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Liu Q, Zhou Y, Cogan JD, Mitchell DB, Sheng Q, Zhao S, Bai Y, Ciombor KK, Sabusap CM, Malabanan MM, Markin CR, Douglas K, Ding G, Banovich NE, Nickerson DA, Blue EE, Bamshad MJ, Brown KK, Schwartz DA, Phillips JA, Martinez-Barricarte R, Salisbury ML, Shyr Y, Loyd JE, Kropski JA, Blackwell TS. The Genetic Landscape of Familial Pulmonary Fibrosis. Am J Respir Crit Care Med 2023; 207:1345-1357. [PMID: 36622818 PMCID: PMC10595451 DOI: 10.1164/rccm.202204-0781oc] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 01/09/2023] [Indexed: 01/10/2023] Open
Abstract
Rationale and Objectives: Up to 20% of idiopathic interstitial lung disease is familial, referred to as familial pulmonary fibrosis (FPF). An integrated analysis of FPF genetic risk was performed by comprehensively evaluating for genetic rare variants (RVs) in a large cohort of FPF kindreds. Methods: Whole-exome sequencing and/or candidate gene sequencing from affected individuals in 569 FPF kindreds was performed, followed by cosegregation analysis in large kindreds, gene burden analysis, gene-based risk scoring, cell-type enrichment analysis, and coexpression network construction. Measurements and Main Results: It was found that 14.9-23.4% of genetic risk in kindreds could be explained by RVs in genes previously linked to FPF, predominantly telomere-related genes. New candidate genes were identified in a small number of families-including SYDE1, SERPINB8, GPR87, and NETO1-and tools were developed for evaluation and prioritization of RV-containing genes across kindreds. Several pathways were enriched for RV-containing genes in FPF, including focal adhesion and mitochondrial complex I assembly. By combining single-cell transcriptomics with prioritized candidate genes, expression of RV-containing genes was discovered to be enriched in smooth muscle cells, type II alveolar epithelial cells, and endothelial cells. Conclusions: In the most comprehensive FPF genetic study to date, the prevalence of RVs in known FPF-related genes was defined, and new candidate genes and pathways relevant to FPF were identified. However, new RV-containing genes shared across multiple kindreds were not identified, thereby suggesting that heterogeneous genetic variants involving a variety of genes and pathways mediate genetic risk in most FPF kindreds.
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Affiliation(s)
- Qi Liu
- Department of Biostatistics
| | | | - Joy D. Cogan
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics
| | | | | | | | | | | | | | | | | | | | - Guixiao Ding
- Division of Allergy, Pulmonary and Critical Care Medicine
| | | | | | | | - Michael J. Bamshad
- Department of Genome Sciences
- Brotman-Baty Institute, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, Washington
| | | | - David A. Schwartz
- Department of Medicine, School of Medicine, University of Colorado Denver, Denver, Colorado; and
| | - John A. Phillips
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics
| | | | | | | | - James E. Loyd
- Division of Allergy, Pulmonary and Critical Care Medicine
| | - Jonathan A. Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
| | - Timothy S. Blackwell
- Division of Allergy, Pulmonary and Critical Care Medicine
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
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Ciani M, Bonvicini C, Scassellati C, Carrara M, Maj C, Fostinelli S, Binetti G, Ghidoni R, Benussi L. The Missing Heritability of Sporadic Frontotemporal Dementia: New Insights from Rare Variants in Neurodegenerative Candidate Genes. Int J Mol Sci 2019; 20:ijms20163903. [PMID: 31405128 PMCID: PMC6721049 DOI: 10.3390/ijms20163903] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/02/2019] [Accepted: 08/08/2019] [Indexed: 12/13/2022] Open
Abstract
Frontotemporal dementia (FTD) is a common form of dementia among early-onset cases. Several genetic factors for FTD have been revealed, but a large proportion of FTD cases still have an unidentified genetic origin. Recent studies highlighted common pathobiological mechanisms among neurodegenerative diseases. In the present study, we investigated a panel of candidate genes, previously described to be associated with FTD and/or other neurodegenerative diseases by targeted next generation sequencing (NGS). We focused our study on sporadic FTD (sFTD), devoid of disease-causing mutations in GRN, MAPT and C9orf72. Since genetic factors have a substantially higher pathogenetic contribution in early onset patients than in late onset dementia, we selected patients with early onset (<65 years). Our study revealed that, in 50% of patients, rare missense potentially pathogenetic variants in genes previously associated with Alzheimer's disease, Parkinson disease, amyotrophic lateral sclerosis and Lewy body dementia (GBA, ABCA7, PARK7, FUS, SORL1, LRRK2, ALS2), confirming genetic pleiotropy in neurodegeneration. In parallel, a synergic genetic effect on FTD is suggested by the presence of variants in five different genes in one single patient. Further studies employing genome-wide approaches might highlight pathogenic variants in novel genes that explain the still missing heritability of FTD.
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Affiliation(s)
- Miriam Ciani
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy
| | - Cristian Bonvicini
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy
| | - Catia Scassellati
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy
| | - Matteo Carrara
- Service of Statistics, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy
| | - Carlo Maj
- Institute of Genomic Statistics and Bioinformatics, University of Bonn, 53127 Bonn, Germany
| | - Silvia Fostinelli
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy
| | - Giuliano Binetti
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy
| | - Roberta Ghidoni
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy
| | - Luisa Benussi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, 25125 Brescia, Italy.
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Ciani M, Benussi L, Bonvicini C, Ghidoni R. Genome Wide Association Study and Next Generation Sequencing: A Glimmer of Light Toward New Possible Horizons in Frontotemporal Dementia Research. Front Neurosci 2019; 13:506. [PMID: 31156380 PMCID: PMC6532367 DOI: 10.3389/fnins.2019.00506] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/02/2019] [Indexed: 12/12/2022] Open
Abstract
Frontotemporal Dementia (FTD) is a focal neurodegenerative disease, with a strong genetic background, that causes early onset dementia. The present knowledge about the risk loci and causative mutations of FTD mainly derives from genetic linkage analysis, studies of candidate genes, Genome-Wide Association Studies (GWAS) and Next-Generation Sequencing (NGS) applications. In this review, we report recent insights into the genetics of FTD, and, specifically, the results achieved thanks to GWAS and NGS approaches. Linkage studies of large FTD pedigrees have prompted the identification of causal mutations in different genes: mutations in C9orf72, MAPT, and GRN genes explain the large majority of cases with a high family history of the disease. In cases with a less clear inheritance, GWAS and NGS have contributed to further understand the genetic picture of FTD. GWAS identified several common genetic variants with a modest risk effect. Of interest, many of these variants are in genes belonging to the endo-lysosomal pathway, the immune response and neuronal survival. On the opposite, the NGS approach allowed the identification of rare variants with a strong risk effect. These variants were identified in known FTD-associated genes and again in genes involved in the endo-lysosomal pathway and in the immune response. Interestingly, both approaches demonstrated that several genes are associated to multiple neurodegenerative disorders including FTD. Thanks to these complementary approaches, the genetic picture of FTD is becoming more clear and novel key molecular processes are emerging. This will foster opportunities to move toward prevention and therapy for this incurable disease.
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Affiliation(s)
- Miriam Ciani
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Luisa Benussi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Cristian Bonvicini
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Roberta Ghidoni
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
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