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McCarthy-Leo C, Baughan S, Dlugas H, Abraham P, Gibbons J, Baldwin C, Chung S, Feldman GL, Dyson G, Finley RL, Tainsky MA. Germline variant profiling of CHEK2 sequencing variants in breast cancer patients. Cancer Genet 2024; 288-289:10-19. [PMID: 39208550 DOI: 10.1016/j.cancergen.2024.08.081] [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: 05/06/2024] [Revised: 07/17/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
The cell cycle checkpoint kinase 2 (CHEK2) is a tumor suppressor gene coding for a protein kinase with a role in the cell cycle and DNA repair pathways. Variants within CHEK2 are associated with an increased risk of developing breast, colorectal, prostate and several other types of cancer. Comprehensive genetic risk assessment leads to early detection of hereditary cancer and provides an opportunity for better survival. Multigene panel screening can identify the presence of pathogenic variants in hereditary cancer predisposition genes (HCPG), including CHEK2. Multigene panels, however, also result in large quantities of genetic data some of which cannot be interpreted and are classified as variants of uncertain significance (VUS). A VUS provides no information for use in medical management and leads to ambiguity in genetic counseling. In the absence of variant segregation data, in vitro functional analyses can be used to clarify variant annotations, aiding in accurate clinical management of patient risk and treatment plans. In this study, we performed whole exome sequencing (WES) to investigate the prevalence of germline variants in 210 breast cancer (BC) patients and conspicuously among the many variants in HCPGs that we found, we identified 16 individuals with non-synonymous or frameshift CHEK2 variants, sometimes along with additional variants within other BC susceptibility genes. Using this data, we investigated the prevalence of these CHEK2 variants in African American (AA) and Caucasian (CA) populations identifying the presence of two novel frameshift variants, c.1350delA (p.Val451Serfs*18) and c.1528delC (p.Gln510Argfs*3) and a novel missense variant, c262C>T (p.Pro88Ser). Along with the current clinical classifications, we assembled available experimental data and computational predictions of function for these CHEK2 variants, as well as explored the role these variants may play in polygenic risk assessment.
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Affiliation(s)
- Claire McCarthy-Leo
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Scott Baughan
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Hunter Dlugas
- Biostatistics and Bioinformatics Core, Karmanos Cancer Institute, Detroit, MI, United States
| | - Prisca Abraham
- Wayne State University School of Medicine, Detroit, MI, United States
| | - Janice Gibbons
- Wayne State University School of Medicine, Detroit, MI, United States
| | - Carolyn Baldwin
- Wayne State University School of Medicine, Detroit, MI, United States
| | - Sarah Chung
- Wayne State University School of Medicine, Detroit, MI, United States
| | - Gerald L Feldman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Gregory Dyson
- Biostatistics and Bioinformatics Core, Karmanos Cancer Institute, Detroit, MI, United States; Department of Oncology, Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States
| | - Russell L Finley
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Michael A Tainsky
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States; Department of Oncology, Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States.
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Surmeli ZG, Ibrahim RHM, Alkhalfan N, Mahmood Z. Cisplatin-induced bone marrow failure in an adult patient with Fanconi anemia. J Oncol Pharm Pract 2024:10781552241268468. [PMID: 39095039 DOI: 10.1177/10781552241268468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
INTRODUCTION Fanconi anemia (FA) is a genetic disorder characterized by bone marrow failure typically developing in the first decade of life, congenital abnormalities, and an increased predisposition to malignancy. However, patients with FA can remain undiagnosed until adulthood and present with solid organ malignancies. Due to impaired DNA repair mechanisms, patients with FA are highly susceptible to severe bone marrow toxicity when treated with cisplatin. CASE REPORT A 38-year-old woman, diagnosed with locally advanced squamous cell carcinoma (SCC) of the uterine cervix, underwent treatment with weekly cisplatin concurrent with radiotherapy. After the second week of cisplatin treatment, she presented with severe pancytopenia. The prolonged and severe pancytopenia following cisplatin and radiation, along with cervical SCC in the absence of risk factors and the presence of parental consanguinity, raised the possibility of FA as the underlying cause. Whole exome sequencing revealed a homozygous FANCI c.668A > C (p.Lys223Thr) missense variant confirming the diagnosis of FA. MANAGEMENT AND OUTCOME The pancytopenia exhibited a protracted course, necessitating admission and supportive treatment with antibiotics, red blood cell and platelet transfusions, as well as filgrastim and eltrombopag. Eventually, the pancytopenia improved after approximately 40 days of hospitalization. DISCUSSION SCC of the head and neck or gynecologic organs in a young adult without known risk factors should prompt consideration of FA. Cisplatin should be avoided in patients with FA.
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Affiliation(s)
| | | | - Nawaf Alkhalfan
- Department of Medical Oncology, Bahrain Oncology Center, Muharraq, Bahrain
| | - Zeyad Mahmood
- Department of Medical Oncology, Bahrain Oncology Center, Muharraq, Bahrain
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Ma R, Xu X. Deciphering the role of post-translational modifications in fanconi anemia proteins and their influence on tumorigenesis. Cancer Gene Ther 2024; 31:1113-1123. [PMID: 38879655 DOI: 10.1038/s41417-024-00797-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 08/17/2024]
Abstract
Fanconi anemia (FA) is an autosomal or X-linked human disease, characterized by bone marrow failure, cancer susceptibility and various developmental abnormalities. So far, at least 22 FA genes (FANCA-W) have been identified. Germline inactivation of any one of these FA genes causes FA symptoms. Proteins encoded by FA genes are involved in the Fanconi anemia pathway, which is known for its roles in DNA inter-strand crosslinks (ICLs) repair. Besides, its roles in genome maintenance upon replication stress has also been reported. Post-translational modifications (PTMs) of FA proteins, particularly phosphorylation and ubiquitination, emerge as critical determinants in the activation of the FA pathway during ICL repair or replication stress response. Consequent inactivation of the FA pathway engenders heightened chromosomal instability, thereby constituting a genetic susceptibility conducive to cancer predisposition and the exacerbation of tumorigenesis. In this review, we have combined recent structural analysis of FA proteins and summarized knowledge on the functions of different PTMs in regulating FA pathways, and discuss potential contributions stemming from mutations at PTMs to the genesis and progression of tumorigenesis.
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Affiliation(s)
- Rui Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xinlin Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
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Snyder AJ, Campbell KM, Lane A, Mehta PA, Myers K, Davies SM, Koo J. Liver abnormalities are frequent and persistent in patients with Fanconi anemia. Blood Adv 2024; 8:1427-1438. [PMID: 38231120 PMCID: PMC10955649 DOI: 10.1182/bloodadvances.2023012215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/02/2024] [Accepted: 01/07/2024] [Indexed: 01/18/2024] Open
Abstract
ABSTRACT Liver disease has not been well described in patients with Fanconi anemia (FA). Improvements in outcomes of transplant mean that more individuals with FA are reaching adulthood and new features of the FA phenotype are being discovered. We performed a retrospective review of liver function in a cohort of 97 patients with FA followed-up for at least 10 years at a single center. We identified a high frequency of transaminitis (n = 31, 32%) without elevation of bilirubin and with no evidence of structural hepatic abnormality in patients with FA. Transaminitis was persistent in many cases, sometimes lasting more than a decade without clinical manifestation, although 2 patients with prolonged transaminitis are deceased from liver failure, indicating important long-term clinical consequences. Transaminitis was found in patients who had and had not received transplant but was more frequent in recipients of transplant. Exposure to total body irradiation increased risk (odds ratio, 15.5 [95% confidence interval, 2.44-304.54]; P = .01), whereas treatment with androgens did not. Review of limited numbers of liver biopsies and autopsy material showed a cholestatic pattern of liver injury, with progressive fibrosis, in the majority of patients. Occurrence in cases without transplant as well as cases with transplant argues against a potential diagnosis of atypical liver graft-versus-host disease. Limited data regarding therapy suggest no benefit from treatment with steroids or other immune suppressive medications or ursodeoxycholic acid. Our data show that liver disease is common in patients with FA, and because most children with FA now reach adulthood, end-stage liver disease in young adulthood means systematic testing of potential therapies is urgently needed.
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Affiliation(s)
- Alana J. Snyder
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Kathleen M. Campbell
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Adam Lane
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Parinda A. Mehta
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Kasiani Myers
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Stella M. Davies
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH
| | - Jane Koo
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH
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Minello A, Carreira A. BRCA1/2 Haploinsufficiency: Exploring the Impact of Losing one Allele. J Mol Biol 2024; 436:168277. [PMID: 37714298 DOI: 10.1016/j.jmb.2023.168277] [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: 07/04/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
Since their discovery in the late 20th century, significant progress has been made in elucidating the functions of the tumor suppressor proteins BRCA1 and BRCA2. These proteins play vital roles in maintaining genome integrity, including DNA repair, replication fork protection, and chromosome maintenance. It is well-established that germline mutations in BRCA1 and BRCA2 increase the risk of breast and ovarian cancer; however, the precise mechanism underlying tumor formation in this context is not fully understood. Contrary to the long-standing belief that the loss of the second wild-type allele is necessary for tumor development, a growing body of evidence suggests that tumorigenesis can occur despite the presence of a single functional allele. This entails that heterozygosity in BRCA1/2 confers haploinsufficiency, where a single copy of the gene is not sufficient to fully suppress tumor formation. Here we provide an overview of the findings and the ongoing debate regarding BRCA haploinsufficiency. We further put out the challenges in studying this topic and discuss its potential relevance in the prevention and treatment of BRCA-related cancers.
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Affiliation(s)
- Anna Minello
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France
| | - Aura Carreira
- Institut Curie, PSL Research University, CNRS, UMR3348, F-91405 Orsay, France; Paris-Saclay University CNRS, UMR3348, F-91405 Orsay, France; Genome Instability and Cancer Predisposition Lab, Department of Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa (CBMSO, CSIC-UAM), Madrid 28049, Spain.
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Kawamoto H, Hitaka T, Saito-Sasaki N, Okada E, Sawada Y. Identification of Multiple Bowen's Disease Skin Lesions by Careful Physical Examination in a Patient With Fanconi Anemia. Cureus 2023; 15:e50016. [PMID: 38186461 PMCID: PMC10767468 DOI: 10.7759/cureus.50016] [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] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Because Fanconi anemia is a hereditary bone marrow failure disease caused by DNA repair dysfunction, malignant skin tumors have been recognized in patients with Fanconi anemia. Herein, we report a 32-year-old male with Fanconi anemia presenting multiple Bowen's disease skin lesions. He first recognized skin eruption in his scrotum, which was diagnosed with Bowen's disease by dermoscopy examination and histological analysis. Due to the elevated risk of skin cancers in Fanconi anemia, we conducted additional meticulous examinations using dermoscopy on the entire body's skin, revealing another skin tumor on his back. A skin biopsy confirmed the diagnosis of another site of Bowen's disease. Therefore, additional thorough examinations using dermoscopy might aid in identifying multiple skin tumors in high-risk cases of skin malignancies, such as Fanconi anemia.
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Affiliation(s)
- Hirofumi Kawamoto
- Dermatology, University of Occupational and Environmental Health, Kitakyushu, JPN
| | - Taiyo Hitaka
- Dermatology, University of Occupational and Environmental Health, Kitakyushu, JPN
| | - Natsuko Saito-Sasaki
- Dermatology, University of Occupational and Environmental Health, Kitakyushu, JPN
| | - Etsuko Okada
- Dermatology, University of Occupational and Environmental Health, Kitakyushu, JPN
| | - Yu Sawada
- Dermatology, University of Occupational and Environmental Health, Kitakyushu, JPN
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Chang L, Zhang L, Zhao B, Cheng X, Wan Y, Zhang R, Yuan W, Gao X, Zhu X. Mutation spectrum, expression profiling, and prognosis evaluation of Fanconi anemia signaling pathway genes for 4259 patients with myelodysplastic syndromes or acute myeloid leukemia. BMC Med Genomics 2023; 16:290. [PMID: 37974167 PMCID: PMC10652513 DOI: 10.1186/s12920-023-01730-5] [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: 11/02/2022] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Individuals diagnosed with Fanconi anemia (FA), an uncommon disorder characterized by chromosomal instability affecting the FA signaling pathway, exhibit heightened vulnerability to the onset of myelodysplastic syndromes (MDS) or acute myeloid leukemia (AML). METHODS Herein, we employed diverse bioinformatics and statistical analyses to investigate the potential associations between the expression/mutation patterns of FA pathway genes and MDS/AML. RESULTS The study included 4295 samples, comprising 3235 AML and 1024 MDS from our and nine other online cohorts. We investigated the distinct proportion of race, age, French-American-British, and gender factors. Compared to the FA wild-type group, we observed a decrease in the expression of FNACD2, FANCI, and RAD51C in the FA mutation group. The FA mutation group exhibited a more favorable clinical overall survival prognosis. We developed a random forest classifier and a decision tree based on FA gene expression for cytogenetic risk assessment. Furthermore, we created an FA-related Nomogram to predict survival rates in AML patients. CONCLUSIONS This investigation facilitates a deeper understanding of the functional links between FA and MDS/AML.
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Affiliation(s)
- Lixian Chang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Li Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Beibei Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Xuelian Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Yang Wan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Ranran Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
| | - Xingjie Gao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Excellent Talent Project, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Heping District Qixiangtai Road No.22, Tianjin, 300070, China.
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, 300020, China.
- Tianjin Institutes of Health Science, Tianjin, 301600, China.
