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OP0153 BROADENING OUR UNDERSTANDING OF THE GENETICS OF JUVENILE IDIOPATHIC ARTHRITIS: INTERROGATION OF THREE DIMENSIONAL CHROMATIN STRUCTURES WITHIN JIA-ASSOCIATED RISK LOCI

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Annals of the Rheumatic Diseases 2019年 78卷 151-152页

作者： Haeja Kessler Evan Tarbell Yungki Park Jim Jarvis University at Buffalo Pediatrics Buffalo United States of America University at Buffalo Biochemistry Buffalo United States of America University at Buffalo Genetics Genomics and Bioinformatics Program Buffalo United States of America

Background Our group has shown that, like most complex traits, the risk loci for juvenile idiopathic arthritis (JIA) identified on genome-wide association studies (GWAS) and genetic fine mapping studies are highly enriched for enhancers. Enhancers are regulatory elements that fine-tune gene expression to specific physiologic circumstances. Enhancers do not always regulate the nearest gene, and may regulate more than one gene. Enhancers typically regulate genes within the same chromatin loop, or topologically associated domain (TAD). Objectives To gain a better understanding of the genetics of JIA by examining the broader chromatin architecture that encompasses the known risk haplotypes. Methods We used publically available chromatin conformation HiC data and the online JuiceBox software suite to query known JIA risk haplotypes for evidence of physical interactions between putative enhancers within the haplotypes and immunologically relevant genes. We specifically queried 20 haplotypes in which H3K4me1/H3K27ac marks were prominent within both lymphoid and myeloid cells. We queried data from GM12787 (B cell), K562 (lymphoblast), and THP-1 (monocyte/macrophage) cells, as well as human cord blood T cells. To identify TADs associated with specific enhancers, we used a 5KB resolution (which allowed us to visualize chromatin loops as peaks), setting the cursor at the center of each putative enhancer. We also identified the genes within the identified chromatin loop domains and used gene ontology (GO) analyses to identify functional associations among genes within the TADs incorporating the JIA risk loci. Results We identified at least one chromatin loop structure in all 20 of the JIA risk haplotypes for each of the 4 cell lines we queried. These loops were not cell type specific. That is, almost identical loops structures could be seen in each of the cell lines at each of the loci, suggesting that these enhancers regulate a broad range of common leukocyte functions. The TA

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Repurposed Nrf2 activator dimethyl fumarate rescues muscle inflammation and fibrosis in an aggravated mdx mouse model of Duchenne muscular dystrophy

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Redox Biology 2025年 84卷 103676页

作者： Stephanie Kourakis Cara A. Timpani Ryan M. Bagaric Bo Qi Benazir A. Ali Rebecca Boyer Guinevere Spiesberger Nitika Kandhari Xu Yan Jujiao Kuang Ankita Tulangekar Judy B. de Haan Deanna Deveson-Lucas Nicole Stupka Dirk Fischer Emma Rybalka Institute for Health and Sport (IHeS) Victoria University Melbourne Victoria Australia Inherited and Acquired Myopathies Program Australian Institute for Musculoskeletal Science (AIMSS) St Albans Victoria Australia Department of Medicine – Western Health Melbourne Medical School The University of Melbourne St Albans Victoria Australia Monash Genomics and Bioinformatics Platform Biomedical Discovery Institute Monash University Clayton Victoria Australia Sarcopenia Research Program Australian Institute for Musculoskeletal Science (AIMSS) St Albans Victoria Australia Basic Science Domain Oxidative Stress Laboratory Baker Heart and Diabetes Institute Melbourne Victoria Australia Baker Department of Cardiometabolic Health University of Melbourne Parkville Victoria Australia Division of Neuropediatric and Developmental Medicine University Children's Hospital of Basel (UKBB) Basel Switzerland

