WO2014183301A1 - Réactif et méthode pour la détection et le traitement des tumeurs - Google Patents

Réactif et méthode pour la détection et le traitement des tumeurs Download PDF

Info

Publication number
WO2014183301A1
WO2014183301A1 PCT/CN2013/075836 CN2013075836W WO2014183301A1 WO 2014183301 A1 WO2014183301 A1 WO 2014183301A1 CN 2013075836 W CN2013075836 W CN 2013075836W WO 2014183301 A1 WO2014183301 A1 WO 2014183301A1
Authority
WO
WIPO (PCT)
Prior art keywords
rars
fusion gene
madili
gene
eif2s3
Prior art date
Application number
PCT/CN2013/075836
Other languages
English (en)
Inventor
Musheng ZENG
Qian Zhong
Lihua Xu
Zhirui LIN
Lijuan HU
Zedong HU
Li Yuan
Original Assignee
Sun Yat-Sen University
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Sun Yat-Sen University filed Critical Sun Yat-Sen University
Priority to PCT/CN2013/075836 priority Critical patent/WO2014183301A1/fr
Publication of WO2014183301A1 publication Critical patent/WO2014183301A1/fr

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • the present invention relates to compositions and methods for cancer diagnosis and therapy, including but not limited to, cancer markers.
  • the present invention relates to recurrent gene fusions as diagnostic markers and clinical targets for tumors.
  • Cancer especially malignant cancer, is harmful for human health and brings large economic burdens for the patients.
  • the difficulty in curing, curing rate, and life quality are variable. Usually, it is relative easier to treat early stage cancer with less side effects, high curing rates and longer survival time with high life quality.
  • US20110065113A1 disclosed a method for identifying prostate cancer in a patient comprising: (a) providing a sample from the patient; and (b) detecting the presence or absence in the sample of a gene fusion having a 5' portion from a transcriptional regulatory region of an SLC45A3 gene and a 3' portion from a RAF family gene, wherein detecting the presence in the sample of the gene fusion identifies prostate cancer in the patient.
  • the disclosures of US20110065113A1 are hereby incorporated by reference in its entirety.
  • RARS arginyl-tRNA synthetase
  • GI:40068503 is one component of a macromolecular aminoacyl-tRNA synthetase complex during protein synthesis (C LingJ Biol Chem. 2005 Oct 14;280(41):34755-63.).
  • RARS has been shown to be associated with a reduced AIMP1 secretion , probably leading to the generation of the cytokine, EMAP II (A Bottoni, J Cell Physiol. 2007 Aug;212(2):293-7.).
  • MAD1L1 Mitotic arrest deficient 1-like protein 1 (GL62243373) is a component of the mitotic spindle-assembly checkpoint that prevents the onset of anaphase until all chromosome are properly aligned at the metaphase plate ( DY Jin, Genomics. 1999 Feb l;55(3):363-4.). It also binds to the TERT promoter and represses telomerase expression(SY Lin, Cell. 2003 Jun 27; 113(7):881-9. ) .
  • EIF2S3 (Eukaryotic translation initiation factor 2 subunit 3), ( GI: 83656782) functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex in order, for eIF-2, to recycle and catalyze another round of initiation. (SR Kimball, Int J Biochem Cell Biol. 1999 Jan;31(l):25-9.).
  • TXNDCll Thioredoxin domain-containing protein 11
  • GI: 54633316 may act as a redox regulator involved in DUOX proteins folding.
  • the interaction with DUOX1 and DUOX2 suggest that it belongs to a multi-protein complex constituting the thyroid H(2)0(2) generating system (J Biol Chem. 2005 Jan 28;280(4):3096-103).
  • the aim of present invention is to provide a tumor detection method.
  • the aim of present invention is to provide a tumor diagnosis method.
  • the aim of present invention is to provide a tumor therapy method.
  • the present invention provides the transcript of RARS-MADILI fusion gene contains exons 1-7 of RARS gene and exon 19 of MAD1L1.
  • the present invention provides a tumor detection kit comprising at least one of the following reagents:
  • oligonucleotide probe comprising a sequence that hybridizes to the DNA of RARS-MADILI fusion gene
  • oligonucleotide probe comprising a sequence that hybridizes to the mRNA of RARS-MADILI fusion gene
