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Yu Z, Zhang Z, Liu J, Wu X, Fan X, Pang J, Bao H, Yin J, Wu X, Shao Y, Liu Z, Liu F. Identification of pathogenic germline variants in a large Chinese lung cancer cohort by clinical sequencing. Mol Oncol 2024; 18:1301-1315. [PMID: 37885353 PMCID: PMC11076998 DOI: 10.1002/1878-0261.13548] [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: 06/01/2023] [Revised: 09/29/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023] Open
Abstract
Genetic factors play significant roles in the tumorigenicity of lung cancer; however, there is lack of systematic and large-scale characterization of pathogenic germline variants for lung cancer. In this study, germline variants in 146 preselected cancer-susceptibility genes were detected in 17 904 Chinese lung cancer patients by clinical next-generation sequencing. Among 17 904 patients, 1738 patients (9.7%) carried 1840 pathogenic/likely pathogenic (P/LP) variants from 87 cancer-susceptibility genes. SBDS (SBDS ribosome maturation factor) (1.37%), TSHR (thyroid stimulating hormone receptor) (1.20%), BLM (BLM RecQ like helicase) (0.62%), BRCA2 (BRCA2 DNA repair associated) (0.62%), and ATM (ATM serine/threonine kinase) (0.45%) were the top five genes with the highest overall prevalence. The top mutated pathways were all involved in DNA damage repair (DDR). Case-control analysis showed SBDS c.184A>T(p.K62*), TSHR c.1574T>C(p.F525S), BRIP1 (BRCA1 interacting helicase 1) c.1018C>T(p.L340F), and MUTYH (mutY DNA glycosylase) c.55C>T(p.R19*) were significantly associated with increased lung cancer risk (q value < 0.05). P/LP variants in certain genes were associated with early onset of lung cancer. Our study indicates that Chinese lung cancer patients have a higher prevalence of P/LP variants than previously reported. P/LP variants are distributed in multiple pathways and dominated by DNA damage repair-associated pathways. The association between identified P/LP variants and lung cancer risk requires further studies for verification.
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Affiliation(s)
- Zhe Yu
- Department of Respiratory MedicineNingbo NO.2 HospitalChina
| | - Zirui Zhang
- Department of Cardiovascular and Thoracic SurgeryNanjing Drum Tower Hospital Affiliated to Nanjing University School of MedicineChina
| | - Jun Liu
- Department of ChemotherapyAffiliated Hospital of Nantong UniversityChina
| | | | | | | | - Hua Bao
- Nanjing Geneseeq Technology Inc.China
| | - Jiani Yin
- Nanjing Geneseeq Technology Inc.China
| | - Xue Wu
- Nanjing Geneseeq Technology Inc.China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc.China
- School of Public HealthNanjing Medical UniversityChina
| | - Zhengcheng Liu
- Department of Cardiovascular and Thoracic SurgeryNanjing Drum Tower Hospital Affiliated to Nanjing University School of MedicineChina
| | - Fang Liu
- Senior Department of OncologyThe Fifth Medical Center of PLA General HospitalBeijingChina
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2
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Chen C, Lin CJ, Pei YC, Ma D, Liao L, Li SY, Fan L, Di GH, Wu SY, Liu XY, Wang YJ, Hong Q, Zhang GL, Xu LL, Li BB, Huang W, Shi JX, Jiang YZ, Hu X, Shao ZM. Comprehensive genomic profiling of breast cancers characterizes germline-somatic mutation interactions mediating therapeutic vulnerabilities. Cell Discov 2023; 9:125. [PMID: 38114467 PMCID: PMC10730692 DOI: 10.1038/s41421-023-00614-3] [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: 07/13/2023] [Accepted: 10/08/2023] [Indexed: 12/21/2023] Open
Abstract
Germline-somatic mutation interactions are universal and associated with tumorigenesis, but their role in breast cancer, especially in non-Caucasians, remains poorly characterized. We performed large-scale prospective targeted sequencing of matched tumor-blood samples from 4079 Chinese females, coupled with detailed clinical annotation, to map interactions between germline and somatic alterations. We discovered 368 pathogenic germline variants and identified 5 breast cancer DNA repair-associated genes (BCDGs; BRCA1/BRCA2/CHEK2/PALB2/TP53). BCDG mutation carriers, especially those with two-hit inactivation, demonstrated younger onset, higher tumor mutation burden, and greater clinical benefits from platinum drugs, PARP inhibitors, and immune checkpoint inhibitors. Furthermore, we leveraged a multiomics cohort to reveal that clinical benefits derived from two-hit events are associated with increased genome instability and an immune-activated tumor microenvironment. We also established an ethnicity-specific tool to predict BCDG mutation and two-hit status for genetic evaluation and therapeutic decisions. Overall, this study leveraged the large sequencing cohort of Chinese breast cancers, optimizing genomics-guided selection of DNA damaging-targeted therapy and immunotherapy within a broader population.
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Affiliation(s)
- Chao Chen
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cai-Jin Lin
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu-Chen Pei
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ding Ma
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Li Liao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Si-Yuan Li
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lei Fan
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gen-Hong Di
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Song-Yang Wu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi-Yu Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yun-Jin Wang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Qi Hong
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Guo-Liang Zhang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lin-Lin Xu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Bei-Bei Li
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wei Huang
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Jin-Xiu Shi
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Xin Hu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Precision Cancer Medical Center Affiliated to Fudan University Shanghai Cancer Center, Shanghai, China.
