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Article ; Online: Precision Medicine: Solving the Mystery of Myocarditis in the Aftermath of SARS-CoV-2.

Feldman, Arthur M / Kasper, Edward K / Qu, Hui-Qi

2023 Volume 11, Issue 4, Page(s) 478–480

MeSH term(s)	Humans ; Myocarditis ; SARS-CoV-2 ; COVID-19 ; Precision Medicine ; Heart Failure
Language	English
Publishing date	2023-04-03
Publishing country	United States
Document type	Editorial
ZDB-ID	2705621-1
ISSN	2213-1787 ; 2213-1779
ISSN (online)	2213-1787
ISSN	2213-1779
DOI	10.1016/j.jchf.2023.02.002
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Article ; Online: Single-Cell RNA Sequencing Technology Landscape in 2023.

Qu, Hui-Qi / Kao, Charlly / Hakonarson, Hakon

Stem cells (Dayton, Ohio)

2023 Volume 42, Issue 1, Page(s) 1–12

Abstract: Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity and the dynamics of gene expression, bearing profound significance in stem cell research. Depending on the starting materials used for analysis, scRNA- ... ...

Abstract	Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity and the dynamics of gene expression, bearing profound significance in stem cell research. Depending on the starting materials used for analysis, scRNA-seq encompasses scRNA-seq and single-nucleus RNA sequencing (snRNA-seq). scRNA-seq excels in capturing cellular heterogeneity and characterizing rare cell populations within complex tissues, while snRNA-seq is advantageous in situations where intact cell dissociation is challenging or undesirable (eg, epigenomic studies). A number of scRNA-seq technologies have been developed as of late, including but not limited to droplet-based, plate-based, hydrogel-based, and spatial transcriptomics. The number of cells, sequencing depth, and sequencing length in scRNA-seq can vary across different studies. Addressing current technical challenges will drive the future of scRNA-seq, leading to more comprehensive and precise insights into cellular biology and disease mechanisms informing therapeutic interventions.
MeSH term(s)	Single-Cell Analysis ; Gene Expression Profiling ; Sequence Analysis, RNA ; RNA, Small Nuclear ; Base Sequence
Chemical Substances	RNA, Small Nuclear
Language	English
Publishing date	2023-11-07
Publishing country	England
Document type	Journal Article
ZDB-ID	1143556-2
ISSN	1549-4918 ; 1066-5099
ISSN (online)	1549-4918
ISSN	1066-5099
DOI	10.1093/stmcls/sxad077
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Article ; Online: Genetics of BAG3

Hui‐Qi Qu / Arthur M. Feldman / Hakon Hakonarson

Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease, Vol 11, Iss

A Paradigm for Developing Precision Therapies for Dilated Cardiomyopathies

2022 Volume 23

Abstract: Nonischemic dilated cardiomyopathy is a common form of heart muscle disease in which genetic factors play a critical etiological role. In this regard, both rare disease‐causing mutations and common disease‐susceptible variants, in the Bcl‐2–associated ... ...

Abstract	Nonischemic dilated cardiomyopathy is a common form of heart muscle disease in which genetic factors play a critical etiological role. In this regard, both rare disease‐causing mutations and common disease‐susceptible variants, in the Bcl‐2–associated athanogene 3 (BAG3) gene have been reported, highlighting the critical role of BAG3 in cardiomyocytes and in the development of dilated cardiomyopathy. The phenotypic effects of the BAG3 mutations help investigators understand the structure and function of the BAG3 gene. Indeed, we report herein that all of the known pathogenic/likely pathogenic variants affect at least 1 of 3 protein functional domains, ie, the WW domain, the second IPV (Ile‐Pro‐Val) domain, or the BAG domain, whereas none of the missense nontruncating pathogenic/likely pathogenic variants affect the proline‐rich repeat (PXXP) domain. A common variant, p.Cys151Arg, associated with reduced susceptibility to dilated cardiomyopathy demonstrated a significant difference in allele frequencies among diverse human populations, suggesting evolutionary selective pressure. As BAG3‐related therapies for heart failure move from the laboratory to the clinic, the ability to provide precision medicine will depend in large part on having a thorough understanding of the potential effects of both common and uncommon genetic variants on these target proteins. The current review article provides a roadmap that investigators can utilize to determine the potential interactions between a patient's genotype, their phenotype, and their response to therapeutic interventions with both gene delivery and small molecules.
Keywords	BAG3 ; dilated cardiomyopathy ; genetics ; heart failure ; INPP5F ; precision medicine ; Diseases of the circulatory (Cardiovascular) system ; RC666-701
Subject code	610
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
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Article ; Online: Genetics of BAG3: A Paradigm for Developing Precision Therapies for Dilated Cardiomyopathies.

