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Lin MS, Jo SY, Luebeck J, Chang HY, Wu S, Mischel PS, Bafna V. Transcriptional immune suppression and up-regulation of double-stranded DNA damage and repair repertoires in ecDNA-containing tumors. eLife 2024; 12:RP88895. [PMID: 38896472 PMCID: PMC11186631 DOI: 10.7554/elife.88895] [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] [Indexed: 06/21/2024] Open
Abstract
Extrachromosomal DNA is a common cause of oncogene amplification in cancer. The non-chromosomal inheritance of ecDNA enables tumors to rapidly evolve, contributing to treatment resistance and poor outcome for patients. The transcriptional context in which ecDNAs arise and progress, including chromosomally-driven transcription, is incompletely understood. We examined gene expression patterns of 870 tumors of varied histological types, to identify transcriptional correlates of ecDNA. Here, we show that ecDNA-containing tumors impact four major biological processes. Specifically, ecDNA-containing tumors up-regulate DNA damage and repair, cell cycle control, and mitotic processes, but down-regulate global immune regulation pathways. Taken together, these results suggest profound alterations in gene regulation in ecDNA-containing tumors, shedding light on molecular processes that give rise to their development and progression.
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Affiliation(s)
- Miin S Lin
- Bioinformatics and Systems Biology Graduate Program, University of California, San DiegoLa JollaUnited States
| | - Se-Young Jo
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of MedicineSeoulRepublic of Korea
| | - Jens Luebeck
- Department of Computer Science and Engineering, University of California, San DiegoLa JollaUnited States
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford UniversityStanfordUnited States
- Department of Genetics, Stanford UniversityStanfordUnited States
- Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| | - Sihan Wu
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical CenterDallasUnited States
| | - Paul S Mischel
- Sarafan Chemistry, Engineering, and Medicine for Human Health (Sarafan ChEM-H), Stanford UniversityStanfordUnited States
- Department of Pathology, Stanford University School of MedicineStanfordUnited States
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San DiegoLa JollaUnited States
- Halıcıoğlu Data Science Institute, University of California, San DiegoLa JollaUnited States
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2
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Ma Z, Gu Q, Dai Y, Wang Q, Shi W, Jiao Z. Therapeutic potential of SHCBP1 inhibitor AZD5582 in pancreatic cancer treatment. Cancer Sci 2024; 115:820-835. [PMID: 38151993 PMCID: PMC10921007 DOI: 10.1111/cas.16059] [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: 08/22/2023] [Revised: 12/07/2023] [Accepted: 12/10/2023] [Indexed: 12/29/2023] Open
Abstract
Pancreatic cancer (PC) is a highly aggressive and deadly malignancy with limited treatment options and poor prognosis. Identifying new therapeutic targets and developing effective strategies for PC treatment is of utmost importance. Here, we revealed that SHCBP1 is significantly overexpressed in PC and negatively correlated with patient prognosis. Knockout of SHCBP1 inhibits the proliferation and migration of PC cells in vitro, and suppresses the tumor growth in vivo. In addition, we identified AZD5582 as a novel inhibitor of SHCBP1, which efficiently restrains the growth of PC in cell lines, organoids, and patient-derived xenografts. Mechanistically, we found that AZD5582 induced the apoptosis of PC cells by inhibiting the activity of PI3K/AKT signaling and preventing the degradation of TP53. Collectively, our study highlights SHCBP1 as a potential therapeutic target and its inhibitor AZD5582 as a viable agent for PC treatment strategies.
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Affiliation(s)
- Zhijian Ma
- The Second Clinical Medical CollegeLanzhou UniversityLanzhouChina
| | - Qianlin Gu
- The Second Clinical Medical CollegeLanzhou UniversityLanzhouChina
| | - Yiwei Dai
- The Second Clinical Medical CollegeLanzhou UniversityLanzhouChina
| | - Qiaoyan Wang
- The Second Clinical Medical CollegeLanzhou UniversityLanzhouChina
| | - Wengui Shi
- Cuiying Biomedical Research CenterLanzhou University Second HospitalLanzhouChina
| | - Zuoyi Jiao
- The Department of General SurgeryLanzhou University Second HospitalLanzhouChina
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3
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Balraj AS, Muthamilselvan S, Raja R, Palaniappan A. PRADclass: Hybrid Gleason Grade-Informed Computational Strategy Identifies Consensus Biomarker Features Predictive of Aggressive Prostate Adenocarcinoma. Technol Cancer Res Treat 2024; 23:15330338231222389. [PMID: 38226611 PMCID: PMC10793196 DOI: 10.1177/15330338231222389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/18/2023] [Accepted: 12/06/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Prostate adenocarcinoma (PRAD) is a common cancer diagnosis among men globally, yet large gaps in our knowledge persist with respect to the molecular bases of its progression and aggression. It is mostly indolent and slow-growing, but aggressive prostate cancers need to be recognized early for optimising treatment, with a view to reducing mortality. METHODS Based on TCGA transcriptomic data pertaining to PRAD and the associated clinical metadata, we determined the sample Gleason grade, and used it to execute: (i) Gleason-grade wise linear modeling, followed by five contrasts against controls and ten contrasts between grades; and (ii) Gleason-grade wise network modeling via weighted gene correlation network analysis (WGCNA). Candidate biomarkers were obtained from the above analysis and the consensus found. The consensus biomarkers were used as the feature space to train ML models for classifying a sample as benign, indolent or aggressive. RESULTS The statistical modeling yielded 77 Gleason grade-salient genes while the WGCNA algorithm yielded 1003 trait-specific key genes in grade-wise significant modules. Consensus analysis of the two approaches identified two genes in Grade-1 (SLC43A1 and PHGR1), 26 genes in Grade-4 (including LOC100128675, PPP1R3C, NECAB1, UBXN10, SERPINA5, CLU, RASL12, DGKG, FHL1, NCAM1, and CEND1), and seven genes in Grade-5 (CBX2, DPYS, FAM72B, SHCBP1, TMEM132A, TPX2, UBE2C). A RandomForest model trained and optimized on these 35 biomarkers for the ternary classification problem yielded a balanced accuracy ∼ 86% on external validation. CONCLUSIONS The consensus of multiple parallel computational strategies has unmasked candidate Gleason grade-specific biomarkers. PRADclass, a validated AI model featurizing these biomarkers achieved good performance, and could be trialed to predict the differentiation of prostate cancers. PRADclass is available for academic use at: https://apalania.shinyapps.io/pradclass (online) and https://github.com/apalania/pradclass (command-line interface).