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Chang L, Cheng X, Gao X, Zou Y, Yuan W, Zhang L, Zhu X. Establishing a novel Fanconi anemia signaling pathway-associated prognostic model and tumor clustering for pediatric acute myeloid leukemia patients. Open Med (Wars) 2023; 18:20230847. [PMID: 38025539 PMCID: PMC10655686 DOI: 10.1515/med-2023-0847] [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: 06/27/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Considering the connection between the Fanconi anemia (FA) signaling pathway and tumor development, we aim to investigate the links between the FA gene expression and the survival prognosis of acute myeloid leukemia (AML) patients. Our study begins by identifying two distinct clusters of pediatric AML patients. Following the batch matching of the TARGET-AML, TCGA-LAML GSE71014, GSE12417, and GSE37642 cohorts, the samples were divided into a training set and an internal validation set. A Lasso regression modeling analysis was performed to identify five signatures: BRIP1, FANCC, FANCL, MAD2L2, and RFWD3. The AML samples were stratified into high- and low-risk groups by evaluating the risk scores. The AML high-risk patients showed a poorer overall survival prognosis. To predict the survival rates, we developed an FA Nomogram incorporating risk score, gender, age, and French-American-British classification. We further utilized the BEAT-AML cohort for the external validation of FA-associated prognostic models and observed good clinical validity. Additionally, we found a correlation between DNA repair, cell cycle, and peroxide-related metabolic events and FA-related high/low risk or cluster 1/2. In summary, our novel FA-associated prognostic models promise to enhance the prediction of pediatric AML prognosis.
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Affiliation(s)
- Lixian Chang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Xuelian Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Xingjie Gao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Key Laboratory of Cellular and Molecular Immunology in Tianjin, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Medical University, Tianjin, 300070, China
| | - Yao Zou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
- Tianjin Institutes of Health Science, Tianjin, 301600, China
| | - Li Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
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9
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Kaldunski ML, Smith JR, Brodie KC, De Pons JL, Demos WM, Gibson AC, Hayman GT, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj MA, Tutaj M, Vedi M, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. Rare disease research resources at the Rat Genome Database. Genetics 2023; 224:iyad078. [PMID: 37119810 PMCID: PMC10411567 DOI: 10.1093/genetics/iyad078] [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: 01/13/2023] [Revised: 04/05/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023] Open
Abstract
Rare diseases individually affect relatively few people, but as a group they impact considerable numbers of people. The Rat Genome Database (https://rgd.mcw.edu) is a knowledgebase that offers resources for rare disease research. This includes disease definitions, genes, quantitative trail loci (QTLs), genetic variants, annotations to published literature, links to external resources, and more. One important resource is identifying relevant cell lines and rat strains that serve as models for disease research. Diseases, genes, and strains have report pages with consolidated data, and links to analysis tools. Utilizing these globally accessible resources for rare disease research, potentiating discovery of mechanisms and new treatments, can point researchers toward solutions to alleviate the suffering of those afflicted with these diseases.
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Affiliation(s)
- Mary L Kaldunski
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jennifer R Smith
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kent C Brodie
- Clinical and Translational Science Institute, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jeffrey L De Pons
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Wendy M Demos
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Adam C Gibson
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - G Thomas Hayman
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Logan Lamers
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stanley J F Laulederkind
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ketaki Thorat
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jyothi Thota
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marek A Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Monika Tutaj
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mahima Vedi
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shur-Jen Wang
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stacy Zacher
- Finance and Administration, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Melinda R Dwinell
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Anne E Kwitek
- The Rat Genome Database, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Joint Department of Biomedical Engineering, Marquette University & Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Kumpula TA, Vorimo S, Mattila TT, O’Gorman L, Astuti G, Tervasmäki A, Koivuluoma S, Mattila TM, Grip M, Winqvist R, Kuismin O, Moilanen J, Hoischen A, Gilissen C, Mantere T, Pylkäs K. Exome sequencing identified rare recurrent copy number variants and hereditary breast cancer susceptibility. PLoS Genet 2023; 19:e1010889. [PMID: 37578974 PMCID: PMC10449128 DOI: 10.1371/journal.pgen.1010889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/24/2023] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
Copy number variants (CNVs) are a major source of genetic variation and can disrupt genes or affect gene dosage. They are known to be causal or underlie predisposition to various diseases. However, the role of CNVs in inherited breast cancer susceptibility has not been thoroughly investigated. To address this, we performed whole-exome sequencing based analysis of rare CNVs in 98 high-risk Northern Finnish breast cancer cases. After filtering, selected candidate alleles were validated and characterized with a combination of orthogonal methods, including PCR-based approaches, optical genome mapping and long-read sequencing. This revealed three recurrent alterations: a 31 kb deletion co-occurring with a retrotransposon insertion (delins) in RAD52, a 13.4 kb deletion in HSD17B14 and a 64 kb partial duplication of RAD51C. Notably, all these genes encode proteins involved in pathways previously identified as essential for breast cancer development. Variants were genotyped in geographically matched cases and controls (altogether 278 hereditary and 1983 unselected breast cancer cases, and 1229 controls). The RAD52 delins and HSD17B14 deletion both showed significant enrichment among cases with indications of hereditary disease susceptibility. RAD52 delins was identified in 7/278 cases (2.5%, P = 0.034, OR = 2.86, 95% CI = 1.10-7.45) and HSD17B14 deletion in 8/278 cases (2.9%, P = 0.014, OR = 3.28, 95% CI = 1.31-8.23), the frequency of both variants in the controls being 11/1229 (0.9%). This suggests a role for RAD52 and HSD17B14 in hereditary breast cancer susceptibility. The RAD51C duplication was very rare, identified only in 2/278 of hereditary cases and 2/1229 controls (P = 0.157, OR = 4.45, 95% CI = 0.62-31.70). The identification of recurrent CNVs in these genes, and especially the relatively high frequency of RAD52 and HSD17B14 alterations in the Finnish population, highlights the importance of studying CNVs alongside single nucleotide variants when searching for genetic factors underlying hereditary disease predisposition.
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Affiliation(s)
- Timo A. Kumpula
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Sandra Vorimo
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Taneli T. Mattila
- Department of Pathology, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Luke O’Gorman
- Department of Human Genetics and Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Galuh Astuti
- Department of Human Genetics and Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Anna Tervasmäki
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Susanna Koivuluoma
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Tiina M. Mattila
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Mervi Grip
- Department of Surgery, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Outi Kuismin
- Department of Clinical Genetics, Medical Research Center Oulu and PEDEGO Research Unit, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Jukka Moilanen
- Department of Clinical Genetics, Medical Research Center Oulu and PEDEGO Research Unit, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Alexander Hoischen
- Department of Human Genetics and Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics and Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tuomo Mantere
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Human Genetics and Radboud Institute of Medical Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Research Unit of Translational Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland
- Northern Finland Laboratory Centre Nordlab, Oulu, Finland
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11
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Zemet R, Du H, Gambin T, Lupski JR, Liu P, Stankiewicz P. SNV/indel hypermutator phenotype in biallelic RAD51C variant: Fanconi anemia. Hum Genet 2023; 142:721-733. [PMID: 37031326 PMCID: PMC10996436 DOI: 10.1007/s00439-023-02550-4] [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: 02/25/2023] [Accepted: 03/24/2023] [Indexed: 04/10/2023]
Abstract
We previously reported a fetus with Fanconi anemia (FA), complementation group O due to compound heterozygous variants involving RAD51C. Interestingly, the trio exome sequencing analysis also detected eight apparent de novo mosaic variants with variant allele fraction (VAF) ranging between 11.5 and 37%. Here, using whole genome sequencing and a 'home-brew' variant filtering pipeline and DeepMosaic module, we investigated the number and signature of de novo heterozygous and mosaic variants and the hypothesis of a rare phenomenon of hypermutation. Eight-hundred-thirty apparent de novo SNVs and 21 de novo indels had VAFs below 37.41% and were considered postzygotic somatic mosaic variants. The VAFs showed a bimodal distribution, with one component having an average VAF of 25% (range: 18.7-37.41%) (n = 446), representing potential postzygotic first mitotic events, and the other component with an average VAF of 12.5% (range 9.55-18.69%) (n = 384), describing potential second mitotic events. No increased rate of CNV formation was observed. The mutational pattern analysis for somatic single base substitution showed SBS40, SBS5, and SBS3 as the top recognized signatures. SBS3 is a known signature associated with homologous recombination-based DNA damage repair error. Our data demonstrate that biallelic RAD51C variants show evidence for defective genomic DNA damage repair and thereby result in a hypermutator phenotype with the accumulation of postzygotic de novo mutations, at least in the prenatal period. This 'genome hypermutator phenomenon' might contribute to the observed hematological manifestations and the predisposition to tumors in patients with FA. We propose that other FA groups should be investigated for genome-wide de novo variants.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Baylor Genetics, Houston, TX, USA.
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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Nassani M, Fakih RE, Passweg J, Cesaro S, Alzahrani H, Alahmari A, Bonfim C, Iftikhar R, Albeihany A, Halkes C, Ahmed SO, Dufour C, Aljurf M. The role of androgen therapy in acquired aplastic anemia and other bone marrow failure syndromes. Front Oncol 2023; 13:1135160. [PMID: 37223686 PMCID: PMC10200973 DOI: 10.3389/fonc.2023.1135160] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 04/06/2023] [Indexed: 05/25/2023] Open
Abstract
Bone marrow failure syndromes are a heterogeneous group of diseases. With the major advancements in diagnostic tools and sequencing techniques, these diseases may be better classified and therapies may be further tailored. Androgens, a historic group of drugs, were found to stimulate hematopoiesis by enhancing the responsiveness of progenitors. These agents have been used for decades to treat different forms of bone marrow failure. With the availability of more effective pathways to treat BMF, androgens are less used currently. Nevertheless, this group of drugs may serve BMF patients where standard therapy is contraindicated or not available. In this article, we review the published literature addressing the use of androgens in BMF patients and we make recommendations on how to best use this class of drugs within the current therapeutic landscape.
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Affiliation(s)
- Momen Nassani
- Department of Hematology, Stem Cell Transplant & Cellular Therapy, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Riad El Fakih
- Department of Hematology, Stem Cell Transplant & Cellular Therapy, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Jakob Passweg
- Department of Hematology, University Hospital Basel, Basel, Switzerland
| | - Simone Cesaro
- Pediatric Hematology Oncology, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Hazzaa Alzahrani
- Department of Hematology, Stem Cell Transplant & Cellular Therapy, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ali Alahmari
- Department of Hematology, Stem Cell Transplant & Cellular Therapy, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Carmem Bonfim
- Transplantation Unit, Department of Hematology, Hospital de Clinicas, Federal University of Parana, Curitiba, Brazil
| | - Raheel Iftikhar
- Department of Hematology, Armed Forces Bone Marrow Transplant Centre, Rawalpindi, Pakistan
| | - Amal Albeihany
- Department of Hematology, Stem Cell Transplant & Cellular Therapy, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Constantijn Halkes
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands
| | - Syed Osman Ahmed
- Department of Hematology, Stem Cell Transplant & Cellular Therapy, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Carlo Dufour
- Hematology Unit, Hemato.Oncology Department, IRCCS, G. Gaslini Children Research Institute, Genova, Italy
| | - Mahmoud Aljurf
- Department of Hematology, Stem Cell Transplant & Cellular Therapy, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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13
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Zemet R, Du H, Gambin T, Lupski JR, Liu P, Stankiewicz P. SNV/indel hypermutator phenotype in biallelic RAD51C variant - Fanconi anemia. RESEARCH SQUARE 2023:rs.3.rs-2628288. [PMID: 36909564 PMCID: PMC10002829 DOI: 10.21203/rs.3.rs-2628288/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
We previously reported a fetus with Fanconi anemia (FA), complementation group O due to compound heterozygous variants involving RAD51C . Interestingly, the trio exome sequencing analysis also detected eight apparent de novo mosaic variants with variant allele fraction (VAF) ranging between 11.5%-37%. Here, using whole genome sequencing and a 'home-brew' variant filtering pipeline and DeepMosaic module, we investigated the number and signature of de novo heterozygous and mosaic variants and the rare phenomenon of hypermutation. Eight-hundred-thirty apparent dnSNVs and 21 de novo indels had VAFs below 37.41% and were considered postzygotic somatic mosaic variants. The VAFs showed a bimodal distribution, with one component with an average VAF of 25% (range: 18.7-37.41%) (n=446), representing potential postzygotic first mitotic events, and the other component with an average VAF of 12.5% (range: 9.55-18.69%) (n=384), describing potential second mitotic events. No increased rate of CNV formation was observed. The mutational pattern analysis for somatic single base substitution showed SBS40, SBS5, and SBS3 as the top recognized signatures. SBS3 is a known signature associated with homologous recombination-based DNA damage repair error. Our data demonstrate that biallelic RAD51C variants show evidence for defective genomic DNA damage repair and thereby result in a hypermutator phenotype with the accumulation of postzygotic de novo mutations, at least in the prenatal period. This 'genome hypermutator phenomenon' might contribute to the observed hematological manifestations and the predisposition to tumors in patients with FA, and pregnancy loss in general. We propose that other FA groups should be investigated for genome-wide de novo variants.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
- Baylor Genetics, Houston, TX
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
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Chang L, Zhang L, An W, Wan Y, Cai Y, Lan Y, Zhang A, Liu L, Ruan M, Liu X, Guo Y, Yang W, Chen X, Chen Y, Wang S, Zou Y, Yuan W, Zhu X. Phenotypic and genotypic correlation evaluation of 148 pediatric patients with Fanconi anemia in a Chinese rare disease cohort. Clin Chim Acta 2023; 539:41-49. [PMID: 36463940 DOI: 10.1016/j.cca.2022.11.030] [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: 10/15/2022] [Revised: 11/11/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022]
Abstract
BACKGROUND Fanconi anemia (FA) is a rare autosomal recessive, X-linked or autosomal dominant disease. Few large-scale FA investigations of rare disease cohorts have been conducted in China. METHODS We enrolled 148 patients diagnosed with FA according to evidence from the clinical phenotype, family history, and a set of laboratory tests. Next, the clinical manifestations and correlation between the genotype and phenotype of FA pediatric cases were investigated. RESULTS The most common FA subtype in our cohort was FA-A (51.4 %), followed by FA-D2 and FA-P. Finger (26 %) and skin (25 %) deformities were the most common malformations. Based on family history, blood system diseases (51 %) had the highest incidence rate, followed by digestive system tumours. A set of new or prognosis-related mutation sites was identified. For example, c.2941 T > G was a new most common missense mutation site for FANCA. FANCP gene mutation sites were mainly concentrated in exons 12/14/15. The mutations of FANCI/FANCD2 were mainly located at the α helix and β corners of the protein complex. FA-A/D1 patients with splicing or deletion mutations showed more severe disease than those with missense mutations. Chromosome 1/3/7/8 abnormalities were closely linked to the progression of FA to leukemia. CONCLUSION Our study investigated the clinical features and genotype/phenotype correlation of 148 Chinese pediatric FA patients, providing new insight into FA.
