Journal of Genetics and Genomics

Exploring noncoding variants in genetic diseases: from detection to functional insights

Ke Wu, Fengxiao Bu, Yang Wu, Gen Zhang, Xin Wang, Shunmin He, Mo-Fang Liu, Runsheng Chen, Huijun Yuan

2024, 51(2): 111-132. doi: 10.1016/j.jgg.2024.01.001

Abstract (4) PDF (1)

Abstract:
Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases.

Gene therapy for monogenic disorders: challenges, strategies, and perspectives

Yi Zhang, Zhi-Ying Wu

2024, 51(2): 133-143. doi: 10.1016/j.jgg.2023.08.001

Abstract (326) PDF (41)

Abstract:
Monogenic disorders refer to a group of human diseases caused by mutations in single genes. While disease-modifying therapies have offered some relief from symptoms and delayed progression for some monogenic diseases, most of these diseases still lack effective treatments. In recent decades, gene therapy has emerged as a promising therapeutic strategy for genetic disorders. Researchers have developed various gene manipulation tools and gene delivery systems to treat monogenic diseases. Despite this progress, concerns about inefficient delivery, persistent expression, immunogenicity, toxicity, capacity limitation, genomic integration, and limited tissue specificity still need to be addressed. This review gives an overview of commonly used gene therapy and delivery tools, along with the challenges they face and potential strategies to counter them.

Unraveling the complexity of polycystic ovary syndrome with animal models

Huanju Liu, Mixue Tu, Zhiyong Yin, Dan Zhang, Jun Ma, Feng He

2024, 51(2): 144-158. doi: 10.1016/j.jgg.2023.09.012

Abstract (352) PDF (10)

Abstract:
Polycystic ovary syndrome (PCOS) is a highly familial and heritable endocrine disorder. Over half of the daughters born to women with PCOS may eventually develop their own PCOS-related symptoms. Progress in the treatment of PCOS is currently hindered by the complexity of its clinical manifestations and incomplete knowledge of its etiopathogenesis. Various animal models, including experimentally induced, naturally occurring, and spontaneously arising ones, have been established to emulate a wide range of phenotypical and pathological traits of human PCOS. These studies have led to a paradigm shift in understanding the genetic, developmental, and evolutionary origins of this disorder. Furthermore, emerging evidence suggests that animal models are useful in evaluating state-of-the-art drugs and treatments for PCOS. This review aims to provide a comprehensive summary of recent studies of PCOS in animal models, highlighting the power of these disease models in understanding the biology of PCOS and aiding high-throughput approaches.

Current therapies for osteoarthritis and prospects of CRISPR-based genome, epigenome, and RNA editing in osteoarthritis treatment

Yuxi Chen, Xiao Luo, Rui Kang, Kaixin Cui, Jianping Ou, Xiya Zhang, Puping Liang

2024, 51(2): 159-183. doi: 10.1016/j.jgg.2023.07.007

Abstract (121) PDF (4)

Abstract:
Osteoarthritis (OA) is one of the most common degenerative joint diseases worldwide, causing pain, disability, and decreased quality of life. The balance between regeneration and inflammation-induced degradation results in multiple etiologies and complex pathogenesis of OA. Currently, there is a lack of effective therapeutic strategies for OA treatment. With the development of CRISPR-based genome, epigenome, and RNA editing tools, OA treatment has been improved by targeting genetic risk factors, activating chondrogenic elements, and modulating inflammatory regulators. Supported by cell therapy and in vivo delivery vectors, genome, epigenome, and RNA editing tools may provide a promising approach for personalized OA therapy. This review summarizes CRISPR-based genome, epigenome, and RNA editing tools that can be applied to the treatment of OA and provides insights into the development of CRISPR-based therapeutics for OA treatment. Moreover, in-depth evaluations of the efficacy and safety of these tools in human OA treatment are needed.

