Biology subjects

Miyagawa, T.

Publications and source records attributed to Miyagawa, T..

6 recordsLinked to original sources

bioRxiv2026

Somatic DDX41 mutations confer neomorphic splicing activity in the pathogenesis of myelodysplastic neoplasms

Germline mutations in the RNA helicase DDX41 are the most common genetic predisposition to myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), representing 5-7% of AML. Over 70% of patients acquire a somatic mutation at specific hotspots (R525H/G530D) in the helicase domain of DDX41 in trans, which is linked to disease progression. DDX41 has diverse cellular functions, including RNA splicing, ribosome biogenesis, R-loop resolution and inflammation. However, the mechanisms by which somatic DDX41 mutations drive MDS/AML pathogenesis are yet to be determined. Here, we systematically evaluated the function of pathogenic, missense germline and somatic DDX41 mutations. We report that DDX41 somatic mutations are gain of function alleles and fail to rescue AML cell growth, distinct from germline DDX41 mutations. DDX41 somatic mutations R525H and G530D drive widespread splicing changes in isogenic AML cell lines, consistent in genetically engineered murine bone marrow HSPCs and CD34+ cells from DDX41-mutant MDS/AML patients. Mechanistically, DDX41-R525H exhibits increased RNA binding affinity compared to wildtype, with aberrantly spliced RNA targets overlapping with enriched binding. Strikingly, aberrant splicing of SEPTIN7 is enriched exclusively in CD34+ HSPCs of patients harboring both germline and somatic DDX41 mutations but absent in samples with germline mutation alone or lacking DDX41 mutations altogether. SEPTIN7 mis-splicing introduces a premature stop codon resulting in its downregulation at the protein level. SEPTIN7 is a known regulator of cytokinesis, HSC polarity and repopulation capacity. Our results identify a novel mis-spliced candidate, SEPTIN7, whose deregulation implicates a mechanism by which the DDX41 somatic mutations promote dysplastic hematopoiesis.

cancer biology↗

bioRxiv2026

Structural basis for alternative 3' splice site selection in the human spliceosome active center

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/741260v1_ufig1.gif" ALT="Figure 1"> View larger version (97K): org.highwire.dtl.DTLVardef@279388org.highwire.dtl.DTLVardef@46d636org.highwire.dtl.DTLVardef@997672org.highwire.dtl.DTLVardef@12f40ee_HPS_FORMAT_FIGEXP M_FIG C_FIG Key findingsO_LICryo-EM reveals SDE2 as a novel factor stabilizing the spliceosome active center C_LIO_LISDE2 {Delta}N structures visualize a stalled C* state with impaired docking-factor engagement. C_LIO_LISDE2, Prp18, and FAM32A read a cis-code to stabilize weaker proximal 3'-ss. C_LIO_LISDE2 {Delta}N destabilizes 3'-ss docking and rescues BRCA1 and CFTR mis-splicing in vivo. C_LI Accurate alternative splicing requires discrimination between adjacent 3' splice sites (3'-ss) during catalysis and is disrupted by pathogenic AG-gain mutations that create competing 3'-ss. Here, we present cryo-EM structures of human spliceosomes assembled on native-sequence pre-mRNAs, revealing how the catalytic core controls alternative 3'-ss selection. SDE2 is a previously unrecognized active-center component that promotes a docking-competent spliceosome conformation. Machine learning, in vivo transcriptomics, and in vitro biochemistry show how SDE2 cooperates with FAM32A and Prp18 to act as readers of a cis-regulatory code that governs 3'-ss selection during catalysis. These factors promote weaker, proximal site use by counteracting an intrinsic distal bias generated by active-site interactions with the distal-site -4 nucleotide. Structural or genetic perturbation of these exon-ligation factors destabilizes proximal 3'-ss docking and restores canonical splicing in disease-relevant CFTR and BRCA1 AG-gain alleles. Our work establishes the spliceosome active center as a tunable regulatory hub for alternative splicing.

molecular biology↗

bioRxiv2025

Passive and active demethylation in immune diseases with proliferation driving global hypomethylation