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Affiliation(s)
- Lixian Chang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
| | - Li Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Wenbin An
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yang Wan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yuli Cai
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yang Lan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Aoli Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Lipeng Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Min Ruan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xiaoming Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Ye Guo
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Wenyu Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xiaojuan Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yumei Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Shuchun Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yao Zou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Xiaofan Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
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15
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Bhat DS, Spies MA, Spies M. A moving target for drug discovery: Structure activity relationship and many genome (de)stabilizing functions of the RAD52 protein. DNA Repair (Amst) 2022; 120:103421. [PMID: 36327799 PMCID: PMC9888176 DOI: 10.1016/j.dnarep.2022.103421] [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: 07/29/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 02/02/2023]
Abstract
BRCA-ness phenotype, a signature of many breast and ovarian cancers, manifests as deficiency in homologous recombination, and as defects in protection and repair of damaged DNA replication forks. A dependence of such cancers on DNA repair factors less important for survival of BRCA-proficient cells, offers opportunities for development of novel chemotherapeutic interventions. The first drugs targeting BRCA-deficient cancers, poly-ADP-ribose polymerase (PARP) inhibitors have been approved for the treatment of advanced, chemotherapy resistant cancers in patients with BRCA1/2 germline mutations. Nine additional proteins that can be targeted to selectively kill BRCA-deficient cancer cells have been identified. Among them, a DNA repair protein RAD52 is an especially attractive target due to general tolerance of the RAD52 loss of function, and protective role of an inactivating mutation. Yet, the effective pharmacological inhibitors of RAD52 have not been forthcoming. In this review, we discuss advances in the state of our knowledge of the RAD52 structure, activities and cellular functions, with a specific focus on the features that make RAD52 an attractive, but difficult drug target.
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Affiliation(s)
- Divya S Bhat
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - M Ashley Spies
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA; Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Maria Spies
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA.
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Peng Q, Zhang Y, Xian B, Wu L, Ding J, Ding W, Zhang X, Ding B, Li D, Wu J, Hu X, Lu G. A synonymous variant contributes to a rare Wiedemann-Rautenstrauch syndrome complicated with mild anemia via affecting pre-mRNA splicing. Front Mol Neurosci 2022; 15:1026530. [DOI: 10.3389/fnmol.2022.1026530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/11/2022] [Indexed: 11/13/2022] Open
Abstract
Wiedemann-Rautenstrauch syndrome (WDRTS) is an extremely rare autosomal recessive neonatal disorder. Currently, over 50 cases with variable phenotypes of WDRTS have been reported. In our cohort of prenatal and postnatal growth retardation, a female proband was found to have general growth retardation, neurocutaneous syndrome, and anemia. Karyotype test and array-CGH detected no obvious chromosomal aberrations. Trio-based whole-exome sequencing (Trio-WES) identified bi-allelic compound mutations in the coding sequence (CDS) of POLR3A gene (c.3342C > T, p.Ser1114 = and c.3718G > A, p.Gly1240Ser). For the mild anemia phenotype, the underlying causal genetic factors could be attributed to the compound heterozygous mutations in FANCA gene (c.2832dup, p.Ala945CysfsTer6 and c.1902 T > G, p.Asp634Glu). Mini-gene reporter assays revealed that the synonymous variant of POLR3A and the missense variant of FANCA could affect pre-mRNA splicing of each gene. For POLR3A, the synonymous mutation (c.3342C > T, p.Ser1114=) generated three types of aberrant isoforms. Therefore, the female patient was finally diagnosed as WDRTS caused by POLR3A. For FANCA, the missense variant (c.1902 T > G, p.Asp634Glu) disrupted the normal splicing between exon 21 and 22, and produced two types of abnormal isoforms, one carrying the 1902G and the other spliced between exon 21 and 23 to exclude exon 22. Network analysis showed that POLR3A and FANCA could be STRINGed, indicating both proteins might collaborate for some unknown functions. Current investigation would broaden the knowledge for clinicians and genetic counselors and remind them to interpret those synonymous or predicted “benign” variants more carefully.
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17
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Hater N, Iwaniuk KM, Leifeld C, Grüten P, Wiek C, Raba K, Zhang F, Fischer JC, Andreassen PR, Hanenberg H, Trompeter HI. Identification of new RAD51D-regulating microRNAs that also emerge as potent inhibitors of the Fanconi anemia/homologous recombination pathways. Hum Mol Genet 2022; 31:4241-4254. [PMID: 35904444 PMCID: PMC9759333 DOI: 10.1093/hmg/ddac177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/28/2022] [Accepted: 07/27/2022] [Indexed: 01/21/2023] Open
Abstract
The Fanconi anemia (FA) and homologous recombination (HR) pathways, which partially overlap and include RAD51 and its paralogs, are key for the repair of different types of DNA damage, such as DNA interstrand crosslinks. First, to broadly assess the impact of microRNA-mediated regulation, we examined microRNA expression profiles in five isogenic fibroblast cell pairs, either deficient in DNA repair due to germline mutations in FANCA, FANCB, FANCC, FANCI or BRIP1/FANCJ or proficient due to correction with retroviral vectors. In each pair, we observed lower abundance of specific microRNAs in the FA-deficient cells. From the list of microRNAs, we experimentally confirmed the effects of miR-141-3p and miR-369-3p targeting RAD51B and miR-15a-5p, miR-494-3p as well as miR-544a targeting RAD51D. However, by western blotting, only RAD51D protein was reduced by a mixture of its regulating microRNAs. Gene ontology analyses and identification of additional FA/HR factors as targets of miR-15a-5p, miR-494-3p and miR-544a strongly suggested the widespread influence of these microRNAs on HR. Interestingly, only miR-494-3p directly reduced RAD51 foci formation, while a mixture of miR-15a-5p, miR-494-3p and miR-544a strongly reduced HR activity in green fluorescent protein (GFP) repair assays. In summary, by successfully employing this novel loss- and gain-of-function strategy, we have identified new microRNAs strongly inhibiting HR in mammalian cells. Understanding and modulating such miRNA regulation of DNA repair genes/pathways might help to overcome the reduced repair capacity of FA patients with biallelic hypomorphic mutations or help to engineer synthetic lethality strategies for patients with mutations in cancer-associated FA/HR genes.
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Affiliation(s)
- Nina Hater
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Katharina M Iwaniuk
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Carina Leifeld
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Pia Grüten
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Constanze Wiek
- Department of Otorhinolaryngology & Head/Neck Surgery, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Katharina Raba
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Fan Zhang
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Johannes C Fischer
- Institute for Transplantation Diagnostics and Cell Therapeutics, University Hospital Düsseldorf, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Paul R Andreassen
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | | | - Hans-Ingo Trompeter
- To whom correspondence should be addressed. Tel: +49 211 8118751; Fax: +49 211 8119109;
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18
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Stackhouse CT, Anderson JC, Yue Z, Nguyen T, Eustace NJ, Langford CP, Wang J, Rowland JR, Xing C, Mikhail FM, Cui X, Alrefai H, Bash RE, Lee KJ, Yang ES, Hjelmeland AB, Miller CR, Chen JY, Gillespie GY, Willey CD. An in vivo model of glioblastoma radiation resistance identifies long non-coding RNAs and targetable kinases. JCI Insight 2022; 7:148717. [PMID: 35852875 PMCID: PMC9462495 DOI: 10.1172/jci.insight.148717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/07/2022] [Indexed: 12/03/2022] Open
Abstract
Key molecular regulators of acquired radiation resistance in recurrent glioblastoma (GBM) are largely unknown, with a dearth of accurate preclinical models. To address this, we generated 8 GBM patient-derived xenograft (PDX) models of acquired radiation therapy–selected (RTS) resistance compared with same-patient, treatment-naive (radiation-sensitive, unselected; RTU) PDXs. These likely unique models mimic the longitudinal evolution of patient recurrent tumors following serial radiation therapy. Indeed, while whole-exome sequencing showed retention of major genomic alterations in the RTS lines, we did detect a chromosome 12q14 amplification that was associated with clinical GBM recurrence in 2 RTS models. A potentially novel bioinformatics pipeline was applied to analyze phenotypic, transcriptomic, and kinomic alterations, which identified long noncoding RNAs (lncRNAs) and targetable, PDX-specific kinases. We observed differential transcriptional enrichment of DNA damage repair pathways in our RTS models, which correlated with several lncRNAs. Global kinomic profiling separated RTU and RTS models, but pairwise analyses indicated that there are multiple molecular routes to acquired radiation resistance. RTS model–specific kinases were identified and targeted with clinically relevant small molecule inhibitors. This cohort of in vivo RTS patient-derived models will enable future preclinical therapeutic testing to help overcome the treatment resistance seen in patients with GBM.
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Affiliation(s)
| | | | - Zongliang Yue
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA. Birmingham, Alabama, USA
| | - Thanh Nguyen
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA. Birmingham, Alabama, USA
| | | | | | - Jelai Wang
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA. Birmingham, Alabama, USA
| | - James R. Rowland
- Department of Physics, The Ohio State University, Columbus, Ohio, USA
| | | | - Fady M. Mikhail
- Department of Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Xiangqin Cui
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | | | - Ryan E. Bash
- Division of Neuropathology, Department of Pathology, and
| | | | | | - Anita B. Hjelmeland
- Department of Cell, Developmental, and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - C. Ryan Miller
- Division of Neuropathology, Department of Pathology, and
| | - Jake Y. Chen
- Informatics Institute, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA. Birmingham, Alabama, USA
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19
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Kogan AA, Topper MJ, Dellomo AJ, Stojanovic L, McLaughlin LJ, Creed TM, Eberly CL, Kingsbury TJ, Baer MR, Kessler MD, Baylin SB, Rassool FV. Activating STING1-dependent immune signaling in TP53 mutant and wild-type acute myeloid leukemia. Proc Natl Acad Sci U S A 2022; 119:e2123227119. [PMID: 35759659 PMCID: PMC9271208 DOI: 10.1073/pnas.2123227119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 04/05/2022] [Indexed: 12/30/2022] Open
Abstract
DNA methyltransferase inhibitors (DNMTis) reexpress hypermethylated genes in cancers and leukemias and also activate endogenous retroviruses (ERVs), leading to interferon (IFN) signaling, in a process known as viral mimicry. In the present study we show that in the subset of acute myeloid leukemias (AMLs) with mutations in TP53, associated with poor prognosis, DNMTis, important drugs for treatment of AML, enable expression of ERVs and IFN and inflammasome signaling in a STING-dependent manner. We previously reported that in solid tumors poly ADP ribose polymerase inhibitors (PARPis) combined with DNMTis to induce an IFN/inflammasome response that is dependent on STING1 and is mechanistically linked to generation of a homologous recombination defect (HRD). We now show that STING1 activity is actually increased in TP53 mutant compared with wild-type (WT) TP53 AML. Moreover, in TP53 mutant AML, STING1-dependent IFN/inflammatory signaling is increased by DNMTi treatment, whereas in AMLs with WT TP53, DNMTis alone have no effect. While combining DNMTis with PARPis increases IFN/inflammatory gene expression in WT TP53 AML cells, signaling induced in TP53 mutant AML is still several-fold higher. Notably, induction of HRD in both TP53 mutant and WT AMLs follows the pattern of STING1-dependent IFN and inflammatory signaling that we have observed with drug treatments. These findings increase our understanding of the mechanisms that underlie DNMTi + PARPi treatment, and also DNMTi combinations with immune therapies, suggesting a personalized approach that statifies by TP53 status, for use of such therapies, including potential immune activation of STING1 in AML and other cancers.
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Affiliation(s)
- Aksinija A. Kogan
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Michael J. Topper
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231
| | - Anna J. Dellomo
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Lora Stojanovic
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Lena J. McLaughlin
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - T. Michael Creed
- Center for Stem Cell Biology and Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Christian L. Eberly
- Center for Stem Cell Biology and Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Tami J. Kingsbury
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Center for Stem Cell Biology and Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Maria R. Baer
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Michael D. Kessler
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231
| | - Stephen B. Baylin
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21231
- Van Andel Research Institute, Grand Rapids, MI 49503
| | - Feyruz V. Rassool
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD 21201
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20
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Munding J, Tannapfel A. [Pathological processing in pancreatic ductal adenocarcinoma-What is new?]. Chirurg 2022; 93:453-460. [PMID: 35290470 DOI: 10.1007/s00104-022-01615-w] [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] [Accepted: 02/14/2022] [Indexed: 11/25/2022]
Abstract
The macroscopic and microscopic assessments of pancreatic cancer resection specimens belong to the standard repertoire of any department of pathology. In recent years standards have been developed regarding both macroscopic and microscopic assessments, which are laid down in international and national guidelines and classifications and are regularly updated. In this way the reporting of results and interdisciplinary communication are facilitated. These classifications and guidelines are influenced by current studies and the data from them provide information on which histopathological factors are particularly relevant for the prognosis and treatment. Due to the increasing use of neoadjuvant therapy the assessment of tumor regression in histopathological specimens is also gaining in importance. Finally, individual targeted treatments are also now available for pancreatic cancer, which require extended molecular pathological diagnostics.
