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Mougeot JLC, Beckman MF, Hovan AJ, Hasséus B, Legert KG, Johansson JE, von Bültzingslöwen I, Brennan MT, Bahrani Mougeot F. Identification of single nucleotide polymorphisms (SNPs) associated with chronic graft-versus-host disease in patients undergoing allogeneic hematopoietic cell transplantation. Support Care Cancer 2023; 31:587. [PMID: 37731134 PMCID: PMC10511391 DOI: 10.1007/s00520-023-08044-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/06/2023] [Indexed: 09/22/2023]
Abstract
INTRODUCTION Chronic graft-versus-host disease (cGVHD) is a debilitating side effect of allogeneic hematopoietic cell transplantation (HCT), affecting the quality of life of patients. We used whole exome sequencing to identify candidate SNPs and complete a multi-marker gene-level analysis using a cohort of cGVHD( +) (N = 16) and cGVHD( -) (N = 66) HCT patients. METHODS Saliva samples were collected from HCT patients (N = 82) pre-conditioning in a multi-center study from March 2011 to May 2018. Exome sequencing was performed and FASTQ files were processed for sequence alignments. Significant SNPs were identified by logistic regression using PLINK2v3.7 and Fisher's exact test. One cGVHD( -) patient sample was excluded from further analysis since no SNP was present in at least 10% of the sample population. The FUMA platform's SNP2GENE was utilized to annotate SNPs and generate a MAGMA output. Chromatin state visualization of lead SNPs was completed using Epilogos tool. FUMA's GENE2FUNC was used to obtain gene function and tissue expression from lead genomic loci. RESULTS Logistic regression classified 986 SNPs associated with cGVHD( +). SNP2GENE returned three genomic risk loci, four lead SNPs, 48 candidate SNPs, seven candidate GWAS tagged SNPs, and four mapped genes. Fisher's exact test identified significant homozygous genotypes of four lead SNPs (p < 0.05). GENE2FUNC analysis of multi-marker SNP sets identified one positional gene set including lead SNPs for KANK1 and KDM4C and two curated gene sets including lead SNPs for PTPRD, KDM4C, and/or KANK1. CONCLUSIONS Our data suggest that SNPs in three genes located on chromosome 9 confer genetic susceptibility to cGVHD in HCT patients. These genes modulate STAT3 expression and phosphorylation in cancer pathogenesis. The findings may have implications in the modulation of pathways currently targeted by JAK inhibitors in cGVHD clinical trials.
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Affiliation(s)
- Jean-Luc C Mougeot
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA.
| | - Micaela F Beckman
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA
| | - Allan J Hovan
- BC Cancer, Oral Oncology and Dentistry, Vancouver, BC, Canada
| | - Bengt Hasséus
- Department of Oral Medicine and Pathology, University of Gothenburg, Gothenburg, Sweden
| | | | - Jan-Erik Johansson
- Department of Hematology and Coagulation, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Michael T Brennan
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA
- Department of Otolaryngology/Head & Neck Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Farah Bahrani Mougeot
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA.
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Alkhamis FA, Alabdali MM, Alsulaiman AA, Alamri AS, Alali R, Akhtar MS, Alsalman SA, Cyrus C, Albakr AI, Alduhalan AS, Gandla D, Al-Romaih K, Abouelhoda M, Loza BL, Keating B, Al-Ali AK. Whole-exome sequencing analyses in a Saudi Ischemic Stroke Cohort reveal association signals, and shows polygenic risk scores are related to Modified Rankin Scale Risk. Funct Integr Genomics 2023; 23:102. [PMID: 36973604 PMCID: PMC10042957 DOI: 10.1007/s10142-023-01039-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023]
Abstract
Ischemic stroke represents a significant societal burden across the globe. Rare high penetrant monogenic variants and less pathogenic common single nucleotide polymorphisms (SNPs) have been described as being associated with risk of diseases. Genetic studies in Saudi Arabian patients offer a greater opportunity to detect rare high penetrant mutations enriched in these consanguineous populations. We performed whole exome sequencing on 387 ischemic stroke subjects from Saudi Arabian hospital networks with up to 20,230 controls from the Saudi Human Genome Project and performed gene burden analyses of variants in 177 a priori loci derived from knowledge-driven curation of monogenic and genome-wide association studies of stroke. Using gene-burden analyses, we observed significant associations in numerous loci under autosomal dominant and/or recessive modelling. Stroke subjects with modified Rankin Scale (mRSs) above 3 were found to carry greater cumulative polygenic risk score (PRS) from rare variants in stroke genes (standardized PRS mean > 0) compared to the population average (standardized PRS mean = 0). However, patients with mRS of 3 or lower had lower cumulative genetic risk from rare variants in stroke genes (OR (95%CI) = 1.79 (1.29-2.49), p = 0.0005), with the means of standardized PRS at or lower than 0. In conclusion, gene burden testing in Saudi stroke populations reveals a number of statistically significant signals under different disease inheritance models. However, interestingly, stroke subjects with mRS of 3 or lower had lower cumulative genetic risk from rare variants in stroke genes and therefore, determining the potential mRS cutoffs to use for clinical significance may allow risk stratification of this population.
