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Shahid M, Azfaralariff A, Zubair M, Abdulkareem Najm A, Khalili N, Law D, Firasat S, Fazry S. In silico study of missense variants of FANCA, FANCC and FANCG genes reveals high risk deleterious alleles predisposing to Fanconi anemia pathogenesis. Gene 2021; 812:146104. [PMID: 34864095 DOI: 10.1016/j.gene.2021.146104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 11/05/2021] [Accepted: 11/16/2021] [Indexed: 11/04/2022]
Abstract
Among the 22 Fanconi anemia (FA) reported genes, 90% of mutational spectra were found in three genes, namely FANCA (64%), FANCC (12%) and FANCG (8%). Therefore, this study aimed to identify the high-risk deleterious variants in three selected genes (FANCA, FANCC, and FANCG) through various computational approaches. The missense variant datasets retrieved from the UCSC genome browser were analyzed for their pathogenicity, stability, and phylogenetic conservancy. A total of 23 alterations, of which 16 in FANCA, 6 in FANCC and one variant in FANCG, were found to be highly deleterious. The native and mutant structures were generated, which demonstrated a profound impact on the respective proteins. Besides, their pathway analysis predicted many other pathways in addition to the Fanconi anemia pathway, homologous recombination, and mismatch repair pathways. Hence, this is the first comprehensive study that can be useful for understanding the genetic signatures in the development of FA.
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Affiliation(s)
- Muhammad Shahid
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Ahmad Azfaralariff
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Muhammad Zubair
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Pattoki Campus, Pakistan
| | - Ahmed Abdulkareem Najm
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Nahid Khalili
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
| | - Douglas Law
- Faculty of Health and Life Sciences, Inti International University, Persiaran Perdana BBN Putra Nilai, 71800 Nilai, Negeri Sembilan
| | - Sabika Firasat
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad, 45320 Islamabad, Pakistan
| | - Shazrul Fazry
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia; ZACH Biotech Depot Private Limited, Cheras, 43300, Selangor, Malaysia; Tasik Chini Research Center, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia.
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Lee RH, Kang H, Yom SS, Smogorzewska A, Johnson DE, Grandis JR. Treatment of Fanconi Anemia-Associated Head and Neck Cancer: Opportunities to Improve Outcomes. Clin Cancer Res 2021; 27:5168-5187. [PMID: 34045293 DOI: 10.1158/1078-0432.ccr-21-1259] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 05/06/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022]
Abstract
Fanconi anemia, the most frequent genetic cause of bone marrow failure, is characterized by an extreme predilection toward multiple malignancies, including a greater than 500-fold incidence of head and neck squamous cell carcinoma (HNSCC) relative to the general population. Fanconi anemia-associated HNSCC and esophageal SCC (FA-HNSCC) often present at advanced stages with poor survival. Surgical resection remains the primary treatment for FA-HNSCC, and there is often great reluctance to administer systemic agents and/or radiotherapy to these patients given their susceptibility to DNA damage. The paucity of FA-HNSCC case reports limits evidence-based management, and such cases have not been analyzed collectively in detail. We present a systematic review of FA-HNSCC treatments reported from 1966 to 2020, defining a cohort of 119 patients with FA-HNSCC including 16 esophageal SCCs (131 total primary tumors), who were treated with surgery, radiotherapy, systemic therapy (including cytotoxic agents, EGFR inhibitors, or immune checkpoint inhibitors), or a combination of modalities. We summarize the clinical responses and regimen-associated toxicities by treatment modality. The collective evidence suggests that when possible, surgical resection with curative intent should remain the primary treatment modality for FA-HNSCC. Radiation can be administered with acceptable toxicity in the majority of cases, including patients who have undergone stem cell transplantation. Although there is little justification for cytotoxic chemotherapy, EGFR inhibitors and tyrosine kinase inhibitors may be both safe and effective. Immunotherapy may also be considered. Most oncologists have little personal experience with FA-HNSCC. This review is intended as a comprehensive resource for clinicians.
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Affiliation(s)
- Rex H Lee
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, California
| | - Hyunseok Kang
- Department of Medicine, University of California San Francisco, San Francisco, California
| | - Sue S Yom
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York
| | - Daniel E Johnson
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, California
| | - Jennifer R Grandis
- Department of Otolaryngology - Head and Neck Surgery, University of California San Francisco, San Francisco, California
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Thompson AS, Saba N, McReynolds LJ, Munir S, Ahmed P, Sajjad S, Jones K, Yeager M, Donovan FX, Chandrasekharappa SC, Alter BP, Savage SA, Rehman S. The causes of Fanconi anemia in South Asia and the Middle East: A case series and review of the literature. Mol Genet Genomic Med 2021; 9:e1693. [PMID: 33960719 PMCID: PMC8372062 DOI: 10.1002/mgg3.1693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/16/2021] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
Background Fanconi anemia (FA) is an inherited bone marrow failure syndrome associated with characteristic dysmorphology primarily caused by biallelic pathogenic germline variants in any of 22 different DNA repair genes. There are limited data on the specific molecular causes of FA in different ethnic groups. Methods We performed exome sequencing and copy number variant analyses on 19 patients with FA from 17 families undergoing hematopoietic cell transplantation evaluation in Pakistan. The scientific literature was reviewed, and we curated germline variants reported in patients with FA from South Asia and the Middle East. Results The genetic causes of FA were identified in 14 of the 17 families: seven FANCA, two FANCC, one FANCF, two FANCG, and two FANCL. Homozygous and compound heterozygous variants were present in 12 and two families, respectively. Nine families carried variants previously reported as pathogenic, including two families with the South Asian FANCL founder variant. We also identified five novel likely deleterious variants in FANCA, FANCF, and FANCG in affected patients. Conclusions Our study supports the importance of determining the genomic landscape of FA in diverse populations, in order to improve understanding of FA etiology and assist in the counseling of families.