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3
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Abdeltwab RM, Yacoub E, Rashad AH, Shohdy KS. Molecular Basis of Tumorigenesis of Bladder Cancer and Emerging Concepts in Developing Therapeutic Targets. Bladder Cancer 2023; 9:313-322. [PMID: 38994247 PMCID: PMC11165923 DOI: 10.3233/blc-230025] [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: 03/22/2023] [Accepted: 09/15/2023] [Indexed: 07/13/2024]
Abstract
BACKGROUND Advanced urothelial carcinoma (UC) is an aggressive disease whose mutagenic processes are yet to be elucidated. Targeted therapies are urgently needed, but the road from bench to bedside is slowly progressing. In this review, we discuss urothelial carcinoma etiology, along with the most recent advances in UC candidate targeted therapies. METHODOLOGY A comprehensive database search was performed. We aimed to review the most recent updates on UC genomics and targeted therapies. Pre-clinical as well as clinical studies were included. RESULTS Our review highlights the advances in understanding the molecular basis of urothelial tumorigenesis, including smoking, chemical parasitic carcinogens, inheritance, and APOBEC3 editing enzymes. We discussed how these factors contributed to the current mutational landscape of UC. Therapeutic options for UC are still very limited. However, several promising therapeutic approaches are in development to leverage our knowledge of molecular targets, such as targeting fibroblast growth factor receptors (FGFR), DNA damage repair pathways, and HER2. CONCLUSIONS Blindly testing targeted therapies based on other cancer data is not sufficient. UC-specific biomarkers are needed to precisely use the appropriate drug for the appropriate population. More efforts to understand UC biology and evolution are urgently needed.
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Affiliation(s)
| | - Elaria Yacoub
- Department of Clinical Oncology, Cairo University, Cairo, Egypt
| | - Ahmed H. Rashad
- Department of Clinical Oncology, Cairo University, Cairo, Egypt
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Chen Z, Liang H, Wei P. Data-adaptive and pathway-based tests for association studies between somatic mutations and germline variations in human cancers. Genet Epidemiol 2023; 47:617-636. [PMID: 37822029 DOI: 10.1002/gepi.22537] [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: 10/20/2022] [Revised: 07/22/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023]
Abstract
Cancer is a disease driven by a combination of inherited genetic variants and somatic mutations. Recently available large-scale sequencing data of cancer genomes have provided an unprecedented opportunity to study the interactions between them. However, previous studies on this topic have been limited by simple, low statistical power tests such as Fisher's exact test. In this paper, we design data-adaptive and pathway-based tests based on the score statistic for association studies between somatic mutations and germline variations. Previous research has shown that two single-nucleotide polymorphism (SNP)-set-based association tests, adaptive sum of powered score (aSPU) and data-adaptive pathway-based (aSPUpath) tests, increase the power in genome-wide association studies (GWASs) with a single disease trait in a case-control study. We extend aSPU and aSPUpath to multi-traits, that is, somatic mutations of multiple genes in a cohort study, allowing extensive information aggregation at both SNP and gene levels.p $p$ -values from different parameters assuming varying genetic architecture are combined to yield data-adaptive tests for somatic mutations and germline variations. Extensive simulations show that, in comparison with some commonly used methods, our data-adaptive somatic mutations/germline variations tests can be applied to multiple germline SNPs/genes/pathways, and generally have much higher statistical powers while maintaining the appropriate type I error. The proposed tests are applied to a large-scale real-world International Cancer Genome Consortium whole genome sequencing data set of 2583 subjects, detecting more significant and biologically relevant associations compared with the other existing methods on both gene and pathway levels. Our study has systematically identified the associations between various germline variations and somatic mutations across different cancer types, which potentially provides valuable utility for cancer risk prediction, prognosis, and therapeutics.
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Affiliation(s)
- Zhongyuan Chen
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Peng Wei
- Department of Biostatistics, MD Anderson Cancer Center, Houston, Texas, USA
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5
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Guo Y, Jiang Z, Chen Q, Xie D, Zhou Y, Yin W, Wang Z, Wang B, Ren C, Jiang X. Construction and experimental validation of a signature for predicting prognosis and immune infiltration analysis of glioma based on disulfidptosis-related lncRNAs. Front Immunol 2023; 14:1291385. [PMID: 38022537 PMCID: PMC10655028 DOI: 10.3389/fimmu.2023.1291385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Backgrounds Disulfidptosis, a newly discovered mechanism of programmed cell death, is believed to have a unique role in elucidating cancer progression and guiding cancer therapy strategies. However, no studies have yet explored this mechanism in glioma. Methods We downloaded data on glioma patients from online databases to address this gap. Subsequently, we identified disulfidptosis-related genes from published literature and verified the associated lncRNAs. Results Through univariate, multivariate, and least absolute shrinkage and selection operator (LASSO) regression algorithms analyses, we identified 10 lncRNAs. These were then utilized to construct prognostic prediction models, culminating in a risk-scoring signature. Reliability and validity tests demonstrated that the model effectively discerns glioma patients' prognosis outcomes. We also analyzed the relationship between the risk score and immune characteristics, and identified several drugs that may be effective for high-risk patients. In vitro experiments revealed that LINC02525 could enhances glioma cells' migration and invasion capacities. Additionally, knocking down LINC02525 was observed to promote glioma cell disulfidptosis. Conclusion This study delves into disulfidptosis-related lncRNAs in glioma, offering novel insights into glioma therapeutic strategies.
