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Geraghty S, Boyer JA, Fazel-Zarandi M, Arzouni N, Ryseck RP, McBride MJ, Parsons LR, Rabinowitz JD, Singh M. Integrative Computational Framework, Dyscovr, Links Mutated Driver Genes to Expression Dysregulation Across 19 Cancer Types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.20.624509. [PMID: 39605479 PMCID: PMC11601522 DOI: 10.1101/2024.11.20.624509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Though somatic mutations play a critical role in driving cancer initiation and progression, the systems-level functional impacts of these mutations-particularly, how they alter expression across the genome and give rise to cancer hallmarks-are not yet well-understood, even for well-studied cancer driver genes. To address this, we designed an integrative machine learning model, Dyscovr, that leverages mutation, gene expression, copy number alteration (CNA), methylation, and clinical data to uncover putative relationships between nonsynonymous mutations in key cancer driver genes and transcriptional changes across the genome. We applied Dyscovr pan-cancer and within 19 individual cancer types, finding both broadly relevant and cancer type-specific links between driver genes and putative targets, including a subset we further identify as exhibiting negative genetic relationships. Our work newly implicates-and validates in cell lines-KBTBD2 and mutant PIK3CA as putative synthetic lethals in breast cancer, suggesting a novel combinatorial treatment approach.
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Affiliation(s)
- Sara Geraghty
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Jacob A. Boyer
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
- Ludwig Cancer Institute, Princeton Branch, Princeton University, Princeton, NJ 08554
| | - Mahya Fazel-Zarandi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Nibal Arzouni
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Rolf-Peter Ryseck
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Matthew J. McBride
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854
| | - Lance R. Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
| | - Joshua D. Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
- Ludwig Cancer Institute, Princeton Branch, Princeton University, Princeton, NJ 08554
- Department of Chemistry, Princeton University, Princeton, NJ 08544
| | - Mona Singh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544
- Department of Computer Science, Princeton University, Princeton, NJ 08544
- Lead Contact
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Huang H, Pan Y, Mai Q, Zhang C, Du Q, Liao Y, Qin S, Chen Y, Huang J, Li J, Liu T, Zou Q, Zhou Y, Yuan L, Wang W, Liang Y, Pan CY, Liu J, Yao S. Targeting CDCP1 boost CD8+ T cells-mediated cytotoxicity in cervical cancer via the JAK/STAT signaling pathway. J Immunother Cancer 2024; 12:e009416. [PMID: 39455095 PMCID: PMC11529519 DOI: 10.1136/jitc-2024-009416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2024] [Indexed: 10/28/2024] Open
Abstract
BACKGROUND Cervical cancer remains a global health challenge. The identification of new immunotherapeutic targets may provide a promising platform for advancing cervical cancer treatment. OBJECTIVE This study aims to investigate the role of CUB domain-containing protein 1 (CDCP1) in cervical cancer progression and evaluate its potential as a therapeutic target. METHODS We performed comprehensive analyses using patient cohorts and preclinical models to examine the association between CDCP1 expression and cervical cancer prognosis. Then in immunodeficient and immunocompetent mouse models, we further investigated the impact of CDCP1 on the tumor immune microenvironment, focusing on its effects on tumor-infiltrating T cells, including cytotoxic T lymphocytes (CTLs) and regulatory T cells (Tregs). Mechanistic studies were performed to elucidate the pathways involved in CDCP1-mediated immune modulation, in particular its interaction with the T cell receptor CD6 and the activation of the JAK-STAT signaling pathway. RESULTS Our results show that CDCP1 overexpression is associated with poor prognosis and T cell infliction in cervical cancer. Specifically, it affects the activity of CTLs and Tregs. Mechanistically, CDCP1 binds to CD6 and inhibits the JAK-STAT pathway of T cells. The study further demonstrates that targeting CDCP1 with the inhibitor 8-prenylnaringenin (8PN) effectively suppresses tumor growth in vivo and enhances antitumor immunity. CONCLUSIONS CDCP1 plays a critical role in cervical cancer progression by modulating the tumor immune microenvironment. Targeting CDCP1 offers a promising therapeutic strategy to improve the outcome of patients with cervical cancer.
