TRACE-seq: A transgenic system for unbiased and non-invasive transcriptome profiling of living cells

Dynamic profiling of changes in gene expression in response to stressors in specific microenvironments without requiring cellular destruction remains challenging. Current methodologies that seek to interrogate gene expression at a molecular level require sampling of cellular transcriptome and therefore lysis of the cell, preventing serial analysis of cellular transcriptome. To address this area of unmet need, we have recently developed a technology allowing transcriptomic analysis over time without cellular destruction. Our method, TRACE-seq (TRanscriptomic Analysis Captured in Extracellular vesicles using sequencing), is characterized by a cell-type specific transgene expression. It provides data on the transcriptome inside extracellular vesicles that provides an accurate representation of stress-responsive cellular transcriptomic changes. Thus, the transcriptome of cells expressing TRACE can be followed over time without destroying the source cell, which is a powerful tool for many fields of fundamental and translational biology research.

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TRanscriptomic Analysis Captured in Extracellular vesicles using RNA-sequencing

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Excellent correlation of cellular and EV transcriptome using this method

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Accurate profiling of gene expression changes in response to stress signals

Distilling complexity to advance cardiac tissue engineering

The promise of cardiac tissue engineering is in the ability to recapitulate in vitro the functional aspects of a healthy heart and disease pathology as well as to design replacement muscle for clinical therapy. Parts of this promise have been realized; others have not. In a meeting of scientists in this field, five central challenges or "big questions" were articulated that, if addressed, could substantially advance the current state of the art in modeling heart disease and realizing heart repair.

Distinct carbon sources affect structural and functional maturation of cardiomyocytes derived from human pluripotent stem cells

The immature phenotype of human pluripotent stem cell derived cardiomyocytes (hPSC-CMs) constrains their potential in cell therapy and drug testing. In this study, we report that shifting hPSC-CMs from glucose-containing to galactose- and fatty acid-containing medium promotes their fast maturation into adult-like CMs with higher oxidative metabolism, transcriptional signatures closer to those of adult ventricular tissue, higher myofibril density and alignment, improved calcium handling, enhanced contractility, and more physiological action potential kinetics. Integrated "-Omics" analyses showed that addition of galactose to culture medium improves total oxidative capacity of the cells and ameliorates fatty acid oxidation avoiding the lipotoxicity that results from cell exposure to high fatty acid levels. This study provides an important link between substrate utilization and functional maturation of hPSC-CMs facilitating the application of this promising cell type in clinical and preclinical applications.

CITED2 Cooperates with ISL1 and Promotes Cardiac Differentiation of Mouse Embryonic Stem Cells

The transcriptional regulator CITED2 is essential for heart development. Here, we investigated the role of CITED2 in the specification of cardiac cell fate from mouse embryonic stem cells (ESC). The overexpression of CITED2 in undifferentiated ESC was sufficient to promote cardiac cell emergence upon differentiation. Conversely, the depletion of Cited2 at the onset of differentiation resulted in a decline of ESC ability to generate cardiac cells. Moreover, loss of Cited2 expression impairs the expression of early mesoderm markers and cardiogenic transcription factors (Isl1, Gata4, Tbx5). The cardiogenic defects in Cited2-depleted cells were rescued by treatment with recombinant CITED2 protein. We showed that Cited2 expression is enriched in cardiac progenitors either derived from ESC or mouse embryonic hearts. Finally, we demonstrated that CITED2 and ISL1 proteins interact physically and cooperate to promote ESC differentiation toward cardiomyocytes. Collectively, our results show that Cited2 plays a pivotal role in cardiac commitment of ESC.