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Affiliation(s)
- Youwei Guo
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhipeng Jiang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Quan Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Dongcheng Xie
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yi Zhou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wen Yin
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zihan Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Binbin Wang
- Department of Neurosurgery, the First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Caiping Ren
- Cancer Research Institute, Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Health Commission (NHC) Key Laboratory of Carcinogenesis and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Xingjun Jiang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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6
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Sun Z, Bai C, Su M, Tang H, Wu X, Wang Y, Bao H, Liu X, Wu X, Shao Y, Xu B. Comprehensive profiling of pathogenic germline large genomic rearrangements in a pan-cancer analysis. Mol Oncol 2023; 17:1917-1929. [PMID: 37013911 PMCID: PMC10483597 DOI: 10.1002/1878-0261.13430] [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: 12/21/2022] [Revised: 03/07/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023] Open
Abstract
The presence of large genomic rearrangements (LGRs) has been heavily investigated in breast and ovarian cancer. However, correlations between LGRs and cancer types beyond these two have not been extensively profiled, likely due to the highly inefficient methods of detecting these types of alterations. This study utilized next-generation sequencing (NGS) to analyze and classify the germline LGR profile in 17 025 cancer patients across 22 cancer types. We characterized newly identified LGRs based on predicted pathogenicity and took a closer look at genes that acquire both germline and somatic mutations within our samples. The detection method for LGRs was validated using droplet digital polymerase chain reaction (ddPCR) assay of commonly investigated LGR genes. In total, 15 659 samples from across 22 cancer types were retained for analysis after filtering. We observed that, in our cohort, the cancer types with the highest proportion of germline LGRs were ovarian cancer (4.7%), renal cell carcinoma (2.5%), breast cancer (2%), glioma (1.8%) and thyroid carcinoma (1.8%). Annotation of detected germline variants revealed several genes-MSH2, FANCA and PMS2-that contain novel LGRs. We observed co-occurrences between germline LGRs in MSH2 and somatic single nucleotide variants/insertion and deletions (SNVs/InDels) in BRCA2, KTM2B, KDM5A, CHD8, and HNF1A. Furthermore, our analysis showed that samples with pathogenic and likely pathogenic germline LGRs tended to also have higher mutational burden, chromosomal instability, and microsatellite instability ratio compared to samples with pathogenic germline SNVs/InDels. In this study, we demonstrated the prevalence of pathogenic germline LGRs beyond breast and ovarian cancer. The profiles of these pathogenic or likely pathogenic alterations will fuel further investigations and highlight new understanding of LGRs across multiple cancer types.
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Affiliation(s)
- Zhe Sun
- The First Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangdongChina
| | - Chujie Bai
- Department of Bone and Soft Tissue Tumor, Key Laboratory of Carcinogenesis and Translational ResearchPeking University Cancer Hospital and InstituteBeijingChina
| | - Miaoyi Su
- Department of Radiation OncologyGuangqian HospitalQuanzhouChina
| | - Haimeng Tang
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Xiaoying Wu
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Yue Wang
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Hua Bao
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Xunbiao Liu
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Xue Wu
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Yang Shao
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
- School of Public HealthNanjing Medical UniversityChina
| | - Bei Xu
- Department of Medical OncologyZhongshan HospitalShanghaiChina
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7
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Jubber I, Ong S, Bukavina L, Black PC, Compérat E, Kamat AM, Kiemeney L, Lawrentschuk N, Lerner SP, Meeks JJ, Moch H, Necchi A, Panebianco V, Sridhar SS, Znaor A, Catto JWF, Cumberbatch MG. Epidemiology of Bladder Cancer in 2023: A Systematic Review of Risk Factors. Eur Urol 2023; 84:176-190. [PMID: 37198015 DOI: 10.1016/j.eururo.2023.03.029] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/01/2023] [Accepted: 03/24/2023] [Indexed: 05/19/2023]
Abstract
CONTEXT Bladder cancer (BC) is common worldwide and poses a significant public health challenge. External risk factors and the wider exposome (totality of exposure from external and internal factors) contribute significantly to the development of BC. Therefore, establishing a clear understanding of these risk factors is the key to prevention. OBJECTIVE To perform an up-to-date systematic review of BC's epidemiology and external risk factors. EVIDENCE ACQUISITION Two reviewers (I.J. and S.O.) performed a systematic review using PubMed and Embase in January 2022 and updated it in September 2022. The search was restricted to 4 yr since our previous review in 2018. EVIDENCE SYNTHESIS Our search identified 5177 articles and a total of 349 full-text manuscripts. GLOBOCAN data from 2020 revealed an incidence of 573 000 new BC cases and 213 000 deaths worldwide in 2020. The 5-yr prevalence worldwide in 2020 was 1 721 000. Tobacco smoking and occupational exposures (aromatic amines and polycyclic aromatic hydrocarbons) are the most substantial risk factors. In addition, correlative evidence exists for several risk factors, including specific dietary factors, imbalanced microbiome, gene-environment risk factor interactions, diesel exhaust emission exposure, and pelvic radiotherapy. CONCLUSIONS We present a contemporary overview of the epidemiology of BC and the current evidence for BC risk factors. Smoking and specific occupational exposures are the most established risk factors. There is emerging evidence for specific dietary factors, imbalanced microbiome, gene-external risk factor interactions, diesel exhaust emission exposure, and pelvic radiotherapy. Further high-quality evidence is required to confirm initial findings and further understand cancer prevention. PATIENT SUMMARY Bladder cancer is common, and the most substantial risk factors are smoking and workplace exposure to suspected carcinogens. On-going research to identify avoidable risk factors could reduce the number of people who get bladder cancer.
