Biology subjects

Kuroki, K.

Publications and source records attributed to Kuroki, K..

6 recordsLinked to original sources

bioRxiv2026

Pathway-Centric Integration of CRISPR Fitness with Molecular Features Draws Cancer State Maps

Cancer cells display heterogeneous pathway activity that shapes therapeutic vulnerability, but mapping it remains challenging. Transcriptomic scores do not directly measure functional activity, and CRISPR knockout data alone lack molecular interpretability. We introduce StateMap, a pathway-centric framework integrating gene expression and genome-wide CRISPR knockout fitness data from the Cancer Dependency Map. For a given pathway, StateMap selects features by co-dependency and mutual information, then projects cell lines into a low-dimensional space reflecting pathway activity and molecular state. Applied to the Hippo pathway, it resolved five functional states refining the YAP-on/YAP-off dichotomy. Notably, the Hippo-strong state showed selective dependence on integrin V{beta}5; ITGAV depletion triggered Hippo-dependent cell aggregation and G1 arrest via enhanced cell-cell adhesion. Machine learning transfer to TCGA identified a matching subtype with poor prognosis, nominated NNMT as a biomarker, and predicted sensitivity to the V inhibitor Cilengitide. StateMap enables pathway-specific state mapping and discovery of state-selective therapeutic vulnerabilities.

cancer biology↗

bioRxiv2023

The human immune checkpoint molecule, HLA-G2, induces tolerance in monocytes and dendritic cells via upregulation of PD-L1

Human leukocyte antigen (HLA)-G is a non-classical HLA class I immunomodulatory molecule with restricted expression in the placenta, thymus and regulatory T cells. The spliced isoforms of HLA-G include an 2 domain-deleted isoform, HLA-G2, which specifically binds to the immune checkpoint leukocyte immunoglobulin-like receptor B2 (LILRB2), to suppress immune responses in myelomonocytic cells. We previously reported the structural and receptor binding characteristics of recombinant HLA-G2 protein and its immunosuppressive effects on inflammation in mouse models. However, the function and the mechanism of action of HLA-G2 on human immune cells have not been elucidated. In the present study, we demonstrate the immunosuppressive effect of HLA-G2 on human CD14-positive monocytic cells. HLA-G2 induced the production of the immunosuppressive cytokine, IL-10, and stimulated IL-6/STAT3/indoleamine-2,3-dioxygenase signaling by binding to LILRB2. HLA-G2 binding to LILRB2 also down-regulated cell surface expression of HLA-DR and CD86. Unexpectedly, HLA-G2 up-regulated cell surface expression of PD-L1 in both CD14-positive monocytic cells and interferon-induced dendritic cells (IFN-DCs). This observation suggests HLA-G2/LILRB2 signaling promotes PD-L1 expression. Furthermore, HLA-G2 treatment of IFN-DCs suppressed T cell proliferation in mixed lymphocyte reactions. These findings provide novel insights into the modulation of human immune responses of tolerogenic myelomonocytic cells induced by HLA-G2 binding to LILRB2, and suggest that targeting the HLA-G2-LILRB2 interaction could be a novel approach for immune checkpoint therapy. Significance statementDuring pregnancy, HLA-G isoforms are expressed by fetal trophoblasts to suppress maternal immune responses. Among various HLA-G isoforms, the HLA-G2 homodimer has been expected as an immunosuppressive biologic targeting myelomonocytic antigen-presenting cells via leukocyte immunoglobulin-like receptor B2. We previously reported significant immunosuppressive effects of HLA-G2 in autoimmune mouse models. Here, we first demonstrate that HLA-G2 isoform induces tolerogenic phenotypes of human peripheral immune cells by significantly upregulating an immune checkpoint molecule, PD-L1. Monocyte-derived dendritic cells stimulated by HLA-G2 suppressed T cell proliferation in mixed lymphocyte reactions. These results suggest that HLA-G2 can be a novel candidate for immune checkpoint therapy.

immunology↗

bioRxiv2022

PlantServation: time-series phenotyping using machine learning revealed seasonal pigment fluctuation in diploid and polyploid Arabidopsis

Long-term field monitoring of leaf pigment content is informative for understanding plant responses to environments distinct from regulated chambers, but is impractical by conventional destructive measurements. We developed PlantServation, a method incorporating robust image-acquisition hardware and deep learning-based software to analyze field images, where the plant shape, color, and background vary over months. We estimated the anthocyanin contents of small individuals of four Arabidopsis species using color information and verified the results experimentally. We obtained >4 million plant images over three field seasons to study anthocyanin fluctuations. We found significant effects of past radiation, coldness, and precipitation on the anthocyanin content in the field. The synthetic allopolyploid A. kamchatica recapitulated the fluctuations of natural polyploids by integrating diploid responses. The data support a long-standing hypothesis stating that allopolyploids can inherit and combine the traits of progenitors. PlantServation pipeline facilitates the study of plant responses to complex environments termed "in natura."

plant biology↗

bioRxiv2020

A new domestic cat genome assembly based on long sequence reads empowers feline genomic medicine and identifies a novel gene for dwarfism.

