Bio


Han had been a postdoc with Dr. Steinmetz at the genetics department for five years, working on both cancers and heart diseases, trying to understand the mechanisms linking from variants to disease phenotypes. This led to a few very interesting findings of aberrant splicing regulation, such as splicing-mediated readthrough stabilization (SRS), one more mechanism for oncogene activation in multiple types of cancers, and tissue-specific splicing of a mitochondrial inner membrane protein, suggesting a molecular connection between deficiency in energy-supplying and dilated cardiomyopathy.

After being a senior computational biologist with Dr. Gloyn, who has been dedicated to the research of type 2 diabetes for decades, Han switched to the field of this multifactorial metabolic disease. It did take some courage to make such a switch at his post-postdoc stage, however, Han has a consistent interest in studying PG&E, which is not pacific gas and electric nearby, but the interaction between phenotype, genotype, and environment. With years of hands-on experience in statistical modeling and the analysis of next-generation sequencing and mass spectrometry data, in addition to a good understanding of disease genetics, cancer biology, and systems biology, Han is highly confident that he will enjoy the adventure and contribute to our understanding of diabetes.

Supervisors


Professional Education


  • Bachelor of Science, East China Normal University (2008)
  • Doctor of Philosophy, Shanghai Institute Of Biochemistry (2014)

Stanford Advisors


All Publications


  • Patient-derived gene and protein expression signatures of NGLY1 deficiency. Journal of biochemistry Rauscher, B., Mueller, W. F., Clauder-Munster, S., Jakob, P., Islam, M. S., Sun, H., Ghidelli-Disse, S., Boesche, M., Bantscheff, M., Pflaumer, H., Collier, P., Haase, B., Chen, S., Hoffman, R., Wang, G., Benes, V., Drewes, G., Snyder, M., Steinmetz, L. M. 2021

    Abstract

    N-Glycanase 1 (NGLY1) deficiency is a rare and complex genetic disorder. Although recent studies have shed light on the molecular underpinnings of NGLY1 deficiency, a systematic characterization of gene and protein expression changes in patient-derived cells has been lacking. Here, we performed RNA-sequencing and mass spectrometry to determine the transcriptomes and proteomes of 66 cell lines representing 4 different cell types derived from 14 NGLY1 deficient patients and 17 controls. Although NGLY1 protein levels were up to 9.5-fold downregulated in patients compared to parents, residual and likely non-functional NGLY1 protein was detectable in all patient-derived lymphoblastoid cell lines. Consistent with the role of NGLY1 as a regulator of the transcription factor Nrf1, we observed a cell type-independent downregulation of proteasomal genes in NGLY1 deficient cells. In contrast, genes involved in ribosome biogenesis and mRNA processing were upregulated in multiple cell types. In addition, we observed cell type-specific effects. For example, genes and proteins involved in glutathione synthesis, such as the glutamate-cysteine ligase subunits GCLC and GCLM, were downregulated specifically in lymphoblastoid cells. We provide a web application that enables access to all results generated in this study at https://apps.embl.de/ngly1browser. This resource will guide future studies of NGLY1 deficiency in directions that are most relevant to patients.

    View details for DOI 10.1093/jb/mvab131

    View details for PubMedID 34878535

  • Single-molecule, full-length transcript isoform sequencing reveals disease-associated RNA isoforms in cardiomyocytes. Nature communications Zhu, C., Wu, J., Sun, H., Briganti, F., Meder, B., Wei, W., Steinmetz, L. M. 2021; 12 (1): 4203

    Abstract

    Alternative splicing generates differing RNA isoforms that govern phenotypic complexity of eukaryotes. Its malfunction underlies many diseases, including cancer and cardiovascular diseases. Comparative analysis of RNA isoforms at the genome-wide scale has been difficult. Here, we establish an experimental and computational pipeline that performs de novo transcript annotation and accurately quantifies transcript isoforms from cDNA sequences with a full-length isoform detection accuracy of 97.6%. We generate a searchable, quantitative human transcriptome annotation with 31,025 known and 5,740 novel transcript isoforms ( http://steinmetzlab.embl.de/iBrowser/ ). By analyzing the isoforms in the presence of RNA Binding Motif Protein 20 (RBM20) mutations associated with aggressive dilated cardiomyopathy (DCM), we identify 121 differentially expressed transcript isoforms in 107 cardiac genes. Our approach enables quantitative dissection of complex transcript architecture instead of mere identification of inclusion or exclusion of individual exons, as exemplified by the discovery of IMMT isoforms mis-spliced by RBM20 mutations. Thereby we achieve a path to direct differential expression testing independent of an existing annotation of transcript isoforms, providing more immediate biological interpretation and higher resolution transcriptome comparisons.

