Biology subjects

Hirakawa, Y.

Publications and source records attributed to Hirakawa, Y..

9 recordsLinked to original sources

bioRxiv2026

REN-former prioritizes candidate regulators of kidney disease-state transitions through single-cell foundation modeling and human genetics

Background Acute kidney injury (AKI)-to-chronic kidney disease (CKD) transition is associated with dynamic changes in tubular cell state. However, conventional single-cell transcriptomic analyses primarily identify genes differentially expressed between disease states and do not directly evaluate genes associated with directional transitions between cellular states. Methods We developed REN-former by fine-tuning Geneformer using the GSE183276 single-cell RNA-sequencing dataset from 45 participants representing Normal Reference, AKI, and CKD states. In silico gene deletion and overexpression analyses were used to estimate directional transcriptomic shifts, with a focus on proximal tubular cells. Selected genes were evaluated using summary-data-based Mendelian randomization (SMR), colocalization and expression analysis in additional KPMP participants not included in GSE183276. Results REN-former achieved recall values of 0.99, 0.80, and 0.79 for Normal Reference, AKI, and CKD, respectively. In silico perturbation analyses identified distinct gene programs associated with transitions from Normal Reference to AKI, from Normal Reference to CKD, from AKI to CKD, and from CKD to Normal Reference. Conventional analysis showed metabolic suppression and increased inflammatory and stress-response activation. SMR identified IFITM3, CALR, TTR, CALM1, MUC13, and RPL13, and colocalization supported IFITM3, CALR, TTR, and CALM1. In additional KPMP data, IFITM3 was higher, whereas TTR and CALM1 were lower, in CKD proximal tubules; CALR did not differ significantly. The observed expression changes were concordant with the REN-former-predicted directions for TTR and CALM1 but discordant for IFITM3. Conclusion REN-former provides a framework for prioritizing candidate regulators of kidney disease-associated cell states by integrating predicted perturbation effects with human genetic and transcriptomic evidence.

bioinformatics↗

bioRxiv2026

Initiation of asexual reproduction by the AP2/ERF gene GEMMIFER in Marchantia polymorpha

Plants can propagate their own clones through asexual reproduction. Genetic and hormonal factors regulating asexual reproduction have begun to be elucidated in the liverwort Marchantia polymorpha, which produce asexual propagules called gemmae within the gemma cups. Here, we report an AP2/ERF family gene, GEMMIFER (MpGMFR), as a key regulator of asexual reproduction in M. polymorpha. Suppression of MpGMFR function using genome editing and amiRNA results in the loss of gemma and gemma cup formation. In contrast, activation of MpGMFR function using a dexamethasone inducible system promotes gemma and/or gemma cup formation depending on the induction conditions. Notably, transient strong activation of MpGMFR induced gemma initial cells at the meristem, which develop into mature gemmae capable of reproducing as new individuals after detachment. These results show that MpGMFR is necessary and sufficient for the initiation of asexual reproduction at the meristem. MpGMFR expression was detected from the meristem through to the early stages of gemma development including the gemma cup floor cells. MpGMFR expression precedes the expression of GEMMA CUP-ASSOCIATED MYB1 (MpGCAM1) in early gemma development, supporting the notion that MpGMFR initiates asexual reproduction. We anticipate this finding to be a foundation to study the evolution of extra meristem formation in plant bodies that may have made a significant contribution to the prosperity of plants on land.

plant biology↗

bioRxiv2025

The minimal cell-cycle control system in Marchantia as a framework for understanding plant cell proliferation

The regulation of cell division is broadly conserved across eukaryotes, governed by cyclins and cyclin-dependent kinases (CDKs) to coordinate progression through the cell cycle. Plants have evolved a complex set of cell-cycle genes with unique features. The high number of cyclin-CDK pairs in flowering plants complicates functional studies due to redundancy and diversification. It is critical to study simple systems in other plant lineages to better understand the functional integration of the cell-cycle control machinery and its evolution across land plants. Through a comprehensive phylogenetic analysis, we show that non-seed plants possess a simple repertoire of cyclin and CDK proteins, suggesting that the observed complexity in seed plants is a derived trait. The liverwort Marchantia polymorpha possesses a streamlined set of core cell cycle genes with minimal redundancy during vegetative development. Using single-cell RNA-seq and fluorescent reporters, we found a precise, phase-specific expression pattern for cell cycle genes. We demonstrated in vivo that only three cyclins are active, one at a given phase, without redundancy. Functional analyses revealed that MpCYCD;1 promotes cell cycle re-entry and disrupts differentiation, while overexpression of MpCYCA or MpCYCB;1 arrests the cell cycle, consistent with their respective roles at G1, S, and G2/M progression. Our findings highlight the functional conservation of mechanisms for cell-cycle control across eukaryotes and provide insights into its ancestral state, revealing a minimal set of functional components required for multicellular development. This study advances our understanding of fundamental aspects of cell-cycle regulation and opens new possibilities for engineering plant growth.