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Affiliation(s)
- Ibrahim Jubber
- Academic Urology Unit, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK.
| | - Sean Ong
- EJ Whitten Foundation Prostate Cancer Research Centre, Epworth HealthCare, Melbourne, Australia; Department of Surgery, University of Melbourne, Melbourne, Australia
| | | | - Peter C Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eva Compérat
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Ashish M Kamat
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Nathan Lawrentschuk
- EJ Whitten Foundation Prostate Cancer Research Centre, Epworth HealthCare, Melbourne, Australia; Department of Surgery, University of Melbourne, Melbourne, Australia; Department of Surgery, Royal Melbourne Hospital, Melbourne, Australia
| | - Seth P Lerner
- Scott Department of Urology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Joshua J Meeks
- Departments of Urology and Biochemistry, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Andrea Necchi
- Department of Medical Oncology, IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, Milan, Italy
| | - Valeria Panebianco
- Department of Radiological Sciences, Oncology, and Pathology, Sapienza University of Rome, Rome, Italy
| | - Srikala S Sridhar
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Ariana Znaor
- Cancer Surveillance Branch, International Agency for Research on Cancer, Lyon, France
| | - James W F Catto
- Academic Urology Unit, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Marcus G Cumberbatch
- Academic Urology Unit, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
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8
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Orji P, Sun H, Isali I, Bell S, Zaorsky N, Mishra K, Gupta S, Correa A, Smaldone M, Calaway A, Viterbo R, Bukavina L. Female sexual function evaluation and intraoperative vaginal reconstruction in bladder cancer. World J Urol 2023; 41:1751-1762. [PMID: 37419972 DOI: 10.1007/s00345-023-04502-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/12/2023] [Indexed: 07/09/2023] Open
Abstract
RC significantly negatively impacts sexual function (SF) in both men and women. While significant research resources have been allocated to examine the deleterious effects of post prostatectomy erectile dysfunction, little attention has been directed towards female sexual function and organ preservation post cystectomy. These academic shortcomings often result in poor provider awareness and inadequate preoperative assessment. As such, it is crucial for all providers involved in female RC care to understand the necessary and available tools for preoperative evaluation, in addition to the anatomic and reconstructive techniques. This review aims to summarize the current preoperative evaluation and available tools of SF assessment and describe in detail the varying operative techniques in the preservation or restoration of SF in women after RC. The review explores the intricacies of preoperative evaluation tools, and intraoperative techniques for organ- and nerve-sparing during radical cystectomy in females. Particular emphasis on vaginal reconstruction after partial or complete resection is provided, including split-thickness skin (STF) graft vaginoplasy, pedicled flaps, myocutaneous flaps and use of bowel segments. In conclusion, this narrative review highlights the importance of understanding anatomic considerations and nerve-sparing strategies in promoting postoperative SF and quality of life. Furthermore, the review describes the advantages and limitations of each organ- and nerve-sparing technique and their impact on sexual function and overall well-being.
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Affiliation(s)
- Peace Orji
- Case Western Reserve School of Medicine, Cleveland, OH, USA
| | - Helen Sun
- Case Western Reserve School of Medicine, Cleveland, OH, USA
- Department of Urology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Ilaha Isali
- Case Western Reserve School of Medicine, Cleveland, OH, USA
- Department of Urology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Spencer Bell
- Department of Urologic Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Nicholas Zaorsky
- Case Western Reserve School of Medicine, Cleveland, OH, USA
- Department of Urology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Kirtishri Mishra
- Case Western Reserve School of Medicine, Cleveland, OH, USA
- Department of Urology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Shubham Gupta
- Case Western Reserve School of Medicine, Cleveland, OH, USA
- Department of Urology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Andres Correa
- Department of Urologic Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Marc Smaldone
- Department of Urologic Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Adam Calaway
- Case Western Reserve School of Medicine, Cleveland, OH, USA
- Department of Urology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Rosalia Viterbo
- Department of Urologic Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Laura Bukavina
- Department of Urologic Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA.
- Department of Urologic Oncology, Fox Chase Cancer Center, Temple Health Medical Center, Philadelphia, PA, 19111, USA.
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9
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Global trends in the epidemiology of bladder cancer: challenges for public health and clinical practice. Nat Rev Clin Oncol 2023; 20:287-304. [PMID: 36914746 DOI: 10.1038/s41571-023-00744-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2023] [Indexed: 03/16/2023]
Abstract
Bladder cancer is among the ten most common cancers globally, causes considerable morbidity and mortality and is, therefore, a substantial burden for health-care systems. The incidence of bladder cancer is affected by demographic trends, most notably population growth and ageing, as well as exposure to risk factors, especially tobacco smoking. Consequently, the incidence has not been stable throughout the world over time, nor will it be in the near future. Further primary prevention efforts are of the utmost importance to reduce the medical and financial burden of bladder cancer on populations and health-care systems. Simultaneously, less-invasive and lower-cost approaches for the diagnosis of both primary and recurrent bladder cancers are required to address challenges posed by the increasing shortage of health-care professionals and limited financial resources worldwide. In this regard, urinary biomarkers have demonstrated promising diagnostic accuracy and efficiency. Awareness of the risk factors and symptoms of bladder cancer should also be increased in society, particularly among health-care professionals and high-risk groups. Studies investigating the associations between lifestyle factors and bladder cancer outcomes are scarce and should be a research priority. In this Review, we outline global trends in bladder cancer incidence and mortality, and discuss the main risk factors influencing bladder cancer occurrence and outcomes. We then discuss the implications, challenges and opportunities of these epidemiological trends for public health and clinical practice.
