Biology subjects

Lanzer, J. D.

Publications and source records attributed to Lanzer, J. D..

3 recordsLinked to original sources

bioRxiv2024

A cross-study transcriptional patient map of heart failure defines conserved multicellular coordination in cardiac remodeling

Heart failure (HF) is characterized by severely reduced cardiac function and tissue remodeling, driven by complex multicellular regulatory processes. Extensive studies have generated molecular profiles at both bulk and single-cell levels; however, systematic integration that describes tissue-wide changes as a function of cell type coordination remains challenging. This disconnect hampers our understanding of the complex multicellular interactions driving heart failure, limiting our ability to translate molecular insights into actionable therapeutic strategies. Here, we integrated bulk and single-cell transcriptional profiles from cardiac tissues of HF and control patients across 25 studies, covering 1,524 individuals and seven cell-types, to delineate consensus multicellular transcriptional changes associated with cardiac remodeling. Our analyses revealed conserved cellular coordination events involving fibrotic, metabolic, inflammatory, and hypertrophic mechanisms, with fibroblasts playing a central role in predicting cardiomyocyte stress. Further analysis of fibroblast populations suggested that their activation in HF represents a broad phenotypic shift rather than solely accumulating distinct cell states. The integration of bulk and single-cell data within our data collection indicated that transcriptional responses to HF across cell types occur independently of tissue composition. Mapping independent data into our consensus programs demonstrated that recovery after left ventricular assist device implantation aligns with molecular recovery, highlighting the clinical relevance of the multicellular molecular state. Overall, our work synthesizes independent cardiac transcriptomics studies and makes the conserved HF associated insights available, establishing a reference for detailed exploration of HF-related multicellular molecular events. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/621815v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1b6fa5borg.highwire.dtl.DTLVardef@1ee9853org.highwire.dtl.DTLVardef@152a259org.highwire.dtl.DTLVardef@209640_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

systems biology↗

bioRxiv2023

Single-cell transcriptomics reveal distinctive patterns of fibroblast activation in murine heart failure with preserved ejection fraction

Inflammation, fibrosis and metabolic stress critically promote heart failure with preserved ejection fraction (HFpEF). Exposure to high-fat diet and nitric oxide synthase inhibitor N[w]-nitro-l-arginine methyl ester (L-NAME) recapitulate features of HFpEF in mice. To identify disease specific traits during adverse remodeling, we profiled interstitial cells in early murine HFpEF using single-cell RNAseq (scRNAseq). Diastolic dysfunction and perivascular fibrosis were accompanied by an activation of cardiac fibroblast and macrophage subsets. Integration of fibroblasts from HFpEF with two murine models for heart failure with reduced ejection fraction (HFrEF) identified a catalog of conserved fibroblast phenotypes across mouse models. Moreover, HFpEF specific characteristics included induced metabolic, hypoxic and inflammatory transcription factors and pathways, including enhanced expression of Angiopoietin-like 4 next to basement membrane compounds. Fibroblast activation was further dissected into transcriptional and compositional shifts and thereby highly responsive cell states for each HF model were identified. In contrast to HFrEF, where myofibroblast and matrifibrocyte activation were crucial features, we found that these cell-states played a subsidiary role in early HFpEF. These disease-specific fibroblast signatures were corroborated in human myocardial bulk transcriptomes. Furthermore, we found an expansion of pro-inflammatory Ly6Chigh macrophages in HFpEF, and we identified a potential cross-talk between macrophages and fibroblasts via SPP1 and TNF[a]. Finally, a marker of murine HFpEF fibroblast activation, Angiopoietin-like 4, was elevated in plasma samples of HFpEF patients and associated with disease severity. Taken together, our study provides a comprehensive characterization of molecular fibroblast and macrophage activation patterns in murine HFpEF, as well as the identification of a novel biomarker for disease progression in patients.

cell biology↗

bioRxiv2023

Multicellular factor analysis of single-cell data for a tissue-centric understanding of disease

Single-cell atlases across conditions are essential in the characterization of human disease. In these complex experimental designs, patient samples are profiled across distinct cell-types and clinical conditions to describe disease processes at the cellular level. However, most of the current analysis tools are limited to pairwise cross-condition comparisons, disregarding the multicellular nature of disease processes and the effects of other biological and technical factors in the variation of gene expression. Here we propose a computational framework for an unsupervised analysis of samples from cross-condition single-cell atlases and for the identification of multicellular programs associated with disease. Our strategy, that repurposes multi-omics factor analysis, incorporates the variation of patient samples across cell-types and enables the joint analysis of multiple patient cohorts, facilitating integration of atlases. We applied our analysis to a collection of acute and chronic human heart failure single-cell datasets and described multicellular processes of cardiac remodeling that were conserved in independent spatial and bulk transcriptomics datasets. In sum, our framework serves as an exploratory tool for unsupervised analysis of cross-condition single-cell atlas and allows for the integration of the measurements of patient cohorts across distinct data modalities, facilitating the generation of comprehensive tissue-centric understanding of disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/529642v1_ufig1.gif" ALT="Figure 1"> View larger version (16K): org.highwire.dtl.DTLVardef@72269org.highwire.dtl.DTLVardef@645808org.highwire.dtl.DTLVardef@1cf9d6dorg.highwire.dtl.DTLVardef@1686e65_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