1
|
Ramanagoudr-Bhojappa R, Tryon R, Lach FP, Donovan FX, Maxwell R, Rosenberg A, MacMillan ML, Wagner JE, Auerbach AD, Smogorzewska A, Chandrasekharappa SC. FANCA c.3624C>T (p.Ser1208=) is a hypomorphic splice variant associated with delayed onset of Fanconi anemia. Blood Adv 2024; 8:899-908. [PMID: 38191666 PMCID: PMC10875269 DOI: 10.1182/bloodadvances.2023011888] [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: 10/09/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/10/2024] Open
Abstract
ABSTRACT Fanconi anemia (FA) is a hereditary, DNA repair deficiency disorder caused by pathogenic variants in any 1 of 22 known genes (FANCA-FANCW). Variants in FANCA account for nearly two-thirds of all patients with FA. Clinical presentation of FA can be heterogeneous and include congenital abnormalities, progressive bone marrow failure, and predisposition to cancer. Here, we describe a relatively mild disease manifestation among 6 individuals diagnosed with FA, each compound heterozygous for 1 established pathogenic FANCA variant and 1 FANCA exon 36 variant, c.3624C>T. These individuals had delayed onset of hematological abnormalities, increased survival, reduced incidence of cancer, and improved fertility. Although predicted to encode a synonymous change (p.Ser1208=), the c.3624C>T variant causes a splicing error resulting in a FANCA transcript missing the last 4 base pairs of exon 36. Deep sequencing and quantitative reverse transcription polymerase chain reaction analysis revealed that 6% to 10% of the FANCA transcripts included the canonical splice product, which generated wild-type FANCA protein. Consistently, functional analysis of cell lines from the studied individuals revealed presence of residual FANCD2 ubiquitination and FANCD2 foci formation, better cell survival, and decreased late S/G2 accumulation in response to DNA interstrand cross-linking agent, indicating presence of residual activity of the FA repair pathway. Thus, the c.3624C>T variant is a hypomorphic allele, which contributes to delayed manifestation of FA disease phenotypes in individuals with at least 1 c.3624C>T allele.
Collapse
Affiliation(s)
- Ramanagouda Ramanagoudr-Bhojappa
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Rebecca Tryon
- Department of Genetics, University of Minnesota, Minneapolis, MN
| | - Francis P. Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY
| | - Frank X. Donovan
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Rochelle Maxwell
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY
| | - Allana Rosenberg
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY
| | - Margaret L. MacMillan
- Division of Pediatric Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN
| | - John E. Wagner
- Division of Pediatric Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN
| | - Arleen D. Auerbach
- Human Genetics and Hematology Program, The Rockefeller University, New York, NY
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY
| | - Settara C. Chandrasekharappa
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| |
Collapse
|
2
|
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.
Collapse
|
3
|
Wieland J, Buchan S, Sen Gupta S, Mantzouratou A. Genomic instability and the link to infertility: A focus on microsatellites and genomic instability syndromes. Eur J Obstet Gynecol Reprod Biol 2022; 274:229-237. [PMID: 35671666 DOI: 10.1016/j.ejogrb.2022.06.001] [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: 03/21/2022] [Revised: 05/25/2022] [Accepted: 06/01/2022] [Indexed: 12/01/2022]
Abstract
Infertility is associated to multiple types of different genomic instabilities and is a genetic feature of genomic instability syndromes. While the mismatch repair machinery contributes to the maintenance of genome integrity, surprisingly its potential role in infertility is overlooked. Defects in mismatch repair mechanisms contribute to microsatellite instability and genomic instability syndromes, due to the inability to repair newly replicated DNA. This article reviews the literature to date to elucidate the contribution of microsatellite instability to genomic instability syndromes and infertility. The key findings presented reveal microsatellite instability is poorly researched in genomic instability syndromes and infertility.
Collapse
Affiliation(s)
- Jack Wieland
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole BH12 5BB, UK.
| | - Sarah Buchan
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole BH12 5BB, UK.
| | - Sioban Sen Gupta
- Institute for Women's Health, 86-96 Chenies Mews, University College London, London WC1E 6HX, UK.
| | - Anna Mantzouratou
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole BH12 5BB, UK.
| |
Collapse
|
4
|
Altintas B, Giri N, McReynolds LJ, Best A, Alter BP. Genotype-phenotype and outcome associations in patients with Fanconi anemia: the National Cancer Institute cohort. Haematologica 2022; 108:69-82. [PMID: 35417938 PMCID: PMC9827153 DOI: 10.3324/haematol.2021.279981] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Indexed: 02/04/2023] Open
Abstract
Fanconi anemia (FA) is caused by pathogenic variants in the FA/BRCA DNA repair pathway genes, and is characterized by congenital abnormalities, bone marrow failure (BMF) and increased cancer risk. We conducted a genotype-phenotype and outcomes study of 203 patients with FA in our cohort. We compared across the genes, FA/BRCA DNA repair pathways (upstream, ID complex and downstream), and type of pathogenic variants (hypomorphic or null). We explored differences between the patients evaluated in our clinic (clinic cohort) and those who provided data remotely (field cohort). Patients with variants in upstream complex pathway had less severe phenotype [lacked VACTERL-H (Vertebral, Anal, Cardiac, Trachea-esophageal fistula, Esophageal/duodenal atresia, Renal, Limb, Hydrocephalus) association and/or PHENOS (Pigmentation, small-Head, small-Eyes, Neurologic, Otologic, Short stature) features]. ID complex was associated with VACTERL-H. The clinic cohort had more PHENOS features than the field cohort. PHENOS was associated with increased risk of BMF, and VACTERL-H with hypothyroidism. The cumulative incidence of severe BMF was 70%, solid tumors (ST) 20% and leukemia 6.5% as the first event. Head and neck and gynecological cancers were the most common ST, with further increased risk after hematopoietic cell transplantation. Among patients with FANCA, variants in exons 27-30 were associated with higher frequency of ST. Overall median survival was 37 years; patients with leukemia or FANCD1/BRCA2 variants had poorest survival. Patients with variants in the upstream complex had better survival than ID or downstream complex (p=0.001 and 0.016, respectively). FA is phenotypically and genotypically heterogeneous; detailed characterization provides new insights towards understanding this complex syndrome and guiding clinical management.
Collapse
Affiliation(s)
- Burak Altintas
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute
| | - Neelam Giri
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute,N. Giri
| | - Lisa J. McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute
| | - Ana Best
- Biostatistics Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA
| | - Blanche P. Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
McReynolds LJ, Biswas K, Giri N, Sharan SK, Alter BP. Genotype-cancer association in patients with Fanconi anemia due to pathogenic variants in FANCD1 (BRCA2) or FANCN (PALB2). Cancer Genet 2021; 258-259:101-109. [PMID: 34687993 DOI: 10.1016/j.cancergen.2021.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/28/2021] [Accepted: 10/02/2021] [Indexed: 02/07/2023]
Abstract
Fanconi anemia (FA) is the most common inherited bone marrow failure syndrome and a cancer predisposition disorder. Cancers in FA include acute leukemia and solid tumors; the most frequent solid tumor is head and neck squamous cell carcinoma. FA is a primarily autosomal recessive disorder. Several of the genes in which biallelic pathogenic variants cause FA are also autosomal monoallelic cancer predisposition genes e.g. FANCD1 (BRCA2) and FANCN (PALB2). We observed that patients with FA due to biallelic or homozygous pathogenic variants in FANCD1 and FANCN have a unique cancer association. We curated published cases plus our NCI cohort cases, including 71 patients in the FANCD1 group (94 cancers and 69 variants) and 16 patients in the FANCN group (23 cancers and 20 variants). Only patients in FANCD1 and FANCN groups had one or more of these tumors: brain tumors (primarily medulloblastoma), Wilms tumor and neuroblastoma; this is a genotype-specific cancer combination of tumors of embryonal origin. Acute leukemias, seen in all FA genotypes, also occurred in FANCD1 and FANCN group patients at young ages. In silico predictions of pathogenicity for FANCD1 variants were compared with results from a mouse embryonic stem cell-based functional assay. Patients with two null FANCD1 variants did not have an increased frequency of cancer nor earlier onset of cancer compared with those with hypomorphic variants. Patients with FA and these specific cancers should consider genetic testing focused on FANCD1 and FANCN, and patients with these genotypes may consider ongoing surveillance for these specific cancers.
Collapse
Affiliation(s)
- Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| | - Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Neelam Giri
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| |
Collapse
|
7
|
Doubaj Y, Zrhidri A, Elalaoui SC, Lyahyai J, El Kadiri Y, Elkassimi N, Sbiti A, El Kababri M, Hessissen L, Sefiani A. Clinical, cytogenetic and molecular findings in nine Moroccan patients with Fanconi anemia. Pan Afr Med J 2021; 39:72. [PMID: 34422195 PMCID: PMC8363957 DOI: 10.11604/pamj.2021.39.72.27220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/12/2021] [Indexed: 11/30/2022] Open
Abstract
Introduction Fanconi anemia (FA) is a rare inherited hematological disease due to a defect in the DNA repair pathway resulting in congenital abnormalities and high susceptibility to develop cancers. The cytogenetic analysis using alkylating agents is still a reference test to establish the diagnosis. Despite the genetic heterogeneity, the identification of the causal mutation is actually performed especially after the development of next generation sequencing (NGS). Methods we report here nine Moroccan patients referred to the department of Medical Genetics for suspicion of FA. We realized a genetic consultation to establish a clinical record with biological data before carrying out the genetic analysis. Karyotyping with mitomycin was performed for all the probands before elaborating molecular study. We used massively parallel sequencing to analyse the three most frequent mutated genes FANCA, FANCC, and FANCG, representing 84% of all genes involved in FA. Results all the patients showed hematological signs associated with at least one extra-hematological congenital anomaly. The chromosomal breaks were significantly higher for the nine patients, compared to the controls. The molecular diagnosis was confirmed in 8 of the 9 families tested (88.8%) with 4 novel mutations. The next generation based sequencing identified 9 variations: 6 in the FANCA gene (66.6%), 3 in the FANCG gene (33.3%) and no FANCC variation was found. Of those, 7 were homozygous and 2 were compounds heterozygous. Conclusion to the best of our knowledge, this is the first molecular report of Moroccan patients with FA suggesting the predominance of two genes without any recurrent mutation. The molecular analysis of FANCA and FANCG genes should be offered first for all patients in Morocco.