The domestic cat (Felis catus) numbers over 94 million in the USA alone, occupies households as a companion animal, and, like humans, suffers from cancer and common and rare diseases. However, genome-wide sequence variant information is limited for this species. To empower trait analyses, a new cat genome reference assembly was developed from PacBio long sequence reads that significantly improve sequence representation and assembly contiguity. The whole genome sequences of 54 domestic cats were aligned to the reference to identify single nucleotide variants (SNVs) and structural variants (SVs). Across all cats, 16 SNVs predicted to have deleterious impacts and in a singleton state were identified as high priority candidates for causative mutations. One candidate was a stop gain in the tumor suppressor FBXW7. The SNV is found in cats segregating for feline mediastinal lymphoma and is a candidate for inherited cancer susceptibility. SV analysis revealed a complex deletion coupled with a nearby potential duplication event that was shared privately across three unrelated dwarfism cats and is found within a known dwarfism associated region on cat chromosome B1. This SV interrupted UDP-glucose 6-dehydrogenase (UGDH), a gene involved in the biosynthesis of glycosaminoglycans. Importantly, UGDH has not yet been associated with human dwarfism and should be screened in undiagnosed patients. The new high-quality cat genome reference and the compilation of sequence variation demonstrate the importance of these resources when searching for disease causative alleles in the domestic cat and for identification of feline biomedical models. Author summaryThe practice of genomic medicine is predicated on the availability of a high quality reference genome and an understanding of the impact of genome variation. Such resources have lead to countless discoveries in humans, however by working exclusively within the framework of human genetics, our potential for understanding diseases biology is limited, as similar analyses in other species have often lead to novel insights. The generation of Felis_catus_9.0, a new high quality reference genome for the domestic cat, helps facilitate the expansion of genomic medicine into the felis lineage. Using Felis_catus_9.0 we analyze the landscape of genomic variation from a collection of 54 cats within the context of human gene constraint. The distribution of variant impacts in cats is correlated with patterns of gene constraint in humans, indicating the utility of this reference for identifying novel mutations that cause phenotypes relevant to human and cat health. Moreover, structural variant analysis revealed a novel variant for feline dwarfism in UGDH, a gene that has not been associated with dwarfism in any other species, suggesting a role for UGDH in cases of undiagnosed dwarfism in humans.

genomics↗

bioRxiv2019

Structure of HIV-2 Nef reveals unique features distinct from HIV-1 involved in immune regulation

The HIV accessory protein Nef plays a major role in establishing and maintaining infection, particularly through immune evasion. Many HIV-2 infected people experience long-term viral control and survival, resembling HIV-1 elite control. HIV-2 Nef has overlapping but also distinct functions from HIV-1 Nef. Here we report the crystal structure of HIV-2 Nef core. The dileucine sorting motif forms a helix bound to neighboring molecules, and moreover, isothermal titration calorimetry demonstrated that the CD3 endocytosis motif can directly bind to HIV-2 Nef, ensuring AP-2 mediated endocytosis for CD3. The highly-conserved C-terminal region forms a -helix, absent from HIV-1. We further determined the structure of SIV Nef harboring this region, demonstrating similar C-terminal -helix, which may contribute to AP-1 binding for MHC-I downregulation. These results provide new insights into the distinct pathogenesis of HIV-2 infection.

biophysics↗

bioRxiv2019

Feedback loops in the Plk4-STIL-HsSAS6 network coordinate site selection for procentriole formation

Centrioles are duplicated once in every cell cycle, ensuring the bipolarity of the mitotic spindle. Although the core components have been identified, how they cooperate to achieve high fidelity in centriole duplication remains poorly understood. Here, we show that in centriole duplication the accumulation of STIL and HsSAS6, components of the cartwheel structure, provides negative feedback in the centriolar dynamics of Plk4. By live-cell imaging of endogenously tagged proteins in human cells throughout the entire cell cycle, we quantitatively tracked the dynamics of the critical duplication factors: Plk4, STIL, and HsSAS6. Centriolar Plk4 peaks and then starts decreasing during the late G1 phase, which coincides with the accumulation of STIL at centrioles. Shortly thereafter, the HsSAS6 level increases steeply at the procentriole assembly site. We also show that both STIL and HsSAS6 are necessary for attenuating Plk4 levels. Furthermore, our mathematical modeling and simulation convincingly reproduce the dynamics of these three proteins at centrioles, and suggest that the STIL-HsSAS6 complex in the cartwheel has a negative feedback effect on centriolar Plk4. Combined, these findings illustrate how the dynamic behavior of and interactions between the critical duplication factors coordinate the centriole-duplication process.

cell biology↗