  • said RARS-MADILI fusion gene comprises a 5' portion of the chimeric genomic DNA from RARS gene and a 3' portion of the chimeric genomic DNA from MAD1L1 gene.
  • the junction of the RARS-MADILI fusion gene at least contains the sequence as below: GGTCTTTTATAAGGCCACCAGCCCC (SEQ ID NO: 1), in which the oligonucleotide underlined is the part sequencing from RARS and the rest is from part of sequencing of exon 19 of MAD1L1 gene.
  • the cDNA transcribed from RARS-MADILI mRNA at least contains the sequence as below:
  • the protein products of RARS-MADILI should contain at least:
  • Tumors can be detected by this invention include but not limited to nasopharyngeal carcinoma, head and neck cancer, lung cancer, liver cancer, and gastric cancer.
  • a method for identifying tumor in a patient comprising:
  • a tumor therapy kit including at least one of the following reagents:
  • the reagents repressing the transcripts of 5' portion of RARS and a 3' portion of MAD1L1 are promoter inhibitor, transcription inhibitor, and siRNA.
  • the transcript of EIF2S3-TXNDC11 fusion gene contains exons 1-2 of EIF2S3 gene and exon 2-12 of TXNDC11.
  • a tumor detection reagent contains at least one of the probes:
  • genomic DNA of EIF2S3-TXNDC11 at least contain part of cadherin-11 and cadherin-5 gene.
  • the fusion site of EIF2S3-TXNDC11 gene at least have the following sequencing:
  • the mRNA of EIF2S3-TXNDC 11 fusion gene should contain at least: CTAACAGTTTCACCTCCTATTGGGGATCTTCAGGTCTTTTATAAGGCCACCAGCCCCTCGGGTTCCAAGATG CAGCTACTGGAGACAGAGTTCTCACAC (SEQ ID NO: 5).
  • Tumors detected are nasopharyngeal carcinoma, head and neck cancer, lung cancer, liver cancer, and gastric cancer.
  • a method for identifying tumor in a patient comprising:
  • a tumor therapy kit including at least one of the following reagents:
  • the reagents repressing the transcripts of 5' portion of EIF2S3 and a 3' portion of TXNDC 11 are promoter inhibitor, transcription inhibitor, and siRNA.
  • the gene or protein product of present invention could be used as molecular diagnostic marker and therapeutic targets of many types of tumors, such as nasopharyngeal carcinoma.
  • Present invention will contribute to the early diagnosis and therapy of tumors, increasing the screening efficiency, decreasing the screening cost, enhancing the early diagnostic rate, and improving the patients' survival.
  • Fig. 1 shows the discovery of RARS-MADILI gene fusion in many kinds of cancer, including (A) Histogram of gene fusion nomination scores in clinically localized nasopharyngeal carcinoma, Head & Neck Squamous Cell Carcinoma, and other types of cancer; (B) Schematic representation of paired-end reads supporting the inter-chromosomal gene fusion between RARS and MAD1L1, resulting in fusion gene RARS-MADILI.
  • Fig. 2 shows the exon structure of RARS (A) and MAD1L1 (B) normal and fusion transcript RARS-MADILI (C).
  • Fig. 3 a circos plot of the genomic landscape of RARS-MADILI gene fusion discovered by RNA-seq in NPC samples. The outer ring shows RARS and MAD1L1 chromosome ideograms. The RARS-MADILI gene fusion is shown as an arc linking the two genomic loci.
  • Fig. 4 shows validation of RNA expression of RARS-MADILI gene fusions.
  • A qRT-PCR validation of RARS-MADILI gene fusion in C666-1 cells by electrophoresis, and
  • B result by sequencing.
  • Fig. 5 shows validation of protein expression of RARS-MADILI gene fusions.
  • A Western blot analysis showing the expression of 34 kDa RARS-MADILI fusion protein in C666-1 and in Hela cells transfected with RARS-MADILI full length fusion construct by N-terminal RARS antibody.
  • B Western blot analysis showing the over-expression of 72kDa RARS protein, 90kDa MAD1L1 protein, 34 kDa RARS-MADILI fusion protein in HNE1 cells transfected with empty vector, RARS gene, MAD1L1 gene, and RARS-MADILI full length fusion construct by anti-flag antibody (upper panel) and RARS-MADILI antibody ascites (lower panel).
  • Fig. 6 shows RARS-MADILI fusion transcripts by cancer.
  • Fig. 7 shows genomic organization and FISH validation of RARS and MAD1L1 gene rearrangement.