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Affiliation(s)
- Alex Stanley Balraj
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Sangeetha Muthamilselvan
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Rachanaa Raja
- Department of Pharmaceutical Technology, UCE, Anna University (BIT campus), Trichy, India
| | - Ashok Palaniappan
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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4
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Dai Y, Hu C, Zhou H, Liu W, Lai W, Xu R, Liao J, Wang J, Li G, Zhang R. Rucaparib inhibits lung adenocarcinoma cell proliferation and migration via the SHCBP1/CDK1 pathway. FEBS J 2023; 290:5720-5743. [PMID: 37581853 DOI: 10.1111/febs.16933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 06/17/2023] [Accepted: 07/14/2023] [Indexed: 08/16/2023]
Abstract
Src homolog and collagen homolog binding protein 1 (SHCBP1) binds to the SH2 domain of SHC-transforming protein 1 (SHC1) and is involved in midbody organization and cytokinesis completion. SHCBP1 has been reported to be a cancer driver gene, promoting cancer progression. However, the functional role and underlying mechanism of SHCBP1 in regulating lung adenocarcinoma (LUAD) cell proliferation and migration are incompletely understood. Here, we discovered that SHCBP1 is overexpressed in LUAD tissues and is associated with a poor prognosis. SHCBP1 knockdown inhibited LUAD cell proliferation and migration by arresting the cell cycle and preventing epithelial-mesenchymal transition (EMT) via decreasing cyclin-dependent kinase 1 (CDK1) expression. Mechanistically, CDK1 overexpression reversed SHCBP1 knockdown-induced inhibition of proliferation and migration, confirming CDK1 as a key downstream target of SHCBP1. In addition, we proposed that rucaparib may be a small-molecule inhibitor of SHCBP1 and validated both in vitro and in vivo that rucaparib inhibits cell proliferation and migration via suppression of the SHCBP1/CDK1 pathway in LUAD. Our study elucidates a newly identified role of SHCBP1 in promoting cell proliferation and migration in LUAD, and suggests rucaparib as a potential inhibitor for LUAD treatment.
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Affiliation(s)
- Yue Dai
- Department of Pharmacy, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Changpeng Hu
- Department of Pharmacy, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Huyue Zhou
- Department of Pharmacy, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Wuyi Liu
- Department of Pharmacy, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Wenjing Lai
- Department of Pharmacy, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Rufu Xu
- Department of Pharmacy, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Jiaxing Liao
- Department of Pharmacy, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Jie Wang
- Department of Pharmacy, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Guobing Li
- Department of Pharmacy, The Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Rong Zhang
- Department of Pharmacy, The Second Affiliated Hospital of Army Medical University, Chongqing, China
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5
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Peng M, Chu X, Peng Y, Li D, Zhang Z, Wang W, Zhou X, Xiao D, Yang X. Targeted therapies in bladder cancer: signaling pathways, applications, and challenges. MedComm (Beijing) 2023; 4:e455. [PMID: 38107059 PMCID: PMC10724512 DOI: 10.1002/mco2.455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023] Open
Abstract
Bladder cancer (BC) is one of the most prevalent malignancies in men. Understanding molecular characteristics via studying signaling pathways has made tremendous breakthroughs in BC therapies. Thus, targeted therapies including immune checkpoint inhibitors (ICIs), antibody-drug conjugates (ADCs), and tyrosine kinase inhibitor (TKI) have markedly improved advanced BC outcomes over the last few years. However, the considerable patients still progress after a period of treatment with current therapeutic regimens. Therefore, it is crucial to guide future drug development to improve BC survival, based on the molecular characteristics of BC and clinical outcomes of existing drugs. In this perspective, we summarize the applications and benefits of these targeted drugs and highlight our understanding of mechanisms of low response rates and immune escape of ICIs, ADCs toxicity, and TKI resistance. We also discuss potential solutions to these problems. In addition, we underscore the future drug development of targeting metabolic reprogramming and cancer stem cells (CSCs) with a deep understanding of their signaling pathways features. We expect that finding biomarkers, developing novo drugs and designing clinical trials with precisely selected patients and rationalized drugs will dramatically improve the quality of life and survival of patients with advanced BC.
