WO2022144815A1 - Aptamère à double spécificité déclenchant une cytotoxicité à médiation cellulaire pour lyser des cellules cancéreuses positives au her2 - Google Patents

Aptamère à double spécificité déclenchant une cytotoxicité à médiation cellulaire pour lyser des cellules cancéreuses positives au her2 Download PDF

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WO2022144815A1
WO2022144815A1 PCT/IB2021/062450 IB2021062450W WO2022144815A1 WO 2022144815 A1 WO2022144815 A1 WO 2022144815A1 IB 2021062450 W IB2021062450 W IB 2021062450W WO 2022144815 A1 WO2022144815 A1 WO 2022144815A1
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her2
dual
segment
nucleic acid
aptamer
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PCT/IB2021/062450
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Majid TALKHABIFARD
Majid Shahbazi
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Talkhabifard Majid
Majid Shahbazi
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Publication of WO2022144815A1 publication Critical patent/WO2022144815A1/fr

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/115—Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith ; Nucleic acids binding to non-nucleic acids, e.g. aptamers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/16—Aptamers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/30—Chemical structure
    • C12N2310/35—Nature of the modification
    • C12N2310/351—Conjugate
    • C12N2310/3519—Fusion with another nucleic acid
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/50—Physical structure
    • C12N2310/51—Physical structure in polymeric form, e.g. multimers, concatemers

Definitions

  • the present disclosure generally relates to a dual-specific aptamer and compositions comprising the same; more particularly, the present disclosure relates to a dual-specific aptamer that may include an anti-HER2 segment configured to specifically bind a HER2 marker, and an anti-CD16 segment configured to specifically bind a CD 16 marker.
  • Nucleic acid aptamers are small oligonucleotides capable of forming different three- dimensional structures; these oligonucleotides have shown binding affinity to a wide range of target molecules via non-covalent interactions. Aptamers have demonstrated remarkable advantages, such as high affinity, excellent specificity, low immunogenicity, simple synthesis, and simple modification; these properties have made aptamers promising candidates for use in various diagnostic and therapeutic applications. In recent years, aptamers have gained an increasing attention as modem therapeutic agents in oncology studies. Main strategies of aptamer-based therapeutics may include blockade of receptor-ligand interactions through antagonistic activity of aptamer, and targeted drag delivery.
  • Human epidermal growth factor receptor 2 (Her2/neu) is one of the four members of epidermal growth factor receptor (EGFR) family involved in growth, proliferation, and differentiation of cells. Heterodimerization of HER2 with any of the three members of the EGFR family may result in autophosphorylation of tyrosine residues inside the receptors' cytoplasmic domain and activation of a variety of signaling pathways. Over-expression of HER2 may play an essential role in the development and progression of different cancers, such as breast cancer, gastric/gastroesophageal cancers, etc. HER2 may be a suitable target for anticancer-therapy of tumors having an overexpression of HER2/neu receptor.
  • EGFR epidermal growth factor receptor
  • HER2-targeted therapies for treating HER2-positive breast cancers are based on tyrosine kinase inhibitors (e.g., neratinib and lapatinib) and monoclonal antibodies (mAbs; e.g., Trastuzumab and pertuzumab) that may lead to pathological signaling inhibition or activation of immune system.
  • the anti-HER2 monoclonal antibodies such as Trastuzumab, may block HER2 by preventing dimerization; they may also activate antibodydependent cell-mediated cytotoxicity (ADCC) mechanism against HER2-positive cancer cells by binding, through their Fc-region, to Natural Killer (NK) cells expressing FcyRIIIA/CD16.
  • ADCC antibodydependent cell-mediated cytotoxicity
  • NK Natural Killer
  • the present disclosure relates to a dual-specific aptamer.
  • the dual-specific aptamer may include: an anti-HER2 segment capable of binding to a HER2 marker/receptor; an anti -CD 16 segment capable of binding to a CD 16 marker/receptor; and a linker that may attach a 3’ end of the anti-HER2 segment to a 5’ end of the anti-CD16 segment.
  • the anti-HER2 segment may be disposed at a 5’ arm of the dual-specific aptamer and may include the nucleic acid sequence set forth in SEQ ID NO: 1. Meanwhile, the anti-HER2 segment may be capable of binding to the HER2 marker on a HER2-positive cancer cell, such as a HER2 -positive breast cancer cell.
  • the anti-CD16 segment may be disposed at a 3’ arm of the dual-specific aptamer and may include the nucleic acid sequence set forth in SEQ ID NO: 3.
  • the anti-CD 16 segment may be capable of binding to the CD 16 marker on a cytotoxic effector cell.
  • the dual-specific aptamer may activate/trigger aptamer-dependent cell-mediated cytotoxicity (ADCC) mechanism by binding to the CD 16 marker on the cytotoxic effector cell.
  • ADCC aptamer-dependent cell-mediated cytotoxicity
  • the dual-specific aptamer may further comprise a linker that may attach the 3’ end of the anti-HER2 segment to the 5’ end of the anti-CD16 segment.
  • the linker may be a nucleic acid linker and may include a single-stranded nucleic acid linker or a double-stranded nucleic acid linker.
  • the single-stranded nucleic acid linker may include the poly-Adenosine/ Adenine (A) sequence set forth in SEQ ID NO: 6.
  • the double-stranded nucleic acid linker may include the poly- A sequence set forth in SEQ ID NO: 6 that may be hybridized to a poly-Thymidine/Thymine (T) set forth in SEQ ID NO: 7.
  • T poly-Thymidine/Thymine
  • the dual-specific aptamer may have the nucleic acid sequence set forth in
  • Another aspect of the present disclosure may be directed to a pharmaceutical composition comprising said dual-specific aptamer.
  • the pharmaceutical composition may be used for treating HER2-psotive cancers.
  • FIG, 1 illustrates predicted secondary structures of dual-specific aptamers (dsAl to 10) and their corresponding flow cytometry binding analysis after incubation with the PBMCs (peripheral blood mononuclear cells) and the enriched NK (natural killer) cells, consistent with one or more exemplary embodiments of the present disclosure;
  • FIG. 2 illustrates the predicted secondary structure of the dual-specific aptamers (ds Al to 10) and their corresponding flow cytometry binding analysis after incubation with the SKBR3 cells as HER2-positive breast cancer cells, consistent with one or more exemplary embodiments of the present disclosure
  • FIG. 3A shows cytotoxic effect of the dsA7 and dsAlO dual-specific aptamers (SEQ ID NO: 14) on SKBR3 cells lysis in a 2D (two-dimensional) culture system comprising the PBMCs and the enriched NK cells, consistent with one or more exemplary embodiments of the present disclosure
  • FIG. 3A shows cytotoxic effect of the dsA7 and dsAlO dual-specific aptamers (SEQ ID NO: 14) on SKBR3 cells lysis in a 2D (two-dimensional) culture system comprising the PBMCs and the enriched NK cells, consistent with one or more exemplary embodiments of the present disclosure
  • FIG. 1 shows cytotoxic effect
  • 3B shows cytotoxic effect of the dsA7 dual-specific aptamer (SEQ ID NO: 14) on MDAMB231 cells lysis in a 2D culture system comprising the PBMCs and the enriched NK cells, consistent with one or more exemplary embodiments of the present disclosure
  • FIG. 4A shows inhibitory effect of a fixed concentration (10 nM) of the dsA7 dualspecific aptamer (SEQ ID NO: 14) on SKBR3 and MDAMB231 cells proliferation, as compared to the inhibitory effect of Trastuzumab and the non-binding NC aptamer, consistent with one or more exemplary embodiments of the present disclosure;
  • FIG. 4B shows inhibitory effect of different concentrations (0.25, 2, and 10 nM) of the dsA7 dual-specific aptamer (SEQ ID NO: 14) on the SKBR3 cells proliferation, compared to the same concentrations of Trastuzumab, consistent with one or more exemplary embodiments of the present disclosure;
  • FIG. 5 illustrates flow cytometry binding analysis of the primary anti-HER2 aptamers set forth in SEQ ID NOs: 1, 15 and 16 and a non-binding NC aptamer to SKBR3 and MDAMB231 cells, consistent with one or more exemplary embodiments of the present disclosure
  • FIG. 6A illustrates flow cytometry binding analysis of the primary anti-CD16 aptamer set forth in SEQ ID NO: 3 and the non-binding NC aptamer to PBMCs, as compared to a 3G8 antibody and an isotype control, consistent with one or more exemplary embodiments of the present disclosure
  • FIG. 6B illustrates flow cytometry binding analysis of the primary anti-CD16 aptamer set forth in SEQ ID NO: 3 and the non-binding NC aptamer to enriched NK cells, as compared to the 3G8 antibody and the isotype control, consistent with one or more exemplary embodiments of the present disclosure
  • FIG. 6A illustrates flow cytometry binding analysis of the primary anti-CD16 aptamer set forth in SEQ ID NO: 3 and the non-binding NC aptamer to enriched NK cells, as compared to the 3G8 antibody and the isotype control, consistent with one or more exemplary embodiments of the present disclosure
  • FIG. 6A illustrates flow cytometry binding
  • FIG. 8 shows the amount of SKBR3 cells lysis in the presence of the dsA7 dual-specific aptamer (SEQ ID NO: 14) alone and in the presence of a combination of the 3G8 antibody and the dsA7 dual-specific aptamer, consistent with one or more exemplary embodiments of the present disclosure.
