1
|
Yu Q, Zhang Y, Ni J, Shen Y, Hu W. Identification and analysis of significant genes in nonalcoholic steatohepatitis-hepatocellular carcinoma transformation: Bioinformatics analysis and machine learning approach. Mol Immunol 2024; 174:18-31. [PMID: 39142007 DOI: 10.1016/j.molimm.2024.07.015] [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: 02/11/2024] [Revised: 07/15/2024] [Accepted: 07/30/2024] [Indexed: 08/16/2024]
Abstract
PURPOSE Nonalcoholic steatohepatitis (NASH) has been an increasingly significant contributor to hepatocellular carcinoma (HCC). Understanding the progression from NASH to HCC is critical to early diagnosis and elucidating the underlying mechanisms. RESULTS 5 significant prognostic genes related to NASH-HCC transformation were identified through algorithm selection, which were ME1, TP53I3, SOCS2, GADD45G and CYP7A1. A diagnostic model for NASH prediction was established (AUC=0.988). TP53I3 and SOCS2 were selected as potential critical genes in the progression of NASH-HCC by external dataset validation and in vitro experiments on NASH and HCC cell lines. Immune infiltration analysis illustrated the correlation between 5 significant prognostic genes and immune cells. Single-cell analysis identified hepatocytes related to NASH-HCC transformation markers, revealing their promoting role in the transformation from NASH to HCC. CONCLUSION With bulk-seq analysis and single-cell analysis, 5 significant prognostic genes related to NASH-HCC transformation were identified and validated at both dataset and in vitro experiment level. Among them, TP53I3 and SOCS2 might be potential critical genes in NASH-HCC progression. Single-cell analysis identified and revealed the critical role that NASH-HCC related hepatocytes play in NASH-HCC tansformation. Our research may introduce a new perspective to the diagnosis, treatment of NASH-related HCC.
Collapse
Affiliation(s)
- Qiyi Yu
- Center for New Drug Safety Evaluation and Research, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Yidong Zhang
- Center for New Drug Safety Evaluation and Research, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Jiaping Ni
- Center for New Drug Safety Evaluation and Research, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Yumeng Shen
- Center for New Drug Safety Evaluation and Research, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China.
| | - Weiwei Hu
- Center for New Drug Safety Evaluation and Research, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; Lingang Laboratory, Shanghai 200032, China.
| |
Collapse
|
2
|
Qian J, Peng M, Li Y, Liu W, Zou X, Chen H, Zhou S, Xiao S, Zhou J. Case report: A germline CHEK1 c.613 + 2T>C leads to a splicing error in a family with multiple cancer patients. Front Oncol 2024; 14:1380093. [PMID: 38686193 PMCID: PMC11056527 DOI: 10.3389/fonc.2024.1380093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/21/2024] [Indexed: 05/02/2024] Open
Abstract
Background Genome instability plays a crucial role in promoting tumor development. Germline mutations in genes responsible for DNA repair are often associated with familial cancer syndromes. A noticeable exception is the CHEK1 gene. Despite its well-established role in homologous recombination, germline mutations in CHEK1 are rarely reported. Case presentation In this report, we present a patient diagnosed with ovarian clear cell carcinoma who has a family history of cancer. Her relatives include a grandfather with esophageal cancer, a father with gastric cancer, and an uncle with a brain tumor. The patient carried a typical genomic profile of clear cell carcinoma including mutations in KRAS, PPP2R1A, and PIK3R1. Importantly, her paired peripheral blood cells harbored a germline CHEK1 mutation, CHEK1 exon 6 c.613 + 2T>C, which was also found in her father. Unfortunately, the CHEK1 status of her grandfather and uncle remains unknown due to the unavailability of their specimens. Further evaluation via RT-PCR confirmed a splicing error in the CHEK1 gene, resulting in truncation at the kinase domain region, indicative of a loss-of-function mutation. Conclusion This case highlights a rare germline CHEK1 mutation within a family with a history of cancer. The confirmed splicing error at the mRNA level underscores the functional consequences of this mutation. Documenting such cases is vital for future evaluation of inheritance patterns, clinical penetrance of the mutation, and its association with specific cancer types.
