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Keshavarz-Rahaghi F, Pleasance E, Kolisnik T, Jones SJM. A p53 transcriptional signature in primary and metastatic cancers derived using machine learning. Front Genet 2022; 13:987238. [PMID: 36134028 PMCID: PMC9483853 DOI: 10.3389/fgene.2022.987238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
The tumor suppressor gene, TP53, has the highest rate of mutation among all genes in human cancer. This transcription factor plays an essential role in the regulation of many cellular processes. Mutations in TP53 result in loss of wild-type p53 function in a dominant negative manner. Although TP53 is a well-studied gene, the transcriptome modifications caused by the mutations in this gene have not yet been explored in a pan-cancer study using both primary and metastatic samples. In this work, we used a random forest model to stratify tumor samples based on TP53 mutational status and detected a p53 transcriptional signature. We hypothesize that the existence of this transcriptional signature is due to the loss of wild-type p53 function and is universal across primary and metastatic tumors as well as different tumor types. Additionally, we showed that the algorithm successfully detected this signature in samples with apparent silent mutations that affect correct mRNA splicing. Furthermore, we observed that most of the highly ranked genes contributing to the classification extracted from the random forest have known associations with p53 within the literature. We suggest that other genes found in this list including GPSM2, OR4N2, CTSL2, SPERT, and RPE65 protein coding genes have yet undiscovered linkages to p53 function. Our analysis of time on different therapies also revealed that this signature is more effective than the recorded TP53 status in detecting patients who can benefit from platinum therapies and taxanes. Our findings delineate a p53 transcriptional signature, expand the knowledge of p53 biology and further identify genes important in p53 related pathways.
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Affiliation(s)
- Faeze Keshavarz-Rahaghi
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Tyler Kolisnik
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
| | - Steven J. M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
- *Correspondence: Steven J. M. Jones,
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Novak J, Zamostna B, Vopalensky V, Buryskova M, Burysek L, Doleckova D, Pospisek M. Interleukin-1α associates with the tumor suppressor p53 following DNA damage. Sci Rep 2020; 10:6995. [PMID: 32332775 PMCID: PMC7181607 DOI: 10.1038/s41598-020-63779-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Accepted: 04/06/2020] [Indexed: 01/07/2023] Open
Abstract
Interleukin-1α (IL-1α) is a dual-function proinflammatory mediator. In addition to its role in the canonical IL-1 signaling pathway, which employs membrane-bound receptors, a growing body of evidence shows that IL-1α has some additional intracellular functions. We identified the interaction of IL-1α with the tumor suppressor p53 in the nuclei and cytoplasm of both malignant and noncancerous mammalian cell lines using immunoprecipitation and the in situ proximity ligation assay (PLA). This interaction was enhanced by treatment with the antineoplastic drug etoposide, which suggests a role for the IL-1α•p53 interaction in genotoxic stress.
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Affiliation(s)
- J Novak
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - B Zamostna
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - V Vopalensky
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - M Buryskova
- Protean s.r.o., Dobra Voda u Ceskych Budejovic, Czech Republic
| | - L Burysek
- Protean s.r.o., Dobra Voda u Ceskych Budejovic, Czech Republic
| | - D Doleckova
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - M Pospisek
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic.
