1
|
Cheng YHH, Bohaczuk SC, Stergachis AB. Functional categorization of gene regulatory variants that cause Mendelian conditions. Hum Genet 2024; 143:559-605. [PMID: 38436667 PMCID: PMC11078748 DOI: 10.1007/s00439-023-02639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/30/2023] [Indexed: 03/05/2024]
Abstract
Much of our current understanding of rare human diseases is driven by coding genetic variants. However, non-coding genetic variants play a pivotal role in numerous rare human diseases, resulting in diverse functional impacts ranging from altered gene regulation, splicing, and/or transcript stability. With the increasing use of genome sequencing in clinical practice, it is paramount to have a clear framework for understanding how non-coding genetic variants cause disease. To this end, we have synthesized the literature on hundreds of non-coding genetic variants that cause rare Mendelian conditions via the disruption of gene regulatory patterns and propose a functional classification system. Specifically, we have adapted the functional classification framework used for coding variants (i.e., loss-of-function, gain-of-function, and dominant-negative) to account for features unique to non-coding gene regulatory variants. We identify that non-coding gene regulatory variants can be split into three distinct categories by functional impact: (1) non-modular loss-of-expression (LOE) variants; (2) modular loss-of-expression (mLOE) variants; and (3) gain-of-ectopic-expression (GOE) variants. Whereas LOE variants have a direct corollary with coding loss-of-function variants, mLOE and GOE variants represent disease mechanisms that are largely unique to non-coding variants. These functional classifications aim to provide a unified terminology for categorizing the functional impact of non-coding variants that disrupt gene regulatory patterns in Mendelian conditions.
Collapse
Affiliation(s)
- Y H Hank Cheng
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Stephanie C Bohaczuk
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
| |
Collapse
|
2
|
Brown A, Mead ME, Steenwyk JL, Goldman GH, Rokas A. Extensive non-coding sequence divergence between the major human pathogen Aspergillus fumigatus and its relatives. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:802494. [PMID: 36866034 PMCID: PMC9977105 DOI: 10.3389/ffunb.2022.802494] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/09/2022] [Indexed: 11/13/2022]
Abstract
Invasive aspergillosis is a deadly fungal disease; more than 400,000 patients are infected worldwide each year and the mortality rate can be as high as 50-95%. Of the ~450 species in the genus Aspergillus only a few are known to be clinically relevant, with the major pathogen Aspergillus fumigatus being responsible for ~50% of all invasive mold infections. Genomic comparisons between A. fumigatus and other Aspergillus species have historically focused on protein-coding regions. However, most A. fumigatus genes, including those that modulate its virulence, are also present in other pathogenic and non-pathogenic closely related species. Our hypothesis is that differential gene regulation - mediated through the non-coding regions upstream of genes' first codon - contributes to A. fumigatus pathogenicity. To begin testing this, we compared non-coding regions upstream of the first codon of single-copy orthologous genes from the two A. fumigatus reference strains Af293 and A1163 and eight closely related Aspergillus section Fumigati species. We found that these non-coding regions showed extensive sequence variation and lack of homology across species. By examining the evolutionary rates of both protein-coding and non-coding regions in a subset of orthologous genes with highly conserved non-coding regions across the phylogeny, we identified 418 genes, including 25 genes known to modulate A. fumigatus virulence, whose non-coding regions exhibit a different rate of evolution in A. fumigatus. Examination of sequence alignments of these non-coding regions revealed numerous instances of insertions, deletions, and other types of mutations of at least a few nucleotides in A. fumigatus compared to its close relatives. These results show that closely related Aspergillus species that vary greatly in their pathogenicity exhibit extensive non-coding sequence variation and identify numerous changes in non-coding regions of A. fumigatus genes known to contribute to virulence.