Collapse
Affiliation(s)
- Yassamine Doubaj
- Centre de Recherche en Génomique et Pathologies Humaines (Centre GENOPATH), Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc.,Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Maroc
| | - Abdelali Zrhidri
- Centre de Recherche en Génomique et Pathologies Humaines (Centre GENOPATH), Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Siham Chafai Elalaoui
- Centre de Recherche en Génomique et Pathologies Humaines (Centre GENOPATH), Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc.,Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Maroc
| | - Jaber Lyahyai
- Centre de Recherche en Génomique et Pathologies Humaines (Centre GENOPATH), Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Youssef El Kadiri
- Centre de Recherche en Génomique et Pathologies Humaines (Centre GENOPATH), Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc
| | - Nadia Elkassimi
- Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Maroc
| | - Aziza Sbiti
- Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Maroc
| | - Maria El Kababri
- Centre d´Hématologie et Oncologie Pédiatrique, Hôpital d´Enfants, Rabat, Maroc
| | - Laila Hessissen
- Centre d´Hématologie et Oncologie Pédiatrique, Hôpital d´Enfants, Rabat, Maroc
| | - Abdelaziz Sefiani
- Centre de Recherche en Génomique et Pathologies Humaines (Centre GENOPATH), Faculté de Médecine et de Pharmacie, Université Mohammed V, Rabat, Maroc.,Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Maroc
| |
Collapse
|
8
|
Next-generation Sequencing in Bone Marrow Failure Syndromes and Isolated Cytopenias: Experience of the Spanish Network on Bone Marrow Failure Syndromes. Hemasphere 2021; 5:e539. [PMID: 33718801 PMCID: PMC7951136 DOI: 10.1097/hs9.0000000000000539] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/11/2021] [Indexed: 11/26/2022] Open
Abstract
Inherited bone marrow failure syndromes (IBMFSs) are a group of congenital rare diseases characterized by bone marrow failure, congenital anomalies, high genetic heterogeneity, and predisposition to cancer. Appropriate treatment and cancer surveillance ideally depend on the identification of the mutated gene. A next-generation sequencing (NGS) panel of genes could be 1 initial genetic screening test to be carried out in a comprehensive study of IBMFSs, allowing molecular detection in affected patients. We designed 2 NGS panels of IBMFS genes: version 1 included 129 genes and version 2 involved 145 genes. The cohort included a total of 204 patients with suspected IBMFSs without molecular diagnosis. Capture-based targeted sequencing covered > 99% of the target regions of 145 genes, with more than 20 independent reads. No differences were seen between the 2 versions of the panel. The NGS tool allowed a total of 91 patients to be diagnosed, with an overall molecular diagnostic rate of 44%. Among the 167 patients with classified IBMFSs, 81 patients (48%) were diagnosed. Unclassified IBMFSs involved a total of 37 patients, of whom 9 patients (24%) were diagnosed. The preexisting diagnosis of 6 clinically classified patients (6%) was amended, implying a change of therapy for some of them. Our NGS IBMFS gene panel assay is a useful tool in the molecular diagnosis of IBMFSs and a reasonable option as the first tier genetic test in these disorders.
Collapse
|
9
|
Ben Haj Ali A, Messaoud O, Elouej S, Talmoudi F, Ayed W, Mellouli F, Ouederni M, Hadiji S, De Sandre-Giovannoli A, Delague V, Lévy N, Bogliolo M, Surrallés J, Abdelhak S, Amouri A. FANCA Gene Mutations in North African Fanconi Anemia Patients. Front Genet 2021; 12:610050. [PMID: 33679882 PMCID: PMC7933650 DOI: 10.3389/fgene.2021.610050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/22/2021] [Indexed: 11/27/2022] Open
Abstract
Populations in North Africa (NA) are characterized by a high rate of consanguinity. Consequently, the proportion of founder mutations might be higher than expected and could be a major cause for the high prevalence of recessive genetic disorders like Fanconi anemia (FA). We report clinical, cytogenetic, and molecular characterization of FANCA in 29 North African FA patients from Tunisia, Libya, and Algeria. Cytogenetic tests revealed high rates of spontaneous chromosome breakages for all patients except two of them. FANCA molecular analysis was performed using three different molecular approaches which allowed us to identify causal mutations as homozygous or compound heterozygous forms. It included a nonsense mutation (c.2749C > T; p.Arg917Ter), one reported missense mutation (c.1304G > A; p.Arg435His), a novel missense variant (c.1258G > A; p.Asp409Glu), and the FANCA most common reported mutation (c.3788_3790delTCT; p.Phe1263del). Furthermore, three founder mutations were identified in 86.7% of the 22 Tunisian patients: (1) a deletion of exon 15, in 36.4% patients (8/22); (2), a deletion of exons 4 and 5 in 23% (5/22) and (3) an intronic mutation c.2222 + 166G > A, in 27.3% (6/22). Despite the relatively small number of patients studied, our results depict the mutational landscape of FA among NA populations and it should be taken into consideration for appropriate genetic counseling.
Collapse
Affiliation(s)
- Abir Ben Haj Ali
- Department of Histology and Cytogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Olfa Messaoud
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Sahar Elouej
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,INSERM, MMG, UMR 1251, Aix Marseille University, Marseille, France
| | - Faten Talmoudi
- Department of Histology and Cytogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Wiem Ayed
- Department of Histology and Cytogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Fethi Mellouli
- Department of Peadiatric Immuno-Haematology, National Bone Marrow Transplantation, Tunis, Tunisia
| | - Monia Ouederni
- Department of Peadiatric Immuno-Haematology, National Bone Marrow Transplantation, Tunis, Tunisia
| | - Sondes Hadiji
- Haematology Department, Hedi Chaker Hospital, University of Sfax, Sfax, Tunisia
| | | | - Valérie Delague
- INSERM, MMG, UMR 1251, Aix Marseille University, Marseille, France
| | - Nicolas Lévy
- INSERM, MMG, UMR 1251, Aix Marseille University, Marseille, France
| | - Massimo Bogliolo
- Research Institute IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Jordi Surrallés
- Research Institute IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Ahlem Amouri
- Department of Histology and Cytogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| |
Collapse
|
10
|
Farouk Sait S, Walsh MF, Karajannis MA. Genetic syndromes predisposing to pediatric brain tumors. Neurooncol Pract 2021; 8:375-390. [PMID: 34277017 DOI: 10.1093/nop/npab012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The application of high-throughput sequencing approaches including paired tumor/normal sampling with therapeutic intent has demonstrated that 8%-19% of pediatric CNS tumor patients harbor a germline alteration in a classical tumor predisposition gene (NF1, P53). In addition, large-scale germline sequencing studies in unselected cohorts of pediatric neuro-oncology patients have demonstrated novel candidate tumor predisposition genes (ELP1 alterations in sonic hedgehog medulloblastoma). Therefore, the possibility of an underlying tumor predisposition syndrome (TPS) should be considered in all pediatric patients diagnosed with a CNS tumor which carries critical implications including accurate prognostication, selection of optimal therapy, screening, risk reduction, and family planning. The Pediatric Cancer Working Group of the American Association for Cancer Research (AACR) recently published consensus screening recommendations for children with the most common TPS. In this review, we provide an overview of the most relevant as well as recently identified TPS associated with the most frequently encountered pediatric CNS tumors with an emphasis on pathogenesis, genetic testing, clinical features, and treatment implications.
Collapse
Affiliation(s)
- Sameer Farouk Sait
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael F Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthias A Karajannis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| |
Collapse
|
11
|
Blombery P, Fox L, Ryland GL, Thompson ER, Lickiss J, McBean M, Yerneni S, Hughes D, Greenway A, Mechinaud F, Wood EM, Lieschke GJ, Szer J, Barbaro P, Roy J, Wight J, Lynch E, Martyn M, Gaff C, Ritchie D. Utility of clinical comprehensive genomic characterization for diagnostic categorization in patients presenting with hypocellular bone marrow failure syndromes. Haematologica 2021; 106:64-73. [PMID: 32054657 PMCID: PMC7776333 DOI: 10.3324/haematol.2019.237693] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/07/2020] [Indexed: 12/26/2022] Open
Abstract
Bone marrow failure (BMF) related to hypoplasia of hematopoietic elements in the bone marrow is a heterogeneous clinical entity with a broad differential diagnosis including both inherited and acquired causes. Accurate diagnostic categorization is critical to optimal patient care and detection of genomic variants in these patients may provide this important diagnostic and prognostic information. We performed real-time, accredited (ISO15189) comprehensive genomic characterization including targeted sequencing and whole exome sequencing in 115 patients with BMF syndromes (median age 24 years, range: 3 months - 81 years). In patients with clinical diagnoses of inherited BMF syndromes, acquired BMF syndromes or clinically unclassifiable BMF we detected variants in 52% (12 of 23), 53% (25 of 47) and 56% (25 of 45) respectively. Genomic characterization resulted in a change of diagnosis in 30 of 115 (26%) including the identification of germline causes for 3 of 47 and 16 of 45 cases with pre-test diagnoses of acquired and clinically unclassifiable BMF respectively. The observed clinical impact of accurate diagnostic categorization included choice to perform allogeneic stem cell transplantation, disease-specific targeted treatments, identification of at-risk family members and influence of sibling allogeneic stem cell donor choice. Multiple novel pathogenic variants and copy number changes were identified in our cohort including in TERT, FANCA, RPS7 and SAMD9. Whole exome sequence analysis facilitated the identification of variants in two genes not typically associated with a primary clinical manifestation of BMF but also demonstrated reduced sensitivity for detecting low level acquired variants. In conclusion, genomic characterization can improve diagnostic categorization of patients presenting with hypoplastic BMF syndromes and should be routinely performed in this group of patients.
Collapse
Affiliation(s)
- Piers Blombery
- Clinical Haematology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Lucy Fox
- Clinical Haematology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Georgina L Ryland
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Ella R Thompson
- University of Melbourne, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Jennifer Lickiss
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Michelle McBean
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Satwica Yerneni
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | | | | | - Erica M Wood
- Transfusion Research Unit, Monash University, Melbourne
| | - Graham J Lieschke
- Clinical Haematology, Peter MacCallum Cancer Centre/Royal Melbourne Hospital, Melbourne
| | - Jeff Szer
- Clinical Haematology, Peter MacCallum Cancer Centre/Royal Melbourne Hospital, Melbourne
| | - Pasquale Barbaro
- Children Health Queensland and University of Queensland, South Brisbane, QLD
| | - John Roy
- Children Health Queensland and University of Queensland, South Brisbane, QLD
| | - Joel Wight
- Department of Hematology, Austin Health, Melbourne
| | - Elly Lynch
- Melbourne Genomics Health Alliance, Parkville VIC, Australia
| | | | - Clara Gaff
- Melbourne Genomics Health Alliance, Parkville VIC, Australia
| | - David Ritchie
- Clinical Haematology, Peter MacCallum Cancer Centre/Royal Melbourne Hospital, Melbourne, Australia
| |
Collapse
|
12
|
Lach FP, Singh S, Rickman KA, Ruiz PD, Noonan RJ, Hymes KB, DeLacure MD, Kennedy JA, Chandrasekharappa SC, Smogorzewska A. Esophageal cancer as initial presentation of Fanconi anemia in patients with a hypomorphic FANCA variant. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005595. [PMID: 33172906 PMCID: PMC7784490 DOI: 10.1101/mcs.a005595] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/26/2020] [Indexed: 11/24/2022] Open
Abstract
Fanconi anemia (FA) is a clinically heterogenous and genetically diverse disease with 22 known complementation groups (FA-A to FA-W), resulting from the inability to repair DNA interstrand cross-links. This rare disorder is characterized by congenital defects, bone marrow failure, and cancer predisposition. FANCA is the most commonly mutated gene in FA and a variety of mostly private mutations have been documented, including small and large indels and point and splicing variants. Genotype-phenotype associations in FA are complex, and a relationship between particular FANCA variants and the observed cellular phenotype or illness severity remains unclear. In this study, we describe two siblings with compound heterozygous FANCA variants (c.3788_3790delTCT and c.4199G > A) who both presented with esophageal squamous cell carcinoma at the age of 51. The proband came to medical attention when he developed pancytopenia after a single cycle of low-dose chemotherapy including platinum-based therapy. Other than a minor thumb abnormality, neither patient had prior findings to suggest FA, including normal blood counts and intact fertility. Patient fibroblasts from both siblings display increased chromosomal breakage and hypersensitivity to interstrand cross-linking agents as seen in typical FA. Based on our functional data demonstrating that the c.4199G > A/p.R1400H variant represents a hypomorphic FANCA allele, we conclude that the residual activity of the Fanconi anemia repair pathway accounts for lack of spontaneous bone marrow failure or infertility with the late presentation of malignancy as the initial disease manifestation. This and similar cases of adult-onset esophageal cancer stress the need for chromosome breakage testing in patients with early onset of aerodigestive tract squamous cell carcinomas before platinum-based therapy is initiated.