  • A Schematic diagrams in the top panel showing the genomic location of RARS and MAD1L1 genes, respectively.
  • B-D FISH validation of RARS-MADILI gene fusion in C666-1 (B), PALM (C), NPC patients (D), respectively.
  • Fig. 8 shows the representative gel picture of rapid amplification of 5' cDNA ends (RLM-5'RACE) in C666 cells.
  • Fig. 9 shows rapid amplification of 3' cDNA ends (RLM-3'RACE) in C666 cells.
  • RLM-3' RACE results for C666 cells.
  • B The DNA sequencing of RLM-3' RACE results for C666 cells.
  • Fig. 10 shows fusion fragment between RARS and MAD1L1 of genomic DNA in C666 and PALM cells by long-range
  • Fig. 11 shows the oncogenic potential of the RARS-MADILI fusion.
  • A Expression of the RARS-MADILI fusion in nasopharyngeal carcinoma cells (CNE1 and HNE1) leads to increased cellular proliferation.
  • B HNE1 stable cells expressing the RARS-MADILI fusion showed increased cell invasion potential by transwell assay.
  • C The CNE1 stable cells expressing the RARS-MADILI fusion showed increased cell progression potential under X-ray irradiation.
  • CNE2 stable cells expressing the RARS-MADILI fusion showed increased cell progression potential by colony formation assay.
  • Fig. 12 shows transformation of BaF3 cells by RARS-MADILI fusion transcript. Fusion constructs RARS-MADILI promoted proliferation in BaF3 cells deprived of IL3.
  • Fig. 13 shows induction of chromosome instability of Hela cells by RARS-MADILI fusion transcript.
  • A Ratio of micronuclei induced by fusion constructs RARS-MADILI and vector control in Hela cells.
  • B Multi-spindle poles by fusion construct RARS- in Hela cells.
  • Fig. 14 shows qPCR confirmation of siRNA knockdown of RARS-MADILI fusion.
  • A the schematic depicting the positions of gene specific siRNA on wild-type RARS, wild-type MAD1L1, and RARS-MADILI fusion
  • B qPCR confirmation of RARS-MADILI knockdown by siRNA against the fusion junction, wild-type RARS, and wild-type MAD1L1 on C666.
  • Fig. 15 shows knocking-down of RARS-MADILI fusion reduced the tumor progression and invasive abilities of C666 cells by (A) shRNA and (B) siRNA with soft-agar assay.
  • RARS-MADILI induces side population in NPC cells.
  • A The expression of RARS-MADILI fusion transcript in C666 SP cells.
  • B RARS-MADILI induces side population in CNE2 cells.
  • C SP cells from
  • CNE2-RARS-MAD1L1 stable cell line have increased cell progression potential by colony formation assay.
  • SP cells from CNE2-RARS-MAD1L1 stable cell line have induced invasion capacity by soft-agar assay.
  • Fig. 17 shows the exon structure of EIF2S3 (A) and TXNDCll (B) normal and fusion transcript EIF2S3- TXNDCll
  • Fig. 18 shows validation of expression of EIF2S3- TXNDCll gene fusions.
  • A qRT-PCR validation of EIF2S3- TXNDC 11 gene fusion in SUNE2 cells and (B) result by sequencing.
  • Fig. 19 shows EIF2S3-TXNDC11 fusion transcripts by cancer.
  • Fig. 20 shows genomic organization and FISH validation of EIF2S3 and TXNDCll gene rearrangement.
  • A Schematic diagrams in the top panel showing the genomic location of EIF2S3 and TXNDCll genes, respectively. FISH validation of EIF2S3- TXNDCll gene fusion in (B) CNE2, (C) SUNE2 and HONE1 cells, respectively.
  • Fig. 21 shows rapid amplification of 5' EIF2S3-TXNDC11 cDNA ends (RLM-5'RACE) in CNE2 cells.
  • RLM-5'RACE The representative gel picture of RLM-5' RACE results for CNE2 cells.
  • B The two different versions of DNA sequencing results of RLM-5' RACE in CNE2 cells.
  • C, D two versions of 5' EIF2S3-TXNDC 11 cDNA ends after aligning by BLAST analysis.
  • Fig. 22 shows fusion fragment between EIF2S3 and TXNDCll of genomic DNA in SUNE2 cells by long-range PCR.
  • A The schematic depicting the positions of gene specific primers (dark line) on EIF2S3 part and specific primers (dot line) on TXNDCll part of the fusion used for EIF2S3- TXNDCll.
  • B The representative gel picture of EIF2S3- TXNDC11 fusion fragment results for SUNE2 cells.
  • C The schematic depicting the genomic rearrangement of EIF2S3- TXNDC11 fusion.