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Affiliation(s)
- Johanna Munding
- Institut für Pathologie, Georgius Agricola Stiftung Ruhr, Ruhr-Universität Bochum, Bürkle-de-la-Camp-Platz 1, 44879, Bochum, Deutschland.
| | - Andrea Tannapfel
- Institut für Pathologie, Georgius Agricola Stiftung Ruhr, Ruhr-Universität Bochum, Bürkle-de-la-Camp-Platz 1, 44879, Bochum, Deutschland
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21
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Palles C, Martin L, Domingo E, Chegwidden L, McGuire J, Cuthill V, Heitzer E, Kerr R, Kerr D, Kearsey S, Clark SK, Tomlinson I, Latchford A. The clinical features of polymerase proof-reading associated polyposis (PPAP) and recommendations for patient management. Fam Cancer 2022; 21:197-209. [PMID: 33948826 PMCID: PMC8964588 DOI: 10.1007/s10689-021-00256-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/07/2021] [Indexed: 10/28/2022]
Abstract
Pathogenic germline exonuclease domain (ED) variants of POLE and POLD1 cause the Mendelian dominant condition polymerase proof-reading associated polyposis (PPAP). We aimed to describe the clinical features of all PPAP patients with probably pathogenic variants. We identified patients with a variants mapping to the EDs of POLE or POLD1 from cancer genetics clinics, a colorectal cancer (CRC) clinical trial, and systematic review of the literature. We used multiple evidence sources to separate ED variants into those with strong evidence of pathogenicity and those of uncertain importance. We performed quantitative analysis of the risk of CRC, colorectal adenomas, endometrial cancer or any cancer in the former group. 132 individuals carried a probably pathogenic ED variant (105 POLE, 27 POLD1). The earliest malignancy was colorectal cancer at 14. The most common tumour types were colorectal, followed by endometrial in POLD1 heterozygotes and duodenal in POLE heterozygotes. POLD1-mutant cases were at a significantly higher risk of endometrial cancer than POLE heterozygotes. Five individuals with a POLE pathogenic variant, but none with a POLD1 pathogenic variant, developed ovarian cancer. Nine patients with POLE pathogenic variants and one with a POLD1 pathogenic variant developed brain tumours. Our data provide important evidence for PPAP management. Colonoscopic surveillance is recommended from age 14 and upper-gastrointestinal surveillance from age 25. The management of other tumour risks remains uncertain, but surveillance should be considered. In the absence of strong genotype-phenotype associations, these recommendations should apply to all PPAP patients.
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Affiliation(s)
- Claire Palles
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Lynn Martin
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Enric Domingo
- Department of Oncology, Old Road Campus Research Building, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Laura Chegwidden
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Josh McGuire
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Vicky Cuthill
- Polyposis Registry, St Mark's Hospital, Harrow, London, HA1 3UJ, UK
| | - Ellen Heitzer
- Diagnostic and Research Institute of Human Genetics, University of Gratz, Graz, Austria
| | - Rachel Kerr
- Department of Oncology, Old Road Campus Research Building, University of Oxford, Roosevelt Drive, Oxford, UK
| | - David Kerr
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Stephen Kearsey
- ZRAB, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Susan K Clark
- Polyposis Registry, St Mark's Hospital, Harrow, London, HA1 3UJ, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Andrew Latchford
- Polyposis Registry, St Mark's Hospital, Harrow, London, HA1 3UJ, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
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22
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Hoes LR, van Berge Henegouwen JM, van der Wijngaart H, Zeverijn LJ, van der Velden DL, van de Haar J, Roepman P, de Leng WJ, Jansen AM, van Werkhoven E, van der Noort V, Huitema AD, Gort EH, de Groot JWB, Kerver ED, de Groot DJ, Erdkamp F, Beerepoot LV, Hendriks MP, Smit EF, van der Graaf WT, van Herpen CM, Labots M, Hoeben A, Morreau H, Lolkema MP, Cuppen E, Gelderblom H, Verheul HM, Voest EE. Patients with Rare Cancers in the Drug Rediscovery Protocol (DRUP) Benefit from Genomics-Guided Treatment. Clin Cancer Res 2022; 28:1402-1411. [PMID: 35046062 PMCID: PMC9365364 DOI: 10.1158/1078-0432.ccr-21-3752] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/22/2021] [Accepted: 01/13/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Patients with rare cancers (incidence less than 6 cases per 100,000 persons per year) commonly have less treatment opportunities and are understudied at the level of genomic targets. We hypothesized that patients with rare cancer benefit from approved anticancer drugs outside their label similar to common cancers. EXPERIMENTAL DESIGN In the Drug Rediscovery Protocol (DRUP), patients with therapy-refractory metastatic cancers harboring an actionable molecular profile are matched to FDA/European Medicines Agency-approved targeted therapy or immunotherapy. Patients are enrolled in parallel cohorts based on the histologic tumor type, molecular profile and study drug. Primary endpoint is clinical benefit (complete response, partial response, stable disease ≥ 16 weeks). RESULTS Of 1,145 submitted cases, 500 patients, including 164 patients with rare cancers, started one of the 25 available drugs and were evaluable for treatment outcome. The overall clinical benefit rate was 33% in both the rare cancer and nonrare cancer subgroup. Inactivating alterations of CDKN2A and activating BRAF aberrations were overrepresented in patients with rare cancer compared with nonrare cancers, resulting in more matches to CDK4/6 inhibitors (14% vs. 4%; P ≤ 0.001) or BRAF inhibitors (9% vs. 1%; P ≤ 0.001). Patients with rare cancer treated with small-molecule inhibitors targeting BRAF experienced higher rates of clinical benefit (75%) than the nonrare cancer subgroup. CONCLUSIONS Comprehensive molecular testing in patients with rare cancers may identify treatment opportunities and clinical benefit similar to patients with common cancers. Our findings highlight the importance of access to broad molecular diagnostics to ensure equal treatment opportunities for all patients with cancer.
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Affiliation(s)
- Louisa R. Hoes
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute Amsterdam, the Netherlands
- Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Jade M. van Berge Henegouwen
- Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hanneke van der Wijngaart
- Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Medical Oncology, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Laurien J. Zeverijn
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute Amsterdam, the Netherlands
- Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Daphne L. van der Velden
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute Amsterdam, the Netherlands
| | - Joris van de Haar
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute Amsterdam, the Netherlands
- Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Paul Roepman
- Hartwig Medical Foundation, Amsterdam, the Netherlands
| | - Wendy J. de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Anne M.L. Jansen
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Erik van Werkhoven
- Biometrics Department, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Alwin D.R. Huitema
- Department of Clinical Pharmacy, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Pharmacy & Pharmacology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Pharmacology, Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Eelke H. Gort
- Department of Medical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Emile D. Kerver
- Department of Medical Oncology, Onze Lieve Vrouwe Gasthuis, Amsterdam, the Netherlands
| | - Derk Jan de Groot
- Medical Oncology, University Medical Centre Groningen, Groningen, the Netherlands
| | - Frans Erdkamp
- Department of Medical Oncology, Zuyderland Hospital, Sittard-Geleen, the Netherlands
| | - Laurens V. Beerepoot
- Department of Medical Oncology, Elisabeth-Tweesteden Hospital, Tilburg, the Netherlands
| | | | - Egbert F. Smit
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Carla M.L. van Herpen
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ann Hoeben
- Division of Medical Oncology, Department of Internal Medicine, GROW-School of Oncology and Developmental Biology, Maastricht University Medical Center, the Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Martijn P. Lolkema
- Department of Medical Oncology, Erasmus Medical Center Cancer Institute, Rotterdam, the Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, the Netherlands
| | - Edwin Cuppen
- Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
- Hartwig Medical Foundation, Amsterdam, the Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hans Gelderblom
- Department of Medical Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Henk M.W. Verheul
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Emile E. Voest
- Division of Molecular Oncology & Immunology, Netherlands Cancer Institute Amsterdam, the Netherlands
- Oncode Institute, the Netherlands Cancer Institute, Amsterdam, the Netherlands
- Center for Personalized Cancer Treatment, Rotterdam, the Netherlands
- Corresponding Author: Emile E. Voest, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands. Phone: 312-0512-9111; E-mail:
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23
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Shah SM, Demidova EV, Lesh RW, Hall MJ, Daly MB, Meyer JE, Edelman MJ, Arora S. Therapeutic implications of germline vulnerabilities in DNA repair for precision oncology. Cancer Treat Rev 2022; 104:102337. [PMID: 35051883 PMCID: PMC9016579 DOI: 10.1016/j.ctrv.2021.102337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/30/2021] [Accepted: 12/31/2021] [Indexed: 12/12/2022]
Abstract
DNA repair vulnerabilities are present in a significant proportion of cancers. Specifically, germline alterations in DNA repair not only increase cancer risk but are associated with treatment response and clinical outcomes. The therapeutic landscape of cancer has rapidly evolved with the FDA approval of therapies that specifically target DNA repair vulnerabilities. The clinical success of synthetic lethality between BRCA deficiency and poly(ADP-ribose) polymerase (PARP) inhibition has been truly revolutionary. Defective mismatch repair has been validated as a predictor of response to immune checkpoint blockade associated with durable responses and long-term benefit in many cancer patients. Advances in next generation sequencing technologies and their decreasing cost have supported increased genetic profiling of tumors coupled with germline testing of cancer risk genes in patients. The clinical adoption of panel testing for germline assessment in high-risk individuals has generated a plethora of genetic data, particularly on DNA repair genes. Here, we highlight the therapeutic relevance of germline aberrations in DNA repair to identify patients eligible for precision treatments such as PARP inhibitors (PARPis), immune checkpoint blockade, chemotherapy, radiation therapy and combined treatment. We also discuss emerging mechanisms that regulate DNA repair.
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Affiliation(s)
- Shreya M Shah
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Science Scholars Program, Temple University, Philadelphia, PA, United States
| | - Elena V Demidova
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Kazan Federal University, Kazan, Russian Federation
| | - Randy W Lesh
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Geisinger Commonwealth School of Medicine, Scranton, PA, United States
| | - Michael J Hall
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Mary B Daly
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Joshua E Meyer
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States; Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Martin J Edelman
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States.
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States; Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States.
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24
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Vanni VS, Campo G, Cioffi R, Papaleo E, Salonia A, Viganò P, Lambertini M, Candiani M, Meirow D, Orvieto R. The neglected members of the family: non-BRCA mutations in the Fanconi anemia/BRCA pathway and reproduction. Hum Reprod Update 2022; 28:296-311. [PMID: 35043201 DOI: 10.1093/humupd/dmab045] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND BReast CAncer (BRCA) genes are extensively studied in the context of fertility and reproductive aging. BRCA proteins are part of the DNA repair Fanconi anemia (FA)/BRCA pathway, in which more than 20 proteins are implicated. According to which gene is mutated and which interactions are lost owing to the mutation, carriers and patients with monoallelic or biallelic FA/BRCA mutations exhibit very different phenotypes, from overt FA to cancer predisposition or no pathological implications. The effect of the so far neglected non-BRCA FA mutations on fertility also deserves consideration. OBJECTIVE AND RATIONALE As improved treatments allow a longer life expectancy in patients with biallelic FA mutations and overt FA, infertility is emerging as a predominant feature. We thus reviewed the mechanisms for such a manifestation, as well as whether they also occur in monoallelic carriers of FA non-BRCA mutations. SEARCH METHODS Electronic databases PUBMED, EMBASE and CENTRAL were searched using the following term: 'fanconi' OR 'FANC' OR 'AND' 'fertility' OR 'pregnancy' OR 'ovarian reserve' OR 'spermatogenesis' OR 'hypogonadism'. All pertinent reports in the English-language literature were retrieved until May 2021 and the reference lists were systematically searched in order to identify any potential additional studies. OUTCOMES Biallelic FA mutations causing overt FA disease are associated with premature ovarian insufficiency (POI) occurring in the fourth decade in women and with primary non-obstructive azoospermia (NOA) in men. Hypogonadism in FA patients seems mainly associated with a defect in primordial germ cell proliferation in fetal life. In recent small, exploratory whole-exome sequencing studies, biallelic clinically occult mutations in the FA complementation group A (Fanca) and M (Fancm) genes were found in otherwise healthy patients with isolated NOA or POI, and also monoallelic carrier status for a loss-of-function mutation in Fanca has been implicated as a possible cause for POI. In those patients with known monoallelic FA mutations undergoing pre-implantation genetic testing, poor assisted reproduction outcomes are reported. However, the mechanisms underlying the repeated failures and the high miscarriage rates observed are not fully known. WIDER IMPLICATIONS The so far 'neglected' members of the FA/BRCA family will likely emerge as a relevant focus of investigation in the genetics of reproduction. Several (rather than a single) non-BRCA genes might be implicated. State-of-the-art methods, such as whole-genome/exome sequencing, and further exploratory studies are required to understand the prevalence and mechanisms for occult FA mutations in infertility and recurrent miscarriage.