Collapse
Affiliation(s)
- Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York, 10065 USA
| | - Sonia Singh
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York, 10065 USA.,Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, 10065 USA
| | - Kimberly A Rickman
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York, 10065 USA
| | - Penelope D Ruiz
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York, 10065 USA
| | - Raymond J Noonan
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York, 10065 USA
| | - Kenneth B Hymes
- New York University School of Medicine, Division of Hematology and Oncology, Department of Internal Medicine, Laura and Isaac Perlmutter Cancer Center, New York, New York, 10016 USA
| | - Mark D DeLacure
- Department of Otolaryngology-Head and Neck Surgery, New York University School of Medicine, New York, New York 10003, USA.,Departments of Plastic Surgery and Neurosurgery, New York University, New York, New York 10016, USA
| | - Jennifer A Kennedy
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York, 10065 USA
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York, 10065 USA
| |
Collapse
|
13
|
Nie D, Zhang J, Wang F, Zhang W, Liu L, Chen X, Zhang Y, Cao P, Xiong M, Wang T, Wu P, Ma X, Tian W, Wang M, Chen KN, Liu H. Comprehensive analysis on phenotype and genetic basis of Chinese Fanconi anemia patients: dismal outcomes call for nationwide studies. BMC MEDICAL GENETICS 2020; 21:118. [PMID: 32487094 PMCID: PMC7268325 DOI: 10.1186/s12881-020-01057-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 05/24/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND Fanconi anemia (FA) is the most common inherited bone marrow failure (BMF) syndrome with 22 related genes identified. The ALDH2 rs671variant has been proved related to accelerate the progression of BMF in FA patients. The phenotype and genetic basis of Chinese FA patients have not been investigated yet. METHODS We analyzed the 22 FA-related genes of 63 BMF patients suspected to be FA. Clinical manifestations, morphological and cytogenetic feathers, ALDH2 genotypes, treatment, and outcomes of the definite cases were retrospectively studied. RESULTS A total of 21 patients were confirmed the diagnosis of FA with the median age of BMF onset was 4-year-old. The number of patients manifested as congenital malformations and growth retardation were 20/21 and 14/21, respectively. BM dysplasia and cytogenetic abnormalities were found in 13/20 and 8/19 patients. All the patients with abnormal karyotypes also manifested as BM dysplasia or had evident blasts. Thirty-five different mutations were identified involving six genes and including twenty novel mutations. FANCA mutations contributed to 66.67% of cases. Eight patients harboring ALDH2-G/A genotype have a significantly younger age of BMF onset (p = 0.025). Within the 19 patients adhering to continuous follow-up, 15 patients underwent hematopoietic stem cell transplantations (HSCTs). During the 29 months of follow-up, 8/19 patients died, seven of which were HSCT-related, and one patient who did not receive HSCT died from severe infection. CONCLUSIONS The phenotypic and genetic spectrum of Chinese FA patients is broad. Bone marrow dysplasia and cytogenetic abnormalities are prevalent and highly consistent. The overall outcome of HSCTs is disappointing. Nationwide multicenter studies are needed for the rarity and adverse outcome of this disease.
Collapse
Affiliation(s)
- Daijing Nie
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
- Beijing Lu Daopei Institute of Hematology, Beijing, 100176, China
| | - Jing Zhang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Fang Wang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Wei Zhang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Lili Liu
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Xue Chen
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Yang Zhang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Panxiang Cao
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Min Xiong
- Department of Hematology, Hebei Yanda Lu Daopei Hospital, Langfang, 065201, China
| | - Tong Wang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Ping Wu
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Xiaoli Ma
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China
| | - Wenjun Tian
- Department of Clinical Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250000, China
| | - Mangju Wang
- Department of Hematology, Peking University First Hospital, Beijing, 100034, China
| | - Kylan N Chen
- Beijing Lu Daopei Institute of Hematology, Beijing, 100176, China
| | - Hongxing Liu
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 6 Sipulan Road, Langfang, 065201, China.
- Beijing Lu Daopei Institute of Hematology, Beijing, 100176, China.
- Division of Pathology & Laboratory Medicine, Beijing Lu Daopei Hospital, Beijing, 100176, China.
| |
Collapse
|
14
|
Steinberg-Shemer O, Goldberg TA, Yacobovich J, Levin C, Koren A, Revel-Vilk S, Ben-Ami T, Kuperman AA, Zemer VS, Toren A, Kapelushnik J, Ben-Barak A, Miskin H, Krasnov T, Noy-Lotan S, Dgany O, Tamary H. Characterization and genotype-phenotype correlation of patients with Fanconi anemia in a multi-ethnic population. Haematologica 2019; 105:1825-1834. [PMID: 31558676 PMCID: PMC7327661 DOI: 10.3324/haematol.2019.222877] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 09/25/2019] [Indexed: 12/16/2022] Open
Abstract
Fanconi anemia (FA), an inherited bone marrow failure (BMF) syndrome, caused by mutations in DNA repair genes, is characterized by congenital anomalies, aplastic anemia, high risk of malignancies and extreme sensitivity to alkylating agents. We aimed to study the clinical presentation, molecular diagnosis and genotype-phenotype correlation among patients with FA from the Israeli inherited BMF registry. Overall, 111 patients of Arab (57%) and Jewish (43%) descent were followed for a median of 15 years (range: 0.1-49); 63% were offspring of consanguineous parents. One-hundred patients (90%) had at least one congenital anomaly; over 80% of the patients developed bone marrow failure; 53% underwent hematopoietic stem-cell transplantation; 33% of the patients developed cancer; no significant association was found between hematopoietic stem-cell transplant and solid tumor development. Nearly 95% of the patients tested had confirmed mutations in the Fanconi genes FANCA (67%), FANCC (13%), FANCG (14%), FANCJ (3%) and FANCD1 (2%), including twenty novel mutations. Patients with FANCA mutations developed cancer at a significantly older age compared to patients with mutations in other Fanconi genes (mean 18.5 and 5.2 years, respectively, P=0.001); however, the overall survival did not depend on the causative gene. We hereby describe a large national cohort of patients with FA, the vast majority genetically diagnosed. Our results suggest an older age for cancer development in patients with FANCA mutations and no increased incidence of solid tumors following hematopoietic stem-cell transplant. Further studies are needed to guide individual treatment and follow-up programs.
Collapse
Affiliation(s)
- Orna Steinberg-Shemer
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva .,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv.,Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva
| | - Tracie A Goldberg
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva
| | - Joanne Yacobovich
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv
| | - Carina Levin
- Pediatric Hematology Unit, Emek Medical Center, Afula.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa
| | - Ariel Koren
- Pediatric Hematology Unit, Emek Medical Center, Afula.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa
| | - Shoshana Revel-Vilk
- Pediatric Hematology/Oncology Unit, Shaare Zedek Medical Center, Jerusalem, affiliated with Hadassah- Hebrew University Medical School, Jerusalem
| | - Tal Ben-Ami
- Pediatric Hematology Unit, Kaplan Medical Center, Rehovot
| | - Amir A Kuperman
- Blood Coagulation Service and Pediatric Hematology Clinic, Galilee Medical Center, Nahariya.,Azrieli Faculty of Medicine, Bar-Ilan University, Safed
| | - Vered Shkalim Zemer
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv
| | - Amos Toren
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv.,Department of Pediatric Hemato-Oncology, Children's Hospital (Edmond and Lily), Sheba Medical Center, Tel-Hashomer
| | - Joseph Kapelushnik
- Pediatric Hematology, Soroka University Medical Center, Ben-Gurion University, Beer Sheva
| | - Ayelet Ben-Barak
- Pediatric Hematology-Oncology Department, Rambam Medical Center, Haifa, Israel
| | - Hagit Miskin
- Pediatric Hematology/Oncology Unit, Shaare Zedek Medical Center, Jerusalem, affiliated with Hadassah- Hebrew University Medical School, Jerusalem
| | - Tanya Krasnov
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva
| | - Sharon Noy-Lotan
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva
| | - Orly Dgany
- Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva
| | - Hannah Tamary
- Department of Hematology-Oncology, Schneider Children's Medical Center of Israel, Petach Tikva .,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv.,Pediatric Hematology Laboratory, Felsenstein Medical Research Center, Petach Tikva
| |
Collapse
|
15
|
Engel NW, Schliffke S, Schüller U, Frenzel C, Bokemeyer C, Kubisch C, Lessel D. Fatal Myelotoxicity Following Palliative Chemotherapy With Cisplatin and Gemcitabine in a Patient With Stage IV Cholangiocarcinoma Linked to Post Mortem Diagnosis of Fanconi Anemia. Front Oncol 2019; 9:420. [PMID: 31192125 PMCID: PMC6540739 DOI: 10.3389/fonc.2019.00420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022] Open
Abstract
Unrecognized genome instability syndromes can potentially impede the rational treatment of cancer in rare patients. Identification of cancer patients with a hereditary condition is a compelling necessity for oncologists, giving varying hypersensitivities to various chemotherapeutic agents or radiation, depending on the underlying genetic cause. Omission of genetic testing in the setting of an overlooked hereditary syndrome may lead to unexpected and unbearable toxicity from oncological standard approaches. We present a case of a 33-year-old man with an early-onset stage IV intrahepatic cholangiocarcinoma, who experienced unusual bone marrow failure and neutropenic fever syndrome as a consequence of palliative chemotherapy containing cisplatin and gemcitabine, leading to a fatal outcome on day 25 of his first chemotherapeutic cycle. The constellation of bone marrow failure after exposure to the platinum-based agent cisplatin, the presence of an early-onset solid malignancy and the critical appraisal of further phenotypical features raised suspicion of a hereditary genome instability syndrome. Whole-exome sequencing from buccal swab DNA enabled the post mortem diagnosis of Fanconi anemia, most likely linked to the fatal outcome due to utilization of the DNA crosslinking agent cisplatin. The patient's phenotype was exceptional, as he never displayed significant hematologic abnormalities, which is the hallmark of Fanconi anemia. As such, this case stresses the importance to at least question the possibility of a hereditary basis in cases of relatively early-onset malignancy before defining an oncological treatment strategy.