  • references herein to “one embodiment,” “an embodiment,” “some embodiments,” “one or more embodiments,” “one exemplary embodiment,” “an exemplary embodiment,” “some exemplary embodiments,” and “one or more exemplary embodiments” indicate that a particular feature, structure or characteristic described in connection or association with the embodiment may be included in at least one of such embodiments. However, the appearance of such phrases in various places in the present disclosure do not necessarily refer to a same embodiment or embodiments.
  • an exemplary dual-specific aptamer or a variant/analog thereof method(s) for producing thereof, compositions comprising the same, and method(s) of cancer treatment using the same.
  • the exemplary dual-specific aptamer disclosed herein, and/or the compositions comprising the same may be effective for treating HER2-positive cancers (i.e., cancer cells that may overexpress HER2 marker/receptor).
  • HER2-positive cancers i.e., cancer cells that may overexpress HER2 marker/receptor.
  • Exemplary embodiments of the present disclosure are described primarily in context of said dual-specific aptamer, method(s) of preparation, and compositions comprising the same.
  • Such applications and products may include, but are not limited to, any composition/product comprising said exemplary dual-specific aptamer, any medical treatment method, diagnostic/detection methods, tools and kits, and any catalytic process related to the exemplary dualspecific aptamer disclosed herein.
  • the exemplary dual-specific aptamer disclosed herein, and/or the compositions comprising the same may have a wide range of therapeutic effects including treatment of all HER2- positive cancers in which tumor/cancer cells may overexpress HER2 protein/marker.
  • the exemplary dual-specific aptamer and the compositions comprising the same may be useful for treating cancer diseases including, but not limited to, breast cancer, endometrial cancer, bladder carcinomas, gallbladder, anal cancer, colorectal cancer, uterine serous cancer (e.g., uterine papillary serous carcinoma), lung cancer (e.g., non- small-cell lung cancer), liver cancer, kidney cancer, gastroesophageal cancer, extrahepatic cholangio carcinomas, cervical cancer, uterine cancer, testicular cancer, ovarian cancer, pancreatic cancer, stomach cancer, etc.
  • cancer diseases including, but not limited to, breast cancer, endometrial cancer, bladder carcinomas, gallbladder, anal cancer, colorectal cancer, uterine serous cancer (e.g., uterine papillary serous carcinoma), lung cancer (e.g., non- small-cell lung cancer), liver cancer, kidney cancer, gastroesophageal cancer, extrahepatic cholangio carcinomas, cervical
  • the exemplary dual-specific aptamer of the present disclosure and the compositions comprising the same may also be effective for treating other medical conditions associated with HER2 marker/receptor dysregulation, e.g., overexpression.
  • medical conditions include, but are not limited to, restenosis, arthritis, schizophrenia, and hyperproliferative diseases such as psoriasis.
  • An exemplary dual-specific aptamer of the present disclosure and the compositions comprising the same may have an improved therapeutic effect on HER2 -positive cancers, compared to monovalent/mono- specific anti-HER2 aptamers.
  • Therapeutic effect of the disclosed dual-specific aptamer may be similar to therapeutic effect of anti-HER2 antibodies, such as Herceptin/Trastuzumab, Pertuzumab, etc.
  • Such improved therapeutic effect may be due to an exemplary structure and function of said dual-specific aptamer, consistent with one or more exemplary embodiments of the present disclosure.
  • the provided dual-specific aptamer similar the anti-HER2 antibodies, may be capable of binding specifically and simultaneously to both of the HER2 and CD 16 markers/receptors.
  • Such bispecific binding may lead to activation of antibody/ap tamer-dependent cell-mediated cytotoxicity (ADCC) against HER2-positive cancer/tumor cells, by binding to a CD16 marker/receptor on a cytotoxic effector cell.
  • ADCC antibody/ap tamer-dependent cell-mediated cytotoxicity
  • “Aptamer” may refer to single-stranded or double-stranded DNA (deoxyribonucleic acid) and/or RNA (ribonucleic acid) oligonucleotides capable of binding to different classes of molecules including, but not limited to, a protein, polypeptide, glycoprotein, lipid, glycopeptide, glycolipid, polysaccharide, and saccharide. They may be capable of forming secondary and/or tertiary and/or quaternary structures that may allow both specific and highly affine molecular interactions with various targets. Meanwhile, aptamers may vary in length and molecular weight. A tertiary structure of an aptamer may be due to intramolecular Watson-Crick base and Hoogsteen base pairings (quadruplex).
  • a typical aptamer may be at least 6 kDa (at least 20 nucleotides) and may bind to a molecule with sub-nanomolar to micromolar affinity.
  • An aptamer may be capable of discriminating a target molecule from closely related molecules; for example, aptamers may selectively bind to a specific protein from a group of proteins in a family.
  • Aptamers may bind to a specific target molecule via intermolecular interactions, such as electrostatic interactions, hydrogen bonds, steric exclusion, and hydrophobic interactions.
  • Aptamers may have a number of prioritized aspects including, but not limited to, low immunogenicity, high affinity, high specificity, suitable pharmacokinetic properties, and biological efficacy.
  • ‘Dual-specific aptamer” may refer to an aptamer/a nucleic acid molecule capable of binding, concurrently and specifically, to two markers/molecules/receptors, such as a protein marker on a cell surface. “Dual-specific” may be used interchangeably with the terms “bispecific” and “bivalent”. It may also be implemented as the abbreviated form “dsA”.
  • HER2 may stand for “Human Epidermal growth factor Receptor 2”; HER2 may be a member of human EGFR (epidermal growth factor receptor) family. “HER2” may also be referred to as “ErbB2” (erythroblastic oncogene B) and “neu”.
  • HER2-positive cancer may refer to cancers and/or disorders/diseases with an increased expression (overexpression) of HER2 protein/gene/RNA transcript.
  • any tumor/cancer cell exhibiting an upregulation of HER2 gene/transcript/protein may be identified as HER2-positive. Said upregulation may be detected at gene level, transcript level, and protein level.
  • a “cancer/tumor cell” may refer to a single cell of a cancerous tissue.
  • a tumor (either benign, pre-malignant, or malignant) may be generated by an abnormal growth or proliferation of cells.
  • cancer (cell) and tumor (cell) may be used, interchangeably, for those cancers that form tumors.
  • CD 16 also known as FcyRIIIA, may refer to a cell-surface receptor on surface of a cytotoxic effector cell, capable of binding to a constant region (i.e., Fc) of antibodies and activating the ADCC mechanism.
  • CD 16 receptor may include all FcyRIIIA isoforms, fragments and variants that may have CD16 biological activity.
  • Two Isoforms of the CD16 marker/receptor may include CD16a and CD16p.
  • CD16a may be an intermediate affinity receptor for IgGl and IgG3, but not for IgG2 and IgG4.
  • CD16a may be involved in secretion of enzymes, phagocytosis, ADCC, inflammatory mediators, and clearance of immune complexes.
  • Cytotoxic effector cell may refer to the cells, generated through hematopoiesis, having cytolytical apoptosis-mediating or phagocytic properties. Cytotoxic effector cells may include T-lymphocytes (T-cells), monocytes, granulocytes, NK (natural killer) cells, mast cells, macrophages, and Langerhans cells.
  • ADCC antibody/aptamer-dependent cell-mediated cytotoxicity
  • FcyR Fey receptors
  • CD 16 Fey receptors
  • the ADCC mechanism may be activated upon interaction of the Fc- region of immunoglobulins with the FcyRIIIA/CD 16 receptor expressed on a cytotoxic effector cells’ surface. Binding of the CD 16 marker/receptor to the Fc-region may lead to secretion of granzyme and perforin that may enhance lysis of target cells. It may also lead to release of IFNy (y interferon) and recruitment of adaptive immune cells. Meanwhile, the cytotoxic effector cells may induce death signals in the target cells via death receptor/ligand ligation.
  • Marker also called as “biomarker”, may refer to a biological molecule, such as a protein (e.g., HER2) or a nucleic acid.
  • Nucleic acid may be employed interchangeably with the terms “polynucleotide” and “nucleic acid molecule/sequence”, and may refer to a polymer of nucleotides, i.e., deoxyribonucleotides, ribonucleotides, or variants thereof. Nucleic acid molecules may be involved in various biological functions due to their ability to form different three-dimensional (3D/tertiary) structures. “Nucleic acid” may also include nucleic-acid molecules having synthetic backbones.
