate and gelatin.
  • One aspect of the present technology includes methods of treating a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1. Additionally or alternatively, in some embodiments, the present technology includes methods of treating a RAS-mutant cancer.
  • the three major isoforms of RAS (KRAS, NRAS, and HRAS) together are mutated in about 20% of human cancers, primarily in the active site at residues G12, G13, and Q61 near the g-phosphate of the guanosine triphosphate (GTP) substrate (See Marcus & Mattos, Clin Cancer Res 21(8): 1810-1818 (2015)).
  • the RAS-mutant cancer comprises a KRAS, NRAS, or HRAS mutation selected from the group consisting of G12C, G12D, G12V, G12A, G12S, G12R, G13D, G13C, G13S, G13R, G13A, G13V, Q61H, Q61L, Q61R, Q61K, Q61P, and Q61E.
  • the present technology includes methods of treating a
  • the present disclosure provides a method for inhibiting proliferation of a RAS-mutant cancer in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of at least one TXNRD1 inhibitor disclosed herein, and wherein the subject suffers from a RAS-mutant cancer characterized by elevated expression levels and/or increased activity of TXNRD1.
  • the subject is diagnosed as having, suspected as having, or at risk of having a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1. Additionally or alternatively, in some embodiments, the subject is diagnosed as having a RAS-mutant cancer.
  • the RAS- mutant cancer comprises a KRAS, NRAS, or HRAS mutation selected from the group consisting of G12C, G12D, G12V, G12A, G12S, G12R, G13D, G13C, G13S, G13R, G13A, G13V, Q61H, Q61L, Q61R, Q61K, Q61P, and Q61E.
  • the subject is diagnosed as having lung cancer (e.g ., lung adenocarcinoma), mucinous adenoma, pancreatic cancer (e.g., PDAC), colorectal cancer, skin cancer (e.g., melanoma), endometrial cancer, testicular germ cell cancer, or adrenal gland cancer.
  • lung cancer e.g ., lung adenocarcinoma
  • pancreatic cancer e.g., PDAC
  • colorectal cancer e.g., skin cancer (e.g., melanoma)
  • endometrial cancer e.g., testicular germ cell cancer, or adrenal gland cancer.
  • the subject is diagnosed as having pancreatic cancer.
  • the subject is diagnosed as having a RAS-mutant pancreatic cancer.
  • compositions or medicaments comprising a TXNRD1 inhibitor disclosed herein are administered to a subject suspected of, or already suffering from such a disease or condition (such as, a subject diagnosed with a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1 and/or a subject diagnosed with a RAS-mutant cancer and/or a subject diagnosed with pancreatic cancer), in an amount sufficient to cure, or at least partially arrest, the symptoms of the disease, including its complications and intermediate pathological phenotypes in development of the disease.
  • a subject suspected of, or already suffering from such a disease or condition such as, a subject diagnosed with a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1 and/or a subject diagnosed with a RAS-mutant cancer and/or a subject diagnosed with pancreatic cancer
  • Subjects suffering from a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1 and/or a subject diagnosed with a RAS-mutant cancer can be identified by any or a combination of diagnostic or prognostic assays known in the art.
  • the subject may exhibit one or more mutations in KRAS.
  • the subject may exhibit one or more mutations in at least one of TP53, CDKN2A , SMAD4 , MLL3 , TGFBR2 , ARID l A and SF3B1, EPC1 and ARID2 , ATM, ZIM2 , MAP2K4 ,
  • the subject may exhibit at least one mutation in one or more of a core set of twelve cellular signaling pathways and processes. Jones e/ a/., Science 321(5897): 1801-1806 (2008).
  • subjects with a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1, and/or subjects suffering from a RAS-mutant pancreatic cancer that are treated with the TXNRD1 inhibitor will show amelioration or elimination of one or more of the following symptoms: pain in the upper abdomen that radiates towards the back, loss of appetite or unintended weight loss, depression, new-onset diabetes, blood clots, fatigue, yellowing of skin and the whites of eyes (jaundice), bloating, nausea, and vomiting.
  • subjects with a disease or condition characterized by elevated expression levels of TXNRD1 and/or increased activity levels of TXNRD1, and/or subjects suffering from a RAS-mutant cancer, and/or subjects suffering from pancreatic cancer that are treated with the TXNRD1 inhibitor will show reduced RAS-mutant cell proliferation and/or increased survival compared to untreated subjects with RAS-mutant cancer.
  • subjects with a disease or condition characterized by elevated expression levels of TXNDR1 and/or increased activity of TXNRD1, and/or subjects suffering from a RAS-mutant cancer, and/or subjects suffering from pancreatic cancer that are treated with the TXNRD1 inhibitor will show reduced TXNPD1 and/or RAS expression levels and/or reduced TXNRD1 and/or RAS activity levels compared to untreated subjects with RAS-mutant cancer.
  • the present disclosure provides a method for monitoring the therapeutic efficacy of a TXNRD1 inhibitor in a subject diagnosed with a RAS-mutant cancer comprising: (a) detecting TXNRD1 protein levels in a test sample obtained from the subject after the subject has been administered the TXNRD1 inhibitor; and (b) determining that the TXNRD1 inhibitor is effective when the TXNRD1 protein levels in the test sample are reduced compared to that observed in a control sample obtained from the subject prior to administration of the TXNRD1 inhibitor.
  • the TXNRDl inhibitor may be auranofm,
  • test sample may be tissues, cells or biological fluids (blood, plasma, saliva, urine, serum etc.) present within a subject.
  • RAS e.g., KRAS, HRAS, NRAS
  • TXNRDl expression levels may be used to determine the efficacy of the TXNRDl inhibitor in the subject (see Example 6 described herein).
  • the method further comprises detecting expression levels of RAS (e.g., KRAS, HRAS, NRAS) and/or TXNRDl in the subject, wherein a decrease in RAS (e.g, KRAS, HRAS, NRAS) and/or TXNRDl expression levels relative to those observed in the subject prior to treatment is indicative of the therapeutic efficacy of the TXNRDl inhibitor.
  • the method further comprises detecting activity of RAS (e.g, KRAS, HRAS, NRAS) and/or TXNRDl protein in the subject, wherein a decrease in RAS (e.g, KRAS, HRAS, NRAS) and/or TXNRDl activity relative to those observed in the subject prior to treatment is indicative of the therapeutic efficacy of the TXNRDl inhibitor.
  • RAS e.g, KRAS, HRAS, NRAS
  • TXNRDl protein e.g, a decrease in RAS (e.g, KRAS, HRAS, NRAS) and/or TXNRDl activity relative to those observed in the subject prior to treatment is indicative of the therapeutic efficacy of the TXNRDl inhibitor.
  • the RAS-mutant cancer comprises a KRAS, NRAS, or HRAS mutation selected from the group consisting of G12C, G12D, G12V, G12A, G12S, G12R, G13D, G13C, G13S, G13R, G13A, G13V, Q61H, Q61L, Q61R, Q61K, Q61P, and Q61E.
  • the KRAS, NRAS, or HRAS mutation is detected via DNA sequencing.
  • TXNRDl and/or RAS e.g, KRAS, HRAS, NRAS expression levels are detected via RNA-seq, northern blotting, microarrays, dot or slot blots, fluorescent in situ hybridization, Reverse transcription polymerase chain reaction (RT-PCR), ribonuclease protection assay (RPA), real-time quantitative RT-PCR, high-performance liquid chromatography (HPLC), liquid
  • the present technology provides a method for preventing or delaying the onset of a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1. Additionally or alternatively, in some aspects, the present technology provides a method for preventing or delaying the onset a RAS-mutant cancer.
  • the RAS-mutant cancer comprises a KRAS, NRAS, or HRAS mutation selected from the group consisting of G12C, G12D, G12V, G12A, G12S, G12R, G13D, G13C, G13S, G13R, G13A, G13V, Q61H, Q61L, Q61R, Q61K, Q61P, and Q61E.
  • the RAS-mutant cancer may be lung cancer (e.g ., lung adenocarcinoma), mucinous adenoma, pancreatic cancer (e.g., PDAC), colorectal cancer, skin cancer (e.g., melanoma), endometrial cancer, testicular germ cell cancer, or adrenal gland cancer.
  • lung cancer e.g ., lung adenocarcinoma
  • mucinous adenoma e.g., pancreatic cancer (e.g., PDAC)
  • colorectal cancer e.g., skin cancer (e.g., melanoma)
  • endometrial cancer e.g., testicular germ cell cancer, or adrenal gland cancer.
  • Subjects at risk or susceptible to a disease or condition characterized by elevated expression levels and/or increased activity of TXNRDl, and/or subjects at risk or susceptible to a RAS-mutant cancer, and/or subjects at risk or susceptible to pancreatic cancer include those that exhibit one or more mutations in RAS (e.g, KRAS, HRAS, NRAS).
  • RAS e.g, KRAS, HRAS, NRAS
  • the subjects may exhibit one or more point mutations in one or more of TP53, CDKN2A,
  • the subjects may exhibit at least one mutation in one or more of a core set of twelve cellular signaling pathways and processes.
  • the RAS-mutant cancer comprises a KRAS, NRAS, or HRAS mutation selected from the group consisting of G12C, G12D, G12V, G12A, G12S, G12R, G13D, G13C, G13S, G13R, G13A, G13V, Q61H, Q61L, Q61R, Q61K, Q61P, and Q61E.
  • compositions or medicaments comprising a TXNRD1 inhibitor disclosed herein are administered to a subject susceptible to, or otherwise at risk of a disease or condition characterized by (a) elevated expression levels and/or increased activity of TXNRD1, and/or (b) a subject susceptible to, or otherwise at risk of a RAS-mutant cancer, and/or a subject susceptible to, or otherwise at risk of pancreatic cancer, in an amount sufficient to eliminate or reduce the risk, or delay the onset of the disease, including biochemical, histologic and/or behavioral symptoms of the disease, its complications and intermediate pathological phenotypes presenting during development of the disease.
  • Administration of a prophylactic TXNRD1 inhibitor can occur prior to the manifestation of symptoms characteristic of the disease or disorder, such that the disease or disorder is prevented or, alternatively, delayed in its progression.
  • treatment with the TXNRD1 inhibitor will prevent or delay the onset of one or more of the following symptoms: pain in the upper abdomen that radiates towards the back, loss of appetite or unintended weight loss, depression, new-onset diabetes, blood clots, fatigue, yellowing of skin and the whites of eyes (jaundice), bloating, nausea, and vomiting.
  • subjects with a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1, and/or (b) subjects with a RAS-mutant cancer, and/or subjects with pancreatic cancer that are treated with the TXNRD1 inhibitor will show TXNRD1 and/or RAS expression levels that resemble those observed in healthy control subjects.
  • a composition comprising a TXNRD1 inhibitor disclosed herein, is administered to the subject.
  • the TXNRD1 inhibitor is administered one, two, three, four, or five times per day. In some embodiments, the TXNRD1 inhibitor is administered more than five times per day.
  • the TXNRDl inhibitor is administered every day, every other day, every third day, every fourth day, every fifth day, or every sixth day. In some embodiments, the TXNRDl inhibitor is administered weekly, bi-weekly, tri- weekly, or monthly. In some embodiments, the TXNRDl inhibitor is administered for a period of one, two, three, four, or five weeks. In some embodiments, the TXNRDl inhibitor is administered for six weeks or more. In some embodiments, the TXNRD1 inhibitor is administered for twelve weeks or more. In some embodiments, the TXNRD1 inhibitor is administered for a period of less than one year. In some embodiments, the TXNRD1 inhibitor is administered for a period of more than one year. In some embodiments, the TXNRD1 inhibitor is administered throughout the subject’s life.
  • the TXNRD1 inhibitor is administered daily for 1 week or more. In some embodiments of the methods of the present technology, the TXNRD1 inhibitor is administered daily for 2 weeks or more. In some embodiments of the methods of the present technology, the TXNRD1 inhibitor is administered daily for 3 weeks or more. In some embodiments of the methods of the present technology, the TXNRD1 inhibitor is administered daily for 4 weeks or more. In some embodiments of the methods of the present technology, the TXNRD1 inhibitor is
  • the TXNRD1 inhibitor is administered daily for 6 weeks or more. In some embodiments of the methods of the present technology, the TXNRD1 inhibitor is administered daily for 12 weeks or more. In some embodiments, the TXNRD1 inhibitor is administered daily throughout the subject’s life.
  • suitable in vitro or in vivo assays are performed to determine the effect of a specific TXNRD1 inhibitor and whether its administration is indicated for treatment.
  • in vitro assays can be performed with representative animal models, to determine if a given TXNRD1 inhibitor exerts the desired effect on reducing or eliminating signs and/or symptoms of a RAS-mutant cancer.
  • Compounds for use in therapy can be tested in suitable animal model systems including, but not limited to rats, mice, chicken, cows, monkeys, rabbits, and the like, prior to testing in human subjects.
  • suitable animal model systems including, but not limited to rats, mice, chicken, cows, monkeys, rabbits, and the like, prior to testing in human subjects.
  • any of the animal model system known in the art can be used prior to administration to human subjects.
  • in vitro or in vivo testing is directed to the biological function of one or more TXNDR1 inhibitors of the present technology.
  • Animal models of a RAS-mutant cancer, and/or pancreatic cancer may be generated using techniques known in the art (see Example 7 described herein). Such models may be used to demonstrate the biological effect of TXNRD1 inhibitors in the prevention and treatment of conditions arising from disruption of a particular gene, and/or inhibition of activity of a specific protein and for determining what comprises a therapeutically effective amount of the one or more TXNRD1 inhibitors disclosed herein in a given context.
  • any method known to those in the art for contacting a cell, organ or tissue with one or more TXNRD1 inhibitors disclosed herein may be employed. Suitable methods include in vitro , ex vivo , or in vivo methods. In vivo methods typically include the administration of one or more TXNRD1 inhibitors to a mammal, suitably a human. When used in vivo for therapy, the one or more TXNRD1 inhibitors described herein are administered to the subject in effective amounts (i.e., amounts that have desired therapeutic effect). The dose and dosage regimen will depend upon the degree of the disease state of the subject, the characteristics of the particular TXNRD1 inhibitor used, e.g. , its therapeutic index, and the subject’s history.
  • the effective amount may be determined during pre-clinical trials and clinical trials by methods familiar to physicians and clinicians.
  • An effective amount of one or more TXNRD1 inhibitors useful in the methods may be administered to a mammal in need thereof by any of a number of well-known methods for administering pharmaceutical compounds.
  • the TXNRD1 inhibitor may be administered systemically or locally.
  • compositions for administration, singly or in combination, to a subject for the treatment or prevention of a RAS-mutant cancer, and / or a subject for the treatment or prevention of pancreatic cancer.
  • Such compositions typically include the active agent and a pharmaceutically acceptable carrier.
  • pharmaceutically acceptable carrier includes saline, solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration.
  • Supplementary active compounds can also be incorporated into the compositions.
  • compositions are typically formulated to be compatible with its intended route of administration.
  • routes of administration include parenteral (e.g., intravenous, intradermal, intraperitoneal or subcutaneous), oral, inhalation, transdermal (topical), intraocular, iontophoretic, and transmucosal administration.
  • Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide.
  • a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents
  • antibacterial agents such as benzyl alcohol or methyl parabens
  • antioxidants
  • the parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
  • the dosing formulation can be provided in a kit containing all necessary equipment (e.g ., vials of drug, vials of diluent, syringes and needles) for a treatment course (e.g ., 7 days of treatment).
  • compositions suitable for injectable use can include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion.
  • suitable carriers include physiological saline, bacteriostatic water,
  • CREMOPHOR ELTM BASF, Parsippany, N. J.
  • PBS phosphate buffered saline
  • a composition for parenteral administration must be sterile and should be fluid to the extent that easy syringability exists. It should be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi.
  • compositions having one or more TXNRDl inhibitors disclosed herein can include a carrier, which can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof.
  • a carrier which can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof.
  • the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thiomerasol, and
  • Glutathione and other antioxidants can be included to prevent oxidation.
  • isotonic agents for example, sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride in the composition.
  • Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent that delays absorption, for example, aluminum monostearate or gelatin.
  • Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating the active compound into a sterile vehicle, which contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • typical methods of preparation include vacuum drying and freeze drying, which can yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • Oral compositions generally include an inert diluent or an edible carrier.
  • the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules, e.g ., gelatin capsules.
  • Oral compositions can also be prepared using a fluid carrier for use as a mouthwash.
  • compositions can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or com starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.
  • a binder such as microcrystalline cellulose, gum tragacanth or gelatin
  • an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or com starch
  • a lubricant such as magnesium stearate or Sterotes
  • a glidant such as colloidal silicon dioxide
  • a sweetening agent such as sucrose or saccharin
  • the compounds can be delivered in the form of an aerosol spray from a pressurized container or dispenser, which contains a suitable propellant, e.g. , a gas such as carbon dioxide, or a nebulizer.
  • a suitable propellant e.g. , a gas such as carbon dioxide, or a nebulizer.
  • Systemic administration of a therapeutic compound as described herein can also be by transmucosal or transdermal means.
  • penetrants appropriate to the barrier to be permeated are used in the formulation.
  • penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives.
  • Transmucosal administration can be accomplished through the use of nasal sprays.
  • the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art.
  • transdermal administration may be performed by iontophoresis.
  • a therapeutic agent can be formulated in a carrier system.
  • the carrier can be a colloidal system.
  • the colloidal system can be a liposome, a phospholipid bilayer vehicle, or a lipid nanoparticle.
  • the therapeutic agent is encapsulated in a liposome while maintaining the agent’s structural integrity.
  • One skilled in the art would appreciate that there are a variety of methods to prepare liposomes. (See Lichtenberg, et al, Methods Biochem. Anal., 33:337-462 (1988); Anselem, et al. , Liposome Technology , CRC Press (1993)). Liposomal formulations can delay clearance and increase cellular uptake (See Reddy, Ann.
  • An active agent can also be loaded into a particle prepared from pharmaceutically acceptable ingredients including, but not limited to, soluble, insoluble, permeable, impermeable, biodegradable or gastroretentive polymers or liposomes.
  • Such particles include, but are not limited to, nanoparticles, biodegradable nanoparticles, microparticles, biodegradable microparticles, nanospheres, biodegradable nanospheres, microspheres, biodegradable microspheres, capsules, emulsions, liposomes, micelles and viral vector systems.
  • the carrier can also be a polymer, e.g. , a biodegradable, biocompatible polymer matrix.
  • the therapeutic agent can be embedded in the polymer matrix, while maintaining the agent’s structural integrity.
  • the polymer may be natural, such as polypeptides, proteins or polysaccharides, or synthetic, such as poly a-hydroxy acids.
  • Examples include carriers made of, e.g. , collagen, fibronectin, elastin, cellulose acetate, cellulose nitrate, polysaccharide, fibrin, gelatin, and combinations thereof.
  • carriers made of, e.g. , collagen, fibronectin, elastin, cellulose acetate, cellulose nitrate, polysaccharide, fibrin, gelatin, and combinations thereof.
  • the polymer is poly-lactic acid (PLA) or copoly lactic/glycolic acid (PGLA).
  • the polymeric matrices can be prepared and isolated in a variety of forms and sizes, including microspheres and nanospheres. Polymer formulations can lead to prolonged duration of therapeutic effect. (See Reddy, Ann. Pharmacother ., 34(7-8):915-923 (2000)). A polymer formulation for human growth hormone (hGH) has been used in clinical trials. (See Kozarich and Rich, Chemical Biology , 2:548-552 (1998)). [00134] Examples of polymer microsphere sustained release formulations are described in PCT publication WO 99/15154 (Tracy, et al), U.S. Pat. Nos.
  • the therapeutic compounds are prepared with carriers that will protect the therapeutic compounds against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems.
  • a controlled release formulation including implants and microencapsulated delivery systems.
  • Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid.
  • Such formulations can be prepared using known techniques.
  • the materials can also be obtained commercially, e.g., from Alza Corporation and Nova Pharmaceuticals, Inc.
  • Liposomal suspensions (including liposomes targeted to specific cells with monoclonal antibodies to cell-specific antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Pat. No. 4,522,811.
  • the therapeutic compounds can also be formulated to enhance intracellular delivery.
  • liposomal delivery systems are known in the art, see, e.g, Chonn and Cullis,“Recent Advances in Liposome Drug Delivery Systems,” Current Opinion in
  • Dosage, toxicity and therapeutic efficacy of any therapeutic agent can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g, for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population).
  • the dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50.
  • Compounds that exhibit high therapeutic indices are advantageous. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.
  • the data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans.
  • the dosage of such compounds may be within a range of circulating concentrations that include the ED50 with little or no toxicity.
  • the dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.
  • the therapeutically effective dose can be estimated initially from cell culture assays.
  • a dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (z.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture.
  • IC50 z.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms
  • levels in plasma may be measured, for example, by high performance liquid chromatography.
  • an effective amount of the one or more TXNRD1 inhibitors disclosed herein sufficient for achieving a therapeutic or prophylactic effect range from about
  • the dosage ranges are from about 0.0001 mg per kilogram body weight per day to about 100 mg per kilogram body weight per day.
  • dosages can be 1 mg/kg body weight or 10 mg/kg body weight every day, every two days or every three days or within the range of 1-10 mg/kg every week, every two weeks or every three weeks.
  • a single dosage of the therapeutic compound ranges from 0.001- 10,000 micrograms per kg body weight.
  • one or more TXNRD1 inhibitor concentrations in a carrier range from 0.2 to 2000 micrograms per delivered milliliter.
  • An exemplary treatment regime entails administration once per day or once a week. In therapeutic applications, a relatively high dosage at relatively short intervals is sometimes required until progression of the disease is reduced or terminated, or until the subject shows partial or complete amelioration of symptoms of disease. Thereafter, the patient can be administered a prophylactic regime.
  • TXNRD1 inhibitors may be defined as a concentration of inhibitor at the target tissue of 10 32 to 10 6 molar, e.g, approximately 10 7 molar. This concentration may be delivered by systemic doses of 0.001 to 100 mg/kg or equivalent dose by body surface area. The schedule of doses would be optimized to maintain the therapeutic concentration at the target tissue, such as by single daily or weekly administration, but also including continuous
  • administration e.g, parenteral infusion or transdermal application.
  • treatment of a subject with a therapeutically effective amount of the therapeutic compositions described herein can include a single treatment or a series of treatments.
  • the mammal treated in accordance with the present methods can be any mammal, including, for example, farm animals, such as sheep, pigs, cows, and horses; pet animals, such as dogs and cats; laboratory animals, such as rats, mice and rabbits.
  • farm animals such as sheep, pigs, cows, and horses
  • pet animals such as dogs and cats
  • laboratory animals such as rats, mice and rabbits.
  • the mammal is a human.
  • one or more of the TXNRD1 inhibitors disclosed herein may be combined with one or more additional therapies for the prevention or treatment of a RAS-mutant cancer or pancreatic cancer.
  • Additional therapeutic agents include, but are not limited to, ABRAXANE® (albumin-bound paclitaxel), GEMZAR® (gemcitabine), 5-FU (fluorouracil), ONIVYDE® (irinotecan liposome injection), surgery, radiation, or a combination thereof.
  • the one or more TXNRD1 inhibitors disclosed herein may be separately, sequentially or simultaneously administered with at least one additional therapeutic agent selected from the group consisting of immunotherapeutic agents, alkylating agents, topoisomerase inhibitors, endoplasmic reticulum stress inducing agents,
  • the at least one additional therapeutic agent is a chemotherapeutic agent.
  • chemotherapeutic agents include, but are not limited to,
  • cyclophosphamide fluorouracil (or 5-fluorouracil or 5-FU), methotrexate, edatrexate (10- ethyl- 10-deaza-aminopterin), thiotepa, carboplatin, cisplatin, taxanes, paclitaxel, protein- bound paclitaxel, docetaxel, vinorelbine, tamoxifen, raloxifene, toremifene, fulvestrant, gemcitabine, irinotecan, ixabepilone, temozolmide, topotecan, vincristine, vinblastine, eribulin, mutamycin, capecitabine, anastrozole, exemestane, letrozole, leuprolide, abarelix, buserlin, goserelin, megestrol acetate, risedronate, pamidronate, ibandronate, alendronate, deno
  • antimetabolites include 5-fluorouracil (5-FU), 6-mercaptopurine (6- MP), capecitabine, cytarabine, floxuridine, fludarabine, gemcitabine, hydroxyurea, methotrexate, pemetrexed, and mixtures thereof.
  • Examples of taxanes include accatin III, 10-deacetyltaxol, 7-xylosyl-10- deacetyltaxol, cephalomannine, 10-deacetyl-7-epitaxol, 7-epitaxol, 10-deacetylbaccatin III, 10-deacetyl cephalomannine, and mixtures thereof.
  • Examples of DNA alkylating agents include cyclophosphamide, chlorambucil, melphalan, bendamustine, uramustine, estramustine, carmustine, lomustine, nimustine, ranimustine, streptozotocin; busulfan, mannosulfan, and mixtures thereof.
  • topoisomerase I inhibitor examples include SN-38, ARC, NPC, camptothecin, topotecan, 9-nitrocamptothecin, exatecan, lurtotecan, lamellarin D9-aminocamptothecin, rubifen, gimatecan, diflomotecan, BN80927, DX-8951f, MAG-CPT, and mixtures thereof.
  • topoisomerase II inhibitors include amsacrine, etoposide, etoposide phosphate, teniposide, daunorubicin, mitoxantrone, amsacrine, ellipticines, aurintricarboxylic acid, doxorubicin, and HU-331 and combinations thereof.
  • immunotherapeutic agents include immune checkpoint inhibitors e.g ., antibodies targeting CTLA-4, PD-1, PD-L1), ipilimumab, 90Y-Clivatuzumab tetraxetan, pembrolizumab, nivolumab, trastuzumab, cixutumumab, ganitumab, demcizumab, cetuximab, nimotuzumab, dalotuzumab, sipuleucel-T, CRS-207, and GVAX.
  • immune checkpoint inhibitors e.g ., antibodies targeting CTLA-4, PD-1, PD-L1), ipilimumab, 90Y-Clivatuzumab tetraxetan, pembrolizumab, nivolumab, trastuzumab, cixutumumab, ganitumab, demcizumab, cetuxim
  • RAS inhibitors include AMG 510, MRTX849, ARS-3248, BI 1701963, ARS-1620, ARS-853, thiol-reactive GDP analogs, BBP-454, mRNA-5671, KRAS
  • G12D inhibitors and the like.
  • the multiple therapeutic agents may be administered in any order or even simultaneously. If simultaneously, the multiple therapeutic agents may be provided in a single, unified form, or in multiple forms (by way of example only, either as a single pill or as two separate pills). One of the therapeutic agents may be given in multiple doses, or both may be given as multiple doses. If not simultaneous, the timing between the multiple doses may vary from more than zero weeks to less than four weeks. In addition, the combination methods, compositions and formulations are not to be limited to the use of only two agents.
  • RAS-mutant cancer e.g., RAS mutant pancreatic cancer
  • TXNRD1 inhibitors one or more TXNRD1 inhibitors.
  • the above described components of the kits of the present technology are packed in suitable containers and labeled for the prevention and/or treatment of a RAS- mutant cancer (e.g., RAS mutant pancreatic cancer).
  • the above-mentioned components may be stored in unit or multi-dose containers, for example, sealed ampoules, vials, bottles, syringes, and test tubes, as an aqueous, preferably sterile, solution or as a lyophilized, preferably sterile, formulation for reconstitution.
  • the kit may further comprise a second container which holds a diluent suitable for diluting the pharmaceutical composition towards a higher volume. Suitable diluents include, but are not limited to, the pharmaceutically acceptable excipient of the pharmaceutical composition and a saline solution.
  • the kit may comprise instructions for diluting the pharmaceutical composition and/or instructions for administering the pharmaceutical composition, whether diluted or not.
  • the containers may be formed from a variety of materials such as glass or plastic and may have a sterile access port (for example, the container may be an intravenous solution bag or a vial having a stopper which may be pierced by a hypodermic injection needle).
  • the kit may further comprise more containers comprising a pharmaceutically acceptable buffer, such as phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, culture medium for one or more of the suitable hosts.
  • the kits may optionally include instructions customarily included in commercial packages of therapeutic or diagnostic products, that contain information about, for example, the indications, usage, dosage, manufacture, administration, contraindications and/or warnings concerning the use of such therapeutic or diagnostic products.
  • the kit can also comprise, e.g ., a buffering agent, a preservative or a stabilizing agent.
  • the kit can also contain a control sample or a series of control samples, which can be assayed and compared to the test sample.
  • Each component of the kit can be enclosed within an individual container and all of the various containers can be within a single package, along with instructions for interpreting the results of the assays performed using the kit.
  • the kits of the present technology may contain a written product on or in the kit container. The written product describes how to use the reagents contained in the kit. In certain embodiments, the use of the reagents can be according to the methods of the present technology.
  • the present technology is further illustrated by the following Examples, which should not be construed as limiting in any way.
  • the examples herein are provided to illustrate advantages of the present technology and to further assist a person of ordinary skill in the art with preparing or using the compositions and systems of the present technology.
  • the examples should in no way be construed as limiting the scope of the present technology, as defined by the appended claims.
  • the examples can include or incorporate any of the variations, aspects, or embodiments of the present technology described above.
  • the variations, aspects, or embodiments described above may also further each include or incorporate the variations of any or all other variations, aspects or embodiments of the present technology.
  • the following Examples demonstrate the preparation, characterization, and use of illustrative compositions of the present technology that inhibit TXNRD1 expression and/or activity.
  • Methods of normalization included, but were not limited to: 1) globally scaling cell-level counts to match the median depth across all cells (scalar adjustment), and 2) solving linear systems to obtain unique scaling factors for individual cells. In some cases, inter-sample batch effects were corrected via a mutual nearest neighbors algorithm.
  • cells targeted with an essential gene were also included in construction of the latent space in order to define a region of“toxicity.” Toxicity manifested as, e.g, knocked down a gene induced apoptosis in primary cells.
  • CRISPR target candidates were mapped to the same latent space constructed from the pure cell types in order to quantify their transcriptional shift towards a wild-type expression profile (therapeutic index).
  • Several algorithms were used for supervised dimensionality reduction. In some cases, the Elbow method (Richards et al ., J Shoulder Elbow Surg 8(4): 351-354 (1999)) was used to determine the optimal number of dimensions for the latent space.
  • the target genes interrogated via a pooled CRISPRi library were quantified in terms of their ability to shift the transcriptional profile of cancer cells back to a wild-type-like expression state (therapeutic index).
  • Genes were scored via machine learning algorithms. Briefly, separate, single-class machine learning algorithms were trained on the latent expression profiles of distinct cell types including, but not limited to: 1) pancreatic ductal cells; 2) pancreatic acinar cells; 3) pancreatic adenocarcinomas; and 4) pancreatic adenocarcinomas with an essential gene (e.g, PCNA or MCM6) targeted (via CRISPR/RNAi) as a model for toxicity.
  • an essential gene e.g, PCNA or MCM6
  • Each of the trained machine learning models was then used to score candidate genes based on the output of the decision function applied to latent expression profiles of single cells targeted with the CRISPRi library. In some cases, cells were repeatedly sampled with replacement in order to construct a bootstrap confidence interval for the decision function estimate.