  • the inventor of present invention conducted transcriptome sequencing of C666 cells and found the fusion gene of RARS-MADILI. According to the results of massively parallel sequencing, the inventor designed the specific primers forRARS-MADlLl, validating it in tumor tissues, further confirming the transcriptional structure of this fusion gene.
  • the sequencing of the primer are:
  • RARS-MADILI-F 5'-CTAACAGTTTCACCTCCTATTGGG-3' (SEQ ID NO: 6);
  • RARS-MADILI-R 5'-GTGTGAGAACTCTGTCTCCAGTAGC-3' (SEQ ID NO: 7);
  • Amplifying conditions 50 ° C 2min; 95 ° C 2min; 95 ° C 15sec, 70 ° C 30sec, 3 cycles; 95 ° C 15sec, 68 ° C 30sec, 3 cycles;
  • Figure 1 presents the discovery of RARS-MA1L1 gene fusion in many kinds of cancer, including: (A) Histogram of gene fusion nomination scores in clinically localized nasopharyngeal carcinoma, Head & Neck Squamous Cell Carcinoma, and other types of cancer. (B) Schematic representation of paired-end reads supporting the inter-chromosomal gene fusion between RARS and MAD1L1, resulting in fusion gene RARS-MADILI.
  • Fig. 2 shows the exon structure of RARS (A) and MAD1L1 (B) normal and fusion transcript RARS-MADILI(C).
  • Fig. 3 A Circos plot of the genomic landscape of RARS-MADILI gene fusion discovered by RNA-seq in NPC samples. The outer ring shows RARS and MAD1L1 chromosome ideograms. The RARS-MADILI gene fusion is shown as an arc linking the two genomic loci.
  • RT-PCR combined with Sanger sequencing was applied to detect the fusion gene of RARS-MADILI at mRNA level in C666
  • Fig. 4 A shows validation of expression of RARS-MADILI gene fusions.
  • A qRT-PCR validation of RARS-MADILI gene fusion in C666-1 cells by electrophoresis and
  • B The RARS-MADILI DNA sequencing amplified by above qRT-PCR. The PCR product was further subjected to sequence and the sequencing is:
  • Fig. 5 shows detection of protein expression of RARS-MADILI gene fusions.
  • the endogenous RARS-MADILI fusion protein in C666 cells was detected with the antibody against N-terminal RARS by Western blotting ( FIG. 5 A) .
  • the flag-tagged exogenous proteins wild-type RARS (72kDa), wild-type MAD1L1 (95kDa), and fusion protein RARS-MADILI (34kDa
  • Fig 5B Western blotting
  • the endogenous RARS-MADILI fusion protein in C666 cells was also detected by immune-precipitation (Fig 5C).
  • Fig. 6 shows RARS-MADILI fusion transcripts by cancer.
  • RARS-MADILI fusion transcript exists in many types of tumors. The positive detection rate was different among different types of tumors. The positive rate is higher in nasopharyngeal carcinoma, head & neck cancer, and gastric cancer, implying the potential application in tumor diagnosis and targeted therapy.
  • the genomic rearrangement of RARS gene and MAD1L1 gene was detected using Fluorescence in situ hybridization (FISH).
  • FISH Fluorescence in situ hybridization
  • the bacterial artificial chromosome (BAC) clones containing either of these two genes were found by searching in Ensemble website.
  • the BAC clone probe containing the single strand of RARS gene is labeled with red fluorescence and the BAC clone probe containing the single strand of MAD1L1 gene is labeled with green fluorescence.
  • these probes specifically bound with the single strand nucleotides of genomic DNA in C666 cells (Fig. 7B), PALM cells (Fig.
  • 5' end of cDNA of RARS-MADILI in C666 was amplified by 5' rapid-amplification of cDNA ends (5'RACE) technology.
  • 5'RACE 5' rapid-amplification of cDNA ends
  • GSP1 primer was designed for reverse transcription: 5'-TTGTGTCTAGGGGAGAAGATT-3' ( SEQ ID NO: 5 ) .
  • RNase H is specific for RNA:DNA heteroduplex molecules.
  • TdT Terminal deoxynucleotidyl transferase
  • dCTP are used to add homopolymeric tails to the 3' ends of the cDNA.
  • the Abridged Anchor Primer (AAP: 5'- GGCCACGCGTCGACTAGTACGGGGGGGGGG-3' ( SEQ ID NO: 6), provided by Invitrogen5' RACE kit) is able to bind the homopolymeric tails.
  • the specific primers for 5' RARS gene of fusion gene RARS-MADILI are designed: Gsp2: 5 ' - AGGTC AGGCC AAGC AGAGTG-3 ' (SEQ ID NO: 10);
  • GSP3 5'-TAGTTGACCTCAGGTGGCCTACA-3' (SEQ ID NO: 11)
  • AUAP Universal Amplification Primer