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3
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Chen YS, Liu F, Luo YH, Fan Y, Xu FG, Li P, Zhou B, Pan XY, Wang CC, Cui L. EDNRB isoform 3 confers Temozolomide resistance in A375 melanoma cells by modulating membrane potential, reactive oxygen species and mitochondrial Ca 2. Cancer Manag Res 2019; 11:7353-7367. [PMID: 31496797 PMCID: PMC6689146 DOI: 10.2147/cmar.s208604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/10/2019] [Indexed: 12/24/2022] Open
Abstract
Background The role of endothelin receptor type B (EDNRB) isoform 3 involved in Temozolomide (TMZ)-induced melanoma cell death has not yet been elucidated. Methods The subcellular localization of EDNRB isoform 3 was determined by confocal and immunoblotting assays. Silencing EDNRB isoform 3 was performed by CRISPR/Cas9. Apoptosis was assessed by annexin V/propium iodide staining and caspases 3/7/9 activity. Mitochondrial membrane potential, reactive oxygen species and mitochondrial Ca2+ were measured by flow cytometry. Apoptosis protein array was applied. Results Confocal and immunoblot analyses indicate mitochondrial localization of EDNRB isoform 3 and the first N-terminal (1–22) amino acids are sufficient for its mitochondrial targeting. EDNRB isoform 3 depleted A375 cells significantly confers chemoresistance with mitochondrial depolarization, reduced reactive oxygen species, enhanced mitochondrial Ca2+ uptake and decreased caspase 9 activation. Additionally, apoptosis array shows that lack of EDNRB isoform 3 has relatively lower expression of phosphorylation of p53 at S392 and a slightly higher expression of Paraoxonase 2. Conclusion Our findings raise the possibility of targeting EDNRB isoform 3 as a new therapeutic strategy in combination with TMZ for melanoma treatment.
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Affiliation(s)
- Yun Shan Chen
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, People's Republic of China
| | - Fen Liu
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, People's Republic of China
| | - Yi Hong Luo
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, People's Republic of China
| | - Yue Fan
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, People's Republic of China
| | - Fang Gui Xu
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, People's Republic of China
| | - Pin Li
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, People's Republic of China
| | - Bei Zhou
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, People's Republic of China
| | - Xiu Yu Pan
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, People's Republic of China
| | - Chi Chiu Wang
- Reproduction and Development Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.,School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong.,Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Long Cui
- Department of Obstetrics and Gynaecology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, People's Republic of China.,Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
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Methotrexate-induced senescence of human colon cancer cells depends on p53 acetylation, but not genomic aberrations. Anticancer Drugs 2019; 30:374-382. [DOI: 10.1097/cad.0000000000000731] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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5
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Upreti M, Jyoti A, Johnson SE, Swindell EP, Napier D, Sethi P, Chan R, Feddock JM, Weiss HL, O'Halloran TV, Evers BM. Radiation-enhanced therapeutic targeting of galectin-1 enriched malignant stroma in triple negative breast cancer. Oncotarget 2018; 7:41559-41574. [PMID: 27223428 PMCID: PMC5173078 DOI: 10.18632/oncotarget.9490] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/04/2016] [Indexed: 12/14/2022] Open
Abstract
Currently there are no FDA approved targeted therapies for Triple Negative Breast Cancer (TNBC). Ongoing clinical trials for TNBC have focused primarily on targeting the epithelial cancer cells. However, targeted delivery of cytotoxic payloads to the non-transformed tumor associated-endothelium can prove to be an alternate approach that is currently unexplored. The present study is supported by recent findings on elevated expression of stromal galectin-1 in clinical samples of TNBC and our ongoing findings on stromal targeting of radiation induced galectin-1 by the anginex-conjugated arsenic-cisplatin loaded liposomes using a novel murine tumor model. We demonstrate inhibition of tumor growth and metastasis in response to the multimodal nanotherapeutic strategy using a TNBC model with orthotopic tumors originating from 3D tumor tissue analogs (TTA) comprised of tumor cells, endothelial cells and fibroblasts. The ‘rigorous’ combined treatment regimen of radiation and targeted liposomes is also shown to be well tolerated. More importantly, the results presented provide a means to exploit clinically relevant radiation dose for concurrent receptor mediated enhanced delivery of chemotherapy while limiting overall toxicity. The proposed study is significant as it falls in line with developing combinatorial therapeutic approaches for stroma-directed tumor targeting using tumor models that have an appropriate representation of the TNBC microenvironment.