  • nucleic acid molecule may constitute modified nucleotides, such as methylated nucleotides, nucleotide variants, etc.; nucleotide modifications may be generated before or after assembly of the polymer.
  • a sequence of nucleotides may further include non-nucleotide components and nucleotide-mimetic.
  • a nucleic acid molecule may be modified after polymerization, for example by conjugation to a detectable label.
  • ‘Variant” may refer to molecules that may differ in their nucleic acid sequence from a reference sequence.
  • the nucleic acid sequence variants may include deletions, insertions, and/or substitutions at certain positions within the nucleic acid sequence, as compared to a reference sequence.
  • nucleic acid variants may have at least 50% identity to a reference sequence.
  • nucleic acid variants may have at least 80% or at least 90% identity with a reference sequence.
  • the present disclosure is directed to an exemplary dual-specific aptamer comprising an anti-HER2 segment and an anti-CD16 segment.
  • the dual-specific aptamer may specifically bind to a HER2 marker through the anti-HER2 segment and to a CD 16 marker through the anti-CD16 segment.
  • each of the anti-HER2 and anti-CD16 segments may be disposed at either of 5’ arm or 3’ arm of the dual-specific aptamer.
  • the anti-HER2 segment may be disposed at the 5’ arm of the dual-specific aptamer and the anti-CD16 segment may be disposed at the 3’ arm of the dual-specific aptamer.
  • the anti-HER2 segment may be configured to specifically bind to a HER2 marker on a HER2-positive cell
  • the anti-CD16 segment may be configured to specifically bind to a CD16 marker on a cytotoxic effector cell.
  • the dual- specific aptamer may comprise: i) a 5’ segment that may specifically bind to a HER2 marker on a HER2 -positive cell (anti-HER2 segment), ii) a 3’ segment that may specifically bind to a CD 16 marker on a cytotoxic effector cell (anti-CD16 segment), and iii) a linker adapted to attach one end of the 5’ segment to one end of the 3’ segment.
  • “5’ arm” and “3’ arm” may have a same meaning as the terms “5’ segment” and “3’ segment”.
  • “5’ arm” may refer to a portion of the dual-specific aptamer that may be disposed at 5’ end of the dualspecific aptamer, or may constitute at least 10%, at least 20%, at least 30%, at least 40%, and at least 60% of nucleotides disposed near/next to the 5’ end of the dual-specific aptamer.
  • “3’ arm” may refer to a portion of the dual-specific aptamer that may be disposed at 3’ end of the dual-specific aptamer, or may constitute at least 10%, at least 20%, at least 30%, at least 40%, and at least 60% of nucleotides disposed near/next to the 3’ end of the dual-specific aptamer.
  • Linker may refer to all nucleosidic and non-nucleosidic molecules or moieties that may physically couple/connect the 5’ segment/arm to the 3’ segment/arm.
  • the nucleosidic linkers may not be limited to a precise sequence and length.
  • the linker may connect one end of the 5’ segment to one end of the 3’ segment.
  • Non-nucleosidic linkers may include, but are not limited to, glycol (e.g., polyethylene glycol), alkyl and amine linkers.
  • the HER2-positive cell may include a HER2- positive cancer cell.
  • the HER2-positive cancer (cell) may include any cancer (cell) with an upregulated/increased expression of HER2 gene/transcript/protein.
  • a HER2 -positive cancer cell may have an increased number of HER2 receptors/protein (bio)markers on its surface.
  • the HER2-positive cancer may include, but is not limited to, breast cancer, endometrial cancer, bladder carcinomas, gallbladder, anal cancer, colorectal cancer, uterine serous cancer (e.g., uterine papillary serous carcinoma), lung cancer (e.g., non- small-cell lung cancer), liver cancer, kidney cancer, gastroesophageal cancer, extrahepatic cholangio carcinomas, cervical cancer, uterine cancer, testicular cancer, ovarian cancer, pancreatic cancer, and stomach cancer.
  • the cytotoxic effector cell may include NK cells, T-cells, neutrophils, eosinophils lymphokine-activated killer (LAK) cells, and macrophages.
  • the HER2-positive cancer may be HER2-positive breast cancer; thus, the dual-specific aptamer may bind to a HER2 marker/receptor on a HER2-positive breast cancer cell via its anti-HER2 segment which may be disposed at the 5’ arm of the dual-specific aptamer.
  • binding of the dual-specific aptamer to a HER2- positive cancer cell may lead to degradation and/or internalization of the HER2 markers/receptors, prevention from HER2 dimerization with other EGFRs, cell cycle arrest, suppression of cell growth and/or proliferation (e.g., through inhibition of the MAPK (Mitogen-activated protein kinase) and PI3K (Phosphoinositide 3-kinases)/Akt signaling pathways), and cell lysis through the ADCC mechanism.
  • MAPK Mitogen-activated protein kinase
  • PI3K Phosphoinositide 3-kinases
  • Specifically binds and equivalents thereof may describe an aptamer that may bind to or interact with a defined biological element (e.g., a protein marker) but may not bind to or interact with other biological elements.
  • a defined biological element e.g., a protein marker
  • the anti-HER2 segment of the dual- specific aptamer may be adapted to bind specifically to the HER2 marker on surface of the HER2 -positive cancer cells, but not to other expressed markers on surface of the HER2-positive cancer cells or the markers expressed by non-cancerous cells.
  • the anti-HER2 segment may have a nucleic acid sequence with at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% sequence identity to SEQ ID NO: 1.
  • the anti-HER2 segment may be at least 95 to 99.5% identical to SEQ ID NO: 1.
  • the anti-HER2 segment may be at least 98% identical to SEQ ID NO: 1.
  • the anti-CD16 segment may have a nucleic acid sequence selected from the group consisting of SEQ ID NO: 2 and SEQ ID NO: 3.
  • the anti- CD16 segment may have a nucleic acid sequence with at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% sequence identity to any of SEQ ID NOs: 2 and/or 3.
  • the anti-HER2 segment may be at least 95 to 99.5% identical to any of SEQ ID NOs: 2 and/or 3.
  • the anti-HER2 segment may be at least 98% identical to any of SEQ ID NOs: 2 and/or 3.
  • each of the anti-HER2 and the anti-CD16 segments may be disposed at either of the 5’ or the 3’ arms of the dual-specific aptamer.
  • the 5’ arm of the dualspecific aptamer may be occupied with the anti-HER2 segment and the 3’ arm of the dual-specific aptamer may be preferably occupied with the anti-CD16 segment.
  • “identity” an “identical” may refer to a degree of relationship between the sequences, calculated by determining number of matches between residues of two or more nucleic acid strings.
  • Identity may be determined by comparing nucleic acid sequences of two or more polynucleotides. Identity may be obtained by calculating the number of identical matches between two or more sequences (preferably the smaller one) by further considering gap alignments (if any) addressed by a computer program (e.g. "algorithms") or a particular mathematical model.
  • the “% identity” applied to two or more polynucleotide sequences may refer to a percentage of residues (i.e., nucleic acid residues) in a candidate nucleic acid sequence that may be identical with the residues in a second nucleic acid sequence after aligning the sequences and gap alignment, if necessary, to achieve a maximum percent identity.
  • Alignment methods and computer programs configured for alignment and/or calculating identity may be utilized that are known in the art. It may be understood in the art that identity or percent identity may differ in value due to penalties and gaps introduced in the calculation. Generally, variants of a particular polynucleotide (i.e., a reference polynucleotide) may have at least 40% to at least 99%, but less than 100%, sequence identity to the reference polynucleotide. In one or more exemplary embodiments, length of a sequence aligned for comparison purposes may differ from at least 30% to 100% of the length of the reference sequence. The residues at corresponding positions may then be compared.
  • the molecules may be identical at a determined position, when that position in a first sequence string is occupied by the same residue as the corresponding position in a second sequence.
  • the percent identity between the two or more sequences may be a function of the total number of identical positions within the sequences. It may be understood that the number of gaps and length of each gap may also be considered for optimal alignment of the two or more sequences.
  • the dual- specific aptamer may further include a linker between the anti-HER2 and the anti-CD16 segments or the 5’ and the 3’ segments.
  • the linker may be a nucleic acid linker including a single-stranded and/or a double- stranded nucleic acid linker.
  • the nucleic acid linker may help the dual- specific aptamer to fold into a correct conformation/tertiary structure.
  • the nucleic acid linker may be selected from a wide variety of nucleic acid sequences having different nucleotide contents.
  • the nucleic acid linker may be a poly- Adenosine/Adenine (A) sequence ranging from 0 to 40 Adenine nucleotides.
  • the nucleic acid linker may have a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 4, 5 and 6; said nucleic acid sequence may have at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or 100% to SEQ ID NOs: 4, 5 and 6.