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Affiliation(s)
- Valeria Stella Vanni
- Università Vita-Salute San Raffaele, Milan, Italy.,Obstetrics and Gynecology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Raffaella Cioffi
- Università Vita-Salute San Raffaele, Milan, Italy.,Obstetrics and Gynecology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Enrico Papaleo
- Obstetrics and Gynecology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Salonia
- Università Vita-Salute San Raffaele, Milan, Italy.,Division of Experimental Oncology/Unit of Urology, URI, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Paola Viganò
- Reproductive Sciences Laboratory, Obstetrics and Gynecology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Lambertini
- Department of Medical Oncology, U.O.C Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova, Italy.,Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genova, Genova, Italy
| | - Massimo Candiani
- Università Vita-Salute San Raffaele, Milan, Italy.,Obstetrics and Gynecology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dror Meirow
- Department of Obstetrics and Gynecology, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel
| | - Raoul Orvieto
- Department of Obstetrics and Gynecology, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv-Yafo, Israel
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25
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Shen K, Zhang M, Wang J, Mu W, Wang J, Wang C, Xing S, Hong Z, Xiao M. Inherited heterozygous Fanconi anemia gene mutations in a therapy-related CMML patient with a rare NUP98-HOXC11 fusion: A case report. Front Oncol 2022; 12:1036511. [PMID: 36338706 PMCID: PMC9626966 DOI: 10.3389/fonc.2022.1036511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 09/28/2022] [Indexed: 02/05/2023] Open
Abstract
Fanconi anemia (FA) genes play critical roles in the repair of DNA lesions. Non-FA (or underlying FA) patients harboring heterozygous germline FA gene mutations may also face an increased risk of developing bone marrow failure, primary immunodeficiency disease, and hereditary cancer predisposition syndromes. We report a female patient who suffered from ovarian cancer at 50 years of age. During the initial treatment, six cycles of docetaxel and carboplatin (DC) combination chemotherapy were administered followed by two cycles of docetaxel maintenance therapy. Then, she received a routine follow-up every 3 months for the next 3 years, and all the results of the examination and laboratory tests were normal. Unfortunately, at 54 years of age, she developed a secondary cancer of therapy-related (t-) chronic myelomonocytic leukemia (t-CMML). After two courses of a highly intensive induction chemotherapy regimen with DAC (decitabine) and HAA (homoharringtonine, cytarabine), the patient suffered from severe and persistent bone marrow failure (BMF). Targeted next-generation sequencing (NGS) of a panel of 80 genes was performed on her initial bone marrow aspirate sample and identified PTPN11, NRAS, and DNMT3A somatic mutations. In addition, RNA sequencing (RNA-seq) revealed a rare NUP98-HOXC11 fusion. Whole-exome sequencing (WES) verified RAD51C, BRIP1, PALB2, and FANCG heterozygous germline mutations of the FA pathway, which were further confirmed in buccal swab samples by Sanger sequencing. For this patient, we hypothesized that an altered FA pathway resulted in genomic instability, hypersensitivity to DNA-crosslinking agents or cytotoxic chemotherapeutics, and unsuccessful DNA damage repair. Consequently, she developed ovarian cancer and secondary t-CMML and then suffered from BMF and delayed post-chemotherapy bone marrow recovery after several chemotherapy courses. This case highlights the importance of genetic counseling in patients with hematopoietic neoplasms with high clinical suspicion for carrying cancer susceptibility gene mutations, which require timely diagnosis and personalized management.
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Bartlett TE, Jia P, Chandna S, Roy S. Inference of tissue relative proportions of the breast epithelial cell types luminal progenitor, basal, and luminal mature. Sci Rep 2021; 11:23702. [PMID: 34880407 PMCID: PMC8655091 DOI: 10.1038/s41598-021-03161-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/26/2021] [Indexed: 12/15/2022] Open
Abstract
Single-cell analysis has revolutionised genomic science in recent years. However, due to cost and other practical considerations, single-cell analyses are impossible for studies based on medium or large patient cohorts. For example, a single-cell analysis usually costs thousands of euros for one tissue sample from one volunteer, meaning that typical studies using single-cell analyses are based on very few individuals. While single-cell genomic data can be used to examine the phenotype of individual cells, cell-type deconvolution methods are required to track the quantities of these cells in bulk-tissue genomic data. Hormone receptor negative breast cancers are highly aggressive, and are thought to originate from a subtype of epithelial cells called the luminal progenitor. In this paper, we show how to quantify the number of luminal progenitor cells as well as other epithelial subtypes in breast tissue samples using DNA and RNA based measurements. We find elevated levels of cells which resemble these hormone receptor negative luminal progenitor cells in breast tumour biopsies of hormone receptor negative cancers, as well as in healthy breast tissue samples from BRCA1 (FANCS) mutation carriers. We also find that breast tumours from carriers of heterozygous mutations in non-BRCA Fanconi Anaemia pathway genes are much more likely to be hormone receptor negative. These findings have implications for understanding hormone receptor negative breast cancers, and for breast cancer screening in carriers of heterozygous mutations of Fanconi Anaemia pathway genes.
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Affiliation(s)
- Thomas E Bartlett
- Department of Statistical Science, University College London, London, UK.
| | - Peiwen Jia
- Department of Statistical Science, University College London, London, UK
| | - Swati Chandna
- Department of Economics, Mathematics and Statistics, Birkbeck University of London, London, UK
| | - Sandipan Roy
- Department of Mathematical Sciences, University of Bath, Bath, UK
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Hu HF, Ye Z, Qin Y, Xu XW, Yu XJ, Zhuo QF, Ji SR. Mutations in key driver genes of pancreatic cancer: molecularly targeted therapies and other clinical implications. Acta Pharmacol Sin 2021; 42:1725-1741. [PMID: 33574569 PMCID: PMC8563973 DOI: 10.1038/s41401-020-00584-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/16/2020] [Indexed: 02/08/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers, with a minimal difference between its incidence rate and mortality rate. Advances in oncology over the past several decades have dramatically improved the overall survival of patients with multiple cancers due to the implementation of new techniques in early diagnosis, therapeutic drugs, and personalized therapy. However, pancreatic cancers remain recalcitrant, with a 5-year relative survival rate of <9%. The lack of measures for early diagnosis, strong resistance to chemotherapy, ineffective adjuvant chemotherapy and the unavailability of molecularly targeted therapy are responsible for the high mortality rate of this notorious disease. Genetically, PDAC progresses as a complex result of the activation of oncogenes and inactivation of tumor suppressors. Although next-generation sequencing has identified numerous new genetic alterations, their clinical implications remain unknown. Classically, oncogenic mutations in genes such as KRAS and loss-of-function mutations in tumor suppressors, such as TP53, CDNK2A, DPC4/SMAD4, and BRCA2, are frequently observed in PDAC. Currently, research on these key driver genes is still the main focus. Therefore, studies assessing the functions of these genes and their potential clinical implications are of paramount importance. In this review, we summarize the biological function of key driver genes and pharmaceutical targets in PDAC. In addition, we conclude the results of molecularly targeted therapies in clinical trials and discuss how to utilize these genetic alterations in further clinical practice.
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Affiliation(s)
- Hai-feng Hu
- grid.452404.30000 0004 1808 0942Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,grid.452404.30000 0004 1808 0942Shanghai Pancreatic Cancer Institute, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Pancreatic Cancer Institute, Fudan University, Shanghai, 200032 China
| | - Zeng Ye
- grid.452404.30000 0004 1808 0942Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,grid.452404.30000 0004 1808 0942Shanghai Pancreatic Cancer Institute, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Pancreatic Cancer Institute, Fudan University, Shanghai, 200032 China
| | - Yi Qin
- grid.452404.30000 0004 1808 0942Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,grid.452404.30000 0004 1808 0942Shanghai Pancreatic Cancer Institute, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Pancreatic Cancer Institute, Fudan University, Shanghai, 200032 China
| | - Xiao-wu Xu
- grid.452404.30000 0004 1808 0942Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,grid.452404.30000 0004 1808 0942Shanghai Pancreatic Cancer Institute, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Pancreatic Cancer Institute, Fudan University, Shanghai, 200032 China
| | - Xian-jun Yu
- grid.452404.30000 0004 1808 0942Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,grid.452404.30000 0004 1808 0942Shanghai Pancreatic Cancer Institute, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Pancreatic Cancer Institute, Fudan University, Shanghai, 200032 China
| | - Qi-feng Zhuo
- grid.452404.30000 0004 1808 0942Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,grid.452404.30000 0004 1808 0942Shanghai Pancreatic Cancer Institute, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Pancreatic Cancer Institute, Fudan University, Shanghai, 200032 China
| | - Shun-rong Ji
- grid.452404.30000 0004 1808 0942Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,grid.452404.30000 0004 1808 0942Shanghai Pancreatic Cancer Institute, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Pancreatic Cancer Institute, Fudan University, Shanghai, 200032 China
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Jung I, Kim M, Rhee S, Lim S, Kim S. MONTI: A Multi-Omics Non-negative Tensor Decomposition Framework for Gene-Level Integrative Analysis. Front Genet 2021; 12:682841. [PMID: 34567063 PMCID: PMC8461247 DOI: 10.3389/fgene.2021.682841] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/12/2021] [Indexed: 11/13/2022] Open
Abstract
Multi-omics data is frequently measured to enrich the comprehension of biological mechanisms underlying certain phenotypes. However, due to the complex relations and high dimension of multi-omics data, it is difficult to associate omics features to certain biological traits of interest. For example, the clinically valuable breast cancer subtypes are well-defined at the molecular level, but are poorly classified using gene expression data. Here, we propose a multi-omics analysis method called MONTI (Multi-Omics Non-negative Tensor decomposition for Integrative analysis), which goal is to select multi-omics features that are able to represent trait specific characteristics. Here, we demonstrate the strength of multi-omics integrated analysis in terms of cancer subtyping. The multi-omics data are first integrated in a biologically meaningful manner to form a three dimensional tensor, which is then decomposed using a non-negative tensor decomposition method. From the result, MONTI selects highly informative subtype specific multi-omics features. MONTI was applied to three case studies of 597 breast cancer, 314 colon cancer, and 305 stomach cancer cohorts. For all the case studies, we found that the subtype classification accuracy significantly improved when utilizing all available multi-omics data. MONTI was able to detect subtype specific gene sets that showed to be strongly regulated by certain omics, from which correlation between omics types could be inferred. Furthermore, various clinical attributes of nine cancer types were analyzed using MONTI, which showed that some clinical attributes could be well explained using multi-omics data. We demonstrated that integrating multi-omics data in a gene centric manner improves detecting cancer subtype specific features and other clinical features, which may be used to further understand the molecular characteristics of interest. The software and data used in this study are available at: https://github.com/inukj/MONTI.
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Affiliation(s)
- Inuk Jung
- Department of Computer Science and Engineering, Kyungpook National University, Daegu, South Korea
| | - Minsu Kim
- Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Sungmin Rhee
- Department of Computer Science and Engineering, Seoul National University, Seoul, South Korea
| | - Sangsoo Lim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Gwanak-Gu, Seoul, South Korea
| | - Sun Kim
- Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Department of Computer Science and Engineering, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Gwanak-Gu, Seoul, South Korea
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Coordinating DNA Replication and Mitosis through Ubiquitin/SUMO and CDK1. Int J Mol Sci 2021; 22:ijms22168796. [PMID: 34445496 PMCID: PMC8395760 DOI: 10.3390/ijms22168796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/30/2022] Open
Abstract
Post-translational modification of the DNA replication machinery by ubiquitin and SUMO plays key roles in the faithful duplication of the genetic information. Among other functions, ubiquitination and SUMOylation serve as signals for the extraction of factors from chromatin by the AAA ATPase VCP. In addition to the regulation of DNA replication initiation and elongation, we now know that ubiquitination mediates the disassembly of the replisome after DNA replication termination, a process that is essential to preserve genomic stability. Here, we review the recent evidence showing how active DNA replication restricts replisome ubiquitination to prevent the premature disassembly of the DNA replication machinery. Ubiquitination also mediates the removal of the replisome to allow DNA repair. Further, we discuss the interplay between ubiquitin-mediated replisome disassembly and the activation of CDK1 that is required to set up the transition from the S phase to mitosis. We propose the existence of a ubiquitin–CDK1 relay, where the disassembly of terminated replisomes increases CDK1 activity that, in turn, favors the ubiquitination and disassembly of more replisomes. This model has important implications for the mechanism of action of cancer therapies that induce the untimely activation of CDK1, thereby triggering premature replisome disassembly and DNA damage.
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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.
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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.
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31
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Kar SP, Considine DP, Tyrer JP, Plummer JT, Chen S, Dezem FS, Barbeira AN, Rajagopal PS, Rosenow WT, Moreno F, Bodelon C, Chang-Claude J, Chenevix-Trench G, deFazio A, Dörk T, Ekici AB, Ewing A, Fountzilas G, Goode EL, Hartman M, Heitz F, Hillemanns P, Høgdall E, Høgdall CK, Huzarski T, Jensen A, Karlan BY, Khusnutdinova E, Kiemeney LA, Kjaer SK, Klapdor R, Köbel M, Li J, Liebrich C, May T, Olsson H, Permuth JB, Peterlongo P, Radice P, Ramus SJ, Riggan MJ, Risch HA, Saloustros E, Simard J, Szafron LM, Titus L, Thompson CL, Vierkant RA, Winham SJ, Zheng W, Doherty JA, Berchuck A, Lawrenson K, Im HK, Manichaikul AW, Pharoah PD, Gayther SA, Schildkraut JM. Pleiotropy-guided transcriptome imputation from normal and tumor tissues identifies candidate susceptibility genes for breast and ovarian cancer. HGG ADVANCES 2021; 2:100042. [PMID: 34317694 PMCID: PMC8312632 DOI: 10.1016/j.xhgg.2021.100042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Familial, sequencing, and genome-wide association studies (GWASs) and genetic correlation analyses have progressively unraveled the shared or pleiotropic germline genetics of breast and ovarian cancer. In this study, we aimed to leverage this shared germline genetics to improve the power of transcriptome-wide association studies (TWASs) to identify candidate breast cancer and ovarian cancer susceptibility genes. We built gene expression prediction models using the PrediXcan method in 681 breast and 295 ovarian tumors from The Cancer Genome Atlas and 211 breast and 99 ovarian normal tissue samples from the Genotype-Tissue Expression project and integrated these with GWAS meta-analysis data from the Breast Cancer Association Consortium (122,977 cases/105,974 controls) and the Ovarian Cancer Association Consortium (22,406 cases/40,941 controls). The integration was achieved through application of a pleiotropy-guided conditional/conjunction false discovery rate (FDR) approach in the setting of a TWASs. This identified 14 candidate breast cancer susceptibility genes spanning 11 genomic regions and 8 candidate ovarian cancer susceptibility genes spanning 5 genomic regions at conjunction FDR < 0.05 that were >1 Mb away from known breast and/or ovarian cancer susceptibility loci. We also identified 38 candidate breast cancer susceptibility genes and 17 candidate ovarian cancer susceptibility genes at conjunction FDR < 0.05 at known breast and/or ovarian susceptibility loci. The 22 genes identified by our cross-cancer analysis represent promising candidates that further elucidate the role of the transcriptome in mediating germline breast and ovarian cancer risk.