  • Transduced cells were selected for 5 days using 1 mg/mL G418 (Invitrogen). At each passage, >20 million cells were maintained to preserve library representation throughout the experiment. After drug selection, TO samples were obtained (20 million cells per replicate) and sorted for Venus + cells. After 12 days (six passages, T12), 20 million shRNA-expressing (dsRed + Venus + ) cells were sorted for each replicate using a FACSAriall (BD Biosciences). Genomic DNA from TO and T12 samples was isolated by two rounds of phenol extraction using PhaseLock tubes (5 Prime) followed by isopropanol precipitation.
  • Proliferation assays Competitive proliferation assays using shRNAs in TRMPV-Neo vector (with miR-30 or miR-E backbone) were performed as described previously (Huang et al., Genes Dev. 28(16): 1800-1814 (2014)). Assays for in vitro growth inhibition by auranofm or piperlongumine were performed by counting the viable cell numbers using CellTiter-Glo Luminescent Cell Viability Assay (Promega) after incubation of cells in the presence of increasing concentrations of auranofm or piperlongumine for 72 hr. Proliferation rates were calculated by dividing viable cell numbers at 72 hr by the viable cell numbers at 0 hr. Relative proliferation rates were calculated by normalizing to the proliferation rate of vehicle-treated cells.
  • mice Tet-On murine PD AC cells were transduced with luciferase-hygro and TRMPV-Neo-miR-E shRNA constructs.
  • One million murine PD AC cells were orthotopically transplanted into female nude recipient mice (NCR nu/nu, purchased from Charles River laboratories and Harlan Laboratories).
  • mice were intraperitoneally injected with 50 mg/kg D-Luciferin (Goldbio), and after 10 min, analyzed using an IVIS Spectrum system (Caliper LifeSciences). Quantification was performed using Living Image software (Caliper LifeSciences) with standardized round regions of interests covering the mouse trunk and extremities.
  • shRNA induction animals were treated with doxycycline in drinking water (2 mg/ml with 2% sucrose; Sigma-Aldrich) and food (625 mg/kg, Harlan Laboratories).
  • RNA sequencing and Gene set enrichment analysis (GSEA) analyses were performed.
  • GSEA Gene set enrichment analysis
  • RNA sequencing total RNA from mPDAC cells harboring shRNAs targeting control Renilla Luciferase or TXNRD1 was isolated using RNeasy Mini Kit, QIAshredder Columns and RNase-Free DNase Set (Qiagen).
  • RNA-Seq library construction and sequencing were performed according to protocols used by the Integrated Genomics Operation (IGO) Core at MSKCC. 5-10 million reads were acquired per replicate sample. After removing adaptor sequences with Trimmomatic (Bolger et al ., 2014), RNA-seq reads were aligned to
  • GRCh37.75(hgl9) using the STAR alignment tool (Dobin et al ., 2013). Genome wide transcript counting was performed by HTSeq to generate FPKM matrix (Anders et al., 2015 Bioinformatics). Gene set enrichment analysis (Subramanian et al., 2005) was performed using GSEA v2.07 software.
  • Auranofm pharmacokinetics The plasma and pancreas pharmacokinetics of gold were analyzed in 9 NCR nu/nu mice following administration of a single dose of 10 mg/kg auranofm suspension via intraperitoneal injection. Plasma and pancreas samples for determination of gold concentration were obtained at 2, 4, and 24 hours following
  • ICPMS inductively coupled plasma mass spectrometry
  • FIGs. 1A-1B provide a pipeline for computational discovery of therapeutic targets in RAS-mutant pancreatic cancer.
  • Kras-mutant pancreatic cell lines were screened using a CRISPRi library transduced at a low multiplicity of infection (MOI).
  • the transcriptomes of single cells were isolated and converted to DNA libraries using a Chromium instrument (10X Genomics) and an enzyme kit (10X Genomics), and were sequenced using Hiseq4000 system (Illumina).
  • Single-cell RNA sequencing (scRNA-seq) profiles of individual cells were matched to their respective CRISPR targets via paired-end sequencing and using barcodes.
  • the raw reads in FASTQ format were aligned with whole genome and mapped to an appropriate genomic coordinate and HGNC gene for each cell, resulting in a count matrix comprised of N cells c M genes (See FIG. 1A).
  • This N c M matrix was further reduced to a N x 50 matrix via supervised dimensionality reduction (See FIG. 1A).
  • the dimensionality reduction model was trained to identify pure cell types (e.g. cancer cells, ductal cells, acinar cells, or cancer cells expressing a non-targeted guide RNA, which served as the negative controls) such that the lower-dimensional latent space maximally separated healthy cells and cancer cells from each other (See FIG. 1A-2A).
  • CRISPR targets that maximally drove mRNA expression pattern away from the negative controls, and towards healthy cells (ductal cells or acinar cells) were identified using this algorithm, and such CRISPR targets constituted the most promising targets that were pursued in preclinical development.
  • the therapeutic index was quantified using machine learning algorithms. Briefly, separate machine learning models were trained to identify distinct cell populations, including: 1) pancreatic ductal cells (positive control for therapeutic index); 2) pancreatic acinar cells (positive control for therapeutic index); 3) Kras-mutant PD AC cells expressing a non-target guide RNA (negative control for therapeutic index); and 4) Kras-mutant PD AC cells expressing an essential gene targeted (positive control for a toxic target). As shown in FIGs.
  • the trained machine learning models were then applied to RNA-seq data of Kras-mutant PD AC cells expressing a CRISPR targets to detect cells that exhibited RNA-seq profiles similar to pancreatic acinar cells and distinguishable from Kras- mutant PD AC cells expressing negative control for therapeutic index. Identities of the CRISPR targets expressed by such cells were identified based on paired-end sequencing and barcodes. Targets with maximal therapeutic index were chosen to pursue in preclinical development.
  • the scRNA-seq profiles of individual Kras-mutant PD AC cells expressing CRISPRi targets were analyzed using decision functions of machine learning algorithms trained on two non-target guide RNAs, a toxic target, and a healthy ductal cell line as described above.
  • the outputs of the decision functions were further transformed via a variety of methods, including but not limited to: effect size, K.S.- statistic, z-score, or p-value relative to a control population.
  • TXNRD1 was identified as a CRISPRi target that transformed Kras-mutant PD AC cells to exhibit RNA-seq profiles similar to pancreatic acinar cells.
  • shRNAs short hairpin RNAs directed toward known drug targets was screened for negative selection in a genetically defined murine HCC model ( Kras G12D ; Myc; shp53). The results were cross-analyzed with prior negative selection results from a murine HCC model (Myc; p53 ⁇ ⁇ ) (Huang et al., Genes Dev. 28(16): 1800-1814 (2014)). As shown in Fig.
  • shRNAs targeting Txnrdl , Acpp, and Amt were found to be selectively depleted in the Kras-mutant PD AC cells, compared to the negative control shRNAs, which remained unchanged in both cell lines. In comparison, positive control shRNAs were depleted in both murine HCC and murine HCC (See Fig. 3A).
  • Kras.247 (a positive control for mPDAC-specific growth inhibition). The percentage of cells expressing these shRNAs was determined on day 0 and on day 12 of shRNA induction.
  • shRNA Ren.713 which is a non-targeting negative control (against Renilla luciferase) had no effect in any cells
  • the positive control shRNA Rpa3.561 was depleted in all cell types tested.
  • the mPDAC-specific positive control Kras.247 was depleted in mPDAC compared to mHCC and iMEFs. As shown in Fig.
  • TXNRDl dependency was further investigated in various cell lines. As shown in FIGs. 6A-6B, knocking out or knocking down replication genes RAPl or PCNA resulted in general lethality to almost all cell lines. In contrast, TXNRDl is conditionally required for certain cell lines which exhibit similar dependency for KRAS, HRAS, and NRAS.
  • TXNRDl inhibitor compositions of the present technology are useful in methods for treating a disease or condition characterized by elevated levels of RAS expression and/or elevated levels of TXNRDl expression in a subject in need thereof.
  • Example 5 KRAS-mutant PD AC growth is sensitive to pharmacolosical TXNRD1 inhibition
  • Auranofm is an inhibitor of enzymatic activity of TXNRDl ⁇ See Gromer et al., J Biol Chem 273(32): 20096-20101).
  • Myricetin, manumycin A and protoporphyrin IX are also inhibitors of enzymatic activity of TXNRDl.
  • mPDAC cells were treated with the TXNRDl inhibitor auranofm or DMSO for 72 hr, and viability was measured. DMSO treatment served as a negative control causing a lack of growth inhibition. Viable cell number of DMSO- treated cells was set to 1.
  • TXNRD1 inhibitor compositions of the present technology are useful in methods for treating a disease or condition characterized by RAS mutations, elevated levels of RAS expression and/or elevated levels of TXNRD1 expression in a subject in need thereof.
  • KRAS mutant cells were generally more sensitive to auranofm than the wild-type KRAS cells.
  • RNA-seq analyses of the mPDAC cells harboring shRNAs targeting control Renilla or Txnrdl were performed.
  • FIGs. 4F-4G suppression of Cdk9 resulted in reversion of both KRAS dependency (FIG. 4F) and pancreatic cancer signatures (FIG. 4G), further validating the findings that TXNRD1 is required for KRAS oncogenic signaling.
  • FIG. 4H suppression of TXNRD1 showed a downregulation of gene signatures related to amino acid transporter and ferroptosis including a gene called SLC7A11.
  • TXNRD1 inhibitor compositions of the present technology are useful in methods for treating a disease or condition characterized by elevated levels of RAS expression and/or elevated levels of TXNRD1 expression in a subject in need thereof.
  • TXNRD1 is Required for Maintenance of KRAS-Mutant Pancreatic Tumors.
  • TXNRD1 The relevance of TXNRD1 on PD AC progression in vivo was also investigated.
  • mPDAC cells were transduced with Luciferase and dox inducible TRMPV-Neo-miR-E constructs containing Txnrdl shRNAs or control shRNAs (Renilla and Kras) and were transplanted into the pancreas of recipient mice by orthotopic injection (See FIG. 5A).
  • the animals were treated without or with dox to induce the corresponding shRNA expression. As shown in FIG.
  • tumor weights from mice from the untreated group displayed larger pancreatic tumors compared to the mice having knockdown of Txnrdl or Kras led to a comparable delay in tumor growth.
  • Weighs of tumors expressing Ren.713E were not affected by doxycycline treatment (compare the two sets of replicates in Ren.713 column of FIG. 5B).
  • Weighs of tumors expressing Txnrdl and KRAS shRNA were comparably inhibited by doxycycline treatment (compare the two sets of replicates between groups and within groups in
  • TXNRD1 inhibitor compositions of the present technology such as an agent that inhibit expression of TXNRD1 are useful in methods for treating a RAS-mutant cancer in a subject in need thereof.
  • TXNRD1 inhibition growth inhibitory effects of pharmacological TXNRD1 inhibition was found in human xenograft models generated by KRAS-mutant PD AC cells (MIAPaCa-2: KRAS mutant) but not in KRAS wild-type cells (Colo357: KRAS wild-type).
  • TXNRDl is required for the maintenance of KRAS-mutant tumors and dependency in vivo.
  • FIG. 10 demonstrates that auranofm is delivered into the pancreas.
  • FIG. 9 demonstrates that patients with pancreatic adenocarcinoma (PD AC) who exhibit TXNRDl mRNA upregulation show reduced overall survival compared with PD AC patients that express low levels of TXNRDL
  • FIGs. 7A-7D show the antiproliferative effects of TXNRDl inhibitor Auranofm in KRAS-mutant pancreatic cancer cells and potential synergistic inhibitory effects when combined with Gemcitabine.
  • FIGs. 8A-8D show the antiproliferative effects of TXNRDl inhibitor Auranofm in KRAS-mutant pancreatic cancer cells and potential synergistic inhibitory effects when combined with KRAS G12C inhibitor AMG 510.
  • a group having 1-3 cells refers to groups having 1, 2, or 3 cells.
  • a group having 1-5 cells refers to groups having 1, 2, 3, 4, or 5 cells, and so forth.

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Abstract

The present disclosure relates generally to compositions and methods for the treatment of a RAS-mutant cancer. In particular, the present technology relates to administering a therapeutically effective amount of one or more TXNRD1 inhibitors to a subject diagnosed with, or at risk for a RAS-mutant cancer (e.g., RAS-mutant pancreatic cancer).

Description

COMPOSITIONS AND METHODS FOR TREATING RAS-MUTANT CANCERS
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims the benefit of and priority to U.S. Provisional Patent
Application No. 62/838,065, filed April 24, 2019, the entire contents of which are incorporated herein by reference.
TECHNICAL FIELD
[0002] The present technology relates generally to compositions and methods for treating, preventing, and/or ameliorating a RAS-mutant cancer in a subject in need thereof. In particular, the present technology relates to methods for treating, preventing, and/or ameliorating RAS-mutant pancreatic cancer by administration of a therapeutically effective amount of a TXNRD1 inhibitor.
BACKGROUND
[0003] The following description of the background of the present technology is provided simply as an aid in understanding the present technology and is not admitted to describe or constitute prior art to the present technology.
[0004] About 90% of all pancreatic cancers are pancreatic ductal adenocarcinoma (PD AC), which is one of the deadliest types of cancer. PD AC has only a 7% 5-year survival rate. Detailed genetic profiles have suggested significant variability among cancers. For example, genome sequencing has revealed that the genes that are frequently mutated in PD AC include KRAS, TP53 , CDKN2A , SMAD4 , MLL3 , TGFBR2 , ARID 1 A and SF3B1, EPC1 and ARID 2, ATM , ZIM2, MAP2K4 , NALCN, SLC16A4 , MAGEA6 , ROB02 , KDM6A , PREX2, ERBB2 , MET ; FGFR1, CDK6 , PIK3R3, PIK3CA , BRCA1, BRCA2 , /M/.//2, efc. Despite the variability, it is clear that KRAS is mutated in 95% of PD AC cases. See, e.g., Biankin et al., Nature 491(7424): 399-405 (2012); Waddell et al. , Nature 518(7540):495-501 (2015); and Jones et al., Science 321(5897): 1801-1806 (2008).
[0005] KRAS protein is a GTPase that plays an important role in cellular signal transduction pathways. KRAS protein is considered to act as a binary ON-OFF switch, cycling between an active guanosine triphosphate (GTP)-bound and inactive guanosine diphosphate (GDP)- bound state. In normal quiescent cells, KRAS is mostly found in the GDP-bound inactive state. Cell-surface receptors transiently promote formation of the active KRAS-GTP, in response to extracellular stimuli. The KRAS mutations in PD AC and other types of cancer are typically missense mutations that render KRAS protein constitutively GTP -bound, resulting in overstimulation of signaling pathways that drive cancer growth. The oncogenic mutant KRAS protein drives tumor progression in multiple cancer types. For example, in case of PD AC, the mutant KRAS proteins regulate reprogramming of pancreatic acinar cell to ductal cell intraepithelial neoplasia. KRAS is also required in the growth and maintenance of PDAC and other cancers. See, e.g., Ying et al., Cell 149(3):656-70 (2012). Indeed, PDAC is considered to be one of the most“KRAS-addicted” types of cancer.
[0006] Accordingly, KRAS is considered an important therapeutic target against PDAC and other KRAS mutant cancers. See, e.g., Waters and Der, Cold Spring Harb PerspectMed. 8(9): a031435 (2018).
SUMMARY OF THE PRESENT TECHNOLOGY
[0007] In one aspect, the present disclosure provides methods for treating a RAS-mutant cancer in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a TXNRDl inhibitor selected from the group consisting of auranofm, Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, protoporphyrin IX, an anti-TXNRDl antibody, and any derivatives thereof. Also disclosed herein are methods for treating a RAS-mutant cancer in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of an inhibitory nucleic acid that inhibits TXNRDl expression. In some
embodiments, the inhibitory nucleic acid comprises a sequence selected from the group consisting of TCTAATATCATTAACACCATGG (SEQ ID NO: 1; human shTXNRDl),
T A A AT A A A ACTGA AT AT GGT C A (SEQ ID NO: 2; human shTXNRDl),
TTAATAATAACTTATGATATTA (SEQ ID NO: 3; human shTXNRDl),
TTT GT A AC A A A A AT AC AT GGA A (SEQ ID NO: 4; human shTXNRDl),
TTTAAATGAAAATCCTTCACAT (SEQ ID NO: 5; human shTXNRDl),
TTTTAAATGAAAATCCTTCACA (SEQ ID NO: 6; human shTXNRDl),
T AAGAAAAGAGAAT C AC AAC AT (SEQ ID NO: 7; human shTXNRDl),
TTTTCATTTATCTTCACCCCTA (SEQ ID NO: 8; human shTXNRDl),
T T AG A A AG A A AT AG AT AC C C A A (SEQ ID NO: 9; human shTXNRDl),
T A AT A AT A AC TT AT GAT ATT A A (SEQ ID NO: 10; human shTXNRDl), TTT AGTC AC AGGGT AATTCGT C (SEQ ID NO: 11; murine shTxnrdl), and TTCGTCACTGACAACGTTGTGA (SEQ ID NO: 12; murine shTxnrdl), or any
complement thereof. The RAS-mutant cancer may be lung cancer (e.g., lung
adenocarcinoma), mucinous adenoma, pancreatic cancer (e.g., PD AC), colorectal cancer, skin cancer (e.g., melanoma), endometrial cancer, testicular germ cell cancer, or adrenal gland cancer. In certain embodiments, the RAS-mutant cancer comprises a KRAS, NRAS, or HRAS mutation selected from the group consisting of G12C, G12D, G12V, G12A, G12S, G12R, G13D, G13C, G13S, G13R, G13A, G13V, Q61H, Q61L, Q61R, Q61K, Q61P, and Q61E. Additionally or alternatively, in some embodiments, the KRAS, NRAS, or HRAS mutation is detected via DNA sequencing.
[0008] Additionally or alternatively, in some embodiments of the methods disclosed herein, the subject displays elevated expression levels of RAS protein (e.g., KRAS, HRAS, NRAS) in cancer cells prior to treatment. In any of the embodiments of the methods disclosed herein, the subject exhibits one or more signs or symptoms selected from among pain in the upper abdomen that radiates towards the back, loss of appetite or unintended weight loss, depression, new-onset diabetes, blood clots, fatigue, yellowing of skin and the whites of eyes (jaundice), bloating, nausea, and vomiting.
[0009] Additionally or alternatively, in some embodiments of the methods disclosed herein, the subject harbors one or more point mutations in TP53, CDKN2A, SMAD4, MLL3,
TGFBR2, ARID 1 A, SF3B1, EPC1, ARID2, ATM, ZIM2, MAP2K4, NALCN, SLC16A4, MAGEA6, ROB02, KDM6A, PREX2, ERBB2, MET, FGFR1, CDK6, PIK3R3, PIK3CA, BRCA1, BRCA2, or PALB2. In some embodiments, the subject is human.
[0010] In any of the embodiments of the methods disclosed herein, the TXNRDl inhibitor or the inhibitory nucleic acid that inhibits TXNRDl expression may be administered orally, topically, intranasally, systemically, intravenously, subcutaneously, intraperitoneally, intradermally, intraocularly, iontophoretically, transmucosally, or intramuscularly. In some embodiments, the TXNRDl inhibitor or the inhibitory nucleic acid is administered daily for 6 weeks or more. In other embodiments, the TXNRDl inhibitor or the inhibitory nucleic acid is administered daily for 12 weeks or more.
[0011] Additionally or alternatively, in some embodiments, the methods further comprise separately, sequentially or simultaneously administering one or more additional therapeutic agents to the subject. Examples of the additional therapeutic agents include, but are not limited to, paclitaxel, gemcitabine, AMG 510, 5-FU (fluorouracil), and irinotecan.
[0012] In another aspect, the present disclosure provides a method for monitoring the therapeutic efficacy of a TXNRD1 inhibitor in a subject diagnosed with a RAS-mutant cancer comprising: (a) detecting TXNRD1 protein levels in a test sample obtained from the subject after the subject has been administered the TXNRD1 inhibitor; and (b) determining that the TXNRD1 inhibitor is effective when the TXNRD1 protein levels in the test sample are reduced compared to that observed in a control sample obtained from the subject prior to administration of the TXNRD1 inhibitor. Examples of TXNRD1 inhibitors include auranofm, Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, protoporphyrin IX, an anti-TXNRDl antibody, an inhibitory nucleic acid that inhibits TXNRD1 expression, or any derivatives thereof. In some embodiments, the inhibitory RNA is a shRNA, an antisense oligonucleotide, or a sgRNA.
[0013] In one aspect, the present disclosure provides a method for inhibiting RAS-mutant cell proliferation in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of at least one TXNRD1 inhibitor, wherein the at least one TXNRD1 inhibitor is selected from the group consisting of auranofm, Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, protoporphyrin IX, an anti-TXNRDl antibody, an inhibitory nucleic acid that inhibits TXNRDl expression, and any derivatives thereof, and wherein the subject suffers from a disease or condition characterized by elevated expression levels and/or increased activity of RAS ( e.g ., KRAS, HRAS, NRAS) and/or TXNRDl . In some embodiments, the inhibitory nucleic acid comprises a nucleic acid sequence selected from the group consisting of TCTAATATCATTAACACCATGG (SEQ ID NO: 1; human
shTXNRDl), T A A AT A A A AC T GA AT AT GGT C A (SEQ ID NO: 2; human shTXNRDl), TTAATAATAACTTATGATATTA (SEQ ID NO: 3; human shTXNRDl),
TTT GT A AC A A A A AT AC AT GGA A (SEQ ID NO: 4; human shTXNRDl),
TTTAAATGAAAATCCTTCACAT (SEQ ID NO: 5; human shTXNRDl),
TTTTAAATGAAAATCCTTCACA (SEQ ID NO: 6; human shTXNRDl),
T AAGAAAAGAGAAT C AC AAC AT (SEQ ID NO: 7; human shTXNRDl),
TTTTCATTTATCTTCACCCCTA (SEQ ID NO: 8; human shTXNRDl), T T AG A A AG A A AT AG AT AC C C A A (SEQ ID NO: 9; human shTXNRDl),
T A AT A AT A AC TT AT GAT ATT A A (SEQ ID NO: 10; human shTXNRDl),
TTT AGTC AC AGGGT AATTCGT C (SEQ ID NO: 11; murine shTxnrdl), and
TTCGTCACTGACAACGTTGTGA (SEQ ID NO: 12; murine shTxnrdl).
[0014] In any and all embodiments of the methods disclosed herein, TXNRD1 and/or RAS ( e.g ., KRAS, HRAS, NRAS) expression levels are detected via RNA-seq, northern blotting, microarrays, dot or slot blots, fluorescent in situ hybridization, Reverse transcription polymerase chain reaction (RT-PCR), ribonuclease protection assay (RPA), real-time quantitative RT-PCR, high-performance liquid chromatography (HPLC), liquid
chromatography-mass spectrometry (LC/MS), enzyme-linked immunosorbent assay
(ELISA), immunoprecipitation, immunoelectrophoresis, immunostaining,
immunohistochemistry, or western blotting.
[0015] Additionally or alternatively, in some embodiments of the methods disclosed herein, the method further comprises administering to the subject a therapeutically effective amount of gemcitabine. In any of the preceding embodiments of the methods disclosed herein, the method further comprises administering to the subject a therapeutically effective amount of a KRASg12C inhibitor, optionally wherein the KRASG12C inhibitor is AMG 510.
BRIEF DESCRIPTION OF THE DRAWINGS
[0016] FIG. 1A shows a schematic diagram illustrating the pipeline used in the present disclosure for discovery of therapeutic targets in KRAS-mutant pancreatic cancer. The pipeline included low multiplicity-of-infection (MOI) transduction of KRAS-mutant pancreatic cancer cells with a clustered regularly interspaced short palindromic repeats based interference (CRISPRi) library (See, e.g., Gilbert et al., Cell 154: 442-451 (2013)), single-cell RNA sequencing (scRNA-seq), genomic alignments and generation of count matrix (See, e.g., Tang et al., Nature Methods 6: 377-382 (2009)), supervised dimensionality reduction, and machine learning algorithms to identify novel targets in which suppression maximally and selectively target cancer cells.
[0017] FIG. IB shows a scatter plot of z-transformed therapeutic scores for several CRISPR target candidates. The therapeutic index was scored across two negative guide RNAs based on a machine learning algorithm, which collectively established negative control benchmarks for identifying therapeutic targets. [0018] FIG. 2A shows the distribution of cell type populations along a single dimension after supervised dimensionality reduction using machine learning algorithms. The following populations are shown: 1) Cancer cell: cancer cells with a non-targeting guide RNA gene targeted (N = 120), 2) Ineffective target: cancer cells with a negative control gene targeted (N = 122), 3) TXNRD1 : cancer cells with TXNRD1 targeted (N = 87) , and 4) Healthy cell: healthy ductal cells (N = 600).
[0019] FIG. 2B shows a heat map illustrating z-transformed therapeutic scores for the top 20 candidate targets. The candidate targets are displayed in descending order based on average rank across the four indicated decision functions from a machine learning algorithm. As shown, TXNRD1 exhibited the highest average rank.
[0020] FIG. 2C shows a graph depicting weight-averaged decision function scores for therapeutic index across a panel of candidate targets. TXNRD1 emerged as the highest- ranking target.
[0021] FIG. 3A shows the results of cross-analysis of shRNA-mediated pooled negative selection screening. shRNA-mediated pooled negative selection screening was performed in
(1) KrasG12D; Myc; shp53 murine pancreatic ductal adenocarcinoma (mPDAC) cells, and
(2) Myc; p53 /_ murine hepatocellular carcinoma (mHCC) cells. The results of shRNA- mediated pooled negative selection screening from the two cell types were cross-analyzed for comparative purposes.
[0022] FIG. 3B shows a bar graph demonstrating validation of candidate genes obtained from FIG. 3A. Competitive proliferation assays were performed in mPDAC cells, mHCC cells, and nontransformed immortalized mouse embryonic fibroblasts (iMEF). These cells were transduced with a Venus+ virus carrying an inducible shRNA. The following controls shRNAs were used: Ren.713 (a non-targeting shRNA serving as a negative control),
Rpa3.561 (a positive control for growth inhibition in all proliferating cells), Kras.247 (a positive control for mPDAC-specific growth inhibition). G418-selected Venus+ cells were mixed with untransduced cells and cultured in the presence of doxy cy cline to induce shRNA. The percentage of Venus+ and dsRed+ (shRNA-expressing) cells was determined at different time points (TO: day 0; T12: day 12). Changes served as readout of growth inhibitory effects of the expressed shRNA. [0023] FIG. 3C shows immunoblots illustrating TXNRD1 knockdown in mPDAC, mHCC and iMEF cells.
[0024] FIG. 3D shows the effect of pharmacological inhibition of TXNRD1 in pancreatic cancer cells. mPDAC cells were treated with increasing doses of auranofm for 72 hours. Relative proliferation was calculated by measuring viable cell numbers, and normalizing to the viable cell numbers of DMSO-treated cells, which were set to 1. Relative proliferation was then plotted as a function of auranofm concentration and fit to an exponential curve.
[0025] FIG. 3E shows the effect of pharmacological inhibition of TXNRD1 in human pancreatic cancer cells, as measured by the change in viable cell numbers after 72 hours in culture with increasing doses of auranofm. Relative proliferation was calculated by measuring viable cell numbers, and normalizing to the viable cell numbers of DMSO-treated cells, which were set to 1. Relative proliferation was then plotted as a function of auranofm concentration and fit to an exponential curve. L3.3, Colo357, and BXPC3 have wild-type KRAS , and rest of the cell lines harbor a KRAS mutation.
[0026] FIG. 4A shows a bar graph illustrating the correlation of ICso value of the TXNRD1 inhibitor auranofm with KRAS status in human pancreatic cancer cell lines (n = 12).
[0027] FIG. 4B shows a bar graph illustrating the correlation of ICso of auranofm with p53 status in human pancreatic cancer cell lines (n = 9).
[0028] FIG. 4C shows a scatter plot illustrating the correlation of ICso of auranofm with Myc expression levels in human pancreatic cancer cell lines (n = 9).
[0029] FIG. 4D shows the effect of pharmacological inhibition of TXNRD1 as measured by treatment of pancreatic cancer cells with piperlongumine (another TXNRD1 inhibitor) for 72 hours. Cancer cells harboring different KRAS mutations (G12C, G12D, G12V) or wild-type allele were assayed. Relative proliferation was calculated by measuring viable cell numbers, and normalizing to the viable cell numbers of DMSO-treated cells, which were set to 1. Relative proliferation was then plotted as a function of auranofm concentration and fit to an exponential curve.
[0030] FIG. 4E shows a scatter plot illustrating the correlation between TXNRDl and KRAS expression levels in TCGA human pancreatic cancer tumors (n = 149).
[0031] FIGs. 4F-4H show evaluation of changes in the gene signatures upon TXNRDl knockdown in mPDAC cells. Gene set enrichment analysis (GSEA) was used to evaluate changes in the gene signatures of KRAS dependency (FIG. 4F), pancreatic cancer (FIG.
4G), and Amino acid transporter/ferroptosis (FIG. 4H) upon TXNRD1 knockdown in mPDAC cells compared to the cells harboring shRen (a non-targeting shRNA serving as a negative control).
[0032] FIG. 5A shows a schematic representation of conditional RNAi experiments. Tet-On competent murine PD AC cells were transduced with TRMPV-Neo-miR-E shRNAs and a luciferase-hygro vector. The transduced cells were selected for G418 and hygromycin resistance, and transplanted into the pancreas of recipient mice. Upon disease onset, as determined using bioluminescent imaging (which typically occurred after seven days), shRNA expression was induced in a subset of mice by doxycycline (dox) supplementation in drinking water and chow.
[0033] FIG. 5B shows a scatter plot illustrating tumor weights in animals treated with or without doxycycline to induce corresponding shRNAs (n = 4-5).
[0034] FIG. 5C shows bioluminescent imaging of representative mice orthotopically transplanted with mPDAC cells harboring the indicated TRMPV-Neo-miR-E shRNAs with and without dox treatment for 7 days. Dox was administered upon disease onset.
Bioluminescent images on Day 0 (DO) and Day 7 (D7) are shown.
[0035] FIG. 5D shows a bar graph illustrating in vivo tumor weigh reduction caused by auranofm treatment. KRasG12D; p53~ ~ organoids were transplanted in recipient mice, and the mice were treated with vehicle only or auranofm (n = 3-4) for 1 week. Tumor weights were measured and plotted.
[0036] FIG. 5E shows a bar graph illustrating in vivo effects of auranofm treatment on human pancreatic cancer cell line tumor weights. MIAPaCa-2 (KRAS mutant) or Colo357 (KRAS wild-type) organoids were transplanted into the pancreases of recipient mice. The mice were treated with vehicle only or auranofm (n = 5) for 2 weeks. Tumor weights were measured and plotted.
[0037] FIGs. 6A-6B show heat maps illustrating the survival dependency of the indicated cell lines on listed genes. Each column represents a cell line that exhibited the highest average rank and each row represents a gene. Gene dependency score was calculated by taking the average of log2FC (abundance fold change relative to non-diseased tissue) of all corresponding sgRNAs (FIG. 6A) or shRNAs (FIG. 6B). Zero represents no change, negative number represents depletion, and positive number represents an enrichment of indicated cell lines. Un-supervised clustering was used to cluster genes with similar phenotypes. As shown, knocking out or knocking down replication genes RAP1 or PCNA resulted in general lethality to almost all cell lines. In contrast, TXNRD1 is conditionally required for certain cell lines which exhibit similar dependency for KRAS, HRAS, and NRAS.