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Affiliation(s)
- Hua Huang
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Yuwen Pan
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Qiuwen Mai
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Chunyu Zhang
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Qiqiao Du
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Yuandong Liao
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Shuhang Qin
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Yili Chen
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Jiaming Huang
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Jie Li
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Tianyu Liu
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Qiaojian Zou
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Yijia Zhou
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Li Yuan
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Wei Wang
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Yanchun Liang
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Chao Yun Pan
- Department of Biochemistry, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Junxiu Liu
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Shuzhong Yao
- Department of Obstetrics and Gynecology, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, China
- Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
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Li C, Zang X, Liu H, Yin S, Cheng X, Zhang W, Meng X, Chen L, Lu S, Wu J. Olink Proteomics for the Identification of Biomarkers for Early Diagnosis of Postmenopausal Osteoporosis. J Proteome Res 2024; 23:4567-4578. [PMID: 39226440 PMCID: PMC11460326 DOI: 10.1021/acs.jproteome.4c00470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/25/2024] [Accepted: 08/13/2024] [Indexed: 09/05/2024]
Abstract
This investigation aims to employ Olink proteomics in analyzing the distinct serum proteins associated with postmenopausal osteoporosis (PMOP) and identifying prognostic markers for early detection of PMOP via molecular mechanism research on postmenopausal osteoporosis. Postmenopausal women admitted to Beijing Jishuitan Hospital were randomly selected and categorized into three groups based on their dual-energy X-ray absorptiometry (DXA) T-scores: osteoporosis group (n = 24), osteopenia group (n = 20), and normal bone mass group (n = 16). Serum samples from all participants were collected for clinical and bone metabolism marker measurements. Olink proteomics was utilized to identify differentially expressed proteins (DEPs) that are highly associated with postmenopausal osteoporosis. The functional analysis of DEPs was performed using Gene Ontology and Kyto Encyclopedia Genes and Genomes (KEGG). The biological characteristics of these proteins and their correlation with PMOP were subsequently analyzed. ROC curve analysis was performed to identify potential biomarkers with the highest diagnostic accuracy for early stage PMOP. Through Olink proteomics, we identified five DEPs highly associated with PMOP, including two upregulated and three downregulated proteins. TWEAK and CDCP1 markers exhibited the highest area under the curve (0.8188 and 0.8031, respectively). TWEAK and CDCP1 have the potential to serve as biomarkers for early prediction of postmenopausal osteoporosis.
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Affiliation(s)
- Chunyan Li
- Beijing
Jishuitan Hospital, Capital Medical University, Xicheng District, Beijing 100035, China
| | - Xinwei Zang
- Beijing
Jishuitan Hospital, Capital Medical University, Xicheng District, Beijing 100035, China
- Cell
Therapy Center, Beijing Institute of Geriatrics, Xuanwu Hospital Capital Medical University, National Clinical Research
Center for Geriatric Diseases, and Key Laboratory of Neurodegenerative
Diseases, Ministry of Education, Beijing 100053, China
| | - Heng Liu
- Beijing
Jishuitan Hospital, Capital Medical University, Xicheng District, Beijing 100035, China
| | - Shangqi Yin
- Beijing
Jishuitan Hospital, Capital Medical University, Xicheng District, Beijing 100035, China
| | - Xiang Cheng
- Beijing
Jishuitan Hospital, Capital Medical University, Xicheng District, Beijing 100035, China
| | - Wei Zhang
- Beijing
Jishuitan Hospital, Capital Medical University, Xicheng District, Beijing 100035, China
| | - Xiangyu Meng
- Beijing
Jishuitan Hospital, Capital Medical University, Xicheng District, Beijing 100035, China
| | - Liyuan Chen
- Shijiazhuang
People’s Hospital, Shijiazhuang Changan District, Hebei 050000, China
| | - Shuai Lu
- Beijing
Jishuitan Hospital, Capital Medical University, Xicheng District, Beijing 100035, China
| | - Jun Wu
- Beijing
Jishuitan Hospital, Capital Medical University, Xicheng District, Beijing 100035, China
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Li K, Xie G, Deng X, Zhang Y, Jia Z, Huang Z. Antibody-drug conjugates in urinary tumors: clinical application, challenge, and perspectives. Front Oncol 2023; 13:1259784. [PMID: 38173833 PMCID: PMC10761427 DOI: 10.3389/fonc.2023.1259784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
Urinary tumors primarily consist of kidney, urothelial, and prostate malignancies, which pose significant treatment challenges, particularly in advanced stages. Antibody-drug conjugates (ADCs) have emerged as a promising therapeutic approach, combining monoclonal antibody specificity with cytotoxic chemotherapeutic payloads. This review highlights recent advancements, opportunities, and challenges in ADC application for urinary tumors. We discuss the FDA-approved ADCs and other novel ADCs under investigation, emphasizing their potential to improve patient outcomes. Furthermore, we explore strategies to address challenges, such as toxicity management, predictive biomarker identification, and resistance mechanisms. Additionally, we examine the integration of ADCs with other treatment modalities, including immune checkpoint inhibitors, targeted therapies, and radiation therapy. By addressing these challenges and exploring innovative approaches, the development of ADCs may significantly enhance therapeutic options and outcomes for patients with advanced urinary tumor.
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Affiliation(s)
- Keqiang Li
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Guoqing Xie
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xiyue Deng
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yu Zhang
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhankui Jia
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhenlin Huang
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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