    View details for DOI 10.1038/s41467-021-24484-z

    View details for PubMedID 34244519

  • A Circulating Bioreactor Reprograms Cancer Cells Toward a More Mesenchymal Niche. Advanced biosystems Calamak, S., Ermis, M., Sun, H., Islam, S., Sikora, M., Nguyen, M., Hasirci, V., Steinmetz, L. M., Demirci, U. 2020; 4 (2): e1900139

    Abstract

    Cancer is a complex and heterogeneous disease, and cancer cells dynamically interact with the mechanical microenvironment such as hydrostatic pressure, fluid shear, and interstitial flow. These factors play an essential role in cell fate and circulating tumor cell heterogeneity, and can influence the cellular phenotype. In this study, a peristaltic continuous flow reactor is designed and applied to HCT-116 colorectal carcinoma cells to mimic the fluid dynamics of circulation. With this intervention, a CD44/CD24-cell subpopulation emerges, and 100 genes are significantly regulated. The expression of cells at 4 h in the flow reactor is very similar to TGF-ß treatment, which is an inducer of epithelial-mesenchymal transition. ATF3 and SERPINE1 are significantly upregulated in these groups, suggesting that the mesenchymal transition is induced through this signaling pathway. This flow reactor model is satisfactory on its own to reprogram colorectal cancer cells toward a more mesenchymal niche mimicking circulation of the blood.

    View details for DOI 10.1002/adbi.201900139

    View details for PubMedID 32293132

  • iPSC Modeling of RBM20-Deficient DCM Identifies Upregulation of RBM20 as a Therapeutic Strategy. Cell reports Briganti, F. n., Sun, H. n., Wei, W. n., Wu, J. n., Zhu, C. n., Liss, M. n., Karakikes, I. n., Rego, S. n., Cipriano, A. n., Snyder, M. n., Meder, B. n., Xu, Z. n., Millat, G. n., Gotthardt, M. n., Mercola, M. n., Steinmetz, L. M. 2020; 32 (10): 108117

    Abstract

    Recent advances in induced pluripotent stem cell (iPSC) technology and directed differentiation of iPSCs into cardiomyocytes (iPSC-CMs) make it possible to model genetic heart disease in vitro. We apply CRISPR/Cas9 genome editing technology to introduce three RBM20 mutations in iPSCs and differentiate them into iPSC-CMs to establish an in vitro model of RBM20 mutant dilated cardiomyopathy (DCM). In iPSC-CMs harboring a known causal RBM20 variant, the splicing of RBM20 target genes, calcium handling, and contractility are impaired consistent with the disease manifestation in patients. A variant (Pro633Leu) identified by exome sequencing of patient genomes displays the same disease phenotypes, thus establishing this variant as disease causing. We find that all-trans retinoic acid upregulates RBM20 expression and reverts the splicing, calcium handling, and contractility defects in iPSC-CMs with different causal RBM20 mutations. These results suggest that pharmacological upregulation of RBM20 expression is a promising therapeutic strategy for DCM patients with a heterozygous mutation in RBM20.

    View details for DOI 10.1016/j.celrep.2020.108117

    View details for PubMedID 32905764

  • Loss of N-glycanase 1 Alters Transcriptional and Translational Regulation in K562 Cell Lines. G3 (Bethesda, Md.) Mueller, W. F., Jakob, P. n., Sun, H. n., Clauder-Münster, S. n., Ghidelli-Disse, S. n., Ordonez, D. n., Boesche, M. n., Bantscheff, M. n., Collier, P. n., Haase, B. n., Benes, V. n., Paulsen, M. n., Sehr, P. n., Lewis, J. n., Drewes, G. n., Steinmetz, L. M. 2020

    Abstract

    N-Glycanase 1 (NGLY1) deficiency is an ultra-rare, complex and devastating neuromuscular disease, with multi-organ symptoms. NGLY1 is a deglycosylating protein involved in the degradation of misfolded proteins retrotranslocated from the endoplasmic reticulum (ER). We show that the loss of NGLY1 causes substantial changes in the RNA and protein landscape of K562 cells. We employed the CMap database to predict compounds that can modulate NGLY1 activity. Utilizing our robust K562 screening system, we demonstrate that the compound NVP-BEZ235 promotes degradation of NGLY1-dependent substrates, concurrent with increased autophagic flux, suggesting that autophagy may assist in clearing aberrant substrates during NGLY1 deficiency.