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Overexpression of CITED2 in ESC promotes cardiogenesis upon differentiation

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Cited2 depletion reduces ESC ability to generate cardiac cells

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Cited2 expression is enriched in cardiac progenitors

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CITED2 and ISL1 cooperate to promote ESC differentiation toward cardiomyocytes

Functional differences in engineered myocardium from embryonic stem cell-derived versus neonatal cardiomyocytes

Stem cell-derived cardiomyocytes represent unique tools for cell- and tissue-based regenerative therapies, drug discovery and safety, and studies of fundamental heart-failure mechanisms. However, the degree to which stem cell-derived cardiomyocytes compare to mature cardiomyocytes is often debated. We reasoned that physiological metrics of engineered cardiac tissues offer a means of comparison. We built laminar myocardium engineered from cardiomyocytes that were differentiated from mouse embryonic stem cell-derived cardiac progenitors or harvested directly from neonatal mouse ventricles, and compared their anatomy and physiology in vitro. Tissues assembled from progenitor-derived myocytes and neonate myocytes demonstrated similar cytoskeletal architectures but different gap junction organization and electromechanical properties. Progenitor-derived myocardium had significantly less contractile stress and slower longitudinal conduction velocity than neonate-derived myocardium, indicating that the developmental state of the cardiomyocytes affects the electromechanical function of the resultant engineered tissue. These data suggest a need to establish performance metrics for future stem cell applications.

Essential and unexpected role of Yin Yang 1 to promote mesodermal cardiac differentiation

RATIONALE

Cardiogenesis is regulated by a complex interplay between transcription factors. However, little is known about how these interactions regulate the transition from mesodermal precursors to cardiac progenitor cells (CPCs).

OBJECTIVE

To identify novel regulators of mesodermal cardiac lineage commitment.

METHODS AND RESULTS

We performed a bioinformatic-based transcription factor binding site analysis on upstream promoter regions of genes that are enriched in embryonic stem cell-derived CPCs. From 32 candidate transcription factors screened, we found that Yin Yang 1 (YY1), a repressor of sarcomeric gene expression, is present in CPCs in vivo. Interestingly, we uncovered the ability of YY1 to transcriptionally activate Nkx2.5, a key marker of early cardiogenic commitment. YY1 regulates Nkx2.5 expression via a 2.1-kb cardiac-specific enhancer as demonstrated by in vitro luciferase-based assays, in vivo chromatin immunoprecipitation, and genome-wide sequencing analysis. Furthermore, the ability of YY1 to activate Nkx2.5 expression depends on its cooperative interaction with Gata4 at a nearby chromatin. Cardiac mesoderm-specific loss-of-function of YY1 resulted in early embryonic lethality. This was corroborated in vitro by embryonic stem cell-based assays in which we showed that the overexpression of YY1 enhanced the cardiogenic differentiation of embryonic stem cells into CPCs.

CONCLUSIONS

These results demonstrate an essential and unexpected role for YY1 to promote cardiogenesis as a transcriptional activator of Nkx2.5 and other CPC-enriched genes.

Assembly of the Photosystem II oxygen-evolving complex is inhibited in psbA site-directed mutants of Chlamydomonas reinhardtii. Aspartate 170 of the D1 polypeptide

Photosystem II catalyzes the photooxidation of water to molecular oxygen, providing electrons to the photosynthetic electron transfer chain. The D1 and D2 chloroplast-encoded reaction center polypeptides bind cofactors essential for Photosystem II function. Transformation of the chloroplast genome of the eukaryotic green alga Chlamydomonas reinhardtii has allowed us to engineer site-directed mutants in which aspartate residue 170 of D1 is replaced by histidine (D170H), asparagine (D170N), threonine (D170T), or proline (D170P). Mutants D170T and D170P are completely deficient in oxygen evolution, but retain normal (D170T) or 50% (D170P) levels of Photosystem II reaction centers. D170H and D170N accumulate wild-type levels of PSII centers, yet evolve oxygen at rates approximately 45% and 15% those of control cells, respectively. Kinetic analysis of chlorophyll fluorescence in the mutants reveals a specific defect in electron donation to the reaction center. Measurements of oxygen flash yields in D170H show, however, that those reaction centers capable of evolving oxygen function normally. We conclude that aspartate residue 170 of the D1 polypeptide plays a critical role in the initial binding of manganese as the functional chloroplast oxygen-evolving complex is assembled.