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Sun Q, Zheng S, Tang W, Wang X, Wang Q, Zhang R, Zhang N, Ping W. Prediction of lung adenocarcinoma prognosis and diagnosis with a novel model anchored in circadian clock-related genes. Sci Rep 2024; 14:18202. [PMID: 39107445 PMCID: PMC11303802 DOI: 10.1038/s41598-024-68256-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Lung adenocarcinoma is the most common primary lung cancer seen in the world, and identifying genetic markers is essential for predicting the prognosis of lung adenocarcinoma and improving treatment outcomes. It is well known that alterations in circadian rhythms are associated with a higher risk of cancer. Moreover, circadian rhythms play a regulatory role in the human body. Therefore, studying the changes in circadian rhythms in cancer patients is crucial for optimizing treatment. The gene expression data and clinical data were sourced from TCGA database, and we identified the circadian clock-related genes. We used the obtained TCGA-LUAD data set to build the model, and the other 647 lung adenocarcinoma patients' data were collected from two GEO data sets for external verification. A risk score model for circadian clock-related genes was constructed, based on the identification of 8 genetically significant genes. Based on ROC analyses, the risk model demonstrated a high level of accuracy in predicting the overall survival times of lung adenocarcinoma patients in training folds, as well as external data sets. This study has successfully constructed a risk model for lung adenocarcinoma prognosis, utilizing circadian rhythm as its foundation. This model demonstrates a dependable capacity to forecast the outcome of the disease, which can further guide the relevant mechanism of lung adenocarcinoma and combine behavioral therapy with treatment to optimize treatment decision-making.
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Affiliation(s)
- Qihang Sun
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shubin Zheng
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Tang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoyu Wang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qi Wang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ruijie Zhang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ni Zhang
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Wei Ping
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Penrod NM, Greene CS, Moore JH. Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity. Genome Med 2014; 6:33. [PMID: 24944582 PMCID: PMC4062052 DOI: 10.1186/gm550] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 04/22/2014] [Indexed: 01/05/2023] Open
Abstract
Background Molecularly targeted drugs promise a safer and more effective treatment modality than conventional chemotherapy for cancer patients. However, tumors are dynamic systems that readily adapt to these agents activating alternative survival pathways as they evolve resistant phenotypes. Combination therapies can overcome resistance but finding the optimal combinations efficiently presents a formidable challenge. Here we introduce a new paradigm for the design of combination therapy treatment strategies that exploits the tumor adaptive process to identify context-dependent essential genes as druggable targets. Methods We have developed a framework to mine high-throughput transcriptomic data, based on differential coexpression and Pareto optimization, to investigate drug-induced tumor adaptation. We use this approach to identify tumor-essential genes as druggable candidates. We apply our method to a set of ER+ breast tumor samples, collected before (n = 58) and after (n = 60) neoadjuvant treatment with the aromatase inhibitor letrozole, to prioritize genes as targets for combination therapy with letrozole treatment. We validate letrozole-induced tumor adaptation through coexpression and pathway analyses in an independent data set (n = 18). Results We find pervasive differential coexpression between the untreated and letrozole-treated tumor samples as evidence of letrozole-induced tumor adaptation. Based on patterns of coexpression, we identify ten genes as potential candidates for combination therapy with letrozole including EPCAM, a letrozole-induced essential gene and a target to which drugs have already been developed as cancer therapeutics. Through replication, we validate six letrozole-induced coexpression relationships and confirm the epithelial-to-mesenchymal transition as a process that is upregulated in the residual tumor samples following letrozole treatment. Conclusions To derive the greatest benefit from molecularly targeted drugs it is critical to design combination treatment strategies rationally. Incorporating knowledge of the tumor adaptation process into the design provides an opportunity to match targeted drugs to the evolving tumor phenotype and surmount resistance.