  • AAP Abridged Universal Amplification Primer
  • GSP2 DNA polymerase
  • the cDNA first strand was used as a template for regular PCR to obtain double strand DNA.
  • PCR products from the primary PCR with the Abridged Anchor Primer were preceded to nest PCR with the AUAP and GSP3 primers. Then after gel electrophoresis and gel extraction of the PCR products, the purified PCR products were inserted into TA clones.
  • Analyzing with BLAST in the sequence, the italic characters are aligned with part of human RARS mRNA (NM_002887.3), the underlined characters are aligned with the 5'UTR, and the bold characters are aligned with CDs.
  • First strand cDNA synthesis is initiated at the poly(A) tail of mRNA using the Abridged Anchor Primer(AAP). After first strand cDNA synthesis, the original mRNA template is destroyed with RNase H, which is specific for RNA:DNA heteroduplex molecules.
  • the inventor designed a GSP1 primer cross the fusion site of RARS gene and MADlLlgene ( GSP1: 5'-GTCTTTTATAAGgccaccagcc-3', the 11 Upper cases is from RARS gene, and the 10 lower cases is from MAD1L1 gene);
  • GSP1 5'-GTCTTTTATAAGgccaccagcc-3', the 11 Upper cases is from RARS gene, and the 10 lower cases is from MAD1L1 gene
  • AAP GSP1 and DNA polymerase
  • the cDNA first strand was used as a template for regular PCR to obtain double strand DNA with a poly(A) tail.
  • the purified PCR products are inserted into TA clones, and subjected to sequence.
  • Fig. 9A shows the representative gel picture of 3' RACE results for C666 cells.
  • CNE2 was used as a negative control.
  • the italic characters are aligned with part of human MAD1L1 mRNA (NM_003550.2, NM 001013836.1, NM_001013837.1), the underlined characters are aligned with the CDs, and the bold characters are aligned with 3'UTR.
  • RARS-MADILI fusion gene was amplified by long range PCR at genomic DNA level.
  • forward primers are designed to target RARS gene as Rl
  • the reverse primers are designed to target MAD1L1 gene as M1-M19.
  • the PCR amplified products by primer sets (R1M12, R2M12, R3M12) were subjected to sequence shown in Fig 10 B and IOC.
  • the inventor applied colony formation assay, Transwell experiment, MTT assay to study the function and possible mechanisms of the fusion gene RARS-MADILI, the empty vector was used as a negative control.
  • the expression of the RARS-MADILI fusion in nasopharyngeal carcinoma cells (CNE1 and HNEl) leads to increased cellular proliferation (Fig. 11A); HNEl stable cells expressing the RARS-MADILI fusion showed increased cell invasion potential by Transwell assay (Fig. 11B);
  • the CNE1 stable cells expressing the RARS-MADILI fusion showed increased cell invasion potential under X-ray irradiation (Fig.
  • the inventor infected IL-dependent BaF3 cells with retrovirus encoded with RARS-MADILI fusion gene. As shown in Fig. 12, upon removal of IL3, the overexpression of fusion constructs RARS-MADILI still induces the proliferation of BaF3 cells. Then using the immunostaining with anti-a-tubulin (green) and nuclei (DAPI, blue), the number of micronuclei and multipolar spindle were calculated in the Hela cells with overexpression of RARS-MADILI.
  • siRNAs were designed to knock-down the mRNA of RARS gene, MAD1L1 gene, or RARS-MADILI gene and to further explore the function of RARS-MADILI in tumor cells.
  • the scheme of each target sequence by different siRNA was shown in Fig 14A.
  • Real-time analysis showed that siRNA-RARS-05 (siRARS-5) and siRNA-M AD 1 L 1 -03 (siMADlLl-3) knocked-down both RARS-MADILI and wild-type gene (either RARS or MAD1L1), while the rest siRNA only can knock down the related wild-type gene.
  • the colony formation abilities and invasion abilities of C666 cells were reduced after knocking-down by siRARS-5 and siMADlLl-3 (Fig. 15, left panel) and by shRNA (Fig. 15, right panel).
  • SP cells are isolated from of C666 by cell sorting and subjected to analyze the endogenous RARS-MADILI expression.
  • the expression level of RARS-MADILI was higher in SP cells than non-SP cells in C666 cell line.
  • the number of SP cells was induced in CNE2 cells after overexpression of RARS-MADILI (Fig. 16B).