plant biology↗

bioRxiv2024

Conserved role of the SERK-BIR module in development and immunity across land plants

SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASES (SERKs), which are subfamily II of leucine-rich repeat receptor-like kinases (LRR-RLKs), play diverse roles in development and immunity in the angiosperm Arabidopsis thaliana. AtSERKs act as co-receptors for many LRR-RLKs, including BRASSINOSTEROID INSENSITIVE 1 (BRI1) and FLAGELLIN SENSITIVE 2 (FLS2).1-4 The conserved tyrosine (Y) residue in AtSERK3 is crucial for signaling specificity in differentiating BRI1- and FLS2-mediated pathways.5 BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1)-INTERACTING RECEPTOR-LIKE KINASES (BIRs) interact with SERKs under resting conditions, negatively regulating SERK-mediated pathways.6,7 SERK and BIR are highly conserved in land plants, whereas BRI1 and FLS2 homologs are absent or poorly conserved in bryophyte lineages.8,9 The biological functions of SERK homologs in non-flowering plants are largely unknown. The genome of the liverwort Marchantia polymorpha encodes single homologs for SERK and BIR, namely MpSERK and MpBIR.9 We here show that Mpserk disruptants display growth and developmental defects with no observable sexual or vegetative reproduction. Complementation analysis revealed a contribution of the conserved Y residue of MpSERK to growth. Proximity labelling-based interactomics identified MpBIR as a MpSERK interactor. Mpbir disruptants displayed defects in reproductive organ development. Patterns of development- and immunity-related gene expression in Mpserk and Mpbir were antagonistic, suggesting that MpBIR functions as a MpSERK repressor. The pathogenic bacterium Pseudomonas syringae pv. tomato DC3000 grew poorly on Mpbir, indicating a significant role of the MpSERK1MpBIR module in immunity. Taken together, we propose that the SERK-BIR functional module was already regulating both development and immunity in the last common ancestor of land plants.

plant biology↗

bioRxiv2023

Encyclopaedia of DNA polymerases localized in organelles: Contribution of genes from diverse bacteria including the proto-mitochondrion.

DNA polymerases (DNAPs) synthesize DNA from deoxyribonucleotides in a semi-conservative manner and serve as the core of DNA replication and repair machineries. In eukaryotic cells, there are two genome-containing organelles, mitochondria and plastids, that were derived from an -proteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids, both organelles must be served by nucleus-encoded DNAPs that localize and work in them to maintain their genomes. The evolution of organellar DNAPs has yet to be fully understood because of two unsettled issues. First, the diversity of organellar DNAPs has not been elucidated in the full spectrum of eukaryotes. Second, it is unclear when the DNAPs that were used originally in the endosymbiotic bacteria giving rise to mitochondria and plastids were discarded, as the organellar DNAPs known to date show no phylogenetic affinity to those of the extant -proteobacteria or cyanobacteria. In this study, we identified from diverse eukaryotes 134 family A DNAP sequences, which were classified into 10 novel types, and explored their evolutionary origins. The subcellular localizations of selected DNAPs were further examined experimentally. The results presented here suggest that the diversity of organellar DNAPs has been shaped by multiple transfers of the PolI gene from phylogenetically broad bacteria, and their occurrence in eukaryotes was additionally impacted by secondary plastid endosymbioses. Finally, we propose that the last eukaryotic common ancestor may have possessed two mitochondrial DNAPs, POP and a candidate of the direct descendant of the proto-mitochondrial DNAP, rdxPolA, identified in this study.

evolutionary biology↗

bioRxiv2023

Control of stem cell behavior by CLE-JINGASA signaling in the shoot apical meristem in Marchantia polymorpha

Land plants undergo indeterminate growth by the activity of meristems in both gametophyte (haploid) and sporophyte (diploid) generations1-3. In the sporophyte of the flowering plant Arabidopsis thaliana, the apical meristems are located at the shoot and root tips, in which a number of regulatory gene homologs are shared for their development, implying deep evolutionary origins4-7. However, little is known about their functional conservation with gametophytic meristems in distantly related land plants such as bryophytes8-17, even though genomic studies have revealed the subfamily-level diversity of regulatory genes is mostly conserved throughout land plants18-23. Here we show that a NAM/ATAF/CUC (NAC) domain transcription factor, JINGASA (MpJIN), acts downstream of CLV3/ESR-related (CLE) peptide signaling and controls stem cell behavior in the gametophytic shoot apical meristem of the liverwort Marchantia polymorpha. We found that MpJIN shows heterogeneous expression in space and time within the stem cell zone, associated with the loss and de novo specification of stem cell identity at the branching event. Consistent with the expression pattern, induction of MpJIN results in ectopic periclinal cell division in the stem cell zone and meristem termination. Comparative expression analysis suggests that the function of JIN/FEZ subfamily genes was shared between the shoot apical meristems in the gametophyte and sporophyte generations in early land plants but was lost in certain lineages including the flowering plant A. thaliana.