CGG repeat expansion in LOC642361/NUTM2B-AS1 typically presents as oculopharyngodistal myopathy

Yan Shi, Chunyan Cao, Yiheng Zeng, Yuanliang Ding, Long Chen, Fuze Zheng, Xuejiao Chen, Fanggui Zhou, Xiefeng Yang, Jinjing Li, Liuqing Xu, Guorong Xu, Minting Lin, Hiroyuki Ishiura, Shoji Tsuji, Ning Wang, Zhiqiang Wang, Wan-Jin Chen, Kang Yang

2024, 51(2): 184-196. doi: 10.1016/j.jgg.2023.12.009

Abstract (0) PDF (0)

Abstract:
CGG repeat expansions in LOC642361/NUTM2B-AS1 have recently been identified as a cause of oculopharyngeal myopathy with leukoencephalopathy. However, since only three patients from a single family were reported, it remains unknown whether their clinicopathological features are typical for CGG repeat expansions in LOC642361/NUTM2B-AS1. Here, using repeat-primed-polymerase chain reaction and long-read sequencing, we identify 12 individuals from 3 unrelated families with CGG repeat expansions in LOC642361/NUTM2B-AS1, typically presenting with oculopharyngodistal myopathy. The CGG repeat expansions range from 161 to 669 repeat units. Most of the patients present with ptosis, restricted eye movements, dysphagia, dysarthria, and diffuse limb muscle weakness. Only one patient shows T2-weighted hyperintensity in the cerebellar white matter surrounding the deep cerebellar nuclei on brain magnetic resonance imaging. Muscle biopsies from three patients show a myopathic pattern and rimmed vacuoles. Analyses of muscle biopsies suggest that CGG repeat expansions in LOC642361/NUTM2B-AS1 may deleteriously affect aggrephagic capacity, suggesting that RNA toxicity and mitochondrial dysfunction may contribute to pathogenesis. Our study thus expands the phenotypic spectrum for the CGG repeat expansion of LOC642361/NUTM2B-AS1 and indicates that this genetic variant typically manifests as oculopharyngodistal myopathy with chronic myopathic changes with rimmed vacuoles and filamentous intranuclear inclusions in muscle fibers.

Correction of a CADASIL point mutation using adenine base editors in hiPSCs and blood vessel organoids

Jingwen Wang, Lei Zhang, Guanglan Wu, Jinni Wu, Xinyao Zhou, Xiaolin Chen, Yongxia Niu, Yiren Jiao, Qianyi Liu, Puping Liang, Guang Shi, Xueqing Wu, Junjiu Huang

2024, 51(2): 197-207. doi: 10.1016/j.jgg.2023.04.013

Abstract (159) PDF (21)

Abstract:
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a monogenic small vessel disease caused by mutations in the NOTCH3 gene. However, the pathogenesis of CADASIL remains unclear, and patients have limited treatment options. Here, we use human induced pluripotent stem cells (hiPSCs) generated from the peripheral blood mononuclear cells of a patient with CADASIL carrying a heterozygous NOTCH3 mutation (c.1261C>T, p.R421C) to develop a disease model. The correction efficiency of different adenine base editors (ABEs) is tested using the HEK293T-NOTCH3 reporter cell line. ABEmax is selected based on its higher efficiency and minimization of predicted off-target effects. Vascular smooth muscle cells (VSMCs) differentiated from CADASIL hiPSCs show NOTCH3 deposition and abnormal actin cytoskeleton structure, and the abnormalities are recovered in corrected hiPSC-derived VSMCs. Furthermore, CADASIL blood vessel organoids generated for in vivo modeling show altered expression of genes related to disease phenotypes, including the downregulation of cell adhesion, extracellular matrix organization, and vessel development. The dual adeno-associated virus (AAV) split-ABEmax system is applied to the genome editing of vascular organoids with an average editing efficiency of 8.82%. Collectively, we present potential genetic therapeutic strategies for patients with CADASIL using blood vessel organoids and the dual AAV split-ABEmax system.