  • the SP cells from RARS-MADlLl-expressed CNE2 formed more and larger colonies by colony formation assay (Fig. 16C) and soft-agar assay (Fig. 16D), comparing to vector control, suggesting that SP cells isolated from RARS-MADlLl-expressed CNE2 have more aggressive invasion and proliferation abilities.
  • the structure of EIF2S3-TXNDC11 is shown in Fig. 17.
  • the amplified sequence of EIF2S3-TXNDC11 is:
  • ACGTTCGACGGGATTCAGAGGTGGTACTGCTCTTCTTCTATGCCCCT (SEQ ID NO: 20) (the bold characters are from part of EIF2S3, the rest are from part of TXNDC 11 ) .
  • the PCR primers are:
  • EIF2S3-TXNDC 11 -F 5 ' -GGATGTTACC AAGTTGACGCC-3 ' (SEQ ID NO: 21);
  • EIF2S3-TXNDC 11 -R 5'-ACAGGTGGCTTTGCTGGTATTA-3' (SEQ ID NO: 22);
  • EIF2S3-TXNDCll-Probe 5'- fam+CAGACAAGCCACAATTAACATAGTCGAGCA+tamra -3' (SEQ ID NO: 23) ; Additional 100 NPC samples were analyzed with the expression of EIF2S3-TXNDC11 by real-time PCR. Amplifying conditions: 50 ° C 2min; 95 ° C 2min; 95 ° C 15sec, 70 ° C 30sec, 3 cycles; 95 ° C 15sec, 68 ° C 30sec, 3 cycles; 95 ° C 15sec, 66 ° C 30sec, 3 cycles; 95 ° C 15sec, 64 ° C 30sec, total 45 cycles; Then statistically analyzing the amplifying results. Only two cases were examined the presence of EIF2S3-TXNDC11. The result was showed as figure 19.
  • the genomic rearrangement of EIF2S3 gene and TXNDC 11 gene was detected using Fluorescence in situ hybridization (FISH).
  • FISH Fluorescence in situ hybridization
  • the bacterial artificial chromosome (BAC) clones containing any of these two genes were found by searching in Ensemble website.
  • the BAC clone probe containing the single strand of EIF2S3 gene is labeled with red fluorescence and the BAC clone probe containing the single strand of TXNDC 11 gene is labeled with green fluorescence.
  • these probes specifically bound with the single strand nucleotides of genomic DNA in CNE2 cells (Fig.
  • 5' end of cDNA of EIF2S3-TXNDC 11 in C666 was amplified by 5' rapid-amplification of cDNA ends (5'RACE) technology.
  • 5'RACE 5' rapid-amplification of cDNA ends
  • GSP1 primer was designed for reverse transcription: 5'-GCTTTGCTGGTATTATCACATCTTT-3' (SEQ ID NO: 24).
  • TdT Terminal deoxynucleotidyl transferase
  • dCTP dCTP
  • Abridged Anchor Primer AAP: 5'- GGCCACGCGTCGACTAGTACGGGGGGGGGG-3' (SEQ ID NO: 25), provided by Invitrogen5' RACE kit
  • EIF2S3-TXNDC 11 -GSP2 5'-GTGGCTTGTCTGCTGATAACT-3' (SEQ ID NO: 26) ( from human EIF2S3 mRNA sequencing NM_001415.3 ) ;
  • EIF2S3-TXNDC 11 -GSP3 5'-AGTGGCGTCAACTTGGTAA-3' (SEQ ID NO: 27) ( from human EIF2S3 mRNA sequencing NM_001415.3 ) ;
  • AUAP Abridged Universal Amplification Primer
  • AUAP 5' -GGCCACGCGTCGACTAGTAC-3' (provided by Invitrogen 5' RACE kit).
  • AAP GSP2 and DNA polymerase
  • the cDNA first strand was used as a template for regular PCR to obtain double strand DNA.
  • PCR products from the primary PCR with the Abridged Anchor Primer were preceded to nest PCR with the AUAP and GSP3 primers.
  • the purified 150 bp PCR products were inserted into TA clones and then the TA colonies were digested to confirm the correct insertion (Fig.
  • EIF2S3-TXNDC11 fusion gene was amplified by long range PCR with LA Taq® Hot Start Version DNA polymerase (TAKARA provided) at genomic DNA level.
  • TAKARA LA Taq® Hot Start Version DNA polymerase
  • forward primers are designed to target the second exon of EIF2S3 gene as El primer 5'-TTGACGCCACTTTCACACGAAG-3' (SEQ ID NO: 30) (from human EIF2S3 mRNA sequence NM_001415.3)
  • the reverse primers are designed to target the second exon of TXNDC11 gene as Tl primer 5' -CCTCTGAATCCCGTCGAACGTA-3' (SEQ ID NO: 31) (from human TXNDC11 mRNA sequence NW_004078085.1).
  • the amplifying condition is 93 ; ⁇ 33m in , ° C68L0sec ;&fMmche cycle, adding 10 seconds to the extension time of every consecutive cycle till the 40th cycle, at last extend additional 6
  • RARS-MADILI and EIF2S3-TXNDC11 fusion genes play important roles in tumor genesis and development of cancers, and might be useful in early diagnosis and targeted therapy as molecular diagnostic markers and therapeutic targets.