  • the nucleic acid linker may be double- stranded and may include a poly- A sequence ranging from 0 to 40 Adenine nucleotides that may be hybridized to a complementary poly- Thymidine (T) sequence.
  • the poly-A sequence of the double- stranded nucleic acid linker may have the nucleic acid sequence set forth in SEQ ID NOs: 4, 5 and 6, or a nucleic acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, or 100% sequence identity to SEQ ID NOs: 4, 5 and 6.
  • the single-stranded nucleic acid linker may include the poly-A sequence set forth in SEQ ID NO: 6.
  • the double-stranded nucleic acid linker may include the poly-A sequence set forth in SEQ ID NO: 6 that may be hybridized to the poly-T sequence set forth in SEQ ID NO: 7. Content and length of nucleic acid linkers may have a significant effect on binding affinity and binding durability of the dual-specific aptamer to both of the HER2 and CD 16 markers.
  • various bivalent/dual-specific aptamers including anti-HER2 and anti-CD16 segments may be designed based on different criteria including, but not limited to, position and content of each of the anti-HER2 and anti-CD16 segments (disposed either on 5’ or 3’ arms of the bivalent aptamer), presence of a linker, type of the linker (whether nucleosidic or non-nucleosidic), length of the nucleosidic linker, content of the nucleosidic linker, and being double-stranded or single-stranded through the entire length or only at the linker segment.
  • the dual-specific aptamer may have a nucleic acid sequence with at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% sequence identity to any of SEQ ID NOs: 8 to 14.
  • the dual-specific aptamer may be at least 95 to 99.5% identical to any of SEQ ID NOs: 8 to 14.
  • the dual-specific aptamer may be at least 98% identical to any of SEQ ID NOs: 8 to 14.
  • Table 1 below shows a number of dual-specific aptamers (dsAl to dsAlO) that may have an anti-HER2 segment (SEQ ID NO: 1) and an anti-CD16 segment (any of SEQ ID NOs: 2 and 3), consistent with one or more exemplary embodiments of the present disclosure.
  • dsA(l to 10) as used herein may stand for “double-specific aptamer (1 to 10)”; for example, dsAl may refer to “double-specific aptamer (1)”.
  • Dual-specific aptamers (dsAl to dsAlO) against HER2 and CD16 markers, consistent with one or more exemplary embodiments of the present disclosure.
  • the dual-specific aptamers referred to as ds Al to dsA7 may have a single-stranded nucleic acid linker.
  • the dual-specific aptamers referred to as dsA8 to 10 may have a double- stranded nucleic acid linker, in which the poly-A sequence of SEQ ID NO: 6 may be hybridized to the poly-T sequence set forth in SEQ ID NO: 7.
  • the anti-CD16 segment/aptamer and the anti-HER2 segment/aptamer may be disposed at the 5’ arm and the 3’ arm of the dual-specific aptamer, respectively.
  • the anti-HER2 segment/aptamer may be disposed at the 5’ arm thereof and the anti-CD16 segment/aptamer may be disposed at the 3’ arm thereof.
  • the dual-specific aptamer of the present disclosure may have the nucleic acid sequence set forth in SEQ ID NO: 14 and may include any of dsA7 and dsAlO set forth in Table 1. Both of the dsA7 and dsAlO may have a similar nucleic acid sequence as set forth in SEQ ID NO: 14, but differing only in the nucleic acid linker segment.
  • dsA7 may have the single-stranded nucleic acid linker set forth in SEQ ID NO: 6 that may be disclosed as A43 (i.e., Adenosine 43) to A62 of SEQ ID NO: 14; while, dsAlO may have a double-stranded nucleic acid linker that may be obtained from hybridization of said A43 to A62 of SEQ ID NO: 14 to the poly-T sequence set forth in SEQ ID NO: 7.
  • the nucleic acid linker may be adapted to attach/link one end of the anti-HER2 segment to one end of the anti-CD16 segment.
  • the nucleic acid linker may link/attach 3’ end of the anti-CD16 segment to 5’ end of the anti-HER2 segment.
  • the nucleic acid linker may link/attach the 3’ end of the anti-HER2 segment to the 5’ end of the anti-CD16 segment.
  • FIG. 1 and FIG. 2 show flow cytometry binding analysis of each of the dual-specific aptamers (dsAl to dsAlO) to HER2 and CD16 markers/receptors, consistent with one or more exemplary embodiments of the present disclosure.
  • FIG. 1 illustrates predicted secondary structures of the dual-specific aptamers (dsAl to 10) and their corresponding flow cytometry binding analysis after incubation with PBMCs (peripheral blood mononuclear cell) and enriched NK cells, consistent with one or more exemplary embodiments of the present disclosure.
  • PBMCs and NK cell may have CD 16 markers/receptors expressed on their surface.
  • FIG. 2 illustrates the predicted secondary structures of the dual- specific aptamers (ds Al to 10) and their corresponding flow cytometry binding analysis after incubation with SKBR3 cells as HER2 -positive breast cancer cells, consistent with one or more exemplary embodiments of the present disclosure.
  • the dual-specific aptamers referred to as dsA7 and dsAlO may demonstrate a stronger and more durable binding to both of the SKBR3 cells and the PBMCs/NK cells, as compared to other dual-specific aptamers disclosed herein (dsAl to 6, dsA8, and dsA9).
  • dsA7 and dsAlO may have a similar binding performance to binding performance of the anti-HER2 aptamer set forth in SEQ ID NO: 1 and the anti-CD16 aptamer of SEQ ID NO: 3 (i.e. , the monovalent aptamers) that both may have an optimal binding affinity to HER2 and CD 16 markers, respectively (see FIGs. 1 and 2).
  • nucleic acid molecules i.e., dual-specific aptamers
  • a wide variety of nucleic acid molecules having at least two segments with anti-HER2 and anti-CD16 activity may be contemplated to be within the scope of the present disclosure, even if their nucleic acid sequences are not explicitly addressed herein for the sake of conciseness.
  • any polynucleotide comprising insertions and/or additions, substitutions, covalent modifications, and deletions with respect to the nucleic acid sequences described herein, may be included within the scope of this disclosure.
  • the aptamers disclosed in the present disclosure may comprise RNAs alone, DNAs alone, or a combination of DNAs and RNAs.
  • the polynucleotides disclosed herein may comprise a modification or segment (e.g., a sequence) that may lead to a desirable feature, such as increased stability, durability and affinity; and/or an additional moiety for subcellular targeting or tracking, such as a detectable label/tag, etc.
  • exemplary modifications of the polynucleotides disclosed herein may include, but are not limited to, modifications that may provide other chemical groups having or incorporating additional charge, hydrophobicity, polarizability, electrostatic interaction, hydrogen bonding, and fluxionality to the polynucleotide bases or to the polynucleotide as a whole.
  • modifications may provide nuclease-resistant oligonucleotides; such modifications may include one or more substituted inter-nucleotide linkages, altered bases, altered sugars, and a combinations thereof.
  • Modifications may further include, but are not limited to, 5’-position pyrimidine modifications, 2'-position sugar modifications, modifications at exocyclic amines, 8-position purine modifications, substitution of 5-bromo or 5-iodo-uracil, and 4- thiouridine substitution, phosphorothioate or alkyl phosphate modifications, methylations, backbone modifications, and unusual base-pairing combinations such as isoguanidine and isobases isocytidine.
  • Modifications may further comprise 5’ and 3’ modifications such as capping.
  • Non-natural nucleotide may refer to an artificially-constructed nucleotide that may resemble, in chemical properties and/or structure, to natural nucleotide.
  • Examples of the non-natural nucleotide may include abasic nucleoside, arabinonucleoside, 2’-deoxyuridine, a-deoxyribonucleoside, P-L-deoxyribonucleoside, and other glycosylated nucleosides.
  • the glycosylated nucleosides may include glycosylated nucleosides having substituted pentose (2’-O-methylribose, 2’-deoxy-2’-fluororibose, 3’-O-methyl ribose, or 1’, 2’ -deoxyribose), arabinose, substituted arabinose sugar, substituted hexose, or alpha anomer.
  • the non-natural nucleoside may further include an artificially constructed base analog or an artificially chemically modified base.
  • Examples of the “base analog” may include a 2-oxo(lH)- pyridin-3-yl group, a 5-substituted 2-oxo(lH)-pyridin-3-yl group, a 2-amino-6-(2-thiazolyl)purin-9- yl group, and a 2-amino-6-(2-oxazolyl)purin-9-yl group.
  • Examples of the modified base may include modified pyrimidine (e.g., 5-hydroxycytosine, 5-fluorouracil and 4-thiouracil), modified purine (e.g., 6-methyladenine and 6-thioguanosine), and other heterocyclic bases.
