A5101070851- Cancer Genomics and Diagnostics
- Cancer Cells and Metastasis
- CRISPR and Genetic Engineering
- Cancer Mechanisms and Therapy
- Gastric Cancer Management and Outcomes
- Ferroptosis and cancer prognosis
- Cancer Immunotherapy and Biomarkers
- Immune cells in cancer
- Chromatin Remodeling and Cancer
- Gastrointestinal Tumor Research and Treatment
- Colorectal Cancer Treatments and Studies
- HER2/EGFR in Cancer Research
- Advanced Data Storage Technologies
- Monoclonal and Polyclonal Antibodies Research
- Esophageal Cancer Research and Treatment
- Caching and Content Delivery
- Parallel Computing and Optimization Techniques
- RNA and protein synthesis mechanisms
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- RNA modifications and cancer
- Intraperitoneal and Appendiceal Malignancies
- Gene Regulatory Network Analysis
- Helicobacter pylori-related gastroenterology studies
- Immunotherapy and Immune Responses
Agency for Science, Technology and Research
2024-2025
Genome Institute of Singapore
2024-2025
Duke-NUS Medical School
2019-2025
Wuhan National Laboratory for Optoelectronics
2021
Huazhong University of Science and Technology
2021
Zhejiang University
2016
Abstract Gastric cancer (GC) is a major cause of global mortality with high levels heterogeneity. To explore geospatial interactions in tumor ecosystems, we integrated 2,138 spatial transcriptomic regions-of-interest (ROIs) 152,423 single-cell expression profiles across 226 GC samples from 121 patients. We observed pervasive expression-based intratumor heterogeneity, recapitulating progression through spatially localized and functionally ordered subgroups associated specific immune...
Peritoneal metastasis (PM) in gastric cancer (GC) is associated with poor prognosis and significant morbidity. We sought to understand the genomic, transcriptomic, tumor microenvironment (TME) features that contribute peritoneal organotropism GC.
Abstract Background Within the tumor microenvironment (TME), association of B lymphocytes (B cells) with prognosis and therapy response in gastric cancer (GC) remains poorly characterized. We investigated predictive prognostic value cells, including their spatial organization within TME, one largest multi-cohort studies to date. Methods Using CD20 immunohistochemistry, we evaluated cell density resection specimens from 977 patients resectable GC across three cohorts, randomized phase III...
<div>Abstract<p>Gastric cancer is a major cause of global mortality. To explore geospatial interactions in gastric tumors, we integrated 2,138 spatial transcriptomic regions interest with 152,423 single-cell expression profiles across 226 samples from 121 patients. We observed pervasive expression-based intratumor heterogeneity, recapitulating tumor progression through spatially localized and functionally ordered subgroups associated specific immune microenvironments, checkpoint...
<p>(1) Supplementary Figure 1 shows morphologies of different ROI categories and their representative genes, pathways similarities with paired scRNA-seq data. (2) 2 validation findings from the discovery GeoMx DSP cohort in whole-section also TMA cohort. (3) 3 experiments validating that intratumor G1/G2 subregion expression is tumor-intrinsic using multiplexed IHC, Stereoseq spatial transcriptomics, vitro drug treatment profiling. (4) 4 individual immune checkpoints, chemokines,...
Abstract Purpose: Peritoneal metastases (PM) in colorectal cancer (CRC) portend a poor prognosis. We sought to elucidate molecular features differentiating primary tumors (PTs) from PMs and actionable targets facilitating transcoelomic dissemination progression. Experimental Design: performed multi-omic profiling of 227 samples 136 patients, including 56 tumor (PT) 120 synchronous comprising 34 matched PT-PM pairs. Whole exome, bulk RNA-seq analysis was conducted identify underlying genomic...
Abstract Introduction Genes contain multiple promoters that can drive the expression of various transcript isoforms. Although isoforms from same gene could have diverse and non-overlapping functions, current loss-of-function methodologies are not able to differentiate between isoform-specific phenotypes. Results Here, we show CRISPR interference (CRISPRi) be adopted for targeting specific within a gene, enabling genetic screens. We use this strategy test functional dependencies 820 gained in...
Abstract PURPOSE HER2-positive gastric cancer (HER2+ GC) exhibits significant intra-tumoral heterogeneity and frequent development of resistance to HER2-targeted therapies. This study aimed characterize the spatial tumor microenvironment (TME) in HER2+ GC identify mechanisms HER2 blockade including trastuzumab deruxtecan (T-DXd), with goal informing novel therapeutic strategies. PATIENTS AND METHODS We performed transcriptomics on pre-and post-treatment samples from patients metastatic who...
Gap filling for the reconstruction of metabolic networks is to restore connectivity metabolites via finding high-confidence reactions that could be missed in target organism. Current methods gap either fall into network topology or have limited capability missing are indirectly related dead-end but biological importance model.We present an automated (DEF) approach, which derived from wisdom endosymbiosis theory, fill gaps by most efficient utilization paths a constructed quasi-endosymbiosis...
Abstract Peritoneal metastases (PM) in gastric cancer (GC) portend a poor prognosis, yet our understanding of tumor microenvironmental (TME) characteristics associated with GCPM remain limited. Here, we analyzed intrinsic genomic alterations and transcriptomic programs predictive prospective cohort 248 patients, identifying CDH1 , PIGR ELF3 mutations as predictors. By inspecting the spatial dynamics TME, find that compartment infiltration pro-tumorigenic cell types such inflammatory...
Abstract Objective Gastric cancer (GC) is a leading cause of mortality, with ARID1A being the second most frequently mutated driver gene in GC. We sought to decipher ARID1A-specific GC regulatory networks and examine therapeutic vulnerabilities arising from loss. Design Genomic profiling patients including Singapore cohort (&gt;200 patients) was performed derive mutational signatures inactivation across molecular subtypes. Single-cell transcriptomic profiles ARID1A-mutated GCs were...
An amendment to this paper has been published and can be accessed via the original article.
Non-volatile Memory (NVM) with extremely high storage performance is the key device to build next generation of systems. Various key-value (KV) store index structures have been designed for NVM, but these designs based on single level NVM suffer from significant write consistency overhead. The DRAM-NVM hybrid schemes improve at cost very long recovery time. In this study, we proposed a novel structure named HBTree (Hybrid B+ Tree), which not only achieves better basic KV operating...