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Pathology (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Genetics & Genomics (AREA)
  • Wood Science & Technology (AREA)
  • Physics & Mathematics (AREA)
  • Biotechnology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Hospice & Palliative Care (AREA)
  • Biophysics (AREA)
  • Oncology (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

Cette invention concerne des réactifs et des méthodes pour la détection et le traitement des tumeurs. Le séquençage massivement parallèle a identifié les gènes de fusion RARS-MAD1L1 et EIF2S3-TXNDC11, et découvert que ces deux gènes de fusion sont associés au développement du cancer. Selon les résultats de différentes expériences, il est facile de détecter des tumeurs par étude de ces gènes de fusion et de les traiter par régulation de l'expression desdits deux gènes de fusion.
PCT/CN2013/075836 2013-05-17 2013-05-17 Réactif et méthode pour la détection et le traitement des tumeurs WO2014183301A1 (fr)

Priority Applications (1)

Application Number Priority Date Filing Date Title
PCT/CN2013/075836 WO2014183301A1 (fr) 2013-05-17 2013-05-17 Réactif et méthode pour la détection et le traitement des tumeurs

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
PCT/CN2013/075836 WO2014183301A1 (fr) 2013-05-17 2013-05-17 Réactif et méthode pour la détection et le traitement des tumeurs

Publications (1)

Publication Number Publication Date
WO2014183301A1 true WO2014183301A1 (fr) 2014-11-20

Family

ID=51897614

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/CN2013/075836 WO2014183301A1 (fr) 2013-05-17 2013-05-17 Réactif et méthode pour la détection et le traitement des tumeurs

Country Status (1)