  • aptamers may have a sufficient capacity to form various nucleic acid primary, secondary (two-dimensional), and tertiary (three-dimensional) structures.
  • aptamers may comprise motifs and structures that may be involved in non-Watson-Crick type interactions; these motifs and structures may include, but are not limited to, symmetric and asymmetric bulges, hairpin loops, pseudoknots, and myriad combinations of pseudoknots.
  • aptamers may be generated using a technique known as “systematic evolution of ligands by exponential enrichment (SELEX)”.
  • SELEX may comprise selection of aptamers on whole cells (“cell SELEX”) or on isolated recombinant protein (“filter SELEX”).
  • filter SELEX may be a method for in vitro evolution of highly specific nucleic acid molecules (i.e., aptamers) against target molecules.
  • Each SELEX-identified nucleic acid ligand (i.e., each aptamer) may be a specific ligand of a given target compound or molecule.
  • SELEX may be based on nucleic acids capability to form a variety of secondary and tertiary structures.
  • the chemical versatility of the nucleic acid monomers may enable nucleic acid molecules to form specific binding interactions with almost any chemical or biological compound. Molecules having any size or composition may be used as targets.
  • SELEX process may start with a pool of single- stranded oligonucleotides or a large library having randomized sequences.
  • the oligonucleotides may include modified or unmodified RNA, DNA, or DNA/RNA hybrids.
  • the library may comprise 100% random or partially random oligonucleotides, random oligonucleotides having one or more fixed/conserved sequence(s) within the randomized sequences or at their 5' and/or 3' ends shared by all oligonucleotides of the pool.
  • Fixed sequences may comprise promoter sequences for RNA polymerases, hybridization sites for PCR (polymerase chain reaction) primers, homopolymeric sequences, restriction sites, selective binding sites to affinity columns, catalytic cores, and other sequences configured for sequencing and/or cloning.
  • conserveed sequences may comprise sequences, other than said fixed sequences, shared by a number of aptamers that may bind to a same target.
  • the pool of oligonucleotides may preferably have both of the randomized sequences and the fixed sequences requisite for efficient amplification or production. Meanwhile, the oligonucleotides may have fixed terminal flanks at 5' and 3' ends of a region with 30-50 random nucleotides.
  • the randomized nucleotides may be produced by chemical synthesis or by size selection from randomly cleaved cellular nucleic acids.
  • the random portion of the oligonucleotides may include any length and any type of RNAs and/or DNAs, and any modified or artificial nucleotides.
  • random oligonucleotides may be synthesized using solid-phase oligonucleotide synthesis techniques, or solution-phase methods, such as triester synthesis methods known in the art. Automated DNA synthesis techniques may yield 1014-1016 individual oligonucleotides that may be sufficient for most of the SELEX experiments.
  • SELEX procedures may preferably be initiated with polynucleotides having a random segment ranging from about 20 to about 50 nucleotides.
  • any of the nucleic acid sequences disclosed herein may also be prepared synthetically, preferably using a commercially available poly/oligo-nucleotide synthesizer.
  • Methods of synthetic oligonucleotide synthesis include, but are not limited to solid-phase oligonucleotide synthesis, liquid-phase oligonucleotide synthesis, and other techniques known in the art.
  • the present disclosure further relates to an exemplary composition comprising the aforementioned dual-specific aptamer(s).
  • the exemplary composition may include a dual-specific aptamer having a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 8 to 14 or variants thereof.
  • the exemplary composition may include any of the dual- specific aptamers referred to as dsAl to dsAlO within the present disclosure (Table 1).
  • said composition may comprise any of the aforementioned dsA7 and dsAlO dualspecific aptamers.
  • composition may comprise the dual-specific aptamer set forth in SEQ ID NO: 14, or dual-specific aptamers having at least 60%, at least 70%, at least 80%, at least 90, at least 95%, or at least 99.5% sequence identity to SEQ ID NO: 14.
  • the present disclosure may be directed to an exemplary pharmaceutical composition
  • an exemplary pharmaceutical composition comprising a dual-specific aptamer having the nucleic acid sequence selected from the group consisting of SEQ ID NOs: 8 to 14 or variants thereof, and optionally, a pharmaceutically acceptable/effective carrier and/or excipient.
  • an exemplary pharmaceutical composition may include any of the dual-specific aptamers referred to as dsAl to dsAlO within the present disclosure (Table 1).
  • an exemplary pharmaceutical composition may comprise any of the aforementioned dsA7 and dsAlO dual-specific aptamers.
  • an exemplary pharmaceutical composition may preferably comprise the dual-specific aptamer set forth in SEQ ID NO: 14 or the dual-specific aptamers having at least 60%, at least 70%, at least 80%, at least 90, at least 95%, or at least 99.5% sequence identity to SEQ ID NO: 14.
  • a pharmaceutical composition may be effective for treating all or a wide range of HER2 -positive cancers in which tumor/cancer cells may overexpress HER2 marker/receptor (i.e., may generate an increased level of HER2 gene/RNA transcript/protein).
  • an exemplary pharmaceutical composition may be useful for treating cancer diseases including, but not limited to, breast cancer, endometrial cancer, bladder carcinomas, gallbladder, anal cancer, colorectal cancer, uterine serous cancer (e.g., uterine papillary serous carcinoma), lung cancer (e.g., non- small -cell lung cancer), liver cancer, kidney cancer, gastroesophageal cancer, extrahepatic cholangio carcinomas, cervical cancer, uterine cancer, testicular cancer, ovarian cancer, pancreatic cancer, stomach cancer, etc.
  • cancer diseases including, but not limited to, breast cancer, endometrial cancer, bladder carcinomas, gallbladder, anal cancer, colorectal cancer, uterine serous cancer (e.g., uterine papillary serous carcinoma), lung cancer (e.g., non- small -cell lung cancer), liver cancer, kidney cancer, gastroesophageal cancer, extrahepatic cholangio carcinomas, cervical cancer, uterine cancer, testicular cancer
  • Said pharmaceutical composition may also be effective for treating other medical conditions associated with HER2 marker/receptor dysregulation, e.g., overexpression.
  • medical conditions may include, but are not limited to, restenosis, arthritis, schizophrenia, and hyperproliferative diseases such as psoriasis.
  • said pharmaceutical composition may be used for treating HER2-positive breast cancer. It is to be understood that the pharmaceutical composition disclosed herein may be administered alone or in combination with anti-HER2 antibodies, chemotherapy, radiotherapy, etc. In an exemplary embodiment, the pharmaceutical composition may eliminate or suppress HER2-overexpressing cancer cells (e.g., HER2-positive breast cancer cells) by binding, specifically and concurrently, to both of HER2 marker(s) expressed by cancerous cells and CD 16 marker(s)/receptor(s) on cytotoxic effector cells.
  • HER2-overexpressing cancer cells e.g., HER2-positive breast cancer cells
  • the pharmaceutical composition may lead to degradation and/or internalization of the HER2 marker s/recep tors, prevention from HER2 dimerization with other EGFRs, cell cycle arrest, suppression of cell growth and proliferation (e.g., through inhibition of the MAPK (Mitogen-activated protein kinase) and/or PI3K (Phosphoinositide 3-kinases)/Akt signaling pathways), and cell lysis through the ADCC mechanism.
  • MAPK Mitogen-activated protein kinase
  • PI3K Phosphoinositide 3-kinases
  • Treatment may refer to partially or completely ameliorating, alleviating, delaying onset of, improving, inhibiting progression of, relieving, reducing incidence of, and/or reducing severity of features or symptom(s) of a disease.
  • “treating” breast cancer may refer to prolonging lifespan (increase the survival rate) of patients, reducing symptoms and features associate with the disease, delaying or preventing onset of the disease, reducing severity of the disease, etc. It is to be understood that treatment may be provided to a subject who may not exhibit symptoms of a disorder, disease, and/or condition with the aim of decreasing the risk of increasing pathology associated with the disorder, disease, and/or condition.
  • an exemplary pharmaceutical composition may further comprise a pharmaceutically acceptable excipient, stabilizer, carrier or any additional element that may provide advantageous properties for administration or activity of the pharmaceutical composition (e.g., administration to a human subject in need thereof).
  • “Pharmaceutically acceptable excipient and/or carrier” may refer to an excipient and/or a carrier that may be physiologically and/or pharmacologically compatible with an active ingredient or a subject.
  • pH regulators may comprise, but are not limited to, buffers, surfactants (e.g., anion surfactants, cation surfactants, or non-ionic surfactants), and ionic strength enhancers such as NaCl.
  • surfactants e.g., anion surfactants, cation surfactants, or non-ionic surfactants
  • ionic strength enhancers such as NaCl.