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Affiliation(s)
- Siddhartha P. Kar
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Daniel P.C. Considine
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan P. Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Jasmine T. Plummer
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Stephanie Chen
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Felipe S. Dezem
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Alvaro N. Barbeira
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Padma S. Rajagopal
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Will T. Rosenow
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Fernando Moreno
- Department of Oncology, Hospital Clínico San Carlos, Madrid, Spain
| | - Clara Bodelon
- Divison of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Anna deFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, Australia
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Arif B. Ekici
- Institute of Human Genetics, University Hospital Erlangen, Erlangen, Germany
- Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen, Erlangen, Germany
| | - Ailith Ewing
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki School of Medicine, Thessaloniki, Greece
| | - Ellen L. Goode
- Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Mikael Hartman
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Florian Heitz
- Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte/Evang., Essen, Germany
- Department of Gynecology, Center for Oncologic Surgery, Charité Campus Virchow-Klinikum, Berlin, Germany
| | - Peter Hillemanns
- Department of Gynecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Estrid Høgdall
- Department of Virus, Lifestyle, and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Molecular Unit, Department of Pathology, Herlev Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Claus K. Høgdall
- The Juliane Marie Centre, Department of Gynecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Tomasz Huzarski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
- Department of Genetics and Pathology, University of Zielona Góra, Zielona Góra, Poland
| | - Allan Jensen
- Department of Lifestyle, Reproduction, and Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Beth Y. Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Lambertus A. Kiemeney
- Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne K. Kjaer
- Department of Virus, Lifestyle, and Genes, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Rüdiger Klapdor
- Department of Gynecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Foothills Medical Center, Calgary, AB, Canada
| | - Jingmei Li
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Genome Institute of Singapore, Human Genetics, Singapore, Singapore
| | - Clemens Liebrich
- Department of Obstetrics and Gynecology, Klinikum Wolfsburg, Wolfsburg, Germany
| | - Taymaa May
- Division of Gynecologic Oncology, University Health Network, Princess Margaret Hospital, Toronto, ON, Canada
| | - Håkan Olsson
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Jennifer B. Permuth
- Departments of Cancer Epidemiology and Gastrointestinal Oncology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM-The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Susan J. Ramus
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Marjorie J. Riggan
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Harvey A. Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | | | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Lukasz M. Szafron
- Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Linda Titus
- Muskie School of Public Service, University of Southern Maine, Portland, ME, USA
| | - Cheryl L. Thompson
- Department of Nutrition, Case Western Reserve University, Cleveland, OH, USA
| | - Robert A. Vierkant
- Department of Quantitative Health Sciences, Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN, USA
| | - Stacey J. Winham
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Jennifer A. Doherty
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Andrew Berchuck
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Kate Lawrenson
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Women’s Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Ani W. Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Paul D.P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics, Department of Biomedical Science, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joellen M. Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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Mehibel M, Xu Y, Li CG, Moon EJ, Thakkar KN, Diep AN, Kim RK, Bloomstein JD, Xiao Y, Bacal J, Saldivar JC, Le QT, Cimprich KA, Rankin EB, Giaccia AJ. Eliminating hypoxic tumor cells improves response to PARP inhibitors in homologous recombination-deficient cancer models. J Clin Invest 2021; 131:146256. [PMID: 34060485 PMCID: PMC8266208 DOI: 10.1172/jci146256] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/21/2021] [Indexed: 12/21/2022] Open
Abstract
Hypoxia, a hallmark feature of the tumor microenvironment, causes resistance to conventional chemotherapy, but was recently reported to synergize with poly(ADP-ribose) polymerase inhibitors (PARPis) in homologous recombination-proficient (HR-proficient) cells through suppression of HR. While this synergistic killing occurs under severe hypoxia (<0.5% oxygen), our study shows that moderate hypoxia (2% oxygen) instead promotes PARPi resistance in both HR-proficient and -deficient cancer cells. Mechanistically, we identify reduced ROS-induced DNA damage as the cause for the observed resistance. To determine the contribution of hypoxia to PARPi resistance in tumors, we used the hypoxic cytotoxin tirapazamine to selectively kill hypoxic tumor cells. We found that the selective elimination of hypoxic tumor cells led to a substantial antitumor response when used with PARPi compared with that in tumors treated with PARPi alone, without enhancing normal tissue toxicity. Since human breast cancers with BRAC1/2 mutations have an increased hypoxia signature and hypoxia reduces the efficacy of PARPi, then eliminating hypoxic tumor cells should enhance the efficacy of PARPi therapy.
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Affiliation(s)
- Manal Mehibel
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University Medical Center, Stanford, California, USA
| | - Yu Xu
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University Medical Center, Stanford, California, USA
| | - Caiyun G. Li
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University Medical Center, Stanford, California, USA
| | - Eui Jung Moon
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University Medical Center, Stanford, California, USA
| | - Kaushik N. Thakkar
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University Medical Center, Stanford, California, USA
| | - Anh N. Diep
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University Medical Center, Stanford, California, USA
| | - Ryan K. Kim
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University Medical Center, Stanford, California, USA
| | - Joshua D. Bloomstein
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University Medical Center, Stanford, California, USA
| | - Yiren Xiao
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University Medical Center, Stanford, California, USA
| | - Julien Bacal
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Joshua C. Saldivar
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Quynh-Thu Le
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University Medical Center, Stanford, California, USA
| | - Karlene A. Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Erinn B. Rankin
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University Medical Center, Stanford, California, USA
- Department of Obstetrics and Gynecology, Stanford University Medical Center, Stanford, California, USA
| | - Amato J. Giaccia
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University Medical Center, Stanford, California, USA
- Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
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Incidence of squamous cell carcinomas of the head and neck following prolonged pegylated liposomal doxorubicin. Anticancer Drugs 2021; 31:747-750. [PMID: 32697468 DOI: 10.1097/cad.0000000000000950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite numerous case reports, the incidence of a secondary diagnosis of head and neck squamous cell carcinoma (HNC) following pegylated liposomal doxorubicin (PLD) treatment is unknown. Computerized pharmacy records were searched at a large, multi-center healthcare system for patients who received PLD. Electronic medical records were searched to identify the patient's age at treatment initiation of PLD, diagnosis for which they were treated with PLD, number of courses and total cumulative dose of PLD (TCDPLD) and secondary malignancies. Published PLD associated HNC was utilized to determine the lowest and median TCDPLD doses associated with HNC. One thousand two hundred ninety eligible patients who had been treated with PLD were identified. The lowest TCDPLD associated HNC in the literature is 405 mg/m2. In our healthcare system, 275 patients received more than 400 mg/m2 yielding a risk of 0.004%. One hundred fifty-one patients received the lowest TCDPLD associated with HNC cancer in our series which was 640 mg/m2 yielding a risk of 0.007%. Four of 30 patients (13.3%) developed HNC who received the median TCDPLD associated with HNC in the literature of 1440 mg/m2. Five of 20 patients (25%) receiving 1650 mg/m2 developed HNC in our healthcare system. Prolonged therapy with PLD is associated with an increased risk of HNC. This risk appears to be related to the cumulative dose varying from 0.004 to 13.3% at the lowest and median TCDPLD of reported cases in the literature, respectively. Oncologists need to be aware of this risk and to screen patients appropriately.
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Zheng Y, Li B, Pan D, Cao J, Zhang J, Wang X, Li X, Hou W, Bao D, Ren L, Yang J, Wang S, Qiu Y, Zhou F, Liu Z, Zhu S, Zhang L, Qing T, Wang Y, Yu Y, Wu J, Hu X, Shi L. Functional consequences of a rare missense BARD1 c.403G>A germline mutation identified in a triple-negative breast cancer patient. Breast Cancer Res 2021; 23:53. [PMID: 33933153 PMCID: PMC8088670 DOI: 10.1186/s13058-021-01428-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 04/13/2021] [Indexed: 11/30/2022] Open
Abstract
We identified a rare missense germline mutation in BARD1 (c.403G>A or p.Asp135Asn) as pathogenic using integrated genomics and transcriptomics profiling of germline and tumor samples from an early-onset triple-negative breast cancer patient who later was administrated with a PARP inhibitor for 2 months. We demonstrated in cell and mouse models that, compared to the wild-type, (1) c.403G>A mutant cell lines were more sensitive to irradiation, a DNA damage agent, and a PARP inhibitor; (2) c.403G>A mutation inhibited interaction between BARD1 and RAD51 (but not BRCA1); and (3) c.403G>A mutant mice were hypersensitive to ionizing radiation. Our study shed lights on the clinical interpretation of rare germline mutations of BARD1.
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Affiliation(s)
- Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Bingying Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Dejing Pan
- Cambridge-Suda Genomic Resource Center and Jiangsu Key Laboratory of Neuropsychiatric Diseases Research, Soochow University, Suzhou, China
| | - Jun Cao
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jian Zhang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiaolin Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Xiangnan Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Wanwan Hou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ding Bao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Luyao Ren
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Shangzi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yangyang Qiu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, China
| | - Fei Zhou
- Cambridge-Suda Genomic Resource Center and Jiangsu Key Laboratory of Neuropsychiatric Diseases Research, Soochow University, Suzhou, China
| | - Zhiwei Liu
- Cambridge-Suda Genomic Resource Center and Jiangsu Key Laboratory of Neuropsychiatric Diseases Research, Soochow University, Suzhou, China
| | - Sibo Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Lei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Tao Qing
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Ying Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China.
| | - Jiaxue Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Xichun Hu
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China. .,Human Phenome Institute, Fudan University, Shanghai, China. .,Fudan-Gospel Joint Research Center for Precision Medicine, Fudan University, Shanghai, China.
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35
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Raghu VK, Ge X, Balajiee A, Shirer DJ, Das I, Benos PV, Chrysanthis PK. A Pipeline for Integrated Theory and Data-Driven Modeling of Biomedical Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:811-822. [PMID: 32841121 PMCID: PMC8237279 DOI: 10.1109/tcbb.2020.3019237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Genome sequencing technologies have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level. However, to truly understand mechanisms of disease and predict the effects of medical interventions, high-throughput data must be integrated with demographic, phenotypic, environmental, and behavioral data from individuals. Further, effective knowledge discovery methods must infer relationships between these data types. We recently proposed a pipeline (CausalMGM) to achieve this. CausalMGM uses probabilistic graphical models to infer the relationships between variables in the data; however, CausalMGM's graphical structure learning algorithm can only handle small datasets efficiently. We propose a new methodology (piPref-Div) that selects the most informative variables for CausalMGM, enabling it to scale. We validate the efficacy of piPref-Div against other feature selection methods and demonstrate how the use of the full pipeline improves breast cancer outcome prediction and provides biologically interpretable views of gene expression data.
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36
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Deng S, Ye W, Zhang S, Zhu G, Zhang P, Song Y, Duan F, Lang J, Lu S. Oral Tongue Cancer in a Patient with Fanconi Anemia: A Case Report and Literature Review. Cancer Manag Res 2021; 13:3145-3154. [PMID: 33883933 PMCID: PMC8053604 DOI: 10.2147/cmar.s301582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/17/2021] [Indexed: 02/05/2023] Open
Abstract
Purpose Fanconi anemia (FA) is a rare genetic disorder characterized by congenital anomalies, progressive bone marrow failure and high susceptibility to solid tumors, especially head and neck squamous cell carcinoma (HNSCC). Management of FA patients with head and neck cancer is a challenge due to increased risk of surgery, poor tolerance of chemotherapy, and severe myelotoxicity of radiotherapy. Patients and Methods We present a case of a 33-year-old man with carcinoma of oral tongue (T1N2M0), who experienced prolonged and profound bone marrow failure as a consequence of concurrent cisplatin/radiation. The young patient who developed HNSCC without risk factors, the myelotoxicity after exposure to platinum-based agent cisplatin and the further evaluation of phenotypic characteristics raised suspicion of FA. Whole exome sequencing performed for the patient and parents ultimately established the diagnosis of FA. Results Genetic testing in 23 FANC genes revealed two novel heterozygous mutations, c.367C>T and c.3971_3972delCGinsTT in FANCA gene of the patient, which were inherited from his father and mother, respectively. Radiotherapy with reduced dose has successfully alleviated the symptoms of tumor invasion and progression, and the radiation-related side effects were acceptable. Unfortunately, the patient eventually died of locoregional disease progression. Conclusion This case highlights the importance of considering the diagnosis of FA in young patients who develop HNSCC in the absence of risk factors, thus permitting more effective oncological treatment strategies and improved outcomes. In conclusion, any decision on different modalities of management in such patients should be based on a balance between locoregional control and therapeutic toxicity.