Collapse
Affiliation(s)
- Jun Qian
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Min Peng
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yanan Li
- Molecular Genetics Laboratory, Suzhou Sano Precision Medicine Ltd., Suzhou, China
| | - Wei Liu
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xinwei Zou
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Huafei Chen
- Molecular Genetics Laboratory, Suzhou Sano Precision Medicine Ltd., Suzhou, China
| | - Sujuan Zhou
- Molecular Genetics Laboratory, Suzhou Sano Precision Medicine Ltd., Suzhou, China
| | - Sheng Xiao
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Jinhua Zhou
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Soochow University, Suzhou, China
| |
Collapse
|
3
|
Wang T, Li X, Liao G, Wang Z, Han X, Gu J, Mu X, Qiu J, Qian Y. AFB1 Triggers Lipid Metabolism Disorders through the PI3K/Akt Pathway and Mediates Apoptosis Leading to Hepatotoxicity. Foods 2024; 13:163. [PMID: 38201191 PMCID: PMC10778638 DOI: 10.3390/foods13010163] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
As the most prevalent mycotoxin in agricultural products, aflatoxin B1 not only causes significant economic losses but also poses a substantial threat to human and animal health. AFB1 has been shown to increase the risk of hepatocellular carcinoma (HCC) but the underlying mechanism is not thoroughly researched. Here, we explored the toxicity mechanism of AFB1 on human hepatocytes following low-dose exposure based on transcriptomics and lipidomics. Apoptosis-related pathways were significantly upregulated after AFB1 exposure in all three hES-Hep, HepaRG, and HepG2 hepatogenic cell lines. By conducting a comparative analysis with the TCGA-LIHC database, four biomarkers (MTCH1, PPM1D, TP53I3, and UBC) shared by AFB1 and HCC were identified (hazard ratio > 1), which can be used to monitor the degree of AFB1-induced hepatotoxicity. Simultaneously, AFB1 induced abnormal metabolism of glycerolipids, sphingolipids, and glycerophospholipids in HepG2 cells (FDR < 0.05, impact > 0.1). Furthermore, combined analysis revealed strong regulatory effects between PIK3R1 and sphingolipids (correlation coefficient > 0.9), suggesting potential mediation by the phosphatidylinositol 3 kinase (PI3K) /protein kinase B (AKT) signaling pathway within mitochondria. This study revealed the dysregulation of lipid metabolism induced by AFB1 and found novel target genes associated with AFB-induced HCC development, providing reliable evidence for elucidating the hepatotoxicity of AFB as well as assessing food safety risks.
Collapse
Affiliation(s)
- Tiancai Wang
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (X.L.); (G.L.); (Z.W.); (J.G.); (X.M.); (J.Q.)
- Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Xiabing Li
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (X.L.); (G.L.); (Z.W.); (J.G.); (X.M.); (J.Q.)
- Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Guangqin Liao
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (X.L.); (G.L.); (Z.W.); (J.G.); (X.M.); (J.Q.)
- Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Zishuang Wang
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (X.L.); (G.L.); (Z.W.); (J.G.); (X.M.); (J.Q.)
- Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Xiaoxu Han
- National Center of Technology Innovation for Dairy, Hohhot 010100, China;
| | - Jingyi Gu
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (X.L.); (G.L.); (Z.W.); (J.G.); (X.M.); (J.Q.)
- Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Xiyan Mu
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (X.L.); (G.L.); (Z.W.); (J.G.); (X.M.); (J.Q.)
- Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Jing Qiu
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (X.L.); (G.L.); (Z.W.); (J.G.); (X.M.); (J.Q.)
- Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| | - Yongzhong Qian
- Key Laboratory of Agro-Product Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (T.W.); (X.L.); (G.L.); (Z.W.); (J.G.); (X.M.); (J.Q.)
- Key Laboratory of Agri-Food Quality and Safety, Ministry of Agriculture and Rural Affairs, Beijing 100081, China
| |
Collapse
|
4
|
Li WJ, Huang Y, Lin YA, Zhang BD, Li MY, Zou YQ, Hu GS, He YH, Yang JJ, Xie BL, Huang HH, Deng X, Liu W. Targeting PRMT1-mediated SRSF1 methylation to suppress oncogenic exon inclusion events and breast tumorigenesis. Cell Rep 2023; 42:113385. [PMID: 37938975 DOI: 10.1016/j.celrep.2023.113385] [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: 01/14/2023] [Revised: 08/10/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023] Open
Abstract
PRMT1 plays a vital role in breast tumorigenesis; however, the underlying molecular mechanisms remain incompletely understood. Herein, we show that PRMT1 plays a critical role in RNA alternative splicing, with a preference for exon inclusion. PRMT1 methylome profiling identifies that PRMT1 methylates the splicing factor SRSF1, which is critical for SRSF1 phosphorylation, SRSF1 binding with RNA, and exon inclusion. In breast tumors, PRMT1 overexpression is associated with increased SRSF1 arginine methylation and aberrant exon inclusion, which are critical for breast cancer cell growth. In addition, we identify a selective PRMT1 inhibitor, iPRMT1, which potently inhibits PRMT1-mediated SRSF1 methylation, exon inclusion, and breast cancer cell growth. Combination treatment with iPRMT1 and inhibitors targeting SRSF1 phosphorylation exhibits an additive effect of suppressing breast cancer cell growth. In conclusion, our study dissects a mechanism underlying PRMT1-mediated RNA alternative splicing. Thus, PRMT1 has great potential as a therapeutic target in breast cancer treatment.
Collapse
Affiliation(s)
- Wen-Juan Li
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Ying Huang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Yi-An Lin
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Bao-Ding Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China
| | - Mei-Yan Li
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Yi-Qin Zou
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Guo-Sheng Hu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Yao-Hui He
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Jing-Jing Yang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China
| | - Bing-Lan Xie
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China
| | - Hai-Hua Huang
- Department of Pathology, The Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Xianming Deng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China.
| | - Wen Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian, China; Xiang An Biomedicine Laboratory, School of Pharmaceutical Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiang'an South Road, Xiamen, Fujian 361102, China.