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Affiliation(s)
- Nadia M Penrod
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth College, HB7937 One Medical Center Dr, Lebanon NH 03766, USA
| | - Casey S Greene
- Department of Genetics, Geisel School of Medicine at Dartmouth College, HB7937 One Medical Center Dr, Lebanon NH 03766, USA ; Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth College, HB7937 One Medical Center Dr, Lebanon NH 03766, USA
| | - Jason H Moore
- Department of Genetics, Geisel School of Medicine at Dartmouth College, HB7937 One Medical Center Dr, Lebanon NH 03766, USA ; Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth College, HB7937 One Medical Center Dr, Lebanon NH 03766, USA
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Kwok HF, Buick RJ, Kuehn D, Gormley JA, Doherty D, Jaquin TJ, McClurg A, Ward C, Byrne T, Jaworski J, Leung KL, Snoddy P, McAnally C, Burden RE, Gray B, Lowry J, Sermadiras I, Gruszka N, Courtenay-Luck N, Kissenpfennig A, Scott CJ, Johnston JA, Olwill SA. Antibody targeting of Cathepsin S induces antibody-dependent cellular cytotoxicity. Mol Cancer 2011; 10:147. [PMID: 22168338 PMCID: PMC3267679 DOI: 10.1186/1476-4598-10-147] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 12/14/2011] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Proteolytic enzymes have been implicated in driving tumor progression by means of their cancer cell microenvironment activity where they promote proliferation, differentiation, apoptosis, migration, and invasion. Therapeutic strategies have focused on attenuating their activity using small molecule inhibitors, but the association of proteases with the cell surface during cancer progression opens up the possibility of targeting these using antibody dependent cellular cytotoxicity (ADCC). Cathepsin S is a lysosomal cysteine protease that promotes the growth and invasion of tumour and endothelial cells during cancer progression. Our analysis of colorectal cancer patient biopsies shows that cathepsin S associates with the cell membrane indicating a potential for ADCC targeting. RESULTS Here we report the cell surface characterization of cathepsin S and the development of a humanized antibody (Fsn0503h) with immune effector function and a stable in vivo half-life of 274 hours. Cathepsin S is expressed on the surface of tumor cells representative of colorectal and pancreatic cancer (23%-79% positive expression). Furthermore the binding of Fsn0503h to surface associated cathepsin S results in natural killer (NK) cell targeted tumor killing. In a colorectal cancer model Fsn0503h elicits a 22% cytotoxic effect. CONCLUSIONS This data highlights the potential to target cell surface associated enzymes, such as cathepsin S, as therapeutic targets using antibodies capable of elicitingADCC in tumor cells.
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Affiliation(s)
- Hang Fai Kwok
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Richard J Buick
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Diana Kuehn
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Julie A Gormley
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Declan Doherty
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Thomas J Jaquin
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Angela McClurg
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Claire Ward
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Teresa Byrne
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Jacob Jaworski
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Ka Lai Leung
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Philip Snoddy
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Christine McAnally
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Roberta E Burden
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
- Molecular Therapeutics, School of Pharmacy, Queen's University Belfast, BT9 7BL, Northern Ireland
| | - Breena Gray
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Jenny Lowry
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Isabelle Sermadiras
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Natalia Gruszka
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Nigel Courtenay-Luck
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
| | - Adrien Kissenpfennig
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL, Northern Ireland
| | - Christopher J Scott
- Molecular Therapeutics, School of Pharmacy, Queen's University Belfast, BT9 7BL, Northern Ireland
| | - James A Johnston
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, BT9 7BL, Northern Ireland
| | - Shane A Olwill
- Fusion Antibodies Ltd., Springbank Ind. Est. Belfast, BT17 0QL, Northern Ireland
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Münz M, Murr A, Kvesic M, Rau D, Mangold S, Pflanz S, Lumsden J, Volkland J, Fagerberg J, Riethmüller G, Rüttinger D, Kufer P, Baeuerle PA, Raum T. Side-by-side analysis of five clinically tested anti-EpCAM monoclonal antibodies. Cancer Cell Int 2010; 10:44. [PMID: 21044305 PMCID: PMC2989956 DOI: 10.1186/1475-2867-10-44] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 11/02/2010] [Indexed: 12/12/2022] Open
Abstract
Background Epithelial cell adhesion molecule (EpCAM) is frequently and highly expressed on human carcinomas. The emerging role of EpCAM as a signalling receptor and activator of the wnt pathway, and its expression on tumor-initiating cells, further add to its attractiveness as target for immunotherapy of cancer. Thus far, five conventional monoclonal IgG antibodies have been tested in cancer patients. These are murine IgG2a edrecolomab and its murine/human chimeric IgG1 antibody version, and humanized, human-engineered and fully human IgG1 antibodies 3622W94, ING-1, and adecatumumab (MT201), respectively. Here we compared all anti-EpCAM antibodies in an attempt to explain differences in clinical activity and safety. Methods We recombinantly produced all antibodies but murine edrecolomab and investigated them for binding affinity, EpCAM epitope recognition, ADCC and CDC, and inhibition of breast cancer cell proliferation. Results ING-1 and 3622W94 bound to EpCAM with much higher affinity than adecatumumab and edrecolomab. Edrecolomab, ING-1, and 3622W94 all recognized epitopes in the exon 2-encoded N-terminal domain of EpCAM, while adecatumumab recognized a more membrane proximal epitope encoded by exon 5. All antibodies induced lysis of EpCAM-expressing cancer cell lines by both ADCC and CDC with potencies that correlated with their binding affinities. The chimeric version of edrecolomab with a human Fcγ1 domain was much more potent in ADCC than the murine IgG2a version. Only adecatumumab showed a significant inhibition of MCF-7 breast cancer cell proliferation in the absence of complement and immune cells. Conclusion A moderate binding affinity and recognition of a distinct domain of EpCAM may best explain why adecatumumab showed a larger therapeutic window in cancer patients than the two high-affinity IgG1 antibodies ING-1 and 3622W94, both of which caused acute pancreatitis.