The m⁶A reader YTHDC2 maintains visual function and retinal photoreceptor survival through modulating translation of PPEF2 and PDE6B

Yeming Yang, Xiaoyan Jiang, Junyao Chen, Lu Liu, Guo Liu, Kuanxiang Sun, Wenjing Liu, Xianjun Zhu, Qiuyue Guan

2024, 51(2): 208-221. doi: 10.1016/j.jgg.2023.12.007

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Abstract:
Inherited retinal dystrophies (IRDs) are major causes of visual impairment and irreversible blindness worldwide, while the precise molecular and genetic mechanisms are still elusive. N-methyladenosine (m⁶A) modification is the most prevalent internal modification in eukaryotic mRNA. YTH domain containing 2 (YTHDC2), an m⁶A reader protein, has recently been identified as a key player in germline development and human cancer. However, its contribution to retinal function remains unknown. Here, we explore the role of YTHDC2 in the visual function of retinal rod photoreceptors by generating rod-specific Ythdc2 knockout mice. Results show that Ythdc2 deficiency in rods causes diminished scotopic ERG responses and progressive retinal degeneration. Multi-omics analysis further identifies Ppef2 and Pde6b as the potential targets of YTHDC2 in the retina. Specifically, via its YTH domain, YTHDC2 recognizes and binds m⁶A-modified Ppef2 mRNA at the coding sequence and Pde6b mRNA at the 5′-UTR, resulting in enhanced translation efficiency without affecting mRNA levels. Compromised translation efficiency of Ppef2 and Pde6b after YTHDC2 depletion ultimately leads to decreased protein levels in the retina, impaired retinal function, and progressive rod death. Collectively, our finding highlights the importance of YTHDC2 in visual function and photoreceptor survival, which provides an unreported elucidation of IRD pathogenesis via epitranscriptomics.

Rare loss-of-function variants in FLNB cause non-syndromic orofacial clefts

Wenbin Huang, Shiying Zhang, Jiuxiang Lin, Yi Ding, Nan Jiang, Jieni Zhang, Huaxiang Zhao, Feng Chen

2024, 51(2): 222-229. doi: 10.1016/j.jgg.2023.03.012

Abstract (179) PDF (30)

Abstract:
Orofacial clefts (OFCs) are the most common congenital craniofacial disorders, of which the etiology is closely related to rare coding variants. Filamin B (FLNB) is an actin-binding protein implicated in bone formation. FLNB mutations have been identified in several types of syndromic OFCs and previous studies suggest a role of FLNB in the onset of non-syndromic OFCs (NSOFCs). Here, we report two rare heterozygous variants (p.P441T and p.G565R) in FLNB in two unrelated hereditary families with NSOFCs. Bioinformatics analysis suggests that both variants may disrupt the function of FLNB. In mammalian cells, p.P441T and p.G565R variants are less potent to induce cell stretches than wild type FLNB, suggesting that they are loss-of-function mutations. Immunohistochemistry analysis demonstrates that FLNB is abundantly expressed during palatal development. Importantly, Flnb^−/− embryos display cleft palates and previously defined skeletal defects. Taken together, our findings reveal that FLNB is required for development of palates in mice and FLNB is a bona fide causal gene for NSOFCs in humans.