Country Link
WO (1) WO2014183301A1 (fr)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN109813912A (zh) * 2019-01-04 2019-05-28 深圳大学 一组血清差异蛋白组合在制备用于检测孤独症的试剂中的应用
CN111733240A (zh) * 2020-06-19 2020-10-02 四川大学华西医院 一种肿瘤生物标志物及其应用

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6943241B2 (en) * 2001-11-05 2005-09-13 Research Association For Biotechnology Full-length cDNA
CN102159729A (zh) * 2008-09-22 2011-08-17 怡发科技股份有限公司 肺癌及结肠直肠癌的分子标记

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6943241B2 (en) * 2001-11-05 2005-09-13 Research Association For Biotechnology Full-length cDNA
CN102159729A (zh) * 2008-09-22 2011-08-17 怡发科技股份有限公司 肺癌及结肠直肠癌的分子标记

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
MAHER C.A. ET AL.: "Transcriptome sequencing to detect gene fusions in cancer.", NATURE, vol. 458, 5 March 2009 (2009-03-05), pages 97 - 101 *
WANG XIAO-SONG ET AL., NATURE BIOTECHNOLOGY, vol. 27, no. 11, 1 November 2009 (2009-11-01), pages 1005 - 1011 *

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN109813912A (zh) * 2019-01-04 2019-05-28 深圳大学 一组血清差异蛋白组合在制备用于检测孤独症的试剂中的应用
CN109813912B (zh) * 2019-01-04 2021-12-28 深圳大学 一组血清差异蛋白组合在制备用于检测孤独症的试剂中的应用
CN111733240A (zh) * 2020-06-19 2020-10-02 四川大学华西医院 一种肿瘤生物标志物及其应用
CN111733240B (zh) * 2020-06-19 2021-05-07 四川大学华西医院 一种肿瘤生物标志物及其应用

Similar Documents

Publication Publication Date Title
Jia et al. Expression, regulation and roles of miR‐26a and MEG3 in tongue squamous cell carcinoma
Tripathi et al. Direct regulation of alternative splicing by SMAD3 through PCBP1 is essential to the tumor-promoting role of TGF-β
Takahashi et al. Long noncoding RNA in liver diseases
US9109259B2 (en) Detection method for novel ROS1 fusions
JP2008532477A5 (fr)
CN109097477B (zh) 一种用于乳腺癌诊断的circRNA标志物及其应用
Yang et al. LncRNA SNHG8 participates in the development of endometrial carcinoma through regulating c-MET expression by miR-152.
Wozniak et al. Diminution of miR-340-5p levels is responsible for increased expression of ABCB5 in melanoma cells under oxygen-deprived conditions
JP2012501164A5 (fr)
WO2010011642A2 (fr) Procédés et compositions employant des protéines de régulation de l'épissage impliquées dans la suppression de tumeurs
CN113718035B (zh) 环状RNA hsa_circ_0003552的应用及检测其的试剂盒
CN111304326A (zh) 检测及靶向lncRNA生物标志物的试剂及其在肝细胞癌中的应用
JP2005511023A5 (fr)
WO2014183301A1 (fr) Réactif et méthode pour la détection et le traitement des tumeurs
US20210292853A1 (en) Detection of cldn18-arhgap6 fusion gene or cldn18-arhgap26 fusion gene in pancreatic cancer
CN111676219B (zh) 一种长链非编码RNA Lnc-EPC1-4及其应用
CN109467596B (zh) 转录因子sp1在调控猪rtl1基因表达中的应用
US20220145395A1 (en) Transpochimeric Gene Transcripts (TCGTS) As Cancer Biomarkers
Hu et al. PUS1 promotes hepatocellular carcinoma via mRNA pseudouridylation to enhance the translation of oncogenic mRNAs
JP2009502111A5 (fr)
JP5704545B2 (ja) 甲状腺癌の検出方法
KR102293777B1 (ko) 신규한 UQCRB-관련 순환 miRNA 바이오 마커 및 이를 이용한 대장암의 진단 방법
JP2010022236A (ja) 甲状腺癌の検出方法
CN108841964B (zh) Loc105370108在直肠腺癌诊治中的应用
CN112760382B (zh) 人fitm1和hist1h2bj基因甲基化位点的检测和应用

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 13884759

Country of ref document: EP

Kind code of ref document: A1

NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 13884759

Country of ref document: EP

Kind code of ref document: A1