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Affiliation(s)
- Markus Münz
- Micromet AG, Staffelseestr, 2, 81477 Munich, Germany.
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Kurtz JE, Dufour P. Adecatumumab: an anti-EpCAM monoclonal antibody, from the bench to the bedside. Expert Opin Biol Ther 2010; 10:951-8. [PMID: 20426706 DOI: 10.1517/14712598.2010.482098] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
IMPORTANCE OF THE FIELD In developing new anticancer drugs, the identification of relevant targets is a key issue of growing importance. Ideally, an anticancer drug target should be specific to cancer cells, in order to both increase efficacy and decrease toxicity of the compound. AREAS COVERED IN THIS REVIEW Epithelial cell adhesion molecule (EpCAM) is a membrane protein with proto-oncogenic properties that is expressed in a number of endothelium-derived cancers and is a promising anticancer drug target. Adecatumumab is a monoclonal, fully human IgG1 antibody that targets EpCAM, development of which is at present reaching Phase III trials. WHAT THE READER WILL GAIN From a review of literature, we here update the rationale for using EpCAM as an anticancer target for monoclonal antibodies, with a special focus on adecatumumab. The fully human nature of adecatumumab is also discussed to put the drug in perspective with other related anti-EpCAM monoclonal antibodies, such as edrecolomab and catumaxomab. Adecatumumab studies are recapitulated, in order to provide the reader with a comprehensive view of the development of this promising anticancer agent. TAKE HOME MESSAGE Adecatumumab is a promising fully human monoclonal antibody targeting EpCAM which is expressed in almost all adenocarcinomas and its activity is not dependent of K-Ras status.
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Affiliation(s)
- Jean-Emmanuel Kurtz
- Département d'Hématologie et d'Oncologie, Hôpitaux Universitaires de Strasbourg, Avenue Molière, 67200 Strasbourg, France
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Surrogate approaches in development of monoclonal antibodies. Drug Discov Today 2009; 14:1159-65. [DOI: 10.1016/j.drudis.2009.09.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 09/10/2009] [Accepted: 09/10/2009] [Indexed: 12/31/2022]
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The Novel Chimeric Anti-NCAM (Neural Cell Adhesion Molecule) Antibody ch.MK1 Displays Antitumor Activity in SCID Mice but Does not Activate Complement-Dependent Cytolysis (CDC). J Immunother 2009; 32:442-51. [DOI: 10.1097/cji.0b013e31819f8b69] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Abstract
Human pancreatic cancer is a malignant disease with almost equal incidence and mortality. Effective diagnostic and therapeutic strategies are still urgently needed to improve its survival rate. With advances in structural and functional genomics, recent work has focused on targeted molecular therapy using monoclonal antibodies. This review summarizes the target molecules on the tumor cell surface and normal tissue stroma, which are related to pancreatic cancer oncogenesis, tumor growth or resistance to chemotherapy, as well as molecules involved in regulating inflammation and host immunoresponses. Targeted molecules include cell-surface receptors, such as the EGF receptor, HER2, death receptor 5 and IGF-1 receptor. Effects of monoclonal antibodies against these target molecules alone or in combination with chemotherapy, small-molecule signal transduction inhibitors, or radiation therapy are also discussed. Also discussed are the use of toxin or radioisotope conjugates, and information relating to the use of these targeting agents in pancreatic cancer clinical trials. Although targeted molecular therapy with monoclonal antibodies has made some progress in pancreatic cancer treatment, especially in preclinical studies, its clinical application to improve the survival rate of pancreatic cancer patients requires further investigation.