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10
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Lobo N, Afferi L, Moschini M, Mostafid H, Porten S, Psutka SP, Gupta S, Smith AB, Williams SB, Lotan Y. Epidemiology, Screening, and Prevention of Bladder Cancer. Eur Urol Oncol 2022; 5:628-639. [PMID: 36333236 DOI: 10.1016/j.euo.2022.10.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/09/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022]
Abstract
CONTEXT Bladder cancer (BC) represents a significant health problem due to the potential morbidity and mortality associated with disease burden, which has remained largely unaltered over time. OBJECTIVE To provide an expert collaborative review and describe the incidence, prevalence, and mortality of BC and to evaluate current evidence for BC screening and prevention. EVIDENCE ACQUISITION Data on the estimated incidence and mortality of BC for 2020 in 185 countries were derived from the International Agency for Research on Cancer GLOBOCAN database. A review of English-language articles published over the past 5 yr was conducted using PubMed/MEDLINE to identify risk factors in addition to contemporary evidence on BC screening and prevention. EVIDENCE SYNTHESIS BC is the tenth most common cancer worldwide, with 573 278 cases in 2020. BC incidence is approximately fourfold higher in men than women. Tobacco smoking remains the principal risk factor, accounting for approximately 50% of cases. There is insufficient evidence to recommend routine BC screening. However, targeted screening of high-risk individuals (defined according to smoking history or occupational exposure) may reduce BC mortality and should be the focus of prospective randomized trials. In terms of disease prevention, smoking cessation represents the most important intervention, followed by a reduction in exposure to occupational and environmental carcinogens. CONCLUSIONS BC confers a significant disease burden. An understanding of BC epidemiology and risk factors provides an optimal foundation for disease prevention and the care of affected patients. PATIENT SUMMARY Bladder cancer is the tenth most common cancer worldwide and is approximately four times more common among men than among women. The main risk factors are tobacco smoking, followed by exposure to carcinogens in the workplace or the environment. Routine screening is not currently recommended, but may be beneficial in individuals at high risk, such as heavy smokers. Primary prevention is extremely important, and smoking cessation represents the most important action for reducing bladder cancer cases and deaths.
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Affiliation(s)
- Niyati Lobo
- Royal Surrey NHS Foundation Trust, Guildford, UK
| | | | - Marco Moschini
- Urological Research Institute, IRCCS San Raffaele Hospital, Milan, Italy
| | | | - Sima Porten
- University of California-San Francisco, San Francisco, CA, USA
| | - Sarah P Psutka
- University of Washington, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Angela B Smith
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, USA
| | | | - Yair Lotan
- University of Texas Southwestern Medical Centre, Dallas, TX, USA.
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11
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Pietzak EJ, Whiting K, Srinivasan P, Bandlamudi C, Khurram A, Joseph V, Walasek A, Bochner E, Clinton T, Almassi N, Truong H, de Jesus Escano MR, Wiseman M, Mandelker D, Kemel Y, Zhang L, Walsh MF, Cadoo KA, Coleman JA, Al-Ahmadie H, Rosenberg JE, Iyer GV, Solit DB, Ostrovnaya I, Offit K, Robson ME, Stadler ZK, Berger MF, Bajorin DF, Carlo M, Bochner BH. Inherited Germline Cancer Susceptibility Gene Variants in Individuals with Non-Muscle-Invasive Bladder Cancer. Clin Cancer Res 2022; 28:4267-4277. [PMID: 35833951 PMCID: PMC9527498 DOI: 10.1158/1078-0432.ccr-22-1006] [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: 03/30/2022] [Revised: 06/07/2022] [Accepted: 07/12/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Identification of inherited germline variants can guide personalized cancer screening, prevention, and treatment. Pathogenic and likely pathogenic (P/LP) germline variants in cancer predisposition genes are frequent among patients with locally advanced or metastatic urothelial carcinoma, but their prevalence and significance in patients with non-muscle-invasive bladder cancer (NMIBC), the most common form of urothelial carcinoma, is understudied. EXPERIMENTAL DESIGN Germline analysis was conducted on paired tumor/normal sequencing results from two distinct cohorts of patients initially diagnosed with NMIBC. Associations between clinicopathologic features and clinical outcomes with the presence of P/LP germline variants in ≥76 hereditary cancer predisposition genes were analyzed. RESULTS A similar frequency of P/LP germline variants were seen in our two NMIBC cohorts [12% (12/99) vs. 8.7% (10/115), P = 0.4]. In the combined analysis, P/LP germline variants were found only in patients with high-grade NMIBC (22/163), but none of the 46 patients with low-grade NMIBC (13.5% vs. 0%, P = 0.005). Fifteen (9.2%) patients with high-grade NMIBC had P/LP variants in DNA damage response genes, most within the nucleotide excision repair (ERCC2/3) and homologous recombination repair (BRCA1, NBN, RAD50) pathways. Contrary to prior reports in patients with NMIBC not receiving Bacillus Calmette-Guerin (BCG), P/LP germline variants were not associated with worse recurrence-free or progression-free survival in patients treated with BCG or with risk of developing upper tract urothelial carcinoma. CONCLUSIONS Our results support offering germline counseling and testing for all patients with high-grade bladder cancer, regardless of initial tumor stage. Therapeutic strategies that target impaired DNA repair may benefit patients with high-grade NMIBC.