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Affiliation(s)
- Ashley S Thompson
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nusrat Saba
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Saeeda Munir
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Parvez Ahmed
- Quaid-i-Azam International Hospital, Islamabad, Pakistan
| | - Sumaira Sajjad
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, 20850, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, 20850, USA
| | - Frank X Donovan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Sadia Rehman
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan
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Xing L, Mi W, Zhang Y, Tian S, Zhang Y, Qi R, Lou G, Zhang C. The identification of six risk genes for ovarian cancer platinum response based on global network algorithm and verification analysis. J Cell Mol Med 2020; 24:9839-9852. [PMID: 32762026 PMCID: PMC7520306 DOI: 10.1111/jcmm.15567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 05/31/2020] [Accepted: 06/16/2020] [Indexed: 02/06/2023] Open
Abstract
Ovarian cancer is the most lethal gynaecological cancer, and resistance of platinum‐based chemotherapy is the main reason for treatment failure. The aim of the present study was to identify candidate genes involved in ovarian cancer platinum response by analysing genes from homologous recombination and Fanconi anaemia pathways. Associations between these two functional genes were explored in the study, and we performed a random walk algorithm based on reconstructed gene‐gene network, including protein‐protein interaction and co‐expression relations. Following the random walk, all genes were ranked and GSEA analysis showed that the biological functions focused primarily on autophagy, histone modification and gluconeogenesis. Based on three types of seed nodes, the top two genes were utilized as examples. We selected a total of six candidate genes (FANCA, FANCG, POLD1, KDM1A, BLM and BRCA1) for subsequent verification. The validation results of the six candidate genes have significance in three independent ovarian cancer data sets with platinum‐resistant and platinum‐sensitive information. To explore the correlation between biomarkers and clinical prognostic factors, we performed differential analysis and multivariate clinical subgroup analysis for six candidate genes at both mRNA and protein levels. And each of the six candidate genes and their neighbouring genes with a mutation rate greater than 10% were also analysed by network construction and functional enrichment analysis. In the meanwhile, the survival analysis for platinum‐treated patients was performed in the current study. Finally, the RT‐qPCR assay was used to determine the performance of candidate genes in ovarian cancer platinum response. Taken together, this research demonstrated that comprehensive bioinformatics methods could help to understand the molecular mechanism of platinum response and provide new strategies for overcoming platinum resistance in ovarian cancer treatment.
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Affiliation(s)
- Linan Xing
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Wanqi Mi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yongjian Zhang
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Songyu Tian
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yunyang Zhang
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Rui Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ge Lou
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Shahid M, Firasat S, Satti HS, Satti TM, Ghafoor T, Sharif I, Afshan K. Screening of the FANCA gene mutational hotspots in the Pakistani fanconi anemia patients revealed 19 sequence variations. Congenit Anom (Kyoto) 2020; 60:32-39. [PMID: 30809872 DOI: 10.1111/cga.12331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/04/2019] [Accepted: 02/21/2019] [Indexed: 02/06/2023]
Abstract
Fanconi anemia (FA) is a recessive disorder that predispose to bone marrow failure and multiple congenital anomalies in affected individuals worldwide. To date, 22 FA genes are known to harbor sequence variations in disease phenotype. Among these, mutations in the FANCA gene are associated with 60% to 70% of FA cases. The aim of the present study was to screen FA cases belonging to consanguineous Pakistani families for selected exons of FANCA gene which are known mutational hotspots for Asian populations. Blood samples were collected from 20 FA cases and 20 controls. RNA was extracted and cDNA was synthesized from blood samples of cases. DNA was extracted from blood samples of cases and ethnically matched healthy controls. Sanger's sequencing of the nine selected exons of FANCA gene in FA cases revealed 19 genetic alterations of which 15 were single nucleotide variants, three were insertions and one was microdeletion. Of the total 19 sequence changes, 13 were novel and six were previously reported. All identified variants were evaluated by computational programs including SIFT, PolyPhen-2 and Mutation taster. Seven out of 20 analyzed patients were carrying homozygous novel sequence variations, predicted to be associated with FA. These disease associated novel variants were not detected in ethnically matched controls and depict genetic heterogeneity of disease.
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Affiliation(s)
- Muhammad Shahid
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sabika Firasat
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Humayoon Shafique Satti
- Armed Forces Bone Marrow Transplant Centre (AFBMTC), CMH Medical Complex, Rawalpindi, Pakistan
| | - Tariq Mahmood Satti
- Armed Forces Bone Marrow Transplant Centre (AFBMTC), CMH Medical Complex, Rawalpindi, Pakistan
| | - Tariq Ghafoor
- Armed Forces Bone Marrow Transplant Centre (AFBMTC), CMH Medical Complex, Rawalpindi, Pakistan
| | - Imtenan Sharif
- Department of Community Medicine, Army Medical College (AMC), National University of Medical Sciences, Rawalpindi, Pakistan
| | - Kiran Afshan
- Department of Animal Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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