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Affiliation(s)
- Mei Peng
- Department of PharmacyXiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Xuetong Chu
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Yan Peng
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Duo Li
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Zhirong Zhang
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Weifan Wang
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Xiaochen Zhou
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Di Xiao
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
| | - Xiaoping Yang
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan ProvinceThe Research Center of Reproduction and Translational Medicine of Hunan ProvinceKey Laboratory of Chemical Biology & Traditional Chinese Medicine Research of Ministry of EducationDepartment of PharmacySchool of MedicineHunan Normal UniversityChangshaHunanChina
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Lin MS, Jo SY, Luebeck J, Chang HY, Wu S, Mischel PS, Bafna V. Transcriptional immune suppression and upregulation of double stranded DNA damage and repair repertoires in ecDNA-containing tumors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.537925. [PMID: 37162993 PMCID: PMC10168239 DOI: 10.1101/2023.04.24.537925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Extrachromosomal DNA is a common cause of oncogene amplification in cancer. The non-chromosomal inheritance of ecDNA enables tumors to rapidly evolve, contributing to treatment resistance and poor outcome for patients. The transcriptional context in which ecDNAs arise and progress, including chromosomally-driven transcription, is incompletely understood. We examined gene expression patterns of 870 tumors of varied histological types, to identify transcriptional correlates of ecDNA. Here we show that ecDNA containing tumors impact four major biological processes. Specifically, ecDNA containing tumors upregulate DNA damage and repair, cell cycle control, and mitotic processes, but downregulate global immune regulation pathways. Taken together, these results suggest profound alterations in gene regulation in ecDNA containing tumors, shedding light on molecular processes that give rise to their development and progression.
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Affiliation(s)
- Miin S. Lin
- Bioinformatics and Systems Biology Graduate Program, University of California at San Diego, La Jolla, CA, USA
| | - Se-Young Jo
- Department of Biomedical Systems Informatics and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Jens Luebeck
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
| | - Howard Y. Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Sihan Wu
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Paul S. Mischel
- Sarafan Chemistry, Engineering, and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
- Halıcıoğlu Data Science Institute, University of California at San Diego, La Jolla, CA, USA
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Deng B, Li A, Zhu Y, Zhou Y, Fei J, Miao Y. SHCBP1 contributes to the proliferation and self‑renewal of cervical cancer cells and activation of the NF‑κB signaling pathway through EIF5A. Oncol Lett 2023; 25:246. [PMID: 37153055 PMCID: PMC10161342 DOI: 10.3892/ol.2023.13832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/24/2023] [Indexed: 05/09/2023] Open
Abstract
Cervical cancer (CC) is the most common human papillomavirus-related disease. Continuous activation of the NF-κB signaling pathway has been observed in CC. SHC binding and spindle associated 1 (SHCBP1) contributes to tumorigenesis and activation of the NF-κB pathway in multiple cancer types, while its function in CC remains unclear. In the present study, three Gene Expression Omnibus datasets were used to identify differentially expressed genes (DEGs) in CC. Loss- and gain-of-function experiments were performed using stable SHCBP1-silenced and SHCBP1-overexpressing CC cells. To further explore the molecular mechanism of SHCBP1 in CC, small interfering RNA targeting eukaryotic translation initiation factor 5A (EIF5A) was transfected into stable SHCBP1-overexpressing CC cells. The results demonstrated that SHCBP1 was an upregulated DEG in CC tissues compared with healthy control cervical tissues. Functional experiments revealed the pro-proliferative and pro-stemness role of SHCBP1 in CC cells (CaSki and SiHa cells), in vitro. Furthermore, the NF-κB signaling pathway in CC cells was activated by SHCBP1. Increases in cell proliferation, stemness and activation of NF-κB, induced by SHCBP1 overexpression in CC cells, were reversed by EIF5A knockdown. Taken together, the results indicated that SHCBP1 serves an important role in regulation of CC cell proliferation, self-renewal and activation of NF-κB via EIF5A. The present study demonstrated a potential molecular mechanism underlying the progression of CC.
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Affiliation(s)
- Boya Deng
- Department of Gynecology, The Second Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
- Correspondence to: Dr Boya Deng, Department of Gynecology, The Second Affiliated Hospital of Zhejiang University, 88 Jiefang Road, Shangcheng, Hangzhou, Zhejiang 310009, P.R. China, E-mail:
| | - Ailin Li
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Ying Zhu
- Department of Gynecology, The Second Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Yingying Zhou
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Jing Fei
- Department of Gynecology, The Second Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Yuan Miao
- Department of Pathology, The College of Basic Medicine Science and The First Hospital of China Medical University, Shenyang, Liaoning 110001, P.R. China
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Biological functions and therapeutic potential of SHCBP1 in human cancer. Biomed Pharmacother 2023; 160:114362. [PMID: 36739763 DOI: 10.1016/j.biopha.2023.114362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The incidence of cancer is increasing globally, and it is the most common cause of death. The identification of novel cancer diagnostic and prognostic biomarkers is important for developing cancer treatment strategies and reducing mortality. SHCSH2 domain-binding protein 1 (SHCBP1) is a protein that specifically binds to the SH2 domain of Src homology-collagen. It participates in the regulation of a variety of signal transduction pathways and can activate a variety of signaling molecules to perform a series of physiological functions. SHCBP1 is expressed in a variety of human tissues, but its abnormal expression in various systems is associated with cancer. SHCBP1 is abnormally expressed in a variety of tumors, and plays roles in almost all aspects of cancer biology (such as cell proliferation, apoptosis prevention, invasion, and metastasis) through various possible mechanisms. Its expression level is related to the clinicopathological characteristics of patients. In addition, the SHCBP1 expression pattern is closely related to cancer type, stage, and other clinical variables. Therefore, SHCBP1 is a promising tumor biomarker for cancer diagnosis and prognosis and a potential therapeutic target. This article reviews the expression, biological functions, mechanisms, and potential clinical significance of SHCBP1 in various human tumors to provide a new theoretical basis for clinical molecular diagnosis, molecular targeted therapy, and scientific research on cancer.
