Biology subjects

Ogino, S.

Publications and source records attributed to Ogino, S..

6 recordsLinked to original sources

bioRxiv2026

Task- and experience-dependent modulation of head-eye coordination during ball interception

Head-eye coordination during ball interception depends on both task demands and motor experience. The purpose of this study is to determine how these factors influence head-eye contributions to gaze control. Twenty-five female university students (novices with no ball sport experience, n = 13; experienced softball players, n = 12) performed two tasks: visually tracking an approaching ball (tracking task) and, in addition, moving the hand to the ball's landing position (reaching task). Head, eye, and gaze velocities, cross-correlation coefficients between gaze and head velocity, and gaze-head lag time were analyzed using linear mixed models. The results showed that although gaze velocity remained unchanged regardless of tasks or groups, decomposing gaze into head and eye components revealed task-dependent contributions. Compared with the tracking task, the reaching task showed significantly larger head velocity and smaller eye velocity, indicating complementary adjustments that were not revealed by gaze movements alone. The cross-correlation between head and gaze was significantly higher in the reaching task than the tracking task, indicating stronger temporal coupling under greater task demand. Furthermore, the experienced group showed greater task-dependent modulation of eye velocity than the novice group, demonstrating greater flexibility in adjusting the magnitude of head-eye movements to task demands. In addition, the experienced group showed a consistently near-zero gaze-head lag regardless of task, whereas the novice group showed a prolonged gaze-leads-head interval. These findings suggest that ball sport experience shapes two distinct aspects of head-eye coordination: task-dependent flexibility in movement magnitude, and stable, temporally synchronized gaze-head control.

physiology↗

bioRxiv2024

Analysis of Categorical Data with Logistic Regression and the Cochran-Mantel-Haenszel Tests in Biological Experiments

The choice of statistical test is a fundamentally important one when analyzing experimental data. Here, we consider the question of categorical data, defined by their properties (for example color) rather than by continuous numbering. Using simple and complex example datasets generated from Caenorhabditis elegans research, we conduct a statistical analysis of (1) a rare cellular event involving the formation of a neuronal extrusion called an exopher, and of (2) a variable behavioral response across a timescale. Two tests we use here are the Cochran- Mantel-Haenszel (CMH) test and logistic regression. These two tests pose practical challenges to researchers that include lack of easy access to statistical software and the need for prior programming knowledge. To this end we provide step-by-step tutorials and example code. We emphasize the flexibility of logistic regression in handling both simple and complex datasets, emphasizing the capacity of logistic regression to provide more comprehensive insights into experimental outcomes than simpler tests like CMH. By analyzing real biological examples and demonstrating their analysis with R code, we provide a practical guide for biologists to enhance the rigor and reproducibility of categorical data analysis in experimental studies.

genetics↗

bioRxiv2020

Tumor-Immune Partitioning and Clustering (TIPC) algorithm reveals distinct signatures of tumor-immune cell interactions within the tumor microenvironment

Growing evidence supports the importance of understanding tumor-immune spatial relationship in the tumor microenvironment in order to achieve precision cancer therapy. However, existing methods, based on oversimplistic cell-to-cell proximity, are largely confounded by immune cell density and are ineffective in capturing tumor-immune spatial patterns. Here we developed a novel computational algorithm, termed Tumor-Immune Partitioning and Clustering (TIPC), to offer an effective solution for spatially informed tumor subtyping. Our method could measure the extent of immune cell partitioning between tumor epithelial and stromal areas as well as the degree of immune cell clustering. Using a U.S. nation-wide colorectal cancer database, we showed that TIPC could determine tumor subtypes with unique tumor-immune spatial patterns that were significantly associated with patient survival and key tumor molecular features. We also demonstrated that TIPC was robust to parameter settings and readily applicable to different immune cell types. The capability of TIPC in delineating clinically relevant patient subtypes that encapsulate tumor-immune spatial relationship, immune density, and tumor morphology is expected to shed light on underlying immune mechanisms. Hence, TIPC can be a useful bioinformatics tool for effective characterization of the spatial composition of the tumor-immune microenvironment to inform precision immunotherapy.

cancer biology↗

bioRxiv2018

Genome Scale Epigenetic Profiling Reveals Five Distinct Subtypes of Colorectal Cancer