Collapse
Affiliation(s)
- Nils W Engel
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon Schliffke
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Pediatric Hematology and Oncology, University Medical Center, Hamburg-Eppendorf, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Christian Frenzel
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Carsten Bokemeyer
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
16
|
Novel Variations of FANCA Gene Provokes Fanconi Anemia: Molecular Diagnosis in a Special Chinese Family. J Pediatr Hematol Oncol 2018; 40:e299-e304. [PMID: 29702541 DOI: 10.1097/mph.0000000000001197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fanconi anemia (FA) is a rare autosomal recessive or X-linked disorder with highly variable clinical manifestations and an incidence of ∼1 to 5 in 1 million births. To date, 15 bona fide FA genes have been reported to be responsible for the known FA complementation groups and the FANCA gene accounts for almost 60%. In the present study, we report a special Chinese family, which has 2 children with classic FA characteristics. Via 2-step analysis of the whole-exome sequencing data and verification using multiplex ligation-dependent probe amplification test, one child was found to have a novel compound heterozygous mutation of a splicing variant (c.1471-1G>A) and a large intragenic deletion (exons 23-30 del) of the FANCA gene. The other child had the same splicing variant and another novel large deletion (exons 1-18 del) in the FANCA gene. Clone sequencing showed the c.1471-1G>A variant generate an altered transcript with 1 cryptic splice site in intron 15, resulting in a premature termination codon (p.Val490HisfsX6). This study not only shows the complexity of FA molecular diagnosis via comprehensively studying the FA pathogenic genes and the mutational spectrum, but also has significant reference value for the future molecular diagnosis of FA.
Collapse
|
17
|
Kimble DC, Lach FP, Gregg SQ, Donovan FX, Flynn EK, Kamat A, Young A, Vemulapalli M, Thomas JW, Mullikin JC, Auerbach AD, Smogorzewska A, Chandrasekharappa SC. A comprehensive approach to identification of pathogenic FANCA variants in Fanconi anemia patients and their families. Hum Mutat 2018; 39:237-254. [PMID: 29098742 PMCID: PMC5762269 DOI: 10.1002/humu.23366] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/20/2017] [Accepted: 10/22/2017] [Indexed: 11/11/2022]
Abstract
Fanconi anemia (FA) is a rare recessive DNA repair deficiency resulting from mutations in one of at least 22 genes. Two-thirds of FA families harbor mutations in FANCA. To genotype patients in the International Fanconi Anemia Registry (IFAR) we employed multiple methodologies, screening 216 families for FANCA mutations. We describe identification of 57 large deletions and 261 sequence variants, in 159 families. All but seven families harbored distinct combinations of two mutations demonstrating high heterogeneity. Pathogenicity of the 18 novel missense variants was analyzed functionally by determining the ability of the mutant cDNA to improve the survival of a FANCA-null cell line when treated with MMC. Overexpressed pathogenic missense variants were found to reside in the cytoplasm, and nonpathogenic in the nucleus. RNA analysis demonstrated that two variants (c.522G > C and c.1565A > G), predicted to encode missense variants, which were determined to be nonpathogenic by a functional assay, caused skipping of exons 5 and 16, respectively, and are most likely pathogenic. We report 48 novel FANCA sequence variants. Defining both variants in a large patient cohort is a major step toward cataloging all FANCA variants, and permitting studies of genotype-phenotype correlations.
Collapse
Affiliation(s)
- Danielle C Kimble
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York
| | - Siobhan Q Gregg
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York
| | - Frank X Donovan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland
| | - Elizabeth K Flynn
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland
| | - Aparna Kamat
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland
| | - Alice Young
- NIH Intramural Sequencing Center, National Human Genome Research Institute, Bethesda, Maryland
| | - Meghana Vemulapalli
- NIH Intramural Sequencing Center, National Human Genome Research Institute, Bethesda, Maryland
| | - James W Thomas
- NIH Intramural Sequencing Center, National Human Genome Research Institute, Bethesda, Maryland
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, Bethesda, Maryland
| | - Arleen D Auerbach
- Human Genetics and Hematology Program, The Rockefeller University, New York, New York
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland
| |
Collapse
|
18
|
Pilonetto DV, Pereira NF, Bonfim CMS, Ribeiro LL, Bitencourt MA, Kerkhoven L, Floor K, Ameziane N, Joenje H, Gille JJP, Pasquini R. A strategy for molecular diagnostics of Fanconi anemia in Brazilian patients. Mol Genet Genomic Med 2017; 5:360-372. [PMID: 28717661 PMCID: PMC5511800 DOI: 10.1002/mgg3.293] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 03/20/2017] [Accepted: 03/24/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Fanconi anemia (FA) is a predominantly autosomal recessive disease with wide genetic heterogeneity resulting from mutations in several DNA repair pathway genes. To date, 21 genetic subtypes have been identified. We aimed to identify the FA genetic subtypes in the Brazilian population and to develop a strategy for molecular diagnosis applicable to routine clinical use. METHODS We screened 255 patients from Hospital de Clínicas, Universidade Federal do Paraná for 11 common FA gene mutations. Further analysis by multiplex ligation-dependent probe amplification (MLPA) for FANCA and Sanger sequencing of all coding exons of FANCA, -C, and -G was performed in cases who harbored a single gene mutation. RESULTS We identified biallelic mutations in 128/255 patients (50.2%): 89, 11, and 28 carried FANCA,FANCC, and FANCG mutations, respectively. Of these, 71 harbored homozygous mutations, whereas 57 had compound heterozygous mutations. In 4/57 heterozygous patients, both mutations were identified by the initial screening, in 51/57 additional analyses was required for classification, and in 2/57 the second mutation remained unidentified. We found 52 different mutations of which 22 were novel. CONCLUSION The proposed method allowed genetic subtyping of 126/255 (49.4%) patients at a significantly reduced time and cost, which makes molecular diagnosis of FA Brazilian patients feasible.
Collapse
Affiliation(s)
- Daniela V. Pilonetto
- Immunogenetics LaboratoryHospital de ClínicasUniversidade Federal do ParanáCuritibaPRBrazil
| | - Noemi F. Pereira
- Immunogenetics LaboratoryHospital de ClínicasUniversidade Federal do ParanáCuritibaPRBrazil
| | - Carmem M. S. Bonfim
- Bone Marrow Transplantation ServiceHospital de ClínicasUniversidade Federal do ParanáCuritibaPRBrazil
| | - Lisandro L. Ribeiro
- Bone Marrow Transplantation ServiceHospital de ClínicasUniversidade Federal do ParanáCuritibaPRBrazil
| | - Marco A. Bitencourt
- Bone Marrow Transplantation ServiceHospital de ClínicasUniversidade Federal do ParanáCuritibaPRBrazil
| | - Lianne Kerkhoven
- Department of Clinical GeneticsVU University Medical CenterAmsterdamThe Netherlands
| | - Karijn Floor
- Department of Clinical GeneticsVU University Medical CenterAmsterdamThe Netherlands
| | - Najim Ameziane
- Department of Clinical GeneticsVU University Medical CenterAmsterdamThe Netherlands
| | - Hans Joenje
- Department of Clinical GeneticsVU University Medical CenterAmsterdamThe Netherlands
| | - Johan J. P. Gille
- Department of Clinical GeneticsVU University Medical CenterAmsterdamThe Netherlands
| | - Ricardo Pasquini
- Bone Marrow Transplantation ServiceHospital de ClínicasUniversidade Federal do ParanáCuritibaPRBrazil
| |
Collapse
|
19
|
Moghadam AAS, Mahjoubi F, Reisi N, Vosough P. Investigation of FANCA gene in Fanconi anaemia patients in Iran. Indian J Med Res 2017; 143:184-96. [PMID: 27121516 PMCID: PMC4859127 DOI: 10.4103/0971-5916.180206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND & OBJECTIVES Fanconi anaemia (FA) is a syndrome with a predisposition to bone marrow failure, congenital anomalies and malignancies. It is characterized by cellular hypersensitivity to cross-linking agents such as mitomycin C (MMC). In the present study, a new approach was selected to investigate FANCA (Fanconi anaemia complementation group A) gene in patients clinically diagnosed with cellular hypersensitivity to DNA cross-linking agent MMC. METHODS Chromosomal breakage analysis was performed to prove the diagnosis of Fanconi anaemia in 318 families. Of these, 70 families had a positive result. Forty families agreed to molecular genetic testing. In total, there were 27 patients with unknown complementary types. Genomic DNA was extracted and total RNA was isolated from fresh whole blood of the patients. The first-strand cDNA was synthesized and the cDNA of each patient was then tested with 21 pairs of overlapping primers. High resolution melting curve analysis was used to screen FANCA, and LinReg software version 1.7 was utilized for analysis of expression. RESULTS In total, six sequence alterations were identified, which included two stop codons, two frames-shift mutations, one large deletion and one amino acid exchange. FANCA expression was downregulated in patients who had sequence alterations. INTERPRETATION & CONCLUSIONS The results of the present study show that high resolution melting (HRM) curve analysis may be useful in the detection of sequence alteration. It is simpler and more cost-effective than the multiplex ligation-dependent probe amplification (MLPA) procedure.
Collapse
Affiliation(s)
| | - Frouzandeh Mahjoubi
- Medical Biotechnology Institute, National Institute of Genetic Engineering & Biotechnology (NIGEB), Tehran, Iran
| | | | | |
Collapse
|
20
|
|
21
|
Tryon R, Zierhut H, MacMillan ML, Wagner JE. Phenotypic variability in patients with Fanconi anemia and biallelic FANCF mutations. Am J Med Genet A 2016; 173:260-263. [PMID: 27714961 DOI: 10.1002/ajmg.a.37998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/18/2016] [Indexed: 11/09/2022]
Abstract
Fanconi anemia is a heterogeneous genetic disorder that is characterized by progressive bone marrow failure, congenital anomalies, and markedly increased risk for malignancies. Mutations in the FANCF (FA-F) gene represent approximately 2% of affected patients. Currently, information on the phenotypic findings of patients with Fanconi anemia from biallelic mutations in FANCF is limited. Here, we report three patients who illustrate the clinical variability within the FA-F group. This analysis suggests a more severe phenotype for those with the common c.484_485delCT mutation. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Rebecca Tryon
- University of Minnesota Health, Minneapolis, Minnesota
| | | | - Margaret L MacMillan
- Department of Pediatrics, Blood and Marrow Transplant Program, University of Minnesota, Minneapolis, Minnesota
| | - John E Wagner
- Department of Pediatrics, Blood and Marrow Transplant Program, University of Minnesota, Minneapolis, Minnesota
| |
Collapse
|
22
|
Loizidou MA, Hadjisavvas A, Tanteles GA, Spanou-Aristidou E, Kyriacou K, Christophidou-Anastasiadou V. Fanconi anemia-D1 due to homozygosity for the BRCA2 gene Cypriot founder mutation: A case report. Oncol Lett 2016; 11:471-473. [PMID: 26834852 DOI: 10.3892/ol.2015.3852] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 09/04/2015] [Indexed: 11/05/2022] Open
Abstract
Fanconi anemia (FA) is a rare disorder characterized by multiple congenital malformations, progressive bone marrow failure and susceptibility to malignancies. Biallelic mutations in the breast cancer 2, early onset (BRCA2) gene are responsible for the FA-D1 subgroup, which accounts for ~3% of all the FA cases. Patients with biallelic BRCA2 mutations generally display a more severe phenotype, with earlier onset and increased incidence of leukaemia and other solid tumors, than other patients with FA. In the present report, the first Cypriot patient with FA-D1 is described, which is the fifth case of a homozygote for the same null allele reported thus far, and the third known case of neuroblastoma in association with FA-D1.