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Affiliation(s)
| | - Donald J Buchsbaum
- Author for correspondence: Department of Radiation Oncology, Division of Radiation Biology, 1530 3rd Avenue South, WTI 674 Birmingham, AL 35294-6832, USA, Tel.: +1 205 934 7077, Fax: +1 205 975 7060
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Presta LG. Molecular engineering and design of therapeutic antibodies. Curr Opin Immunol 2009; 20:460-70. [PMID: 18656541 DOI: 10.1016/j.coi.2008.06.012] [Citation(s) in RCA: 365] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 06/02/2008] [Accepted: 06/04/2008] [Indexed: 10/21/2022]
Abstract
Since the first murine monoclonal antibody was approved for human therapeutic use over a decade ago, the realization that monoclonal antibody therapeutics could be engineered to improve their efficacy has inspired an astonishing array of novel antibody constructs. Early focus was on reducing the immunogenicity of rodent antibodies via humanization and generation of antibodies in transgenic mice; as those techniques were being established and then provided marketed therapeutic antibodies, the focus expanded to include engineering for enhanced effector functions, control of half-life, tumor and tissue accessibility, augmented biophysical characteristics such as stability, and more efficient (and less costly) production. Over the past two years significant progress in designing antibodies with improved pharmacokinetic properties, via modified interaction with the neonatal Fc receptor (FcRn), has been achieved. Likewise, the ability to alter the communication of a therapeutic antibody with the immune system has been advanced, using both manipulation of the immunoglobulin protein sequence and its glycosylation. Although clinical evaluation of these engineered modifications has yet to be reported, results in primates are encouraging.
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Type II (tositumomab) anti-CD20 monoclonal antibody out performs type I (rituximab-like) reagents in B-cell depletion regardless of complement activation. Blood 2008; 112:4170-7. [PMID: 18583569 DOI: 10.1182/blood-2008-04-149161] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anti-CD20 monoclonal antibodies (mAbs) are classified into type I (rituximab-like) or type II (tositumomab-like) based on their ability to redistribute CD20 molecules in the plasma membrane and activate various effector functions. To compare type I and II mAbs directly in vivo and maximize Fc effector function, we selected and engineered mAbs with the same mouse IgG(2)a isotype and assessed their B-cell depleting activity in human CD20 transgenic mice. Despite being the same isotype, having similar affinity, opsonizing activity for phagocytosis, and in vivo half-life, the type II mAb tositumomab (B1) provided substantially longer depletion of B cells from the peripheral blood compared with the type I mAb rituximab (Rit m2a), and 1F5. This difference was also evident within the secondary lymphoid organs, in particular, the spleen. Failure to engage complement did not explain the efficacy of the type II reagents because type I mAbs mutated in the Fc domain (K322A) to prevent C1q binding still did not display equivalent efficacy. These results give support for the use of type II CD20 mAbs in human B-cell diseases.
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Amann M, Brischwein K, Lutterbuese P, Parr L, Petersen L, Lorenczewski G, Krinner E, Bruckmeier S, Lippold S, Kischel R, Lutterbuese R, Kufer P, Baeuerle PA, Schlereth B. Therapeutic window of MuS110, a single-chain antibody construct bispecific for murine EpCAM and murine CD3. Cancer Res 2008; 68:143-51. [PMID: 18172306 DOI: 10.1158/0008-5472.can-07-2182] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
EpCAM (CD326) is one of the most frequently and highly expressed tumor-associated antigens known and recently has also been found on cancer stem cells derived from human breast, colon, prostate, and pancreas tumors. However, like many other tumor-associated antigens used for antibody-based immunotherapeutic approaches, EpCAM is expressed on normal tissues including epithelia of pancreas, colon, lung, bile ducts, and breast. To assess the therapeutic window of an EpCAM/CD3-bispecific single-chain antibody construct of the bispecific T-cell engager (BiTE) class, we constructed murine surrogate of MT110 (muS110) from single-chain antibodies specific for murine EpCAM and CD3 antigens. Immunhistochemical analysis showed that, with minor differences, the expression of EpCAM protein on a large variety of tissues from man and mouse was similar with respect to distribution and level. MuS110 exhibited significant antitumor activity at as low as 5 microg/kg in both syngeneic 4T1 orthotopic breast cancer and CT-26 lung cancer mouse models. Dosing of muS110 for several weeks up to 400 microg/kg by intraanimal dose escalation was still tolerated, indicating existence of a significant therapeutic window for an EpCAM-specific BiTE antibody in mice. MuS110 was found to have similar in vitro characteristics and in vivo antitumor activity as MT110, a human EpCAM/human CD3-bispecific BiTE antibody that currently is in formal preclinical development.
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