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Identification of Recurrent Chromosome Breaks Underlying Structural Rearrangements in Mammary Cancer Cell Lines. Genes (Basel) 2022; 13:genes13071228. [PMID: 35886011 PMCID: PMC9319013 DOI: 10.3390/genes13071228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/10/2022] [Accepted: 06/28/2022] [Indexed: 02/04/2023] Open
Abstract
Cancer genomes are characterized by the accumulation of small-scale somatic mutations as well as large-scale chromosomal deletions, amplifications, and complex structural rearrangements. This characteristic is at least partially dependent on the ability of cancer cells to undergo recurrent chromosome breakage. In order to address the extent to which chromosomal structural rearrangement breakpoints correlate with recurrent DNA double-strand breaks (DSBs), we simultaneously mapped chromosome structural variation breakpoints (using whole-genome DNA-seq) and spontaneous DSB formation (using Break-seq) in the estrogen receptor (ER)-positive breast cancer cell line MCF-7 and a non-cancer control breast epithelium cell line MCF-10A. We identified concurrent DSBs and structural variation breakpoints almost exclusively in the pericentromeric region of chromosome 16q in MCF-7 cells. We fine-tuned the identification of copy number variation breakpoints on 16q. In addition, we detected recurrent DSBs that occurred in both MCF-7 and MCF-10A. We propose a model for DSB-driven chromosome rearrangements that lead to the translocation of 16q, likely with 10q, and the eventual 16q loss that does not involve the pericentromere of 16q. We present evidence from RNA-seq data that select genes, including SHCBP1, ORC6, and MYLK3, which are immediately downstream from the 16q pericentromere, show heightened expression in MCF-7 cell line compared to the control. Data published by The Cancer Genome Atlas show that all three genes have increased expression in breast tumor samples. We found that SHCBP1 and ORC6 are both strong poor prognosis and treatment outcome markers in the ER-positive breast cancer cohort. We suggest that these genes are potential oncogenes for breast cancer progression. The search for tumor suppressor loss that accompanies the 16q loss ought to be augmented by the identification of potential oncogenes that gained expression during chromosomal rearrangements.
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Puhka M, Thierens L, Nicorici D, Forsman T, Mirtti T, af Hällström T, Serkkola E, Rannikko A. Exploration of Extracellular Vesicle miRNAs, Targeted mRNAs and Pathways in Prostate Cancer: Relation to Disease Status and Progression. Cancers (Basel) 2022; 14:cancers14030532. [PMID: 35158801 PMCID: PMC8833493 DOI: 10.3390/cancers14030532] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/10/2022] [Accepted: 01/17/2022] [Indexed: 02/08/2023] Open
Abstract
Simple Summary Prostate cancer lacks non-invasive specific biomarkers for aggressive disease. Urinary extracellular vesicles (uEV) could provide such markers; however, due to technical challenges, little is known regarding the pathogenesis pathways reflected in uEV. We performed a miRNA, target mRNA and pathway study focused on uEV, exploring the differences between cancer (1) status groups (Gleason score) and (2) progression groups. The uEV provided a surprisingly comprehensive presentation of differentially expressed miRNAs, target mRNAs and pathogenesis pathways. The miRNAs associated with prostate cancer status or progression were mostly unique, but still targeted overlapping sets of signalling, resistance, hormonal and immune pathways. Interestingly, mRNA targets of the key miRNAs (miR-892a, miR-223-3p, miR-146a-5p) were widely expressed in both uEV and plasma EV from PCa patients. The study thus suggests that uEV carry a vast presentation of PCa status and progression-linked RNAs that are worth further exploration in large personalized medicine trials. Abstract Background: Prostate cancer (PCa) lacks non-invasive specific biomarkers for aggressive disease. We studied the potential of urinary extracellular vesicles (uEV) as a liquid PCa biopsy by focusing on the micro RNA (miRNA) cargo, target messenger RNA (mRNA) and pathway analysis. Methods: We subjected uEV samples from 31 PCa patients (pre-prostatectomy) to miRNA sequencing and matched uEV and plasma EV (pEV) from three PCa patients to mRNA sequencing. EV quality control was performed by electron microscopy, Western blotting and particle and RNA analysis. We compared miRNA expression based on PCa status (Gleason Score) and progression (post-prostatectomy follow-up) and confirmed selected miRNAs by quantitative PCR. Expression of target mRNAs was mapped in matched EV. Results: Quality control showed typical small uEV, pEV, RNA and EV-protein marker enriched samples. Comparisons between PCa groups revealed mostly unique differentially expressed miRNAs. However, they targeted comprehensive and largely overlapping sets of cancer and progression-associated signalling, resistance, hormonal and immune pathways. Quantitative PCR confirmed changes in miR-892a (Gleason Score 7 vs. ≥8), miR-223-3p (progression vs. no progression) and miR-146a-5p (both comparisons). Their target mRNAs were expressed widely in PCa EV. Conclusions: PCa status and progression-linked RNAs in uEV are worth exploration in large personalized medicine trials.