Qu, Hui-Qi / Feldman, Arthur M / Hakonarson, Hakon

Journal of the American Heart Association

2022 Volume 11, Issue 23, Page(s) e027373

Abstract: Nonischemic dilated cardiomyopathy is a common form of heart muscle disease in which genetic factors play a critical etiological role. In this regard, both rare disease-causing mutations and common disease-susceptible variants, in the Bcl-2-associated ... ...

Abstract	Nonischemic dilated cardiomyopathy is a common form of heart muscle disease in which genetic factors play a critical etiological role. In this regard, both rare disease-causing mutations and common disease-susceptible variants, in the Bcl-2-associated athanogene 3 (
MeSH term(s)	Humans ; Cardiomyopathy, Dilated/genetics ; Cardiomyopathy, Dilated/therapy ; Adaptor Proteins, Signal Transducing/genetics ; Apoptosis Regulatory Proteins/genetics
Chemical Substances	BAG3 protein, human ; Adaptor Proteins, Signal Transducing ; Apoptosis Regulatory Proteins
Language	English
Publishing date	2022-11-16
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2653953-6
ISSN	2047-9980 ; 2047-9980
ISSN (online)	2047-9980
ISSN	2047-9980
DOI	10.1161/JAHA.122.027373
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Article ; Online: Mendelian randomization study of obesity and type 2 diabetes in hospitalized COVID-19 patients.

Qu, Hui-Qi / Qu, Jingchun / Glessner, Joseph / Hakonarson, Hakon

Metabolism: clinical and experimental

2022 Volume 129, Page(s) 155156

Abstract: Background: Both obesity and type 2 diabetes (T2D) are reported to be highly enriched in hospitalized COVID-19 patients. Due to the close correlation between obesity and T2D, it is important to examine whether obesity and T2D are independently related ... ...

Abstract	Background: Both obesity and type 2 diabetes (T2D) are reported to be highly enriched in hospitalized COVID-19 patients. Due to the close correlation between obesity and T2D, it is important to examine whether obesity and T2D are independently related to COVID-19 hospitalization. Objective: To examine the causal effect of obesity and T2D in hospitalized COVID-19 patients using Mendelian randomization (MR). Research design and methods: This two-sample MR analysis applied genetic markers of obesity identified in the genome wide association study (GWAS) by the GIANT Consortium as instrumental variables (IVs) of obesity; and genetic markers of T2D identified by the DIAGRAM Consortium as IVs of T2D. The MR analysis was performed in hospitalized COVID-19 patient by the COVID-19 Host Genetics Initiative using the MR-Base platform. Results: All 3 classes of obesity (Class 1/2/3) were shown as the causal risk factors of COVID-19 hospitalization; however, T2D doesn't increase the risk of hospitalization or critically ill COVID-19 as an independent factor. Conclusions: Obesity, but not T2D, is a primary risk factor of COVID-19 hospitalization.
MeSH term(s)	Body Mass Index ; COVID-19/epidemiology ; COVID-19/genetics ; COVID-19/therapy ; Causality ; Comorbidity ; Diabetes Mellitus, Type 2/epidemiology ; Diabetes Mellitus, Type 2/genetics ; Genome-Wide Association Study ; Hospitalization/statistics & numerical data ; Humans ; Mendelian Randomization Analysis ; Obesity/classification ; Obesity/epidemiology ; Obesity/genetics ; Polymorphism, Single Nucleotide/genetics ; Risk Factors ; SARS-CoV-2 ; Severity of Illness Index
Language	English
Publishing date	2022-01-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80230-x
ISSN	1532-8600 ; 0026-0495
ISSN (online)	1532-8600
ISSN	0026-0495
DOI	10.1016/j.metabol.2022.155156
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Article ; Online: Mitochondrial DNA Haplogroup K Is Protective Against Autism Spectrum Disorder Risk in Populations of European Ancestry.

