Quantitative Evaluation of Cardiac Cell Interactions and Responses to Cyclic Strain

The heart has a dynamic mechanical environment contributed by its unique cellular composition and the resultant complex tissue structure. In pathological heart tissue, both the mechanics and cell composition can change and influence each other. As a result, the interplay between the cell phenotype and mechanical stimulation needs to be considered to understand the biophysical cell interactions and organization in healthy and diseased myocardium. In this work, we hypothesized that the overall tissue organization is controlled by varying densities of cardiomyocytes and fibroblasts in the heart. In order to test this hypothesis, we utilized a combination of mechanical strain, co-cultures of different cell types, and inhibitory drugs that block intercellular junction formation. To accomplish this, an image analysis pipeline was developed to automatically measure cell type-specific organization relative to the stretch direction. The results indicated that cardiac cell type-specific densities influence the overall organization of heart tissue such that it is possible to model healthy and fibrotic heart tissue in vitro. This study provides insight into how to mimic the dynamic mechanical environment of the heart in engineered tissue as well as providing valuable information about the process of cardiac remodeling and repair in diseased hearts.

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Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia

Communications Biology ◽

10.1038/s42003-020-01418-x ◽

2020 ◽

Vol 3 (1) ◽

Cited By ~ 1

Author(s):

Ana J. Chucair-Elliott ◽

Sarah R. Ocañas ◽

David R. Stanford ◽

Victor A. Ansere ◽

Kyla B. Buettner ◽

...

Keyword(s):

Gene Expression ◽

Affinity Purification ◽

Regulation Of Gene Expression ◽

Cell Types ◽

Tissue Level ◽

Cell Phenotype ◽

Specific Gene ◽

Cell Type ◽

A Cell ◽

Cell Type Specific

AbstractEpigenetic regulation of gene expression occurs in a cell type-specific manner. Current cell-type specific neuroepigenetic studies rely on cell sorting methods that can alter cell phenotype and introduce potential confounds. Here we demonstrate and validate a Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) approach for temporally controlled labeling and isolation of ribosomes and nuclei, and thus RNA and DNA, from specific central nervous system cell types. Analysis of gene expression and DNA modifications in astrocytes or microglia from the same animal demonstrates differential usage of DNA methylation and hydroxymethylation in CpG and non-CpG contexts that corresponds to cell type-specific gene expression. Application of this approach in LPS treated mice uncovers microglia-specific transcriptome and epigenome changes in inflammatory pathways that cannot be detected with tissue-level analysis. The NuTRAP model and the validation approaches presented can be applied to any brain cell type for which a cell type-specific cre is available.

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Cardiac cell type–specific gene regulatory programs and disease risk association

Science Advances ◽

10.1126/sciadv.abf1444 ◽

2021 ◽

Vol 7 (20) ◽

pp. eabf1444

Author(s):

James D. Hocker ◽

Olivier B. Poirion ◽

Fugui Zhu ◽

Justin Buchanan ◽

Kai Zhang ◽

...

Keyword(s):

Disease Risk ◽

Cell Types ◽

Regulatory Elements ◽

Specific Gene ◽

Dependent Manner ◽

Cardiac Cell ◽

Limited Information ◽

Cell Type ◽

Functional Studies ◽

Cell Type Specific

Misregulated gene expression in human hearts can result in cardiovascular diseases that are leading causes of mortality worldwide. However, the limited information on the genomic location of candidate cis-regulatory elements (cCREs) such as enhancers and promoters in distinct cardiac cell types has restricted the understanding of these diseases. Here, we defined >287,000 cCREs in the four chambers of the human heart at single-cell resolution, which revealed cCREs and candidate transcription factors associated with cardiac cell types in a region-dependent manner and during heart failure. We further found cardiovascular disease–associated genetic variants enriched within these cCREs including 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Additional functional studies revealed that two of these variants affect a cCRE controlling KCNH2/HERG expression and action potential repolarization. Overall, this atlas of human cardiac cCREs provides the foundation for illuminating cell type–specific gene regulation in human hearts during health and disease.

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Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia

10.1101/862722 ◽

2019 ◽

Author(s):

Ana J. Chucair-Elliott ◽

Sarah R. Ocañas ◽

David R. Stanford ◽

Victor A. Ansere ◽

Kyla B. Buettner ◽

...

Keyword(s):

Gene Expression ◽

Regulation Of Gene Expression ◽

Cell Types ◽

Tissue Level ◽

Cell Phenotype ◽

Specific Gene ◽

Cell Type ◽

Current Cell ◽

A Cell ◽

Cell Type Specific

AbstractEpigenetic regulation of gene expression occurs in a cell type-specific manner. Current cell-type specific neuroepigenetic studies rely on cell sorting methods that can alter cell phenotype and introduce potential confounds. Here we demonstrate and validate a Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) approach for temporally controlled labeling and isolation of ribosomes and nuclei, and thus RNA and DNA, from specific CNS cell types. Paired analysis of the transcriptome and DNA modifications in astrocytes and microglia demonstrates differential usage of DNA methylation and hydroxymethylation in CG and non-CG contexts that corresponds to cell type-specific gene expression. Application of this approach in LPS treated mice uncovers microglia-specific transcriptome and epigenome changes in inflammatory pathways that cannot be detected with tissue-level analysis. The NuTRAP model and the validation approaches presented can be applied to any CNS cell type for which a cell type-specific cre is available.