[0038] FIGs. 7A-7D show the antiproliferative effects of TXNRD1 inhibitor Auranofm in KRAS-mutant pancreatic cancer cells and potential synergistic inhibitory effects when combined with Gemcitabine. FIG. 7 A shows dose-dependent effects of Auranofm,
Gemcitabine, and their combination on MIAPaCa-2 (KRASG12C) and PSN1 (KRASG12R) pancreatic cancer cell lines. FIG. 7B shows percent growth inhibition at each concentration of Auranofm and Gemcitabine in MIAPaCa-2 (KRASG12C) and PSN1 (KRASg12R) cells from FIG. 7A. Data presented as mean of three independent experiments (n = 3). FIG. 7C shows Combination Index (Cl) plots for MIAPaCa-2 (KRASG12C) and PSN1 (KRASg12R) cells treated with Auranofm in combination with Gemcitabine. According to FIG. 7C, Cl values of <1 indicated synergism between Auranofm and Gemcitabine. FIG. 7D shows
Combination Index (Cl) scores for MIAPaCa-2 (KRASG12C) and PSN1 (KRASG12R) cells treated with Auranofm in combination with Gemcitabine at the indicated concentrations. Each Cl score represents data from at least three independent experiments.
[0039] FIGs. 8A-8D show the antiproliferative effects of TXNRD1 inhibitor Auranofm in KRAS-mutant pancreatic cancer cells and potential synergistic inhibitory effects when combined with KRASG12C inhibitor AMG 510. FIG. 8A shows dose-dependent effects of Auranofm, AMG 510, and their combination on MIAPaCa-2 (KRASG12C) and PSN1 (KRASg12R) pancreatic cancer cell lines. FIG. 8B shows percent growth inhibition at each concentration of Auranofm and AMG 510 in MIAPaCa-2 (KRASG12C) and PSN1
(KRASg12R) cells from FIG. 8A. Data presented as mean of three independent experiments (n = 3). FIG. 8C shows Cl plots presenting Cl values of <1 indicated synergism between Auranofm and AMG 510. FIG. 8D shows Combination Index (Cl) scores for MIAPaCa-2 (KRASg12C) and PSN1 (KRASG12R) cells treated with Auranofm in combination with AMG 510 at the indicated concentrations. Each Cl score represents data from at least three independent experiments. [0040] FIG. 9 shows overall survival in patients with pancreatic adenocarcinoma who have TXNRD1 mRNA upregulation. 178 patients were separated to two groups, TXNRD1 low and TXNRD1 high/medium. Proportion cutoff (0-100%) for high/medium and low is > 15.87% (Z score > -1, n = 145) and <= 15.87% (Z score <= -1, n = 33), respectively. Data analysis is based on available TCGA data.
[0041] FIG. 10 shows plasma and pancreas gold concentration in NCR nu/nu mice following a single intraperitoneal injection dose of 10 mg/kg auranofm suspension. Three serial samples (2h, 4h, 24h) collected over 24 hours (n = 3).
DETAILED DESCRIPTION
[0042] It is to be appreciated that certain aspects, modes, embodiments, variations and features of the present methods are described below in various levels of detail in order to provide a substantial understanding of the present technology.
[0043] In practicing the present methods, many conventional techniques in molecular biology, protein biochemistry, cell biology, microbiology and recombinant DNA are used.
See , e.g., Sambrook and Russell eds. (2001) Molecular Cloning: A Laboratory Manual, 3rd edition; the series Ausubel et al ., eds. (2007) Current Protocols in Molecular Biology, the series Methods in Enzymology (Academic Press, Inc., N.Y.); MacPherson et al., (1991) PCR 1: A Practical Approach (IRL Press at Oxford University Press); MacPherson el al., (1995) PCR 2: A Practical Approach, Harlow and Lane eds. (1999) Antibodies, A Laboratory Manual, Freshney (2005) Culture of Animal Cells: A Manual of Basic Technique, 5th edition; Gait ed. (1984) Oligonucleotide Synthesis, U.S. Patent No. 4,683,195; Hames and Higgins eds. (1984) Nucleic Acid Hybridization ; Anderson (1999) Nucleic Acid Hybridization ;
Hames and Higgins eds. (1984) Transcription and Translation; Immobilized Cells and Enzymes (IRL Press (1986)); Perbal (1984) A Practical Guide to Molecular Cloning; Miller and Calos eds. (1987) Gene Transfer Vectors for Mammalian Cells (Cold Spring Harbor Laboratory); Makrides ed. (2003) Gene Transfer and Expression in Mammalian Cells;
Mayer and Walker eds. (1987) Immunochemical Methods in Cell and Molecular Biology (Academic Press, London); and Herzenberg et al., eds (1996) Weir’s Handbook of
Experimental Immunology.
[0044] The present disclosure is based, in part, on the discovery that TXNRDl is a therapeutic target for treating RAS-mutant pancreatic cancer, and that pharmacological inhibition of TXNRD1 in pancreatic cancer cells was effective in treating RAS mutant pancreatic cancer.
Definitions
[0045] Unless defined otherwise, all technical and scientific terms used herein generally have the same meaning as commonly understood by one of ordinary skill in the art to which this technology belongs. As used in this specification and the appended claims, the singular forms“a”,“an” and“the” include plural referents unless the content clearly dictates otherwise. For example, reference to“a cell” includes a combination of two or more cells, and the like. Generally, the nomenclature used herein and the laboratory procedures in cell culture, molecular genetics, organic chemistry, analytical chemistry and nucleic acid chemistry and hybridization described below are those well-known and commonly employed in the art.
[0046] As used herein, the term“about” in reference to a number is generally taken to include numbers that fall within a range of 1%, 5%, or 10% in either direction (greater than or less than) of the number unless otherwise stated or otherwise evident from the context (except where such number would be less than 0% or exceed 100% of a possible value).
[0047] As used herein, the“administration” of an agent or drug to a subject includes any route of introducing or delivering to a subject a compound to perform its intended function. Administration can be carried out by any suitable route, including orally, intranasally, parenterally (intravenously, intramuscularly, intraperitoneally, or subcutaneously), or topically. Administration includes self-administration and the administration by another.
[0048] As used herein, the term“antibody” collectively refers to immunoglobulins or immunoglobulin-like molecules including by way of example and without limitation, IgA, IgD, IgE, IgG and IgM, combinations thereof, and similar molecules produced during an immune response in any vertebrate, for example, in mammals such as humans, goats, rabbits and mice, as well as non-mammalian species, such as shark immunoglobulins. As used herein,“antibodies” (includes intact immunoglobulins) and“antigen binding fragments” specifically bind to a molecule of interest (or a group of highly similar molecules of interest) to the substantial exclusion of binding to other molecules (for example, antibodies and antibody fragments that have a binding constant for the molecule of interest that is at least 103 M 1 greater, at least 104 M 1 greater or at least 105 M 1 greater than a binding constant for other molecules in a biological sample). The term“antibody” also includes genetically engineered forms such as chimeric antibodies (for example, humanized murine antibodies), heteroconjugate antibodies (such as, bispecific antibodies). See also, Pierce Catalog and Handbook, 1994-1995 (Pierce Chemical Co., Rockford, Ill.); Kuby, J., Immunology , 3rd Ed., W.H. Freeman & Co., New York, 1997.
[0049] More particularly, antibody refers to a polypeptide ligand comprising at least a light chain immunoglobulin variable region or heavy chain immunoglobulin variable region which specifically recognizes and binds an epitope of an antigen. Antibodies are composed of a heavy and a light chain, each of which has a variable region, termed the variable heavy (VH) region and the variable light (VL) region. Together, the VH region and the VL region are responsible for binding the antigen recognized by the antibody. Typically, an
immunoglobulin has heavy (H) chains and light (L) chains interconnected by disulfide bonds. There are two types of light chain, lambda (l) and kappa (K). There are five main heavy chain classes (or isotypes) which determine the functional activity of an antibody molecule: IgM, IgD, IgG, IgA and IgE. Each heavy and light chain contains a constant region and a variable region, (the regions are also known as“domains”). In combination, the heavy and the light chain variable regions specifically bind the antigen. Light and heavy chain variable regions contain a“framework” region interrupted by three hypervariable regions, also called “complementarity-determining regions” or“CDRs”. The extent of the framework region and CDRs have been defined (see, Rabat et al., Sequences of Proteins of Immunological Interest , U.S. Department of Health and Human Services, 1991, which is hereby incorporated by reference). The Rabat database is now maintained online. The sequences of the framework regions of different light or heavy chains are relatively conserved within a species. The framework region of an antibody, that is the combined framework regions of the constituent light and heavy chains, largely adopt a b-sheet conformation and the CDRs form loops which connect, and in some cases form part of, the b-sheet structure. Thus, framework regions act to form a scaffold that provides for positioning the CDRs in correct orientation by inter chain, non-covalent interactions.
[0050] The CDRs are primarily responsible for binding to an epitope of an antigen. The CDRs of each chain are typically referred to as CDR1, CDR2, and CDR3, numbered sequentially starting from the N-terminus, and are also typically identified by the chain in which the particular CDR is located. Thus, a VH CDR3 is located in the variable domain of the heavy chain of the antibody in which it is found, whereas a VL CDRl is the CDR1 from the variable domain of the light chain of the antibody in which it is found. An antibody that binds TXNRD1 protein will have a specific VH region and the VL region sequence, and thus specific CDR sequences. Antibodies with different specificities (i.e. different combining sites for different antigens) have different CDRs. Although it is the CDRs that vary from antibody to antibody, only a limited number of amino acid positions within the CDRs are directly involved in antigen binding. These positions within the CDRs are called specificity determining residues (SDRs). “Immunoglobulin-related compositions” as used herein, refers to antibodies (including monoclonal antibodies, polyclonal antibodies, humanized antibodies, chimeric antibodies, recombinant antibodies, multi-specific antibodies, bispecific antibodies, etc.,) as well as antibody fragments. An antibody or antigen binding fragment thereof specifically binds to an antigen.
[0051] As used herein, the term“antibody-related polypeptide” means antigen-binding antibody fragments, including single-chain antibodies, that can comprise the variable region(s) alone, or in combination, with all or part of the following polypeptide elements: hinge region, CHi, CFh, and CFE domains of an antibody molecule. Also included in the technology are any combinations of variable region(s) and hinge region, CHi, CFh, and CFE domains. Antibody-related molecules useful in the present methods, e.g ., but are not limited to, Fab, Fab' and F(ab')2, Fd, single-chain Fvs (scFv), single-chain antibodies, disulfide- linked Fvs (sdFv) and fragments comprising either a VL or VH domain. Examples include: (i) a Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CHi domains; (ii) a F(ab')2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the VH and CHi domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al. , Nature 341 : 544-546, 1989), which consists of a VH domain; and (vi) an isolated complementarity determining region (CDR). As such“antibody fragments” or “antigen binding fragments” can comprise a portion of a full length antibody, generally the antigen binding or variable region thereof. Examples of antibody fragments or antigen binding fragments include Fab, Fab1, F(ab')2, and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules; and multi-specific antibodies formed from antibody fragments.
[0052] The term“antigen binding fragment” refers to a fragment of the whole immunoglobulin structure which possesses a part of a polypeptide responsible for binding to antigen. Examples of the antigen binding fragment useful in the present technology include scFv, (SCFV)2, SCFVFC, Fab, Fab' and F(ab')2, but are not limited thereto.
[0053] As used herein, the term“diabodies” refers to small antibody fragments with two antigen-binding sites, which fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) in the same polypeptide chain (VH VL). By using a linker that is too short to allow pairing between the two domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create two antigen binding sites. Diabodies are described more fully in, e.g ., EP 404,097;
WO 93/11161; and Hollinger et al. , Proc. Natl. Acad. Sci. USA , 90: 6444-6448 (1993).
[0054] As used herein, the terms“single-chain antibodies” or“single-chain Fv (scFv)” refer to an antibody fusion molecule of the two domains of the Fv fragment, VL and VH. Single-chain antibody molecules may comprise a polymer with a number of individual molecules, for example, dimer, trimer or other polymers. Furthermore, although the two domains of the Fv fragment, VL and VH, are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single-chain Fv (scFv)). Bird et al. (1988) Science 242:423-426 and Huston et al. (1988) Proc. Natl. Acad Sci. USA 85:5879-5883. Such single-chain antibodies can be prepared by recombinant techniques or enzymatic or chemical cleavage of intact antibodies.
[0055] Any of the above-noted antibody fragments are obtained using conventional techniques known to those of skill in the art, and the fragments are screened for binding specificity and neutralization activity in the same manner as are intact antibodies.
[0056] The terms“complementary” or“complementarity” as used herein with reference to polynucleotides (i.e., a sequence of nucleotides such as an oligonucleotide or a target nucleic acid) refer to the base-pairing rules. The complement of a nucleic acid sequence as used herein refers to an oligonucleotide which, when aligned with the nucleic acid sequence such that the 5' end of one sequence is paired with the 3' end of the other, is in“antiparallel association.” For example, the sequence“5'-A-G-T-3'” is complementary to the sequence “3'-T-C-A-5” Certain bases not commonly found in naturally-occurring nucleic acids may be included in the nucleic acids described herein. These include, for example, inosine, 7- deazaguanine, Locked Nucleic Acids (LNA), and Peptide Nucleic Acids (PNA).
Complementarity need not be perfect; stable duplexes may contain mismatched base pairs, degenerative, or unmatched bases. Those skilled in the art of nucleic acid technology can determine duplex stability empirically considering a number of variables including, for example, the length of the oligonucleotide, base composition and sequence of the
oligonucleotide, ionic strength and incidence of mismatched base pairs. A complementary sequence can also be an RNA sequence complementary to the DNA sequence or its complementary sequence, and can also be a cDNA.
[0057] As used herein, the term“consensus FR” means a framework (FR) antibody region in a consensus immunoglobulin sequence. The FR regions of an antibody do not contact the antigen.
[0058] As used herein, a "control" is an alternative sample used in an experiment for comparison purpose. A control can be "positive" or "negative." For example, where the purpose of the experiment is to determine a correlation of the efficacy of a therapeutic agent for the treatment for a particular type of disease or condition, a positive control (a compound or composition known to exhibit the desired therapeutic effect) and a negative control (a subject or a sample that does not receive the therapy or receives a placebo) are typically employed.
[0059] As used herein, the term“effective amount” refers to a quantity sufficient to achieve a desired therapeutic and/or prophylactic effect, e.g ., an amount which results in the prevention of, or a decrease in a disease or condition described herein or one or more signs or symptoms associated with a disease or condition described herein. In the context of therapeutic or prophylactic applications, the amount of a composition administered to the subject will vary depending on the composition, the degree, type, and severity of the disease and on the characteristics of the individual, such as general health, age, sex, body weight and tolerance to drugs. The skilled artisan will be able to determine appropriate dosages depending on these and other factors. The compositions can also be administered in combination with one or more additional therapeutic compounds. In the methods described herein, the therapeutic compositions may be administered to a subject having one or more signs or symptoms of a RAS-mutant cancer. As used herein, a“therapeutically effective amount” of a composition refers to composition levels in which the physiological effects of a disease or condition are ameliorated or eliminated. A therapeutically effective amount can be given in one or more administrations.
[0060] As used herein,“expression” includes one or more of the following: transcription of the gene into precursor mRNA; splicing and other processing of the precursor mRNA to produce mature mRNA; mRNA stability; translation of the mature mRNA into protein (including codon usage and tRNA availability); and glycosylation and/or other modifications of the translation product, if required for proper expression and function.
[0061] As used herein, the term“gene” means a segment of DNA that contains all the information for the regulated biosynthesis of an RNA product, including promoters, exons, introns, and other untranslated regions that control expression.
[0062] “Homology” or“identity” or“similarity” refers to sequence similarity between two peptides or between two nucleic acid molecules. Homology can be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same nucleobase or amino acid, then the molecules are homologous at that position. A degree of homology between sequences is a function of the number of matching or homologous positions shared by the sequences. A polynucleotide or polynucleotide region (or a polypeptide or polypeptide region) has a certain percentage (for example, at least 60%, 65%, 70%, 75%, 80%, 85%,
90%, 95%, 98% or 99%) of“sequence identity” to another sequence means that, when aligned, that percentage of bases (or amino acids) are the same in comparing the two sequences. This alignment and the percent homology or sequence identity can be determined using software programs known in the art. In some embodiments, default parameters are used for alignment. One alignment program is BLAST, using default parameters. In particular, programs are BLASTN and BLASTP, using the following default parameters: Genetic code=standard; filter=none; strand=both; cutoff=60; expect=10;
Matrix=BLOSUM62; Descriptions=50 sequences; sort by =HIGH SCORE; Databases=non- redundant, GenBank+EMBL+DDBJ+PDB+GenBank CDS
translations+SwissProtein+SPupdate+PIR. Details of these programs can be found at the National Center for Biotechnology Information. Biologically equivalent polynucleotides are those having the specified percent homology and encoding a polypeptide having the same or similar biological activity. Two sequences are deemed“unrelated” or“non-homologous” if they share less than 40% identity, or less than 25% identity, with each other.
[0063] As used herein, the term“hypervariable region” refers to the amino acid residues of an antibody which are responsible for antigen-binding. The hypervariable region generally comprises amino acid residues from a“complementarity determining region” or“CDR” (e.g, around about residues 24-34 (LI), 50-56 (L2) and 89-97 (L3) in the VL, and around about 31- 35B (HI), 50-65 (H2) and 95-102 (H3) in the VH (Kabat et al. , Sequences of Proteins of Immunological Interest , 5th Ed. Public Health Service, National Institutes of Health,
Bethesda, MD. (1991)) and/or those residues from a“hypervariable loop” (e.g, residues 26- 32 (LI), 50-52 (L2) and 91-96 (L3) in the VL, and 26-32 (HI), 52A-55 (H2) and 96-101 (H3) in the VH (Chothia and Lesk J Mol. Biol. 196:901-917 (1987)).
[0064] The term“hybridize” as used herein refers to a process where two substantially complementary nucleic acid strands (at least about 65% complementary over a stretch of at least 14 to 25 nucleotides, at least about 75%, or at least about 90% complementary) anneal to each other under appropriately stringent conditions to form a duplex or heteroduplex through formation of hydrogen bonds between complementary base pairs. Nucleic acid hybridization techniques are well known in the art. See , e.g, Sambrook, et al., 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Press, Plainview, N.Y. Hybridization and the strength of hybridization (; i.e ., the strength of the association between the nucleic acids) is influenced by such factors as the degree of complementarity between the nucleic acids, stringency of the conditions involved, and the thermal melting point (Tm) of the formed hybrid. Those skilled in the art understand how to estimate and adjust the stringency of hybridization conditions such that sequences having at least a desired level of complementarity will stably hybridize, while those having lower complementarity will not. For examples of hybridization conditions and parameters, see, e.g., Sambrook, et al., 1989, Molecular Cloning: A Laboratory Manual, Second Edition,
Cold Spring Harbor Press, Plainview, N.Y. ; Ausubel, F. M. et al., 1994, Current Protocols in Molecular Biology, John Wiley & Sons, Secaucus, N.J. In some embodiments, specific hybridization occurs under stringent hybridization conditions. An oligonucleotide or polynucleotide ( e.g ., a probe or a primer) that is specific for a target nucleic acid will “hybridize” to the target nucleic acid under suitable conditions.
[0065] As used herein,“oligonucleotide” refers to a molecule that has a sequence of nucleic acid bases on a backbone comprised mainly of identical monomer units at defined intervals. The bases are arranged on the backbone in such a way that they can bind with a nucleic acid having a sequence of bases that are complementary to the bases of the oligonucleotide. The most common oligonucleotides have a backbone of sugar phosphate units. A distinction may be made between oligodeoxyribonucleotides that do not have a hydroxyl group at the 2' position and oligoribonucleotides that have a hydroxyl group at the 2' position.
Oligonucleotides may also include derivatives, in which the hydrogen of the hydroxyl group is replaced with organic groups, e.g., an allyl group. One or more bases of the
oligonucleotide may also be modified to include a phosphorothioate bond (e.g, one of the two oxygen atoms in the phosphate backbone which is not involved in the internucleotide bridge, is replaced by a sulfur atom) to increase resistance to nuclease degradation. The exact size of the oligonucleotide will depend on many factors, which in turn depend on the ultimate function or use of the oligonucleotide. The oligonucleotide may be generated in any manner, including, for example, chemical synthesis, DNA replication, restriction endonuclease digestion of plasmids or phage DNA, reverse transcription, PCR, or a combination thereof. The oligonucleotide may be modified e.g, by addition of a methyl group, a biotin or digoxigenin moiety, a fluorescent tag or by using radioactive nucleotides.
[0066] As used herein, the term“pharmaceutically-acceptable carrier” is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal compounds, isotonic and absorption delaying compounds, and the like, compatible with pharmaceutical administration. Pharmaceutically-acceptable carriers and their formulations are known to one skilled in the art and are described, for example, in Remington's
Pharmaceutical Sciences (20th edition, ed. A. Gennaro, 2000, Lippincott, Williams &
Wilkins, Philadelphia, Pa.).
[0067] As used herein, the term“polynucleotide” or“nucleic acid” means any RNA or DNA, which may be unmodified or modified RNA or DNA. Polynucleotides include, without limitation, single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, RNA that is mixture of single- and double-stranded regions, and hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double- stranded regions. In addition, polynucleotide refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The term polynucleotide also includes DNAs or RNAs containing one or more modified bases and DNAs or RNAs with backbones modified for stability or for other reasons.
[0068] As used herein,“prevention,”“prevent,” or“preventing” of a disorder or condition refers to one or more compounds that, in a statistical sample, reduces the occurrence of the disorder or condition in the treated sample relative to an untreated control sample, or delays the onset of one or more symptoms of the disorder or condition relative to the untreated control sample. As used herein, preventing a RAS-mutant cancer, includes preventing or delaying the initiation of symptoms of a RAS-mutant cancer. As used herein, prevention of a RAS-mutant cancer also includes preventing a recurrence of one or more signs or symptoms of a RAS-mutant cancer.
[0069] As used herein, the term“sample” refers to clinical samples obtained from a subject. Biological samples may include tissues, cells, protein or membrane extracts of cells, mucus, sputum, bone marrow, bronchial alveolar lavage (BAL), bronchial wash (BW), and biological fluids ( e.g ., ascites fluid or cerebrospinal fluid (CSF)) isolated from a subject, as well as tissues, cells and fluids (blood, plasma, saliva, urine, serum etc.) present within a subject.
[0070] As used herein, the term“separate” therapeutic use refers to an administration of at least two active ingredients at the same time or at substantially the same time by different routes.
[0071] As used herein, the term“sequential” therapeutic use refers to administration of at least two active ingredients at different times, the administration route being identical or different. More particularly, sequential use refers to the whole administration of one of the active ingredients before administration of the other or others commences. It is thus possible to administer one of the active ingredients over several minutes, hours, or days before administering the other active ingredient or ingredients. There is no simultaneous treatment in this case. [0072] As used herein, the term“simultaneous” therapeutic use refers to the administration of at least two active ingredients by the same route and at the same time or at substantially the same time.
[0073] As used herein, the terms“subject,”“individual,” or“patient” are used
interchangeably and refer to an individual organism, a vertebrate, a mammal, or a human. In certain embodiments, the individual, patient or subject is a human.
[0074] As used herein, the terms“target sequence” and“target nucleic acid sequence” refer to a specific nucleic acid sequence to be modulated ( e.g ., inhibited or downregulated).
[0075] The term“TXNRD1 inhibitor” as used herein refers to an agent that inhibits gene expression or biological activity of TXNRD1. Examples of TXNRD1 biological activity include, but are not limited to, enzymatic activity, substrate binding activity, homo- or hetero dimerization activity, and binding to a cellular structure. Several different isoforms of thioredoxin reductase 1 exist. The TXNRD1 inhibitors of the present disclosure inhibit at least one biological activity of at least one isoform. Examples of TXNRD1 inhibitors include, but are not limited to, auranofm, Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, protoporphyrin IX, shRNAs or siRNAs against TXNRD1, anti-sense oligonucleotides against TXNRD1, anti- TXNRD1 antibodies, or any derivatives thereof.
[0076] “Treating”,“treat”, or“treatment” as used herein covers the treatment of a disease or disorder described herein, in a subject, such as a human, and includes: (i) inhibiting a disease or disorder, i.e., arresting its development; (ii) relieving a disease or disorder, i.e., causing regression of the disorder; (iii) slowing progression of the disorder; and/or (iv) inhibiting, relieving, or slowing progression of one or more symptoms of the disease or disorder. In some embodiments, treatment means that the symptoms associated with the disease are, e.g., alleviated, reduced, cured, or placed in a state of remission.
[0077] It is also to be appreciated that the various modes of treatment or prevention of medical diseases and conditions as described are intended to mean“substantial,” which includes total but also less than total treatment or prevention, and wherein some biologically or medically relevant result is achieved. The treatment may be a continuous prolonged treatment for a chronic disease or a single, or few time administrations for the treatment of an acute condition. TXNRD1 Inhibitors of the Present Technology
[0078] TXNRD1 protein (also known as, thioredoxin reductase 1, GRIM-12, TR, TR1, TRXRl, or TXNR) is a member of the pyridine nucleotide oxidoreductase family, and is a component of the thioredoxin (Trx) system. TXNRDl is a flavoenzyme, which reduces thioredoxins, as well as other substrates, and plays a key role in redox homoeostasis and selenium metabolism. TXNRDl protein functions as a homodimer containing FAD, and has a selenocysteine (Sec) at the active site.
[0079] In one aspect, the present disclosure provides compositions for treating a RAS-mutant cancer. In some embodiments, the TXNRDl inhibitor reduces gene expression and/or activity levels of TXNRDl. In some embodiments, the TXNRDl inhibitor reduces a TXNRDl activity selected from the group consisting of enzymatic activity, substrate binding activity, homo- or hetero-dimerization activity, and binding to a cellular structure.
[0080] In one aspect, the present disclosure provides pharmacological inhibitors including, but not limited to, auranofm, Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, and protoporphyrin IX. Anti- TXNRDl antibodies or any derivatives thereof, may also be used in the methods disclosed herein.
[0081] In another aspect, the present disclosure provides inhibitory RNAs (e.g., sgRNAs, antisense RNAs or shRNAs) that inhibit TXNRDl expression and/or activity levels.
Examples of such inhibitory RNAs include those with sequences comprising
TCTAATATCATTAACACCATGG (SEQ ID NO: 1; human shTXNRDl),
T A A AT A A A ACTGA AT AT GGT C A (SEQ ID NO: 2; human shTXNRDl),
TTAATAATAACTTATGATATTA (SEQ ID NO: 3; human shTXNRDl),
TTT GT A AC A A A A AT AC AT GGA A (SEQ ID NO: 4; human shTXNRDl),
TTTAAATGAAAATCCTTCACAT (SEQ ID NO: 5; human shTXNRDl),
TTTTAAATGAAAATCCTTCACA (SEQ ID NO: 6; human shTXNRDl),
T AAGAAAAGAGAAT C AC AAC AT (SEQ ID NO: 7; human shTXNRDl),
TTTTCATTTATCTTCACCCCTA (SEQ ID NO: 8; human shTXNRDl),
T T AG A A AG A A AT AG AT AC C C A A (SEQ ID NO: 9; human shTXNRDl),
T A AT A AT A AC TT AT GAT ATT A A (SEQ ID NO: 10; human shTXNRDl),
TTT AGTC AC AGGGT AATTCGT C (SEQ ID NO: 11; murine shTxnrdl), and TTCGTCACTGACAACGTTGTGA (SEQ ID NO: 12; murine shTxnrdl), or any complement thereof.