  • pharmaceutical acceptable carriers may include, but are not limited to, saline, sterile water, condensation product of castor oil and ethylene oxide, glucose, lower alcohol (e.g., Ci-4 alcohol), liquid acid, oil (e.g., peanut oil, corn oil, sesame oil), and an emulsifier (e.g., diglyceride, fatty acid monoglyceride or phospholipid such as lecithin, polyvinyl pyrrolidone, polyalkylene glycol, sodium alginate, ethylene glycol and the like).
  • the exemplary pharmaceutically acceptable carriers may further comprise a preservative, an adjuvant, a moistening agent, a stabilizer, a penetration enhancer, an emulsifier, etc.
  • an exemplary pharmaceutical composition may be sterile. Meanwhile, the exemplary pharmaceutical composition may have a controlled and maintained viscosity by using a suitable excipient or solvent.
  • An exemplary pharmaceutical composition may be administered to a patient in need thereof through approaches including, but not limited to injection, oral administration, etc.
  • the pharmaceutical composition may be administered in form of a unit dose.
  • the dose of an exemplary pharmaceutical composition may be essential for treating or preventing a specific condition or symptom and may depend on the severity of the condition or symptom to be treated, administration route, gender, body weight, age, and general healthy condition of a subject, and the like. The amount/dose may be determined by a physician based on practical conditions.
  • Another exemplary aspect of the present disclosure may relate to a method for treating HER2-positive cancers (mentioned earlier in this section) in a subject in need thereof.
  • the method may comprise administering a therapeutically effective amount of the disclosed dual-specific aptamer or the pharmaceutical composition comprising the same to a patient in need thereof.
  • the method may lead to lysis or growth-arrest of the HER2 -positive cancer cells.
  • the method may include administering a therapeutically effective amount of any of the dual-specific aptamers referred to as ds Al to dsAlO in the present disclosure (Table 1) to a patient in need thereof.
  • the dualspecific aptamer may comprise any of the aforementioned dsA7 and dsAlO dual-specific aptamers.
  • the dual-specific aptamer may comprise the dual-specific aptamer set forth in SEQ ID NO: 14 or the dual-specific aptamers having at least 60%, at least 70%, at least 80%, at least 90, at least 95%, or at least 99.5% sequence identity to SEQ ID NO: 14.
  • the method may include administering a therapeutically effective amount of the dual-specific aptamer to treat other medical conditions associated with HER2 marker/receptor dysregulation, e.g., overexpression.
  • medical conditions may include, but are not limited to, restenosis, arthritis, schizophrenia, and hyperproliferative diseases such as psoriasis.
  • the dual-specific aptamer may be used for treating HER2- positive breast cancer.
  • FIG. 3A shows cytotoxic effect of the dsA7 and dsAlO dual-specific aptamers (SEQ ID NO: 14) on SKBR3 cells lysis (as HER2-positive breast cancer cells) in a 2D (two- dimensional) culture system comprising PBMCs and the enriched NK cells (as CD 16-positive cells), consistent with one or more exemplary embodiments of the present disclosure.
  • FIG. 3A is discussed in detail in the “EXAMPLES” section; briefly, based on FIG.
  • both of the dsA7 and the dsAlO dual-specific aptamers may have a similar performance as of commercial anti-HER2 antibody (Trastuzumab) in mediating ADCC mechanism against SKBR3 cells (as HER2-positive breast cancer cells) and SKBR3 cell lysis.
  • FIG. 4A and FIG. 4B show the effect of dsA7 dual-specific aptamer (SEQ ID NO: 14) on SKBR3 cells proliferation, consistent with one or more exemplary embodiments of the present disclosure. In particular, FIG.
  • FIG. 4A shows inhibitory effect of a fixed concentration (10 nM) of the dsA7 dual-specific aptamer (SEQ ID NO: 14) on SKBR3 and MDAMB231 cells proliferation, compared to the inhibitory effect of Trastuzumab and the non-binding NC aptamer, consistent with one or more exemplary embodiments of the present disclosure.
  • FIG. 4B shows inhibitory effect of different concentrations (0.25, 2, and 10 nM) of the dsA7 dual-specific aptamer (SEQ ID NO: 14) on the SKBR3 cells proliferation, compared to the same concentrations of Trastuzumab, consistent with one or more exemplary embodiments of the present disclosure.
  • the dsA7 dual-specific aptamer may be capable of inhibiting SKBR3 cells proliferation, similar to antiproliferation activity of Trastuzumab. Based on FIG. 3 and FIG. 4A and FIG. 4B, it may be concluded that an effective amount of the dsA7 and dsAlO dual-specific aptamers may be effective for eliminating, suppressing, and/or inhibiting HER2-positive breast cancer cells.
  • “Therapeutically effective amount” may refer to an amount of the dual-specific aptamer or the pharmaceutical composition comprising the same that may induce a biological response in a subject including, but not limited to, tissue, system, animal, and human. “Therapeutically effective amount” may further refer to any amount that, in comparison to a reference subject who has not received that amount of the dual-specific aptamer, may decrease a rate of advancement of a disorder or disease, and may improve treatment, prevention, amelioration, or healing of a disorder, disease, or a side effect. “Therapeutically effective amount” may also comprise any amount that may be effective for improving normal physiological function of a subject. [00082]
  • the nucleic acid molecules/sequences described above may be non-naturally occurring. Exemplary embodiments may provide the nucleic acid molecules preferably in synthetic, recombinant, isolated, and/or purified form.
  • Synthetic may refer to polynucleotides prepared, produced, and/or manufactured by the hand of man. Synthesis of polynucleotides of the exemplary embodiments may be enzymatic or chemical.
  • Example 1 Selection and characterization of primary anti-HER2 and anti-CD16 aptamers to be incorporated in the dual-specific aptamer
  • a number of primary anti-HER2 and anti-CD16 aptamers were selected as possible candidates to be incorporated in the dual-specific aptamer. Meanwhile, a random singlestranded DNA with the lowest free energy (dG) was obtained as a non-binding negative control (NC) aptamer using an online tool.
  • the primary anti-HER2 aptamers include SEQ ID NOs: 1, 15 and 16, and the primary anti-CD16 aptamer includes SEQ ID NO: 3.
  • a truncated form of said primary antiCD 16 was also considered as a candidate to be used in designing the dual-specific aptamer; the truncated anti-CD16 segment’s nucleic acid sequence is set forth in SEQ ID NO: 2.
  • the primary aptamers set forth in SEQ ID NOs: 1, 3, 15 and 16, and the non-binding NC aptamer were conjugated to a biotin moiety (the anti-HER2 aptamers and the non-binding NC aptamer were 5 ’-biotinylated and the anti-CD16 aptamer was 3 ’-biotinylated) and HPLC (high performance liquid chromatography) -purified.
  • Biotinylation was performed with the purpose of FETC (fluorescein isothiocyanate)- labeling and flow cytometry analysis. Binding activity of the aforementioned primary aptamers to their targets, i.e., CD16 and HER2, was evaluated on HER2-positive and CD16-positive cells. Therefore, SKBR3 (as HER2-positive breast cancer cells) and MDAMD231 (having low expression of HER2) cell lines were cultured in 10% FBS (fetal bovine serum)-supplemented DMEM (Dulbecco's Modified Eagle's medium) and were incubated at 37 °C with 5% CO2.
  • FBS fetal bovine serum
  • DMEM Dulbecco's Modified Eagle's medium
  • peripheral blood mononuclear cells PBMCs
  • PBMCs peripheral blood mononuclear cells
  • NK Natural Killer
  • MCS magnetic-activated cell sorting
  • binding properties of the primary anti-HER2 aptamers (SEQ ID NOs: 1, 15 and 16) to HER2 and the primary anti-CD16 aptamer (SEQ ID NO: 3) to CD16 was evaluated by flow cytometry.
  • the biotinylated primary aptamers (SEQ ID NOs: 1, 3, 15 and 16) were initially conjugated with streptavidin (SA)-FITC.
  • SKBR3, MDAMB231, PBMCs and the isolated/enriched NK cells were detached, washed with PBS (phosphate buffer saline), and were counted instantly using a Neobar lam; a ratio of dead to living cells was calculated for each cell-type based on the enumeration results.
  • the cells were washed again with a washing buffer (PBS containing 0.1% BSA).
  • the FITC-labeled primary aptamers SEQ ID NOs: 1, 3, 15 and 16
  • the FITC-labeled nonbinding NC aptamer were prepared at a concentration of 1000 nM in separate empty microtubes and heated at 95 ° C for 5 minutes, followed by cooling at 25-37 0 C for further refolding.
  • the SKBR3 and MDAMB231 cells were incubated with said FITC-labeled primary anti-HER2 aptamers, and PBMCs and the enriched NK cells were incubated with FITC-labeled anti-CD16 aptamer at 25° C for 30 minutes; both in a final volume of 100 pL binding buffer (the washing buffer containing 5 mM MgCh).
  • a phycoerythrin (PE)-labeled anti- CD16 monoclonal antibody 3G8 antibody was used as a flow cytometry control (reference).