plant biology↗

bioRxiv2021

In vivo study on the healing of bone defect treated with non-thermal atmospheric pressure gas discharge plasma

Medical treatment using non-thermal atmospheric pressure gas discharge plasma is rapidly gaining recognition. Gas discharge plasma is thought to generate highly reactive species in an ambient atmosphere, which could be exposed to biological targets (e.g., cells and tissues). If plasma-generated reactive species could stimulate bone regeneration, gas discharge plasma could provide a new treatment opportunity in regenerative medicine. We investigated the impact of plasma on bone regeneration using a large bone defect in model rabbits and simple atmospheric pressure plasma (helium microplasma jet). We tracked the recovery progress of the large bone defects by X-ray imaging over eight weeks. The X-ray results showed a clear difference in the filling of the large bone defect among groups with different plasma treatment times, whereas filling was not substantial in the untreated control group. According to the results of micro-computed tomography analysis at eight weeks, the most successful bone regeneration was achieved using a plasma treatment time of 10 min, wherein the new bone volume was 1.51 times larger than that in the control group. Overall, these results suggest that non-thermal atmospheric pressure gas discharge plasma is promising for fracture treatment.

pathology↗

bioRxiv2021

An evolutionarily conserved coreceptor gene is essential for CLAVATA signaling in Marchantia polymorpha

Growth and development of land plants are controlled by CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) family of peptide hormones. In contrast to the genetic diversity of CLE family in flowering plants, the liverwort Marchantia polymorpha possesses a minimal set of CLE, MpCLE1(TDIF homolog) and MpCLE2 (CLV3 homolog). MpCLE1 and MpCLE2 peptides exert distinct function at the apical meristem of M. polymorpha gametophyte via specific receptors, MpTDIF RECEPTOR (MpTDR) and MpCLAVATA1 (MpCLV1), respectively, both belonging to the subclass XI of leucine-rich repeat receptor-like kinases (LRR-RLKs). Biochemical and genetic studies in Arabidopsis have shown that TDR/PXY family and CLV1/BAM family recognize the CLE peptide ligand in a heterodimeric complex with a member of subclass-II coreceptors. Here we show that three LRR-RLK genes of M. polymorpha are classified into subclass II, representing three distinct subgroups evolutionarily conserved in land plants. To address the involvement of subclass-II coreceptors in M. polymorpha CLE signaling, we performed molecular genetic analysis on one of them, MpCLAVATA3 INSENSITIVE RECEPTOR KINASE (MpCIK). Two knockout alleles for MpCIK formed narrow apical meristems marked by promMpYUC2:GUS marker, which were not expanded by MpCLE2 peptide treatment, phenocopying Mpclv1. Loss of sensitivity to MpCLE2 peptide was also observed in gemma cup formation in both Mpclv1 and Mpcik. Biochemical analysis using a Nicotiana benthamiana transient expression system revealed weak association between MpCIK and MpCLV1, as well as MpCIK and MpTDR. While MpCIK may also participate in MpCLE1 signaling, our data show that the conserved CLV3-CLV1-CIK module functions in M. polymorpha, controlling meristem activity for development and organ formation for asexual reproduction.

plant biology↗

bioRxiv2019

Dual Role of Jam3b in Early Hematopoietic and Vascular Development

In order to efficiently derive hematopoietic stem cells (HSCs) from pluripotent precursors, it is crucial to understand how mesodermal cells acquire hematopoietic or endothelial identity due to their close developmental connection. Although Npas4 has been recently identified as a conserved master regulator of hemato-vascular development, the molecular mechanisms underlying the cell fate divergence between hematopoietic and vascular endothelial cells are still unclear. Here, we show in zebrafish that the divergence of hematopoietic and vascular endothelial cells in mesodermal cells is regulated by Junctional adhesion molecule 3b (Jam3b) via two independent signaling pathways. Mutation of jam3b led to the reduction of npas4l expression in the posterior lateral plate mesoderm and defect of both hematopoietic and vascular development. Mechanistically, we uncover that Jam3b promotes endothelial specification by regulating npas4l expression through the repression of the Rap1a-Erk signaling cascade. Jam3b subsequently promotes hematopoietic development including HSCs by regulating lrrc15 expression in endothelial precursors through the activation of an integrin-dependent signaling cascade. Our data provide insight into the divergent mechanisms for instructing hematopoietic or vascular fates from mesodermal cells.

developmental biology↗