Immune checkpoint inhibitors (ICIs) represent a new hot spot in tumor therapy. Programmed cell death has an important role in the prognosis. We explore a programmed cell death gene prognostic model associated with survival and immunotherapy prediction via computational algorithms. Patient details were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases. We used LASSO algorithm and multiple-cox regression to establish a programmed cell death-associated gene prognostic model. Further, we explored whether this model could evaluate the sensitivity of patients to anti-PD-1/PD-L1. In total, 1342 patients were included. We constructed a programmed cell death model in TCGA cohorts, and the overall survival (OS) was significantly different between the high- and low-risk score groups (HR 2.70; 95% CI 1.94-3.75; < 0.0001; 3-year OS AUC 0.71). Specifically, this model was associated with immunotherapy progression-free survival benefit in the validation cohort (HR 2.42; 95% CI 1.59-3.68; = 0.015; 12-month AUC 0.87). We suggest that the programmed cell death model could provide guidance for immunotherapy in LUAD patients.
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http://dx.doi.org/10.3390/jpm13030476 | DOI Listing |
ISME Commun
January 2024
Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, United States.
Alga-dominated geothermal spring communities in Yellowstone National Park (YNP), USA, have been the focus of many studies, however, relatively little is known about the composition and community interactions which underpin these ecosystems. Our goal was to determine, in three neighboring yet distinct environments in Lemonade Creek, YNP, how cells cope with abiotic stressors over the diurnal cycle. All three environments are colonized by two photosynthetic lineages, and , both of which are extremophilic Cyanidiophyceae red algae.
View Article and Find Full Text PDFCrohn's disease (CD) is a complex inflammatory bowel disease resulting from an interplay of genetic, microbial, and environmental factors. Cell-type-specific contributions to CD etiology and genetic risk are incompletely understood. Here we built a comprehensive atlas of cell-type- resolved chromatin accessibility comprising 557,310 candidate cis-regulatory elements (cCREs) in terminal ileum and ascending colon from patients with active and inactive CD and healthy controls.
View Article and Find Full Text PDFLymph node (LN) lymphatic endothelial cells (LEC) actively acquire and archive foreign antigens. Here, we address questions of how LECs achieve durable antigen archiving and whether LECs with high levels of antigen express unique transcriptional programs. We used single cell sequencing in dissociated LN tissue and spatial transcriptomics to quantify antigen levels in LEC subsets and dendritic cell populations at multiple time points after immunization and determined that ceiling and floor LECs archive antigen for the longest duration.
View Article and Find Full Text PDFAlzheimers Dement
December 2024
Department of Laboratory Medicine and Pathobiology and Department of Medicine, University of Toronto, Toronto, Ontario, Canada.
Introduction: Limited research has extensively analyzed neurodegenerative disease-related protein deposition patterns in the hippocampus.
Methods: This study examined the distribution of proteins in hippocampal subregions across major neurodegenerative diseases and explored their relation to each other. The area density of phosphorylated tau (p-tau), amyloid beta (Aβ), α-synuclein, and phosphorylated TDP-43 protein deposits together with pyramidal cell density in each hippocampal subregion, including CA1-4, prosubiculum (ProS), and subiculum was assessed in 166 cases encompassing various neurodegenerative diseases.
Nucleic Acids Res
December 2024
Binzhou People's Hospital Affiliated to Shandong First Medical University/College of Medical Information and Artificial Intelligence, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong 250117, China.
Recent studies have confirmed that certain circRNAs encode proteins that are integral to various biological functions. In this study, we present CICADA, an algorithm specifically designed to assess the protein-coding potential and coding products of circRNAs at high throughput, which enables the identification of previously unknown circRNA-encoded proteins. By harnessing the potential of this algorithm, we identified a variety of functional, protein-coding circRNAs in esophageal squamous cell carcinoma and established circRNA translation profiles for diverse types of cancer.
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