Stephen Chang, MD, PhD

All Publications

• A molecular cell atlas of the human lung from single-cell RNA sequencing. Nature Travaglini, K. J., Nabhan, A. N., Penland, L., Sinha, R., Gillich, A., Sit, R. V., Chang, S., Conley, S. D., Mori, Y., Seita, J., Berry, G. J., Shrager, J. B., Metzger, R. J., Kuo, C. S., Neff, N., Weissman, I. L., Quake, S. R., Krasnow, M. A. 2020

  Abstract

  Although single-cell RNA sequencing studies have begun to provide compendia of cell expression profiles1-9, it has been difficult to systematically identify and localize all molecularcell types in individual organs to create a full molecular cell atlas. Here, using droplet- and plate-based single-cell RNA sequencing of approximately 75,000 human cells across all lung tissue compartments and circulating blood, combined with a multi-pronged cell annotation approach, we create an extensive cell atlas of the human lung. We define the gene expression profiles and anatomical locations of 58 cell populations in the human lung, including 41 out of 45 previously known cell types and 14 previously unknown ones. This comprehensive molecular atlas identifies the biochemical functions of lung cells and the transcription factors and markers for making and monitoring them; defines the cell targets of circulating hormones and predicts local signalling interactions and immune cell homing; and identifies cell types that are directly affected by lung disease genes and respiratory viruses. By comparing human and mouse data, we identified 17 molecular cell types that have been gained or lost during lung evolution and others with substantially altered expression profiles, revealing extensive plasticity of cell types and cell-type-specific gene expression during organ evolution including expression switches between cell types. This atlas provides the molecular foundation for investigating how lung cell identities, functions and interactions are achieved in development and tissue engineering and altered in disease and evolution.

  View details for DOI 10.1038/s41586-020-2922-4

  View details for PubMedID 33208946

• Molecular profiling of dilated cardiomyopathy that progresses to heart failure. JCI insight Burke, M. A., Chang, S., Wakimoto, H., Gorham, J. M., Conner, D. A., Christodoulou, D. C., Parfenov, M. G., Depalma, S. R., Eminaga, S., Konno, T., Seidman, J. G., Seidman, C. E. 2016; 1 (6)

  Abstract

  Dilated cardiomyopathy (DCM) is defined by progressive functional and structural changes. We performed RNA-seq at different stages of disease to define molecular signaling in the progression from pre-DCM hearts to DCM and overt heart failure (HF) using a genetic model of DCM (phospholamban missense mutation, PLN(R9C/+)). Pre-DCM hearts were phenotypically normal yet displayed proliferation of nonmyocytes (59% relative increase vs. WT, P = 8 × 10(-4)) and activation of proinflammatory signaling with notable cardiomyocyte-specific induction of a subset of profibrotic cytokines including TGFβ2 and TGFβ3. These changes progressed through DCM and HF, resulting in substantial fibrosis (17.6% of left ventricle [LV] vs. WT, P = 6 × 10(-33)). Cardiomyocytes displayed a marked shift in metabolic gene transcription: downregulation of aerobic respiration and subsequent upregulation of glucose utilization, changes coincident with attenuated expression of PPARα and PPARγ coactivators -1α (PGC1α) and -1β, and increased expression of the metabolic regulator T-box transcription factor 15 (Tbx15). Comparing DCM transcriptional profiles with those in hypertrophic cardiomyopathy (HCM) revealed similar and distinct molecular mechanisms. Our data suggest that cardiomyocyte-specific cytokine expression, early fibroblast activation, and the shift in metabolic gene expression are hallmarks of cardiomyopathy progression. Notably, key components of these profibrotic and metabolic networks were disease specific and distinguish DCM from HCM.

  View details for PubMedID 27239561

  View details for PubMedCentralID PMC4882118

• 5 ' RNA-Seq identifies Fhl1 as a genetic modifier in cardiomyopathy JOURNAL OF CLINICAL INVESTIGATION Christodoulou, D. C., Wakimoto, H., Onoue, K., Eminaga, S., Gorham, J. M., Depalma, S. R., Herman, D. S., Teekakirikul, P., Conner, D. A., McKean, D. M., Domenighetti, A. A., Aboukhalil, A., Chang, S., Srivastava, G., McDonough, B., De Jager, P. L., Chen, J., Bulyk, M. L., Muehlschlege, J. D., Seidman, C. E., Seidman, J. G. 2014; 124 (3): 1364-1370