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Affiliation(s)
- Siyao Deng
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Wenjing Ye
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Shichuan Zhang
- Department of Radiation Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China.,Radiation Oncology Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Guiquan Zhu
- State Key Laboratory of Oral Diseases, National Clinical Research Centre for Oral Diseases, Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, People's Republic of China
| | - Peng Zhang
- Department of Radiation Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Yanqiong Song
- Department of Radiation Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China
| | - Fanglei Duan
- Radiation Oncology Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Jinyi Lang
- Department of Radiation Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China.,Radiation Oncology Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
| | - Shun Lu
- Department of Radiation Oncology, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, People's Republic of China.,Radiation Oncology Key Laboratory of Sichuan Province, Chengdu, People's Republic of China
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37
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Cui Z, Liu Y, Zhang J, Qiu X. Super-delta2: An Enhanced Differential Expression Analysis Procedure for Multi-Group Comparisons of RNA-seq Data. Bioinformatics 2021; 37:2627-2636. [PMID: 33693477 DOI: 10.1093/bioinformatics/btab155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 01/16/2021] [Accepted: 03/04/2021] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION We developed super-delta2, a differential gene expression analysis pipeline designed for multi-group comparisons for RNA-seq data. It includes a customized one-way ANOVA F-test and a post-hoc test for pairwise group comparisons; both are designed to work with a multivariate normalization procedure to reduce technical noise. It also includes a trimming procedure with bias-correction to obtain robust and approximately unbiased summary statistics used in these tests. We demonstrated the asymptotic applicability of super-delta2 to log-transformed read counts in RNA-seq data by large sample theory based on Negative Binomial Poisson (NBP) distribution. RESULTS We compared super-delta2 with three commonly used RNA-seq data analysis methods: limma/voom, edgeR, and DESeq2 using both simulated and real datasets. In all three simulation settings, super-delta2 not only achieved the best overall statistical power, but also was the only method that controlled type I error at the nominal level. When applied to a breast cancer dataset to identify differential expression pattern associated with multiple pathologic stages, super-delta2 selected more enriched pathways than other methods, which are directly linked to the underlying biological condition (breast cancer). CONCLUSIONS By incorporating trimming and bias-correction in the normalization step, super-delta2 was able to achieve tight control of type I error. Because the hypothesis tests are based on asymptotic normal approximation of the NBP distribution, super-delta2 does not require computationally expensive iterative optimization procedures used by methods such as edgeR and DESeq2, which occasionally have convergence issues. AVAILABILITY Our method is implemented in a R-package, "superdelta2", freely available at: https://github.com/fhlsjs/superdelta2. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zihan Cui
- Department of Statistics, Florida State University, Tallahassee, FL, 32304
| | - Yuhang Liu
- Department of Statistics, Florida State University, Tallahassee, FL, 32304
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, FL, 32304
| | - Xing Qiu
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, 14624
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38
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Janysek DC, Kim J, Duijf PHG, Dray E. Clinical use and mechanisms of resistance for PARP inhibitors in homologous recombination-deficient cancers. Transl Oncol 2021; 14:101012. [PMID: 33516088 PMCID: PMC7847957 DOI: 10.1016/j.tranon.2021.101012] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/14/2020] [Accepted: 12/31/2020] [Indexed: 12/11/2022] Open
Abstract
Cells are continuously subjected to DNA damaging agents. DNA damages are repaired by one of the many pathways guarding genomic integrity. When one or several DNA damage pathways are rendered inefficient, cells can accumulate mutations, which modify normal cellular pathways, favoring abnormal cell growth. This supports malignant transformation, which can occur when cells acquire resistance to cell cycle checkpoints, apoptosis, or growth inhibition signals. Mutations in genes involved in the repair of DNA double strand breaks (DSBs), such as BRCA1, BRCA2, or PALB2, significantly increase the risk of developing cancer of the breast, ovaries, pancreas, or prostate. Fortunately, the inability of these tumors to repair DNA breaks makes them sensitive to genotoxic chemotherapies, allowing for the development of therapies precisely tailored to individuals' genetic backgrounds. Unfortunately, as with many anti-cancer agents, drugs used to treat patients carrying a BRCA1 or BRCA2 mutation create a selective pressure, and over time tumors can become drug resistant. Here, we detail the cellular function of tumor suppressors essential in DNA damage repair pathways, present the mechanisms of action of inhibitors used to create synthetic lethality in BRCA carriers, and review the major molecular sources of drug resistance. Finally, we present examples of the many strategies being developed to circumvent drug resistance.
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Affiliation(s)
- Dawn C Janysek
- School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Jennifer Kim
- School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Pascal H G Duijf
- Queensland University of Technology, IHBI at the Translational Research Institute, Brisbane, QLD, Australia; Centre for Data Science, Queensland University of Technology, Brisbane, QLD, Australia; University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Eloïse Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States; Mays Cancer Center, UT Health San Antonio MD Anderson, San Antonio, TX, United States.
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39
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Shen X, Wang R, Kim MJ, Hu Q, Hsu CC, Yao J, Klages-Mundt N, Tian Y, Lynn E, Brewer TF, Zhang Y, Arun B, Gan B, Andreeff M, Takeda S, Chen J, Park JI, Shi X, Chang CJ, Jung SY, Qin J, Li L. A Surge of DNA Damage Links Transcriptional Reprogramming and Hematopoietic Deficit in Fanconi Anemia. Mol Cell 2021; 80:1013-1024.e6. [PMID: 33338401 DOI: 10.1016/j.molcel.2020.11.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 07/26/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022]
Abstract
Impaired DNA crosslink repair leads to Fanconi anemia (FA), characterized by a unique manifestation of bone marrow failure and pancytopenia among diseases caused by DNA damage response defects. As a germline disorder, why the hematopoietic hierarchy is specifically affected is not fully understood. We find that reprogramming transcription during hematopoietic differentiation results in an overload of genotoxic stress, which causes aborted differentiation and depletion of FA mutant progenitor cells. DNA damage onset most likely arises from formaldehyde, an obligate by-product of oxidative protein demethylation during transcription regulation. Our results demonstrate that rapid and extensive transcription reprogramming associated with hematopoietic differentiation poses a major threat to genome stability and cell viability in the absence of the FA pathway. The connection between differentiation and DNA damage accumulation reveals a novel mechanism of genome scarring and is critical to exploring therapies to counteract the aplastic anemia for the treatment of FA patients.
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Affiliation(s)
- Xi Shen
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Rui Wang
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Moon Jong Kim
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Qianghua Hu
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Chih-Chao Hsu
- Department of Epigenetics and Molecular Carcinogenesis, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Jun Yao
- Department of Molecular Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Naeh Klages-Mundt
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Yanyan Tian
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Erica Lynn
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Thomas F Brewer
- Department of Chemistry, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yilei Zhang
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Banu Arun
- Department of Breast Medical Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Boyi Gan
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Michael Andreeff
- Department of Leukemia, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Shunichi Takeda
- Department of Radiation Biology, Kyoto University, 606-8501 Kyoto, Japan
| | - Junjie Chen
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Jae-Il Park
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA
| | - Christopher J Chang
- Department of Chemistry, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sung Yun Jung
- Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jun Qin
- Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, the University of Texas, MD Anderson Cancer, Houston, TX 77030, USA; Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.
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40
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Rodríguez A, Yang C, Furutani E, García de Teresa B, Velázquez M, Filiatrault J, Sambel LA, Phan T, Flores-Guzmán P, Sánchez S, Monsiváis Orozco A, Mayani H, Bolukbasi OV, Färkkilä A, Epperly M, Greenberger J, Shimamura A, Frías S, Grompe M, Parmar K, D'Andrea AD. Inhibition of TGFβ1 and TGFβ3 promotes hematopoiesis in Fanconi anemia. Exp Hematol 2021; 93:70-84.e4. [PMID: 33166613 PMCID: PMC8686188 DOI: 10.1016/j.exphem.2020.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/28/2020] [Accepted: 11/03/2020] [Indexed: 12/31/2022]
Abstract
Fanconi anemia (FA) is a chromosome instability syndrome with congenital abnormalities, cancer predisposition and bone marrow failure (BMF). Although hematopoietic stem and progenitor cell (HSPC) transplantation is the recommended therapy, new therapies are needed for FA patients without suitable donors. BMF in FA is caused, at least in part, by a hyperactive growth-suppressive transforming growth factor β (TGFβ) pathway, regulated by the TGFβ1, TGFβ2, and TGFβ3 ligands. Accordingly, the TGFβ pathway is an attractive therapeutic target for FA. While inhibition of TGFβ1 and TGFβ3 promotes blood cell expansion, inhibition of TGFβ2 is known to suppress hematopoiesis. Here, we report the effects of AVID200, a potent TGFβ1- and TGFβ3-specific inhibitor, on FA hematopoiesis. AVID200 promoted the survival of murine FA HSPCs in vitro. AVID200 also promoted in vitro the survival of human HSPCs from patients with FA, with the strongest effect in patients progressing to severe aplastic anemia or myelodysplastic syndrome (MDS). Previous studies have indicated that the toxic upregulation of the nonhomologous end-joining (NHEJ) pathway accounts, at least in part, for the poor growth of FA HSPCs. AVID200 downregulated the expression of NHEJ-related genes and reduced DNA damage in primary FA HSPC in vitro and in in vivo models. Collectively, AVID200 exhibits activity in FA mouse and human preclinical models. AVID200 may therefore provide a therapeutic approach to improving BMF in FA.
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Affiliation(s)
- Alfredo Rodríguez
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA; Instituto Nacional de Pediatría, Mexico City, Mexico
| | - Chunyu Yang
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Elissa Furutani
- Dana Farber and Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | | | - Martha Velázquez
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Jessica Filiatrault
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Larissa A Sambel
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Tin Phan
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Patricia Flores-Guzmán
- Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | | | - Héctor Mayani
- Unidad de Investigación Médica en Enfermedades Oncológicas, Hospital de Oncología, Centro Médico Nacional, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Ozge V Bolukbasi
- Dana Farber and Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Anniina Färkkilä
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA; Research Program in Systems Oncology & Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Michael Epperly
- Department of Radiation Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Joel Greenberger
- Department of Radiation Oncology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Akiko Shimamura
- Dana Farber and Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Sara Frías
- Instituto Nacional de Pediatría, Mexico City, Mexico; Instituto de Investigaciones Biomédicas, Universidad Nacional Autonóma de México, Mexico City, Mexico
| | | | - Kalindi Parmar
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Alan D D'Andrea
- Department of Radiation Oncology and Center for DNA Damage and Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA.
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DNA polymerase ι compensates for Fanconi anemia pathway deficiency by countering DNA replication stress. Proc Natl Acad Sci U S A 2020; 117:33436-33445. [PMID: 33376220 DOI: 10.1073/pnas.2008821117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Fanconi anemia (FA) is caused by defects in cellular responses to DNA crosslinking damage and replication stress. Given the constant occurrence of endogenous DNA damage and replication fork stress, it is unclear why complete deletion of FA genes does not have a major impact on cell proliferation and germ-line FA patients are able to progress through development well into their adulthood. To identify potential cellular mechanisms that compensate for the FA deficiency, we performed dropout screens in FA mutant cells with a whole genome guide RNA library. This uncovered a comprehensive genome-wide profile of FA pathway synthetic lethality, including POLI and CDK4 As little is known of the cellular function of DNA polymerase iota (Pol ι), we focused on its role in the loss-of-function FA knockout mutants. Loss of both FA pathway function and Pol ι leads to synthetic defects in cell proliferation and cell survival, and an increase in DNA damage accumulation. Furthermore, FA-deficient cells depend on the function of Pol ι to resume replication upon replication fork stalling. Our results reveal a critical role for Pol ι in DNA repair and replication fork restart and suggest Pol ι as a target for therapeutic intervention in malignancies carrying an FA gene mutation.
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Rageul J, Kim H. Fanconi anemia and the underlying causes of genomic instability. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:693-708. [PMID: 31983075 PMCID: PMC7778457 DOI: 10.1002/em.22358] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/03/2020] [Accepted: 01/21/2020] [Indexed: 05/02/2023]
Abstract
Fanconi anemia (FA) is a rare genetic disorder, characterized by birth defects, progressive bone marrow failure, and a predisposition to cancer. This devastating disease is caused by germline mutations in any one of the 22 known FA genes, where the gene products are primarily responsible for the resolution of DNA interstrand cross-links (ICLs), a type of DNA damage generally formed by cytotoxic chemotherapeutic agents. However, the identity of endogenous mutagens that generate DNA ICLs remains largely elusive. In addition, whether DNA ICLs are indeed the primary cause behind FA phenotypes is still a matter of debate. Recent genetic studies suggest that naturally occurring reactive aldehydes are a primary source of DNA damage in hematopoietic stem cells, implicating that they could play a role in genome instability and FA. Emerging lines of evidence indicate that the FA pathway constitutes a general surveillance mechanism for the genome by protecting against a variety of DNA replication stresses. Therefore, understanding the DNA repair signaling that is regulated by the FA pathway, and the types of DNA lesions underlying the FA pathophysiology is crucial for the treatment of FA and FA-associated cancers. Here, we review recent advances in our understanding of the relationship between reactive aldehydes, bone marrow dysfunction, and FA biology in the context of signaling pathways triggered during FA-mediated DNA repair and maintenance of the genomic integrity. Environ. Mol. Mutagen. 2020. © 2020 Wiley Periodicals, Inc.
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Affiliation(s)
- Julie Rageul
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, New York 11794, USA
- Stony Brook Cancer Center, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York 11794, USA
- Correspondence to: Hyungjin Kim, Ph.D., Department of Pharmacological Sciences, Renaissance School of Medicine at Stony Brook University, Basic Sciences Tower 8-125, 100 Nicolls Rd., Stony Brook, NY 11794, Phone: 631-444-3134, FAX: 631-444-3218,
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43
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Holcomb AJ, Brown L, Tawfik O, Madan R, Shnayder Y, Thomas SM, Wallace NA. DNA repair gene expression is increased in HPV positive head and neck squamous cell carcinomas. Virology 2020; 548:174-181. [PMID: 32838940 DOI: 10.1016/j.virol.2020.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 07/01/2020] [Accepted: 07/03/2020] [Indexed: 12/11/2022]
Abstract
The incidence of head and neck squamous cell carcinomas (HNSCCs) is rising in developed countries. This is driven by an increase in HNSCCs caused by high-risk human papillomavirus (HPV) infections or HPV + HNSCCs. Compared to HNSCCs not caused by HPV (HPV- HNSCCs), HPV + HNSCCs are more responsive to therapy and associated with better oncologic outcomes. As a result, the HPV status of an HNSCC is an important determinant in medical management. One method to determine the HPV status of an HNSCC is increased expression of p16 caused by the HPV E7 oncogene. We identified novel expression changes in HPV + HNSCCs. A comparison of gene expression among HPV+ and HPV- HNSCCs in The Cancer Genome Atlas demonstrated increased DNA repair gene expression in HPV + HNSCCs. Further, DNA repair gene expression correlated with HNSCC survival. Immunohistochemical analysis of a novel HNSCC microarray confirmed that DNA repair protein abundance is elevated in HPV + HNSCCs.
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Affiliation(s)
- Andrew J Holcomb
- The University of Kansas Medical Center, Department of Otolaryngology, Head and Neck Surgery, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - Laura Brown
- The University of Kansas Medical Center, Department of Pathology and Lab Medicine, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Ossama Tawfik
- The University of Kansas Medical Center, Department of Pathology and Lab Medicine, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Rashna Madan
- The University of Kansas Medical Center, Department of Pathology and Lab Medicine, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Yelizaveta Shnayder
- The University of Kansas Medical Center, Department of Otolaryngology, Head and Neck Surgery, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - Sufi Mary Thomas
- The University of Kansas Medical Center, Department of Otolaryngology, Head and Neck Surgery, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - Nicholas A Wallace
- Kansas State University, Department of Biology, 116 Ackert Hall, Manhattan, KS, 66506, USA.