| |
Collapse
|
5
|
Font A, Domenech M, Ramirez JL, Marqués M, Benítez R, Ruiz de Porras V, Gago JL, Carrato C, Sant F, Lopez H, Castellano D, Malats N, Calle ML, Real FX. Predictive signature of response to neoadjuvant chemotherapy in muscle-invasive bladder cancer integrating mRNA expression, taxonomic subtypes, and clinicopathological features. Front Oncol 2023; 13:1155244. [PMID: 37588099 PMCID: PMC10426739 DOI: 10.3389/fonc.2023.1155244] [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: 01/31/2023] [Accepted: 07/10/2023] [Indexed: 08/18/2023] Open
Abstract
Background and objective Neoadjuvant chemotherapy (NAC) followed by cystectomy is the standard of care in muscle-invasive bladder cancer (MIBC). Pathological response has been associated with longer survival, but no currently available clinicopathological variables can identify patients likely to respond, highlighting the need for predictive biomarkers. We sought to identify a predictive signature of response to NAC integrating clinical score, taxonomic subtype, and gene expression. Material and methods From 1994 to 2014, pre-treatment tumor samples were collected from MIBC patients (stage T2-4N0/+M0) at two Spanish hospitals. A clinical score was determined based on stage, hydronephrosis and histology. Taxonomic subtypes (BASQ, luminal, and mixed) were identified by immunohistochemistry. A custom set of 41 genes involved in DNA damage repair and immune response was analyzed in 84 patients with the NanoString nCounter platform. Genes related to pathological response were identified by LASSO penalized logistic regression. NAC consisted of cisplatin/methotrexate/vinblastine until 2000, after which most patients received cisplatin/gemcitabine. The capacity of the integrated signature to predict pathological response was assessed with AUC. Overall survival (OS) and disease-specific survival (DSS) were analyzed with the Kaplan-Meier method. Results LASSO selected eight genes to be included in the signature (RAD51, IFNγ, CHEK1, CXCL9, c-MET, KRT14, HERC2, FOXA1). The highest predictive accuracy was observed with the inclusion in the model of only three genes (RAD51, IFNɣ, CHEK1). The integrated clinical-taxonomic-gene expression signature including these three genes had a higher predictive ability (AUC=0.71) than only clinical score plus taxonomic subtype (AUC=0.58) or clinical score alone (AUC=0.56). This integrated signature was also significantly associated with OS (p=0.02) and DSS (p=0.02). Conclusions We have identified a predictive signature for response to NAC in MIBC patients that integrates the expression of three genes with clinicopathological characteristics and taxonomic subtypes. Prospective studies to validate these results are ongoing.
Collapse
Affiliation(s)
- Albert Font
- Medical Oncology Department, Institut Català d’Oncologia, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
- Badalona Applied Research Group in Oncology (B-ARGO), Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona, Spain
| | - Montserrat Domenech
- Medical Oncology Department, Althaia Xarxa Assistencial Universitària de Manresa, Manresa, Spain
| | - Jose Luis Ramirez
- Hematology Service, Institut Català d'Oncologia (ICO) Badalona-Hospital Germans Trias i Pujol, Lymphoid Neoplasms Group, Josep Carreras Leukemia Research Institute (IJC), Badalona, Spain
| | - Miriam Marqués
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO) and CIBERONC, Madrid, Spain
| | - Raquel Benítez
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), and CIBERONC, Madrid, Spain
| | - Vicenç Ruiz de Porras
- Medical Oncology Department, Institut Català d’Oncologia, Hospital Universitari Germans Trias i Pujol, Badalona, Barcelona, Spain
- Badalona Applied Research Group in Oncology (B-ARGO), Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona, Spain
| | - José L. Gago
- Urology Department, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain
| | - Cristina Carrato
- Pathology Department, Hospital Universitari Germans Trias I Pujol, Badalona, Barcelona, Spain
| | - Francesc Sant
- Pathology Department, Althaia Xarxa Assistencial Universitària de Manresa, Manresa, Spain
| | - Hector Lopez
- Urology Department, Althaia Xarxa Assistencial Universitària de Manresa, Manresa, Spain
| | - Daniel Castellano
- Medical Oncology Department, University Hospital 12 de Octubre, Madrid, Spain
| | - Nuria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), and CIBERONC, Madrid, Spain
| | - M. Luz Calle
- Biosciences Department, Faculty of Sciences, Technology, University of Vic-Central University of Catalonia, Vic, Barcelona, Spain
| | - Francisco X. Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centre for Biomedical Research in Cancer Network (CIBERONC), Madrid, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| |
Collapse
|
6
|
Li L, Zou BJ, Zhao JZ, Liang JB, She ZY, Zhou WY, Lin SX, Tian L, Luo WJ, He FZ. A novel DNA damage repair-related signature for predicting prognositc and treatment response in non-small lung cancer. Front Oncol 2022; 12:961274. [PMID: 36408135 PMCID: PMC9673481 DOI: 10.3389/fonc.2022.961274] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 10/14/2022] [Indexed: 10/06/2023] Open
Abstract
DNA damage repair (DDR) is essential for maintaining genome integrity and modulating cancer risk, progression, and therapeutic response. DDR defects are common among non-small lung cancer (NSCLC), resulting in new challenge and promise for NSCLC treatment. Thus, a thorough understanding of the molecular characteristics of DDR in NSCLC is helpful for NSCLC treatment and management. Here, we systematically analyzed the relationship between DDR alterations and NSCLC prognosis, and successfully established and validated a six-DDR gene prognostic model via LASSO Cox regression analysis based on the expression of prognostic related DDR genes, CDC25C, NEIL3, H2AFX, NBN, XRCC5, RAD1. According to this model, NSCLC patients were classified into high-risk subtype and low-risk subtype, each of which has significant differences between the two subtypes in clinical features, molecular features, immune cell components, gene mutations, DDR pathway activation status and clinical outcomes. The high-risk patients was characterized with worse prognosis, lower proportion and number of DDR mutations, unique immune profile and responsive to immunetherapy. And the low-risk patients tend to have superior survival, while being less responsive to immunotherapy and more sensitive to treatment with DNA-damaging chemotherapy drugs. Overall, this molecular classification based on DDR expression profile enables hierarchical management of patients and personalized clinical treatment, and provides potential therapeutic targets for NSCLC.