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Affiliation(s)
- Maija Puhka
- HiPrep and EV Core, Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00290 Helsinki, Finland;
- Correspondence: (M.P.); (A.R.)
| | - Lisse Thierens
- HiPrep and EV Core, Institute for Molecular Medicine Finland FIMM, University of Helsinki, 00290 Helsinki, Finland;
| | - Daniel Nicorici
- Orion Pharma, Orion Corporation, 02200 Espoo, Finland; (D.N.); (T.F.); (E.S.)
| | - Tarja Forsman
- Orion Pharma, Orion Corporation, 02200 Espoo, Finland; (D.N.); (T.F.); (E.S.)
| | - Tuomas Mirtti
- Department of Pathology, HUS Diagnostic Centre, Helsinki University Hospital, 00290 Helsinki, Finland;
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | | | - Elina Serkkola
- Orion Pharma, Orion Corporation, 02200 Espoo, Finland; (D.N.); (T.F.); (E.S.)
| | - Antti Rannikko
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Urology, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
- Correspondence: (M.P.); (A.R.)
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EGF-induced nuclear translocation of SHCBP1 promotes bladder cancer progression through inhibiting RACGAP1-mediated RAC1 inactivation. Cell Death Dis 2022; 13:39. [PMID: 35013128 PMCID: PMC8748695 DOI: 10.1038/s41419-021-04479-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/01/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022]
Abstract
Bladder cancer is a highly heterogeneous and aggressive malignancy with a poor prognosis. EGF/EGFR activation causes the detachment of SHC-binding protein 1 (SHCBP1) from SHC adapter protein 1 (SHC1), which subsequently translocates into the nucleus and promotes cancer development via multiple signaling pathways. However, the role of the EGF-SHCBP1 axis in bladder cancer progression remains unexplored. Herein, we report that SHCBP1 is upregulated in bladder cancer tissues and cells, with cytoplasmic or nuclear localization. Released SHCBP1 responds to EGF stimulation by translocating into the nucleus following Ser273 phosphorylation. Depletion of SHCBP1 reduces EGF-induced cell migration and invasiveness of bladder cancer cells. Mechanistically, SHCBP1 binds to RACGAP1 via its N-terminal domain of amino acids 1 ~ 428, and this interaction is enhanced following EGF treatment. Furthermore, SHCBP1 facilitates cell migration by inhibiting RACGAP-mediated GTP-RAC1 inactivation, whose activity is indispensable for cell movement. Collectively, we demonstrate that the EGF-SHCBP1-RACGAP1-RAC1 axis acts as a novel regulatory mechanism of bladder cancer progression, which offers a new clinical therapeutic strategy to combat bladder cancer.
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Identification of SHCBP1 as a potential biomarker involving diagnosis, prognosis, and tumor immune microenvironment across multiple cancers. Comput Struct Biotechnol J 2022; 20:3106-3119. [PMID: 35782736 PMCID: PMC9233189 DOI: 10.1016/j.csbj.2022.06.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/29/2022] [Accepted: 06/15/2022] [Indexed: 11/23/2022] Open
Abstract
Shc SH2-domain binding protein 1 (SHCBP1), a protein specific binding to SH2 domain of Src homolog and collagen homolog (Shc), takes part in the regulation of various signal transduction pathways, which has been reported to be associated with tumorigenesis and progression. However, the pathological mechanisms are not completely investigated. Thus, this study aimed to comprehensively elucidate the potential functions of SHCBP1 in multiple cancer types. The comprehensive analyses for SHCBP1 in various tumors, including gene expression, diagnosis, prognosis, immune-related features, genetic alteration, and function enrichment, were conducted based on multiple databases and analysis tools. SHCBP1 was upregulated in most types of cancers. The results of qRT-PCR had confirmed that SHCBP1 mRNA was significantly upregulated in lung adenocarcinoma (LUAD) and liver hepatocellular carcinoma (LIHC) cell lines. Based on the receiver operating characteristic (ROC) and survival analysis, SHCBP1 was considered as a potential diagnostic and prognostic biomarker. Furthermore, SHCBP1 expression was linked with tumor immunity and immunosuppressive microenvironment according to the correlation analysis of SHCBP1 expression with immune cells infiltration, immune checkpoint genes, and immune-related genes (MHC genes, chemokines, and chemokines receptors). Moreover, SHCBP1 expression correlated with tumor mutational burden (TMB), microsatellite instability (MSI), and neoantigens. The feature of SHCBP1 mutational landscape in pan-cancer was identified. Finally, we focused on investigating the clinical significance and the potential biological role of SHCBP1 in LUAD. Our study comprehensively uncovered that SHCBP1 could be identified as an immune-related biomarker for cancer diagnosis and prognosis, and a potential therapeutic target for tumor immunotherapy.
