Biology subjects

Hagiwara, K.

Publications and source records attributed to Hagiwara, K..

7 recordsLinked to original sources

bioRxiv2026

Reactivation of a TAL1 progenitor cell enhancer region by non-coding somatic variants in T-lineage acute lymphoblastic leukemia

Aberrant activation of TAL1, a key oncogenic driver, defines a major subgroup comprising [~]30% of childhood T-lineage acute lymphoblastic leukemias (T-ALLs). We and others have shown that somatic non-coding mutations within upstream and intronic cis-regulatory regions of TAL1 contribute to transformation by creating binding sites for MYB and other transcription factors. Here we investigated cis-regulatory mechanisms mediated by somatic mutations occurring in an intergenic region located 29 kilobase pairs downstream of the canonical TAL1 transcription initiation site, implicated in 6% of TAL1-expressing T-ALLs. These somatic variants include i) complex indels resulting in de novo MYB transcription factor binding sites (TFBSs) and ii) internal tandem duplications (ITDs) encompassing canonical MYB TFBSs. Chromatin immunoprecipitation sequencing (ChIP-seq) revealed binding of the TAL1 core regulatory circuit (CRC) transcription factors MYB, GATA3, and RUNX1, resulting in enhancer activity mediated by sequences with the mutant allele. Strikingly, ChIP-seq peaks for the repressive H3K27me3 mark and the active H3K27ac mark co-existed across TAL1 regulatory sequences but enriched for different haplotypes. TAL1 transcription from the mutant haplotype initiated from a promoter located within exon 4 of the canonical TAL1 transcript, resulting in a short isoform normally expressed by hematopoietic stem cells (HSC). Interestingly, neither the isoform expression nor the enhancer activity could be predicted by the sequence-to-function deep learning artificial intelligence (AI) model AlphaGenome, emphasizing the importance of experimental validation. Our findings indicate that selection for cis-regulatory, non-coding variants leads to reactivation of enhancers normally active in HSC but silenced in differentiated lineages during normal hematopoietic cell development.

cancer biology↗

bioRxiv2026

In vivo xenogenic reconstitution of human alveolar epithelial architecture and function

An urgent need exists for lung models that accurately replicate human physiological profiles. We developed a chimeric mouse model enabling targeted ablation of alveolar type 2 (AT2) cells and lung macrophages, creating niches for endoscopically transplanted human induced pluripotent stem cell (hiPSC)-derived lung progenitors (hLPs). These engrafted cells were retained for 24 weeks, demonstrating self-renewal and differentiation potential, surfactant protein secretion, and maintaining alveolar phosphate homeostasis, suggesting their maturation into AT2 cells. Furthermore, transplantation of hLPs derived from disease-specific hiPSCs recapitulated the phenotype of pulmonary alveolar microlithiasis. The architecture, function, and metabolism of human alveolar epithelium were accurately replicated in vivo. This model has the potential to link experimental models and first-in-human studies, facilitating the development of novel therapies for intractable lung diseases.

developmental biology↗

bioRxiv2025

Confounding factors in assessing the enriched expression of somatic mutant allele in bulk tumor samples

Allele-specific expression (ASE) of somatic mutations can be caused by cis-activation of the mutant allele or silencing of the wildtype allele and has been investigated by examining the enrichment of mutant allele in RNA relative to DNA. Here we show that this mutation-based approach can be confounded by gene expression differences in tumor and normal cells which co-exist in most bulk tumor samples. We modeled mutant allele expression by incorporating tumor/normal expression difference, mutant allele dosage, tumor purity, and nonsense-mediated decay (NMD) efficiency, projecting that the enrichment can occur without ASE. This confounding effect is exacerbated with low tumor purity and is dependent on mutant allele dosage for NMD-sensitive mutations. The model was validated empirically using somatic insertions/deletions (indels) from 9,101 the Cancer Genome Atlas (TCGA) samples, showing three-fold higher enrichment in driver genes vs. non-drivers. To explore if the enriched mutant allele expression can be leveraged to complement DNA-based somatic mutation detection, we performed de novo somatic indel calling using TCGA RNA-Seq, increasing the TCGA driver indel repertoire by [~]14%, mostly in samples with lower tumor purity. Our study not only revealed confounding factors in ASE analysis but also demonstrated the utility of leveraging RNA-Seq for driver mutation analysis.