[0082] The present disclosure provides an antisense nucleic acid comprising a nucleic acid sequence that is complementary to and specifically hybridizes with a portion of any one of
NM_182729.2 Homo sapiens thioredoxin reductase 1 (TXNRD1), transcript variant 1, mRNA (SEQ ID NO: 13)
1 agaccctcac gtgatgacaa cagctagcaa agttctgtag ctactgcctt agggcatagt
61 ctaatttctt cagtaaaaac acacttattc caaatttggt tccagaattg ccttaaattg
121 tttttgctct gttcttaggt tgggggcggc tatgagcagg cagaggatgt ggtgtcaccc
181 aattaggagc tctcagctta cgaggcaatt agcataggtt gccagggctg cacgaggagt
241 ggatttctgc tttgtcattc tgactctggc agttagcccg cccgctcggc gcagggcgtg
301 gcttctcgta gccattagga aacagcaacc ctttcacctc agttttcttc actccggcat
361 ttgcagcaga gcgaaaggtg gtcgagtcct gaaggagggc ctgatgtctt catcattctc
421 aaattcttag gacggtcggg ccctggaagg aacgctctcg gaattggccg cggaaaccga
481 tctgcccgtt gtgtttgtga aacagagaaa gataggcggc catggtccaa ccttgaaggc
541 ttatcaggag ggcagacttc aaaagctact aaaaatgaac ggccctgaag atcttcccaa
601 gtcctatgac tatgacctta tcatcattgg aggtggctca ggaggtctgg cagctgctaa
661 ggaggcagcc caatatggca agaaggtgat ggtcctggac tttgtcactc ccacccctct
721 tggaactaga tggggtctcg gaggaacatg tgtgaatgtg ggttgcatac ctaaaaaact
781 gatgcatcaa gcagctttgt taggacaagc cctgcaagac tctcgaaatt atggatggaa
841 agtcgaggag acagttaagc atgattggga cagaatgata gaagctgtac agaatcacat
901 tggctctttg aattggggct accgagtagc tctgcgggag aaaaaagtcg tctatgagaa
961 tgcttatggg caatttattg gtcctcacag gattaaggca acaaataata aaggcaaaga
1021 aaaaatttat tcagcagaga gatttctcat tgccactggt gaaagaccac gttacttggg
1081 catccctggt gacaaagaat actgcatcag cagtgatgat cttttctcct tgccttactg
1141 cccgggtaag accctggttg ttggagcatc ctatgtcgct ttggagtgcg ctggatttct
1201 tgctggtatt ggtttagacg tcactgttat ggttaggtcc attcttctta gaggatttga
1261 ccaggacatg gccaacaaaa ttggtgaaca catggaagaa catggcatca agtttataag
1321 acagttcgta ccaattaaag ttgaacaaat tgaagcaggg acaccaggcc gactcagagt
1381 agtagctcag tccaccaata gtgaggaaat cattgaagga gaatataata cggtgatgct
1441 ggcaatagga agagatgctt gcacaagaaa aattggctta gaaaccgtag gggtgaagat
1501 aaatgaaaag actggaaaaa tacctgtcac agatgaagaa cagaccaatg tgccttacat
1561 ctatgccatt ggcgatatat tggaggataa ggtggagctc accccagttg caatccaggc
1621 aggaagattg ctggctcaga ggctctatgc aggttccact gtcaagtgtg actatgaaaa
1681 tgttccaacc actgtattta ctcctttgga atatggtgct tgtggccttt ctgaggagaa
1741 agctgtggag aagtttgggg aagaaaatat tgaggtttac catagttact tttggccatt
1801 ggaatggacg attccgtcaa gagataacaa caaatgttat gcaaaaataa tctgtaatac
1861 taaagacaat gaacgtgttg tgggctttca cgtactgggt ccaaatgctg gagaagttac
1921 acaaggcttt gcagctgcgc tcaaatgtgg actgaccaaa aagcagctgg acagcacaat
1981 tggaatccac cctgtctgtg cagaggtatt cacaacattg tctgtgacca agcgctctgg
2041 ggcaagcatc ctccaggctg gctgctgagg ttaagcccca gtgtggatgc tgttgccaag
2101 actgcaaacc actggctcgt ttccgtgccc aaatccaagg cgaagttttc tagagggttc
2161 ttgggctctt ggcacctgcg tgtcctgtgc ttaccaccgc ccaaggcccc cttggatctc
2221 ttggatagga gttggtgaat agaaggcagg cagcatcaca ctggggtcac tgacagactt
2281 gaagctgaca tttggcaggg catcgaaggg atgcatccat gaagtcacca gtctcaagcc
2341 catgtggtag gcggtgatgg aacaactgtc aaatcagttt tagcatgacc tttccttgtg
2401 gattttctta ttctcgttgt caagttttct agggttgaat ttttttcttt tttctccatg
2461 gtgttaatga tattagagat gaaaaacgtt agcagttgat ttttgtccaa aagcaagtca
2521 tggctagagt atccatgcaa ggtgtcttgt tgcatggaag ggatagtttg gctcccttgg 2581 aggctatgta ggcttgtccc gggaaagaga actgtcctgc agctgaaatg gactgttctt 2641 tactgacctg ctcagcagtt tcttctctca tatattccca aaacaagtac atctgcgatc 2701 aactctagcc aaatttgccc ctgtgtgcta catgatggat gattattatt ttaaggtctg 2761 tttaggaagg gaaatggcta cttggccagc cattgcctgg catttggtag tatagtatga 2821 ttctcaccat tatttgtcat ggaggcagac atacaccaga aatgggggag aaacagtaca 2881 tatctttctg tctttagttt attgtgtgct ggtctaagca agctgagatc atttgcaatg 2941 gaaaacacgt aacttgttta aaagtttttc tggtagcttt agctttatgc taaaaaaaat 3001 aatgacattg ggtatctatt tctttctaag actacattag taggaaaata agtcttttca 3061 tgcttatgat ttagctgttt tgtggtaatt gctttttaaa ggaagttatt aatatcataa 3121 gttattatta atattttgaa cacaggtgga tgtgaaggat tttcatttaa aaaccaagtg 3181 gttttgactt tttctgttga atgaacaact gtgccttgtg gaatttttgc agaagtgttt 3241 atgctttgtt agcatttcaa cttgcattat tataaagagg tattaatgcc tcagttatgt 3301 gtttgtcaat gtactggctg aggattctat ctcagctgtc ttttctaact gtgtaggttg 3361 agttttgaac acgtgcttgt ggacatcagg cctcctgcca gcagttcttg aagcttcttt 3421 ttcattcctg ctactctacc tgtatttctc agttgcagca ctgagtggtc aaaatacatt 3481 tctgggccac ctcagggaac ccatgcatct gcctggcatt taggcagcag agcccctgac 3541 cgtcccccac agggctctgc ctcacgtcct catctcattt ggctgtgtaa agaaatggga 3601 aaagggaaaa ggagagagca attgaggcag ttgaccatat tcagttttat ttatttattt 3661 ttaatttgtt tttttctcca agtccaccag tctctgaaat tagaacagta ggcggtatga 3721 gataatcagg cctaatcatg ttgtgattct cttttcttag tggagtggaa tgttctatcc 3781 ccacaagaag gattatatct tatagacttg tcttgttcag attctgtatt tacccatttt 3841 attgaaacat atactaagtt ccatgtattt ttgttacaaa tcttctgaaa aaaaacaaaa 3901 caatgtgaaa cattaaaatt aaaaggcatt aataatatcc acgtgtgcct tcttactgaa 3961 aaaaaaaaa
NM_182742.2 Homo sapiens thioredoxin reductase 1 (TXNRD1), transcript variant 2, mRNA (SEQ ID NO: 14)
1 agaccctcac gtgatgacaa cagctagcaa agttctgtag ctactgcctt agggcatagt 61 ctaatttctt cagtaaaaac acacttattc caaatttggt tccagaattg ccttaaattg 121 tttttgctct gttcttaggt tgggggcggc tatgagcagg cagaggatgt ggtgtcaccc 181 aattaggagc tctcagctta cgaggcaatt agcataggtt gccagggctg cacgaggagt 241 ggatttctgc tttgtcattc tgactctggc agttagcccg cccgctcggc gcagggcgtg 301 gcttctcgta gccattagga aacagcaacc ctttcacctc agttttcttc actccggcat 361 ttgcagcaga gcgaaaggtg gtcgagtcct gaaggagggc ctgatgtctt catcattctc 421 aaattcttgt aagctctgcg tcgggtgaaa ccagacaaag ccgcgagccc agggatggga 481 gcacgcgggg gacggcctgc cggcggggac gacagcattg cgcctgggtg cagcagtgtg 541 cgtctcgggg aagggaagat attttaaggc gtgtctgagc agacggggag gcttttccaa 601 acccaggcag cttcgtggcg tgtgcggttt cgacccggtc acacaaagct tcagcatgtc 661 atgtggctta tcaggagggc agacttcaaa agctactaaa aatgaacggc cctgaagatc 721 ttcccaagtc ctatgactat gaccttatca tcattggagg tggctcagga ggtctggcag 781 ctgctaagga ggcagcccaa tatggcaaga aggtgatggt cctggacttt gtcactccca 841 cccctcttgg aactagatgg ggtctcggag gaacatgtgt gaatgtgggt tgcataccta 901 aaaaactgat gcatcaagca gctttgttag gacaagccct gcaagactct cgaaattatg 961 gatggaaagt cgaggagaca gttaagcatg attgggacag aatgatagaa gctgtacaga 1021 atcacattgg ctctttgaat tggggctacc gagtagctct gcgggagaaa aaagtcgtct 1081 atgagaatgc ttatgggcaa tttattggtc ctcacaggat taaggcaaca aataataaag 1141 gcaaagaaaa aatttattca gcagagagat ttctcattgc cactggtgaa agaccacgtt 1201 acttgggcat ccctggtgac aaagaatact gcatcagcag tgatgatctt ttctccttgc 1261 cttactgccc gggtaagacc ctggttgttg gagcatccta tgtcgctttg gagtgcgctg 1321 gatttcttgc tggtattggt ttagacgtca ctgttatggt taggtccatt cttcttagag 1381 gatttgacca ggacatggcc aacaaaattg gtgaacacat ggaagaacat ggcatcaagt 1441 ttataagaca gttcgtacca attaaagttg aacaaattga agcagggaca ccaggccgac 1501 tcagagtagt agctcagtcc accaatagtg aggaaatcat tgaaggagaa tataatacgg 1561 tgatgctggc aataggaaga gatgcttgca caagaaaaat tggcttagaa accgtagggg 1621 tgaagataaa tgaaaagact ggaaaaatac ctgtcacaga tgaagaacag accaatgtgc
1681 cttacatcta tgccattggc gatatattgg aggataaggt ggagctcacc ccagttgcaa
1741 tccaggcagg aagattgctg gctcagaggc tctatgcagg ttccactgtc aagtgtgact
1801 atgaaaatgt tccaaccact gtatttactc ctttggaata tggtgcttgt ggcctttctg
1861 aggagaaagc tgtggagaag tttggggaag aaaatattga ggtttaccat agttactttt
1921 ggccattgga atggacgatt ccgtcaagag ataacaacaa atgttatgca aaaataatct
1981 gtaatactaa agacaatgaa cgtgttgtgg gctttcacgt actgggtcca aatgctggag
2041 aagttacaca aggctttgca gctgcgctca aatgtggact gaccaaaaag cagctggaca
2101 gcacaattgg aatccaccct gtctgtgcag aggtattcac aacattgtct gtgaccaagc
2161 gctctggggc aagcatcctc caggctggct gctgaggtta agccccagtg tggatgctgt
2221 tgccaagact gcaaaccact ggctcgtttc cgtgcccaaa tccaaggcga agttttctag
2281 agggttcttg ggctcttggc acctgcgtgt cctgtgctta ccaccgccca aggccccctt
2341 ggatctcttg gataggagtt ggtgaataga aggcaggcag catcacactg gggtcactga
2401 cagacttgaa gctgacattt ggcagggcat cgaagggatg catccatgaa gtcaccagtc
2461 tcaagcccat gtggtaggcg gtgatggaac aactgtcaaa tcagttttag catgaccttt
2521 ccttgtggat tttcttattc tcgttgtcaa gttttctagg gttgaatttt tttctttttt
2581 ctccatggtg ttaatgatat tagagatgaa aaacgttagc agttgatttt tgtccaaaag
2641 caagtcatgg ctagagtatc catgcaaggt gtcttgttgc atggaaggga tagtttggct
2701 cccttggagg ctatgtaggc ttgtcccggg aaagagaact gtcctgcagc tgaaatggac
2761 tgttctttac tgacctgctc agcagtttct tctctcatat attcccaaaa caagtacatc
2821 tgcgatcaac tctagccaaa tttgcccctg tgtgctacat gatggatgat tattatttta
2881 aggtctgttt aggaagggaa atggctactt ggccagccat tgcctggcat ttggtagtat
2941 agtatgattc tcaccattat ttgtcatgga ggcagacata caccagaaat gggggagaaa
3001 cagtacatat ctttctgtct ttagtttatt gtgtgctggt ctaagcaagc tgagatcatt
3061 tgcaatggaa aacacgtaac ttgtttaaaa gtttttctgg tagctttagc tttatgctaa
3121 aaaaaataat gacattgggt atctatttct ttctaagact acattagtag gaaaataagt
3181 cttttcatgc ttatgattta gctgttttgt ggtaattgct ttttaaagga agttattaat
3241 atcataagtt attattaata ttttgaacac aggtggatgt gaaggatttt catttaaaaa
3301 ccaagtggtt ttgacttttt ctgttgaatg aacaactgtg ccttgtggaa tttttgcaga
3361 agtgtttatg ctttgttagc atttcaactt gcattattat aaagaggtat taatgcctca
3421 gttatgtgtt tgtcaatgta ctggctgagg attctatctc agctgtcttt tctaactgtg
3481 taggttgagt tttgaacacg tgcttgtgga catcaggcct cctgccagca gttcttgaag
3541 cttctttttc attcctgcta ctctacctgt atttctcagt tgcagcactg agtggtcaaa
3601 atacatttct gggccacctc agggaaccca tgcatctgcc tggcatttag gcagcagagc
3661 ccctgaccgt cccccacagg gctctgcctc acgtcctcat ctcatttggc tgtgtaaaga
3721 aatgggaaaa gggaaaagga gagagcaatt gaggcagttg accatattca gttttattta
3781 tttattttta atttgttttt ttctccaagt ccaccagtct ctgaaattag aacagtaggc
3841 ggtatgagat aatcaggcct aatcatgttg tgattctctt ttcttagtgg agtggaatgt
3901 tctatcccca caagaaggat tatatcttat agacttgtct tgttcagatt ctgtatttac
3961 ccattttatt gaaacatata ctaagttcca tgtatttttg ttacaaatct tctgaaaaaa
4021 aacaaaacaa tgtgaaacat taaaattaaa aggcattaat aatatccacg tgtgccttct
4081 tactgaaaaa aaaaaa
Homo sapiens thioredoxin reductase 1 (TXNRD1), transcript variant 3, mRNA
NCBI Reference Sequence: NM_182743.2 (SEQ ID NO: 15)
1 agaccctcac gtgatgacaa cagctagcaa agttctgtag ctactgcctt agggcatagt 61 ctaatttctt cagtaaaaac acacttattc caaatttggt tccagaattg ccttaaattg 121 tttttgctct gttcttaggt tgggggcggc tatgagcagg cagaggatgt ggtgtcaccc 181 aattaggagc tctcagctta cgaggcaatt agcataggtt gccagggctg cacgaggagt 241 ggatttctgc tttgtcattc tgactctggc agttagcccg cccgctcggc gcagggcgtg 301 gcttctcgta gccattagga aacagcaacc ctttcacctc agttttcttc actccggcat 361 ttgcagcaga gcgaaaggtg gtcgagtcct gaaggagggc ctgatgtctt catcattctc 421 aaattcttgc ttatcaggag ggcagacttc aaaagctact aaaaatgaac ggccctgaag 481 atcttcccaa gtcctatgac tatgacctta tcatcattgg aggtggctca ggaggtctgg 541 cagctgctaa ggaggcagcc caatatggca agaaggtgat ggtcctggac tttgtcactc
601 ccacccctct tggaactaga tggggtctcg gaggaacatg tgtgaatgtg ggttgcatac
661 ctaaaaaact gatgcatcaa gcagctttgt taggacaagc cctgcaagac tctcgaaatt
721 atggatggaa agtcgaggag acagttaagc atgattggga cagaatgata gaagctgtac
781 agaatcacat tggctctttg aattggggct accgagtagc tctgcgggag aaaaaagtcg
841 tctatgagaa tgcttatggg caatttattg gtcctcacag gattaaggca acaaataata
901 aaggcaaaga aaaaatttat tcagcagaga gatttctcat tgccactggt gaaagaccac
961 gttacttggg catccctggt gacaaagaat actgcatcag cagtgatgat cttttctcct
1021 tgccttactg cccgggtaag accctggttg ttggagcatc ctatgtcgct ttggagtgcg
1081 ctggatttct tgctggtatt ggtttagacg tcactgttat ggttaggtcc attcttctta
1141 gaggatttga ccaggacatg gccaacaaaa ttggtgaaca catggaagaa catggcatca
1201 agtttataag acagttcgta ccaattaaag ttgaacaaat tgaagcaggg acaccaggcc
1261 gactcagagt agtagctcag tccaccaata gtgaggaaat cattgaagga gaatataata
1321 cggtgatgct ggcaatagga agagatgctt gcacaagaaa aattggctta gaaaccgtag
1381 gggtgaagat aaatgaaaag actggaaaaa tacctgtcac agatgaagaa cagaccaatg
1441 tgccttacat ctatgccatt ggcgatatat tggaggataa ggtggagctc accccagttg
1501 caatccaggc aggaagattg ctggctcaga ggctctatgc aggttccact gtcaagtgtg
1561 actatgaaaa tgttccaacc actgtattta ctcctttgga atatggtgct tgtggccttt
1621 ctgaggagaa agctgtggag aagtttgggg aagaaaatat tgaggtttac catagttact
1681 tttggccatt ggaatggacg attccgtcaa gagataacaa caaatgttat gcaaaaataa
1741 tctgtaatac taaagacaat gaacgtgttg tgggctttca cgtactgggt ccaaatgctg
1801 gagaagttac acaaggcttt gcagctgcgc tcaaatgtgg actgaccaaa aagcagctgg
1861 acagcacaat tggaatccac cctgtctgtg cagaggtatt cacaacattg tctgtgacca
1921 agcgctctgg ggcaagcatc ctccaggctg gctgctgagg ttaagcccca gtgtggatgc
1981 tgttgccaag actgcaaacc actggctcgt ttccgtgccc aaatccaagg cgaagttttc
2041 tagagggttc ttgggctctt ggcacctgcg tgtcctgtgc ttaccaccgc ccaaggcccc
2101 cttggatctc ttggatagga gttggtgaat agaaggcagg cagcatcaca ctggggtcac
2161 tgacagactt gaagctgaca tttggcaggg catcgaaggg atgcatccat gaagtcacca
2221 gtctcaagcc catgtggtag gcggtgatgg aacaactgtc aaatcagttt tagcatgacc
2281 tttccttgtg gattttctta ttctcgttgt caagttttct agggttgaat ttttttcttt
2341 tttctccatg gtgttaatga tattagagat gaaaaacgtt agcagttgat ttttgtccaa
2401 aagcaagtca tggctagagt atccatgcaa ggtgtcttgt tgcatggaag ggatagtttg
2461 gctcccttgg aggctatgta ggcttgtccc gggaaagaga actgtcctgc agctgaaatg
2521 gactgttctt tactgacctg ctcagcagtt tcttctctca tatattccca aaacaagtac
2581 atctgcgatc aactctagcc aaatttgccc ctgtgtgcta catgatggat gattattatt
2641 ttaaggtctg tttaggaagg gaaatggcta cttggccagc cattgcctgg catttggtag
2701 tatagtatga ttctcaccat tatttgtcat ggaggcagac atacaccaga aatgggggag
2761 aaacagtaca tatctttctg tctttagttt attgtgtgct ggtctaagca agctgagatc
2821 atttgcaatg gaaaacacgt aacttgttta aaagtttttc tggtagcttt agctttatgc
2881 taaaaaaaat aatgacattg ggtatctatt tctttctaag actacattag taggaaaata
2941 agtcttttca tgcttatgat ttagctgttt tgtggtaatt gctttttaaa ggaagttatt
3001 aatatcataa gttattatta atattttgaa cacaggtgga tgtgaaggat tttcatttaa
3061 aaaccaagtg gttttgactt tttctgttga atgaacaact gtgccttgtg gaatttttgc
3121 agaagtgttt atgctttgtt agcatttcaa cttgcattat tataaagagg tattaatgcc
3181 tcagttatgt gtttgtcaat gtactggctg aggattctat ctcagctgtc ttttctaact
3241 gtgtaggttg agttttgaac acgtgcttgt ggacatcagg cctcctgcca gcagttcttg
3301 aagcttcttt ttcattcctg ctactctacc tgtatttctc agttgcagca ctgagtggtc
3361 aaaatacatt tctgggccac ctcagggaac ccatgcatct gcctggcatt taggcagcag
3421 agcccctgac cgtcccccac agggctctgc ctcacgtcct catctcattt ggctgtgtaa
3481 agaaatggga aaagggaaaa ggagagagca attgaggcag ttgaccatat tcagttttat
3541 ttatttattt ttaatttgtt tttttctcca agtccaccag tctctgaaat tagaacagta
3601 ggcggtatga gataatcagg cctaatcatg ttgtgattct cttttcttag tggagtggaa
3661 tgttctatcc ccacaagaag gattatatct tatagacttg tcttgttcag attctgtatt
3721 tacccatttt attgaaacat atactaagtt ccatgtattt ttgttacaaa tcttctgaaa
3781 aaaaacaaaa caatgtgaaa cattaaaatt aaaaggcatt aataatatcc acgtgtgcct
3841 tcttactgaa aaaaaaaaa Homo sapiens thioredoxin reductase 1 (TXNRD1), transcript variant 4, mRNA NCBI Reference Sequence: NM_003330.3 (SEQ ID NO: 16)
1 agaccctcac gtgatgacaa cagctagcaa agttctgtag ctactgcctt agggcatagt
61 ctaatttctt cagtaaaaac acacttattc caaatttggt tccagaattg ccttaaattg
121 tttttgctct gttcttaggt tgggggcggc tatgagcagg cagaggatgt ggtgtcaccc
181 aattaggagc tctcagctta cgaggcaatt agcataggtt gccagggctg cacgaggagt
241 ggatttctgc tttgtcattc tgactctggc agttagcccg cccgctcggc gcagggcgtg
301 gcttctcgta gccattagga aacagcaacc ctttcacctc agttttcttc actccggcat
361 ttgcagcaga gcgaaaggtg gtcgagtcct gaaggagggc ctgatgtctt catcattctc
421 aaattcttgt aagctctgcg tcgggtgaaa ccagacaaag ccgcgagccc agggatggga
481 gcacgcgggg gacggcctgc cggcggggac gacagcattg cgcctgggtg cagcagtgtg
541 cgtctcgggg aagggaagat attttaaggc gtgtctgagc agacggggag gcttttccaa
601 acccaggcag cttcgtggcg tgtgcggttt cgacccggtc acacaaagct tcagcatgtc
661 atgtgaggac ggtcgggccc tggaaggaac gctctcggaa ttggccgcgg aaaccgatct
721 gcccgttgtg tttgtgaaac agagaaagat aggcggccat ggtccaacct tgaaggctta
781 tcaggagggc agacttcaaa agctactaaa aatgaacggc cctgaagatc ttcccaagtc
841 ctatgactat gaccttatca tcattggagg tggctcagga ggtctggcag ctgctaagga
901 ggcagcccaa tatggcaaga aggtgatggt cctggacttt gtcactccca cccctcttgg
961 aactagatgg ggtctcggag gaacatgtgt gaatgtgggt tgcataccta aaaaactgat
1021 gcatcaagca gctttgttag gacaagccct gcaagactct cgaaattatg gatggaaagt
1081 cgaggagaca gttaagcatg attgggacag aatgatagaa gctgtacaga atcacattgg
1141 ctctttgaat tggggctacc gagtagctct gcgggagaaa aaagtcgtct atgagaatgc
1201 ttatgggcaa tttattggtc ctcacaggat taaggcaaca aataataaag gcaaagaaaa
1261 aatttattca gcagagagat ttctcattgc cactggtgaa agaccacgtt acttgggcat
1321 ccctggtgac aaagaatact gcatcagcag tgatgatctt ttctccttgc cttactgccc
1381 gggtaagacc ctggttgttg gagcatccta tgtcgctttg gagtgcgctg gatttcttgc
1441 tggtattggt ttagacgtca ctgttatggt taggtccatt cttcttagag gatttgacca
1501 ggacatggcc aacaaaattg gtgaacacat ggaagaacat ggcatcaagt ttataagaca
1561 gttcgtacca attaaagttg aacaaattga agcagggaca ccaggccgac tcagagtagt
1621 agctcagtcc accaatagtg aggaaatcat tgaaggagaa tataatacgg tgatgctggc
1681 aataggaaga gatgcttgca caagaaaaat tggcttagaa accgtagggg tgaagataaa
1741 tgaaaagact ggaaaaatac ctgtcacaga tgaagaacag accaatgtgc cttacatcta
1801 tgccattggc gatatattgg aggataaggt ggagctcacc ccagttgcaa tccaggcagg
1861 aagattgctg gctcagaggc tctatgcagg ttccactgtc aagtgtgact atgaaaatgt
1921 tccaaccact gtatttactc ctttggaata tggtgcttgt ggcctttctg aggagaaagc
1981 tgtggagaag tttggggaag aaaatattga ggtttaccat agttactttt ggccattgga
2041 atggacgatt ccgtcaagag ataacaacaa atgttatgca aaaataatct gtaatactaa
2101 agacaatgaa cgtgttgtgg gctttcacgt actgggtcca aatgctggag aagttacaca
2161 aggctttgca gctgcgctca aatgtggact gaccaaaaag cagctggaca gcacaattgg
2221 aatccaccct gtctgtgcag aggtattcac aacattgtct gtgaccaagc gctctggggc
2281 aagcatcctc caggctggct gctgaggtta agccccagtg tggatgctgt tgccaagact
2341 gcaaaccact ggctcgtttc cgtgcccaaa tccaaggcga agttttctag agggttcttg
2401 ggctcttggc acctgcgtgt cctgtgctta ccaccgccca aggccccctt ggatctcttg
2461 gataggagtt ggtgaataga aggcaggcag catcacactg gggtcactga cagacttgaa
2521 gctgacattt ggcagggcat cgaagggatg catccatgaa gtcaccagtc tcaagcccat
2581 gtggtaggcg gtgatggaac aactgtcaaa tcagttttag catgaccttt ccttgtggat
2641 tttcttattc tcgttgtcaa gttttctagg gttgaatttt tttctttttt ctccatggtg
2701 ttaatgatat tagagatgaa aaacgttagc agttgatttt tgtccaaaag caagtcatgg
2761 ctagagtatc catgcaaggt gtcttgttgc atggaaggga tagtttggct cccttggagg
2821 ctatgtaggc ttgtcccggg aaagagaact gtcctgcagc tgaaatggac tgttctttac
2881 tgacctgctc agcagtttct tctctcatat attcccaaaa caagtacatc tgcgatcaac
2941 tctagccaaa tttgcccctg tgtgctacat gatggatgat tattatttta aggtctgttt
3001 aggaagggaa atggctactt ggccagccat tgcctggcat ttggtagtat agtatgattc 3061 tcaccattat ttgtcatgga ggcagacata caccagaaat gggggagaaa cagtacatat 3121 ctttctgtct ttagtttatt gtgtgctggt ctaagcaagc tgagatcatt tgcaatggaa 3181 aacacgtaac ttgtttaaaa gtttttctgg tagctttagc tttatgctaa aaaaaataat 3241 gacattgggt atctatttct ttctaagact acattagtag gaaaataagt cttttcatgc 3301 ttatgattta gctgttttgt ggtaattgct ttttaaagga agttattaat atcataagtt 3361 attattaata ttttgaacac aggtggatgt gaaggatttt catttaaaaa ccaagtggtt 3421 ttgacttttt ctgttgaatg aacaactgtg ccttgtggaa tttttgcaga agtgtttatg 3481 ctttgttagc atttcaactt gcattattat aaagaggtat taatgcctca gttatgtgtt 3541 tgtcaatgta ctggctgagg attctatctc agctgtcttt tctaactgtg taggttgagt 3601 tttgaacacg tgcttgtgga catcaggcct cctgccagca gttcttgaag cttctttttc 3661 attcctgcta ctctacctgt atttctcagt tgcagcactg agtggtcaaa atacatttct 3721 gggccacctc agggaaccca tgcatctgcc tggcatttag gcagcagagc ccctgaccgt 3781 cccccacagg gctctgcctc acgtcctcat ctcatttggc tgtgtaaaga aatgggaaaa 3841 gggaaaagga gagagcaatt gaggcagttg accatattca gttttattta tttattttta 3901 atttgttttt ttctccaagt ccaccagtct ctgaaattag aacagtaggc ggtatgagat 3961 aatcaggcct aatcatgttg tgattctctt ttcttagtgg agtggaatgt tctatcccca 4021 caagaaggat tatatcttat agacttgtct tgttcagatt ctgtatttac ccattttatt 4081 gaaacatata ctaagttcca tgtatttttg ttacaaatct tctgaaaaaa aacaaaacaa 4141 tgtgaaacat taaaattaaa aggcattaat aatatccacg tgtgccttct tactgaaaaa 4201 aaaaaa
Homo sapiens thioredoxin reductase 1 (TXNRD1), transcript variant 5, mRNA
NCBI Reference Sequence: NM_001261445.1 (SEQ ID NO: 17)
1 agaccctcac gtgatgacaa cagctagcaa agttctgtag ctactgcctt agggcatagt
61 ctaatttctt cagtaaaaac acacttattc caaatttggt tccagaattg ccttaaattg
121 tttttgctct gttcttaggt tgggggcggc tatgagcagg cagaggatgt ggtgtcaccc
181 aattaggagc tctcagctta cgaggcaatt agcataggtt gccagggctg cacgaggagt
241 ggatttctgc tttgtcattc tgactctggc agttagcccg cccgctcggc gcagggcgtg
301 gcttctcgta gccattagga aacagcaacc ctttcacctc agttttcttc actccggcat
361 ttgcagcaga gcgaaaggtg gtcgagtcct gaaggagggc ctgatgtctt catcattctc
421 aaattcttgt aagctctgcg tcgggtgaaa ccagacaaag ccgcgagccc agggatggga
481 gcacgcgggg gacggcctgc cggcggggac gacagcattg cgcctgggtg cagcagtgtg
541 cgtctcgggg aagggaagat attttaaggc gtgtctgagc agacggggag gcttttccaa
601 acccaggcag cttcgtggcg tgtgcggttt cgacccggtc acacaaagct tcagcatgtc
661 atgtggtagg tgaggccggc gcctgtaggc tggcggtttc cttcctcttg gtctttgtag
721 agacagtttg cagaacagcg gagaaaatgg aggacggtcg ggccctggaa ggaacgctct
781 cggaattggc cgcggaaacc gatctgcccg ttgtgtttgt gaaacagaga aagataggcg
841 gccatggtcc aaccttgaag gcttatcagg agggcagact tcaaaagcta ctaaaaatga
901 acggccctga agatcttccc aagtcctatg actatgacct tatcatcatt ggaggtggct
961 caggaggtct ggcagctgct aaggaggcag cccaatatgg caagaaggtg atggtcctgg
1021 actttgtcac tcccacccct cttggaacta gatggggtct cggaggaaca tgtgtgaatg
1081 tgggttgcat acctaaaaaa ctgatgcatc aagcagcttt gttaggacaa gccctgcaag
1141 actctcgaaa ttatggatgg aaagtcgagg agacagttaa gcatgattgg gacagaatga
1201 tagaagctgt acagaatcac attggctctt tgaattgggg ctaccgagta gctctgcggg
1261 agaaaaaagt cgtctatgag aatgcttatg ggcaatttat tggtcctcac aggattaagg
1321 caacaaataa taaaggcaaa gaaaaaattt attcagcaga gagatttctc attgccactg
1381 gtgaaagacc acgttacttg ggcatccctg gtgacaaaga atactgcatc agcagtgatg
1441 atcttttctc cttgccttac tgcccgggta agaccctggt tgttggagca tcctatgtcg
1501 ctttggagtg cgctggattt cttgctggta ttggtttaga cgtcactgtt atggttaggt
1561 ccattcttct tagaggattt gaccaggaca tggccaacaa aattggtgaa cacatggaag
1621 aacatggcat caagtttata agacagttcg taccaattaa agttgaacaa attgaagcag
1681 ggacaccagg ccgactcaga gtagtagctc agtccaccaa tagtgaggaa atcattgaag
1741 gagaatataa tacggtgatg ctggcaatag gaagagatgc ttgcacaaga aaaattggct
1801 tagaaaccgt aggggtgaag ataaatgaaa agactggaaa aatacctgtc acagatgaag 1861 aacagaccaa tgtgccttac atctatgcca ttggcgatat attggaggat aaggtggagc
1921 tcaccccagt tgcaatccag gcaggaagat tgctggctca gaggctctat gcaggttcca
1981 ctgtcaagtg tgactatgaa aatgttccaa ccactgtatt tactcctttg gaatatggtg
2041 cttgtggcct ttctgaggag aaagctgtgg agaagtttgg ggaagaaaat attgaggttt
2101 accatagtta cttttggcca ttggaatgga cgattccgtc aagagataac aacaaatgtt
2161 atgcaaaaat aatctgtaat actaaagaca atgaacgtgt tgtgggcttt cacgtactgg
2221 gtccaaatgc tggagaagtt acacaaggct ttgcagctgc gctcaaatgt ggactgacca
2281 aaaagcagct ggacagcaca attggaatcc accctgtctg tgcagaggta ttcacaacat
2341 tgtctgtgac caagcgctct ggggcaagca tcctccaggc tggctgctga ggttaagccc
2401 cagtgtggat gctgttgcca agactgcaaa ccactggctc gtttccgtgc ccaaatccaa
2461 ggcgaagttt tctagagggt tcttgggctc ttggcacctg cgtgtcctgt gcttaccacc
2521 gcccaaggcc cccttggatc tcttggatag gagttggtga atagaaggca ggcagcatca
2581 cactggggtc actgacagac ttgaagctga catttggcag ggcatcgaag ggatgcatcc
2641 atgaagtcac cagtctcaag cccatgtggt aggcggtgat ggaacaactg tcaaatcagt
2701 tttagcatga cctttccttg tggattttct tattctcgtt gtcaagtttt ctagggttga
2761 atttttttct tttttctcca tggtgttaat gatattagag atgaaaaacg ttagcagttg
2821 atttttgtcc aaaagcaagt catggctaga gtatccatgc aaggtgtctt gttgcatgga
2881 agggatagtt tggctccctt ggaggctatg taggcttgtc ccgggaaaga gaactgtcct
2941 gcagctgaaa tggactgttc tttactgacc tgctcagcag tttcttctct catatattcc
3001 caaaacaagt acatctgcga tcaactctag ccaaatttgc ccctgtgtgc tacatgatgg
3061 atgattatta ttttaaggtc tgtttaggaa gggaaatggc tacttggcca gccattgcct
3121 ggcatttggt agtatagtat gattctcacc attatttgtc atggaggcag acatacacca
3181 gaaatggggg agaaacagta catatctttc tgtctttagt ttattgtgtg ctggtctaag
3241 caagctgaga tcatttgcaa tggaaaacac gtaacttgtt taaaagtttt tctggtagct
3301 ttagctttat gctaaaaaaa ataatgacat tgggtatcta tttctttcta agactacatt
3361 agtaggaaaa taagtctttt catgcttatg atttagctgt tttgtggtaa ttgcttttta
3421 aaggaagtta ttaatatcat aagttattat taatattttg aacacaggtg gatgtgaagg
3481 attttcattt aaaaaccaag tggttttgac tttttctgtt gaatgaacaa ctgtgccttg
3541 tggaattttt gcagaagtgt ttatgctttg ttagcatttc aacttgcatt attataaaga
3601 ggtattaatg cctcagttat gtgtttgtca atgtactggc tgaggattct atctcagctg
3661 tcttttctaa ctgtgtaggt tgagttttga acacgtgctt gtggacatca ggcctcctgc
3721 cagcagttct tgaagcttct ttttcattcc tgctactcta cctgtatttc tcagttgcag
3781 cactgagtgg tcaaaataca tttctgggcc acctcaggga acccatgcat ctgcctggca
3841 tttaggcagc agagcccctg accgtccccc acagggctct gcctcacgtc ctcatctcat
3901 ttggctgtgt aaagaaatgg gaaaagggaa aaggagagag caattgaggc agttgaccat
3961 attcagtttt atttatttat ttttaatttg tttttttctc caagtccacc agtctctgaa