Collapse
Affiliation(s)
- Ling Li
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Bao-jia Zou
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Juan-zhi Zhao
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Jia-bi Liang
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Zi-yue She
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Wen-ying Zhou
- Department of Central Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Si-xiao Lin
- Department of Central Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Lin Tian
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Wen-ji Luo
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Fa-zhong He
- Department of Quality Control, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, Guangdong, China
| |
Collapse
|
7
|
Li Y, Liu X, Chang Y, Fan B, Shangguan C, Chen H, Zhang L. Identification and Validation of a DNA Damage Repair-Related Signature for Diffuse Large B-Cell Lymphoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2645090. [PMID: 36281462 PMCID: PMC9587677 DOI: 10.1155/2022/2645090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/27/2022] [Indexed: 10/06/2023]
Abstract
BACKGROUND Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of non-Hodgkin's lymphoma in adults, whose prognostic scoring system remains to be improved. Dysfunction of DNA repair genes is closely associated with the development and prognosis of diffuse large B-cell lymphoma. The aim of this study was to establish and validate a DNA repair-related gene signature associated with the prognosis of DLBCL and to investigate the clinical predictive value of this signature. METHODS DLBCL cases were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. One hundred ninety-nine DNA repair-related gene sets were retrieved from the GeneCards database. The LASSO Cox regression was used to generate the DNA repair-related gene signature. Subsequently, the level of immune cell infiltration and the correlation between the gene signature and immune cells were analyzed using the CIBERSORT algorithm. Based on the Genomics of Drug Sensitivity in Cancer (GDSC) database, the relationship between the signature and drug sensitivity was analyzed, and together with the nomogram and gene set variation analysis (GSVA), the value of the signature for clinical application was evaluated. RESULTS A total of 14 DNA repair genes were screened out and included in the final risk model. Subgroup analysis of the training and validation cohorts showed that the risk model accurately predicted overall survival of DLBCL patients, with patients in the high-risk group having a worse prognosis than patients in the low-risk group. Subsequently, the risk score was confirmed as an independent prognostic factor by multivariate analysis. Furthermore, by CIBERSORT analysis, we discovered that immune cells, such as regulatory T cells (Tregs), activated memory CD4+ T cells, and gamma delta T cells showed significant differences between the high- and low-risk groups. In addition, we found some interesting associations of our signature with immune checkpoint genes (CD96, TGFBR1, and TIGIT). By analyzing drug sensitivity data in the GDSC database, we were able to identify potential therapeutics for DLBCL patients stratified according to our signature. CONCLUSIONS Our study identified and validated a 14-DNA repair-related gene signature for stratification and prognostic prediction of DLBCL patients, which might guide clinical personalization of treatment.
Collapse
Affiliation(s)
- Yang Li
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou 450000, China
| | - Xiyang Liu
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou 450000, China
| | - Yu Chang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou 450000, China
| | - Bingjie Fan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou 450000, China
| | - Chenxing Shangguan
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou 450000, China
| | - Huan Chen
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou 450000, China
| | - Lei Zhang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou 450000, China
| |
Collapse
|
8
|
Identification and Validation of a Novel Immune Infiltration-Based Diagnostic Score for Early Detection of Hepatocellular Carcinoma by Machine-Learning Strategies. Gastroenterol Res Pract 2022; 2022:5403423. [PMID: 35747248 PMCID: PMC9213192 DOI: 10.1155/2022/5403423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/11/2022] [Indexed: 11/18/2022] Open
Abstract
Objective To investigate the diagnostic gene biomarkers for hepatocellular carcinoma (HCC) and identify the immune cell infiltration characteristics in this pathology. Methods Five gene expression datasets were obtained through Gene Expression Omnibus (GEO) portal. After batch effect removal, differentially expressed genes (DEGs) were conducted between 209 HCC and 146 control tissues and functional correlation analyses were performed. Two machine learning algorithms were used to develop diagnostic signatures. The discriminatory ability of the gene signature was measured by AUC. The expression levels and diagnostic value of the identified biomarkers in HCC were further validated in three independent external cohorts. CIBERSORT algorithm was adopted to explore the immune infiltration of HCC. A correlation analysis was carried out between these diagnostic signatures and immune cells. Results A total of 375 DEGs were identified. GPC3, ACSM3, SPINK1, COL15A1, TP53I3, RRAGD, and CLDN10 were identified as the early diagnostic signatures of HCC and were all validated in external cohorts. The corresponding results of AUC presented excellent discriminatory ability of these feature genes. The immune cell infiltration analysis showed that multiple immune cells associated with these biomarkers may be involved in the development of HCC. Conclusion This study indicates that GPC3, ACSM3, SPINK1, COL15A1, TP53I3, RRAGD, and CLDN10 are potential biomarkers associated with immune infiltration in HCC. Combining these genes can be used for early detection of HCC and evaluating immune cell infiltration. Further studies are needed to explore their roles underlying the occurrence of HCC.