In inherited neuromuscular disease, Duchenne muscular dystrophy (DMD), glucocorticoids significantly slow disease progression yet impart side effects severe enough to preclude use in a significant proportion of patients. Extending our findings that acute treatment with FDA approved multiple sclerosis drug, dimethyl fumarate (DMF), rescues muscle pathology in juvenile mdx mice, we aimed to conduct tiered pre-clinical testing toward translation. To aggravate disease phenotype in adult mdx muscles that usually lack human equivalent muscle pathology, we used bi-weekly treadmill running for 4 weeks which increased plasma DMD biomarker, creatine kinase, by 2-fold and quadriceps fibrosis by ∼30 %. Using this model, we screened DMF for 5 weeks in a head-to-head comparison, and in combination, with standard-of-care prednisone (PRED), to model the most likely clinical trial scenario. We show comparable efficacy between DMF and PRED at reducing inflammation via NF-κB suppression and CD68 + macrophage infiltration. Moderate term DMF monotherapy had additional anti-fibrotic and anti-lipogenic effects on skeletal and cardiac muscle beyond those seen with PRED treatment, although combination therapy exacerbated fibrosis in quadriceps. Our study supports DMF as a repurposing candidate for DMD, especially for patients who cannot tolerate chronic glucocorticoid treatment. We also highlight the importance of evaluating combination therapy to identify potential off-target effects between emerging therapeutics and glucocorticoids towards better designed clinical trials.

关键词： Duchenne muscular dystrophy Dimethyl fumarate Therapeutics Muscle pathology

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A Bayesian mixture model for clustering on the stiefel manifold

arXiv

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arXiv 2017年

作者： Sengupta, Subhajit Pal, Subhadip Mitra, Riten Guo, Ying Banerjee, Arunava Ji, Yuan Program for Computational Genomics and Medicine NorthShore University HealthSystem Department of Bioinformatics and Biostatistics University of Louisville Department of Biostatistics and Bioinformatics Emory University Department of Computer and Information Science and Engineering University of Florida Department of Public Health Sciences University of Chicago

Analysis of a Bayesian mixture model for the Matrix Langevin distribution on the Stiefel manifold is presented. The model exploits a particular parametrization of the Matrix Langevin distribution, various aspects of which are elaborated on. A general, and novel, family of conjugate priors, and an efficient Markov chain Monte Carlo (MCMC) sampling scheme for the corresponding posteriors is then developed for the mixture model. Theoretical properties of the prior and posterior distributions, including posterior consistency, are explored in detail. Extensive simulation experiments are presented to validate the efficacy of the framework. Real-world examples, including a large scale neuroimaging dataset, are analyzed to demonstrate the computational tractability of the approach. Copyright © 2017, The Authors. All rights reserved.

关键词： Mixtures

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The ESCRT protein CHMP5 promotes T cell leukemia by enabling BRD4-p300-dependent transcription

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Nature Communications 2025年第1期16卷 1-19页

作者： Umphred-Wilson, Katharine Ratnayake, Shashikala Tang, Qianzi Wang, Rui Chaudhary, Sneha Ghosh Ballachanda, Devaiah N. Trichka, Josephine Wisniewski, Jan Zhou, Lan Chen, Qingrong Meerzaman, Daoud Singer, Dinah S. Adoro, Stanley Experimental Immunology Branch National Cancer Institute National Institutes of Health Bethesda 20892 MD United States Immunology Training Program Department of Pathology Case Western Reserve University School of Medicine Cleveland 44106 OH United States Computational Genomics and Bioinformatics Branch Center for Biomedical Informatics & Information Technology National Cancer Institute National Institutes of Health Bethesda 20850 MD United States College of Animal Science and Technology Sichuan Agricultural University Chengdu 611130 China Department of Pathology and Genomic Medicine Houston Methodist Hospital Houston 77030 TX United States

Addiction to oncogene-rewired transcriptional networks is a therapeutic vulnerability in cancer cells, underscoring a need to better understand mechanisms that relay oncogene signals to the transcriptional machinery. Here, using human and mouse T cell acute lymphoblastic leukemia (T-ALL) models, we identify an essential requirement for the endosomal sorting complex required for transport protein CHMP5 in T-ALL epigenetic and transcriptional programming. CHMP5 is highly expressed in T-ALL cells where it mediates recruitment of the coactivator BRD4 and the histone acetyl transferase p300 to enhancers and super-enhancers that enable transcription of T-ALL genes. Consequently, CHMP5 depletion causes severe downregulation of critical T-ALL genes, mitigates chemoresistance and impairs T-ALL initiation by oncogenic NOTCH1 in vivo. Altogether, our findings uncover a non-oncogene dependency on CHMP5 that enables T-ALL initiation and maintenance. © This is a U.S. Government work and not under copyright protection in the US;foreign copyright protection may apply 2025.