4021 attagaacag taggcggtat gagataatca ggcctaatca tgttgtgatt ctcttttctt
4081 agtggagtgg aatgttctat ccccacaaga aggattatat cttatagact tgtcttgttc
4141 agattctgta tttacccatt ttattgaaac atatactaag ttccatgtat ttttgttaca
4201 aatcttctga aaaaaaacaa aacaatgtga aacattaaaa ttaaaaggca ttaataatat
4261 ccacgtgtgc cttcttactg aaaaaaaaaa a
Homo sapiens thioredoxin reductase 1 (TXNRD1), transcript variant 6, mRNA
NCBI Reference Sequence: NM_001261446.1 (SEQ ID NO: 18)
1 agaccctcac gtgatgacaa cagctagcaa agttctgtag ctactgcctt agggcatagt
61 ctaatttctt cagtaaaaac acacttattc caaatttggt tccagaattg ccttaaattg
121 tttttgctct gttcttaggt tgggggcggc tatgagcagg cagaggatgt ggtgtcaccc
181 aattaggagc tctcagctta cgaggcaatt agcataggtt gccagggctg cacgaggagt
241 ggatttctgc tttgtcattc tgactctggc agttagcccg cccgctcggc gcagggcgtg
301 gcttctcgta gccattagga aacagcaacc ctttcacctc agttttcttc actccggcat
361 ttgcagcaga gcgaaaggtg gtcgagtcct gaaggagggc ctgatgtctt catcattctc
421 aaattcttag gacggtcggg ccctggaagg aacgctctcg gaattggccg cggaaaccga
481 tctgcccgtt gtgtttgtga aacagagaaa gataggcggc catggtccaa ccttgaagga
541 ggcagcccaa tatggcaaga aggtgatggt cctggacttt gtcactccca cccctcttgg 601 aactagatgg ggtctcggag gaacatgtgt gaatgtgggt tgcataccta aaaaactgat
661 gcatcaagca gctttgttag gacaagccct gcaagactct cgaaattatg gatggaaagt
721 cgaggagaca gttaagcatg attgggacag aatgatagaa gctgtacaga atcacattgg
781 ctctttgaat tggggctacc gagtagctct gcgggagaaa aaagtcgtct atgagaatgc
841 ttatgggcaa tttattggtc ctcacaggat taaggcaaca aataataaag gcaaagaaaa
901 aatttattca gcagagagat ttctcattgc cactggtgaa agaccacgtt acttgggcat
961 ccctggtgac aaagaatact gcatcagcag tgatgatctt ttctccttgc cttactgccc
1021 gggtaagacc ctggttgttg gagcatccta tgtcgctttg gagtgcgctg gatttcttgc
1081 tggtattggt ttagacgtca ctgttatggt taggtccatt cttcttagag gatttgacca
1141 ggacatggcc aacaaaattg gtgaacacat ggaagaacat ggcatcaagt ttataagaca
1201 gttcgtacca attaaagttg aacaaattga agcagggaca ccaggccgac tcagagtagt
1261 agctcagtcc accaatagtg aggaaatcat tgaaggagaa tataatacgg tgatgctggc
1321 aataggaaga gatgcttgca caagaaaaat tggcttagaa accgtagggg tgaagataaa
1381 tgaaaagact ggaaaaatac ctgtcacaga tgaagaacag accaatgtgc cttacatcta
1441 tgccattggc gatatattgg aggataaggt ggagctcacc ccagttgcaa tccaggcagg
1501 aagattgctg gctcagaggc tctatgcagg ttccactgtc aagtgtgact atgaaaatgt
1561 tccaaccact gtatttactc ctttggaata tggtgcttgt ggcctttctg aggagaaagc
1621 tgtggagaag tttggggaag aaaatattga ggtttaccat agttactttt ggccattgga
1681 atggacgatt ccgtcaagag ataacaacaa atgttatgca aaaataatct gtaatactaa
1741 agacaatgaa cgtgttgtgg gctttcacgt actgggtcca aatgctggag aagttacaca
1801 aggctttgca gctgcgctca aatgtggact gaccaaaaag cagctggaca gcacaattgg
1861 aatccaccct gtctgtgcag aggtattcac aacattgtct gtgaccaagc gctctggggc
1921 aagcatcctc caggctggct gctgaggtta agccccagtg tggatgctgt tgccaagact
1981 gcaaaccact ggctcgtttc cgtgcccaaa tccaaggcga agttttctag agggttcttg
2041 ggctcttggc acctgcgtgt cctgtgctta ccaccgccca aggccccctt ggatctcttg
2101 gataggagtt ggtgaataga aggcaggcag catcacactg gggtcactga cagacttgaa
2161 gctgacattt ggcagggcat cgaagggatg catccatgaa gtcaccagtc tcaagcccat
2221 gtggtaggcg gtgatggaac aactgtcaaa tcagttttag catgaccttt ccttgtggat
2281 tttcttattc tcgttgtcaa gttttctagg gttgaatttt tttctttttt ctccatggtg
2341 ttaatgatat tagagatgaa aaacgttagc agttgatttt tgtccaaaag caagtcatgg
2401 ctagagtatc catgcaaggt gtcttgttgc atggaaggga tagtttggct cccttggagg
2461 ctatgtaggc ttgtcccggg aaagagaact gtcctgcagc tgaaatggac tgttctttac
2521 tgacctgctc agcagtttct tctctcatat attcccaaaa caagtacatc tgcgatcaac
2581 tctagccaaa tttgcccctg tgtgctacat gatggatgat tattatttta aggtctgttt
2641 aggaagggaa atggctactt ggccagccat tgcctggcat ttggtagtat agtatgattc
2701 tcaccattat ttgtcatgga ggcagacata caccagaaat gggggagaaa cagtacatat
2761 ctttctgtct ttagtttatt gtgtgctggt ctaagcaagc tgagatcatt tgcaatggaa
2821 aacacgtaac ttgtttaaaa gtttttctgg tagctttagc tttatgctaa aaaaaataat
2881 gacattgggt atctatttct ttctaagact acattagtag gaaaataagt cttttcatgc
2941 ttatgattta gctgttttgt ggtaattgct ttttaaagga agttattaat atcataagtt
3001 attattaata ttttgaacac aggtggatgt gaaggatttt catttaaaaa ccaagtggtt
3061 ttgacttttt ctgttgaatg aacaactgtg ccttgtggaa tttttgcaga agtgtttatg
3121 ctttgttagc atttcaactt gcattattat aaagaggtat taatgcctca gttatgtgtt
3181 tgtcaatgta ctggctgagg attctatctc agctgtcttt tctaactgtg taggttgagt
3241 tttgaacacg tgcttgtgga catcaggcct cctgccagca gttcttgaag cttctttttc
3301 attcctgcta ctctacctgt atttctcagt tgcagcactg agtggtcaaa atacatttct
3361 gggccacctc agggaaccca tgcatctgcc tggcatttag gcagcagagc ccctgaccgt
3421 cccccacagg gctctgcctc acgtcctcat ctcatttggc tgtgtaaaga aatgggaaaa
3481 gggaaaagga gagagcaatt gaggcagttg accatattca gttttattta tttattttta
3541 atttgttttt ttctccaagt ccaccagtct ctgaaattag aacagtaggc ggtatgagat
3601 aatcaggcct aatcatgttg tgattctctt ttcttagtgg agtggaatgt tctatcccca
3661 caagaaggat tatatcttat agacttgtct tgttcagatt ctgtatttac ccattttatt
3721 gaaacatata ctaagttcca tgtatttttg ttacaaatct tctgaaaaaa aacaaaacaa
3781 tgtgaaacat taaaattaaa aggcattaat aatatccacg tgtgccttct tactgaaaaa
3841 aaaaaa Homo sapiens thioredoxin reductase 1 (TXNRD1), transcript variant 7, mRNA
NCBI Reference Sequence: NM OO 1093771.3 (SEQ ID NO: 19)
1 agttcccaca gggccttgtg cgacatgggc tgcgccgagg gcaaggcagt ggcggcggcc
61 gccccaacgg agctgcagac gaaaggcaag aacggcgatg gccgccgtag gtcagctaaa
121 gatcatcacc ctggtaaaac tttgccagag aacccagcag gattcaccag cacggccact
181 gcagactcca gagccctgct tcaggcctat atagatggtc actctgtggt catcttcagt
241 aggtccacat gcacacgctg tactgaggta aagaagttat ttaaatctct gtgtgttcct
301 tattttgtgc ttgaacttga tcaaacagag gacggtcggg ccctggaagg aacgctctcg
361 gaattggccg cggaaaccga tctgcccgtt gtgtttgtga aacagagaaa gataggcggc
421 catggtccaa ccttgaaggc ttatcaggag ggcagacttc aaaagctact aaaaatgaac
481 ggccctgaag atcttcccaa gtcctatgac tatgacctta tcatcattgg aggtggctca
541 ggaggtctgg cagctgctaa ggaggcagcc caatatggca agaaggtgat ggtcctggac
601 tttgtcactc ccacccctct tggaactaga tggggtctcg gaggaacatg tgtgaatgtg
661 ggttgcatac ctaaaaaact gatgcatcaa gcagctttgt taggacaagc cctgcaagac
721 tctcgaaatt atggatggaa agtcgaggag acagttaagc atgattggga cagaatgata
781 gaagctgtac agaatcacat tggctctttg aattggggct accgagtagc tctgcgggag
841 aaaaaagtcg tctatgagaa tgcttatggg caatttattg gtcctcacag gattaaggca
901 acaaataata aaggcaaaga aaaaatttat tcagcagaga gatttctcat tgccactggt
961 gaaagaccac gttacttggg catccctggt gacaaagaat actgcatcag cagtgatgat
1021 cttttctcct tgccttactg cccgggtaag accctggttg ttggagcatc ctatgtcgct
1081 ttggagtgcg ctggatttct tgctggtatt ggtttagacg tcactgttat ggttaggtcc
1141 attcttctta gaggatttga ccaggacatg gccaacaaaa ttggtgaaca catggaagaa
1201 catggcatca agtttataag acagttcgta ccaattaaag ttgaacaaat tgaagcaggg
1261 acaccaggcc gactcagagt agtagctcag tccaccaata gtgaggaaat cattgaagga
1321 gaatataata cggtgatgct ggcaatagga agagatgctt gcacaagaaa aattggctta
1381 gaaaccgtag gggtgaagat aaatgaaaag actggaaaaa tacctgtcac agatgaagaa
1441 cagaccaatg tgccttacat ctatgccatt ggcgatatat tggaggataa ggtggagctc
1501 accccagttg caatccaggc aggaagattg ctggctcaga ggctctatgc aggttccact
1561 gtcaagtgtg actatgaaaa tgttccaacc actgtattta ctcctttgga atatggtgct
1621 tgtggccttt ctgaggagaa agctgtggag aagtttgggg aagaaaatat tgaggtttac
1681 catagttact tttggccatt ggaatggacg attccgtcaa gagataacaa caaatgttat
1741 gcaaaaataa tctgtaatac taaagacaat gaacgtgttg tgggctttca cgtactgggt
1801 ccaaatgctg gagaagttac acaaggcttt gcagctgcgc tcaaatgtgg actgaccaaa
1861 aagcagctgg acagcacaat tggaatccac cctgtctgtg cagaggtatt cacaacattg
1921 tctgtgacca agcgctctgg ggcaagcatc ctccaggctg gctgctgagg ttaagcccca
1981 gtgtggatgc tgttgccaag actgcaaacc actggctcgt ttccgtgccc aaatccaagg
2041 cgaagttttc tagagggttc ttgggctctt ggcacctgcg tgtcctgtgc ttaccaccgc
2101 ccaaggcccc cttggatctc ttggatagga gttggtgaat agaaggcagg cagcatcaca
2161 ctggggtcac tgacagactt gaagctgaca tttggcaggg catcgaaggg atgcatccat
2221 gaagtcacca gtctcaagcc catgtggtag gcggtgatgg aacaactgtc aaatcagttt
2281 tagcatgacc tttccttgtg gattttctta ttctcgttgt caagttttct agggttgaat
2341 ttttttcttt tttctccatg gtgttaatga tattagagat gaaaaacgtt agcagttgat
2401 ttttgtccaa aagcaagtca tggctagagt atccatgcaa ggtgtcttgt tgcatggaag
2461 ggatagtttg gctcccttgg aggctatgta ggcttgtccc gggaaagaga actgtcctgc
2521 agctgaaatg gactgttctt tactgacctg ctcagcagtt tcttctctca tatattccca
2581 aaacaagtac atctgcgatc aactctagcc aaatttgccc ctgtgtgcta catgatggat
2641 gattattatt ttaaggtctg tttaggaagg gaaatggcta cttggccagc cattgcctgg
2701 catttggtag tatagtatga ttctcaccat tatttgtcat ggaggcagac atacaccaga
2761 aatgggggag aaacagtaca tatctttctg tctttagttt attgtgtgct ggtctaagca
2821 agctgagatc atttgcaatg gaaaacacgt aacttgttta aaagtttttc tggtagcttt
2881 agctttatgc taaaaaaaat aatgacattg ggtatctatt tctttctaag actacattag
2941 taggaaaata agtcttttca tgcttatgat ttagctgttt tgtggtaatt gctttttaaa
3001 ggaagttatt aatatcataa gttattatta atattttgaa cacaggtgga tgtgaaggat 3061 tttcatttaa aaaccaagtg gttttgactt tttctgttga atgaacaact gtgccttgtg
312 1 gaatttttgc agaagtgttt atgctttgtt agcatttcaa ettgeattat tataaagagg
318 1 tattaatgee tcagttatgt gtttgtcaat gtactggctg aggattetat ctcagctgtc
324 1 ttttctaact gtgtaggttg agttttgaac acgtgcttgt ggacatcagg cctcctgcca
3301 gcagttcttg aagcttcttt ttcattcctg ctactctacc tgtatttctc agttgcagca
3361 ctgagtggtc aaaatacatt tctgggccac ctcagggaac ccatgcatct gcctggcatt
342 1 taggeageag agcccctgac cgtcccccac agggctctgc ctcacgtcct catctcattt
34 8 1 ggctgtgtaa agaaatggga aaagggaaaa ggagagagea attgaggeag ttgaccatat
354 1 tcagttttat ttatttattt ttaatttgtt tttttctcca agtccaccag tctctgaaat
3601 tagaacagta ggcggtatga gataatcagg cctaatcatg ttgtgattct cttttcttag
3661 tggagtggaa tgttctatcc ccacaagaag gattatatet tatagaettg tcttgttcag
372 1 attctgtatt tacccatttt attgaaacat atactaagtt ccatgtattt ttgttacaaa
37 8 1 tcttctgaaa aaaaacaaaa caatgtgaaa cattaaaatt aaaaggcatt aataatatcc
384 1 acgtgtgcct tcttactgaa
Mus musculus thioredoxm reductase 1 (Txnrdl), transcript variant 1, mRNA
NCBI Reference Sequence: NM_001042513.1 (SEQ ID NO: 20)
1 agtttgcttc cgtcaggcct cgcgtccacg cgggaggtgc gggaegeega caccgcgggg 61 egagaagage tggtggtttc accttccttg ttcatagggc ggcggggcct tgcagcggcg 121 cgggcgagcg gaaaggccgc gggaggegge gagccagcgg aaggtgcgac eggeggaggg 181 cggccatggt ccagccctga agccgaacaa aaaaggccaa cttcaaaagc tgccaacaat 241 gaatggctcc aaagatcccc ctgggtccta tgaettegae ctgatcatca ttggaggagg 301 etcaggagga ctggcagcag etaaggagge agccaaattt gacaagaaag tgctggtctt 361 ggattttgtc acaccgactc ctcttgggac cagatggggt cteggaggaa cgtgtgtgaa 421 tgtgggttgc atacctaaga agetgatgea ccaggcagct ttgeteggae aagctctgaa 481 agactcgcgc aactatggct ggaaagtcga agacacagtg aagcatgact gggagaaaat 541 gaeggaatet gtgcagagtc acatcggctc gctgaactgg ggctaccgcg tagctctccg 601 ggagaaaaag gtcgtctatg agaatgetta cgggaggttc attggtcctc acaggattgt 661 ggcgacaaat aacaaaggta aagaaaaaat ctattcagca gagcggttcc tcatcgccac 721 aggtgagagg ccccgctacc tgggcatccc tggagacaaa gagtactgca tcagcagtga 781 tgatcttttc tccttgcctt actgcccggg gaagacccta gtagttggtg catcctatgt 841 cgccttggaa tgtgcaggat ttctggctgg tateggetta gacgtcactg taatggtgcg 901 gtccattctc ettagaggat ttgaccaaga catggccaac aaaatcggtg aacacatgga 961 agaacatggt atcaagttta taaggcagtt cgtcccaacg aaaattgaac agategaage 1021 aggaacacca ggccgactca gggtgactgc tcaatccaca aacagcgagg agaccataga 1081 gggcgaattt aacacagtgt tgctggcggt aggaagagat tettgtaega gaactattgg 1141 cttagagacc gtgggcgtga agataaaega aaaaaccgga aagatacccg teaeggatga 1201 agagcagacc aatgtgcctt acatctacgc catcggtgac atcctggagg ggaagetaga 1261 gctgactccc gtagccatcc aggcggggag attgctggct cagaggctgt atggaggctc 1321 caatgtcaaa tgtgactatg acaatgtccc aacgactgta tttactcctt tggaatatgg 1381 ctgttgtggc ctctctgaag aaaaagccgt agagaaattt ggggaagaaa atattgaagt 1441 ttaccatagt ttcttttggc cattggaatg gacagtccca tcccgggata acaacaaatg 1501 ttatgcaaaa ataatetgea accttaaaga egatgaaegt gtcgtgggct tccacgtgct 1561 gggtccaaac gctggagagg tgacgcaggg etttgegget gcgctcaagt gtgggctgac 1621 taagcagcag ctggacagca ccatcggcat ccacccggtc tgtgcagaga tattcacaac 1681 gttgtcagtg aegaageget ctgggggaga catcctccag tctggctgct gaggttaagc 1741 cccagtgtgg atgctgttgc caagactaca gaccattgcc ttgcttcctt gcccacgccc 1801 aggtgaagtt caggaaggct cttgggtcct aggegecaat tcaaggtgct gtcctaaggc 1861 caccgggtcc ctgggatctt gtgggtagga ggtggcaggt egaaggagge tgeageateg 1921 cactggggtc accatgacag actcagactg acatctggca gagcatcaca ggcatgcgtc 1981 catgaagtca ctggcctcaa gcccaagtgg tgggcagtga cagaagagct gccgggtctg 2041 ttgagctcaa ccttttcctg tagattgtet tagtctcact ttcaagctgt ctaatgtcaa 2101 ttctgttttt cttttttcct ccatggggtt aatgatacta gagataggga atattagcaa 2161 tcagtttttg tcatggctgg tccatctgca acagtcttta ctgtgtggaa gtgggtgaga 2221 tggcttatga gagccaaacc aatttatccc cagaaagacg aattaccctg tgactaaaat 2281 acactgtctg cttttactaa ctggtgtagc attgtctcct ttaataagtc ttgtgtccaa 2341 aacgagaaaa accattggcc acttttgcaa gtttcctgca gtgtgcttag caagggaggt 2401 ggcgacttgg ctaatctact tgaactgcat cgcatggctc ttgggtagct tagagcatcg 2461 cagggtagag gcagaccagc agtgagtgtc tctcctggta caattattgt ctggttctca 2521 gtggaaaacg cttaatttgc tttaaacttg gtgtttttgt gaggtggatt tagtcttaag 2581 ctgtgtccca taagaactac attcacaggc aagtggctct tcctccacac agcctataca 2641 tcttctgagg taattacttt cataaggaag ctgttcataa cgtaagttat tattattatt 2701 gaacacaggt ggatgtgaag gatttttcat tgaaaaacca aatggttttt ctttttttct 2761 gttcagtgag cccacaggaa ctctgtcagg acagccagta ctctgccggc atggctgctg 2821 gggcgtttac ggtgtagttt agctcctagg ttacatgacc gtgaacatgc tggctgagga 2881 ctacacaaac caggtttccc accatacacg gcctggccct gcagcttctt ttcttgccct 2941 cccctttgcc tgtccccacc tgcagtactg agtggcgttt cacagtaccc ttctgggcca 3001 cctcagggaa gggatttgcc tggtgtccag ccagcagcac ccaccctgcc ccacgaggct 3061 ccctcacacc tgcccccccg tccttgtgtt gaagacagtg ggaagaggag aaaggaccag 3121 ggaaaccaag ggagttgact gttcagtttt atttatttat tttttaagtt tttttttcct 3181 ttcaagtctg ccagtctctg agatcagaac aacagacagt gtagggtaac taatcatgtg 3241 attctcttag tggaatgaaa tgttctaccc ccacaagaag gagtatacgt cattgttcat 3301 attctgtaat cgcacaatgt attgtaatgc aaattccaat tccatgtatt tttattacaa 3361 tttttctgga aaaaaatgtg aaccaataaa agatgttgat gcacacgcgt gccttct
Mus musculus thioredoxin reductase 1 (Txnrdl), transcript variant 3, mRNA
NCBI Reference Sequence: NM_001042514.1 (SEQ ID NO: 21)
1 gtggctacga ggctggtgtt tttagccgcc atgcagagct tttctgagtt ctgggggtcc
61 tggagtcttg ctggcccggc tgcttaaggg tcggagtcca ctggcgagag tgacccaggg
121 cgcgtggcgt cccggaagcc ccgcccggag gaaggctcac tgccgctctg ctttgtgcca
181 cagagggcgg cggggccttg cagcggcgcg ggcgagcgga aaggccgcgg gaggcggcga
241 gccagcggaa ggtgcgaccg gcggagggcg gccatggtcc agccctgaag ccgaacaaaa
301 aaggccaact tcaaaagctg ccaacaatga atggctccaa agatccccct gggtcctatg
361 acttcgacct gatcatcatt ggaggaggct caggaggact ggcagcagct aaggaggcag
421 ccaaatttga caagaaagtg ctggtcttgg attttgtcac accgactcct cttgggacca
481 gatggggtct cggaggaacg tgtgtgaatg tgggttgcat acctaagaag ctgatgcacc
541 aggcagcttt gctcggacaa gctctgaaag actcgcgcaa ctatggctgg aaagtcgaag
601 acacagtgaa gcatgactgg gagaaaatga cggaatctgt gcagagtcac atcggctcgc
661 tgaactgggg ctaccgcgta gctctccggg agaaaaaggt cgtctatgag aatgcttacg
721 ggaggttcat tggtcctcac aggattgtgg cgacaaataa caaaggtaaa gaaaaaatct
781 attcagcaga gcggttcctc atcgccacag gtgagaggcc ccgctacctg ggcatccctg
841 gagacaaaga gtactgcatc agcagtgatg atcttttctc cttgccttac tgcccgggga
901 agaccctagt agttggtgca tcctatgtcg ccttggaatg tgcaggattt ctggctggta
961 tcggcttaga cgtcactgta atggtgcggt ccattctcct tagaggattt gaccaagaca
1021 tggccaacaa aatcggtgaa cacatggaag aacatggtat caagtttata aggcagttcg
1081 tcccaacgaa aattgaacag atcgaagcag gaacaccagg ccgactcagg gtgactgctc
1141 aatccacaaa cagcgaggag accatagagg gcgaatttaa cacagtgttg ctggcggtag
1201 gaagagattc ttgtacgaga actattggct tagagaccgt gggcgtgaag ataaacgaaa
1261 aaaccggaaa gatacccgtc acggatgaag agcagaccaa tgtgccttac atctacgcca
1321 tcggtgacat cctggagggg aagctagagc tgactcccgt agccatccag gcggggagat
1381 tgctggctca gaggctgtat ggaggctcca atgtcaaatg tgactatgac aatgtcccaa
1441 cgactgtatt tactcctttg gaatatggct gttgtggcct ctctgaagaa aaagccgtag
1501 agaaatttgg ggaagaaaat attgaagttt accatagttt cttttggcca ttggaatgga
1561 cagtcccatc ccgggataac aacaaatgtt atgcaaaaat aatctgcaac cttaaagacg
1621 atgaacgtgt cgtgggcttc cacgtgctgg gtccaaacgc tggagaggtg acgcagggct
1681 ttgcggctgc gctcaagtgt gggctgacta agcagcagct ggacagcacc atcggcatcc
1741 acccggtctg tgcagagata ttcacaacgt tgtcagtgac gaagcgctct gggggagaea 1801 tcctccagtc tggctgctga ggttaagccc cagtgtggat gctgttgcca agactacaga
1861 ccattgcctt gcttccttgc ccacgcccag gtgaagttca ggaaggctct tgggtcctag
1921 gcgccaattc aaggtgctgt cctaaggcca ccgggtccct gggatcttgt gggtaggagg
1981 tggcaggtcg aaggaggctg cagcatcgca ctggggtcac catgacagac tcagactgac
2041 atctggcaga gcatcacagg catgcgtcca tgaagtcact ggcctcaagc ccaagtggtg
2101 ggcagtgaca gaagagctgc cgggtctgtt gagctcaacc ttttcctgta gattgtctta
2161 gtctcacttt caagctgtct aatgtcaatt ctgtttttct tttttcctcc atggggttaa
2221 tgatactaga gatagggaat attagcaatc agtttttgtc atggctggtc catctgcaac
2281 agtctttact gtgtggaagt gggtgagatg gcttatgaga gccaaaccaa tttatcccca
2341 gaaagacgaa ttaccctgtg actaaaatac actgtctgct tttactaact ggtgtagcat
2401 tgtctccttt aataagtctt gtgtccaaaa cgagaaaaac cattggccac ttttgcaagt
2461 ttcctgcagt gtgcttagca agggaggtgg cgacttggct aatctacttg aactgcatcg
2521 catggctctt gggtagctta gagcatcgca gggtagaggc agaccagcag tgagtgtctc
2581 tcctggtaca attattgtct ggttctcagt ggaaaacgct taatttgctt taaacttggt
2641 gtttttgtga ggtggattta gtcttaagct gtgtcccata agaactacat tcacaggcaa
2701 gtggctcttc ctccacacag cctatacatc ttctgaggta attactttca taaggaagct
2761 gttcataacg taagttatta ttattattga acacaggtgg atgtgaagga tttttcattg
2821 aaaaaccaaa tggtttttct ttttttctgt tcagtgagcc cacaggaact ctgtcaggac
2881 agccagtact ctgccggcat ggctgctggg gcgtttacgg tgtagtttag ctcctaggtt
2941 acatgaccgt gaacatgctg gctgaggact acacaaacca ggtttcccac catacacggc
3001 ctggccctgc agcttctttt cttgccctcc cctttgcctg tccccacctg cagtactgag
3061 tggcgtttca cagtaccctt ctgggccacc tcagggaagg gatttgcctg gtgtccagcc
3121 agcagcaccc accctgcccc acgaggctcc ctcacacctg cccccccgtc cttgtgttga
3181 agacagtggg aagaggagaa aggaccaggg aaaccaaggg agttgactgt tcagttttat
3241 ttatttattt tttaagtttt tttttccttt caagtctgcc agtctctgag atcagaacaa
3301 cagacagtgt agggtaacta atcatgtgat tctcttagtg gaatgaaatg ttctaccccc
3361 acaagaagga gtatacgtca ttgttcatat tctgtaatcg cacaatgtat tgtaatgcaa
3421 attccaattc catgtatttt tattacaatt tttctggaaa aaaatgtgaa ccaataaaag
3481 atgttgatgc acacgcgtgc cttct
Mus musculus thioredoxin reductase 1 (Txnrdl), transcript variant 2, mRNA
NCBI Reference Sequence: NM_015762.2 (SEQ ID NO: 22)
1 agtttgcttc cgtcaggcct cgcgtccacg cgggaggtgc gggacgccga caccgcgggg
61 cgagaagagc tggtggtttc accttccttg ttcatccgaa caaaaaaggc caacttcaaa
121 agctgccaac aatgaatggc tccaaagatc cccctgggtc ctatgacttc gacctgatca
181 tcattggagg aggctcagga ggactggcag cagctaagga ggcagccaaa tttgacaaga
241 aagtgctggt cttggatttt gtcacaccga ctcctcttgg gaccagatgg ggtctcggag
301 gaacgtgtgt gaatgtgggt tgcataccta agaagctgat gcaccaggca gctttgctcg
361 gacaagctct gaaagactcg cgcaactatg gctggaaagt cgaagacaca gtgaagcatg
421 actgggagaa aatgacggaa tctgtgcaga gtcacatcgg ctcgctgaac tggggctacc
481 gcgtagctct ccgggagaaa aaggtcgtct atgagaatgc ttacgggagg ttcattggtc
541 ctcacaggat tgtggcgaca aataacaaag gtaaagaaaa aatctattca gcagagcggt
601 tcctcatcgc cacaggtgag aggccccgct acctgggcat ccctggagac aaagagtact
661 gcatcagcag tgatgatctt ttctccttgc cttactgccc ggggaagacc ctagtagttg
721 gtgcatccta tgtcgccttg gaatgtgcag gatttctggc tggtatcggc ttagacgtca
781 ctgtaatggt gcggtccatt ctccttagag gatttgacca agacatggcc aacaaaatcg
841 gtgaacacat ggaagaacat ggtatcaagt ttataaggca gttcgtccca acgaaaattg
901 aacagatcga agcaggaaca ccaggccgac tcagggtgac tgctcaatcc acaaacagcg
961 aggagaccat agagggcgaa tttaacacag tgttgctggc ggtaggaaga gattcttgta
1021 cgagaactat tggcttagag accgtgggcg tgaagataaa cgaaaaaacc ggaaagatac
1081 ccgtcacgga tgaagagcag accaatgtgc cttacatcta cgccatcggt gacatcctgg
1141 aggggaaget agagctgact cccgtagcca tccaggcggg gagattgctg gctcagaggc
1201 tgtatggagg ctccaatgtc aaatgtgact atgacaatgt cccaacgact gtatttactc
1261 ctttggaata tggctgttgt ggcctctctg aagaaaaagc cgtagagaaa tttggggaag 1321 aaaatattga agtttaccat agtttctttt ggccattgga atggacagtc ccatcccggg
1381 ataacaacaa atgttatgca aaaataatct gcaaccttaa agacgatgaa cgtgtcgtgg
1441 gcttccacgt gctgggtcca aacgctggag aggtgacgca gggctttgcg gctgcgctca
1501 agtgtgggct gactaagcag cagctggaca gcaccatcgg catccacccg gtctgtgcag
1561 agatattcac aacgttgtca gtgacgaagc gctctggggg agacatcctc cagtctggct
1621 gctgaggtta agccccagtg tggatgctgt tgccaagact acagaccatt gccttgcttc
1681 cttgcccacg cccaggtgaa gttcaggaag gctcttgggt cctaggcgcc aattcaaggt
1741 gctgtcctaa ggccaccggg tccctgggat cttgtgggta ggaggtggca ggtcgaagga
1801 ggctgcagca tcgcactggg gtcaccatga cagactcaga ctgacatctg gcagagcatc
1861 acaggcatgc gtccatgaag tcactggcct caagcccaag tggtgggcag tgacagaaga
1921 gctgccgggt ctgttgagct caaccttttc ctgtagattg tcttagtctc actttcaagc
1981 tgtctaatgt caattctgtt tttctttttt cctccatggg gttaatgata ctagagatag
2041 ggaatattag caatcagttt ttgtcatggc tggtccatct gcaacagtct ttactgtgtg
2101 gaagtgggtg agatggctta tgagagccaa accaatttat ccccagaaag acgaattacc
2161 ctgtgactaa aatacactgt ctgcttttac taactggtgt agcattgtct cctttaataa
2221 gtcttgtgtc caaaacgaga aaaaccattg gccacttttg caagtttcct gcagtgtgct
2281 tagcaaggga ggtggcgact tggctaatct acttgaactg catcgcatgg ctcttgggta
2341 gcttagagca tcgcagggta gaggcagacc agcagtgagt gtctctcctg gtacaattat
2401 tgtctggttc tcagtggaaa acgcttaatt tgctttaaac ttggtgtttt tgtgaggtgg
2461 atttagtctt aagctgtgtc ccataagaac tacattcaca ggcaagtggc tcttcctcca
2521 cacagcctat acatcttctg aggtaattac tttcataagg aagctgttca taacgtaagt
2581 tattattatt attgaacaca ggtggatgtg aaggattttt cattgaaaaa ccaaatggtt
2641 tttctttttt tctgttcagt gagcccacag gaactctgtc aggacagcca gtactctgcc
2701 ggcatggctg ctggggcgtt tacggtgtag tttagctcct aggttacatg accgtgaaca
2761 tgctggctga ggactacaca aaccaggttt cccaccatac acggcctggc cctgcagctt
2821 cttttcttgc cctccccttt gcctgtcccc acctgcagta ctgagtggcg tttcacagta
2881 cccttctggg ccacctcagg gaagggattt gcctggtgtc cagccagcag cacccaccct
2941 gccccacgag gctccctcac acctgccccc ccgtccttgt gttgaagaca gtgggaagag
3001 gagaaaggac cagggaaacc aagggagttg actgttcagt tttatttatt tattttttaa
3061 gttttttttt cctttcaagt ctgccagtct ctgagatcag aacaacagac agtgtagggt
3121 aactaatcat gtgattctct tagtggaatg aaatgttcta cccccacaag aaggagtata
3181 cgtcattgtt catattctgt aatcgcacaa tgtattgtaa tgcaaattcc aattccatgt
3241 atttttatta caatttttct ggaaaaaaat gtgaaccaat aaaagatgtt gatgcacacg
3301 cgtgccttct
Mus musculus thioredoxin reductase 1 (Txnrdl), transcript variant 4, mRNA
NCBI Reference Sequence: NM 001042523.1 (SEQ ID NO: 23)
1 caggctccac cagtgcttct gcagacctca gagcctggcg gctggcctca taaacagccg 61 tgcggtggac actctactaa gtgccctgca ttgaaggaga agccctggtc accatgccag 121 ttgatgactg ctggctgtac ttcccagctt ctcgaggtag aacctttgtg cagactgtct 181 gggtggcacc cacttgcccc aactgttgct ggtttccagg ttttctccct ccagtccccc 241 ggccaccaca tgtgccccgt gtgctgctga ggggccctcg tggggctgtg cttcctgctt 301 cacgtccctc caagacactc ccctcctcat cccagacgcc ctgtcctact gacccctgta 361 tctgccctcc accctccaca cctgatagta ggcaggaaaa aaatacgcaa tctgagctgc 421 cgaacaaaaa aggccaactt caaaagctgc caacaatgaa tggctccaaa gatccccctg 481 ggtcctatga cttcgacctg atcatcattg gaggaggctc aggaggactg gcagcagcta 541 aggaggcagc caaatttgac aagaaagtgc tggtcttgga ttttgtcaca ccgactcctc 601 ttgggaccag atggggtctc ggaggaacgt gtgtgaatgt gggttgcata cctaagaagc 661 tgatgcacca ggcagctttg ctcggacaag ctctgaaaga ctcgcgcaac tatggctgga 721 aagtcgaaga cacagtgaag catgactggg agaaaatgac ggaatctgtg cagagtcaca 781 tcggctcgct gaactggggc taccgcgtag ctctccggga gaaaaaggtc gtctatgaga 841 atgcttacgg gaggttcatt ggtcctcaca ggattgtggc gacaaataac aaaggtaaag 901 aaaaaatcta ttcagcagag cggttcctca tcgccacagg tgagaggccc cgctacctgg 961 gcatccctgg agacaaagag tactgcatca gcagtgatga tcttttctcc ttgccttact 1021 gcccggggaa gaccctagta gttggtgcat cctatgtcgc cttggaatgt gcaggatttc
1081 tggctggtat cggcttagac gtcactgtaa tggtgcggtc cattctcctt agaggatttg
1141 accaagacat ggccaacaaa atcggtgaac acatggaaga acatggtatc aagtttataa
1201 ggcagttcgt cccaacgaaa attgaacaga tcgaagcagg aacaccaggc cgactcaggg
1261 tgactgctca atccacaaac agcgaggaga ccatagaggg cgaatttaac acagtgttgc
1321 tggcggtagg aagagattct tgtacgagaa ctattggctt agagaccgtg ggcgtgaaga
1381 taaacgaaaa aaccggaaag atacccgtca cggatgaaga gcagaccaat gtgccttaca
1441 tctacgccat cggtgacatc ctggagggga agctagagct gactcccgta gccatccagg
1501 eggggagatt gctggctcag aggctgtatg gaggctccaa tgtcaaatgt gactatgaca
1561 atgtcccaac gactgtattt actcctttgg aatatggctg ttgtggcctc tctgaagaaa
1621 aagccgtaga gaaatttggg gaagaaaata ttgaagttta ccatagtttc ttttggccat
1681 tggaatggac agtcccatcc cgggataaca acaaatgtta tgcaaaaata atctgcaacc
1741 ttaaagacga tgaacgtgtc gtgggcttcc acgtgctggg tccaaacgct ggagaggtga
1801 cgcagggctt tgcggctgcg ctcaagtgtg ggctgactaa gcagcagctg gacagcacca
1861 tcggcatcca cccggtctgt gcagagatat tcacaacgtt gtcagtgacg aagcgctctg