Collapse
|
9
|
Dalmasso B, Puccini A, Catalano F, Borea R, Iaia ML, Bruno W, Fornarini G, Sciallero S, Rebuzzi SE, Ghiorzo P. Beyond BRCA: The Emerging Significance of DNA Damage Response and Personalized Treatment in Pancreatic and Prostate Cancer Patients. Int J Mol Sci 2022; 23:ijms23094709. [PMID: 35563100 PMCID: PMC9099822 DOI: 10.3390/ijms23094709] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/07/2022] Open
Abstract
The BRCA1/2 germline and/or somatic pathogenic variants (PVs) are key players in the hereditary predisposition and therapeutic response for breast, ovarian and, more recently, pancreatic and prostate cancers. Aberrations in other genes involved in homologous recombination and DNA damage response (DDR) pathways are being investigated as promising targets in ongoing clinical trials. However, DDR genes are not routinely tested worldwide. Due to heterogeneity in cohort selection and dissimilar sequencing approaches across studies, neither the burden of PVs in DDR genes nor the prevalence of PVs in genes in common among pancreatic and prostate cancer can be easily quantified. We aim to contextualize these genes, altered in both pancreatic and prostate cancers, in the DDR process, to summarize their hereditary and somatic burden in different studies and harness their deficiency for cancer treatments in the context of currently ongoing clinical trials. We conclude that the inclusion of DDR genes, other than BRCA1/2, shared by both cancers considerably increases the detection rate of potentially actionable variants, which are triplicated in pancreatic and almost doubled in prostate cancer. Thus, DDR alterations are suitable targets for drug development and to improve the outcome in both pancreatic and prostate cancer patients. Importantly, this will increase the detection of germline pathogenic variants, thereby patient referral to genetic counseling.
Collapse
Affiliation(s)
- Bruna Dalmasso
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, 16132 Genoa, Italy; (B.D.); (W.B.)
| | - Alberto Puccini
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Fabio Catalano
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Roberto Borea
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Maria Laura Iaia
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - William Bruno
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, 16132 Genoa, Italy; (B.D.); (W.B.)
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy;
| | - Giuseppe Fornarini
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Stefania Sciallero
- IRCCS Ospedale Policlinico San Martino, Medical Oncology Unit 1, 16132 Genoa, Italy; (A.P.); (F.C.); (R.B.); (M.L.I.); (G.F.); (S.S.)
| | - Sara Elena Rebuzzi
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy;
- Ospedale San Paolo, Medical Oncology, 17100 Savona, Italy
| | - Paola Ghiorzo
- IRCCS Ospedale Policlinico San Martino, Genetics of Rare Cancers, 16132 Genoa, Italy; (B.D.); (W.B.)
- Department of Internal Medicine and Medical Specialties, University of Genoa, 16132 Genoa, Italy;
- Correspondence:
| |
Collapse
|
10
|
Baughan SL, Darwiche F, Tainsky MA. Functional Analysis of ATM variants in a high risk cohort provides insight into missing heritability. Cancer Genet 2022; 264-265:40-49. [DOI: 10.1016/j.cancergen.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 11/29/2022]
|
11
|
Gianni P, Matenoglou E, Geropoulos G, Agrawal N, Adnani H, Zafeiropoulos S, Miyara SJ, Guevara S, Mumford JM, Molmenti EP, Giannis D. The Fanconi anemia pathway and Breast Cancer: A comprehensive review of clinical data. Clin Breast Cancer 2021; 22:10-25. [PMID: 34489172 DOI: 10.1016/j.clbc.2021.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/17/2021] [Accepted: 08/05/2021] [Indexed: 02/08/2023]
Abstract
The development of breast cancer depends on several risk factors, including environmental, lifestyle and genetic factors. Despite the evolution of DNA sequencing techniques and biomarker detection, the epidemiology and mechanisms of various breast cancer susceptibility genes have not been elucidated yet. Dysregulation of the DNA damage response causes genomic instability and increases the rate of mutagenesis and the risk of carcinogenesis. The Fanconi Anemia (FA) pathway is an important component of the DNA damage response and plays a critical role in the repair of DNA interstrand crosslinks and genomic stability. The FA pathway involves 22 recognized genes and specific mutations have been identified as the underlying defect in the majority of FA patients. A thorough understanding of the function and epidemiology of these genes in breast cancer is critical for the development and implementation of individualized therapies that target unique tumor profiles. Targeted therapies (PARP inhibitors) exploiting the FA pathway gene defects have been developed and have shown promising results. This narrative review summarizes the current literature on the involvement of FA genes in sporadic and familial breast cancer with a focus on clinical data derived from large cohorts.
Collapse
Affiliation(s)
- Panagiota Gianni
- Department of Internal Medicine III, Hematology, Oncology, Palliative Medicine, Rheumatology and Infectious Diseases, University Hospital Ulm, Germany
| | - Evangelia Matenoglou
- Medical School, Aristotle University of Thessaloniki, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Geropoulos
- Thoracic Surgery Department, University College London Hospitals NHS Foundation Trust, London
| | - Nirav Agrawal
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY
| | - Harsha Adnani
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY
| | - Stefanos Zafeiropoulos
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY; Elmezzi Graduate School of Molecular Medicine, Northwell Health, Manhasset, New York, NY
| | - Santiago J Miyara
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY; Elmezzi Graduate School of Molecular Medicine, Northwell Health, Manhasset, New York, NY
| | - Sara Guevara
- Department of Surgery, North Shore University Hospital, Manhasset, New York, NY
| | - James M Mumford
- Department of Family Medicine, Glen Cove Hospital, Glen Cove, New York, NY; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, NY
| | - Ernesto P Molmenti
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY; Department of Surgery, North Shore University Hospital, Manhasset, New York, NY; Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, NY
| | - Dimitrios Giannis
- Feinstein Institutes for Medical Research at Northwell Health, Manhasset, New York, NY.
