Quasi-spatial single-cell transcriptomics based on physical tissue properties defines early aging-associated niche in liver

Medicine, Hepatobiliary System, Basic Medical Sciences, Geriatrics, Life Sciences, Cell Biology, Biochemistry, Immunology,
single-cell sequencing   fibrotic niche   liver aging   senescent cells   spatial omics   physical tissue properties  

Redefining the Early-Aging Microenvironment in the Liver: Quasi-spatial Single-cell Transcriptomics Reveals Fibrotic Niche Formation and Cellular Heterogeneity Background and Research Motivation Aging is an inevitable process in life, with one of its most significant features being the accumulation of senescent cells within tissues and organs. Thes...

Single-cell and spatial transcriptomics reveal divergent microenvironments and progression signatures in early- and late-onset prostate cancer

Medicine, Basic Medical Sciences, Geriatrics, Urology, Oncology, Life Sciences, Cell Biology, Biochemistry, Immunology,
single-cell sequencing   spatial transcriptomics   prostate cancer   heterogeneity   tumor microenvironment   androgen response   tumor progression  

Background: Age-related Heterogeneity in Prostate Cancer and New Opportunities for Precision Medicine Prostate cancer (PCA) is the second most common malignancy and the fifth leading cause of cancer-related death among men worldwide. With the global aging population and the advancement of health screening, the age of onset for prostate cancer has b...

Microglia Transcriptional States and Their Functional Significance: Context Drives Diversity

Medicine, Neurology, Life Sciences, Cell Biology, Biochemistry, Immunology,
microglia   transcriptional states   single-cell sequencing   brain microenvironment   functional diversity  

Academic Background Microglia are the only resident macrophages in the central nervous system (CNS) and play critical roles in development, homeostasis, and disease. Traditionally, microglia were viewed as homogeneous “resting” or “activated” states, but the advent of single-cell sequencing technologies has revealed their remarkable transcriptional...

Systematic Reconstruction of Molecular Pathway Signatures Using Scalable Single-Cell Perturbation Screens

Medicine, Life Sciences, Cell Biology, Bioengineering, Immunology, Genetics,
single-cell sequencing   gene regulatory networks   CRISPR interference   functional genomics   signaling pathways  

In the field of functional genomics, researchers have long been dedicated to predicting causal regulatory relationships from observational data. However, despite modern technologies enabling the measurement of diverse molecular modalities, inferring causal regulatory relationships from observational data remains challenging. In particular, the iden...

SCICONE: Single-Cell Copy Number Calling and Event History Reconstruction

Information Science, Computer Science, Medicine, Oncology, Life Sciences, Cell Biology, Bioengineering, Genetics,
single-cell sequencing   copy number variation   tumor evolution   SCICONE model   low-depth sequencing  

During tumor development, copy number alterations (CNAs) are key drivers of tumor heterogeneity and evolution. Understanding these variations is crucial for developing personalized cancer diagnostics and therapies. Single-cell sequencing technology offers the highest resolution for copy number analysis, down to the individual cell level. However, l...