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Affiliation(s)
- Meenakshi Upreti
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Department of Pathology, University of Kentucky, Lexington, KY, USA
| | - Amar Jyoti
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Department of Pathology, University of Kentucky, Lexington, KY, USA
| | - Sara E Johnson
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Elden P Swindell
- Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Dana Napier
- Department of Pathology, University of Kentucky, Lexington, KY, USA
| | - Pallavi Sethi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA.,Department of Pathology, University of Kentucky, Lexington, KY, USA
| | - Ryan Chan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Jonathan M Feddock
- Department of Radiation Medicine, University of Kentucky Chandler Hospital, Lexington, KY, USA
| | - Heidi L Weiss
- Department of Pathology, University of Kentucky, Lexington, KY, USA
| | - Thomas V O'Halloran
- Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - B Mark Evers
- Department of Pathology, University of Kentucky, Lexington, KY, USA.,Department of Surgery, University of Kentucky, Lexington, KY, USA
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Altamura G, Corteggio A, Pacini L, Conte A, Pierantoni GM, Tommasino M, Accardi R, Borzacchiello G. Transforming properties of Felis catus papillomavirus type 2 E6 and E7 putative oncogenes in vitro and their transcriptional activity in feline squamous cell carcinoma in vivo. Virology 2016; 496:1-8. [PMID: 27236740 DOI: 10.1016/j.virol.2016.05.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 04/12/2016] [Accepted: 05/20/2016] [Indexed: 01/18/2023]
Abstract
Felis catus papillomavirus type 2 (FcaPV2) DNA is found in feline cutaneous squamous cell carcinomas (SCCs); however, its biological properties are still uncharacterized. In this study, we successfully expressed FcaPV2 E6 and E7 putative oncogenes in feline epithelial cells and demonstrated that FcaPV2 E6 binds to p53, impairing its protein level. In addition, E6 and E7 inhibited ultraviolet B (UVB)-triggered accumulation of p53, p21 and pro-apoptotic markers such as Cleaved Caspase3, Bax and Bak, suggesting a synergistic action of the virus with UV exposure in tumour pathogenesis. Furthermore, FcaPV2 E7 bound to feline pRb and impaired pRb levels, resulting in upregulation of the downstream pro-proliferative genes Cyclin A and Cdc2. Importantly, we demonstrated mRNA expression of FcaPV2 E2, E6 and E7 in feline SCC samples, strengthening the hypothesis of a causative role in the development of feline SCC.
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Affiliation(s)
- Gennaro Altamura
- Department of Veterinary Medicine and Animal Productions, General Pathology and Pathological Anatomy Unit, University of Naples Federico II, Via Delpino 1, 80137 Naples, Italy.
| | - Annunziata Corteggio
- Department of Veterinary Medicine and Animal Productions, General Pathology and Pathological Anatomy Unit, University of Naples Federico II, Via Delpino 1, 80137 Naples, Italy.
| | - Laura Pacini
- Infections and Cancer Biology Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372 Lyon, France.
| | - Andrea Conte
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy.
| | - Giovanna Maria Pierantoni
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy.
| | - Massimo Tommasino
- Infections and Cancer Biology Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372 Lyon, France.
| | - Rosita Accardi
- Infections and Cancer Biology Group, International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372 Lyon, France.
| | - Giuseppe Borzacchiello
- Department of Veterinary Medicine and Animal Productions, General Pathology and Pathological Anatomy Unit, University of Naples Federico II, Via Delpino 1, 80137 Naples, Italy.