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Matsuda T, Miyata Y, Nakamura Y, Otsubo A, Mukae Y, Harada J, Mitsunari K, Matsuo T, Ohba K, Furusato B, Sakai H. Pathological significance and prognostic role of LATS2 in prostate cancer. Prostate 2021; 81:1252-1260. [PMID: 34492128 PMCID: PMC9290072 DOI: 10.1002/pros.24226] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/27/2021] [Accepted: 04/30/2021] [Indexed: 11/11/2022]
Abstract
BACKGROUND Large tumor suppressor 2 (LATS2) is an important regulator of the Hippo pathway and it plays crucial roles in cell survival and behaviors. Herein, we evaluated the pathological roles of LATS2 in prostate cancer (PC), for which very little information is available. METHODS Cell proliferation, migration, and invasion in response to the siRNA-mediated knockdown (KD) LATS2 expression were evaluated in two PC cell lines (LNCaP and PC3). The expression of LATS2 in specimens from 204 PC patients was investigated immunohistochemically, and the relationships between its expression and clinicopathological features, proliferation index (PI; measured using an anti-KI-67 antibody), and biochemical recurrence (BCR) were investigated. RESULTS KD of LATS2 increased the growth, migration, and invasion in LNCaP cells and only increased migration in PC3 cells. The expression of LATS2 was negatively associated with the grade group, T, N, M stage, and PI. In addition, the expression of LATS2 was a useful predictor of the histological effects of neoadjuvant hormonal therapy and BCR-free survival periods. A multivariate analysis model including clinicopathological features showed that negative expression of LATS2 had a significantly higher risk of BCR (odds ratio = 2.95, P < 0.001). CONCLUSIONS LATS2 acts as a tumor suppressor in PC. LATS2 expression is a useful predictor for BCR. LATS2-related activities are possibly dependent on the androgen-dependency of PC cells. Therefore, we suggest that LATS2 could be a potential therapeutic target and a useful predictor for outcome in patients with PC.
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Affiliation(s)
- Tsuyoshi Matsuda
- Department of UrologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Yasuyoshi Miyata
- Department of UrologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Yuichiro Nakamura
- Department of UrologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Asato Otsubo
- Department of UrologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Yuta Mukae
- Department of UrologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Junki Harada
- Department of UrologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Kensuke Mitsunari
- Department of UrologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Tomohiro Matsuo
- Department of UrologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Kojiro Ohba
- Department of UrologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Bungo Furusato
- Department of pathologyNagasaki University Graduate School of Biomedical ScienecesNagasakiJapan
| | - Hideki Sakai
- Department of UrologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
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14
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Geng H, Guo M, Xu W, Zang X, Wu T, Teng F, Wang Y, Liu X, Wang X, Sun Q, Liang J. SHCBP1 Promotes Papillary Thyroid Carcinoma Carcinogenesis and Progression Through Promoting Formation of Integrin and Collagen and Maintaining Cell Stemness. Front Endocrinol (Lausanne) 2021; 11:613879. [PMID: 33716952 PMCID: PMC7953042 DOI: 10.3389/fendo.2020.613879] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 12/31/2020] [Indexed: 01/08/2023] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common thyroid cancer with a rapidly increasing incidence globally. Bioinformatics analyses suggested that SHCBP1 (SHC SH2 Domain-Binding Protein 1) was significantly up-regulated in PTC tumor tissues, which was further confirmed by immunohistochemical staining and qPCR analyses in Xuzhou cohort. Moreover, the results indicated that the mRNA level of SHCBP1 was negatively associated with patients' disease-free survival rate, and further analysis reveals that patients with high SHCBP1 expression tend to have more lymph node metastasis. Afterward, MTT, colony formation, cell-cycle assay, FACS apoptosis assay, invasion, migration, as well as scratch assay were performed to study the phenotypes change of PTC cells after knocking down SHCBP1. The in vivo subcutaneous tumor model was developed to study the proliferation ability of PTC cells after SHCBP1 knockdown. We show that knock down of SHCBP1 significantly inhibits PTC cell proliferation, cell cycle, invasion and migration in vivo and in vitro. Western blot and qRT-PCR showed that knockdown of SHCBP1 could significantly reduce MYC, KLF4, CD44, ITGA6, ITGB1, ITGB5, and COL4A2 expression at both RNA and protein levels, which indicated that SHCBP1 might be involved in PTC carcinogenesis and progression through targeting formation of integrin and collagen and cell stemness pathways, and can be a potential diagnosis biomarker and therapeutic target for PTC.