Collapse
Affiliation(s)
- Maria A Loizidou
- Department of Electron Microscopy/Molecular Pathology, Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus
| | - Andreas Hadjisavvas
- Department of Electron Microscopy/Molecular Pathology, Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus; Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus
| | - George A Tanteles
- Department of Clinical Genetics, Makarios Medical Centre and Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus
| | - Elena Spanou-Aristidou
- Department of Clinical Genetics, Makarios Medical Centre and Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus
| | - Kyriacos Kyriacou
- Department of Electron Microscopy/Molecular Pathology, Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus; Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus
| | - Violetta Christophidou-Anastasiadou
- Cyprus School of Molecular Medicine, Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus; Department of Clinical Genetics, Makarios Medical Centre and Cyprus Institute of Neurology and Genetics, Nicosia 1683, Cyprus
| |
Collapse
|
23
|
Solanki A, Mohanty P, Shukla P, Rao A, Ghosh K, Vundinti BR. FANCA Gene Mutations with 8 Novel Molecular Changes in Indian Fanconi Anemia Patients. PLoS One 2016; 11:e0147016. [PMID: 26799702 PMCID: PMC4723128 DOI: 10.1371/journal.pone.0147016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/27/2015] [Indexed: 11/18/2022] Open
Abstract
Fanconi anemia (FA), a rare heterogeneous genetic disorder, is known to be associated with 19 genes and a spectrum of clinical features. We studied FANCA molecular changes in 34 unrelated and 2 siblings of Indian patients with FA and have identified 26 different molecular changes of FANCA gene, of which 8 were novel mutations (a small deletion c.2500delC, 4 non-sense mutations c.2182C>T, c.2630C>G, c.3677C>G, c.3189G>A; and 3 missense mutations; c.1273G>C, c.3679 G>C, and c.3992 T>C). Among these only 16 patients could be assigned FA-A complementation group, because we could not confirm single exon deletions detected by MLPA or cDNA amplification by secondary confirmation method and due to presence of heterozygous non-pathogenic variations or heterozygous pathogenic mutations. An effective molecular screening strategy should be developed for confirmation of these mutations and determining the breakpoints for single exon deletions.
Collapse
Affiliation(s)
- Avani Solanki
- Department of Cytogenetics, National Institute of Immunohaematology (ICMR), Mumbai, Maharashtra, India
| | - Purvi Mohanty
- Department of Cytogenetics, National Institute of Immunohaematology (ICMR), Mumbai, Maharashtra, India
| | - Pallavi Shukla
- Department of Cytogenetics, National Institute of Immunohaematology (ICMR), Mumbai, Maharashtra, India
| | - Anita Rao
- Department of Cytogenetics, National Institute of Immunohaematology (ICMR), Mumbai, Maharashtra, India
| | - Kanjaksha Ghosh
- Department of Cytogenetics, National Institute of Immunohaematology (ICMR), Mumbai, Maharashtra, India
| | - Babu Rao Vundinti
- Department of Cytogenetics, National Institute of Immunohaematology (ICMR), Mumbai, Maharashtra, India
- * E-mail:
| |
Collapse
|
24
|
Flynn EK, Kamat A, Lach FP, Donovan FX, Kimble DC, Narisu N, Sanborn E, Boulad F, Davies SM, Gillio AP, Harris RE, MacMillan ML, Wagner JE, Smogorzewska A, Auerbach AD, Ostrander EA, Chandrasekharappa SC. Comprehensive analysis of pathogenic deletion variants in Fanconi anemia genes. Hum Mutat 2015; 35:1342-53. [PMID: 25168418 DOI: 10.1002/humu.22680] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 08/09/2014] [Indexed: 11/06/2022]
Abstract
Fanconi anemia (FA) is a rare recessive disease resulting from mutations in one of at least 16 different genes. Mutation types and phenotypic manifestations of FA are highly heterogeneous and influence the clinical management of the disease. We analyzed 202 FA families for large deletions, using high-resolution comparative genome hybridization arrays, single-nucleotide polymorphism arrays, and DNA sequencing. We found pathogenic deletions in 88 FANCA, seven FANCC, two FANCD2, and one FANCB families. We find 35% of FA families carry large deletions, accounting for 18% of all FA pathogenic variants. Cloning and sequencing across the deletion breakpoints revealed that 52 FANCA deletion ends, and one FANCC deletion end extended beyond the gene boundaries, potentially affecting neighboring genes with phenotypic consequences. Seventy-five percent of the FANCA deletions are Alu-Alu mediated, predominantly by AluY elements, and appear to be caused by nonallelic homologous recombination. Individual Alu hotspots were identified. Defining the haplotypes of four FANCA deletions shared by multiple families revealed that three share a common ancestry. Knowing the exact molecular changes that lead to the disease may be critical for a better understanding of the FA phenotype, and to gain insight into the mechanisms driving these pathogenic deletion variants.
Collapse
Affiliation(s)
- Elizabeth K Flynn
- Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, 20892
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Zhang T, Wilson AF, Mahmood Ali A, Namekawa SH, Andreassen PR, Ruhikanta Meetei A, Pang Q. Loss of Faap20 Causes Hematopoietic Stem and Progenitor Cell Depletion in Mice Under Genotoxic Stress. Stem Cells 2015; 33:2320-30. [PMID: 25917546 DOI: 10.1002/stem.2048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 03/11/2015] [Indexed: 11/09/2022]
Abstract
20-kDa FANCA-associated protein (FAAP20) is a recently identified protein that associates with the Fanconi anemia (FA) core complex component, FANCA. FAAP20 contains a conserved ubiquitin-binding zinc-finger domain and plays critical roles in the FA-BRCA pathway of DNA repair and genome maintenance. The function of FAAP20 in animals has not been explored. Here, we report that deletion of Faap20 in mice led to a mild FA-like phenotype with defects in the reproductive and hematopoietic systems. Specifically, hematopoietic stem and progenitor cells (HSPCs) from Faap20(-) (/) (-) mice showed defects in long-term multilineage reconstitution in lethally irradiated recipient mice, with milder phenotype as compared to HSPCs from Fanca(-) (/) (-) or Fancc(-) (/) (-) mice. Faap20(-) (/) (-) mice are susceptible to mitomycin C (MMC)-induced pancytopenia. That is, acute MMC stress induced a significant progenitor loss especially the erythroid progenitors and megakaryocyte-erythrocyte progenitors in Faap20(-) (/) (-) mice. Furthermore, Faap20(-) (/) (-) HSPCs displayed aberrant cell cycle pattern during chronic MMC treatment. Finally, using Faap20(-) (/) (-) Fanca(-) (/) (-) double-knockout mice, we demonstrated a possible dominant effect of FANCA in the interaction between FAAP20 and FANCA. This novel Faap20 mouse model may be valuable in studying the regulation of the FA pathway during bone marrow failure progress in FA patients.
Collapse
Affiliation(s)
| | | | | | - Satoshi H Namekawa
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | | | | | - Qishen Pang
- Division of Experimental Hematology and Cancer Biology
| |
Collapse
|
26
|
Xie J, Kim H, Moreau LA, Puhalla S, Garber J, Al Abo M, Takeda S, D'Andrea AD. RNF4-mediated polyubiquitination regulates the Fanconi anemia/BRCA pathway. J Clin Invest 2015; 125:1523-32. [PMID: 25751062 DOI: 10.1172/jci79325] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/20/2015] [Indexed: 12/13/2022] Open
Abstract
The Fanconi anemia/BRCA (FA/BRCA) pathway is a DNA repair pathway that is required for excision of DNA interstrand cross-links. The 17 known FA proteins, along with several FA-associated proteins (FAAPs), cooperate in this pathway to detect, unhook, and excise DNA cross-links and to subsequently repair the double-strand breaks generated in the process. In the current study, we identified a patient with FA with a point mutation in FANCA, which encodes a mutant FANCA protein (FANCAI939S). FANCAI939S failed to bind to the FAAP20 subunit of the FA core complex, leading to decreased stability. Loss of FAAP20 binding exposed a SUMOylation site on FANCA at amino acid residue K921, resulting in E2 SUMO-conjugating enzyme UBC9-mediated SUMOylation, RING finger protein 4-mediated (RNF4-mediated) polyubiquitination, and proteasome-mediated degradation of FANCA. Mutation of the SUMOylation site of FANCA rescued the expression of the mutant protein. Wild-type FANCA was also subject to SUMOylation, RNF4-mediated polyubiquitination, and degradation, suggesting that regulated release of FAAP20 from FANCA is a critical step in the normal FA pathway. Consistent with this model, cells lacking RNF4 exhibited interstrand cross-linker hypersensitivity, and the gene encoding RNF4 was epistatic with the other genes encoding members of the FA/BRCA pathway. Together, the results from our study underscore the importance of analyzing unique patient-derived mutations for dissecting complex DNA repair processes.
