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Mashup Score: 193Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis - 5 month(s) ago
The human lung is structurally complex, with a diversity of specialized epithelial, stromal and immune cells playing specific functional roles in anatomically distinct locations, and large-scale changes in the structure and cellular makeup of this distal lung is a hallmark of pulmonary fibrosis (PF) and other progressive chronic lung diseases. Single-cell transcriptomic studies have revealed numerous disease-emergent/enriched cell types/states in PF lungs, but the spatial contexts wherein these cells contribute to disease pathogenesis has remained uncertain. Using sub-cellular resolution image-based spatial transcriptomics, we analyzed the gene expression of more than 1 million cells from 19 unique lungs. Through complementary cell-based and innovative cell-agnostic analyses, we characterized the localization of PF-emergent cell-types, established the cellular and molecular basis of classical PF histopathologic disease features, and identified a diversity of distinct molecularly-define
Source: www.biorxiv.orgCategories: General Medicine News, Hem/OncsTweet
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Mashup Score: 4Cell type-specific and disease-associated eQTL in the human lung - 5 month(s) ago
Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis (PF). Defining the genetic control of gene expression in a cell-type-specific and context-dependent manner is critical for understanding the mechanisms through which genetic variation influences complex traits and disease pathobiology. To this end, we performed single-cell RNA-sequencing of lung tissue from 67 PF and 49 unaffected donors. Employing a pseudo-bulk approach, we mapped expression quantitative trait loci (eQTL) across 38 cell types, observing both shared and cell type-specific regulatory effects. Further, we identified disease-interaction eQTL and demonstrated that this class of associations is more likely to be cell-type specific and linked to cellular dysregulation in PF. Finally, we connected PF risk variants to their regulatory targets in disease-relevant cell types. These results indicate that cellular context determines the impact of genetic variation on gene expres
Source: www.biorxiv.orgCategories: General Medicine News, Hem/OncsTweet-
We used the @10xGenomics Xenium platform to profile 343 gene from 28 lung biopsies with and without PF. After filtering we had data from > 1.1M cells. So much data. For comparison this is ~2X the cells than our recent paper which took ~6 years to generate https://t.co/AD1JjWhGb3
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Mashup Score: 5GitHub - weizhou0/qtl - 6 month(s) ago
Contribute to weizhou0/qtl development by creating an account on GitHub.
Source: github.comCategories: General Medicine News, Hem/OncsTweet-
RT @greally: Wei Zhou from the @bmneale lab giving an #ASHG23 standout talk on SAIGE-QTL (https://t.co/cWuN94ION5), which improves on pseud…
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Mashup Score: 6Understanding How Sex-Based Differences Impact Health Outcomes - 6 month(s) ago
Sex is a major determinant in disease prevalence and treatment response, caused by a vast number of genetic differences between men and women. However, the inclusion of both sexes in clinical and scientific research had not been mandated by federal law until nearly the turn of the century.
Source: news.feinberg.northwestern.eduCategories: General Medicine News, Hem/OncsTweet-
RT @be_stranger: Great to see our work highlighted by @NorthwesternU. https://t.co/kKsfSJtutw If you’re attending #ASHG23 and want to talk,…
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Mashup Score: 2Phase I Trial Evaluating Locoregionally-delivered IL13Rα2-targeting CAR T Cells in High-Grade Glioma - 6 month(s) ago
Chimeric antigen receptor (CAR) T cell therapy is at early stages of clinical testing for solid tumors. We report here a completed phase I trial (NCT02208362) evaluating locoregional delivery of IL13Rα2-targeted CAR T cells in 65 patients with recurrent high-grade glioma, the majority being re…
Source: www.researchsquare.comCategories: General Medicine News, Hem/OncsTweet-
As a quick side bar, this CAR and the intraventricular approach were first deployed in an adult trial led by Christine Brown which you can check out here: https://t.co/MCFYT1BNyN. A lot of learnings from the adult trail were applied to what has been done in the pediatric trial.
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Mashup Score: 5Cell type-specific and disease-associated eQTL in the human lung - 6 month(s) ago
Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis (PF). Defining the genetic control of gene expression in a cell-type-specific and context-dependent manner is critical for understanding the mechanisms through which genetic variation influences complex traits and disease pathobiology. To this end, we performed single-cell RNA-sequencing of…
Source: www.biorxiv.orgCategories: General Medicine News, Hem/OncsTweet-
Forgot to mention the great @HeiniMNatri is actually giving 2 talks! Be sure to stop by the @Gencove Industry education session in the Conv Ctr/Room 144B/Level 1 at 3:30pm on Thursday to hear her talk about our work in single cell eQTL! #ASHG23 https://t.co/sZt3E4KlkA
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Mashup Score: 8Do mammals have menopause? - 7 month(s) ago
Semantics and lack of data have clouded our understanding about menopause in non-human mammals. The traditional definition of menopause based on the l…
Source: www.sciencedirect.comCategories: General Medicine News, Hem/OncsTweet-
RT @afilimon: Do mammals have menopause? Happy to share our commentary, just out in @CellCellPress: https://t.co/shbgDJgO00
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Mashup Score: 1A Machine Learning One-Class Logistic Regression Model to Predict Stemness in Single Cell Transcriptomics and Spatial Omics Datasets - 1 year(s) ago
Cell annotation is a crucial methodological component to interpreting single cell and spatial omics data. These approaches are often biased and manually curated. Here we harness an existing stemness model for assessing oncogenic states to transform its application to single cell and spatial omic datasets. This one-class logistic regression machine learning algorithm is used to extract…
Source: bioRxivCategories: Hem/Oncs, Latest HeadlinesTweet-
RT @DrJasPlummer: Check out our preprint of a ML model for cancer stemness in single cell and spatial technologies https://t.co/fZBePEN4ql…
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Mashup Score: 3WEHI Spatial Technology Symposium 2023 - 1 year(s) ago
Join us for a full day symposium exploring everything spatial!
Source: EventbriteCategories: Hem/Oncs, Latest HeadlinesTweet-
RT @rkhyip: It's on! Join us for an exciting full day symposium explore everything spatial (https://t.co/Wko2SIJs4u). Excellent opportunity…
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Mashup Score: 12Cell type-specific and disease-associated eQTL in the human lung - 1 year(s) ago
Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis (PF). Defining the genetic control of gene expression in a cell-type-specific and context-dependent manner is critical for understanding the mechanisms through which genetic variation influences complex traits and disease pathobiology. To this end, we performed single-cell RNA-sequencing of…
Source: bioRxivCategories: Hem/Oncs, Latest HeadlinesTweet-
Incredibly excited to share out latest work using single cell RNA sequencing to identify eQTLs across 38 cell types in primary human lung tissue. https://t.co/6SMFGZtDvZ 1/n
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I'm incredibly excited to share our most recent work: "Image-based spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis" https://t.co/GzxJFXuvDA