Chang, Xiao / Qu, Hui-Qi / Liu, Yichuan / Glessner, Joseph T / Hakonarson, Hakon

Journal of the American Academy of Child and Adolescent Psychiatry

2023

Abstract: Objective: Accumulative evidence indicates a critical role of mitochondrial function in autism spectrum disorders (ASD), implying that ASD risk may be linked to mitochondrial dysfunction due to DNA (mtDNA) variations. Although a few studies have ... ...

Abstract	Objective: Accumulative evidence indicates a critical role of mitochondrial function in autism spectrum disorders (ASD), implying that ASD risk may be linked to mitochondrial dysfunction due to DNA (mtDNA) variations. Although a few studies have explored the association between mtDNA variations and ASD, the role of mtDNA in ASD is still unclear. Here, we aimed to investigate whether mitochondrial DNA haplogroups are associated with the risk of ASD. Method: Two European cohorts and an Ashkenazi Jewish (AJ) cohort were analyzed, including 2,062 ASD patients in comparison with 4,632 healthy controls. DNA samples were genotyped using Illumina HumanHap550/610 and Illumina 1M arrays, inclusive of mitochondrial markers. Mitochondrial DNA (mtDNA) haplogroups were identified from genotyping data using HaploGrep2. A mitochondrial genome imputation pipeline was established to detect mtDNA variants. We conducted a case-control study to investigate potential associations of mtDNA haplogroups and variants with the susceptibility to ASD. Results: We observed that the ancient adaptive mtDNA haplogroup K was significantly associated with decreased risk of ASD by the investigation of 2 European cohorts including a total of 2,006 cases and 4,435 controls (odds ratio = 0.64, P=1.79 × 10 Conclusion: This study helps to shed light on the contribution of mitochondria in ASD and provides new insights into the genetic mechanism underlying ASD, suggesting the potential involvement of mtDNA-encoded proteins in the development of ASD.
Language	English
Publishing date	2023-12-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	392535-3
ISSN	1527-5418 ; 0890-8567
ISSN (online)	1527-5418
ISSN	0890-8567
DOI	10.1016/j.jaac.2023.09.550
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Article ; Online: Genome-wide association study of the age of onset of type 1 diabetes reveals HTATIP2 as a novel T cell regulator.

Cardinale, Christopher J / Chang, Xiao / Wei, Zhi / Qu, Hui-Qi / Bradfield, Jonathan P / Polychronakos, Constantin / Hakonarson, Hakon

Frontiers in immunology

2023 Volume 14, Page(s) 1101488

Abstract: Introduction: Type 1 diabetes, a disorder caused by autoimmune destruction of pancreatic insulin-producing cells, is more difficult to manage when it presents at a younger age. We sought to identify genetic correlates of the age of onset by conducting ... ...