  • the incubated binding reactions were then washed gently with a binding solution and centrifuged.
  • the centrifuged cells were resuspended in 100 pL of the binding buffer containing 10 pL of the SA-FETC solution to make sure all of the biotinylated primary aptamers are FITC-labeled.
  • the incubated binding reactions were washed again with the binding buffer and were centrifuged.
  • the centrifuged cells were resuspended in 500 pL of said binding buffer.
  • the incubated cells were analyzed by flow cytometry to evaluate binding properties of the primary aptamers.
  • the mean fluorescence intensity (MFI) of the cells (SKBR3, MDAMB231,
  • PBMCs, and NK cells bound to the corresponding primary aptamers was used as a reference to evaluate and interpret the specific binding performance of the same.
  • FIG. 5 illustrates flow cytometry binding analysis of the primary anti-HER2 aptamers set forth in SEQ ID NOs: 1, 15 and 16 (502, 504 and 506, respectively) and the non-binding NC aptamer (508) to the SKBR3 and MDAMB231 cells, consistent with one or more exemplary embodiments of the present disclosure.
  • the primary anti-HER2 aptamer set forth in SEQ ID NO: 1 (502) demonstrated a robust binding to the SKBR3 cells, as compared to SEQ ID NOs: 15 (504) and 16 (506), while having no significant binding to the MDAMB231 cells. Therefore, the primary anti-HER2 aptamer of SEQ ID NO: 1 was selected to be incorporated in the dual-specific aptamer.
  • FIG. 6A illustrates flow cytometry binding analysis of the primary anti-CD16 aptamer set forth in SEQ ID NO: 3 (602) and the non-binding NC aptamer (604) to the PBMCs, as compared to the 3G8 antibody (606) and an isotype control (608), consistent with one or more exemplary embodiments of the present disclosure.
  • FIG. 6B illustrates flow cytometry binding analysis of the primary anti-CD16 aptamer set forth in SEQ ID NO: 3 (610) and the non-binding NC aptamer (612) to the enriched NK cells, as compared to the 3G8 antibody (614) and an isotype control (616), consistent with one or more exemplary embodiments of the present disclosure. As illustrated in FIGs.
  • the primary anti-CD16 aptamer of SEQ ID NO: 3 demonstrated a strong and specific binding to the PBMCs (602) and the enriched NK cells (610). Meanwhile, the primary anti-CD16 aptamer of SEQ ID NO: 3 (602 and 610) showed a binding performance similar to that of the 3G8 antibody (606 and 614) to both of the PBMCs and the enriched NK cells.
  • the isotype control i.e., an antibody used against an antigen not found on the sample cells was used to ensure that the obtained MFIs are due to specific binding of the 3G8 antibody to the target cells.
  • the obtained results may approve the binding performance of the primary anti-HER2 aptamer of SEQ ID NO: 1 and the primary anti-CD16 aptamer of SEQ ID NO: 3, and may demonstrate that these primary aptamers may be useful for designing the dual- specific aptamer.
  • Example 2 Designing a plurality of dual-specific aptamers against both of the HERZ and CD16 markers/receptors
  • each of the plurality of dual-specific aptamers may include an anti-HER2 segment and an anti-CD16 segment, wherein the anti-HER2 and the anti-CD16 segments may be disposed at either of the 5’ or the 3’ arm of the dual-specific aptamer.
  • Anti-HER2 segment” and “anti-CD16 segment” as used herein may refer to “anti-HER2 aptamer” and “antiCD 16 aptamer,” respectively.
  • the dual-specific aptamer may be capable of binding, specifically and concurrently, to a HER2 marker through the anti-HER2 segment and to a CD 16 marker through the anti-CD16 segment.
  • the criteria of designing the dual-specific aptamer(s) described in the present disclosure may include, but is not limited to: truncation, orientation and position of the primary aptamers on the dual-specific apatmer; and the nucleic acid linker’s content, length and number of strands (either single- or double-stranded).
  • the nucleic acid linkers may be selected from any of a single- or double- stranded DNA/RNA with a wide variety of nucleotide contents and lengths, ranging from 7 to 20 nucleotides.
  • Final length of the designed dual-specific aptamer(s) may vary from 76 to 100 nucleotides.
  • each of the plurality of dual-specific aptamers were synthesized in both of biotinylated (5’ or 3 ’ -biotinylated) and non-biotinylated forms; the biotinylated form may be used for FITC-labeling and flow cytometry analysis.
  • the anti-CD16 segment in the dual-specific aptamer may be configured to trigger an ADCC (aptamer-dependent cell-mediated cytotoxicity) mechanism against HER2-positive cancer cells. Therefore, it was predicted that length of the nucleic acid linkers may have a significant effect on activation of the ADCC mechanism by the dual- specific aptamer.
  • the optimal length of the linker may be determined based on a spanning distance between the complementarity-determining regions (CDRs) of the anti- HER2 antibodies and their Fc-binding domain in a hinge region thereof. This distance has been estimated to be about 65 A; taking this distance into account, different linkers having lengths ranging from 0 to 128 A were considered in designing the plurality of dual-specific aptamers.
  • Table 1 shown in the “DETAILED DESCRIPION” section represents the plurality of designed and tested dualspecific aptamers (dsAl to dsAlO), consistent with one or more exemplary embodiments of the present disclosure.
  • the linker length in each of the disclosed dual-specific aptamers are set forth in Table 3 below.
  • oligo-dT deoxy Thymidine/Thymine sequence
  • A poly-Adenosine
  • Example 3 Evaluating binding properties of the plurality of dual-specific aptamers to HER2 and CD16 markers/receptors
  • binding properties of the plurality of dual-specific aptamers, set forth in Table 1, to HER2 and CD16 markers were evaluated by flow cytometry analysis.
  • biotinylated forms of the dual-specific aptamers set forth in Table 1 were conjugated with SA-FITC conjugates.
  • the detached cancer cells of SKBR3 and MDAMB231, the PBMCs, and the enriched NK cells were washed with PBS and counted instantly using the Neobar lam. Then, a ratio of dead to living cells was calculated based on the enumeration results.
  • the detached cells were further washed with the washing buffer (PBS containing 0.1% BSA).
  • the FITC-labeled dualspecific aptamers (dsAl to dsAlO) and the FITC-labeled non-binding NC aptamer were prepared, at a concentration of 1000 nM, in separate empty microtubes.
  • the FITC-labeled dual specific aptamers of dsAl to dsAlO were heated at 95 0 C for 5 minutes, followed by cooling at 25 to 37 ° C for aptamer refolding.
  • the cells i.e., the SKBR3, MDAMB231, PBMCs, and the enriched NK cells
  • the cells were incubated with the FITC-labeled dual-specific aptamers at 25° C for 30 minutes in 100 pL of the binding buffer (the washing buffer containing 5 mM MgCh). Then, the incubated binding reactions were gently washed with the binding buffer and centrifuged. The centrifuged cells were resuspended in 100 pL of the binding buffer containing 10 pL of the SA-FITC solution. After 15 minutes of incubation at 25° C, the incubated binding reactions were again washed with the binding buffer, centrifuged, and resuspended in 500 pL of the binding buffer.
  • the incubated cells were analyzed by flow cytometry to evaluate binding properties of said dual-specific aptamers (dsAl to dsAlO).
  • MFIs of the incubated SKBR3 and MDAMB231 cells with the FITC-labeled dual-specific aptamers (ds Al to dsAlO) was considered as a reference to evaluate and interpret their specific binding performance and binding efficacy.
  • the PE-labeled 3G8 antibody was used as a flow cytometry control (reference) to determine purity of CD16-positive cells.
  • FIG. 1 illustrates predicted secondary structures of the dual-specific aptamers (dsAl to 10) and their corresponding flow cytometry binding analysis after incubation with the PBMCs and the enriched NK cells, consistent with one or more exemplary embodiments of the present disclosure.
  • the flow cytometry binding analysis of the non -binding NC aptamer and the PE-labeled 3G8 antibody are also provided as controls/references in FIG. 1.
  • FIG. 2 illustrates the predicted secondary structure of the dual-specific aptamers (dsAl to 10) and their corresponding flow cytometry binding analysis after incubation with the SKBR3 cells as HER2 -positive breast cancer cells, consistent with one or more exemplary embodiments of the present disclosure.
  • the cytometry binding analysis of the non-binding NC aptamer is also shown in FIG. 2. It is to be understood that the predicted secondary structures demonstrated in FIG. 1 and FIG. 2 may be indefinite and may vary based on different biological and/or physiological conditions. Particularly, in case of those dualspecific aptamers having double- stranded nucleic acid linkers (as set forth in Table 1 and 3), the exact secondary structure may not be predictable.