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7
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Pereboeva L, Hubbard M, Goldman FD, Westin ER. Robust DNA Damage Response and Elevated Reactive Oxygen Species in TINF2-Mutated Dyskeratosis Congenita Cells. PLoS One 2016; 11:e0148793. [PMID: 26859482 PMCID: PMC4747510 DOI: 10.1371/journal.pone.0148793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/22/2016] [Indexed: 12/13/2022] Open
Abstract
Dyskeratosis Congenita (DC) is an inherited multisystem premature aging disorder with characteristic skin and mucosal findings as well as a predisposition to cancer and bone marrow failure. DC arises due to gene mutations associated with the telomerase complex or telomere maintenance, resulting in critically shortened telomeres. The pathogenesis of DC, as well as several congenital bone marrow failure (BMF) syndromes, converges on the DNA damage response (DDR) pathway and subsequent elevation of reactive oxygen species (ROS). Historically, DC patients have had poor outcomes following bone marrow transplantation (BMT), perhaps as a consequence of an underlying DNA hypersensitivity to cytotoxic agents. Previously, we demonstrated an activated DDR and increased ROS, augmented by chemotherapy and radiation, in somatic cells isolated from DC patients with a mutation in the RNA component of telomerase, TERC. The current study was undertaken to determine whether previous findings related to ROS and DDR in TERC patients’ cells could be extended to other DC mutations. Of particular interest was whether an antioxidant approach could counter increased ROS and decrease DC pathologies. To test this, we examined lymphocytes from DC patients from different DC mutations (TERT, TINF2, and TERC) for the presence of an active DDR and increased ROS. All DC mutations led to increased steady-state p53 (2-fold to 10-fold) and ROS (1.5-fold to 2-fold). Upon exposure to ionizing radiation (XRT), DC cells increased in both DDR and ROS to a significant degree. Exposing DC cells to hydrogen peroxide also revealed that DC cells maintain a significant oxidant burden compared to controls (1.5-fold to 3-fold). DC cell culture supplemented with N-acetylcysteine, or alternatively grown in low oxygen, afforded significant proliferative benefits (proliferation: maximum 2-fold increase; NAC: 5-fold p53 decrease; low oxygen: maximum 3.5-fold p53 decrease). Together, our data supports a mechanism whereby telomerase deficiency and subsequent shortened telomeres initiate a DDR and create a pro-oxidant environment, especially in cells carrying the TINF2 mutations. Finally, the ameliorative effects of antioxidants in vitro suggest this could translate to therapeutic benefits in DC patients.
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Affiliation(s)
- Larisa Pereboeva
- Department of Medicine, Division of Hematology Oncology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Meredith Hubbard
- Department of Pediatrics, Division of Hematology Oncology, University of Alabama, Birmingham, Alabama, United States of America
| | - Frederick D. Goldman
- Department of Pediatrics, Division of Hematology Oncology, University of Alabama, Birmingham, Alabama, United States of America
| | - Erik R. Westin
- Department of Pediatrics, Division of Hematology Oncology, University of Alabama, Birmingham, Alabama, United States of America
- * E-mail:
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8
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Lu J, Miao J, Su T, Liu Y, He R. Formaldehyde induces hyperphosphorylation and polymerization of Tau protein both in vitro and in vivo. Biochim Biophys Acta Gen Subj 2013; 1830:4102-16. [DOI: 10.1016/j.bbagen.2013.04.028] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/07/2013] [Accepted: 04/18/2013] [Indexed: 12/29/2022]
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9
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M3-mAChR Stimulation Exerts Anti-apoptotic Effect Via Activating the HIF-1α/HO-1/VEGF Signaling Pathway in H9c2 Rat Ventricular Cells. J Cardiovasc Pharmacol 2012; 60:474-82. [DOI: 10.1097/fjc.0b013e31826c1c13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Herr DR. Potential use of G protein-coupled receptor-blocking monoclonal antibodies as therapeutic agents for cancers. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2012; 297:45-81. [PMID: 22608557 DOI: 10.1016/b978-0-12-394308-8.00002-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The therapeutic use of monoclonal antibodies (mAbs) is the fastest growing area of pharmaceutical development and has enjoyed significant clinical success since approval of the first mAb drug in1984. However, despite significant effort, there are still no approved therapeutic mAbs directed against the largest and most attractive family of drug targets: G protein-coupled receptors (GPCRs). GPCRs regulate essentially all cellular processes, including those that are fundamental to cancer pathology, such as proliferation, survival/drug resistance, migration, differentiation, tissue invasion, and angiogenesis. Many different GPCR isoforms are enhanced or dysregulated in multiple tumor types, and several GPCRs have known oncogenic activity. With approximately 350 distinct GPCRs in the genome, these receptors provide a rich landscape for the design of effective, targeted therapies for cancer, a uniquely heterogeneous disease family. While the generation of selective, efficacious mAbs has been problematic for these structurally complex integral membrane proteins, progress in the development of immunotherapeutics has been made by several independent groups. This chapter provides an overview of the roles of GPCRs in cancer and describes the current state of the art of GPCR-targeted mAb drugs.
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Affiliation(s)
- Deron R Herr
- Expression Drug Designs, LLC, San Marcos, California, USA
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