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KAREBrowser: SNP database of Korea Association REsource project

KAREBrowser: SNP database of Korea Association REsource proj...

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IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Chang Bum Hong Young Jin Kim Sanghoon Moon Young-Ah Shin Yoon Shin Cho Jong-Young Lee Division of Structural and functional Genomics Center for Genome Science National Institute of Health Seoul South Korea Interdisciplinary Program in bioinformatics Seoul National University Seoul South Korea

International HapMap Project and the Human Genome Diversity Project (HGDP) provide plentiful resources on human genome information for the public. However, these kinds of information available from HapMap and HGDP are limited mainly due to the small size of samples in both databases. Recently we conducted genome-wide association study (GWAS) with 8,842 Korean subjects (Cho et al., Nature Genetics 2009). In an effort to build a publicly available browsing system for genome data resulted from our large scale GWAS, we developed the browser, namely Korea Association REsource (KARE) browser. This browser provides users with a large scale of single nucleotide polymorphisms (SNP) information comprising 1.5 million SNPs from population-based cohorts of 8,842 samples. KAREBrowser was based on the generic genome browser (GBrowse) that is a web-based application tool developed for users to navigate and visualize the genomic features and annotations in an interactive manner. All SNP information and related functions are available at the web site http://***/karebrowser/.

关键词： bioinformatics genomics Databases Browsers Couplings Humans

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BioSMACK: A linux Live CD for analysis of genome-wide association

BioSMACK: A linux Live CD for analysis of genome-wide associ...

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IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Chang Bum Hong Young Jin Kim Sanghoon Moon Young-Ah Shin Min Jin Go Jong-Young Lee Yoon Shin Cho Division of Structural and functional Genomics Center for Genome Science National Institute of Health Seoul South Korea Interdisciplinary Program in bioinformatics Seoul National University Seoul South Korea

Recent advancement of high-throughput genotyping technologies has enabled us to carry out a genome-wide association study (GWAS) in a large cohort. However, analyzing millions of single nucleotide polymorphisms (SNP) is still a troublesome task for researchers to encounter in conducting GWAS. Several difficulties in using analysis tools are one of the major challenges for researchers such as compatibility and dependencies during installation process of softwares. This is a huge obstacle to research institute without computing facilities and specialists. Thus proper research environment is an urgent demand for researchers working on GWAS. We developed BioSMACK to provide research environment for GWAS with no configuration and easy usage. BioSMACK is based on Ubuntu Live CD that offers complete linux-based operating system environment without installation. Moreover, we provide users with GWAS manual that is consist of series of guidelines for GWAS and useful examples. BioSMACK is freely available at http://***/biosmack.

关键词： bioinformatics genomics Linux Metals Operating systems Manuals

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Resolving p53 to Create Clinically-Relevant Mutation Models

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Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada 2023年第1期29卷 1087-1090页

作者： Solares, Maria J. Jonaid, G.M. Kelly, Deborah F. Molecular Cellular Integrative Biosciences Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park PA United States Department of Biomedical Engineering Pennsylvania State University University Park PA United States Center for Structural Oncology Pennsylvania State University University Park PA United States Bioinformatics and Genomics Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park PA United States

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The phase separation of SGS3 regulates antiviral immunity and fertility in Arabidopsis

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Science China(Life Sciences) 2023年第8期66卷 1938-1941页

作者： Yujie Han Xiaolin Zhang Ran Du Xiaoyi Shan Daoxin Xie MOE Laboratory of Bioinformatics Tsinghua-Peking Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing 100084China Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program School of Life SciencesTsinghua UniversityBeijing 100084China Shenzhen Branch of Guangdong Laboratory for Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China

Dear Editor,As a conserved mechanism among eukaryotic organisms,RNA silencing is vital for suppressing gene expression at the transcriptional or posttranscriptional level to regulate multiple biological *** interfering RNAs(si RNAs)generated by Dicer proteins integrate with Argonaute(AGO)to form an RNA-induced silencing complex(RISC),in which RNA/DNA could be degraded/methylated through a sequence-specific manner(Ding et al.,2004).