1921 ggggagacat cctccagtct ggctgctgag gttaagcccc agtgtggatg ctgttgccaa
1981 gactacagac cattgccttg cttccttgcc cacgcccagg tgaagttcag gaaggctctt
2041 gggtcctagg cgccaattca aggtgctgtc ctaaggccac cgggtccctg ggatcttgtg
2101 ggtaggaggt ggcaggtcga aggaggctgc agcatcgcac tggggtcacc atgacagact
2161 cagactgaca tctggcagag catcacaggc atgcgtccat gaagtcactg gcctcaagcc
2221 caagtggtgg gcagtgacag aagagctgcc gggtctgttg agctcaacct tttcctgtag
2281 attgtcttag tctcactttc aagctgtcta atgtcaattc tgtttttctt ttttcctcca
2341 tggggttaat gatactagag atagggaata ttagcaatca gtttttgtca tggctggtcc
2401 atctgcaaca gtctttactg tgtggaagtg ggtgagatgg cttatgagag ccaaaccaat
2461 ttatccccag aaagacgaat taccctgtga ctaaaataca ctgtctgctt ttactaactg
2521 gtgtagcatt gtctccttta ataagtcttg tgtccaaaac gagaaaaacc attggccact
2581 tttgcaagtt tcctgcagtg tgcttagcaa gggaggtggc gacttggcta atctacttga
2641 actgcatcgc atggctcttg ggtagcttag agcatcgcag ggtagaggca gaccagcagt
2701 gagtgtctct cctggtacaa ttattgtctg gttctcagtg gaaaacgctt aatttgcttt
2761 aaacttggtg tttttgtgag gtggatttag tcttaagctg tgtcccataa gaactacatt
2821 cacaggcaag tggctcttcc tccacacagc ctatacatct tctgaggtaa ttactttcat
2881 aaggaagctg ttcataacgt aagttattat tattattgaa cacaggtgga tgtgaaggat
2941 ttttcattga aaaaccaaat ggtttttctt tttttctgtt cagtgagccc acaggaactc
3001 tgtcaggaca gccagtactc tgccggcatg gctgctgggg cgtttacggt gtagtttagc
3061 tcctaggtta catgaccgtg aacatgctgg ctgaggacta cacaaaccag gtttcccacc
3121 atacacggcc tggccctgca gcttcttttc ttgccctccc ctttgcctgt ccccacctgc
3181 agtactgagt ggcgtttcac agtacccttc tgggccacct cagggaaggg atttgcctgg
3241 tgtccagcca gcagcaccca ccctgcccca cgaggctccc tcacacctgc ccccccgtcc
3301 ttgtgttgaa gacagtggga agaggagaaa ggaccaggga aaccaaggga gttgactgtt
3361 cagttttatt tatttatttt ttaagttttt ttttcctttc aagtctgcca gtctctgaga
3421 tcagaacaac agacagtgta gggtaactaa tcatgtgatt ctcttagtgg aatgaaatgt
3481 tctaccccca caagaaggag tatacgtcat tgttcatatt ctgtaatcgc acaatgtatt
3541 gtaatgcaaa ttccaattcc atgtattttt attacaattt ttctggaaaa aaatgtgaac
3601 caataaaaga tgttgatgca cacgcgtgcc ttct
(i.e., TXNRD1 mRNA isoforms), thereby reducing or inhibiting TXNRD1 expression. The antisense nucleic acid may be antisense RNA, or antisense DNA. Antisense nucleic acids based on the known TXNRD1 gene sequence can be readily designed and engineered using methods known in the art. In some embodiments, the antisense nucleic acid comprises the nucleic acid sequence of any one of SEQ ID NOs: 1-12, or a complement thereof.
[0083] Antisense nucleic acids are molecules which are complementary to a sense nucleic acid strand, e.g ., complementary to the coding strand of a double-stranded DNA molecule (or cDNA) or complementary to an mRNA sequence. Accordingly, an antisense nucleic acid can form hydrogen bonds with a sense nucleic acid. The antisense nucleic acid can be
complementary to an entire TXNRD1 coding strand, or to a portion thereof, e.g, all or part of the protein coding region (or open reading frame). In some embodiments, the antisense nucleic acid is an oligonucleotide which is complementary to only a portion of the coding region of TXNRD1 mRNA. In certain embodiments, an antisense nucleic acid molecule can be complementary to a noncoding region of the TXNRD1 coding strand. In some
embodiments, the noncoding region refers to the 5' and 3' untranslated regions that flank the coding region and are not translated into amino acids. For example, the antisense
oligonucleotide can be complementary to the region surrounding the translation start site of TXNRD1. An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45 or 50 nucleotides in length.
[0084] An antisense nucleic acid can be constructed using chemical synthesis and enzymatic ligation reactions using procedures known in the art. For example, an antisense nucleic acid (e.g, an antisense oligonucleotide) can be chemically synthesized using naturally occurring nucleotides or modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids, e.g, phosphorothioate derivatives and acridine substituted nucleotides. Examples of modified nucleotides which can be used to generate the antisense nucleic acid include 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-hodouracil,
hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl)uracil, 5- carboxymethylaminomethyl-2-thouridine, 5-carboxymethylaminometh-yluracil,
dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-metnylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5- methoxyaminom ethyl-2 -thiouracil, beta-D-mannosylqueosine, 5'- methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopenten-yladenine, uracil- 5-oxyacetic acid (v), wybutosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl-2- thiouracil, 2-thlouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-cxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation ( i.e ., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest).
[0085] The antisense nucleic acid molecules may be administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding the protein of interest to thereby inhibit expression of the protein, e.g. , by inhibiting transcription and/or translation. The hybridization can occur via Watson-Crick base pairing to form a stable duplex, or in the case of an antisense nucleic acid molecule which binds to DNA duplexes, through specific interactions in the major groove of the double helix.
[0086] In some embodiments, the antisense nucleic acid molecules are modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid molecules to peptides or antibodies which bind to cell surface receptors or antigens. In some embodiments, the antisense nucleic acid molecule is an alpha-anomeric nucleic acid molecule. An alpha-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual b- units, the strands run parallel to each other (Gaultier et al., Nucleic Acids. Res. 15:6625- 6641(1987)). The antisense nucleic acid molecule can also comprise a 2'-0 - methylribonucleotide (Inoue et al., Nucleic Acids Res. 15:6131-6148 (1987)) or a chimeric RNA-DNA analogue (Inoue et al., FEBS Lett. 215:327-330 (1987)).
[0087] The present disclosure also provides a short hairpin RNA (shRNA) or small interfering RNA (siRNA) comprising a nucleic acid sequence that is complementary to and specifically hybridizes with a portion of any one of SEQ ID NOs: 13-23 (TXNRDl mRNA isoforms), thereby reducing or inhibiting TXNRDl expression. In some embodiments, the shRNA or siRNA is about 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29 base pairs in length. Double-stranded RNA (dsRNA) can induce sequence-specific post-transcriptional gene silencing (e.g., RNA interference (RNAi)) in many organisms such as C. elegans,
Drosophila, plants, mammals, oocytes and early embryos. RNAi is a process that interferes with or significantly reduces the number of protein copies made by an mRNA. For example, a double-stranded siRNA or shRNA molecule is engineered to complement and hybridize to a mRNA of a target gene. Following intracellular delivery, the siRNA or shRNA molecule associates with an RNA-induced silencing complex (RISC), which then binds and degrades a complementary target mRNA (such as TXNRD1 mRNA). In some embodiments, the shRNA or siRNA comprises the nucleic acid sequence of any one of SEQ ID NOs: 1-12.
[0088] The present disclosure also provides a ribozyme comprising a nucleic acid sequence that is complementary to and specifically hybridizes with a portion of any one of SEQ ID NOs: 13-23 (TXNRDl mRNA isoforms), thereby reducing or inhibiting TXNRD1 expression. Ribozymes are catalytic RNA molecules with ribonuclease activity which are capable of cleaving a complementary single-stranded nucleic acid, such as an mRNA. Thus, ribozymes ( e.g ., hammerhead ribozymes (described in Haselhoff and Gerlach, Nature 334:585-591 (1988))) can be used to catalytically cleave TXNRDl transcripts, thereby inhibiting translation of TXNRDl.
[0089] A ribozyme having specificity for a TXNRDl-e ncoding nucleic acid can be designed based upon a TXNRDl nucleic acid sequence disclosed herein. For example, a derivative of a Tetrahymena L-19 IV S RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in a TXNRDl -mcodlmg mRNA. See, e.g., U.S. Pat. No. 4,987,071 and U.S. Pat. No. 5,116,742. Alternatively, TXNRDl mRNA can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel and Szostak (1993) Science 261 : 1411-1418, incorporated herein by reference.
[0090] The present disclosure also provides a synthetic guide RNA (sgRNA) comprising a nucleic acid sequence that is complementary to and specifically hybridizes with a portion of any one of SEQ ID NOs: 13-23 (TXNRDl mRNA isoforms). Guide RNAs for use in CRISPR-Cas systems are typically generated as a single guide RNA comprising a crRNA segment and a tracrRNA segment. The crRNA segment and a tracrRNA segment can also be generated as separate RNA molecules. The crRNA segment comprises the targeting sequence that binds to a portion of any one of SEQ ID NOs: 13-23 (TXNRDl mRNA isoforms), and a stem portion that hybridizes to a tracrRNA. The tracrRNA segment comprises a nucleotide sequence that is partially or completely complementary to the stem sequence of the crRNA and a nucleotide sequence that binds to the CRISPR enzyme. In some embodiments, the crRNA segment and the tracrRNA segment are provided as a single guide RNA. In some embodiments, the crRNA segment and the tracrRNA segment are provided as separate RNAs. The combination of the CRISPR enzyme with the crRNA and tracrRNA make up a functional CRISPR-Cas system. Exemplary CRISPR-Cas systems for targeting nucleic acids, are described, for example, in WO2015/089465.
[0091] In some embodiments, a synthetic guide RNA is a single RNA represented as comprising the following elements:
5'-Xl-X2-Y-Z-3'
where XI and X2 represent the crRNA segment, where XI is the targeting sequence that binds to a portion of any one of SEQ ID NOs: 13-23, X2 is a stem sequence the hybridizes to a tracrRNA, Z represents a tracrRNA segment comprising a nucleotide sequence that is partially or completely complementary to X2, and Y represents a linker sequence. In some embodiments, the linker sequence comprises two or more nucleotides and links the crRNA and tracrRNA segments. In some embodiments, the linker sequence comprises 2, 3, 4, 5, 6,
7, 8, 9, 10 or more nucleotides. In some embodiments, the linker is the loop of the hairpin structure formed when the stem sequence hybridized with the tracrRNA.
[0092] In some embodiments, a synthetic guide RNA is provided as two separate RNAs where one RNA represents a crRNA segment: 5'-Xl-X2-3' where XI is the targeting sequence that binds to a portion of any one of SEQ ID NOs: 13-23, X2 is a stem sequence the hybridizes to a tracrRNA, and one RNA represents a tracrRNA segment, Z, that is a separate RNA from the crRNA segment and comprises a nucleotide sequence that is partially or completely complementary to X2 of the crRNA.
[0093] Exemplary crRNA stem sequences and tracrRNA sequences are provided, for example, in WO/2015/089465, which is incorporated by reference herein. In general, a stem sequence includes any sequence that has sufficient complementarity with a complementary sequence in the tracrRNA to promote formation of a CRISPR complex at a target sequence, wherein the CRISPR complex comprises the stem sequence hybridized to the tracrRNA. In general, degree of complementarity is with reference to the optimal alignment of the stem and complementary sequence in the tracrRNA, along the length of the shorter of the two sequences. Optimal alignment may be determined by any suitable alignment algorithm, and may further account for secondary structures, such as self-complementarity within either the stem sequence or the complementary sequence in the tracrRNA. In some embodiments, the degree of complementarity between the stem sequence and the complementary sequence in the tracrRNA along the length of the shorter of the two when optimally aligned is about or more than about 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97.5%, 99%, or higher. In some embodiments, the stem sequence is about or more than about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, or more nucleotides in length. In some embodiments, the stem sequence and complementary sequence in the tracrRNA are contained within a single RNA, such that hybridization between the two produces a transcript having a secondary structure, such as a hairpin. In some embodiments, the tracrRNA has additional complementary sequences that form hairpins. In some embodiments, the tracrRNA has at least two or more hairpins. In some embodiments, the tracrRNA has two, three, four or five hairpins. In some embodiments, the tracrRNA has at most five hairpins.
[0094] In a hairpin structure, the portion of the sequence 5' of the final“N” and upstream of the loop corresponds to the crRNA stem sequence, and the portion of the sequence 3' of the loop corresponds to the tracrRNA sequence. Further non-limiting examples of single polynucleotides comprising a guide sequence, a stem sequence, and a tracr sequence are as follows (listed 5' to 3'), where“N” represents a base of a guide sequence ( e.g . a modified oligonucleotide provided herein), the first block of lower case letters represent stem sequence, and the second block of lower case letters represent the tracrRNA sequence, and the final poly-T sequence represents the transcription terminator: (a)
NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaagatttaGAAAtaaatcttgcagaagctacaaagataa ggcttcatgccgaaatcaacaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT (SEQ ID NO: 24); (b) NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaGAAAtgcagaagctacaaagataaggcttcatgccg aaatcaacaccctgtcattttatggcagggtgttttcgttatttaaTTTTTT (SEQ ID NO: 25); (c)
NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaGAAAtgcagaagctacaaagataaggcttcatgccg aaatcaacaccctgtcattttatggcagggtgtTTTTTT (SEQ ID NO: 26); (d)
NNNNNNNNNNNNNNNNNNNNgttttagagctaGAAAtagcaagttaaaataaggctagtccgttatcaactt gaaaaagtggcaccgagtcggtgcTTTTTT (SEQ ID NO: 27); (e)
NNNNNNNNNNNNNNNNNNNNgttttagagctaGAAATAGcaagttaaaataaggctagtccgttatcaac ttgaaaaagtgTTTTTTT (SEQ ID NO: 28); and (f)
NNNNNNNNNNNNNNNNNNNNgttttagagctagAAATAGcaagttaaaataaggctagtccgttatcaTT TTTTTT (SEQ ID NO: 29). [0095] Selection of suitable oligonucleotides for use in as a targeting sequence in a CRISPR Cas system depends on several factors including the particular CRISPR enzyme to be used and the presence of corresponding proto-spacer adjacent motifs (PAMs) downstream of the target sequence in the target nucleic acid. The PAM sequences direct the cleavage of the target nucleic acid by the CRISPR enzyme. In some embodiments, a suitable PAM is 5'- NRG or 5'-NNGRR (where N is any Nucleotide) for SpCas9 or SaCas9 enzymes (or derived enzymes), respectively. Generally, the PAM sequences should be present between about 1 to about 10 nucleotides of the target sequence to generate efficient cleavage of the target nucleic acid. Thus, when the guide RNA forms a complex with the CRISPR enzyme, the complex locates the target and PAM sequence, unwinds the DNA duplex, and the guide RNA anneals to the complementary sequence on the opposite strand. This enables the Cas9 nuclease to create a double-strand break. In some embodiments, the sgRNA comprises the nucleic acid sequence of any one of SEQ ID NOs: 1-12.
[0096] A variety of CRISPR enzymes are available for use in conjunction with the disclosed guide RNAs of the present disclosure. In some embodiments, the CRISPR enzyme is a Type II CRISPR enzyme. In some embodiments, the CRISPR enzyme catalyzes DNA cleavage. In some embodiments, the CRISPR enzyme catalyzes RNA cleavage. In some embodiments, the CRISPR enzyme is any Cas9 protein, for instance any naturally-occurring bacterial Cas9 as well as any chimeras, mutants, homologs or orthologs. Non-limiting examples of Cas proteins include Casl, CaslB, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csnl and Csxl2), CaslO, Csyl, Csy2, Csy3, Csel, Cse2, Cscl, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3, Csxl, Csxl5, Csfl, Csf2, Csf3, Csf4, homologues thereof, or modified variants thereof. In some embodiments, the CRISPR enzyme cleaves both strands of the target nucleic acid at the Protospacer Adjacent Motif
(PAM) site. In some embodiments, the CRISPR enzyme is a nickase, which cleaves only one strand of the target nucleic acid. In some embodiments, the CRISPR enzyme is a dCas9 tagged with additional enzyme activities, which suppress or activate the expression of genes of interest. Pharmaceutical Compositions
[0097] In one aspect, the present disclosure provides pharmaceutical compositions comprising a TXNRD1 inhibitor.
[0098] The pharmaceutical compositions of the present disclosure may be prepared by any of the methods known in the pharmaceutical arts. The amount of active ingredient that can be combined with a carrier material to produce a single dosage form will vary depending upon the host being treated and the particular mode of administration. The amount of active ingredient that can be combined with a carrier material to produce a single dosage form will generally be that amount of the compound that produces a therapeutic effect. Generally, the amount of active compound will be in the range of about 0.1 to 99 percent, more typically, about 5 to 70 percent, and more typically, about 10 to 30 percent.
[0099] In some embodiments, pharmaceutical compositions of the present technology may contain one or more pharmaceutically-acceptable carriers, which as used herein, generally refers to a pharmaceutically-acceptable composition, such as a liquid or solid filler, diluent, excipient, manufacturing aid ( e.g ., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), or solvent encapsulating material, useful for introducing the active agent into the body.
[00100] Examples of suitable aqueous and non-aqueous carriers that may be employed in the pharmaceutical compositions of the present technology include, for example, water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), vegetable oils (such as olive oil), and injectable organic esters (such as ethyl oleate), and suitable mixtures thereof. Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.
[00101] In some embodiments, the formulations may include one or more of sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients, such as cocoa butter and suppository waxes; oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, com oil and soybean oil; glycols, such as propylene glycol; polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; esters, such as ethyl oleate and ethyl laurate; agar; alginic acid; buffering agents, such as magnesium hydroxide and aluminum hydroxide; pyrogen-free water; isotonic saline; Ringer's solution; ethyl alcohol; pH buffered solutions; polyesters, polycarbonates and/or polyanhydrides; preservatives; glidants; fillers; and other non-toxic compatible substances employed in pharmaceutical formulations.
[00102] Various auxiliary agents, such as wetting agents, emulsifiers, lubricants ( e.g ., sodium lauryl sulfate and magnesium stearate), coloring agents, release agents, coating agents, sweetening agents, flavoring agents, preservative agents, and antioxidants can also be included in the pharmaceutical composition of the present technology. Some examples of pharmaceutically-acceptable antioxidants include: water soluble antioxidants, such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabi sulfite, sodium sulfite, and the like; oil-soluble antioxidants, such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propyl gallate, alpha-tocopherol, and the like; and metal chelating agents, such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like. In some embodiments, the
pharmaceutical formulation includes an excipient selected from, for example, celluloses, liposomes, lipid nanoparticles, micelle-forming agents (e.g., bile acids), and polymeric carriers, e.g., polyesters and polyanhydrides. Suspensions, in addition to the active compounds, may contain suspending agents, such as, for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof. Prevention of the action of microorganisms on the active compounds may be ensured by the inclusion of various antibacterial and antifungal agents, such as, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. It may also be desirable to include isotonic agents, such as sugars, sodium chloride, and the like into the compositions. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents that delay absorption, such as aluminum monostearate and gelatin.
Therapeutic Methods
[00103] The following discussion is presented by way of example only, and is not intended to be limiting.
[00104] One aspect of the present technology includes methods of treating a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1. Additionally or alternatively, in some embodiments, the present technology includes methods of treating a RAS-mutant cancer. The three major isoforms of RAS (KRAS, NRAS, and HRAS) together are mutated in about 20% of human cancers, primarily in the active site at residues G12, G13, and Q61 near the g-phosphate of the guanosine triphosphate (GTP) substrate (See Marcus & Mattos, Clin Cancer Res 21(8): 1810-1818 (2015)). In certain embodiments, the RAS-mutant cancer comprises a KRAS, NRAS, or HRAS mutation selected from the group consisting of G12C, G12D, G12V, G12A, G12S, G12R, G13D, G13C, G13S, G13R, G13A, G13V, Q61H, Q61L, Q61R, Q61K, Q61P, and Q61E.
[00105] In some embodiments, the present technology includes methods of treating a
RAS-mutant pancreatic cancer. In one aspect, the present disclosure provides a method for inhibiting proliferation of a RAS-mutant cancer in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of at least one TXNRD1 inhibitor disclosed herein, and wherein the subject suffers from a RAS-mutant cancer characterized by elevated expression levels and/or increased activity of TXNRD1.
[00106] In some embodiments, the subject is diagnosed as having, suspected as having, or at risk of having a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1. Additionally or alternatively, in some embodiments, the subject is diagnosed as having a RAS-mutant cancer. In certain embodiments, the RAS- mutant cancer comprises a KRAS, NRAS, or HRAS mutation selected from the group consisting of G12C, G12D, G12V, G12A, G12S, G12R, G13D, G13C, G13S, G13R, G13A, G13V, Q61H, Q61L, Q61R, Q61K, Q61P, and Q61E. In some embodiments, the subject is diagnosed as having lung cancer ( e.g ., lung adenocarcinoma), mucinous adenoma, pancreatic cancer (e.g., PDAC), colorectal cancer, skin cancer (e.g., melanoma), endometrial cancer, testicular germ cell cancer, or adrenal gland cancer. In some embodiments, the subject is diagnosed as having pancreatic cancer. In some embodiments, the subject is diagnosed as having a RAS-mutant pancreatic cancer.
[00107] In therapeutic applications, compositions or medicaments comprising a TXNRD1 inhibitor disclosed herein are administered to a subject suspected of, or already suffering from such a disease or condition (such as, a subject diagnosed with a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1 and/or a subject diagnosed with a RAS-mutant cancer and/or a subject diagnosed with pancreatic cancer), in an amount sufficient to cure, or at least partially arrest, the symptoms of the disease, including its complications and intermediate pathological phenotypes in development of the disease.
[00108] Subjects suffering from a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1 and/or a subject diagnosed with a RAS-mutant cancer can be identified by any or a combination of diagnostic or prognostic assays known in the art.
[00109] In some embodiments, the subject may exhibit one or more mutations in KRAS.
In addition, the subject may exhibit one or more mutations in at least one of TP53, CDKN2A , SMAD4 , MLL3 , TGFBR2 , ARID l A and SF3B1, EPC1 and ARID2 , ATM, ZIM2 , MAP2K4 ,
N A IX V, SLC16A4 , MAGEA6 , ROB02 , KDM6A , PREX2, ERBB2 , MET , FGFR1, CDK6 , PIK3R3, PIK3CA , BRCA1 , BRCA2 , PALB2 , e/c. Biankin el al ., Nature 491(7424): 399-405 (2012); and Waddell e/ a/., Nature 518(7540):495-501 (2015). Additionally or alternatively, the subject may exhibit at least one mutation in one or more of a core set of twelve cellular signaling pathways and processes. Jones e/ a/., Science 321(5897): 1801-1806 (2008).