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Affiliation(s)
- Houfa Geng
- Department of Endocrinology, Affiliated Hospital of Medical College of Southeast University and Xuzhou Central Hospital, Xuzhou, China
- Xuzhou Clinical School, Xuzhou Medical University, Xuzhou, China
- Xuzhou Clinical School, Nanjing Medical University, Xuzhou, China
| | - Mengzhe Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Wei Xu
- Department of Endocrinology, Affiliated Hospital of Medical College of Southeast University and Xuzhou Central Hospital, Xuzhou, China
- Xuzhou Clinical School, Xuzhou Medical University, Xuzhou, China
- Xuzhou Clinical School, Nanjing Medical University, Xuzhou, China
| | - Xiu Zang
- Department of Endocrinology, Affiliated Hospital of Medical College of Southeast University and Xuzhou Central Hospital, Xuzhou, China
- Xuzhou Clinical School, Xuzhou Medical University, Xuzhou, China
- Xuzhou Clinical School, Nanjing Medical University, Xuzhou, China
| | - Tingting Wu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, China
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Fei Teng
- Department of Endocrinology, Affiliated Hospital of Medical College of Southeast University and Xuzhou Central Hospital, Xuzhou, China
- Xuzhou Clinical School, Xuzhou Medical University, Xuzhou, China
- Xuzhou Clinical School, Nanjing Medical University, Xuzhou, China
| | - Yu Wang
- Department of Endocrinology, Affiliated Hospital of Medical College of Southeast University and Xuzhou Central Hospital, Xuzhou, China
- Xuzhou Clinical School, Xuzhou Medical University, Xuzhou, China
- Xuzhou Clinical School, Nanjing Medical University, Xuzhou, China
| | - Xuekui Liu
- Department of Endocrinology, Affiliated Hospital of Medical College of Southeast University and Xuzhou Central Hospital, Xuzhou, China
- Xuzhou Clinical School, Xuzhou Medical University, Xuzhou, China
- Xuzhou Clinical School, Nanjing Medical University, Xuzhou, China
| | - Xiuli Wang
- Department of Endocrinology, Affiliated Hospital of Medical College of Southeast University and Xuzhou Central Hospital, Xuzhou, China
- Xuzhou Clinical School, Xuzhou Medical University, Xuzhou, China
- Xuzhou Clinical School, Nanjing Medical University, Xuzhou, China
| | - Qiang Sun
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Jun Liang
- Department of Endocrinology, Affiliated Hospital of Medical College of Southeast University and Xuzhou Central Hospital, Xuzhou, China
- Xuzhou Clinical School, Xuzhou Medical University, Xuzhou, China
- Xuzhou Clinical School, Nanjing Medical University, Xuzhou, China
- Xuzhou Institute of Medical Science, Postgraduate Workstation of Soochow University, Xuzhou, China
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15
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Yang C, Hu JF, Zhan Q, Wang ZW, Li G, Pan JJ, Huang L, Liao CY, Huang Y, Tian YF, Shen BY, Chen JZ, Wang YD, Chen S. SHCBP1 interacting with EOGT enhances O-GlcNAcylation of NOTCH1 and promotes the development of pancreatic cancer. Genomics 2021; 113:827-842. [PMID: 33515675 DOI: 10.1016/j.ygeno.2021.01.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/12/2020] [Accepted: 01/21/2021] [Indexed: 01/07/2023]
Abstract
O-GlcNAcylation is important in the development and progression of pancreatic ductal adenocarcinoma (PDAC). The glycosyltransferase EGF domain-specific O-linked GlcNAc transferase (EOGT) acts as a key participant in glycosylating NOTCH1. High-throughput sequencing of specimens from 30 advanced PDAC patients identified SHCBP1 and EOGT as factors of poor prognosis. We hypothesized that they could mediate PDAC progression by influencing NOTCH1 O-GlcNAcylation. Thus, 186 PDAC tissue specimens were immunostained for EOGT and SHCBP1. Pancreatic cancer cell lines and nude mouse models were used for in vitro and in vivo experiments. Respectively, The protein expression of EOGT and SHCBP1 was significantly elevated and correlated with worse prognosis in PDAC patients. In vitro, SHCBP1 overexpression promoted pancreatic cancer cell proliferation, migration and invasion, while knocking down SHCBP1 and EOGT inhibited these malignant processes. In vivo data showed that SHCBP1 overexpression promoted xenograft growth and lung metastasis and shortened survival in mice, whereas knocking down either EOGT or SHCBP1 expression suppressed xenograft growth and metastasis and prolonged survival. We further clarified the molecular mechanisms by which EOGT and SHCBP1 enhance the O-GlcNAcylation of NOTCH1, Subsequently promoting the nuclear localization of the Notch intracellular domain (NICD) and inhibiting the transcription of E-cadherin and P21 in pancreatic cancer cells.
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Affiliation(s)
- Can Yang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, PR China
| | - Jian-Fei Hu
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, PR China
| | - Qian Zhan
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Zu-Wei Wang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, PR China
| | - Ge Li
- Department of Hepatobiliary Surgery, Union Hospital, Fujian Medical University, Fuzhou 350001, PR China
| | - Jing-Jing Pan
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, PR China
| | - Long Huang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, PR China; Department of Hepatobiliary Surgery, Fujian Provincial Hospital, Fujian Medical University, Fuzhou 350001, PR China
| | - Cheng-Yu Liao
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, PR China
| | - Yi Huang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, PR China; Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou 350001, PR China
| | - Yi-Feng Tian
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, PR China; Department of Hepatobiliary Surgery, Fujian Provincial Hospital, Fujian Medical University, Fuzhou 350001, PR China
| | - Bai-Yong Shen
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China
| | - Jiang-Zhi Chen
- Department of Hepatobiliary Surgery, Union Hospital, Fujian Medical University, Fuzhou 350001, PR China; Fujian Medical University Cancer Center, Fuzhou 350001, PR China; Department of Hepatobiliary Surgery, Fujian Institute of Hepatobiliary Surgery, 350001, PR China.
| | - Yao-Dong Wang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, PR China; Department of Hepatobiliary Surgery, Fujian Provincial Hospital, Fujian Medical University, Fuzhou 350001, PR China.
| | - Shi Chen
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou 350001, PR China; Department of Hepatobiliary Surgery, Fujian Provincial Hospital, Fujian Medical University, Fuzhou 350001, PR China.