  Abstract

  The transcriptome is subject to multiple changes during pathogenesis, including the use of alternate 5' start-sites that can affect transcription levels and output. Current RNA sequencing techniques can assess mRNA levels, but do not robustly detect changes in 5' start-site use. Here, we developed a transcriptome sequencing strategy that detects genome-wide changes in start-site usage (5'RNA-Seq) and applied this methodology to identify regulatory events that occur in hypertrophic cardiomyopathy (HCM). Compared with transcripts from WT mice, 92 genes had altered start-site usage in a mouse model of HCM, including four-and-a-half LIM domains protein 1 (Fhl1). HCM-induced altered transcriptional regulation of Fhl1 resulted in robust myocyte expression of a distinct protein isoform, a response that was conserved in humans with genetic or acquired cardiomyopathies. Genetic ablation of Fhl1 in HCM mice was deleterious, which suggests that Fhl1 transcriptional changes provide salutary effects on stressed myocytes in this disease. Because Fhl1 is a chromosome X-encoded gene, stress-induced changes in its transcription may contribute to gender differences in the clinical severity of HCM. Our findings indicate that 5'RNA-Seq has the potential to identify genome-wide changes in 5' start-site usage that are associated with pathogenic phenotypes.

  View details for DOI 10.1172/JCI70108

  View details for Web of Science ID 000332347700050

  View details for PubMedID 24509080

  View details for PubMedCentralID PMC3934171

• Connexin43 Modulates Cell Polarity and Directional Cell Migration by Regulating Microtubule Dynamics PLOS ONE Francis, R., Xu, X., Park, H., Wei, C., Chang, S., Chatterjee, B., Lo, C. 2011; 6 (10)

  Abstract

  Knockout mice deficient in the gap junction gene connexin43 exhibit developmental anomalies associated with abnormal neural crest, primordial germ cell, and proepicardial cell migration. These migration defects are due to a loss of directional cell movement, and are associated with abnormal actin stress fiber organization and a loss of polarized cell morphology. To elucidate the mechanism by which Cx43 regulates cell polarity, we used a wound closure assays with mouse embryonic fibroblasts (MEFs) to examine polarized cell morphology and directional cell movement. Studies using embryonic fibroblasts from Cx43 knockout (Cx43KO) mice showed Cx43 deficiency caused cell polarity defects as characterized by a failure of the Golgi apparatus and the microtubule organizing center to reorient with the direction of wound closure. Actin stress fibers at the wound edge also failed to appropriately align, and stabilized microtubule (Glu-tubulin) levels were markedly reduced. Forced expression of Cx43 with deletion of its tubulin-binding domain (Cx43dT) in both wildtype MEFs and neural crest cell explants recapitulated the cell migration defects seen in Cx43KO cells. However, forced expression of Cx43 with point mutation causing gap junction channel closure had no effect on cell motility. TIRF imaging revealed increased microtubule instability in Cx43KO cells, and microtubule targeting of membrane localized Cx43 was reduced with expression of Cx43dT construct in wildtype cells. Together, these findings suggest the essential role of Cx43 gap junctions in development is mediated by regulation of the tubulin cytoskeleton and cell polarity by Cx43 via a nonchannel function.

  View details for DOI 10.1371/journal.pone.0026379

  View details for Web of Science ID 000295981600056

  View details for PubMedID 22022608

  View details for PubMedCentralID PMC3194834

• Genetics of hypertrophic cardiomyopathy CURRENT OPINION IN CARDIOLOGY Konno, T., Chang, S., Seidman, J. G., Seidman, C. E. 2010; 25 (3): 205-209

  Abstract

  Hypertrophic cardiomyopathy (HCM), the most common inherited cardiac disorder, exhibits remarkable genetic and clinical heterogeneity. This manuscript reviews recent discoveries of disease-causing genes and their clinical consequences, and provides an overview of research that aims to elucidate how HCM ensues from a single-nucleotide mutation.The spectrum of genes that are mutated in HCM has expanded. In combination with newly developed sequencing technologies, there are now robust strategies for gene-based diagnosis in HCM. Understanding the molecular pathophysiology of HCM has emerged from the study of genetically engineered animal models of disease, and new data indicate important roles for altered intracellular Ca²⁺ regulation and oxidative stress. Pharmacologic strategies to normalize these processes show promise in attenuating HCM in experimental models.The current repertoire of HCM genes allows effective gene-based diagnosis, information that enables accurate assessment of disease risk in family members, and provides some insight into clinical course. From mechanistic insights gleaned from fundamental investigations of experimental HCM models, novel therapeutic targets that may provide new benefits for HCM patients have surfaced.

  View details for DOI 10.1097/HCO.0b013e3283375698

  View details for Web of Science ID 000276879500006

  View details for PubMedID 20124998

  View details for PubMedCentralID PMC2932754