[00110] In some embodiments, subjects with a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1, and/or subjects suffering from a RAS-mutant pancreatic cancer that are treated with the TXNRD1 inhibitor will show amelioration or elimination of one or more of the following symptoms: pain in the upper abdomen that radiates towards the back, loss of appetite or unintended weight loss, depression, new-onset diabetes, blood clots, fatigue, yellowing of skin and the whites of eyes (jaundice), bloating, nausea, and vomiting.
[00111] In certain embodiments, subjects with a disease or condition characterized by elevated expression levels of TXNRD1 and/or increased activity levels of TXNRD1, and/or subjects suffering from a RAS-mutant cancer, and/or subjects suffering from pancreatic cancer that are treated with the TXNRD1 inhibitor will show reduced RAS-mutant cell proliferation and/or increased survival compared to untreated subjects with RAS-mutant cancer. In certain embodiments, subjects with a disease or condition characterized by elevated expression levels of TXNDR1 and/or increased activity of TXNRD1, and/or subjects suffering from a RAS-mutant cancer, and/or subjects suffering from pancreatic cancer that are treated with the TXNRD1 inhibitor will show reduced TXNPD1 and/or RAS expression levels and/or reduced TXNRD1 and/or RAS activity levels compared to untreated subjects with RAS-mutant cancer.
[00112] In one aspect, the present disclosure provides a method for monitoring the therapeutic efficacy of a TXNRD1 inhibitor in a subject diagnosed with a RAS-mutant cancer comprising: (a) detecting TXNRD1 protein levels in a test sample obtained from the subject after the subject has been administered the TXNRD1 inhibitor; and (b) determining that the TXNRD1 inhibitor is effective when the TXNRD1 protein levels in the test sample are reduced compared to that observed in a control sample obtained from the subject prior to administration of the TXNRD1 inhibitor. The TXNRDl inhibitor may be auranofm,
Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, Brevetoxin-2, Manumycin A, Ethaselen, Aurothioglucose, Protoporphyrin IX, inhibitory RNAs against TXNRDl, anti- TXNRD1 antibodies, or any derivatives thereof. The test sample may be tissues, cells or biological fluids (blood, plasma, saliva, urine, serum etc.) present within a subject.
Alternatively, RAS (e.g., KRAS, HRAS, NRAS) and/or TXNRDl expression levels may be used to determine the efficacy of the TXNRDl inhibitor in the subject (see Example 6 described herein). Accordingly, in certain embodiments, the method further comprises detecting expression levels of RAS (e.g., KRAS, HRAS, NRAS) and/or TXNRDl in the subject, wherein a decrease in RAS (e.g, KRAS, HRAS, NRAS) and/or TXNRDl expression levels relative to those observed in the subject prior to treatment is indicative of the therapeutic efficacy of the TXNRDl inhibitor. Additionally or alternatively, in certain embodiments, the method further comprises detecting activity of RAS (e.g, KRAS, HRAS, NRAS) and/or TXNRDl protein in the subject, wherein a decrease in RAS (e.g, KRAS, HRAS, NRAS) and/or TXNRDl activity relative to those observed in the subject prior to treatment is indicative of the therapeutic efficacy of the TXNRDl inhibitor. In certain embodiments, the RAS-mutant cancer comprises a KRAS, NRAS, or HRAS mutation selected from the group consisting of G12C, G12D, G12V, G12A, G12S, G12R, G13D, G13C, G13S, G13R, G13A, G13V, Q61H, Q61L, Q61R, Q61K, Q61P, and Q61E. In certain embodiments, the KRAS, NRAS, or HRAS mutation is detected via DNA sequencing.
[00113] In any and all embodiments of the methods disclosed herein, TXNRDl and/or RAS (e.g, KRAS, HRAS, NRAS) expression levels are detected via RNA-seq, northern blotting, microarrays, dot or slot blots, fluorescent in situ hybridization, Reverse transcription polymerase chain reaction (RT-PCR), ribonuclease protection assay (RPA), real-time quantitative RT-PCR, high-performance liquid chromatography (HPLC), liquid
chromatography-mass spectrometry (LC/MS), enzyme-linked immunosorbent assay
(ELISA), immunoprecipitation, immunoelectrophoresis, immunostaining,
immunohistochemistry, or western blotting.
Prophylactic Methods
[00114] In one aspect, the present technology provides a method for preventing or delaying the onset of a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1. Additionally or alternatively, in some aspects, the present technology provides a method for preventing or delaying the onset a RAS-mutant cancer. In certain embodiments, the RAS-mutant cancer comprises a KRAS, NRAS, or HRAS mutation selected from the group consisting of G12C, G12D, G12V, G12A, G12S, G12R, G13D, G13C, G13S, G13R, G13A, G13V, Q61H, Q61L, Q61R, Q61K, Q61P, and Q61E. The RAS-mutant cancer may be lung cancer ( e.g ., lung adenocarcinoma), mucinous adenoma, pancreatic cancer (e.g., PDAC), colorectal cancer, skin cancer (e.g., melanoma), endometrial cancer, testicular germ cell cancer, or adrenal gland cancer.
[00115] Subjects at risk or susceptible to a disease or condition characterized by elevated expression levels and/or increased activity of TXNRDl, and/or subjects at risk or susceptible to a RAS-mutant cancer, and/or subjects at risk or susceptible to pancreatic cancer include those that exhibit one or more mutations in RAS (e.g, KRAS, HRAS, NRAS). In addition, the subjects may exhibit one or more point mutations in one or more of TP53, CDKN2A,
SMAD4, MLL3, TGFBR2, ARID 1 A and SF3B1, EPC1 and ARID2, AIM, ZIM2, MAP2K4, NALCN , SLC16A4, MAGEA6, ROB02, KDM6A, PREX2, ERBB2, MET, FGFR1, CDK6, PIK3R3, PIK3CA, BRCA1, BRCA2, PALB2, etc. Biankin el al., Nature 491(7424): 399-405 (2012); and Waddell et al., Nature 518(7540):495-501 (2015). Additionally or alternatively, the subjects may exhibit at least one mutation in one or more of a core set of twelve cellular signaling pathways and processes. Jones et al., Science 321(5897): 1801-1806 (2008). Such subjects can be identified by, e.g, any or a combination of diagnostic or prognostic assays known in the art. In certain embodiments, the RAS-mutant cancer comprises a KRAS, NRAS, or HRAS mutation selected from the group consisting of G12C, G12D, G12V, G12A, G12S, G12R, G13D, G13C, G13S, G13R, G13A, G13V, Q61H, Q61L, Q61R, Q61K, Q61P, and Q61E.
[00116] In prophylactic applications, pharmaceutical compositions or medicaments comprising a TXNRD1 inhibitor disclosed herein are administered to a subject susceptible to, or otherwise at risk of a disease or condition characterized by (a) elevated expression levels and/or increased activity of TXNRD1, and/or (b) a subject susceptible to, or otherwise at risk of a RAS-mutant cancer, and/or a subject susceptible to, or otherwise at risk of pancreatic cancer, in an amount sufficient to eliminate or reduce the risk, or delay the onset of the disease, including biochemical, histologic and/or behavioral symptoms of the disease, its complications and intermediate pathological phenotypes presenting during development of the disease. Administration of a prophylactic TXNRD1 inhibitor can occur prior to the manifestation of symptoms characteristic of the disease or disorder, such that the disease or disorder is prevented or, alternatively, delayed in its progression.
[00117] In some embodiments, treatment with the TXNRD1 inhibitor will prevent or delay the onset of one or more of the following symptoms: pain in the upper abdomen that radiates towards the back, loss of appetite or unintended weight loss, depression, new-onset diabetes, blood clots, fatigue, yellowing of skin and the whites of eyes (jaundice), bloating, nausea, and vomiting. In certain embodiments, (a) subjects with a disease or condition characterized by elevated expression levels and/or increased activity of TXNRD1, and/or (b) subjects with a RAS-mutant cancer, and/or subjects with pancreatic cancer that are treated with the TXNRD1 inhibitor will show TXNRD1 and/or RAS expression levels that resemble those observed in healthy control subjects.
[00118] For therapeutic and/or prophylactic applications, a composition comprising a TXNRD1 inhibitor disclosed herein, is administered to the subject. In some embodiments, the TXNRD1 inhibitor is administered one, two, three, four, or five times per day. In some embodiments, the TXNRD1 inhibitor is administered more than five times per day.
Additionally or alternatively, in some embodiments, the TXNRDl inhibitor is administered every day, every other day, every third day, every fourth day, every fifth day, or every sixth day. In some embodiments, the TXNRDl inhibitor is administered weekly, bi-weekly, tri- weekly, or monthly. In some embodiments, the TXNRDl inhibitor is administered for a period of one, two, three, four, or five weeks. In some embodiments, the TXNRDl inhibitor is administered for six weeks or more. In some embodiments, the TXNRD1 inhibitor is administered for twelve weeks or more. In some embodiments, the TXNRD1 inhibitor is administered for a period of less than one year. In some embodiments, the TXNRD1 inhibitor is administered for a period of more than one year. In some embodiments, the TXNRD1 inhibitor is administered throughout the subject’s life.
[00119] In some embodiments of the methods of the present technology, the TXNRD1 inhibitor is administered daily for 1 week or more. In some embodiments of the methods of the present technology, the TXNRD1 inhibitor is administered daily for 2 weeks or more. In some embodiments of the methods of the present technology, the TXNRD1 inhibitor is administered daily for 3 weeks or more. In some embodiments of the methods of the present technology, the TXNRD1 inhibitor is administered daily for 4 weeks or more. In some embodiments of the methods of the present technology, the TXNRD1 inhibitor is
administered daily for 6 weeks or more. In some embodiments of the methods of the present technology, the TXNRD1 inhibitor is administered daily for 12 weeks or more. In some embodiments, the TXNRD1 inhibitor is administered daily throughout the subject’s life.
Determination of the Biological Effect of TXNRD1 inhibitor
[00120] In various embodiments, suitable in vitro or in vivo assays are performed to determine the effect of a specific TXNRD1 inhibitor and whether its administration is indicated for treatment. In various embodiments, in vitro assays can be performed with representative animal models, to determine if a given TXNRD1 inhibitor exerts the desired effect on reducing or eliminating signs and/or symptoms of a RAS-mutant cancer.
Compounds for use in therapy can be tested in suitable animal model systems including, but not limited to rats, mice, chicken, cows, monkeys, rabbits, and the like, prior to testing in human subjects. Similarly, for in vivo testing, any of the animal model system known in the art can be used prior to administration to human subjects. In some embodiments, in vitro or in vivo testing is directed to the biological function of one or more TXNDR1 inhibitors of the present technology.
[00121] Animal models of a RAS-mutant cancer, and/or pancreatic cancer may be generated using techniques known in the art (see Example 7 described herein). Such models may be used to demonstrate the biological effect of TXNRD1 inhibitors in the prevention and treatment of conditions arising from disruption of a particular gene, and/or inhibition of activity of a specific protein and for determining what comprises a therapeutically effective amount of the one or more TXNRD1 inhibitors disclosed herein in a given context.
Modes of Administration and Effective Dosages
[00122] Any method known to those in the art for contacting a cell, organ or tissue with one or more TXNRD1 inhibitors disclosed herein may be employed. Suitable methods include in vitro , ex vivo , or in vivo methods. In vivo methods typically include the administration of one or more TXNRD1 inhibitors to a mammal, suitably a human. When used in vivo for therapy, the one or more TXNRD1 inhibitors described herein are administered to the subject in effective amounts (i.e., amounts that have desired therapeutic effect). The dose and dosage regimen will depend upon the degree of the disease state of the subject, the characteristics of the particular TXNRD1 inhibitor used, e.g. , its therapeutic index, and the subject’s history.
[00123] The effective amount may be determined during pre-clinical trials and clinical trials by methods familiar to physicians and clinicians. An effective amount of one or more TXNRD1 inhibitors useful in the methods may be administered to a mammal in need thereof by any of a number of well-known methods for administering pharmaceutical compounds. The TXNRD1 inhibitor may be administered systemically or locally.
[00124] The one or more TXNRD1 inhibitors described herein can be incorporated into pharmaceutical compositions for administration, singly or in combination, to a subject for the treatment or prevention of a RAS-mutant cancer, and / or a subject for the treatment or prevention of pancreatic cancer. Such compositions typically include the active agent and a pharmaceutically acceptable carrier. As used herein the term“pharmaceutically acceptable carrier” includes saline, solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. Supplementary active compounds can also be incorporated into the compositions.
[00125] Pharmaceutical compositions are typically formulated to be compatible with its intended route of administration. Examples of routes of administration include parenteral (e.g., intravenous, intradermal, intraperitoneal or subcutaneous), oral, inhalation, transdermal (topical), intraocular, iontophoretic, and transmucosal administration. Solutions or suspensions used for parenteral, intradermal, or subcutaneous application can include the following components: a sterile diluent such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerine, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl parabens; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for the adjustment of tonicity such as sodium chloride or dextrose. pH can be adjusted with acids or bases, such as hydrochloric acid or sodium hydroxide. The parenteral preparation can be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic. For convenience of the patient or treating physician, the dosing formulation can be provided in a kit containing all necessary equipment ( e.g ., vials of drug, vials of diluent, syringes and needles) for a treatment course ( e.g ., 7 days of treatment).
[00126] Pharmaceutical compositions suitable for injectable use can include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water,
CREMOPHOR EL™ (BASF, Parsippany, N. J.) or phosphate buffered saline (PBS). In all cases, a composition for parenteral administration must be sterile and should be fluid to the extent that easy syringability exists. It should be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi.
[00127] The pharmaceutical compositions having one or more TXNRDl inhibitors disclosed herein can include a carrier, which can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thiomerasol, and the like.
Glutathione and other antioxidants can be included to prevent oxidation. In many cases, it will be advantageous to include isotonic agents, for example, sugars, polyalcohols such as mannitol, sorbitol, or sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent that delays absorption, for example, aluminum monostearate or gelatin.
[00128] Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle, which contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, typical methods of preparation include vacuum drying and freeze drying, which can yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
[00129] Oral compositions generally include an inert diluent or an edible carrier. For the purpose of oral therapeutic administration, the active compound can be incorporated with excipients and used in the form of tablets, troches, or capsules, e.g ., gelatin capsules. Oral compositions can also be prepared using a fluid carrier for use as a mouthwash.
Pharmaceutically compatible binding agents, and/or adjuvant materials can be included as part of the composition. The tablets, pills, capsules, troches and the like can contain any of the following ingredients, or compounds of a similar nature: a binder such as microcrystalline cellulose, gum tragacanth or gelatin; an excipient such as starch or lactose, a disintegrating agent such as alginic acid, Primogel, or com starch; a lubricant such as magnesium stearate or Sterotes; a glidant such as colloidal silicon dioxide; a sweetening agent such as sucrose or saccharin; or a flavoring agent such as peppermint, methyl salicylate, or orange flavoring.
[00130] For administration by inhalation, the compounds can be delivered in the form of an aerosol spray from a pressurized container or dispenser, which contains a suitable propellant, e.g. , a gas such as carbon dioxide, or a nebulizer. Such methods include those described in U.S. Pat. No. 6,468,798.
[00131] Systemic administration of a therapeutic compound as described herein can also be by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid derivatives. Transmucosal administration can be accomplished through the use of nasal sprays. For transdermal administration, the active compounds are formulated into ointments, salves, gels, or creams as generally known in the art. In one embodiment, transdermal administration may be performed by iontophoresis.
[00132] A therapeutic agent can be formulated in a carrier system. The carrier can be a colloidal system. The colloidal system can be a liposome, a phospholipid bilayer vehicle, or a lipid nanoparticle. In one embodiment, the therapeutic agent is encapsulated in a liposome while maintaining the agent’s structural integrity. One skilled in the art would appreciate that there are a variety of methods to prepare liposomes. (See Lichtenberg, et al, Methods Biochem. Anal., 33:337-462 (1988); Anselem, et al. , Liposome Technology , CRC Press (1993)). Liposomal formulations can delay clearance and increase cellular uptake (See Reddy, Ann. Pharmacother ., 34(7-8):915-923 (2000)). An active agent can also be loaded into a particle prepared from pharmaceutically acceptable ingredients including, but not limited to, soluble, insoluble, permeable, impermeable, biodegradable or gastroretentive polymers or liposomes. Such particles include, but are not limited to, nanoparticles, biodegradable nanoparticles, microparticles, biodegradable microparticles, nanospheres, biodegradable nanospheres, microspheres, biodegradable microspheres, capsules, emulsions, liposomes, micelles and viral vector systems.
[00133] The carrier can also be a polymer, e.g. , a biodegradable, biocompatible polymer matrix. In one embodiment, the therapeutic agent can be embedded in the polymer matrix, while maintaining the agent’s structural integrity. The polymer may be natural, such as polypeptides, proteins or polysaccharides, or synthetic, such as poly a-hydroxy acids.
Examples include carriers made of, e.g. , collagen, fibronectin, elastin, cellulose acetate, cellulose nitrate, polysaccharide, fibrin, gelatin, and combinations thereof. In one
embodiment, the polymer is poly-lactic acid (PLA) or copoly lactic/glycolic acid (PGLA). The polymeric matrices can be prepared and isolated in a variety of forms and sizes, including microspheres and nanospheres. Polymer formulations can lead to prolonged duration of therapeutic effect. (See Reddy, Ann. Pharmacother ., 34(7-8):915-923 (2000)). A polymer formulation for human growth hormone (hGH) has been used in clinical trials. (See Kozarich and Rich, Chemical Biology , 2:548-552 (1998)). [00134] Examples of polymer microsphere sustained release formulations are described in PCT publication WO 99/15154 (Tracy, et al), U.S. Pat. Nos. 5,674,534 and 5,716,644 (both to Zale, et al. ), PCT publication WO 96/40073 (Zale, et al. ), and PCT publication WO 00/38651 (Shah, et al). U.S. Pat. Nos. 5,674,534 and 5,716,644 and PCT publication WO 96/40073 describe a polymeric matrix containing particles of erythropoietin that are stabilized against aggregation with a salt.
[00135] In some embodiments, the therapeutic compounds are prepared with carriers that will protect the therapeutic compounds against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Such formulations can be prepared using known techniques. The materials can also be obtained commercially, e.g., from Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted to specific cells with monoclonal antibodies to cell-specific antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art, for example, as described in U.S. Pat. No. 4,522,811.
[00136] The therapeutic compounds can also be formulated to enhance intracellular delivery. For example, liposomal delivery systems are known in the art, see, e.g, Chonn and Cullis,“Recent Advances in Liposome Drug Delivery Systems,” Current Opinion in
Biotechnology 6:698-708 (1995); Weiner,“Liposomes for Protein Delivery: Selecting Manufacture and Development Processes,” Immunomethods , 4(3):201-9 (1994); and
Gregoriadis,“Engineering Liposomes for Drug Delivery: Progress and Problems,” Trends Biotechnol. , 13(12):527-37 (1995). Mizguchi, et al. , Cancer Lett., 100:63-69 (1996), describes the use of fusogenic liposomes to deliver a protein to cells both in vivo and in vitro.
[00137] Dosage, toxicity and therapeutic efficacy of any therapeutic agent can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g, for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Compounds that exhibit high therapeutic indices are advantageous. While compounds that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.
[00138] The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds may be within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the methods, the therapeutically effective dose can be estimated initially from cell culture assays. A dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (z.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to determine useful doses in humans accurately. Levels in plasma may be measured, for example, by high performance liquid chromatography.
[00139] Typically, an effective amount of the one or more TXNRD1 inhibitors disclosed herein sufficient for achieving a therapeutic or prophylactic effect, range from about
0.000001 mg per kilogram body weight per day to about 10,000 mg per kilogram body weight per day. Suitably, the dosage ranges are from about 0.0001 mg per kilogram body weight per day to about 100 mg per kilogram body weight per day. For example, dosages can be 1 mg/kg body weight or 10 mg/kg body weight every day, every two days or every three days or within the range of 1-10 mg/kg every week, every two weeks or every three weeks. In one embodiment, a single dosage of the therapeutic compound ranges from 0.001- 10,000 micrograms per kg body weight. In one embodiment, one or more TXNRD1 inhibitor concentrations in a carrier range from 0.2 to 2000 micrograms per delivered milliliter. An exemplary treatment regime entails administration once per day or once a week. In therapeutic applications, a relatively high dosage at relatively short intervals is sometimes required until progression of the disease is reduced or terminated, or until the subject shows partial or complete amelioration of symptoms of disease. Thereafter, the patient can be administered a prophylactic regime.
[00140] In some embodiments, a therapeutically effective amount of one or more
TXNRD1 inhibitors may be defined as a concentration of inhibitor at the target tissue of 10 32 to 10 6 molar, e.g, approximately 10 7 molar. This concentration may be delivered by systemic doses of 0.001 to 100 mg/kg or equivalent dose by body surface area. The schedule of doses would be optimized to maintain the therapeutic concentration at the target tissue, such as by single daily or weekly administration, but also including continuous
administration (e.g, parenteral infusion or transdermal application).
[00141] The skilled artisan will appreciate that certain factors may influence the dosage and timing required to effectively treat a subject, including but not limited to, the severity of the disease or disorder, previous treatments, the general health and/or age of the subject, and other diseases present. Moreover, treatment of a subject with a therapeutically effective amount of the therapeutic compositions described herein can include a single treatment or a series of treatments.
[00142] The mammal treated in accordance with the present methods can be any mammal, including, for example, farm animals, such as sheep, pigs, cows, and horses; pet animals, such as dogs and cats; laboratory animals, such as rats, mice and rabbits. In some
embodiments, the mammal is a human.
Combination Therapy
[00143] In some embodiments, one or more of the TXNRD1 inhibitors disclosed herein may be combined with one or more additional therapies for the prevention or treatment of a RAS-mutant cancer or pancreatic cancer. Additional therapeutic agents include, but are not limited to, ABRAXANE® (albumin-bound paclitaxel), GEMZAR® (gemcitabine), 5-FU (fluorouracil), ONIVYDE® (irinotecan liposome injection), surgery, radiation, or a combination thereof.
[00144] In some embodiments, the one or more TXNRD1 inhibitors disclosed herein may be separately, sequentially or simultaneously administered with at least one additional therapeutic agent selected from the group consisting of immunotherapeutic agents, alkylating agents, topoisomerase inhibitors, endoplasmic reticulum stress inducing agents,
antimetabolites, mitotic inhibitors, nitrogen mustards, nitrosoureas, alkyl sulfonates, platinum agents, taxanes, vinca agents, anti-estrogen drugs, aromatase inhibitors, ovarian suppression agents, VEGF/VEGFR inhibitors, EGF/EGFR inhibitors, RAS inhibitors, PARP inhibitors, cytostatic alkaloids, cytotoxic antibiotics, antimetabolites, endocrine/hormonal agents, bisphosphonate therapy agents, phenphormin and targeted biological therapy agents (e.g., therapeutic peptides described in US 6306832, WO 2012007137, WO 2005000889, WO 2010096603 etc.). In some embodiments, the at least one additional therapeutic agent is a chemotherapeutic agent.
[00145] Specific chemotherapeutic agents include, but are not limited to,
cyclophosphamide, fluorouracil (or 5-fluorouracil or 5-FU), methotrexate, edatrexate (10- ethyl- 10-deaza-aminopterin), thiotepa, carboplatin, cisplatin, taxanes, paclitaxel, protein- bound paclitaxel, docetaxel, vinorelbine, tamoxifen, raloxifene, toremifene, fulvestrant, gemcitabine, irinotecan, ixabepilone, temozolmide, topotecan, vincristine, vinblastine, eribulin, mutamycin, capecitabine, anastrozole, exemestane, letrozole, leuprolide, abarelix, buserlin, goserelin, megestrol acetate, risedronate, pamidronate, ibandronate, alendronate, denosumab, zoledronate, trastuzumab, tykerb, anthracy clines ( e.g ., daunorubicin and doxorubicin), cladribine, midostaurin, bevacizumab, oxaliplatin, melphalan, etoposide, mechlorethamine, bleomycin, microtubule poisons, annonaceous acetogenins, chlorambucil, ifosfamide, streptozocin, carmustine, lomustine, busulfan, dacarbazine, temozolomide, altretamine, 6-mercaptopurine (6-MP), cytarabine, floxuridine, fludarabine, hydroxyurea, pemetrexed, epirubicin, idarubicin, SN-38, ARC, NPC, campothecin, 9-nitrocamptothecin, 9- aminocamptothecin, rubifen, gimatecan, diflomotecan, BN80927, DX-8951f, MAG-CPT, amsacnne, etoposide phosphate, teniposide, azacitidine (Vidaza), decitabine, accatin III, 10- deacetyltaxol, 7-xylosyl-lO-deacetyltaxol, cephalomannine, 10-deacetyl-7-epitaxol, 7- epitaxol, 10-deacetylbaccatin III, 10-deacetyl cephalomannine, streptozotocin, nimustine, ranimustine, bendamustine, uramustine, estramustine, mannosulfan, camptothecin, exatecan, lurtotecan, lamellarin D9-aminocamptothecin, amsacrine, ellipticines, aurintricarboxylic acid, HU-331, or combinations thereof.
[00146] Examples of antimetabolites include 5-fluorouracil (5-FU), 6-mercaptopurine (6- MP), capecitabine, cytarabine, floxuridine, fludarabine, gemcitabine, hydroxyurea, methotrexate, pemetrexed, and mixtures thereof.
[00147] Examples of taxanes include accatin III, 10-deacetyltaxol, 7-xylosyl-10- deacetyltaxol, cephalomannine, 10-deacetyl-7-epitaxol, 7-epitaxol, 10-deacetylbaccatin III, 10-deacetyl cephalomannine, and mixtures thereof. [00148] Examples of DNA alkylating agents include cyclophosphamide, chlorambucil, melphalan, bendamustine, uramustine, estramustine, carmustine, lomustine, nimustine, ranimustine, streptozotocin; busulfan, mannosulfan, and mixtures thereof.
[00149] Examples of topoisomerase I inhibitor include SN-38, ARC, NPC, camptothecin, topotecan, 9-nitrocamptothecin, exatecan, lurtotecan, lamellarin D9-aminocamptothecin, rubifen, gimatecan, diflomotecan, BN80927, DX-8951f, MAG-CPT, and mixtures thereof. Examples of topoisomerase II inhibitors include amsacrine, etoposide, etoposide phosphate, teniposide, daunorubicin, mitoxantrone, amsacrine, ellipticines, aurintricarboxylic acid, doxorubicin, and HU-331 and combinations thereof.
[00150] Examples of immunotherapeutic agents include immune checkpoint inhibitors e.g ., antibodies targeting CTLA-4, PD-1, PD-L1), ipilimumab, 90Y-Clivatuzumab tetraxetan, pembrolizumab, nivolumab, trastuzumab, cixutumumab, ganitumab, demcizumab, cetuximab, nimotuzumab, dalotuzumab, sipuleucel-T, CRS-207, and GVAX.
[00151] Examples of RAS inhibitors include AMG 510, MRTX849, ARS-3248, BI 1701963, ARS-1620, ARS-853, thiol-reactive GDP analogs, BBP-454, mRNA-5671, KRAS
G12D inhibitors, and the like.
[00152] In any case, the multiple therapeutic agents may be administered in any order or even simultaneously. If simultaneously, the multiple therapeutic agents may be provided in a single, unified form, or in multiple forms (by way of example only, either as a single pill or as two separate pills). One of the therapeutic agents may be given in multiple doses, or both may be given as multiple doses. If not simultaneous, the timing between the multiple doses may vary from more than zero weeks to less than four weeks. In addition, the combination methods, compositions and formulations are not to be limited to the use of only two agents.
Kits
[00153] The present disclosure also provides kits for the prevention and/or treatment of a
RAS-mutant cancer (e.g., RAS mutant pancreatic cancer), comprising one or more TXNRD1 inhibitors. Optionally, the above described components of the kits of the present technology are packed in suitable containers and labeled for the prevention and/or treatment of a RAS- mutant cancer (e.g., RAS mutant pancreatic cancer).
[00154] The above-mentioned components may be stored in unit or multi-dose containers, for example, sealed ampoules, vials, bottles, syringes, and test tubes, as an aqueous, preferably sterile, solution or as a lyophilized, preferably sterile, formulation for reconstitution. The kit may further comprise a second container which holds a diluent suitable for diluting the pharmaceutical composition towards a higher volume. Suitable diluents include, but are not limited to, the pharmaceutically acceptable excipient of the pharmaceutical composition and a saline solution. Furthermore, the kit may comprise instructions for diluting the pharmaceutical composition and/or instructions for administering the pharmaceutical composition, whether diluted or not. The containers may be formed from a variety of materials such as glass or plastic and may have a sterile access port (for example, the container may be an intravenous solution bag or a vial having a stopper which may be pierced by a hypodermic injection needle). The kit may further comprise more containers comprising a pharmaceutically acceptable buffer, such as phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, culture medium for one or more of the suitable hosts. The kits may optionally include instructions customarily included in commercial packages of therapeutic or diagnostic products, that contain information about, for example, the indications, usage, dosage, manufacture, administration, contraindications and/or warnings concerning the use of such therapeutic or diagnostic products.
[00155] The kit can also comprise, e.g ., a buffering agent, a preservative or a stabilizing agent. The kit can also contain a control sample or a series of control samples, which can be assayed and compared to the test sample. Each component of the kit can be enclosed within an individual container and all of the various containers can be within a single package, along with instructions for interpreting the results of the assays performed using the kit. The kits of the present technology may contain a written product on or in the kit container. The written product describes how to use the reagents contained in the kit. In certain embodiments, the use of the reagents can be according to the methods of the present technology.
EXAMPLES
[00156] The present technology is further illustrated by the following Examples, which should not be construed as limiting in any way. The examples herein are provided to illustrate advantages of the present technology and to further assist a person of ordinary skill in the art with preparing or using the compositions and systems of the present technology. The examples should in no way be construed as limiting the scope of the present technology, as defined by the appended claims. The examples can include or incorporate any of the variations, aspects, or embodiments of the present technology described above. The variations, aspects, or embodiments described above may also further each include or incorporate the variations of any or all other variations, aspects or embodiments of the present technology. The following Examples demonstrate the preparation, characterization, and use of illustrative compositions of the present technology that inhibit TXNRD1 expression and/or activity.
Example 1: Experimental Materials and Methods
[0157] Preprocessing of scRNA-seq count data. The raw, HGNC-aligned, UMI count matrix generated via 10x sequencing was preprocessed and scaled prior to analyzing in downstream analysis pipelines. Low-abundance genes ( e.g . average count < 0.25) and genes with reads in <10% of cells as well as cells with non-zero reads for <10% of all genes were removed from the count matrix. To adjust for discrepancies in sequencing depth between individual cells, count matrices were normalized in some cases and scaled prior to carrying forward in subsequent analyses. Methods of normalization included, but were not limited to: 1) globally scaling cell-level counts to match the median depth across all cells (scalar adjustment), and 2) solving linear systems to obtain unique scaling factors for individual cells. In some cases, inter-sample batch effects were corrected via a mutual nearest neighbors algorithm.