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Affiliation(s)
- Eugene J. Pietzak
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.,Corresponding Author: Eugene J. Pietzak, Urology Service, Department of Surgery, Kimmel Center for Prostate and Urologic Cancers, Memorial Sloan Kettering Cancer Center, 353 East 68th Street, New York, NY 10065. Phone: 646-422-4781; Fax: 212-988-0759. E-mail:
| | - Karissa Whiting
- Biostatistics Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Preethi Srinivasan
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chaitanya Bandlamudi
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aliya Khurram
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vijai Joseph
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aleksandra Walasek
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Bochner
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timothy Clinton
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nima Almassi
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hong Truong
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Manuel R. de Jesus Escano
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michal Wiseman
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Diana Mandelker
- Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Kemel
- Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Liying Zhang
- Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F. Walsh
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Karen A. Cadoo
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,St. James's Hospital Dublin, Trinity College Dublin, Trinity St. James's Cancer Institute, Dublin, Ireland
| | - Jonathan A. Coleman
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hikmat Al-Ahmadie
- Genitourinary Pathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jonathan E. Rosenberg
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gopakumar V. Iyer
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B. Solit
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Irina Ostrovnaya
- Biostatistics Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark E. Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zsofia K. Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F. Berger
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dean F. Bajorin
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria Carlo
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bernard H. Bochner
- Urologic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
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Polyploidy as an Adaptation against Loss of Heterozygosity in Cancer. Int J Mol Sci 2022; 23:ijms23158528. [PMID: 35955663 PMCID: PMC9369199 DOI: 10.3390/ijms23158528] [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: 06/30/2022] [Revised: 07/23/2022] [Accepted: 07/28/2022] [Indexed: 12/13/2022] Open
Abstract
Polyploidy is common in cancer cells and has implications for tumor progression and resistance to therapies, but it is unclear whether it is an adaptation of the tumor or the non-adaptive effect of genomic instability. I discuss the possibility that polyploidy reduces the deleterious effects of loss of heterozygosity, which arises as a consequence of mitotic recombination, and which in diploid cells leads instead to the rapid loss of complementation of recessive deleterious mutations. I use computational predictions of loss of heterozygosity to show that a population of diploid cells dividing by mitosis with recombination can be easily invaded by mutant polyploid cells or cells that divide by endomitosis, which reduces loss of complementation, or by mutant cells that occasionally fuse, which restores heterozygosity. A similar selective advantage of polyploidy has been shown for the evolution of different types of asexual reproduction in nature. This provides an adaptive explanation for cyclical ploidy, mitotic slippage and cell fusion in cancer cells.
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13
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New Drug Development and Clinical Trial Design by Applying Genomic Information Management. Pharmaceutics 2022; 14:pharmaceutics14081539. [PMID: 35893795 PMCID: PMC9330622 DOI: 10.3390/pharmaceutics14081539] [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: 07/01/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023] Open
Abstract
Depending on the patients’ genotype, the same drug may have different efficacies or side effects. With the cost of genomic analysis decreasing and reliability of analysis methods improving, vast amount of genomic information has been made available. Several studies in pharmacology have been based on genomic information to select the optimal drug, determine the dose, predict efficacy, and prevent side effects. This paper reviews the tissue specificity and genomic information of cancer. If the tissue specificity of cancer is low, cancer is induced in various organs based on a single gene mutation. Basket trials can be performed for carcinomas with low tissue specificity, confirming the efficacy of one drug for a single gene mutation in various carcinomas. Conversely, if the tissue specificity of cancer is high, cancer is induced in only one organ based on a single gene mutation. An umbrella trial can be performed for carcinomas with a high tissue specificity. Some drugs are effective for patients with a specific genotype. A companion diagnostic strategy that prescribes a specific drug for patients selected with a specific genotype is also reviewed. Genomic information is used in pharmacometrics to identify the relationship among pharmacokinetics, pharmacodynamics, and biomarkers of disease treatment effects. Utilizing genomic information, sophisticated clinical trials can be designed that will be better suited to the patients of specific genotypes. Genomic information also provides prospects for innovative drug development. Through proper genomic information management, factors relating to drug response and effects can be determined by selecting the appropriate data for analysis and by understanding the structure of the data. Selecting pre-processing and appropriate machine-learning libraries for use as machine-learning input features is also necessary. Professional curation of the output result is also required. Personalized medicine can be realized using a genome-based customized clinical trial design.
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14
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Shohdy KS, Villamar DM, Cao Y, Trieu J, Price KS, Nagy R, Tagawa ST, Molina AM, Sternberg CN, Nanus DM, Mosquera JM, Elemento O, Sonpavde GP, Grivas P, Vogelzang NJ, Faltas BM. Serial ctDNA analysis predicts clinical progression in patients with advanced urothelial carcinoma. Br J Cancer 2022; 126:430-439. [PMID: 35046520 PMCID: PMC8810988 DOI: 10.1038/s41416-021-01648-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 10/28/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Targeted sequencing of circulating tumour DNA (ctDNA) is a promising tool to monitor dynamic changes in the variant allele frequencies (VAF) of genomic alterations and predict clinical outcomes in patients with advanced urothelial carcinoma (UC). METHODS We performed targeted sequencing of 182 serial ctDNA samples from 53 patients with advanced UC. RESULTS Serial ctDNA-derived metrics predicted the clinical outcomes in patients with advanced UC. Combining serial ctDNA aggregate VAF (aVAF) values with clinical factors, including age, sex, and liver metastasis, improved the performance of prognostic models. An increase of the ctDNA aVAF by ≥1 in serial ctDNA samples predicted disease progression within 6 months in 90% of patients. The majority of patients with aVAFs ≤0.7 in three consecutive ctDNA samples achieved durable clinical responses (≥6 months). CONCLUSIONS Serial ctDNA analysis predicts disease progression and enables dynamic monitoring to guide precision medicine in patients with advanced UC.