Global DNA hypomethylation is a hallmark of immune-mediated diseases, yet its regulatory significance remains unclear. Replication-associated loss of DNA methylation at solo-WCGW (W = A/T) CpGs has recently been proposed as a consequence of cell division. Here we systematically investigated genome-wide hypomethylation patterns across seven immune-mediated diseases. Most diseases exhibited global hypomethylation, particularly at solo-WCGW CpGs in transcriptionally repressed regions, potentially reflecting increased immune cell proliferation. By contrast, CpG sites whose methylation levels were associated with cytokine exposure or SNP genotypes were predominantly located in transcriptionally active regions. To investigate whether immunological events driving immune cell proliferation may also be imprinted in transcriptionally active regions, we searched for differentially methylated regions (DMRs) correlated with an index reflecting the extent of solo-WCGW hypomethylation. In narcolepsy, we identified a DMR within the T-cell receptor alpha (TRA) locus, and greater hypomethylation was associated with increased clonality of both TRA and TRB repertoires, with a similar pattern in an independent cohort. In multiple sclerosis, a DMR was also detected within the IGH locus encoding the B-cell receptor. Together, these findings suggest that the hypomethylation index captures the impact of disease-specific immune dynamics, while reflecting a shared epigenetic signature of immune cell proliferation across diseases.

genomics↗

bioRxiv2024

Sex differences in the clinical manifestation of autosomal dominant frontotemporal dementia

INTRODUCTIONSex differences are apparent in neurodegenerative diseases, but have not been comprehensively characterized in frontotemporal dementia (FTD). METHODSParticipants included 337 adults with autosomal dominant FTD enrolled in the ALLFTD Consortium. Clinical assessments and plasma were collected annually for up to six years. Linear mixed-effects models investigated how sex and disease stage associated with longitudinal trajectories of cognition, function, and neurofilament light chain (NfL). RESULTSWhile sex differences were not apparent at asymptomatic stages, females showed more rapid declines across all outcomes in symptomatic stages compared to males. In asymptomatic participants, the association between baseline NfL and clinical trajectories was weaker in females versus males, a difference that attenuated in symptomatic participants. DISCUSSIONIn genetic FTD, females show cognitive resilience in early disease stages followed by steeper clinical declines later in disease. Baseline NfL may be a less sensitive prognostic tool for clinical progression in females with FTD-causing mutations.

neuroscience↗

bioRxiv2024

Multiomics analysis of narcolepsy T cells: global hypomethylation in solo-WCGW motif linked to T cell proliferation

Narcolepsy type 1 (NT1) is a chronic sleep disorder caused by a loss of orexin-producing cells in the brain and involves autoimmune mechanisms, including the presence of autoreactive T cells. We performed a genome-wide DNA methylation analysis using CD4+ and CD8+ T cells of NT1 patients. Analysis of differentially methylated regions as well as multiomics analysis with genomic and transcriptomic data obtained from the same samples indicated that cell chemotaxis pathways are implicated as a cause in the pathogenesis of NT1. Additionally, we found global hypomethylation in both the T cells of NT1 cases (CD4+: P = 1.69E-67; CD8+: P = 4.83E-12). These NT1-associated hypomethylated sites were significantly more abundant in solo-WCGW (sequences without neighboring CpGs, where W is an A or T base; P = 9.87E-194). Solo-WCGW tends to lose DNA methylation over the course of cell divisions, suggesting enhanced T cell proliferation in NT1.

genomics↗

bioRxiv2023

Identification of Region-Specific Gene Isoforms in the Human Brain Using Long-Read Transcriptome Sequencing and Their Correlation with DNA Methylation

BackgroundSite specificity is known in neuropsychiatric disorders, and differences in gene expression patterns could potentially explain this mechanism. However, studies using long-read transcriptome sequencing to analyze gene expression in different regions of the human brain have been limited, and none have focused on the hypothalamus, which plays a crucial role in regulating autonomic functions. ResultsWe performed long-read RNA sequencing on 12 samples derived from three different brain regions of the same individuals; the cerebellum, hypothalamus, and temporal cortex. We found that, compared to other regions, many genes with higher expression levels in the cerebellum and temporal cortex were associated with neuronal pathways, whereas those with higher expression levels in the hypothalamus were primarily linked to immune pathways. In addition, we investigated genes with different major isoforms in each brain region, even with similar overall expression levels among regions, and identified several genes, such as GAS7, that express different major isoforms in different regions. Many of these genes are involved in "actin filament-based process" and "cell projection organization" pathways, suggesting that region-dependent isoforms may have distinct roles in dendritic spine and neuronal formation in each region. Furthermore, we investigated the involvement of DNA methylation in these isoforms and found that DNA methylation may be associated with isoforms that have different first exons. ConclusionsOur results provide potentially valuable findings for future research on brain disorders and shed light on the mechanisms underlying isoform diversity in the human brain.

genomics↗