bioinformatics↗

bioRxiv2024

N-Acetylglucosamine Facilitates Coordinated Myoblast Flow, Forming the Foundation for Efficient Myogenesis

Skeletal muscle comprises 30-40% of a mammals body mass, maintaining its integrity through efficient muscle fiber regeneration, which involves myoblast differentiation into myotubes. Previously, we reported that N-acetylglucosamine (GlcNAc) promotes myogenesis in C2C12 cells, although the underlying mechanisms were unclear. UDP-GlcNAc, the activated form of GlcNAc, is critical for the biosynthesis of highly branched (N-acetyllactosamine-rich) N-linked oligosaccharides, which are recognized by galectin-3 (Gal-3), facilitating dynamic cell-cell and cell-matrix interactions. In this study, we used primary myoblasts from wild-type and Gal-3 null (Gal-3KO) mice, observing myotube formation through long-term live-cell imaging and single-cell tracking. We found that GlcNAc enhances myoblast fusion in a dose-dependent manner, and the addition of Gal-3 with GlcNAc leads to the formation of larger myotubes. Gal-3KO myoblasts exhibited a reduced capacity for myotube formation, a deficiency that was rectified by supplementing with GlcNAc and Gal-3. Our results highlight the critical role of Gal-3 interaction with oligosaccharides whose synthesis was promoted by GlcNAc in facilitating myotube formation. Single-cell tracking revealed that GlcNAc and Gal-3 increase myoblast motility, creating a faster-coordinated cell flow--a directed movement of myoblasts, along which myotubes form through cell fusion. Interestingly, myoblasts contributing to myotube formation were pre-positioned along the eventual shape of the myotubes before the establishment of the coordinated flow. These myoblasts moved along the flow, paused, and even moved against the flow, suggesting that both flow and initial positioning play roles in aligning myoblasts into the shape of a myotube. Overall, our findings demonstrate that GlcNAc, in conjunction with Gal-3, enhances myotube formation by fostering an environment conducive to myoblast positioning, establishing coordinated flow, and facilitating fusion. This suggests potential therapeutic applications of GlcNAc in muscle repair and muscle disorders.

cell biology↗

bioRxiv2024

Genetic investigation of GPI anchored Bd37 orthologs in Babesia divergens group and use of recombinant protein for ecological survey in deer.

The Glycosylphosphatidylinositol (GPI) anchored protein group has great potential as an excellent immunodiagnostic marker, because of its high expression and necessity for parasite survival. Babesia divergens /B. capreoli group includes parasites with confirmed or possible zoonotic potential to cause human babesiosis. In this study, we investigated ortholog of Bd37, a GPI-anchored major merozoite surface protein of B. divergens sensu stricto, in the Asia lineage of the B. divergens /B. capreoli group. From two genomic isolates from sporozoites/sporoblasts, three Bd37 gene variants, namely Bd37 JP-A, JP-B, and JP-C, were isolated with 62.3% -64.1% amino acid sequences identity. Discriminative blood direct PCR revealed that JP-A was exclusively encoded in all parasites infecting wild sika deer examined (n=22). While JP-B and JP-C genes were randomly detected in 12 and 11 specimens, respectively. Recombinant JP-A-based ELISA showed an overall positive rate of 13.9% in deer in Japan from north (Hokkaido) to south (Kyushu islands) (24 prefectures, n=360). This positive rate was twice as high as that examined by 18S rRNA-based PCR (6.8%). Antibodies against recombinant JP-B and JP-C were also evident in the deer. This study demonstrated that the presence of three orthologs in the Bd37 gene family in Asia lineage and identified JP- A as an informative marker for serological surveys in Japan. This is the first report that diagnostic antigen of Babesia parasite was identified by a comprehensive analysis of genetic polymorphisms from a various developmental stage in host and vector... ImportanceBabesia divergens Asia lineage in B. divergens/ B. capreoli group is a parasite closely related to zoonotic pathogen B. divergens sensu strict (EU lineage) and Babesia sp. MO1(US-lineage). Large scale serodiagnostic system for this group has not been established. As the nature of the parasites antigenic differentiation to escaping from immunological attack in the host, investigation of diagnostic markers should consider such antigenic diversity inherited (circulating) in the population. We focused on the Glycosylphosphatidylinositol (GPI) anchor protein, Bd37, a major surface protein of the EU lineage, and investigated Asia lineage infecting sika deer and taiga tick in Japan. Three Bd37 ortholog genes (JP-A, JP-B, and JP-C) were isolated from the tick and deer, though only JP-A gene was exclusively encoded in the parasites genomes (n=36). In spite of sequence polymorphism in the N-terminal region, the antibody raised against the representative recombinant antigen, rJP-A2, reacted to various JP- A proteins. rJP-A2-based ELISA system revealed a positive rate in wild sika deer was 13.9% which is two times higher than that examined by genetic examination (PCR). GPI-anchored proteins are densely expressed and required for parasite survival. We showed GPI proteins including Bd37 and its ortholog are potentially excellent immunodiagnostic markers for emerging and growing human babesiosis.