Collapse
Affiliation(s)
- Alec Brown
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Matthew E. Mead
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Jacob L. Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, United States
| |
Collapse
|
3
|
Colaco S, Nadkarni A. Borderline HbA 2 levels: Dilemma in diagnosis of beta-thalassemia carriers. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108387. [PMID: 34893152 DOI: 10.1016/j.mrrev.2021.108387] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 05/27/2021] [Accepted: 06/08/2021] [Indexed: 12/17/2022]
Abstract
There is inconsistency in the exact definition of diagnostic levels of HbA2 for β thalassemia trait. While many laboratories consider HbA2 ≥4.0 % diagnostic, still others consider HbA2 ≥3.3 % or HbA2 ≥3.5 % as the cut-off for establishing β thalassemia carrier diagnosis. This is because, over the years, studies have described β thalassemia carriers showing HbA2 levels that lie above the normal range of HbA2 but below the typical carrier range of β thalassemia. These, "borderline HbA2 levels", though not detrimental to health, are significant in β thalassemia carrier diagnosis because they can lead to misinterpretation of results. In this review, we have evaluated the prevalence of borderline HbA2 levels and discussed the causes of borderline HbA2 values. We have also compiled an extensive catalogue of β globin gene defects associated with borderline HbA2 levels and have discussed strategies to avoid misdiagnosing borderline HbA2 β thalassemia carriers. Our analysis of studies that have delineated the cause of borderline HbA2 levels in different populations shows that 35.4 % [626/1766] of all individuals with borderline HbA2 levels carry a molecular defect. Among the positive samples, 17 % [299/1766] show β globin gene defects, 7.7 % [137/1766] show α thalassemia defects, 2.7 % [49/1766] show KLF1 gene mutations, 2.3 % [41/1766] show the co-inheritance of β and α thalassemia, 2.0 % [37/1766] show the co-inheritance of β and δ thalassemia and 1.8 % [32/1766] show α globin gene triplication. It appears that a comprehensive molecular work up of the β globin gene is the only definite method to detect borderline HbA2 β thalassemia carriers, especially in populations with a high prevalence of the disease. The presence of associated genetic or acquired determinants may subsequently be assessed to identify the cause of borderline HbA2.
Collapse
Affiliation(s)
- Stacy Colaco
- Department of Hematogenetics, ICMR-National Institute of Immunohematology, 13th Floor, K.E.M. Hospital Campus, Parel, Mumbai, 400 012, India
| | - Anita Nadkarni
- Department of Hematogenetics, ICMR-National Institute of Immunohematology, 13th Floor, K.E.M. Hospital Campus, Parel, Mumbai, 400 012, India.
| |
Collapse
|
4
|
Murad H, Moassas F, Fakseh NAL. A rare gene variation cap +1 (A>C) (HBB: c. -50A>C) associated with codon 5 (-CT) (HBB: c.17_18delCT) mutation in Syrian family. Mol Genet Genomic Med 2021; 9:e1602. [PMID: 33491330 PMCID: PMC8104179 DOI: 10.1002/mgg3.1602] [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: 09/20/2020] [Revised: 12/23/2020] [Accepted: 01/04/2021] [Indexed: 12/04/2022] Open
Abstract
Background CAP+1 [A>C] (HBB:c.‐50A>C) is a rare silent β‐thalassemia (β‐thal) mutation. Carrier individuals of this mutation show borderline hemoglobin (Hb), mean corpuscular volume (MCV) and Hb A2 levels. This mutation was previously reported in combination with different β‐thalassemia mutations, leading to variable phenotypes. Case presentation Here, we describe for the first time the combination of silent CAP+1 [A>C] (HBB:c.‐50A>C) mutation with β0 codon 5 [‐CT] (HBB:c.17_18delCT) mutation in a Syrian proband, leading to beta thalassemia intermedia (TI). Conclusions The compound heterozygotes of the silent CAP+1 (A>C) together with another severe beta gene mutation, are phenotypically severe enough to present at an early age and require appropriate therapeutic modalities.