    View details for DOI 10.1534/g3.119.401031

    View details for PubMedID 32265286

  • Dysregulated ribonucleoprotein granules promote cardiomyopathy in RBM20 gene-edited pigs. Nature medicine Schneider, J. W., Oommen, S. n., Qureshi, M. Y., Goetsch, S. C., Pease, D. R., Sundsbak, R. S., Guo, W. n., Sun, M. n., Sun, H. n., Kuroyanagi, H. n., Webster, D. A., Coutts, A. W., Holst, K. A., Edwards, B. S., Newville, N. n., Hathcock, M. A., Melkamu, T. n., Briganti, F. n., Wei, W. n., Romanelli, M. G., Fahrenkrug, S. C., Frantz, D. E., Olson, T. M., Steinmetz, L. M., Carlson, D. F., Nelson, T. J. 2020

    Abstract

    Ribonucleoprotein (RNP) granules are biomolecular condensates-liquid-liquid phase-separated droplets that organize and manage messenger RNA metabolism, cell signaling, biopolymer assembly, biochemical reactions and stress granule responses to cellular adversity. Dysregulated RNP granules drive neuromuscular degenerative disease but have not previously been linked to heart failure. By exploring the molecular basis of congenital dilated cardiomyopathy (DCM) in genome-edited pigs homozygous for an RBM20 allele encoding the pathogenic R636S variant of human RNA-binding motif protein-20 (RBM20), we discovered that RNP granules accumulated abnormally in the sarcoplasm, and we confirmed this finding in myocardium and reprogrammed cardiomyocytes from patients with DCM carrying the R636S allele. Dysregulated sarcoplasmic RBM20 RNP granules displayed liquid-like material properties, docked at precisely spaced intervals along cytoskeletal elements, promoted phase partitioning of cardiac biomolecules and fused with stress granules. Our results link dysregulated RNP granules to myocardial cellular pathobiology and heart failure in gene-edited pigs and patients with DCM caused by RBM20 mutation.

    View details for DOI 10.1038/s41591-020-1087-x

    View details for PubMedID 33188278

  • Biological plasticity rescues target activity in CRISPR knock outs. Nature methods Smits, A. H., Ziebell, F. n., Joberty, G. n., Zinn, N. n., Mueller, W. F., Clauder-Münster, S. n., Eberhard, D. n., Fälth Savitski, M. n., Grandi, P. n., Jakob, P. n., Michon, A. M., Sun, H. n., Tessmer, K. n., Bürckstümmer, T. n., Bantscheff, M. n., Steinmetz, L. M., Drewes, G. n., Huber, W. n. 2019

    Abstract

    Gene knock outs (KOs) are efficiently engineered through CRISPR-Cas9-induced frameshift mutations. While the efficiency of DNA editing is readily verified by DNA sequencing, a systematic understanding of the efficiency of protein elimination has been lacking. Here we devised an experimental strategy combining RNA sequencing and triple-stage mass spectrometry to characterize 193 genetically verified deletions targeting 136 distinct genes generated by CRISPR-induced frameshifts in HAP1 cells. We observed residual protein expression for about one third of the quantified targets, at variable levels from low to original, and identified two causal mechanisms, translation reinitiation leading to N-terminally truncated target proteins or skipping of the edited exon leading to protein isoforms with internal sequence deletions. Detailed analysis of three truncated targets, BRD4, DNMT1 and NGLY1, revealed partial preservation of protein function. Our results imply that systematic characterization of residual protein expression or function in CRISPR-Cas9-generated KO lines is necessary for phenotype interpretation.

    View details for DOI 10.1038/s41592-019-0614-5

    View details for PubMedID 31659326