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Affiliation(s)
- Fahad A Alkhamis
- Department of Neurology, King Fahd Hospital of The University, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Majed M Alabdali
- Department of Neurology, King Fahd Hospital of The University, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Abdulla A Alsulaiman
- Department of Neurology, King Fahd Hospital of The University, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Abdullah S Alamri
- Department of Neurology, King Fahd Hospital of The University, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Rudaynah Alali
- Department of Internal Medicine, King Fahd Hospital of The University, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Mohammed S Akhtar
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Sadiq A Alsalman
- Department of Neurology, King Fahd Hospital, Alhafof, Saudi Arabia
| | - Cyril Cyrus
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Aishah I Albakr
- Department of Neurology, King Fahd Hospital of The University, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Anas S Alduhalan
- Department of Neurology, King Fahd Hospital of The University, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia
| | - Divya Gandla
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | | | | | - Bao-Li Loza
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | - Brendan Keating
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, 19104, USA
| | - Amein K Al-Ali
- Department of Clinical Biochemistry, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31441, Saudi Arabia.
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Eyileten C, Sharif L, Wicik Z, Jakubik D, Jarosz-Popek J, Soplinska A, Postula M, Czlonkowska A, Kaplon-Cieslicka A, Mirowska-Guzel D. The Relation of the Brain-Derived Neurotrophic Factor with MicroRNAs in Neurodegenerative Diseases and Ischemic Stroke. Mol Neurobiol 2021; 58:329-347. [PMID: 32944919 PMCID: PMC7695657 DOI: 10.1007/s12035-020-02101-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 08/25/2020] [Indexed: 03/07/2023]
Abstract
Brain-derived neurotrophic factor (BDNF) is a member of the neurotrophin family of growth factors that plays a crucial role in the development of the nervous system while supporting the survival of existing neurons and instigating neurogenesis. Altered levels of BDNF, both in the circulation and in the central nervous system (CNS), have been reported to be involved in the pathogenesis of neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), multiple sclerosis (MS), and ischemic stroke. MicroRNAs (miRNAs) are a class of non-coding RNAs found in body fluids such as peripheral blood and cerebrospinal fluid. Several different miRNAs, and their target genes, are recognized to be involved in the pathophysiology of neurodegenerative and neurovascular diseases. Thus, they present as promising biomarkers and a novel treatment approach for CNS disorders. Currently, limited studies provide viable evidence of miRNA-mediated post-transcriptional regulation of BDNF. The aim of this review is to provide a comprehensive assessment of the current knowledge regarding the potential diagnostic and prognostic values of miRNAs affecting BDNF expression and its role as a CNS disorders and neurovascular disease biomarker. Moreover, a novel therapeutic approach in neurodegenerative diseases and ischemic stroke targeting miRNAs associated with BDNF will be discussed.
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Affiliation(s)
- Ceren Eyileten
- Department of Experimental and Clinical Pharmacology, Medical University of Warsaw, Center for Preclinical Research and Technology CEPT, Banacha 1B Str., 02-097 Warsaw, Poland
| | - Lucia Sharif
- Department of Experimental and Clinical Pharmacology, Medical University of Warsaw, Center for Preclinical Research and Technology CEPT, Banacha 1B Str., 02-097 Warsaw, Poland
| | - Zofia Wicik
- Department of Experimental and Clinical Pharmacology, Medical University of Warsaw, Center for Preclinical Research and Technology CEPT, Banacha 1B Str., 02-097 Warsaw, Poland
- Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Paulo, Brazil
| | - Daniel Jakubik
- Department of Experimental and Clinical Pharmacology, Medical University of Warsaw, Center for Preclinical Research and Technology CEPT, Banacha 1B Str., 02-097 Warsaw, Poland
| | - Joanna Jarosz-Popek
- Department of Experimental and Clinical Pharmacology, Medical University of Warsaw, Center for Preclinical Research and Technology CEPT, Banacha 1B Str., 02-097 Warsaw, Poland
| | - Aleksandra Soplinska
- Department of Experimental and Clinical Pharmacology, Medical University of Warsaw, Center for Preclinical Research and Technology CEPT, Banacha 1B Str., 02-097 Warsaw, Poland
| | - Marek Postula
- Department of Experimental and Clinical Pharmacology, Medical University of Warsaw, Center for Preclinical Research and Technology CEPT, Banacha 1B Str., 02-097 Warsaw, Poland
| | - Anna Czlonkowska
- 2nd Department of Neurology, Institute of Psychiatry and Neurology, 02-957 Warsaw, Poland
| | | | - Dagmara Mirowska-Guzel
- Department of Experimental and Clinical Pharmacology, Medical University of Warsaw, Center for Preclinical Research and Technology CEPT, Banacha 1B Str., 02-097 Warsaw, Poland
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