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Deconvolving clinically relevant cellular immune crosstalk from bulk gene expression using CODEFACS and LIRICS

10.1101/2021.01.20.427515 ◽

2021 ◽

Author(s):

Kun Wang ◽

Sushant Patkar ◽

Joo Sang Lee ◽

E. Michael Gertz ◽

Welles Robinson ◽

...

Keyword(s):

Gene Expression ◽

Complex Mixture ◽

Cell Types ◽

Cell Interactions ◽

Specific Gene ◽

Cell Type ◽

Patient Response ◽

Receptor Interactions ◽

Cell Type Specific ◽

Cell Cell

AbstractThe tumor microenvironment (TME) is a complex mixture of cell-types that interact with each other to affect tumor growth and clinical outcomes. To accelerate the discovery of such interactions, we developed CODEFACS (COnfident DEconvolution For All Cell Subsets), a deconvolution tool inferring cell-type-specific gene expression in each sample from bulk expression measurements, and LIRICS (LIgand Receptor Interactions between Cell Subsets), a supporting pipeline that analyzes the deconvolved gene expression from CODEFACS to identify clinically relevant ligand-receptor interactions between cell-types. Using 15 benchmark test datasets, we first demonstrate that CODEFACS substantially improves the ability to reconstruct cell-type-specific transcriptomes from individual bulk samples, compared to the state-of-the-art method, CIBERSORTx. Second, analyzing the TCGA, we uncover cell-cell interactions that specifically occur in TME of mismatch-repair-deficient tumors and are associated with their high response rates to anti-PD1 treatment. These results point to specific T-cell co-stimulating interactions that enhance immunotherapy responses in tumors independently of their mutation burden levels. Finally, using machine learning, we identify a subset of cell-cell interactions that predict patient response to anti-PD1 therapy in melanoma better than recently published bulk transcriptomics-based signatures. CODEFACS offers a way to study bulk cancer and normal transcriptomes at a cell type-specific resolution, complementing single-cell transcriptomics.

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Abstract MP143: Harnessing Glycomics to Understand Cardiac Biology and Disease

Circulation Research ◽

10.1161/res.127.suppl_1.mp143 ◽

2020 ◽

Vol 127 (Suppl_1) ◽

Author(s):

Christopher Ashwood ◽

Linda Berg Luecke ◽

Rebekah L Gundry

Keyword(s):

Human Heart ◽

Heart Function ◽

Heart Tissue ◽

Cardiac Biomarkers ◽

Tissue Homogenate ◽

Glycan Structure ◽

Cell Type ◽

Cell Type Specific ◽

Human Heart Tissue

Cell surface glycoproteins play critical roles in maintaining cardiac structure and function, and the glycan-moiety attached to a protein is critical for proper protein folding, stability, and signaling. Despite mounting evidence that glycan structures are key modulators of heart function and must be considered when developing cardiac biomarkers, we currently do not have a comprehensive view of the glycans present in the normal human heart. Here, we used an innovative mass spectrometry approach to generate the first glycan structure libraries for primary human heart tissue, cardiomyocytes (CM) enriched from human heart tissue, and human induced pluripotent stem cell derived CM (hiPSC-CM), containing >260 N- and O- glycans. Comparing the glycome of CM enriched from primary heart tissue to that of heart tissue homogenate, 21 structures significantly differed, and the high mannose class is increased in enriched CM. Moreover, >30% of the glycome significantly changed across 20-100 days of in vitro differentiation, and only 23% of the N -glycan structures were shared between hiPSC-CM and primary CM. Overall, these observations are an important complement to genomic, transcriptomic, and proteomic profiling and reveal new considerations for the use and interpretation of hiPSC-CM models for studies of human development, disease, and drug testing. These data are also expected to aid in the evaluation of the immunogenic potential of hiPSC-CM for transplantation. Finally, harnessing differences observed between immature, proliferative hiPSC-CM and adult primary CM may be exploited to drive in vitro differentiation towards a more mature phenotype. Building on these data, current efforts are underway to develop chamber- and cell-type specific views ( e.g. cardiomyocytes, fibroblasts) of the glycome in the healthy and failing human heart. Such analyses provide a key link to understand the role glycosylation plays in cell-type specific functions and cardiac disease. The structural differences observed here, either among cell types or stages of differentiation, require complex regulation of multiple enzymes in the biosynthetic pathway, and therefore would be challenging to measure with antibody arrays, RNAseq, or proteomics. Therefore, continued application of structure-based glycomics approaches, such as the method used here, will be essential for elucidating the roles that glycans and glycoproteins play during developmental and disease processes in the human heart.

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