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Affiliation(s)
- Kyrillus S Shohdy
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Department of Clinical Oncology, Kasr Alainy School of Medicine, Cairo University, Cairo, Egypt
| | - Dario M Villamar
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yen Cao
- Department of Medical Oncology, Comprehensive Cancer Centers of Nevada, Las Vegas, NV, USA
| | - Janson Trieu
- Department of Medical Oncology, Comprehensive Cancer Centers of Nevada, Las Vegas, NV, USA
| | | | | | - Scott T Tagawa
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ana M Molina
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Cora N Sternberg
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - David M Nanus
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Juan Miguel Mosquera
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Guru P Sonpavde
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Petros Grivas
- Department of Medical Oncology, University of Washington, Seattle, WA, USA
| | - Nicholas J Vogelzang
- Department of Medical Oncology, Comprehensive Cancer Centers of Nevada, Las Vegas, NV, USA.
| | - Bishoy Morris Faltas
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA.
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA.
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15
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Pal SK, Frankel PH, Mortazavi A, Milowsky M, Vaishampayan U, Parikh M, Lyou Y, Weng P, Parikh R, Teply B, Dreicer R, Emamekhoo H, Michaelson D, Hoimes C, Zhang T, Srinivas S, Kim WY, Cui Y, Newman E, Lara PN. Effect of Cisplatin and Gemcitabine With or Without Berzosertib in Patients With Advanced Urothelial Carcinoma: A Phase 2 Randomized Clinical Trial. JAMA Oncol 2021; 7:1536-1543. [PMID: 34436521 PMCID: PMC8391778 DOI: 10.1001/jamaoncol.2021.3441] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/01/2021] [Indexed: 01/10/2023]
Abstract
IMPORTANCE Preclinical studies suggest that inhibition of single-stranded DNA repair by ataxia telangiectasia and Rad3 (ATR) may enhance the cytotoxicity of cisplatin, gemcitabine, and other chemotherapeutic agents. Cisplatin with gemcitabine remains the standard up-front therapy for treatment in patients with metastatic urothelial cancer. OBJECTIVE To determine whether the use of the selective ATR inhibitor, berzosertib, could augment the activity of cisplatin with gemcitabine. DESIGN, SETTING, AND PARTICIPANTS In a phase 2 randomized clinical trial, 87 patients across 23 centers in the National Cancer Institute Experimental Therapeutics Clinical Trials Network were randomized to receive either cisplatin with gemcitabine alone (control arm) or cisplatin with gemcitabine plus berzosertib (experimental arm). Key eligibility criteria included confirmed metastatic urothelial cancer, no prior cytotoxic therapy for metastatic disease, 12 months or more since perioperative therapy, and eligibility for cisplatin receipt based on standard criteria. The study was conducted from January 27, 2017, to December 15, 2020. INTERVENTIONS In the control arm, cisplatin, 70 mg/m2, was given on day 1 and gemcitabine, 1000 mg/m2, was given on days 1 and 8 of a 21-day cycle. In the experimental arm, cisplatin, 60 mg/m2, was given on day 1; gemcitabine, 875 mg/m2, on days 1 and 8; and berzosertib, 90 mg/m2, on days 2 and 9 of a 21-day cycle. MAIN OUTCOMES AND MEASURES The primary end point of the study was progression-free survival. The analysis was on all patients who started therapy. RESULTS Of the total of 87 patients randomized, 41 patients received cisplatin with gemcitabine alone and 46 received cisplatin with gemcitabine plus berzosertib. Median age was 67 (range, 32-84) years, and 68 patients (78%) were men. Median progression-free survival was 8.0 months for both arms (Bajorin risk-adjusted hazard ratio, 1.22; 95% CI, 0.72-2.08). Median overall survival was shorter with cisplatin with gemcitabine plus berzosertib compared with cisplatin with gemcitabine alone (14.4 vs 19.8 months; Bajorin risk-adjusted hazard ratio, 1.42; 95% CI, 0.76-2.68). Higher rates of grade 3 vs grade 4 thrombocytopenia (59% vs 39%) and neutropenia (37% vs 27%) were observed with cisplatin with gemcitabine and berzosertib compared with cisplatin with gemcitabine alone; consequently, more dose reductions were needed in the experimental arm. Patients in the experimental arm received a median cisplatin dose of 250 mg/m2, which was significantly lower than the median dose of 370 mg/m2 in the control arm (P < .001). CONCLUSIONS AND RELEVANCE The addition of berzosertib to cisplatin with gemcitabine did not prolong progression-free survival relative to cisplatin with gemcitabine alone in patients with metastatic urothelial cancer, and a trend toward inferior survival was observed with this combination. Berzosertib plus cisplatin with gemcitabine was associated with significantly higher hematologic toxicities despite attenuated dosing of cisplatin with gemcitabine. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02567409.