| |
Collapse
|
12
|
Germline mutations in apoptosis pathway genes in ovarian cancer; the functional role of a TP53I3 (PIG3) variant in ROS production and DNA repair. Cell Death Discov 2021; 7:62. [PMID: 33782397 PMCID: PMC8007802 DOI: 10.1038/s41420-021-00442-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/05/2021] [Accepted: 02/14/2021] [Indexed: 11/08/2022] Open
Abstract
Approximately 25% of all cases of ovarian cancer (OVCA) cases are associated with inherited risk. However, accurate risk assessment is limited by the presence of variants of unknown significance (VUS). Previously, we performed whole-exome sequencing on 48 OVCA patients with familial predisposition, yet negative for pathogenic BRCA1/2 mutations. In our cohort, we uncovered thirteen truncating mutations in genes associated with apoptosis (~35% of our patient cohort). The TP53I3 p.S252X premature stop gain was identified in two unrelated patients. TP53I3 is transcriptionally activated by p53 and believed to play a role in DNA damage response and reactive oxygen species-induced apoptosis. In addition, nonsense variants in apoptosis-related genes TP53AIP1, BCLAF1, and PIK3C2G were identified in our cohort; highlighting the potential relevance of genes involved in apoptotic processes to hereditary cancer. In the current study, we employed functional assays and demonstrated that cells expressing TP53I3 p.S252X displayed decreased homologous recombination repair efficiency and increased sensitivity to chemotherapeutic drugs bleomycin, mitomycin c, and etoposide. In addition, in the presence of oxidative stress from hydrogen peroxide or etoposide we observed a reduction in the formation of reactive oxygen species, an important precursor to apoptosis with this variant. Our findings suggest that the combination of in silico and wet laboratory approaches can better evaluate VUSs, establish novel germline predisposition genetic loci, and improve individual cancer risk estimates.
Collapse
|
13
|
Arend RC, Jackson-Fisher A, Jacobs IA, Chou J, Monk BJ. Ovarian cancer: new strategies and emerging targets for the treatment of patients with advanced disease. Cancer Biol Ther 2021; 22:89-105. [PMID: 33427569 PMCID: PMC7928025 DOI: 10.1080/15384047.2020.1868937] [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] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 12/01/2020] [Accepted: 12/22/2020] [Indexed: 10/25/2022] Open
Abstract
Recently approved therapies have contributed to a significant progress in the management of ovarian cancer; yet, more options are needed to further improve outcomes in patients with advanced disease. Here we review the rationale and ongoing clinical trials of novel combination strategies involving chemotherapy, poly ADP ribose polymerase, programmed death 1 (PD-1)/PD-ligand 1 immune checkpoint and/or vascular endothelial growth factor receptor inhibitors. Further, we discuss novel agents aimed at targets associated with ovarian cancer growth or progression that are emerging as potential new treatment approaches. Among them, agents targeted to folate receptor α, tissue factor, and protein kinase-mediated pathways (WEE1 kinase, phosphatidylinositol-3 kinase α, cell cycle checkpoint kinase 1/2, ATR kinase) are currently in clinical development as mono- or combination therapies. If successful, findings from these extensive development efforts may further transform treatment of patients with advanced ovarian cancer.
Collapse
Affiliation(s)
- Rebecca C. Arend
- Division of Gynecologic Oncology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Jeffrey Chou
- Research and Development, Pfizer, San Francisco, CA, USA
| | | |
Collapse
|
14
|
Cavaillé M, Uhrhammer N, Privat M, Ponelle-Chachuat F, Gay-Bellile M, Lepage M, Molnar I, Viala S, Bidet Y, Bignon YJ. Analysis of 11 candidate genes in 849 adult patients with suspected hereditary cancer predisposition. Genes Chromosomes Cancer 2020; 60:73-78. [PMID: 33099839 PMCID: PMC7756731 DOI: 10.1002/gcc.22911] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 12/21/2022] Open
Abstract
Hereditary predisposition to cancer concerns between 5% and 10% of cancers. The main genes involved in the most frequent syndromes (hereditary breast and ovarian cancer syndrome, hereditary nonpolyposis colorectal cancer syndrome) were identified in the 1990s. Exploration of their functional pathways then identified novel genes for hereditary predisposition to cancer, and candidate genes whose involvement remains unclear. To determine the contribution of truncating variants in 11 candidate genes (BARD1, FAM175A, FANCM, MLH3, MRE11A, PMS1, RAD50, RAD51, RAD51B, RINT1, and XRCC2) to cancer predisposition in a population of interest, panel sequencing was performed in 849 patients with a suspected hereditary predisposition to cancer for whom a diagnostic panel of 38 genes identified no causal mutation. Sixteen truncating variants were found in FANCM (n = 7), RINT1 (n = 4), RAD50 (n = 2), BARD1, PMS1, and RAD51B. FANCM (adjusted P‐value: .03) and RINT1 (adjusted P‐value: .04) were significantly associated with hereditary breast and ovarian cancer. However, further studies are required to determinate the risk of cancer, including the segregation of the variants in the families of our cases. No mutation was identified in RAD51, MRE11A, FAM175A, XRCC2, or MLH3. The involvement of these genes in the hereditary predisposition to cancer cannot be ruled out, although if it exists it is rare or does not seem to involve truncating variants.