microbiology↗

bioRxiv2020

Color morphs of the coral, Acropora tenuis, show different responses to environmental stress and different expression profiles of fluorescent-protein genes

Corals of the family Acroporidae are key structural components of reefs that support the most diverse marine ecosystems. Due to increasing anthropogenic stresses, coral reefs are in decline. Along the coast of Okinawa, Japan, three different color morphs of Acropora tenuis have been recognized for decades. These include brown (N morph), yellow-green (G) and purple (P) forms. The tips of axial coral polyps exhibit specific fluorescence spectra. This attribute is inherited asexually, and color morphs do not change seasonally. In Okinawa Prefecture, during the summer of 2017, the N and P morphs experienced bleaching, in which some N morphs died while P morphs recovered. In contrast, G morphs successfully withstood the stress. Symbiotic dinoflagellates are essential symbiotic partners of scleractinian corals. Photosynthetic activity of symbionts was reduced in July in N and P morphs; however, the three color-morphs host similar sets of Clade-C zoothanthellae, suggesting that beaching of N and P morphs cannot be attributed to differences in symbiont clades. The decoded Acropora tenuis genome includes five genes for green fluorescent proteins (GFP), two for cyan fluorescent proteins (CFP), three for red fluorescent proteins (RFP), and seven genes for chromoprotein (ChrP). A summer survey of gene expression profiles demonstrated that (a) expression of CFP and REP was quite low in all three morphs, (b) P morphs expressed higher levels of ChrP, (c) both N and G morphs expressed GFP highly, and (d) GFP expression was reduced in N morphs, compared to G morphs, which maintained higher levels of GFP expression throughout the summer. Although further studies are required to understand the biological significance of these color morphs of Acropora tenuis, our results suggest that thermal stress resistance is modified by genetic mechanisms that coincidentally lead to diversification of color morphs.

evolutionary biology↗

bioRxiv2019

RNAIndel: a machine-learning framework for discovery of somatic coding indels using tumor RNA-Seq data

Reliable identification of expressed somatic insertion/deletion (indels) is an unmet demand due to artifacts generated in PCR-based RNA-Seq library preparation and the lack of normal RNA-Seq data, presenting analytical challenges for discovery of somatic indels in tumor trasncriptome.\n\nBy implementing features characterized by PCR-free whole-genome and whole-exome sequencing into a machine-learning framework, we present RNAIndel, a tool for predicting somatic, germline and artifact indels from tumor RNA-Seq data alone. RNAIndel robustly predicts 87{square}93% of somatic indels from 235 samples with heterogeneous conditions, even recovering subclonal (VAF range 0.01-0.15) driver indels missed by targeted deep-sequencing, outperforming the current best-practice for RNA-Seq variant calling which had 57% sensitivity but with 12 times more false positives.\n\nRNAIndel is freely available at https://github.com/stjude/RNAIndel\n\nContactjinghui.zhang@stjude.org

bioinformatics↗