Collapse
|
27
|
Genetic Counseling for Fanconi Anemia: Crosslinking Disciplines. J Genet Couns 2014; 23:910-21. [DOI: 10.1007/s10897-014-9754-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 07/31/2014] [Indexed: 12/22/2022]
|
28
|
Samarakoon PS, Sorte HS, Kristiansen BE, Skodje T, Sheng Y, Tjønnfjord GE, Stadheim B, Stray-Pedersen A, Rødningen OK, Lyle R. Identification of copy number variants from exome sequence data. BMC Genomics 2014; 15:661. [PMID: 25102989 PMCID: PMC4132917 DOI: 10.1186/1471-2164-15-661] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 07/01/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND With advances in next generation sequencing technologies and genomic capture techniques, exome sequencing has become a cost-effective approach for mutation detection in genetic diseases. However, computational prediction of copy number variants (CNVs) from exome sequence data is a challenging task. Whilst numerous programs are available, they have different sensitivities, and have low sensitivity to detect smaller CNVs (1-4 exons). Additionally, exonic CNV discovery using standard aCGH has limitations due to the low probe density over exonic regions. The goal of our study was to develop a protocol to detect exonic CNVs (including shorter CNVs that cover 1-4 exons), combining computational prediction algorithms and a high-resolution custom CGH array. RESULTS We used six published CNV prediction programs (ExomeCNV, CONTRA, ExomeCopy, ExomeDepth, CoNIFER, XHMM) and an in-house modification to ExomeCopy and ExomeDepth (ExCopyDepth) for computational CNV prediction on 30 exomes from the 1000 genomes project and 9 exomes from primary immunodeficiency patients. CNV predictions were tested using a custom CGH array designed to capture all exons (exaCGH). After this validation, we next evaluated the computational prediction of shorter CNVs. ExomeCopy and the in-house modified algorithm, ExCopyDepth, showed the highest capability in detecting shorter CNVs. Finally, the performance of each computational program was assessed by calculating the sensitivity and false positive rate. CONCLUSIONS In this paper, we assessed the ability of 6 computational programs to predict CNVs, focussing on short (1-4 exon) CNVs. We also tested these predictions using a custom array targeting exons. Based on these results, we propose a protocol to identify and confirm shorter exonic CNVs combining computational prediction algorithms and custom aCGH experiments.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Robert Lyle
- Department of Medical Genetics, University of Oslo, Oslo, Norway.
| |
Collapse
|
29
|
Rogers KJ, Fu W, Akey JM, Monnat RJ. Global and disease-associated genetic variation in the human Fanconi anemia gene family. Hum Mol Genet 2014; 23:6815-25. [PMID: 25104853 DOI: 10.1093/hmg/ddu400] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Fanconi anemia (FA) is a human recessive genetic disease resulting from inactivating mutations in any of 16 FANC (Fanconi) genes. Individuals with FA are at high risk of developmental abnormalities, early bone marrow failure and leukemia. These are followed in the second and subsequent decades by a very high risk of carcinomas of the head and neck and anogenital region, and a small continuing risk of leukemia. In order to characterize base pair-level disease-associated (DA) and population genetic variation in FANC genes and the segregation of this variation in the human population, we identified 2948 unique FANC gene variants including 493 FA DA variants across 57,240 potential base pair variation sites in the 16 FANC genes. We then analyzed the segregation of this variation in the 7578 subjects included in the Exome Sequencing Project (ESP) and the 1000 Genomes Project (1KGP). There was a remarkably high frequency of FA DA variants in ESP/1KGP subjects: at least 1 FA DA variant was identified in 78.5% (5950 of 7578) individuals included in these two studies. Six widely used functional prediction algorithms correctly identified only a third of the known, DA FANC missense variants. We also identified FA DA variants that may be good candidates for different types of mutation-specific therapies. Our results demonstrate the power of direct DNA sequencing to detect, estimate the frequency of and follow the segregation of deleterious genetic variation in human populations.
Collapse
Affiliation(s)
| | | | | | - Raymond J Monnat
- Department of Genome Sciences and Department of Pathology, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
30
|
Schrader KA, Stratton KL, Murali R, Laitman Y, Cavallone L, Offit L, Wen YH, Thomas T, Shah S, Rau-Murthy R, Manschreck C, Salo-Mullen E, Otegbeye E, Corines M, Zhang L, Norton L, Hudis C, Klein RJ, Kauff ND, Robson M, Stadler ZK, Haber DA, Lipkin SM, Friedman E, Foulkes WD, Altshuler D, Vijai J, Offit K. Genome Sequencing of Multiple Primary Tumors Reveals a Novel PALB2 Variant. J Clin Oncol 2014; 34:e61-7. [PMID: 24982446 DOI: 10.1200/jco.2013.50.0272] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
| | | | | | - Yael Laitman
- Chaim Sheba Medical Center, Tel-Hashomer, and Tel Aviv University, Tel-Aviv, Israel
| | - Luca Cavallone
- Lady Davis Institute, Jewish General Hospital, Montreal, Québec, Canada
| | - Lily Offit
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Tinu Thomas
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sohela Shah
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Ebun Otegbeye
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Liying Zhang
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Larry Norton
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Noah D Kauff
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark Robson
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Daniel A Haber
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA; and Howard Hughes Medical Institute, Chevy Chase, MD
| | | | - Eitan Friedman
- Chaim Sheba Medical Center, Tel-Hashomer, and Tel Aviv University, Tel-Aviv, Israel
| | - William D Foulkes
- Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Québec, Canada
| | - David Altshuler
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA
| | - Joseph Vijai
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
31
|
De Rocco D, Bottega R, Cappelli E, Cavani S, Criscuolo M, Nicchia E, Corsolini F, Greco C, Borriello A, Svahn J, Pillon M, Mecucci C, Casazza G, Verzegnassi F, Cugno C, Locasciulli A, Farruggia P, Longoni D, Ramenghi U, Barberi W, Tucci F, Perrotta S, Grammatico P, Hanenberg H, Della Ragione F, Dufour C, Savoia A. Molecular analysis of Fanconi anemia: the experience of the Bone Marrow Failure Study Group of the Italian Association of Pediatric Onco-Hematology. Haematologica 2014; 99:1022-31. [PMID: 24584348 DOI: 10.3324/haematol.2014.104224] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Fanconi anemia is an inherited disease characterized by congenital malformations, pancytopenia, cancer predisposition, and sensitivity to cross-linking agents. The molecular diagnosis of Fanconi anemia is relatively complex for several aspects including genetic heterogeneity with mutations in at least 16 different genes. In this paper, we report the mutations identified in 100 unrelated probands enrolled into the National Network of the Italian Association of Pediatric Hematoly and Oncology. In approximately half of these cases, mutational screening was carried out after retroviral complementation analyses or protein analysis. In the other half, the analysis was performed on the most frequently mutated genes or using a next generation sequencing approach. We identified 108 distinct variants of the FANCA, FANCG, FANCC, FANCD2, and FANCB genes in 85, 9, 3, 2, and 1 families, respectively. Despite the relatively high number of private mutations, 45 of which are novel Fanconi anemia alleles, 26% of the FANCA alleles are due to 5 distinct mutations. Most of the mutations are large genomic deletions and nonsense or frameshift mutations, although we identified a series of missense mutations, whose pathogenetic role was not always certain. The molecular diagnosis of Fanconi anemia is still a tiered procedure that requires identifying candidate genes to avoid useless sequencing. Introduction of next generation sequencing strategies will greatly improve the diagnostic process, allowing a rapid analysis of all the genes.
Collapse
Affiliation(s)
| | - Roberta Bottega
- Department of Medical Sciences, University of Trieste, Italy
| | - Enrico Cappelli
- Clinical and Experimental Hematology Unit, G. Gaslini Children's Hospital, Genoa, Italy
| | - Simona Cavani
- Human Genetics laboratory, "E.O. Ospedali Galliera", Genoa, Italy
| | - Maria Criscuolo
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Italy
| | - Elena Nicchia
- Department of Medical Sciences, University of Trieste, Italy
| | - Fabio Corsolini
- Clinical and Experimental Hematology Unit, G. Gaslini Children's Hospital, Genoa, Italy
| | - Chiara Greco
- Pediatric Onco-Hematology, "Azienda Ospedaliero Universitaria Pisana", Pisa, Italy
| | - Adriana Borriello
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Italy
| | - Johanna Svahn
- Clinical and Experimental Hematology Unit, G. Gaslini Children's Hospital, Genoa, Italy
| | - Marta Pillon
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy
| | | | | | - Federico Verzegnassi
- Pediatric Onco-Hematology, "Azienda Ospedaliero Universitaria Pisana", Pisa, Italy
| | - Chiara Cugno
- Pediatric Onco-Hematology, "Fondazione IRCCS Policlinico San Matteo", Pavia, Italy
| | - Anna Locasciulli
- Department of Pediatric and Pediatric Hematology, S.Camillo Hospital, Rome, Italy
| | - Piero Farruggia
- Pediatric Onco-Hematology, ARNAS Civico Hospital, Palermo, Italy
| | - Daniela Longoni
- Pediatrics Unit, University of Milano-Bicocca, Fondazione MBBM, Ospedale San Gerardo, Monza, Italy
| | - Ugo Ramenghi
- Department of Pediatric and Public Health Sciences, Sapienza Università di Roma, Firenze, Italy
| | - Walter Barberi
- Dipartimento di Biotecnologia Cellulari ed Ematologia, Sapienza Università di Roma, Firenze, Italy
| | - Fabio Tucci
- Pediatric Onco-Hematology, "Azienda Ospedaliero-Universitaria" Meyer, Firenze, Italy
| | | | - Paola Grammatico
- Department of Molecular Medicine, "La Sapienza" University, Rome, Italy
| | - Helmut Hanenberg
- Department of Otorhinolaryngology & Head/Neck Surgery, Heinrich Heine University School of Medicine, Duesseldorf, Germany Pediatric Hematology/Oncology, Wells Center for Pediatric Research, Department of Pediatrics, The Riley Hospital, Indiana University School of Medicine, Indianapolis, IN, USA Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Fulvio Della Ragione
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Italy
| | - Carlo Dufour
- Clinical and Experimental Hematology Unit, G. Gaslini Children's Hospital, Genoa, Italy
| | - Anna Savoia
- Department of Medical Sciences, University of Trieste, Italy Pediatric Onco-Hematology, "Azienda Ospedaliero Universitaria Pisana", Pisa, Italy
| | | |
Collapse
|
32
|
Zheng Z, Geng J, Yao RE, Li C, Ying D, Shen Y, Ying L, Yu Y, Fu Q. Molecular defects identified by whole exome sequencing in a child with Fanconi anemia. Gene 2013; 530:295-300. [DOI: 10.1016/j.gene.2013.08.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 08/01/2013] [Accepted: 08/09/2013] [Indexed: 01/25/2023]
|
33
|
Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia. Blood 2013; 121:e138-48. [PMID: 23613520 DOI: 10.1182/blood-2012-12-474585] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Current methods for detecting mutations in Fanconi anemia (FA)-suspected patients are inefficient and often miss mutations. We have applied recent advances in DNA sequencing and genomic capture to the diagnosis of FA. Specifically, we used custom molecular inversion probes or TruSeq-enrichment oligos to capture and sequence FA and related genes, including introns, from 27 samples from the International Fanconi Anemia Registry at The Rockefeller University. DNA sequencing was complemented with custom array comparative genomic hybridization (aCGH) and RNA sequencing (RNA-seq) analysis. aCGH identified deletions/duplications in 4 different FA genes. RNA-seq analysis revealed lack of allele specific expression associated with a deletion and splicing defects caused by missense, synonymous, and deep-in-intron variants. The combination of TruSeq-targeted capture, aCGH, and RNA-seq enabled us to identify the complementation group and biallelic germline mutations in all 27 families: FANCA (7), FANCB (3), FANCC (3), FANCD1 (1), FANCD2 (3), FANCF (2), FANCG (2), FANCI (1), FANCJ (2), and FANCL (3). FANCC mutations are often the cause of FA in patients of Ashkenazi Jewish (AJ) ancestry, and we identified 2 novel FANCC mutations in 2 patients of AJ ancestry. We describe here a strategy for efficient molecular diagnosis of FA.