Collapse
Affiliation(s)
- Mathias Cavaillé
- INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Nancy Uhrhammer
- INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Maud Privat
- INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Flora Ponelle-Chachuat
- INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Mathilde Gay-Bellile
- INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Mathis Lepage
- INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Ioana Molnar
- INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France.,Délégation Recherche Clinique & Innovation, Centre Jean Perrin, Centre de Lutte contre le Cancer, Clermont-Ferrand, France.,Centre d'Investigation Clinique, UMR501, Clermont-Ferrand, France
| | - Sandrine Viala
- INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Yannick Bidet
- INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| | - Yves-Jean Bignon
- INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, Université Clermont Auvergne, Clermont-Ferrand, France.,Département d'Oncogénétique, Centre Jean Perrin, Clermont-Ferrand, France
| |
Collapse
|
15
|
Morton LM, Karyadi DM, Hartley SW, Frone MN, Sampson JN, Howell RM, Neglia JP, Arnold MA, Hicks BD, Jones K, Zhu B, Dagnall CL, Karlins E, Yeager MS, Leisenring WM, Yasui Y, Turcotte LM, Smith SA, Weathers RE, Miller J, Sigel BS, Merino DM, Berrington de Gonzalez A, Bhatia S, Robison LL, Tucker MA, Armstrong GT, Chanock SJ. Subsequent Neoplasm Risk Associated With Rare Variants in DNA Damage Response and Clinical Radiation Sensitivity Syndrome Genes in the Childhood Cancer Survivor Study. JCO Precis Oncol 2020; 4:PO.20.00141. [PMID: 32923912 PMCID: PMC7469586 DOI: 10.1200/po.20.00141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2020] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Radiotherapy for childhood cancer is associated with elevated subsequent neoplasm (SN) risk, but the contribution of rare variants in DNA damage response and radiation sensitivity genes to SN risk is unknown. PATIENTS AND METHODS We conducted whole-exome sequencing in a cohort of childhood cancer survivors originally diagnosed during 1970 to 1986 (mean follow-up, 32.7 years), with reconstruction of doses to body regions from radiotherapy records. We identified patients who developed SN types previously reported to be related to radiotherapy (RT-SNs; eg, basal cell carcinoma [BCC], breast cancer, meningioma, thyroid cancer, sarcoma) and matched controls (sex, childhood cancer type/diagnosis, age, SN location, radiation dose, survival). Conditional logistic regression assessed SN risk associated with potentially protein-damaging rare variants (SnpEff, ClinVar) in 476 DNA damage response or radiation sensitivity genes with exact permutation-based P values using a Bonferroni-corrected significance threshold of P < 8.06 × 10-5. RESULTS Among 5,105 childhood cancer survivors of European descent, 1,108 (21.7%) developed at least 1 RT-SN. Out-of-field RT-SN risk, excluding BCC, was associated with homologous recombination repair (HRR) gene variants (patient cases, 23.2%; controls, 10.8%; odds ratio [OR], 2.6; 95% CI, 1.7 to 3.9; P = 4.79 × 10-5), most notably but nonsignificantly for FANCM (patient cases, 4.0%; matched controls, 0.6%; P = 9.64 × 10-5). HRR variants were not associated with likely in/near-field RT-SNs, excluding BCC (patient cases, 12.7%; matched controls, 12.9%; P = .92). Irrespective of radiation dose, risk for RT-SNs was also associated with EXO1 variants (patient cases, 1.8%; controls, 0.4%; P = 3.31 × 10-5), another gene implicated in DNA double-strand break repair. CONCLUSION In this large-scale discovery study, we identified novel associations between RT-SN risk after childhood cancer and potentially protein-damaging rare variants in genes involved in DNA double-strand break repair, particularly HRR. With replication, these results could affect screening recommendations for childhood cancer survivors and risk-benefit assessments of treatment approaches.