Collapse
Affiliation(s)
- Hossam Murad
- Molecular Biology and Biotechnology Department, Human Genetics Div, Atomic Energy Commission of Syria, Damascus, Syria
| | - Faten Moassas
- Molecular Biology and Biotechnology Department, Human Genetics Div, Atomic Energy Commission of Syria, Damascus, Syria
| | - Nour A L Fakseh
- Molecular Biology and Biotechnology Department, Human Genetics Div, Atomic Energy Commission of Syria, Damascus, Syria
| |
Collapse
|
5
|
Sripusanapan A, Phusua A, Fanhchaksai K, Charoenkwan P. Compound heterozygosity of a silent beta-thalassemia mutation at the 3'-untranslated region (HBB: c.*132 C>T) and beta-zero thalassemia results in thalassemia intermedia. Pediatr Blood Cancer 2020; 67:e28157. [PMID: 31930713 DOI: 10.1002/pbc.28157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/11/2019] [Indexed: 11/05/2022]
Affiliation(s)
- Adivitch Sripusanapan
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Arunee Phusua
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Kanda Fanhchaksai
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Pimlak Charoenkwan
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| |
Collapse
|
6
|
Notarangelo LD, Agostini A, Casale M, Samperi P, Arcioni F, Gorello P, Perrotta S, Masera N, Barone A, Bertoni E, Bonetti E, Burnelli R, Casini T, Del Vecchio GC, Filippini B, Giona F, Giordano P, Gorio C, Marchina E, Nardi M, Petrone A, Colombatti R, Sainati L, Russo G. HbS/β+ thalassemia: Really a mild disease? A National survey from the AIEOP Sickle Cell Disease Study Group with genotype-phenotype correlation. Eur J Haematol 2019; 104:214-222. [PMID: 31788855 DOI: 10.1111/ejh.13362] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 12/20/2022]
Abstract
OBJECTIVES HbS/β+ patients' presence in Italy increased due to immigration; these patients are clinically heterogeneous, and specific guidelines are lacking. Our aim is to describe a cohort of HbS/β+ patients, with genotype-phenotype correlation, in order to offer guidance for clinical management of such patients. METHODS Retrospective cohort study of HbS/β+ patients among 15 AIEOP Centres. RESULTS A total of 41 molecularly confirmed S/β+ patients were enrolled (1-55 years, median 10.9) and classified on β+ mutation: IVS-I-110, IVS-I-6, promoter, and "others." Prediagnostic events included VOC 16/41 (39%), ACS 6/41 (14.6%), sepsis 3/41 (3.7%), and avascular necrosis 3/41 (7,3%). Postdiagnostic events were VOC 22/41 (53.6% %), sepsis 4/41 (9.7%), ACS 4/41 (9.7%), avascular necrosis 3/41 (7.3%), aplastic crisis 2/41 (4.8%), stroke 1/41 (2.4%), ACS 1/41 (2.4%), and skin ulcerations 1/41 (2.4%). The IVS-I-110 group presented the lowest median age at first SCD-related event (P = .02 vs promoter group) and the higher median number of severe events/year (0.26 events/patient/year) (P = .01 vs IVS-I-6 and promoter groups). Promoter group presented a specific skeletal phenotype. Treatment regimen applied was variable among the centers. CONCLUSIONS HbS/β+ is not always a mild disease. Patients with IVS-I-110 mutation could benefit from a standard of care like SS and S/β° patients. Standardization of treatment is needed.
Collapse
Affiliation(s)
| | - Annalisa Agostini
- Pediatrics Clinic, University of Brescia, Spedali Civili di Brescia, Brescia, Italy
| | - Maddalena Casale
- Department of Woman, Child and General and Specialist Surgery, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Piera Samperi
- Unit of Pediatric Hematology and Oncology, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Francesco Arcioni
- Pediatric Hematology and Oncology with Bone Marrow Transplation, Azienda Ospedaliera di Perugia, Perugia, Italy
| | - Paolo Gorello
- Department of Medicine, University of Perugia, CREO, Hematology, Perugia, Italy
| | - Silverio Perrotta
- Department of Woman, Child and General and Specialist Surgery, Università degli Studi della Campania "Luigi Vanvitelli", Napoli, Italy
| | - Nicoletta Masera
- Department of Pediatrics, Università di Milano Bicocca, Fondazione MBBM, Monza, Italy
| | - Angelica Barone
- Department of Pediatric Onco-Hematology, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Elisa Bertoni
- Hematology Oncology Unit, Children's Hospital, ASST Spedali Civili, Brescia, Italy
| | - Elisa Bonetti
- Department of Pediatric Onco-Hematology, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Roberta Burnelli
- Pediatric Oncology University Hospital, Sant'Anna Hospital, Ferrara, Italy
| | - Tommaso Casini
- Pediatric Hematology-Oncology, IRCCS Meyer Children's Hospital, Florence, Italy
| | - Giovanni Carlo Del Vecchio
- Pediatric Unit "F. Vecchio", Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | | | - Fiorina Giona
- Department of Cellular Biotechnologies and Hematology, Policlinico Umberto I, Sapienza University, Hematology, Rome, Italy