[0158] Supervised dimensionality reduction. In order to computationally identify therapeutic targets, high-dimensional count data were mapped to a lower-dimensional, latent space. The latent space was constructed via supervised dimensionality reduction on a collection of pure cell types (e.g, pancreatic adenocarcinoma, ductal, and acinar cells), with cell type serving as the supervised label for reduction. In this way, the latent space maximized the separability between cancer and primary cells. In some cases, cells targeted with an essential gene (e.g, PCNA or MCM6 via RNAi or CRISPR) were also included in construction of the latent space in order to define a region of“toxicity.” Toxicity manifested as, e.g, knocked down a gene induced apoptosis in primary cells. Following model training, cells interrogated with CRISPR target candidates were mapped to the same latent space constructed from the pure cell types in order to quantify their transcriptional shift towards a wild-type expression profile (therapeutic index). [0159] Several algorithms were used for supervised dimensionality reduction. In some cases, the Elbow method (Richards et al ., J Shoulder Elbow Surg 8(4): 351-354 (1999)) was used to determine the optimal number of dimensions for the latent space.
[0160] Scoring of therapeutic index. The target genes interrogated via a pooled CRISPRi library were quantified in terms of their ability to shift the transcriptional profile of cancer cells back to a wild-type-like expression state (therapeutic index). Genes were scored via machine learning algorithms. Briefly, separate, single-class machine learning algorithms were trained on the latent expression profiles of distinct cell types including, but not limited to: 1) pancreatic ductal cells; 2) pancreatic acinar cells; 3) pancreatic adenocarcinomas; and 4) pancreatic adenocarcinomas with an essential gene (e.g, PCNA or MCM6) targeted (via CRISPR/RNAi) as a model for toxicity. Each of the trained machine learning models was then used to score candidate genes based on the output of the decision function applied to latent expression profiles of single cells targeted with the CRISPRi library. In some cases, cells were repeatedly sampled with replacement in order to construct a bootstrap confidence interval for the decision function estimate.
[0161] 2-1) Pooled negative selection RNAi screening. A custom shRNA library focused on 442 drug target genes (2245 shRNAs, five to six per gene) was designed and constructed as previously described (Huang et al., Genes Dev. 28(16): 1800-1814 (2014)). The library was cloned into TRMPV-Neo vector and transduced into Tet-On murine pancreatic ductal adenocarcinoma (mPDAC) cells ( KrasG12D ; Myc; shp53). Lito et al., Cancer Cell 25(5):697- 710 (2014). The conditions used for transduction of the library predominantly led to a single retroviral integration and represented each shRNA in a calculated number of at least 1000 cells. Transduced cells were selected for 5 days using 1 mg/mL G418 (Invitrogen). At each passage, >20 million cells were maintained to preserve library representation throughout the experiment. After drug selection, TO samples were obtained (20 million cells per replicate) and sorted for Venus+ cells. After 12 days (six passages, T12), 20 million shRNA-expressing (dsRed+ Venus+) cells were sorted for each replicate using a FACSAriall (BD Biosciences). Genomic DNA from TO and T12 samples was isolated by two rounds of phenol extraction using PhaseLock tubes (5 Prime) followed by isopropanol precipitation.
[0162] The results obtained from the mPDAC screen were then compared with the results obtained from Myc; p53~ murine hepatocellular carcinoma (mHCC) cells (Huang et al., GenesDev. 28(16): 1800-1814 (2014)), and a two-dimensional RNAi screening plot was constructed. See, e.g, FIG. 3 A.
[0163] Plasmids. For conditional RNAi experiments, shRNAs were expressed from the TRMPV-Neo vector from either miR-E or miR-30 backbones, which have been described previously (Zuber et al ., Nat Biotechnol. 29(l):79-83 (2011); Fellmann el al ., Cell Rep 5(6):
1704-1713 (2013)). Knockdown efficiency or overexpression was evaluated by
immunoblotting.
[0164] Immunoblotting. Cell pellets were lysed in Laemmli buffer (100 mM Tris-HCl pH 6.8, 5% glycerol, 2% SDS, 5% 2-Mercaptoethanol). Equal amounts of protein were resolved on 12% SDS-polyacrylamide gels and transferred to PVDF membranes for 120 minutes under 90V. The abundance of b-actin was monitored to ensure equal loading. Images were analyzed using the AlphaView software (ProteinSimple). Immunoblots were performed using antibodies for TXNRDl (TrxRl) (1 :1000, sc-28321, Santa Cruz Biotechnology),
KRAS (1 :200, WH0003845M1, Sigma-Aldrich), or b-actin-HRP (1 : 10000, A3854, Sigma).
[0165] Proliferation assays. Competitive proliferation assays using shRNAs in TRMPV-Neo vector (with miR-30 or miR-E backbone) were performed as described previously (Huang et al., Genes Dev. 28(16): 1800-1814 (2014)). Assays for in vitro growth inhibition by auranofm or piperlongumine were performed by counting the viable cell numbers using CellTiter-Glo Luminescent Cell Viability Assay (Promega) after incubation of cells in the presence of increasing concentrations of auranofm or piperlongumine for 72 hr. Proliferation rates were calculated by dividing viable cell numbers at 72 hr by the viable cell numbers at 0 hr. Relative proliferation rates were calculated by normalizing to the proliferation rate of vehicle-treated cells.
[0166] Animal studies. All experimental procedures described in this study were approved by the Institutional Animal Care and Use Committee (IACUC) at Memorial Sloan Kettering Cancer Center (NY), under protocol number 11-06-016 and 11-06-018. Mice were maintained under specific pathogen-free conditions, and food and water were provided ad libitum.
[0167] In vivo conditional RNAi experiments. Tet-On murine PD AC cells were transduced with luciferase-hygro and TRMPV-Neo-miR-E shRNA constructs. One million murine PD AC cells were orthotopically transplanted into female nude recipient mice (NCR nu/nu, purchased from Charles River laboratories and Harlan Laboratories). For whole-body bioluminescent imaging, mice were intraperitoneally injected with 50 mg/kg D-Luciferin (Goldbio), and after 10 min, analyzed using an IVIS Spectrum system (Caliper LifeSciences). Quantification was performed using Living Image software (Caliper LifeSciences) with standardized round regions of interests covering the mouse trunk and extremities. For shRNA induction, animals were treated with doxycycline in drinking water (2 mg/ml with 2% sucrose; Sigma-Aldrich) and food (625 mg/kg, Harlan Laboratories).
[0168] In vivo drug treatment experiments. For auranofm treatment trials, 16 mg auranofm was first solved in 4 mL ethanol, and then diluted with 12 mL PBS to a final concentration of 1 mg/ml. Mice were given daily auranofm (10 mg/kg) or a similar volume of vehicle by intraperitoneal injection. The sick animals were sacrificed and pancreatic tissues and tumors were used for further analysis.
[0169] RNA sequencing and Gene set enrichment analysis (GSEA) analyses. For RNA sequencing, total RNA from mPDAC cells harboring shRNAs targeting control Renilla Luciferase or TXNRD1 was isolated using RNeasy Mini Kit, QIAshredder Columns and RNase-Free DNase Set (Qiagen). RNA-Seq library construction and sequencing were performed according to protocols used by the Integrated Genomics Operation (IGO) Core at MSKCC. 5-10 million reads were acquired per replicate sample. After removing adaptor sequences with Trimmomatic (Bolger et al ., 2014), RNA-seq reads were aligned to
GRCh37.75(hgl9) using the STAR alignment tool (Dobin et al ., 2013). Genome wide transcript counting was performed by HTSeq to generate FPKM matrix (Anders et al., 2015 Bioinformatics). Gene set enrichment analysis (Subramanian et al., 2005) was performed using GSEA v2.07 software.
[0170] Statistics. Data are presented as mean ± standard deviation if not otherwise stated. Statistical significance between groups was calculated by two-tailed Student’s t-test.
Correlation was calculated by Pearson test. Prism 7 software was used to calculate the ICso values. Significance values are P < 0.05 (*), P < 0.01 (**), and P < 0.001 (***). Volcano plots were prepared in some cases.
[0171] Analysis of gene dependency. The data of human cancer cell line whole genome sgRNA screen used for all heatmaps was from http://genomecrispr. dkfz.de/. The Log2FC (abundance fold-change with log transformation) was used to calculate the gene dependency score for each gene in each experiment. The gene dependency score was calculated via taking the average of Log2FC of all sgRNAs targeting the same gene. Un-supervised clustering using "Pheatmap" R package was used to cluster genes with similar phenotypes for visualization.
[0172] Determination of fold change in sensitivity to Auranofm and quantitative analysis of drug synergy. CompuSyn software (Version 1.0) (http://www.combosyn.com), which is based on the Median-Effect Principle and the Combination Index-Isobologram Theorem was used to analyze drug synergism. Combination index (Cl) values Cl >1 indicates antagonism; Cl = 0.75-1.25 indicates additive effects; and <1 indicates synergism. Each GI (Growth inhibition) or Cl score represents data from at least three independent experiments.
[0173] Auranofm pharmacokinetics. The plasma and pancreas pharmacokinetics of gold were analyzed in 9 NCR nu/nu mice following administration of a single dose of 10 mg/kg auranofm suspension via intraperitoneal injection. Plasma and pancreas samples for determination of gold concentration were obtained at 2, 4, and 24 hours following
administration of auranofm. Collected plasma and pancreas samples were analyzed using an inductively coupled plasma mass spectrometry (ICPMS) method to quantify gold
concentration.
Example 2: Computational Discovery and Validation of Novel Tarsets in Kras-Mutant Pancreatic Cancer
[0174] FIGs. 1A-1B provide a pipeline for computational discovery of therapeutic targets in RAS-mutant pancreatic cancer. As shown in FIG. 1A, Kras-mutant pancreatic cell lines were screened using a CRISPRi library transduced at a low multiplicity of infection (MOI). The transcriptomes of single cells were isolated and converted to DNA libraries using a Chromium instrument (10X Genomics) and an enzyme kit (10X Genomics), and were sequenced using Hiseq4000 system (Illumina). Single-cell RNA sequencing (scRNA-seq) profiles of individual cells were matched to their respective CRISPR targets via paired-end sequencing and using barcodes. The raw reads in FASTQ format were aligned with whole genome and mapped to an appropriate genomic coordinate and HGNC gene for each cell, resulting in a count matrix comprised of N cells c M genes (See FIG. 1A). This N c M matrix was further reduced to a N x 50 matrix via supervised dimensionality reduction (See FIG. 1A). The dimensionality reduction model was trained to identify pure cell types (e.g. cancer cells, ductal cells, acinar cells, or cancer cells expressing a non-targeted guide RNA, which served as the negative controls) such that the lower-dimensional latent space maximally separated healthy cells and cancer cells from each other (See FIG. 1A-2A). Cells expressing CRISPR targets that maximally drove mRNA expression pattern away from the negative controls, and towards healthy cells (ductal cells or acinar cells) were identified using this algorithm, and such CRISPR targets constituted the most promising targets that were pursued in preclinical development.
[0175] As shown in FIGs. 1A-1B, the therapeutic index was quantified using machine learning algorithms. Briefly, separate machine learning models were trained to identify distinct cell populations, including: 1) pancreatic ductal cells (positive control for therapeutic index); 2) pancreatic acinar cells (positive control for therapeutic index); 3) Kras-mutant PD AC cells expressing a non-target guide RNA (negative control for therapeutic index); and 4) Kras-mutant PD AC cells expressing an essential gene targeted (positive control for a toxic target). As shown in FIGs. 1A-1B, the trained machine learning models were then applied to RNA-seq data of Kras-mutant PD AC cells expressing a CRISPR targets to detect cells that exhibited RNA-seq profiles similar to pancreatic acinar cells and distinguishable from Kras- mutant PD AC cells expressing negative control for therapeutic index. Identities of the CRISPR targets expressed by such cells were identified based on paired-end sequencing and barcodes. Targets with maximal therapeutic index were chosen to pursue in preclinical development.
Example 3: Computational Identification of TXNRD1 as a Therapeutic Target in KRAS- Mutant Pancreatic Cancer
[0176] As shown in FIG. IB, the scRNA-seq profiles of individual Kras-mutant PD AC cells expressing CRISPRi targets were analyzed using decision functions of machine learning algorithms trained on two non-target guide RNAs, a toxic target, and a healthy ductal cell line as described above. The outputs of the decision functions were further transformed via a variety of methods, including but not limited to: effect size, K.S.- statistic, z-score, or p-value relative to a control population. Scores across multiple machine learning algorithms and replicates were further aggregated via various methods, including but not limited to: average, weighted average, rank aggregation, weighted rank aggregation, Stouffer’s method (z- scores), and Fischer’s method (p-values). [0177] As shown in FIG. 2A, TXNRD1 was identified as a CRISPRi target that transformed Kras-mutant PD AC cells to exhibit RNA-seq profiles similar to pancreatic acinar cells.
Distribution of cell type populations was analyzed along a single dimension after supervised dimensionality reduction using machine learning algorithms and plotted. As shown in FIG. 2A, Kras-mutant PD AC cells expressing guide RNA targeting TXNRD1 (N = 87), showed a shift towards healthy ductal cells (N= 600). By comparison, Kras-mutant PD AC cells expressing an ineffective CRISPRi target (a non-targeting guide RNA (N= 122) largely overlapped the profile of cancer cells. As shown in FIG. 2B, the z-transformed therapeutic index of TXNRD1 , averaged across the four decision functions from machine learning algorithms, was the highest of the top 20 candidate targets. Similarly, as shown in FIG. 2C, TXNRD1 exhibited the highest weight-averaged decision function scores for therapeutic index among a panel of over fifty candidate targets.
Example 4: Identification of TXNRD1 as a Therapeutic Target by a 2-D RNAi Screening Approach
[0178] To selectively identify drug targets that are essential for the maintenance of KRAS- mutant PD AC, a custom library of short hairpin RNAs (shRNAs) directed toward known drug targets was screened for negative selection in a genetically defined murine HCC model ( KrasG12D ; Myc; shp53). The results were cross-analyzed with prior negative selection results from a murine HCC model (Myc; p53~ ~) (Huang et al., Genes Dev. 28(16): 1800-1814 (2014)). As shown in Fig. 3A, shRNAs targeting Txnrdl , Acpp, and Amt were found to be selectively depleted in the Kras-mutant PD AC cells, compared to the negative control shRNAs, which remained unchanged in both cell lines. In comparison, positive control shRNAs were depleted in both murine HCC and murine HCC (See Fig. 3A).
[0179] . To detect depletion of cells expressing specific siRNA was quantitated in mPDAC, mHCC and iMEFs, these cells transduced with a virus carrying an inducible shRNA against Txnrdl , Acpp, Amt and controls: Ren.713 (a non-targeting shRNA which served as a negative control), Rpa3.561 (a positive control for growth inhibition in all proliferating cells),
Kras.247 (a positive control for mPDAC-specific growth inhibition). The percentage of cells expressing these shRNAs was determined on day 0 and on day 12 of shRNA induction.
Decrease in the percentage of cells expressing a shRNA indicated inhibitory effects of the shRNA. As shown in Fig. 3B, shRNA Ren.713, which is a non-targeting negative control (against Renilla luciferase) had no effect in any cells, the positive control shRNA Rpa3.561 was depleted in all cell types tested. The mPDAC-specific positive control Kras.247 was depleted in mPDAC compared to mHCC and iMEFs. As shown in Fig. 3B, shRNAs against Txnrdl , Acpp , and Amt exhibited inhibitory effects in Kras-mutant PD AC cells ( KrasG12D ; Myc; shp53 ), compared to the negative control, but not in mHCC cells (Myc; p53~ ) or nontransformed immortalized mouse embryonic fibroblasts (iMEF). The effect of Txnrdl shRNA was more pronounced than shRNA targeting Acpp or Amt. The Western blots shown in Fig. 3B show that the shRNA reduced amounts of proteins they targeted. Therefore, this assay also identified Txnrdl as a promising target. Given that RAS gain of function mutations ( e.g ., at codon 12, 13, or 61) occur in regions that share 100% amino acid sequence identity among the KRAS, NRAS, and HRAS isoforms (See Prior et a/., Cancer Research 72(10) (2012)), inhibition of TXNRDl is anticipated to treat cancers associated with KRAS, NRAS, and HRAS mutations.
[0180] TXNRDl dependency was further investigated in various cell lines. As shown in FIGs. 6A-6B, knocking out or knocking down replication genes RAPl or PCNA resulted in general lethality to almost all cell lines. In contrast, TXNRDl is conditionally required for certain cell lines which exhibit similar dependency for KRAS, HRAS, and NRAS.
[0181] These results demonstrate that the TXNRDl inhibitor compositions of the present technology are useful in methods for treating a disease or condition characterized by elevated levels of RAS expression and/or elevated levels of TXNRDl expression in a subject in need thereof.
Example 5: KRAS-mutant PD AC growth is sensitive to pharmacolosical TXNRD1 inhibition
[0182] To evaluate the effect of pharmacological inhibition of TXNRDl in pancreatic cancer with small molecule drugs, inhibitor studies with myricetin, manumycin A, protoporphyrin IX, and auranofm were undertaken.
[0183] Auranofm is an inhibitor of enzymatic activity of TXNRDl {See Gromer et al., J Biol Chem 273(32): 20096-20101). Myricetin, manumycin A and protoporphyrin IX are also inhibitors of enzymatic activity of TXNRDl. mPDAC cells were treated with the TXNRDl inhibitor auranofm or DMSO for 72 hr, and viability was measured. DMSO treatment served as a negative control causing a lack of growth inhibition. Viable cell number of DMSO- treated cells was set to 1. Viability of auranofm-treated cells, which was normalized to that of DMSO-treated cells, was plotted as a function of auranofm concentration and was fit to an exponential growth curve. Each of myricetin, manumycin A and protoporphyrin IX were also subjected to similar treatment.
[0184] As shown in FIG. 3D, auranofm inhibited growth of mPDAC cells at submicromolar concentration. These results demonstrate that the TXNRD1 inhibitor compositions of the present technology are useful in methods for treating a disease or condition characterized by RAS mutations, elevated levels of RAS expression and/or elevated levels of TXNRD1 expression in a subject in need thereof.
Example 6: KRAS status predicts response to TXNRD1 inhibition
[0185] Since the screening system discussed above and FIGs. 1A-3B was driven by mutant Kras, p53 loss and Myc overexpression, whether alterations in either gene could dictate sensitivity to TXNRD1 inhibition was investigated. Twelve pancreatic cancer cell lines were treated with increasing concentration of auranofm or DMSO. Among the cell lines used in this experiment L3.3, Colo357, and BXPC3 have wild-type KRAS. The cell lines
PANC0327, MIAPaCa-2, PANC0213, ASPC1, 8898, CFP AC-1, L3.6pl, PANC1 and SU8686 harbored KRAS mutations. As shown in FIG. 3E, although there was variability from a cell line to cell line, the KRAS mutant cells were generally more sensitive to auranofm than the wild-type KRAS cells.
[0186] To understand whether the observed difference between sensitivities of wild-type KRAS cells and KRAS mutant cells, was statistically significant, the ICso data of the relative sensitivity of human PD AC cell lines to TXNRD1 inhibition by auranofm was compared. As shown in FIG. 4A, a significant correlation was found between the anti-proliferative response to TXNRD1 inhibition and KRAS mutational status. In contrast, as shown in FIG. 4B-4C, there was a no significant correlation between the response to TXNRD1 inhibition and p53 mutational status or MYC mRNA expression. To understand the effect of KRAS mutations (G12C, G12D, G12V) on auranofm sensitivity, human pancreatic cancer cells harboring different KRAS mutations (G12C, G12D, G12V) or wild-type were treated with another TXNRD1 inhibitor piperlongumine. As shown in FIG. 4D, the KRAS mutant cells were more sensitive to piperlongumine than the wild-type KRAS cells, further reinforcing the above findings. [0187] To understand whether a correlation exists between expression of KRAS and
TXNRD1 , expression of both these genes was quantitated in 149 human pancreatic cancer tumors from the Cancer Genome Atlas Research Network (TCGA) and shown as a scatter plot. As shown in FIG. 4E, a correlation between expression of TXNRD1 and KRAS expression levels was observed (r = 0.36, p < 0.0001).
[0188] To understand the molecular mechanisms of TXNRD1 suppression in the PD AC cells, RNA-seq analyses of the mPDAC cells harboring shRNAs targeting control Renilla or Txnrdl were performed. As shown in FIGs. 4F-4G, suppression of Cdk9 resulted in reversion of both KRAS dependency (FIG. 4F) and pancreatic cancer signatures (FIG. 4G), further validating the findings that TXNRD1 is required for KRAS oncogenic signaling. Interestingly, as shown in FIG. 4H, suppression of TXNRD1 showed a downregulation of gene signatures related to amino acid transporter and ferroptosis including a gene called SLC7A11.
[0189] These results demonstrate that the TXNRD1 inhibitor compositions of the present technology are useful in methods for treating a disease or condition characterized by elevated levels of RAS expression and/or elevated levels of TXNRD1 expression in a subject in need thereof.
Example 7: TXNRD1 is Required for Maintenance of KRAS-Mutant Pancreatic Tumors.
[0190] The relevance of TXNRD1 on PD AC progression in vivo was also investigated. To suppress Txnrdl in established pancreatic tumors, mPDAC cells were transduced with Luciferase and dox inducible TRMPV-Neo-miR-E constructs containing Txnrdl shRNAs or control shRNAs (Renilla and Kras) and were transplanted into the pancreas of recipient mice by orthotopic injection (See FIG. 5A). Upon detection of a luminescent signal, the animals were treated without or with dox to induce the corresponding shRNA expression. As shown in FIG. 5C, bioluminescent imaging revealed that mice from the untreated group (no dox) displayed large pancreatic tumors by day 7. In contrast, knockdown of Txnrdl or Kras led to a comparable delay in tumor growth. Therefore, RNAi-mediated suppression of Txnrdl approximates the effect of Kras inhibition in eliciting anti -turn or effects in Kras-mutant PD AC in vivo. Tumor weights were quantitated from animals treated with or without doxycycline to induce corresponding shRNAs (n = 4-5). As shown in FIG. 5B, tumor weights from mice from the untreated group (no dox) displayed larger pancreatic tumors compared to the mice having knockdown of Txnrdl or Kras led to a comparable delay in tumor growth. Weighs of tumors expressing Ren.713E were not affected by doxycycline treatment (compare the two sets of replicates in Ren.713 column of FIG. 5B). Weighs of tumors expressing Txnrdl and KRAS shRNA were comparably inhibited by doxycycline treatment (compare the two sets of replicates between groups and within groups in
Txnrdl.2057E, Txnrdl.1474E and KRas.247 columns of FIG. 5B).
[0191] These results demonstrate that the TXNRD1 inhibitor compositions of the present technology, such as an agent that inhibit expression of TXNRD1, are useful in methods for treating a RAS-mutant cancer in a subject in need thereof.
[0192] Growth inhibitory effects of pharmacological TXNRD1 inhibition was also examined in additional murine PD AC models generated by transplanting KRasG12D; p53~ ~ pancreatic cancer organoid lines into the pancreas of recipient mice. Mice were treated either with vehicle only, acting as a negative control, or auranofm. As shown in FIG. 5D, consistent with the in vivo RNAi results (FIGs. 5A-5C), treatment with TXNRD1 inhibitor auranofm (10 mg/kg, one per day, 5 days per week) triggered a delay in Kras-mutant tumor growth. In addition, as shown in FIG. 5E, growth inhibitory effects of pharmacological TXNRD1 inhibition was found in human xenograft models generated by KRAS-mutant PD AC cells (MIAPaCa-2: KRAS mutant) but not in KRAS wild-type cells (Colo357: KRAS wild-type). Thus, TXNRDl is required for the maintenance of KRAS-mutant tumors and dependency in vivo. FIG. 10 demonstrates that auranofm is delivered into the pancreas.
[0193] FIG. 9 demonstrates that patients with pancreatic adenocarcinoma (PD AC) who exhibit TXNRDl mRNA upregulation show reduced overall survival compared with PD AC patients that express low levels of TXNRDL
[0194] FIGs. 7A-7D show the antiproliferative effects of TXNRDl inhibitor Auranofm in KRAS-mutant pancreatic cancer cells and potential synergistic inhibitory effects when combined with Gemcitabine. FIGs. 8A-8D show the antiproliferative effects of TXNRDl inhibitor Auranofm in KRAS-mutant pancreatic cancer cells and potential synergistic inhibitory effects when combined with KRASG12C inhibitor AMG 510.
[0195] These results demonstrate that the TXNRDl inhibitor compositions of the present technology are useful in methods for treating a RAS-mutant cancer in a subject in need thereof. EQUIVALENTS
[0196] The present technology is not to be limited in terms of the particular embodiments described in this application, which are intended as single illustrations of individual aspects of the present technology. Many modifications and variations of this present technology can be made without departing from its spirit and scope, as will be apparent to those skilled in the art. Functionally equivalent methods and apparatuses within the scope of the present technology, in addition to those enumerated herein, will be apparent to those skilled in the art from the foregoing descriptions. Such modifications and variations are intended to fall within the scope of the present technology. It is to be understood that this present technology is not limited to particular methods, reagents, compounds compositions or biological systems, which can, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting.
[0197] In addition, where features or aspects of the disclosure are described in terms of Markush groups, those skilled in the art will recognize that the disclosure is also thereby described in terms of any individual member or subgroup of members of the Markush group.
[0198] As will be understood by one skilled in the art, for any and all purposes, particularly in terms of providing a written description, all ranges disclosed herein also encompass any and all possible subranges and combinations of subranges thereof. Any listed range can be easily recognized as sufficiently describing and enabling the same range being broken down into at least equal halves, thirds, quarters, fifths, tenths, etc. As a non-limiting example, each range discussed herein can be readily broken down into a lower third, middle third and upper third, etc. As will also be understood by one skilled in the art all language such as“up to,”
“at least,”“greater than,”“less than,” and the like, include the number recited and refer to ranges which can be subsequently broken down into subranges as discussed above. Finally, as will be understood by one skilled in the art, a range includes each individual member.
Thus, for example, a group having 1-3 cells refers to groups having 1, 2, or 3 cells. Similarly, a group having 1-5 cells refers to groups having 1, 2, 3, 4, or 5 cells, and so forth. [0199] All patents, patent applications, provisional applications, and publications referred to or cited herein are incorporated by reference in their entirety, including all figures and tables, to the extent they are not inconsistent with the explicit teachings of this specification.

Claims

WHAT IS CLAIMED IS:
1. A method for treating a RAS-mutant cancer in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of a TXNRD1 inhibitor selected from the group consisting of auranofm, Piperlongumine, D9, TRi-1, TRi-2,
Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, protoporphyrin IX, and an anti-TXNRDl antibody.
2. A method for treating a RAS-mutant cancer in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of an inhibitory nucleic acid that inhibits TXNRD1 expression.
3. The method of claim 2, wherein the inhibitory nucleic acid comprises a sequence selected from the group consisting of: SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, and SEQ ID NO: 12, or any complement thereof.
4. The method of any one of claims 1-3, wherein the subject displays elevated expression levels of RAS protein in cancer cells prior to treatment.
5. The method of any one of claims 1-4, wherein the RAS-mutant cancer is lung cancer, mucinous adenoma, pancreatic cancer, colorectal cancer, skin cancer, endometrial cancer, testicular germ cell cancer, or adrenal gland cancer.
6. The method of claim 5, wherein the RAS-mutant cancer comprises a KRAS, NRAS, or HRAS mutation selected from the group consisting of G12C, G12D, G12V, G12A, G12S, G12R, G13D, G13C, G13S, G13R, G13A, G13V, Q61H, Q61L, Q61R, Q61K, Q61P, and Q61E.
7. The method of any one of claims 1-6, wherein the subject exhibits one or more signs or symptoms selected from among pain in the upper abdomen that radiates towards the back, loss of appetite or unintended weight loss, depression, new-onset diabetes, blood clots, fatigue, yellowing of skin and the whites of eyes (jaundice), bloating, nausea, and vomiting.
8. The method of any one of claims 1-7, wherein the subject harbors one or more point mutations in TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARABIA, SF3B1, EPC1, ARID2, ATM, ZIM2, MAP2K4, NALCN, SLC16A4, MAGEA6, R0B02, KDM6A, PREX2, ERBB2, MET, FGFR1, CDK6, PIK3R3, PIK3CA, BRCA1, BRCA2, or PALB2.
9. The method of any one of claims 1-8, wherein the subject is human.
10. The method of any one of claims 1 or 3-9, wherein the TXNRD1 inhibitor is administered orally, topically, intranasally, systemically, intravenously, subcutaneously, intraperitoneally, intradermally, intraocularly, iontophoretically, transmucosally, or intramuscularly.
11. The method of any one of claims 2-9, wherein the inhibitory nucleic acid is administered orally, topically, intranasally, systemically, intravenously, subcutaneously, intraperitoneally, intradermally, intraocularly, iontophoretically, transmucosally, or intramuscularly.
12. The method of any one of claims 1-11, further comprising separately, sequentially or simultaneously administering one or more additional therapeutic agents to the subject.
13. The method of claim 12, wherein the additional therapeutic agents are selected from the group consisting of paclitaxel, gemcitabine, AMG 510, 5-FU (fluorouracil), and irinotecan.
14. The method of any one of claims 1-13, wherein the TXNRD1 inhibitor or the inhibitory nucleic acid is administered daily for 6 weeks or more.
15. The method of any one of claims 1-14, wherein the TXNRD1 inhibitor or the inhibitory nucleic acid is administered daily for 12 weeks or more.
16. A method for monitoring the therapeutic efficacy of a TXNRD1 inhibitor in a subject diagnosed with a RAS-mutant cancer comprising:
(a) detecting TXNRD1 protein levels in a test sample obtained from the subject after the subject has been administered the TXNRD1 inhibitor; and
(b) determining that the TXNRD1 inhibitor is effective when the TXNRD1 protein levels in the test sample are reduced compared to that observed in a control sample obtained from the subject prior to administration of the TXNRD1 inhibitor.
17. The method of claim 16, wherein the TXNRD1 inhibitor is auranofm,
Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, protoporphyrin IX, an anti-TXNRDl antibody, or an inhibitory nucleic acid that inhibits TXNRD1 expression.
18. The method of claim 17, wherein the inhibitory RNA is a shRNA, an antisense oligonucleotide, or a sgRNA.
19. A method for inhibiting RAS-mutant cell proliferation in a subject in need thereof, comprising administering to the subject a therapeutically effective amount of at least one TXNRD1 inhibitor,
wherein the at least one TXNRD1 inhibitor is selected from the group consisting of auranofm, Piperlongumine, D9, TRi-1, TRi-2, Myricetin, PMX464, PX12, brevetoxin-2, manumycin A, ethaselen, aurothioglucose, protoporphyrin IX, an anti-TXNRDl antibody, and an inhibitory nucleic acid that inhibits TXNRD1 expression, and
wherein the subject suffers from a disease or condition characterized by elevated expression levels and/or increased activity of RAS and/or TXNRD1.
20. The method of any one of claims 17-19, wherein the inhibitory nucleic acid comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, and SEQ ID NO: 12, or any complement thereof.
21. The method of any one of claims 1-20, further comprising administering to the subject a therapeutically effective amount of gemcitabine.
22. The method of any one of claims 1-20, further comprising administering to the subject a therapeutically effective amount of a KRASG12C inhibitor, optionally wherein the
KRASg12C inhibitor is AMG 510.
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