Collapse
|
34
|
Shukla P, Rao A, Ghosh K, Vundinti BR. Identification of a novel large intragenic deletion in a family with Fanconi anemia: first molecular report from India and review of literature. Gene 2013; 518:470-5. [PMID: 23370339 DOI: 10.1016/j.gene.2013.01.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 12/27/2012] [Accepted: 01/10/2013] [Indexed: 11/28/2022]
Abstract
We report here an Indian case with Fanconi anemia (FA) presented with fever, pallor, short stature, hyperpigmentation and upper limb anomaly. Chromosome breakage analysis together with FANCD2 Western blot monoubiquitination assay confirmed the diagnosis as FA. Multiplex ligation-dependent probe amplification (MLPA) revealed a novel homozygous large intragenic deletion (exons 8-27 del) in the FANCA gene in the proband. His sib and parents were also analyzed and found to be heterozygous for the same mutation. We also reviewed the literature of FANCA large intragenic deletions found in FA patients from different countries and the mechanism involved in the formation of these deletions. To the best of our knowledge, this is the first molecular report from India on FA. The finding expands the mutation spectrum of the FANCA gene. Identification of the mutation confirms the diagnosis of FA at DNA level and helps in providing proper genetic counseling to the family.
Collapse
Affiliation(s)
- Pallavi Shukla
- Department of Cytogenetics, National Institute of Immunohaematology (ICMR), 13th Floor, New Multistoried Building, K.E.M. Hospital Campus, Parel, Mumbai-400012, India
| | | | | | | |
Collapse
|
35
|
Smetsers S, Muter J, Bristow C, Patel L, Chandler K, Bonney D, Wynn RF, Whetton AD, Will AM, Rockx D, Joenje H, Strathdee G, Shanks J, Klopocki E, Gille JJP, Dorsman J, Meyer S. Heterozygote FANCD2 mutations associated with childhood T Cell ALL and testicular seminoma. Fam Cancer 2012; 11:661-5. [DOI: 10.1007/s10689-012-9553-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
36
|
Gille JJP, Floor K, Kerkhoven L, Ameziane N, Joenje H, de Winter JP. Diagnosis of Fanconi Anemia: Mutation Analysis by Multiplex Ligation-Dependent Probe Amplification and PCR-Based Sanger Sequencing. Anemia 2012; 2012:603253. [PMID: 22778927 PMCID: PMC3388349 DOI: 10.1155/2012/603253] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/21/2012] [Indexed: 12/20/2022] Open
Abstract
Fanconi anemia (FA) is a rare inherited disease characterized by developmental defects, short stature, bone marrow failure, and a high risk of malignancies. FA is heterogeneous: 15 genetic subtypes have been distinguished so far. A clinical diagnosis of FA needs to be confirmed by testing cells for sensitivity to cross-linking agents in a chromosomal breakage test. As a second step, DNA testing can be employed to elucidate the genetic subtype of the patient and to identify the familial mutations. This knowledge allows preimplantation genetic diagnosis (PGD) and enables prenatal DNA testing in future pregnancies. Although simultaneous testing of all FA genes by next generation sequencing will be possible in the near future, this technique will not be available immediately for all laboratories. In addition, in populations with strong founder mutations, a limited test using Sanger sequencing and MLPA will be a cost-effective alternative. We describe a strategy and optimized conditions for the screening of FANCA, FANCB, FANCC, FANCE, FANCF, and FANCG and present the results obtained in a cohort of 54 patients referred to our diagnostic service since 2008. In addition, the follow up with respect to genetic counseling and carrier screening in the families is discussed.
Collapse
Affiliation(s)
- Johan J. P. Gille
- Department of Clinical Genetics, VU University Medical Center, Van der Boechorsttraat 7, 1081 BT Amsterdam, The Netherlands
| | - Karijn Floor
- Department of Clinical Genetics, VU University Medical Center, Van der Boechorsttraat 7, 1081 BT Amsterdam, The Netherlands
| | - Lianne Kerkhoven
- Department of Clinical Genetics, VU University Medical Center, Van der Boechorsttraat 7, 1081 BT Amsterdam, The Netherlands
| | - Najim Ameziane
- Department of Clinical Genetics, VU University Medical Center, Van der Boechorsttraat 7, 1081 BT Amsterdam, The Netherlands
| | - Hans Joenje
- Department of Clinical Genetics, VU University Medical Center, Van der Boechorsttraat 7, 1081 BT Amsterdam, The Netherlands
| | - Johan P. de Winter
- Department of Clinical Genetics, VU University Medical Center, Van der Boechorsttraat 7, 1081 BT Amsterdam, The Netherlands
| |
Collapse
|
37
|
Diagnosis of fanconi anemia: mutation analysis by next-generation sequencing. Anemia 2012; 2012:132856. [PMID: 22720145 PMCID: PMC3374947 DOI: 10.1155/2012/132856] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 03/21/2012] [Indexed: 12/31/2022] Open
Abstract
Fanconi anemia (FA) is a rare genetic instability syndrome characterized by developmental defects, bone marrow failure, and a high cancer risk. Fifteen genetic subtypes have been distinguished. The majority of patients (≈85%) belong to the subtypes A (≈60%), C (≈15%) or G (≈10%), while a minority (≈15%) is distributed over the remaining 12 subtypes. All subtypes seem to fit within the “classical” FA phenotype, except for D1 and N patients, who have more severe clinical symptoms. Since FA patients need special clinical management, the diagnosis should be firmly established, to exclude conditions with overlapping phenotypes. A valid FA diagnosis requires the detection of pathogenic mutations in a FA gene and/or a positive result from a chromosomal breakage test. Identification of the pathogenic mutations is also important for adequate genetic counselling and to facilitate prenatal or preimplantation genetic diagnosis. Here we describe and validate a comprehensive protocol for the molecular diagnosis of FA, based on massively parallel sequencing. We used this approach to identify BRCA2, FANCD2, FANCI and FANCL mutations in novel unclassified FA patients.
Collapse
|
38
|
Castella M, Pujol R, Callén E, Trujillo JP, Casado JA, Gille H, Lach FP, Auerbach AD, Schindler D, Benítez J, Porto B, Ferro T, Muñoz A, Sevilla J, Madero L, Cela E, Beléndez C, de Heredia CD, Olivé T, de Toledo JS, Badell I, Torrent M, Estella J, Dasí A, Rodríguez-Villa A, Gómez P, Barbot J, Tapia M, Molinés A, Figuera A, Bueren JA, Surrallés J. Origin, functional role, and clinical impact of Fanconi anemia FANCA mutations. Blood 2011; 117:3759-69. [PMID: 21273304 PMCID: PMC3083295 DOI: 10.1182/blood-2010-08-299917] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 12/30/2010] [Indexed: 12/17/2022] Open
Abstract
Fanconi anemia is characterized by congenital abnormalities, bone marrow failure, and cancer predisposition. To investigate the origin, functional role, and clinical impact of FANCA mutations, we determined a FANCA mutational spectrum with 130 pathogenic alleles. Some of these mutations were further characterized for their distribution in populations, mode of emergence, or functional consequences at cellular and clinical level. The world most frequent FANCA mutation is not the result of a mutational "hot-spot" but results from worldwide dissemination of an ancestral Indo-European mutation. We provide molecular evidence that total absence of FANCA in humans does not reduce embryonic viability, as the observed frequency of mutation carriers in the Gypsy population equals the expected by Hardy-Weinberg equilibrium. We also prove that long distance Alu-Alu recombination can cause Fanconi anemia by originating large interstitial deletions involving FANCA and 2 adjacent genes. Finally, we show that all missense mutations studied lead to an altered FANCA protein that is unable to relocate to the nucleus and activate the FA/BRCA pathway. This may explain the observed lack of correlation between type of FANCA mutation and cellular phenotype or clinical severity in terms of age of onset of hematologic disease or number of malformations.
Collapse
Affiliation(s)
- Maria Castella
- Genome Instability and DNA Repair Group, Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Campus de Bellaterra s/n, Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Alter BP, Giri N, Savage SA, Peters JA, Loud JT, Leathwood L, Carr AG, Greene MH, Rosenberg PS. Malignancies and survival patterns in the National Cancer Institute inherited bone marrow failure syndromes cohort study. Br J Haematol 2010; 150:179-88. [PMID: 20507306 PMCID: PMC3125983 DOI: 10.1111/j.1365-2141.2010.08212.x] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Fanconi anaemia (FA), dyskeratosis congenita (DC), Diamond-Blackfan anaemia (DBA), and Shwachman-Diamond syndrome (SDS) comprise major inherited bone marrow failure syndromes (IBMFS). Adverse events include severe bone marrow failure (BMF), myelodysplastic syndrome (MDS), acute myeloid leukaemia (AML), and solid tumours (ST). The natural history of FA is well characterised; hazard rates in the other syndromes have not yet been quantified. An open cohort was established at the National Cancer Institute (NCI) in 2002. Patients enrolled prior to December, 2007 were followed up to December, 2008. Diagnoses were confirmed with standard tests. Age-associated risks of adverse events were calculated. Most patients in each syndrome survived to young adulthood. Patients with FA had earlier onset of cancers, need for stem cell transplant, and death; followed by DC; DBA and SDS were mildest. While FA and DC patients had markedly increased risks of cancer, AML and MDS, there were no cases of leukaemia in DBA or SDS patients. The NCI cohort provides the first direct quantitative comparison of timing and magnitude of cancer risk in the IBMFS. The findings demonstrate that both FA and DC are major cancer susceptibility syndromes. The IBMFS, historically considered paediatric disorders, have important management implications for physicians treating adult patients.
Collapse
Affiliation(s)
- Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20852-7231, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Zhi G, Chen X, Newcomb W, Brown J, Semmes OJ, Kupfer GM. Purification of FANCD2 sub-complexes. Br J Haematol 2010; 150:88-92. [PMID: 20456353 DOI: 10.1111/j.1365-2141.2010.08217.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Fanconi anaemia (FA) is a recessive genetic disorder characterized by bone marrow failure, birth defects and cancer. Cells from FA patients are particularly defective in removing DNA interstrand crosslinks. We have developed a working chromatography purification scheme for FANCD2, a pivotal player in the FA DNA repair pathway, to facilitate identification of FANCD2 interacting partners. In doing so, at least three distinct FANCD2 subcomplexes were found to be present, designated as large, middle, and small complexes. The small complex is composed of tetramer of FANCD2 polypeptides, which may be the building block for other FANCD2 subcomplexes.
Collapse
Affiliation(s)
- Gang Zhi
- Department of Microbiology, University of Virginia Health System, Virginia, Charlottesville, VA, USA
| | | | | | | | | | | |
Collapse
|
41
|
Abstract
The inherited marrow failure syndromes are a diverse set of genetic disorders characterized by hematopoietic aplasia and cancer predisposition. The clinical phenotypes are highly variable and much broader than previously recognized. The medical management of the inherited marrow failure syndromes differs from that of acquired aplastic anemia or malignancies arising in the general population. Diagnostic workup, molecular pathogenesis, and clinical treatment are reviewed.