| | - Paola Giordano
- Pediatric Unit "F. Vecchio", Department of Biomedical Sciences and Human Oncology, University of Bari "Aldo Moro", Bari, Italy
| | - Chiara Gorio
- Hematology Oncology Unit, Children's Hospital, ASST Spedali Civili, Brescia, Italy
| | - Eleonora Marchina
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Margherita Nardi
- Onco-Hematologic Pediatric Center, University Hospital of Pisa, Pisa, Italy
| | - Angela Petrone
- Department of Pediatrics, Rovereto Hospital, Rovereto, Italy
| | - Raffaella Colombatti
- Clinic of Pediatric Hematology Oncology, Department of Woman's and Child Health, Azienda Ospedaliera-Università di Padova, Padova, Italy
| | - Laura Sainati
- Clinic of Pediatric Hematology Oncology, Department of Woman's and Child Health, Azienda Ospedaliera-Università di Padova, Padova, Italy
| | - Giovanna Russo
- Unit of Pediatric Hematology and Oncology, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| |
Collapse
|
7
|
Murad H, Moassas F, Ali B, Alachkar W. A compound heterozygous −29 A>G and IVS-I-1 G>A mutation of HBB gene leading to β-thalassemia intermedia in a Syrian patient: A case report. COGENT MEDICINE 2019. [DOI: 10.1080/2331205x.2019.1581448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Hossam Murad
- Atomic Energy Commission of Syria (AECS), Damascus, Syria
| | - Faten Moassas
- Atomic Energy Commission of Syria (AECS), Damascus, Syria
| | - Bashar Ali
- Atomic Energy Commission of Syria (AECS), Damascus, Syria
| | - Walid Alachkar
- Atomic Energy Commission of Syria (AECS), Damascus, Syria
| |
Collapse
|
8
|
Moassas F, Alabloog A, Murad H. Description of a Rare β-Globin Gene Mutation: -86 (C>G) (HBB: c.-136C>G) Observed in a Syrian Family. Hemoglobin 2018; 42:203-205. [PMID: 30173596 DOI: 10.1080/03630269.2018.1500918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We present the description of a β-thalassemia (β-thal) -86 (C>G) (HBB: c.-136C>G) mutation in a Syrian family from Damascus, As-Suwayda Province, Syria, who was referred to the laboratory for prenatal diagnosis (PND). The mutation was found in the mother in a homozygous state, while it was in the father and in the amniotic fluid sample in a heterozygous state. This mutation is located at -86 within the proximal CACCC box in the promoter of the β-globin gene and is possibly linked with a phenotype of β+-thal. Polymerase chain reaction-restriction fragment length polymorphism (PCR/RFLP) analysis indicated that the -86 mutation was linked with haplotype I [+ - - - - + +]. We propose that Lebanon may be the origin of this mutation. To the best of our knowledge, this is the first report describing this mutation in As-Suwayda Province. These findings provide novel information on the region-specificity of this mutation in southwestern Syria.
Collapse
Affiliation(s)
- Faten Moassas
- a Molecular Biology and Biotechnology Department, Human Genetics Division , Atomic Energy Commission of Syria , Damascus , Syria
| | - Ayman Alabloog
- a Molecular Biology and Biotechnology Department, Human Genetics Division , Atomic Energy Commission of Syria , Damascus , Syria
| | - Hossam Murad
- a Molecular Biology and Biotechnology Department, Human Genetics Division , Atomic Energy Commission of Syria , Damascus , Syria
| |
Collapse
|
9
|
CRISPR-Cas9 HDR system enhances AQP1 gene expression. Oncotarget 2017; 8:111683-111696. [PMID: 29340084 PMCID: PMC5762352 DOI: 10.18632/oncotarget.22901] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/16/2017] [Indexed: 01/04/2023] Open
Abstract
Ionizing radiation (IR) isthe primarytherapeutic tool to treat patients with cancerous lesions located in the head and neck. In many patients, IR results in irreversible and severe salivary gland dysfunction or xerostomia. Currently there are no effective treatment options to reduce the effects of xerostomia. More recently, salivary gland gene therapy utilizing the water-specific protein aquaporin 1 (AQP1) has been of great interest to potentially correct salivary dysfunction. In this study, we used CRISPR-Cas9 gene editing along with the endogenous promoter of AQP1 within theHEK293 and MDCK cell lines. The successful integration of the cytomegalovirus (CMV) promoterresultedin a significant increase of AQP1 gene transcription and translation. Additionalfunctional experiments involvingthe MDCK cell line confirmedthat over-expressed AQP1increasedtransmembrane fluid flux indicative of increased intracellular fluid flux. The off-target effect of designed guided RNA sequence was analyzed and demonstrateda high specificity for the Cas9 cleavage. Considering the development of new methods for robust DNA knock-in, our results suggest that endogenous promoter replacement may be a potential treatment forsalivary gland dysfunction.
Collapse
|