Abstract	Introduction: Type 1 diabetes, a disorder caused by autoimmune destruction of pancreatic insulin-producing cells, is more difficult to manage when it presents at a younger age. We sought to identify genetic correlates of the age of onset by conducting the first genome-wide association study (GWAS) treating the age of first diagnosis as a quantitative trait. Methods: We performed GWAS with a discovery cohort of 4,014 cases and a replication cohort of 493 independent cases. Genome-wide significant SNPs were mapped to a causal variant by Bayesian conditional analysis and gel shift assay. The causal protein-coding gene was identified and characterized by RNA interference treatment of primary human pan-CD4+ T cells with RNA-seq of the transcriptome. The candidate gene was evaluated functionally in primary cells by CD69 staining and proliferation assays. Results: Our GWAS replicated the known association of the age of diagnosis with the human leukocyte antigen complex (HLA-DQB1). The second signal identified was in an intron of the NELL1 gene on chromosome 11 and fine-mapped to variant rs10833518 (P < 1.54 × 10 Discussion: This study implicates HTATIP2 as a new type 1 diabetes gene acting via T cell regulation. Larger population sample sizes are expected to reveal additional loci.
MeSH term(s)	Humans ; Acetyltransferases ; Age of Onset ; Bayes Theorem ; Diabetes Mellitus, Type 1 ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Transcription Factors ; T-Lymphocytes/immunology
Chemical Substances	Acetyltransferases (EC 2.3.1.-) ; HTATIP2 protein, human (EC 2.3.1.48) ; Transcription Factors
Language	English
Publishing date	2023-02-01
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1101488
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Article ; Online: TOPORS as a novel causal gene for Joubert syndrome.

Strong, Alanna / Qu, Hui-Qi / Cullina, Sinéad / McManus, Morgan L / Zackai, Elaine H / Glessner, Joseph / Kenny, Eimear E / Hakonarson, Hakon

American journal of medical genetics. Part A

2023 Volume 191, Issue 8, Page(s) 2156–2163

Abstract: Joubert syndrome (JBTS) is a Mendelian disorder of the primary cilium defined by the clinical triad of hypotonia, developmental delay, and a distinct cerebellar malformation called the molar tooth sign. JBTS is inherited in an autosomal recessive, ... ...

Abstract	Joubert syndrome (JBTS) is a Mendelian disorder of the primary cilium defined by the clinical triad of hypotonia, developmental delay, and a distinct cerebellar malformation called the molar tooth sign. JBTS is inherited in an autosomal recessive, autosomal dominant, or X-linked recessive manner. Though over 40 genes have been identified as causal for JBTS, molecular diagnosis is not made in 30%-40% of individuals who meet clinical criteria. TOPORS encodes topoisomerase I-binding arginine/serine-rich protein, and homozygosity for a TOPORS missense variant (c.29C > A; p.(Pro10Gln)) was identified in individuals with the ciliopathy oral-facial-digital syndrome in two families of Dominican descent. Here, we report an additional proband of Dominican ancestry with JBTS found by exome sequencing to be homozygous for the identical p.(Pro10Gln) TOPORS missense variant. Query of the Mount Sinai BioMe biobank, which includes 1880 individuals of Dominican ancestry, supports a high carrier frequency of the TOPORS p.(Pro10Gln) variant in individuals of Dominican descent. Our data nominates TOPORS as a novel causal gene for JBTS and suggests that TOPORS variants should be considered in the differential of ciliopathy-spectrum disease in individuals of Dominican ancestry.
MeSH term(s)	Humans ; Cerebellum/abnormalities ; Abnormalities, Multiple/diagnosis ; Abnormalities, Multiple/genetics ; Abnormalities, Multiple/metabolism ; Eye Abnormalities/diagnosis ; Eye Abnormalities/genetics ; Retina/abnormalities ; Kidney Diseases, Cystic/diagnosis ; Kidney Diseases, Cystic/genetics ; Mutation ; Ciliopathies/genetics ; Nervous System Malformations
Language	English
Publishing date	2023-05-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2108614-X
ISSN	1552-4833 ; 0148-7299 ; 1552-4825
ISSN (online)	1552-4833
ISSN	0148-7299 ; 1552-4825
DOI	10.1002/ajmg.a.63303
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Article: Identification of copy number variants contributing to hallux valgus.