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Affiliation(s)
- Sumanta K. Pal
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Paul H. Frankel
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Amir Mortazavi
- Department of Internal Medicine, Ohio State University Comprehensive Cancer Center, Columbus
| | - Matthew Milowsky
- Department of Medicine, UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina
| | - Ulka Vaishampayan
- Department of Internal Medicine, University of Michigan Cancer Center, Ann Arbor
| | - Mamta Parikh
- Department of Internal Medicine, UC Davis Comprehensive Cancer Center, Sacramento, California
| | - Yung Lyou
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Peng Weng
- Department of Internal Medicine, University of Kentucky Markey Cancer Center, Lexington
| | - Rahul Parikh
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
| | - Benjamin Teply
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha
| | - Robert Dreicer
- Department of Medicine, University of Virginia Cancer Center, Charlottesville
| | - Hamid Emamekhoo
- Department of Medicine, University of Wisconsin Cancer Center, Madison
| | - Dror Michaelson
- Department of Medicine, Massachusetts General Hospital, Boston
| | - Christopher Hoimes
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Tian Zhang
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Sandy Srinivas
- Department of Medicine, Stanford Cancer Center, Palo Alto, California
| | - William Y. Kim
- Department of Medicine, UNC Lineberger Comprehensive Cancer Center, Chapel Hill, North Carolina
| | - Yujie Cui
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Edward Newman
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Primo N. Lara
- Department of Internal Medicine, UC Davis Comprehensive Cancer Center, Sacramento, California
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Mamrot J, Hall NE, Lindley RA. Predicting clinical outcomes using cancer progression associated signatures. Oncotarget 2021; 12:845-858. [PMID: 33889305 PMCID: PMC8057277 DOI: 10.18632/oncotarget.27934] [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: 11/05/2020] [Accepted: 03/22/2021] [Indexed: 12/09/2022] Open
Abstract
Somatic mutation signatures are an informative facet of cancer aetiology, however they are rarely useful for predicting patient outcome. The aim of this study is to evaluate the utility of a panel of 142 mutation-signature–associated metrics (P142) for predicting cancer progression in patients from a ‘TCGA PanCancer Atlas’ cohort. The P142 metrics are comprised of AID/APOBEC and ADAR deaminase associated SNVs analyzed for codon context, strand bias, and transitions/transversions. TCGA tumor-normal mutation data was obtained for 10,437 patients, representing 31 of the most prevalent forms of cancer. Stratified random sampling was used to split patients into training, tuning and validation cohorts for each cancer type. Cancer specific machine learning (XGBoost) models were built using the output from the P142 panel to predict patient Progression Free Survival (PFS) status as either “High PFS” or “Low PFS”. Predictive performance of each model was evaluated using the validation cohort. Models accurately predicted PFS status for several cancer types, including adrenocortical carcinoma, glioma, mesothelioma, and sarcoma. In conclusion, the P142 panel of metrics successfully predicted cancer progression status in patients with some, but not all cancer types analyzed. These results pave the way for future studies on cancer progression associated signatures.
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Affiliation(s)
- Jared Mamrot
- GMDx Group Ltd, Melbourne, Victoria, Australia.,Department of Obstetrics and Gynaecology, Monash University, Clayton, VIC, Australia
| | | | - Robyn A Lindley
- GMDx Group Ltd, Melbourne, Victoria, Australia.,Department of Clinical Pathology, The Victorian Comprehensive Cancer Centre, Faculty of Medicine, Dentistry & Health Sciences, University of Melbourne, VIC, Australia
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Fanfani V, Citi L, Harris AL, Pezzella F, Stracquadanio G. The Landscape of the Heritable Cancer Genome. Cancer Res 2021; 81:2588-2599. [PMID: 33731442 DOI: 10.1158/0008-5472.can-20-3348] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/15/2021] [Accepted: 03/02/2021] [Indexed: 12/24/2022]
Abstract
Genome-wide association studies (GWAS) have found hundreds of single-nucleotide polymorphisms (SNP) associated with increased risk of cancer. However, the amount of heritable risk explained by SNPs is limited, leaving most of the cancer heritability unexplained. Tumor sequencing projects have shown that causal mutations are enriched in genic regions. We hypothesized that SNPs located in protein coding genes and nearby regulatory regions could explain a significant proportion of the heritable risk of cancer. To perform gene-level heritability analysis, we developed a new method, called Bayesian Gene Heritability Analysis (BAGHERA), to estimate the heritability explained by all genotyped SNPs and by those located in genic regions using GWAS summary statistics. BAGHERA was specifically designed for low heritability traits such as cancer and provides robust heritability estimates under different genetic architectures. BAGHERA-based analysis of 38 cancers reported in the UK Biobank showed that SNPs explain at least 10% of the heritable risk for 14 of them, including late onset malignancies. We then identified 1,146 genes, called cancer heritability genes (CHG), explaining a significant proportion of cancer heritability. CHGs were involved in hallmark processes controlling the transformation from normal to cancerous cells. Importantly, 60 of them also harbored somatic driver mutations, and 27 are tumor suppressors. Our results suggest that germline and somatic mutation information could be exploited to identify subgroups of individuals at higher risk of cancer in the broader population and could prove useful to establish strategies for early detection and cancer surveillance. SIGNIFICANCE: This study describes a new statistical method to identify genes associated with cancer heritability in the broader population, creating a map of the heritable cancer genome with gene-level resolution.See related commentary by Bader, p. 2586.
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Affiliation(s)
- Viola Fanfani
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Luca Citi
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, United Kingdom
| | - Adrian L Harris
- Molecular Oncology Laboratories, Department of Oncology, The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Francesco Pezzella
- Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Giovanni Stracquadanio
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom.
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Zhang X, Sjöblom T. Targeting Loss of Heterozygosity: A Novel Paradigm for Cancer Therapy. Pharmaceuticals (Basel) 2021; 14:ph14010057. [PMID: 33450833 PMCID: PMC7828287 DOI: 10.3390/ph14010057] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 12/13/2022] Open
Abstract
Loss of heterozygosity (LOH) is a common genetic event in the development of cancer. In certain tumor types, LOH can affect more than 20% of the genome, entailing loss of allelic variation in thousands of genes. This reduction of heterozygosity creates genetic differences between tumor and normal cells, providing opportunities for development of novel cancer therapies. Here, we review and summarize (1) mutations associated with LOH on chromosomes which have been shown to be promising biomarkers of cancer risk or the prediction of clinical outcomes in certain types of tumors; (2) loci undergoing LOH that can be targeted for development of novel anticancer drugs as well as (3) LOH in tumors provides up-and-coming possibilities to understand the underlying mechanisms of cancer evolution and to discover novel cancer vulnerabilities which are worth a further investigation in the near future.
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