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16
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Gu C, Shi X, Dai C, Shen F, Rocco G, Chen J, Huang Z, Chen C, He C, Huang T, Chen C. RNA m 6A Modification in Cancers: Molecular Mechanisms and Potential Clinical Applications. Innovation (N Y) 2020; 1:100066. [PMID: 34557726 PMCID: PMC8454620 DOI: 10.1016/j.xinn.2020.100066] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
N6-Methyladenosine (m6A) RNA modification brings a new dawn for RNA modification researches in recent years. This posttranscriptional RNA modification is dynamic and reversible, and is regulated by methylases ("writers"), demethylases ("erasers"), and proteins that preferentially recognize m6A modifications ("readers"). The change of RNA m6A modification regulates RNA metabolism in eucaryon, including translation, splicing, exporting, decay, and processing. Thereby the dysregulation of m6A may lead to tumorigenesis and progression. Given the tumorigenic role of abnormal m6A expression, m6A regulators may function as potential clinical therapeutic targets for cancers. In this review, we emphasize on the underlying mechanisms of m6A modifications in tumorigenesis and further introduce the potential m6A regulators-associated therapeutic targets for tumor therapy.
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Affiliation(s)
- Chang Gu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Xin Shi
- Department of Cardiology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Chenyang Dai
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Gaetano Rocco
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jiafei Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China
| | - Zhengyu Huang
- Department of Colorectal and Anal Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Chunji Chen
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA,Medical Scientist Training Program/Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA,Corresponding author
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China,Corresponding author
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200433, China,Corresponding author
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17
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Chen SH, Ke ZB, Wu YP, Chen DN, Yu X, Chen Y, Wei Y, Zheng QS, Xue XY, Xu N. Predictors of Prolonged Laparoscopic Radical Prostatectomy and the Creation of a Scoring System for the Duration. Cancer Manag Res 2020; 12:8005-8014. [PMID: 32943933 PMCID: PMC7481309 DOI: 10.2147/cmar.s265480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/07/2020] [Indexed: 11/30/2022] Open
Abstract
Purpose To identify the relevant factors, and create and validate a predictive scoring system for the duration of laparoscopic radical prostatectomy (LRP). Patients and Methods We retrospectively analyzed clinicopathological data from 436 patients who underwent LRP between January 2014 and January 2019, of whom 304 cases were used as a model creation group and 132 were used as a validation group. Uni/multivariate linear regression analysis was performed to determine the predictors of the duration of the procedure and a novel scoring system was created using these predictors. External validation of the scoring system was performed. The Hosmer–Lemeshow test was used to determine the goodness-of-fit of the model and calibration plots were created for visual assessment. Results “Prolonged duration” was defined as a duration of the procedure that was longer than the mean (>150 min) duration. Multivariate analysis showed that body mass index (BMI), prostate volume, intravesicular protrusion of the prostate (IPP), the ratio of the cross-sectional areas of the prostate and the Retzius space (P/R), pelvic lymph node dissection, and neurovascular bundle (NVB) preservation were significant predictors of prolonged duration. A scoring system that included these six parameters was created and the area under the curve achieved during receiver operating characteristic analysis using this scoring system was 0.874 (95% confidence interval [CI]: 0.836–0.913). The Hosmer–Lemeshow test showed that the scoring system was well calibrated (X2=5.339, P=0.376). The external validation showed that the model had high predictive accuracy (AUC=0.835, 95% CI: 0.764–0.906) and goodness-of-fit (X2=4.401, P=0.493). Conclusion The following factors were significantly associated with prolonged duration of laparoscopic radical prostatectomy: BMI, prostate volume, IPP, P/R, pelvic lymph node dissection, and NVB preservation. The novel scoring system created can be used to accurately predict the duration of the procedure, assess the difficulty of surgery, and improve perioperative efficiency.
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Affiliation(s)
- Shao-Hao Chen
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, People's Republic of China
| | - Zhi-Bin Ke
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, People's Republic of China
| | - Yu-Peng Wu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, People's Republic of China
| | - Dong-Ning Chen
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, People's Republic of China
| | - Xiang Yu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, People's Republic of China
| | - Yu Chen
- Cancer Bio-Immunotherapy Center, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, People's Republic of China.,Department of Medical Oncology, Fujian Medical University Cancer Hospital and Fujian Cancer Hospital, Fuzhou, People's Republic of China
| | - Yong Wei
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, People's Republic of China
| | - Qing-Shui Zheng
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, People's Republic of China
| | - Xue-Yi Xue
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, People's Republic of China
| | - Ning Xu
- Department of Urology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350005, People's Republic of China
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