Zhou, Wentao / Jia, Jun / Qu, Hui-Qi / Ma, Feier / Li, Junyi / Qi, Xiaohui / Meng, Xinyi / Ding, Zhiyong / Zheng, Gang / Hakonarson, Hakon / Zeng, Xiantie / Li, Jin / Xia, Qianghua

Frontiers in genetics

2023 Volume 14, Page(s) 1116284

Abstract: Hallux valgus is a common form of foot deformity, and genetic factors contribute substantially to the pathogenesis of hallux valgus deformity. We conducted a genetic study on the structural variants underlying familial hallux valgus using whole exome ... ...

Abstract	Hallux valgus is a common form of foot deformity, and genetic factors contribute substantially to the pathogenesis of hallux valgus deformity. We conducted a genetic study on the structural variants underlying familial hallux valgus using whole exome sequencing approach. Twenty individuals from five hallux valgus families and two sporadic cases were included in this study. A total of 372 copy number variations were found and passed quality control filtering. Among them, 43 were only present in cases but not in controls or healthy individuals in the database of genomic variants. The genes covered by these copy number variations were enriched in gene sets related to immune signaling pathway, and cytochrome P450 metabolism. The hereditary CNVs demonstrate a dominant inheritance pattern. Two candidate pathogenic CNVs were further validated by quantitative-PCR. This study suggests that hallux valgus is a degenerative joint disease involving the dysregulation of immune and metabolism signaling pathways.
Language	English
Publishing date	2023-03-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2023.1116284
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Article ; Online: Target genes regulated by CLEC16A intronic region associated with common variable immunodeficiency.

Huang, Xubo / Huang, Jinxia / Li, Xiumei / Fan, Jingxian / Zhou, Desheng / Qu, Hui-Qi / Glessner, Joseph T / Ji, Dandan / Jia, Qi / Ding, Zhiyong / Wang, Nan / Wei, Wei / Lyu, Xing / Li, Mulin Jun / Liu, Zhe / Liu, Wei / Wei, Yongjie / Hakonarson, Hakon / Xia, Qianghua /

Li, Jin

The Journal of allergy and clinical immunology

2024

Abstract: Background: CLEC16A intron 19 has been identified as a candidate locus for common variable immunodeficiency (CVID).: Objectives: This study sought to elucidate the molecular mechanism by which variants at the CLEC16A intronic locus may contribute to ... ...

Abstract	Background: CLEC16A intron 19 has been identified as a candidate locus for common variable immunodeficiency (CVID). Objectives: This study sought to elucidate the molecular mechanism by which variants at the CLEC16A intronic locus may contribute to the pathogenesis of CVID. Methods: The investigators performed fine-mapping of the CLEC16A locus in a CVID cohort, then deleted the candidate functional SNP in T-cell lines by the CRISPR-Cas9 technique and conducted RNA-sequencing to identify target gene(s). The interactions between the CLEC16A locus and its target genes were identified using circular chromosome conformation capture. The transcription factor complexes mediating the chromatin interactions were determined by proteomic approach. The molecular pathways regulated by the CLEC16A locus were examined by RNA-sequencing and reverse phase protein array. Results: This study showed that the CLEC16A locus is an enhancer regulating expression of multiple target genes including a distant gene ATF7IP2 through chromatin interactions. Distinct transcription factor complexes mediate the chromatin interactions in an allele-specific manner. Disruption of the CLEC16A locus affects the AKT signaling pathway, as well as the molecular response of CD4 Conclusions: Through multiomics and targeted experimental approaches, this study elucidated the underlying target genes and signaling pathways involved in the genetic association of CLEC16A with CVID, and highlighted plausible molecular targets for developing novel therapeutics.
Language	English
Publishing date	2024-01-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	121011-7
ISSN	1097-6825 ; 1085-8725 ; 0091-6749
ISSN (online)	1097-6825 ; 1085-8725
ISSN	0091-6749
DOI	10.1016/j.jaci.2023.12.023
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