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Pharmacologic induction of innate immune signaling directly drives homologous recombination deficiency. Proc Natl Acad Sci U S A 2020; 117:17785-17795. [PMID: 32651270 DOI: 10.1073/pnas.2003499117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Poly(ADP ribose) polymerase inhibitors (PARPi) have efficacy in triple negative breast (TNBC) and ovarian cancers (OCs) harboring BRCA mutations, generating homologous recombination deficiencies (HRDs). DNA methyltransferase inhibitors (DNMTi) increase PARP trapping and reprogram the DNA damage response to generate HRD, sensitizing BRCA-proficient cancers to PARPi. We now define the mechanisms through which HRD is induced in BRCA-proficient TNBC and OC. DNMTi in combination with PARPi up-regulate broad innate immune and inflammasome-like signaling events, driven in part by stimulator of interferon genes (STING), to unexpectedly directly generate HRD. This inverse relationship between inflammation and DNA repair is critical, not only for the induced phenotype, but also appears as a widespread occurrence in The Cancer Genome Atlas datasets and cancer subtypes. These discerned interactions between inflammation signaling and DNA repair mechanisms now elucidate how epigenetic therapy enhances PARPi efficacy in the setting of BRCA-proficient cancer. This paradigm will be tested in a phase I/II TNBC clinical trial.
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Koklesova L, Liskova A, Samec M, Qaradakhi T, Zulli A, Smejkal K, Kajo K, Jakubikova J, Behzadi P, Pec M, Zubor P, Biringer K, Kwon TK, Büsselberg D, Sarria GR, Giordano FA, Golubnitschaja O, Kubatka P. Genoprotective activities of plant natural substances in cancer and chemopreventive strategies in the context of 3P medicine. EPMA J 2020; 11:261-287. [PMID: 32547652 PMCID: PMC7272522 DOI: 10.1007/s13167-020-00210-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 05/16/2020] [Indexed: 12/12/2022]
Abstract
Severe durable changes may occur to the DNA structure caused by exogenous and endogenous risk factors initiating the process of carcinogenesis. By evidence, a large portion of malignancies have been demonstrated as being preventable. Moreover, the targeted prevention of cancer onset is possible, due to unique properties of plant bioactive compounds. Although genoprotective effects of phytochemicals have been well documented, there is an evident lack of articles which would systematically present the spectrum of anticancer effects by phytochemicals, plant extracts, and plant-derived diet applicable to stratified patient groups at the level of targeted primary (cancer development) and secondary (cancer progression and metastatic disease) prevention. Consequently, clinical implementation of knowledge accumulated in the area is still highly restricted. To stimulate coherent co-development of the dedicated plant bioactive compound investigation on one hand and comprehensive cancer preventive strategies on the other hand, the current paper highlights and deeply analyses relevant evidence available in the area. Key molecular mechanisms are presented to detail genoprotective and anticancer activities of plants and phytochemicals. Clinical implementation is discussed. Based on the presented evidence, advanced chemopreventive strategies in the context of 3P medicine are considered.
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Affiliation(s)
- Lenka Koklesova
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Alena Liskova
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Marek Samec
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Tawar Qaradakhi
- Institute for Health and Sport, Victoria University, Melbourne, VIC Australia
| | - Anthony Zulli
- Institute for Health and Sport, Victoria University, Melbourne, VIC Australia
| | - Karel Smejkal
- Department of Natural Drugs, Faculty of Pharmacy, Masaryk University, 612 42 Brno, Czech Republic
| | - Karol Kajo
- Department of Pathology, St. Elisabeth Oncology Institute, 812 50 Bratislava, Slovakia
- Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Jana Jakubikova
- Biomedical Research Center SAS, Cancer Research Institute, Bratislava, Slovakia
| | - Payam Behzadi
- Department of Microbiology, College of Basic Sciences, Shahr-e-Qods Branch, Islamic Azad University, Tehran, Iran
| | - Martin Pec
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia
| | - Pavol Zubor
- Department of Gynecologic Oncology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- OBGY Health & Care, Ltd., 01001 Zilina, Slovakia
| | - Kamil Biringer
- Department of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Taeg Kyu Kwon
- Department of Immunology and School of Medicine, Keimyung University, Dalseo-Gu, Daegu, 42601 Korea
| | - Dietrich Büsselberg
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, P.O. Box 24144, Doha, Qatar
| | - Gustavo R. Sarria
- Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Frank A. Giordano
- Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Olga Golubnitschaja
- Predictive, Preventive and Personalised (3P) Medicine, Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 03601 Martin, Slovakia
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Beddok A, Krieger S, Castera L, Stoppa-Lyonnet D, Thariat J. Management of Fanconi Anemia patients with head and neck carcinoma: Diagnosis and treatment adaptation. Oral Oncol 2020; 108:104816. [PMID: 32480311 DOI: 10.1016/j.oraloncology.2020.104816] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 05/20/2020] [Indexed: 12/18/2022]
Abstract
Fanconi anemia (FA) is a rare genetic disease that is mostly transmitted, according to a recessive model with biallelic germline alterations in one of the 22 genes of the FA pathway, or monoallelic alteration of the 23rd FA gene (RAD51). The FA pathway is implicated in interstrand DNA crosslink repair, induces genome stability, and is a potent driver of tumorigenesis. Patients with FA have a 500 to 1000-fold increased risk of developing head and neck squamous cell carcinoma (HNSCC). Patients with FA developing an HNSCC, usually have severe radiation toxicities. In this context, the modalities of radiation therapy should be adapted. Some patients with FA present a milder phenotype, especially in the case of medullary FA gene spontaneous reversion. Therefore, in an unusual context of HNSCC, such as no risk factors or a young age, it may be very useful to search anemia or development abnormalities, that may unravel a yet undiagnosed FA disease. Besides, in some young patients with HNSCC who did not suffer from FA, a monoallelic germline alteration in an FA gene could be combined with a second risk factor such as HPV infection or APOBEC alteration. Although several in vitro studies showed that normal cells with monoallelic FA gene alteration may have a particular radiosensitivity, these observations have not been confirmed in vivo in FA heterozygotes patients. Finally, some somatic activating alterations have also been found in HSNCC tumor samples and could be associated with radioresistance.
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Affiliation(s)
- Arnaud Beddok
- Department of Radiation Oncology, Curie Institute, Paris, France.
| | - Sophie Krieger
- Department of Cancer Biology and Genetics, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, François Baclesse Center, Caen, France
| | - Laurent Castera
- Department of Cancer Biology and Genetics, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, François Baclesse Center, Caen, France
| | | | - Juliette Thariat
- Department of Radiation Oncology, François Baclesse Center, Caen, France
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47
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Bajpai J, Singh G, Chougule A, Chandrani P. Rare mutations in breast cancer and implications in the clinic: Oscillation between sharp horns of dilemmas! CANCER RESEARCH, STATISTICS, AND TREATMENT 2020. [DOI: 10.4103/crst.crst_136_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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48
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Fang CB, Wu HT, Zhang ML, Liu J, Zhang GJ. Fanconi Anemia Pathway: Mechanisms of Breast Cancer Predisposition Development and Potential Therapeutic Targets. Front Cell Dev Biol 2020; 8:160. [PMID: 32300589 PMCID: PMC7142266 DOI: 10.3389/fcell.2020.00160] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 02/28/2020] [Indexed: 02/05/2023] Open
Abstract
The maintenance of genomic stability is crucial for species survival, and its failure is closely associated with tumorigenesis. The Fanconi anemia (FA) pathway, involving 22 identified genes, plays a central role in repairing DNA interstrand cross-links. Importantly, a germline defect in any of these genes can cause Fanconi's anemia, a heterogeneous genetic disorder, characterized by congenital growth abnormalities, bone marrow failure, and predisposition to cancer. On the other hand, the breast cancer susceptibility genes, BRCA1 and BRCA2, also known as FANCS and FANCD1, respectively, are involved in the FA pathway; hence, researchers have studied the association between the FA pathway and cancer predisposition. Here, we mainly focused on and systematically reviewed the clinical and mechanistic implications of the predisposition of individuals with abnormalities in the FA pathway to cancer, especially breast cancer.
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Affiliation(s)
- Can-Bin Fang
- Chang Jiang Scholar’s Laboratory/Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Shantou University Medical College, Shantou, China
| | - Hua-Tao Wu
- Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Man-Li Zhang
- Chang Jiang Scholar’s Laboratory/Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Shantou University Medical College, Shantou, China
| | - Jing Liu
- Chang Jiang Scholar’s Laboratory/Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Shantou University Medical College, Shantou, China
- Department of Physiology, Shantou University Medical College, Shantou, China
- *Correspondence: Jing Liu,
| | - Guo-Jun Zhang
- Chang Jiang Scholar’s Laboratory/Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Shantou University Medical College, Shantou, China
- The Cancer Center and the Department of Breast-Thyroid Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiang’an, China
- Guo-Jun Zhang, ;
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49
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Gupta M, Iyer R, Fountzilas C. Poly(ADP-Ribose) Polymerase Inhibitors in Pancreatic Cancer: A New Treatment Paradigms and Future Implications. Cancers (Basel) 2019; 11:E1980. [PMID: 31835379 PMCID: PMC6966572 DOI: 10.3390/cancers11121980] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/30/2019] [Accepted: 12/06/2019] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy. Most of the patients of PDAC present at later stages of disease and have a five-year survival rate of less than 10%. About 5-10% PDAC cases are hereditary in nature and have DNA damage repair (DDR) mutations such as BRCA 1 and 2. Besides having implications on screening and prevention strategies, these mutations can confer sensitivity to platinum-based therapies and determine eligibility for poly(ADP-ribose) polymerase inhibitors (PARPi). In the presence of DDR mutations and PARPi, the cells are unable to utilize the error-free process of homologous recombination repair, leading to accumulation of double stranded DNA breaks and cell death eventually. Various PARPi are in clinical development in PDAC in different subgroup of patients as monotherapies and in combination with other therapeutics. This review would focus on the mechanism of action of PARPi, history of development in PDAC, resistance mechanisms and future directions.
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Affiliation(s)
- Medhavi Gupta
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Renuka Iyer
- Department of Medicine/Division of GI Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Christos Fountzilas
- Department of Medicine/Division of GI Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
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50
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Costa S, Costa C, Madureira J, Valdiglesias V, Teixeira-Gomes A, Guedes de Pinho P, Laffon B, Teixeira JP. Occupational exposure to formaldehyde and early biomarkers of cancer risk, immunotoxicity and susceptibility. ENVIRONMENTAL RESEARCH 2019; 179:108740. [PMID: 31563789 DOI: 10.1016/j.envres.2019.108740] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Formaldehyde (FA) is a high-volume production chemical manufactured worldwide to which many people are exposed to both environmentally and occupationally. FA was recently reclassified as a human carcinogen. Several epidemiological studies have revealed an increased risk of cancer development among workers exposed to FA. Although FA genotoxicity was confirmed in a variety of experimental systems, data from human studies are conflicting. The aim of the present study was to evaluate the occupational exposure to FA in a multistage approach relating the exposure with different biomarkers (dose and effect) and individual susceptibility. Air monitoring was performed to estimate the level of exposure to FA during shift work. Eighty-five workers from hospital anatomy-pathology laboratories exposed to FA and 87 controls were tested for cytogenetic alterations in lymphocytes (micronucleus, MN; sister-chromatid exchange, SCE) and T-cell receptor (TCR) mutation assay. The frequency of MN in exfoliated buccal cells, a first contact tissue was also assessed. Percentages of different lymphocyte subpopulations were selected as immunotoxicity biomarkers. The level of formic acid in urine was investigated as a potential biomarker of internal dose. The effects of polymorphic genes of xenobiotic metabolising enzymes and DNA repair enzymes on the endpoints studied were determined. The mean level of FA exposure was 0.38 ± 0.03 ppm. MN (in lymphocytes and buccal cells) and SCE were significantly increased in FA-exposed workers compared to controls. MN frequency positively correlated with FA levels of exposure and duration. Significant alterations in the percentage of T cytotoxic lymphocytes, NK cells and B lymphocytes were found between groups. Polymorphisms in CYP2E1, GSTP1 and FANCA genes were associated with increased genetic damage in FA-exposed subjects. The obtained information may provide new important data to be used by health and safety care programs and by governmental agencies responsible for setting the acceptable levels for occupational exposure to FA.
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Affiliation(s)
- Solange Costa
- National Institute of Health, Environmental Health Department, Rua Alexandre Herculano, 321, 4000-055, Porto, Portugal; EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Rua das Taipas, nº 135, 4050-600, Porto, Portugal.
| | - Carla Costa
- National Institute of Health, Environmental Health Department, Rua Alexandre Herculano, 321, 4000-055, Porto, Portugal; EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Rua das Taipas, nº 135, 4050-600, Porto, Portugal
| | - Joana Madureira
- National Institute of Health, Environmental Health Department, Rua Alexandre Herculano, 321, 4000-055, Porto, Portugal; EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Rua das Taipas, nº 135, 4050-600, Porto, Portugal
| | - Vanessa Valdiglesias
- Universidade da Coruña, DICOMOSA Group, Department of Psychology, Area of Psychobiology, Faculty of Education Sciences, Campus Elviña s/n, 15071-A, Coruña, Spain
| | - Armanda Teixeira-Gomes
- National Institute of Health, Environmental Health Department, Rua Alexandre Herculano, 321, 4000-055, Porto, Portugal; EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Rua das Taipas, nº 135, 4050-600, Porto, Portugal
| | - Paula Guedes de Pinho
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Blanca Laffon
- EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Rua das Taipas, nº 135, 4050-600, Porto, Portugal
| | - João Paulo Teixeira
- National Institute of Health, Environmental Health Department, Rua Alexandre Herculano, 321, 4000-055, Porto, Portugal; EPIUnit - Instituto de Saúde Pública, Universidade do Porto, Rua das Taipas, nº 135, 4050-600, Porto, Portugal
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