Collapse
Affiliation(s)
- Lindsay M. Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Danielle M. Karyadi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Stephen W. Hartley
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Megan N. Frone
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Joshua N. Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Rebecca M. Howell
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Joseph P. Neglia
- Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - Michael A. Arnold
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH
- Department of Pathology, Wexner Medical Center, Ohio State University, Columbus, OH
| | - Belynda D. Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Casey L. Dagnall
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Meredith S. Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Wendy M. Leisenring
- Cancer Prevention and Clinical Statistics Programs, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St Jude Children’s Research Hospital, Memphis, TN
| | | | - Susan A. Smith
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rita E. Weathers
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Byron S. Sigel
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Diana M. Merino
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Amy Berrington de Gonzalez
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL
| | - Leslie L. Robison
- Department of Epidemiology and Cancer Control, St Jude Children’s Research Hospital, Memphis, TN
| | - Margaret A. Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Gregory T. Armstrong
- Department of Epidemiology and Cancer Control, St Jude Children’s Research Hospital, Memphis, TN
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| |
Collapse
|
16
|
Alexandrova E, Pecoraro G, Sellitto A, Melone V, Ferravante C, Rocco T, Guacci A, Giurato G, Nassa G, Rizzo F, Weisz A, Tarallo R. An Overview of Candidate Therapeutic Target Genes in Ovarian Cancer. Cancers (Basel) 2020; 12:cancers12061470. [PMID: 32512900 PMCID: PMC7352306 DOI: 10.3390/cancers12061470] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/31/2020] [Accepted: 06/02/2020] [Indexed: 12/25/2022] Open
Abstract
Ovarian cancer (OC) shows the highest mortality rate among gynecological malignancies and, because of the absence of specific symptoms, it is frequently diagnosed at an advanced stage, mainly due to the lack of specific and early biomarkers, such as those based on cancer molecular signature identification. Indeed, although significant progress has been made toward improving the clinical outcome of other cancers, rates of mortality for OC are essentially unchanged since 1980, suggesting the need of new approaches to identify and characterize the molecular mechanisms underlying pathogenesis and progression of these malignancies. In addition, due to the low response rate and the high frequency of resistance to current treatments, emerging therapeutic strategies against OC focus on targeting single factors and pathways specifically involved in tumor growth and metastasis. To date, loss-of-function screenings are extensively applied to identify key drug targets in cancer, seeking for more effective, disease-tailored treatments to overcome lack of response or resistance to current therapies. We review here the information relative to essential genes and functional pathways recently discovered in OC, often strictly interconnected with each other and representing promising biomarkers and molecular targets to treat these malignancies.
Collapse
Affiliation(s)
- Elena Alexandrova
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Giovanni Pecoraro
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Assunta Sellitto
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Viola Melone
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Carlo Ferravante
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
- Genomix4Life, via S. Allende 43/L, 84081 Baronissi, Italy;
| | - Teresa Rocco
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
- Genomix4Life, via S. Allende 43/L, 84081 Baronissi, Italy;
| | - Anna Guacci
- Genomix4Life, via S. Allende 43/L, 84081 Baronissi, Italy;
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
- CRGS-Genome Research Center for Health, University of Salerno Campus of Medicine, 84081 Baronissi, Italy
- Correspondence: (A.W.); (R.T.); Tel.: +39-089-965043 (A.W.); +39-089-965067 (R.T.)
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitan”, University of Salerno, 84081 Baronissi, Italy; (E.A.); (G.P.); (A.S.); (V.M.); (C.F.); (T.R.); (G.G.); (G.N.); (F.R.)
- Correspondence: (A.W.); (R.T.); Tel.: +39-089-965043 (A.W.); +39-089-965067 (R.T.)
| |
Collapse
|
17
|
Engqvist H, Parris TZ, Kovács A, Rönnerman EW, Sundfeldt K, Karlsson P, Helou K. Validation of Novel Prognostic Biomarkers for Early-Stage Clear-Cell, Endometrioid and Mucinous Ovarian Carcinomas Using Immunohistochemistry. Front Oncol 2020; 10:162. [PMID: 32133296 PMCID: PMC7040170 DOI: 10.3389/fonc.2020.00162] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/29/2020] [Indexed: 12/17/2022] Open
Abstract
Early-stage (I and II) ovarian carcinoma patients generally have good prognosis. Yet, some patients die earlier than expected. Thus, it is important to stratify early-stage patients into risk groups to identify those in need of more aggressive treatment regimens. The prognostic value of 29 histotype-specific biomarkers identified using RNA sequencing was evaluated for early-stage clear-cell (CCC), endometrioid (EC) and mucinous (MC) ovarian carcinomas (n = 112) using immunohistochemistry on tissue microarrays. Biomarkers with prognostic significance were further evaluated in an external ovarian carcinoma data set using the web-based Kaplan-Meier plotter tool. Here, we provide evidence of aberrant protein expression patterns and prognostic significance of 17 novel histotype-specific prognostic biomarkers [10 for CCC (ARPC2, CCT5, GNB1, KCTD10, NUP155, RPL13A, RPL37, SETD3, SMYD2, TRIO), three for EC (CECR1, KIF26B, PIK3CA), and four for MC (CHEK1, FOXM1, KIF23, PARPBP)], suggesting biological heterogeneity within the histotypes. Combined predictive models comprising the protein expression status of the validated CCC, EC and MC biomarkers together with established clinical markers (age, stage, CA125, ploidy) improved the predictive power in comparison with models containing established clinical markers alone, further strengthening the importance of the biomarkers in ovarian carcinoma. Further, even improved predictive powers were demonstrated when combining these models with our previously identified prognostic biomarkers PITHD1 (CCC) and GPR158 (MC). Moreover, the proteins demonstrated improved risk prediction of CCC-, EC-, and MC-associated ovarian carcinoma survival. The novel histotype-specific prognostic biomarkers may not only improve prognostication and patient stratification of early-stage ovarian carcinomas, but may also guide future clinical therapy decisions.
Collapse
Affiliation(s)
- Hanna Engqvist
- Department of Oncology, Sahlgrenska Cancer Center, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Toshima Z. Parris
- Department of Oncology, Sahlgrenska Cancer Center, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Anikó Kovács
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Elisabeth Werner Rönnerman
- Department of Oncology, Sahlgrenska Cancer Center, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Karin Sundfeldt
- Department of Obstetrics and Gynecology, Sahlgrenska Cancer Center, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Per Karlsson
- Department of Oncology, Sahlgrenska Cancer Center, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Khalil Helou
- Department of Oncology, Sahlgrenska Cancer Center, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|