BACKGROUNDColorectal cancer is an epigenetically heterogeneous disease, however the extent and spectrum of the CpG Island Methylator Phenotype (CIMP) is not clear.\n\nRESULTSAn unselected cohort of 216 colorectal cancers clustered into five clinically and molecularly distinct subgroups using Illumina 450K DNA methylation arrays. CIMP-High cancers were most frequent in the proximal colons of female patients. These dichotomised into CIMP-Hl and CIMP-H2 based on methylation profile which was supported by over representation of BRAF (74%, P<0.0001) or KRAS (55%, P<0.0001) mutation, respectively. Congruent with increasing methylation, there was a stepwise increase in patient age from 62 years in the CI MP-Negative subgroup to 75 years in the CIMP-Hl subgroup (P<0.0001). There was a striking association between PRC2-marked loci and those subjected to significant gene body methylation in CIMP-type cancers (P<1.6xl078). We identified oncogenes susceptible to gene body methylation and Wnt pathway antagonists resistant to gene body methylation. CIMP cluster specific mutations were observed for genes involved in chromatin remodelling, such as in the SWI/SNF and NuRD complexes, suggesting synthetic lethality.\n\nCONCLUSIONThere are five clinically and molecularly distinct subgroups of colorectal cancer based on genome wide epigenetic profiling. These analyses highlighted an unidentified role for gene body methylation in progression of serrated neoplasia. Subgroup-specific mutation of distinct epigenetic regulator genes revealed potentially druggable vulnerabilities for these cancers, which may provide novel precision medicine approaches.

genomics↗

bioRxiv2018

Gene regulatory network analysis identifies sex-linked differences in colon cancer drug metabolism processes

Significant sex differences are observed in colon cancer, and understanding these differences is essential to advance disease prevention, diagnosis, and treatment. Males have a higher risk of developing colon cancer and a lower survival rate than women. However, the molecular features that drive these sex differences are poorly understood. We used both transcript-based and gene regulatory network methods to analyze RNA-Seq data from The Cancer Genome Atlas for 445 patients with colon cancer. We compared gene expression between tumors in men and women and found no significant sex differences except for sex-chromosome genes. We then inferred patient-specific gene regulatory networks, and found significant regulatory differences between males and females, with drug and xenobiotics metabolism via cytochrome P450 pathways more strongly targeted in females. This finding was validated in a dataset that included 1,193 patients from five independent studies. While targeting of the drug metabolism pathway did not change the overall survival for males treated with adjuvant chemotherapy, females with greater targeting had an increase in 10-year overall survival probability, with 89% (95% CI: 78%-100%) survival compared to 61% (95% CI: 45%-82%) for women with lower targeting, respectively (p=0.034). Our network analysis uncovered patterns of transcriptional regulation that differentiate male and female colon cancer. Most importantly, targeting of the drug metabolism pathway was predictive of survival in women who received adjuvant chemotherapy. This network-based approach can be used to investigate the molecular features that drive sex differences in other cancers and complex diseases.

systems biology↗

bioRxiv2018

Inherited DNA Repair Defects in Colorectal Cancer

Colorectal cancer (CRC) heritability has been estimated to be around 30%. However, mutations in the known CRC susceptibility genes explain CRC risk in under 10% of the cases. Germline mutations in DNA-repair genes (DRGs) have recently been reported in CRC but their contribution to CRC risk is largely unknown. We evaluated the gene-level germline mutation enrichment of 40 DRGs in 680 unselected CRC individuals compared to 27728 ancestry-matched cancer-free adults. Significant findings were then examined in independent cohorts of 1661 unselected CRC cases and 1456 early-onset CRC cases. Of 680 individuals in the discovery set, 31 (4.56%) individuals harbored germline pathogenic mutations in known CRC susceptibility genes while another 33 (4.85%) individuals had DRG mutations that have not been previously associated with CRC risk. Germline pathogenic mutations in ATM and PALB2 were enriched in both the discovery (OR= 2.81; P= 0.035 and OR= 4.91; P= 0.024, respectively) and validation sets (OR= 2.97; Adjusted P= 0.0013 and OR= 3.42; Adjusted P= 0.034, for ATM and PALB2 respectively). Biallelic loss of ATM was evident in all cases with matched tumor profiling. CRC cases also had higher rates of actionable mutations in the HR pathway that can substantially increase the risk of developing cancers other than CRC. Our analysis provides evidence for ATM and PALB2 as CRC risk genes, underscoring the importance of the homologous recombination pathway in CRC. In addition, we identified frequent complete homologous recombination deficiency in CRC tumors, representing a unique opportunity to explore targeted therapeutic interventions such as PARPi.

genetics↗