Collapse
|
42
|
Chang YH, Shaw CF, Wu KH, Hsieh KH, Su YN, Lu PJ. Treatment with deferiprone for iron overload alleviates bone marrow failure in a Fanconi anemia patient. Hemoglobin 2010; 33:346-51. [PMID: 19814681 DOI: 10.3109/03630260903212563] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fanconi anemia (FA) is a rare inherited disorder characterized by congenital abnormalities, progressive bone marrow failure and cancer susceptibility. There are no reports in the literature about a specific therapy effective in treating the progressive bone marrow failure of FA except for hematopoietic stem cell transplantation (HSCT). A FA patient started to receive deferiprone (L1) therapy due to iron overload. We report here that the white blood cell counts, hemoglobin (Hb) levels and platelet counts were significantly higher during the L1-treated period than when without L1 therapy. Therefore, L1 therapy may be worth considering for FA patients who cannot undergo HSCT.
Collapse
Affiliation(s)
- Yu-Hsiang Chang
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | | | | | | | | | | |
Collapse
|
43
|
Cioc AM, Wagner JE, MacMillan ML, DeFor T, Hirsch B. Diagnosis of myelodysplastic syndrome among a cohort of 119 patients with fanconi anemia: morphologic and cytogenetic characteristics. Am J Clin Pathol 2010; 133:92-100. [PMID: 20023263 DOI: 10.1309/ajcp7w9vmjenzovg] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Predisposition to myelodysplastic syndrome (MDS) and acute leukemia is a hallmark of Fanconi anemia (FA). Morphologic criteria for MDS in FA are not well established, nor is the significance of clonal chromosomal abnormalities. We reviewed bone marrow samples of 119 FA patients: 23 had MDS, with the most common subtype refractory cytopenia with multilineage dysplasia. The presence of MDS was highly correlated with the presence of clonal abnormalities. Neutrophil dysplasia and increased blasts were always associated with the presence of a clone, in contrast with dyserythropoiesis. The most frequent clones had gains of 1q and 3q and/or loss of 7. Karyotype complexity also correlated with MDS. One third of patients with 3q as a sole abnormality had no MDS; patients with 3q and an additional abnormality all had MDS. The data provide a rationale for integrating cytogenetic findings with independently evaluated morphologic findings for monitoring bone marrow status in FA.
Collapse
|
44
|
Rhee DB, Wang Y, Mizesko M, Zhou F, Haneline L, Liu Y. FANCC suppresses short telomere-initiated telomere sister chromatid exchange. Hum Mol Genet 2009; 19:879-87. [PMID: 20022886 DOI: 10.1093/hmg/ddp556] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Telomere shortening has been linked to rare human disorders that present with bone marrow failure including Fanconi anemia (FA). FANCC is one of the most commonly mutated FA genes in FA patients and the FANCC subtype tends to have a relatively early onset of bone marrow failure and hematologic malignancies. Here, we studied the role of Fancc in telomere length regulation in mice. Deletion of Fancc (Fancc(-/-)) did not affect telomerase activity, telomere length or telomeric end-capping in a mouse strain possessing intrinsically long telomeres. However, ablation of Fancc did exacerbate telomere attrition when murine bone marrow cells experienced high cell turnover after serial transplantation. When Fancc(-/-) mice were crossed into a telomerase reverse transcriptase heterozygous or null background (Tert(+/-) or Tert(-/-)) with short telomeres, Fancc deficiency led to an increase in the incidence of telomere sister chromatid exchange. In contrast, these phenotypes were not observed in Tert mutant mice with long telomeres. Our data indicate that Fancc deficiency accelerates telomere shortening during high turnover of hematopoietic cells and promotes telomere recombination initiated by short telomeres.
Collapse
Affiliation(s)
- David B Rhee
- Laboratory of Molecular Gerontology, NIH Biomedical Research Center, National Institute on Aging, Baltimore, MD 21224-6825, USA
| | | | | | | | | | | |
Collapse
|
45
|
Validation of Fanconi anemia complementation Group A assignment using molecular analysis. Genet Med 2009; 11:183-92. [PMID: 19367192 DOI: 10.1097/gim.0b013e318193ba67] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
PURPOSE Fanconi anemia is a genetically heterogeneous chromosomal breakage disorder exhibiting a high degree of clinical variability. Clinical diagnoses are confirmed by testing patient cells for increased sensitivity to crosslinking agents. Fanconi anemia complementation group assignment, essential for efficient molecular diagnosis of the disease, had not been validated for clinical application before this study. The purpose of this study was (1) confirmation of the accuracy of Fanconi anemia complementation group assignment to Group A (FANCA) and (2) development of a rapid mutation detection strategy that ensures the efficient capture of all FANCA mutations. METHODS Using fibroblasts from 29 patients, diagnosis of Fanconi anemia and assignment to complementation Group A was made through breakage analysis studies. FANCA coding and flanking sequences were analyzed using denaturing high pressure liquid chromatography, sequencing, and multiplex ligation-dependent probe amplification. Patients in which two mutations were not identified were analyzed by cDNA sequencing. Patients with no mutations were sequenced for mutations in FANCC, G, E, and F. RESULTS Of the 56 putative mutant alleles studied, 89% had an identifiable FANCA pathogenic mutation. Eight unique novel mutations were identified. CONCLUSION Complementation assignment to Group A was validated in a clinical laboratory setting using our FANCA rapid molecular testing strategy.
Collapse
|
46
|
Sari N, Akyuz C, Aktas D, Gumruk F, Orhan D, Alikasifoglu M, Aydin B, Alanay Y, Buyukpamukcu M. Wilms tumor, AML and medulloblastoma in a child with cancer prone syndrome of total premature chromatid separation and Fanconi anemia. Pediatr Blood Cancer 2009; 53:208-10. [PMID: 19373780 DOI: 10.1002/pbc.21966] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Wilms tumor (WT) is the most common primary renal tumor in childhood. The occurrence of WT in patients with growth retardation, mental retardation and central nervous system abnormalities in association with premature chromatid separation (PCS) and mosaic variegated aneuploidy has been previously described in only 10 patients. Here we report the very rare occurrence of WT with two other malignancies, acute myeloid leukemia and medulloblastoma in association with chromosomal instability. This is a novel presentation of Fanconi anemia with this cytogenetic abnormality.
Collapse
Affiliation(s)
- Neriman Sari
- Department of Pediatric Oncology, Ankara Oncology Hospital, Ankara, Turkey.
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
de Winter JP, Joenje H. The genetic and molecular basis of Fanconi anemia. Mutat Res 2009; 668:11-19. [PMID: 19061902 DOI: 10.1016/j.mrfmmm.2008.11.004] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 10/28/2008] [Accepted: 11/06/2008] [Indexed: 05/27/2023]
Abstract
The capacity to maintain genomic integrity is shared by all living organisms. Multiple pathways are distinguished that safeguard genomic stability, most of which have originated in primitive life forms. In human individuals, defects in these pathways are typically associated with cancer proneness. The Fanconi anemia pathway, one of these pathways, has evolved relatively late during evolution and exists - in its fully developed form - only in vertebrates. This pathway, in which thus far 13 distinct proteins have been shown to participate, appears essential for error-free DNA replication. Inactivating mutations in the corresponding genes underlie the recessive disease Fanconi anemia (FA). In the last decade the genetic basis of this disorder has been uncovered by a variety of approaches, including complementation cloning, genetic linkage analysis and protein association studies. Here we review these approaches, introduce the encoded proteins, and discuss their possible role in ensuring genomic integrity.
Collapse
Affiliation(s)
- Johan P de Winter
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, Van der Boechorststraat 7, Amsterdam 1081 BT, The Netherlands.
| | | |
Collapse
|
48
|
Neveling K, Endt D, Hoehn H, Schindler D. Genotype-phenotype correlations in Fanconi anemia. Mutat Res 2009; 668:73-91. [PMID: 19464302 DOI: 10.1016/j.mrfmmm.2009.05.006] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 03/30/2009] [Accepted: 05/12/2009] [Indexed: 11/30/2022]
Abstract
Although still incomplete, we now have a remarkably detailed and nuanced picture of both phenotypic and genotypic components of the FA spectrum. Initially described as a combination of pancytopenia with a limited number of physical anomalies, it was later recognized that additional features were compatible with the FA phenotype, including a form without detectable malformations (Estren-Dameshek variant). The discovery of somatic mosaicism extended the boundaries of the FA phenotype to cases even without any overt hematological manifestations. This clinical heterogeneity was augmented by new conceptualizations. There was the realization of a constant risk for the development of myelodysplasia and certain malignancies, including acute myelogenous leukemia and squamous cell carcinoma, and there was the emergence of a distinctive cellular phenotype. A striking degree of genetic heterogeneity became apparent with the delineation of at least 12 complementation groups and the identification of their underlying genes. Although functional genetic insights have fostered the interpretation of many phenotypic features, surprisingly few stringent genotype-phenotype connections have emerged. In addition to myriad genetic alterations, less predictable influences are likely to modulate the FA phenotype, including modifier genes, environmental factors and chance effects. In reviewing the current status of genotype-phenotype correlations, we arrive at a unifying hypothesis to explain the remarkably wide range of FA phenotypes. Given the large body of evidence that genomic instability is a major underlying mechanism of accelerated ageing phenotypes, we propose that the numerous FA variants can be viewed as differential modulations and compression in time of intrinsic biological ageing.
Collapse
Affiliation(s)
- Kornelia Neveling
- Department of Human and Medical Genetics, University of Wurzburg, Biozentrum, Am Hubland, Wurzburg D-97074, Germany
| | | | | | | |
Collapse
|
49
|
Impaired FANCD2 monoubiquitination and hypersensitivity to camptothecin uniquely characterize Fanconi anemia complementation group M. Blood 2009; 114:174-80. [PMID: 19423727 DOI: 10.1182/blood-2009-02-207811] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
FANCM is a component of the Fanconi anemia (FA) core complex and one FA patient (EUFA867) with biallelic mutations in FANCM has been described. Strikingly, we found that EUFA867 also carries biallelic mutations in FANCA. After correcting the FANCA defect in EUFA867 lymphoblasts, a "clean" FA-M cell line was generated. These cells were hypersensitive to mitomycin C, but unlike cells defective in other core complex members, FANCM(-/-) cells were proficient in monoubiquitinating FANCD2 and were sensitive to the topoisomerase inhibitor camptothecin, a feature shared only with the FA subtype D1 and N. In addition, FANCM(-/-) cells were sensitive to UV light. FANCM and a C-terminal deletion mutant rescued the cross-linker sensitivity of FANCM(-/-) cells, whereas a FANCM ATPase mutant did not. Because both mutants restored the formation of FANCD2 foci, we conclude that FANCM functions in an FA core complex-dependent and -independent manner.
Collapse
|
50
|
Genetik in der Pädiatrie als Interaktion zwischen Klinik und Labor. Monatsschr Kinderheilkd 2008. [DOI: 10.1007/s00112-008-1681-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|