NCAD v1.0: a database for non-coding variant annotation and interpretation

Xiaoshu Feng, Sihan Liu, Ke Li, Fengxiao Bu, Huijun Yuan

2024, 51(2): 230-242. doi: 10.1016/j.jgg.2023.12.005

Abstract (0) PDF (0)

Abstract:
The application of whole genome sequencing is expanding in clinical diagnostics across various genetic disorders, and the significance of non-coding variants in penetrant diseases is increasingly being demonstrated. Therefore, it is urgent to improve the diagnostic yield by exploring the pathogenic mechanisms of variants in non-coding regions. However, the interpretation of non-coding variants remains a significant challenge, due to the complex functional regulatory mechanisms of non-coding regions and the current limitations of available databases and tools. Hence, we develop the non-coding variant annotation database (NCAD, http://www.ncawdb.net/), encompassing comprehensive insights into 665,679,194 variants, regulatory elements, and element interaction details. Integrating data from 96 sources, spanning both GRCh37 and GRCh38 versions, NCAD v1.0 provides vital information to support the genetic diagnosis of non-coding variants, including allele frequencies of 12 diverse populations, with a particular focus on the population frequency information for 230,235,698 variants in 20,964 Chinese individuals. Moreover, it offers prediction scores for variant functionality, five categories of regulatory elements, and four types of non-coding RNAs. With its rich data and comprehensive coverage, NCAD serves as a valuable platform, empowering researchers and clinicians with profound insights into non-coding regulatory mechanisms while facilitating the interpretation of non-coding variants.

PICOTEES: a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants from Chinese children cohorts

Xinran Dong, Yulan Lu, Lanting Guo, Chuan Li, Qi Ni, Bingbing Wu, Huijun Wang, Lin Yang, Songyang Wu, Qi Sun, Hao Zheng, Wenhao Zhou, Shuang Wang

2024, 51(2): 243-251. doi: 10.1016/j.jgg.2023.09.003

Abstract (87) PDF (5)

Abstract:
The growth in biomedical data resources has raised potential privacy concerns and risks of genetic information leakage. For instance, exome sequencing aids clinical decisions by comparing data through web services, but it requires significant trust between users and providers. To alleviate privacy concerns, the most commonly used strategy is to anonymize sensitive data. Unfortunately, studies have shown that anonymization is insufficient to protect against reidentification attacks. Recently, privacy-preserving technologies have been applied to preserve application utility while protecting the privacy of biomedical data. We present the PICOTEES framework, a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants (https://birthdefectlab.cn:3000/). PICOTEES enables privacy-preserving queries of the phenotype spectrum for a single variant by utilizing trusted execution environment technology, which can protect the privacy of the user's query information, backend models, and data, as well as the final results. We demonstrate the utility and performance of PICOTEES by exploring a bioinformatics dataset. The dataset is from a cohort containing 20,909 genetic testing patients with 3,152,508 variants from the Children's Hospital of Fudan University in China, dominated by the Chinese Han population (>99.9%). Our query results yield a large number of unreported diagnostic variants and previously reported pathogenicity.

Rare variants in FANCJ induce premature ovarian insufficiency in humans and mice

Xi Yang, Shuting Ren, Jialin Yang, Yuncheng Pan, Zixue Zhou, Qing Chen, Yunzheng Fang, Lingyue Shang, Feng Zhang, Xiaojin Zhang, Yanhua Wu

2024, 51(2): 252-255. doi: 10.1016/j.jgg.2023.03.013

Abstract (179) PDF (10)

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enOsCas12f1-mediated exon skipping for Duchenne muscular dystrophy therapy in humanized mouse model

Ming Jin, Jiajia Lin, Yu Zhang, Qingquan Xiao, Xiangfeng Kong, Xiumei Zhang, Zhurui Shao, Yin Wang, Yuyang Yu, Jinjing Li, Wan-Jin Chen, Guoling Li, Hui Yang, Ning Wang

2024, 51(2): 256-259. doi: 10.1016/j.jgg.2023.12.003

Abstract (0) PDF (0)

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GeMemiOM: the curated database on genes, putative methylation study targets, and microRNA targets for otitis media

Kondyarpu Abhishek, Bineet Kumar Mohanta, Pratima Kumari, Anshuman Dixit, Puppala Venkat Ramchander

2024, 51(2): 260-263. doi: 10.1016/j.jgg.2023.07.010

Abstract (430) PDF (41)

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2024 Vol. 51, No. 2