关键词： immunity separation

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0414 Recurrent chimeric transcripts in human and mouseGet access

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Journal of Animal Science 2016年第SUPPL_5期94卷 200–201页

作者： Djebali, S. Rodríguez Martín, B. Palumbo, E. Pervouchine, D. D. Breschi, A. Davis, C. Dobin, A. Alonso, G. Rastrojo, A. Aguado, B. Gingeras, T. R. Guigó, R. GenPhySE INRA Castanet-Tolosan France Universitat Pompeu Fabra (UPF) Barcelona Spain Bioinformatics and Genomics Program Centre for Genomic Regulation (CRG) Barcelona Spain Cold Spring Harbor Laboratory Functional Genomics NY Centro de Biología Molecular Severo Ochoa (CSIC- UAM) Madrid Spain

The formation of chimeric transcripts (chimeras) has been widely reported. Some of them reflect underlying chromosomal rearrangements, or are the results of the propensity of reverse transcriptase to engage in template switching, however, a proportion of cases genuinely appear to correspond totrans-splicing of RNAs, as has previously been *** we use ENCODE and mouse ENCODE deeply sequenced and bio-replicated RNaseq data from 18 human and 30 mouse samples, and the ChimPipe program, to identify chimeras occurring in multiple biological samples (recurrent), and between the same pairs of genes in human and mouse, since they are more likely to be transcriptionally induced and *** common chimeras tend to connect gene pairs located on the same chromosome and relatively near to each other ( < 100kb), therefore pointing to polymerase read-through, however interchromosomal chimeras are also observed, pointing totrans-splicing. Importantly, these recurrent chimeras tend to maintain an open reading frame, and could therefore generate chimeric proteins. We also observe that not only the gene-to-gene connection is conserved, but strikingly so are specific junction sites. The genes connected in common chimeras tend to be involved in morphogenesis and body plan formation, and consistently tend to be detected in cell lines of embryonic *** of human chimeras by RT-PCR yielded a success rate of 50%, and subsequent cloning and sequencing revealed novel transcript structures, of which some preserve the domains from the two parent genes. Applying this method to multiple animal species and breeds will help us understanding chimera evolution as well as reveal some links between genotype and phenotype.

关键词： chimeras transcripts trans-splicing

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Ex vitro rooting of minicutting of Carica papaya L. single shoot from tissue culture

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In Vitro Cellular and Developmental Biology - Plant 2023年第3期59卷 393-400页

作者： Chen, Yu-Ting Yang, Tun-Han Yu, Tsong-Ann Ph.D. Program in Medical Biotechnology National Chung Hsing University 145 Xingda Rd. South Dist Taichung City 402 Taiwan Institute of Genomics and Bioinformatics National Chung Hsing University 145 Xingda Rd. South Dist Taichung City 402 Taiwan Department of Biomedical Sciences Da-Yeh University 168 University Rd Changhua County Dacun Township 515 Taiwan

Papaya (Carica papaya L.) is an important economic crop. An efficient and low-cost propagation ex vitro process is required for commercial papaya plantlet production. In this study, a propagation process of papaya was established by minicutting and evaluating parameters affecting survival. Individual shoots (1.5 cm) were cut from papaya multiple shoots in vitro as the minicuttings. After dipping in 400.0 mg L⁻¹ indole-3-butyric acid (IBA), they were planted into the nursery pro trays with 104 holes containing vermiculite, perlite, and King Root® substrate at 1:1:1 ratio, and then covered with a lid to keep the ratio of humidity (RH) at 100% for root development. After a 3-wk treatment in a growth chamber (28°C), the rooting rate, root number, root length, and stem length were promoted to 91.1%, 2.9, 3.71 cm, and 1.88 cm, respectively. Combining the treatment with 400 mg L⁻¹ IBA and 1/2 Murashige and Skoog (MS) salt solution supplemented at the 14th day after cutting gives the best growth potential for papaya plantlets, especially increasing root length to 4.55 cm. It also effectively enhances the survival rate of plantlets to 93.3%. This process saves the rooting initiation medium and time cost and avoids the complicated procedure of cleaning medium from root surface, which results in root damage. Under this minicutting process, the papaya plantlets thrived and were optimally suited to field cultivation. © 2023, The Society for In Vitro Biology.

关键词： Ex vitro Minicutting Papaya rooting Survival rate

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