  • dsA7 and dsAlO demonstrated a robust binding to both of the SKBR3 cells (i.e. , the HER2 markers on SKBR3 cells surface) and the enriched NK cells or PBMCs as compared to the rest of dual-specific aptamers set forth in Table 1. Meanwhile, no significant unspecific binding was observed. As shown in these figures, dsA7 and dsAlO may have a binding performance similar to that of the primary anti-HER2 and anti-CD16 aptamers set forth in SEQ ID NOs: 1 and 3.
  • dsAlO retained 90.5% and 93.3% of a “primary maximal binding affinity” of the primary aptamers (SEQ ID NOs: 1 and 3) to the SKBR3 and the enriched NK cells, respectively.
  • dsA7 retained 48.5% and 39% of the “primary maximal binding affinity” of the primary aptamers (SEQ ID NOs: 1 and 3) to the SKBR3 and the enriched NK cells, respectively.
  • flow cytometry binding analysis of the FITC-labeled dual-specific aptamers were compared to that of the FITC-labeled non-binding NC aptamer and the isotype control described in “Example 1”. As shown in FIG. 1, flow cytometry binding analysis of the FITC-labeled dual-specific aptamers (dsAl to dsAlO) were also compared to binding performance of the PE-labeled 3G8 antibody as the reference.
  • FIG. 7 shows a comparison of normalized MFI values obtained from the flow cytometry binding analysis of the FITC-labeled dsA7 and dsAlO dual-specific aptamers (SEQ ID NO: 14) to the SKBR3 and the enriched NK cells, consistent with one or more exemplary embodiments of the present disclosure.
  • SEQ ID NO: 14 the following formulae may be used: MFI of a dual specific aptamer — MFI of the nonbinding NC aptamer
  • the normalized MFI was calculated based on incubation of a fixed concentration (1000 nM) of the dsA7 and dsAlO dual-specific aptamers with the SKBR3 and NK cells.
  • the results shown in FIGs. 1 to 3 may further confirm that the dsA7 and dsAlO dual specific aptamers may be suitable candidates for targeting the HER2-overexpressing cancer cells (HER2-positive cancer cells) due to their specific and robust binding to both HER2 and CD16 markers.
  • Example 4 Evaluating cytotoxic effect of the dsA7 and dsAlO dual-specific aptamers by performing ADCC assay
  • cytotoxic effect of the dsA7 and dsAlO dual-specific aptamers, through the ADCC mechanism, was evaluated using a two-dimensional (2D) culture comprising breast cancer cells and enriched NK cells.
  • the ADCC assay may be performed by measuring the amount of Lactate Dehydrogenase (LDH) released from damaged/lysed cells. Therefore, about 104 cells from each of the SKBR3 and MDAMB231 cell lines, having at least 90% viability, were seeded and cultured per each well in a 96-well cell culture microplate using DMEM medium for SKBR3 and RPML1640 for MDAMB231.
  • LDH Lactate Dehydrogenase
  • the culture mediums were removed and the cells were washed once with PBS buffer. Then, 80 pL of DMEM and RPMI-1640 culture mediums, each containing different concentrations of the dsA7 and dsAlO dual-specific aptamers (ranging from 0 to 200 nM) were heated at 95 °C for 5 minutes. The heated culture mediums were cooled at 25 °C, combined withlO pL FBS and added to each well.
  • the “specific cell lysis” was estimated by measuring the amount of LDH released from damaged/lysed cells. For this purpose, cell-free supernatant of the test reactions in each well was separated from the incubated cells by centrifugation. Then, the amount of LDH in the separated cell- free supernatant was measured using a commercial cytotoxicity/LDH assay kit. The obtained signal from a "medium-only sample” was used as background and was subtracted from all measured signals. The following formulae was used to calculate percentage of target cells lysis: sample lysis — spontaneous target cell lysis — spontaneous effector cell lysis
  • FIG. 3A shows cytotoxic effect of the dsA7 and dsAlO dual-specific aptamers (SEQ ID NO: 14) on SKBR3 cells lysis in a 2D culture system comprising the PBMCs and the enriched NK cells, consistent with one or more exemplary embodiments of the present disclosure.
  • the amount of cell lysis in the presence of the dsA7 and dsAlO dual-specific aptamers was compared to: i) the amount of SKBR3 cells lysis in the presence of an anti-HER2 monoclonal antibody (Trastuzumab), as a reference; and ii) the amount of cell lysis in the presence of the non-binding NC aptamer.
  • FIG. 3B shows cytotoxic effect of the dsA7 dual-specific aptamers (SEQ ID NO: 14) on MDAMB231 cells lysis in a 2D culture system comprising the PBMCs and the enriched NK cells, consistent with one or more exemplary embodiments of the present disclosure.
  • the amount of MDAMB231 cells lysis in the presence of the dsA7 dual-specific aptamer was compared to the amount of cell lysis in the presence of the non-binding NC aptamer.
  • ADCC assay results of the dsA7 and dsAlO dualspecific aptamers was similar to that of Trastuzumab antibody. No significant difference was observed between the ADCC assay results of dsA7 and dsAlO. An optimal concentration of the two aptamers led to at least 90% of a maximum cytotoxicity induced by Trastuzumab. As shown in FIGs. 3A and 3B, intensity of the induced cell cytotoxicity by dsA7 and dsAlO was completely dosedependent (up to 150 nM). At higher concentrations of dsA7 and dsAlO, ADCC-mediated cell lysis was significantly decreased.
  • FIG. 8 shows the amount of SKBR3 cells lysis in the presence of the dsA7 dual-specific aptamer (SEQ ID NO: 14) alone and in the presence of a combination of the 3G8 antibody and the dsA7 dual-specific aptamer, consistent with one or more exemplary embodiments of the present disclosure.
  • Example 5 Evaluating ability of the dsA7 dual-specific aptamer to inhibit proliferation of the HER2-overexpressing cells (SKBR3 cells)
  • proliferation inhibition potential of the dsA7 dual-specific aptamer was tested on SKBR3 and MDAMB231 cells, in vitro.
  • 1000 cells from each of the SKBR3 and MDAMB231 cell lines were seeded in each well of a 96-well plate and cultured using DMEM/F12 medium. After 24 h of incubation, the DMEM/F12 medium was removed and 100 pL the DMEM/F12 medium containing 2.5% FBS, in two groups: one comprising different concentrations of the dsA7 dual-specific aptamer and the other comprising Trastuzumab, were added in triplicates to each well.
  • 4A shows inhibitory effect of a fixed concentration (10 nM) of the dsA7 dual-specific aptamer (SEQ ID NO: 14) on SKBR3 and MDAMB231 cells proliferation, as compared to the inhibitory effect of Trastuzumab and the non-binding NC aptamer, consistent with one or more exemplary embodiments of the present disclosure.
  • 10 nM concentration of the dsA7 dual-specific aptamer significantly inhibited proliferation of the SKBR3 cells as compared to the Trastuzumab- treated SKBR3 cells.
  • the MDAMB231 cells were not significantly affected by the dsA7 dual-specific aptamer.
  • FIG. 4B shows inhibitory effect of different concentrations (0.25, 2, and 10 nM) of the dsA7 dual-specific aptamer (SEQ ID NO: 14) on the SKBR3 cells proliferation, as compared to the same concentrations of Trastuzumab, consistent with one or more exemplary embodiments of the present disclosure. Accordingly, referring to FIGs. 4A-B the inhibitory effect of the dsA7 dualspecific aptamer was dose-dependent and no significant difference was observed as compared to Trastuzumab at the specific concentrations shown in FIG. 4B. All experiments, as described herein, were performed in three replicates. Referring to FIG.
  • 4A may refer to a P value ⁇ 0.05, indicating that the dsA7 dual-specific aptamer may significantly inhibit proliferation of the SKBR3 cells; however, it had no significant effect on the MDAMB231 cells proliferation, in vitro. Meanwhile, the inhibitory effect of the dsA7 dual-specific aptamer was directly dose-dependent and was similar and comparable to that of Trastuzumab.

Abstract

La présente invention concerne un aptamère à double spécificité comprenant un segment anti-HER2 disposé au niveau du bras 5', un segment anti-CD16 disposé au niveau du bras 3', et un lieur qui fixe l'extrémité 3' du segment anti-HER2 à l'extrémité 5' du segment anti-CD16. Ledit aptamère à double spécificité est efficace dans le traitement de cancers positifs au HER2 par déclenchement de la cytotoxicité à médiation cellulaire dépendante des aptamères (ADCC).
PCT/IB2021/062450 2021-01-01 2021-12-30 Aptamère à double spécificité déclenchant une cytotoxicité à médiation cellulaire pour lyser des cellules cancéreuses positives au her2 WO2022144815A1 (fr)

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WO2018213791A1 (fr) * 2017-05-18 2018-11-22 Children's National Medical Center Compositions comprenant des aptamères et des charges utiles d'acide nucléique et procédés pour leur utilisation
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