Publications by authors named "Yered H Pita-Juarez"
Formalin-fixed paraffin-embedded (FFPE) samples are valuable but underutilized in single-cell omics research due to their low RNA quality. In this study, leveraging a recent advance in single-cell genomic technology, we introduce snPATHO-seq, a versatile method to derive high-quality single-nucleus transcriptomic data from FFPE samples. We benchmarked the performance of the snPATHO-seq workflow against existing 10x 3' and Flex assays designed for frozen or fresh samples and highlighted the consistency in snRNA-seq data produced by all workflows.
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- The study investigates the role of non-coding mutations, specifically in the 3' untranslated region (3'-UTR), in gastric cancer progression and immune response by analyzing data from 375 patients.
- Through gene expression and immune landscape analyses, the research identifies variants that affect gene expression and immune features like T cell diversity.
- Importantly, a unique variant signature outperforms traditional markers in predicting patient response to immunotherapy, highlighting the potential of these non-coding mutations as therapeutic targets.
Serine and Arginine Rich Splicing Factor 1 (SRSF1) is a splicing factor that binds to exonic enhancers and stimulates splicing and is previously implicated with autoimmunity. Herein, we investigate the role of SRSF1 in regulating innate immune functions that are pertinent in the pathogenesis of auto-inflammatory diseases. Specifically, we show that conditional deletion of SRSF1 in mature lymphocytes resulted in higher expression of il-17a and il-17 f and an expansion of IL17A CD8 T cells.
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- - The study aims to uncover the genetic factors linking to chronic liver disease by analyzing data from over 300,000 participants to identify significant genetic variants related to liver enzyme levels.
- - Researchers found a specific genetic variant (GPAM rs10787429) that correlates with higher levels of liver enzymes and is linked to an increased risk of alcohol-related and fatty liver disease.
- - This variant interacts with factors like body mass index and alcohol consumption, indicating a complex relationship between genetics, lifestyle, and liver health and showing an unusual association with higher cholesterol levels.
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- This study examines the pathophysiology of COVID-19 by analyzing single-cell and spatial atlases from various organ autopsy samples of individuals who died from the virus.
- Findings revealed significant changes in lung tissue, including impaired tissue regeneration and inflammation, indicating how SARS-CoV-2 affects different cell types.
- The research provides crucial insights into the biological impact of severe COVID-19, aiding in the development of potential new treatments.
Article Synopsis
- The SARS-CoV-2 pandemic has led to over 1 million deaths worldwide, primarily due to severe lung injuries and multiple organ failures, but there is limited understanding of the immune responses involved in COVID-19.
- Researchers collected and analyzed over 420 tissue samples from various organs of 17 COVID-19 victims, utilizing advanced techniques like RNA sequencing to map out cellular changes related to their illness.
- Significant findings include alterations in lung tissue cell types, such as the increase of specific progenitor cells and myofibroblasts, indicating impaired tissue repair and failed regenerative processes in severely damaged lungs.