Xinghua Victor Pan M.D., Ph.D.

Research Scientist in Genetics

Research Interests

Single Cell Functional Genomics: My group focuses on the development and application of cutting edge technologies for genome-wide analysis of single cells and low numbers of cells for the functional genomic elements, in aspects of genomics, epigenomics and transcriptomics, with the support of Dr. Sherman Weissman. We began with whole genome amplification technology, WPA (PNAS 2008), which was invented on the basis of my experience in development of REPLIg kit (at Molecular Staging Inc. with Dr. Roger Lasken), and was then adapted for full length and whole transcriptome amplification and expression profiling (RNA-seq) (PNAS 2013a). Combining these together, we established the proof of principle for co-detection and sequencing of gDNA and mRNA from the same single cells (Scientific Reports, 2014). We have in addition developed a simple and robust method for telomere length measurement of single cells (PNAS 2013b). We have also independently renovated RRBS for single cell analysis, and extended the genome-wide bisulfite sequencing to the single cell level. Recently we have been building up on a different method for genome-wide CpG methylation pattern sequencing independent of bisulfite conversion, which are particularly suitable for single cell analysis, and we again approach a new method for detection of condensed chromatin regions for single cells (manuscripts in submission or preparation). We adapt these technologies into other advanced systems and platforms especially high throughput sequencing (NGS) and microfluidics such as Fluidigm platform and collaborate with other investigators to study the gene regulation network for induced pluripotent stem cells (iPSC), embryonic stem cells (ESC), adult stem cells (HSC, hMSC), neurons, cells of the immune system and cancers, and have been starting an effort to apply these technologies into translational medicine.

Research Summary

Single cell genomics - development and application of a sreies of cutting edge novel technologies for genetics and genomics analyssis at single-cell level. Currently we focus on single cell genomics, single cell transcriptomics, single cell epigenomics particularly DNA methylome, and integrated analysis of multi-factors for single cells. Using these technologies and combininbg with other technology platforms such as next generation sequencing (NGS) and Fluidigm platforms, we study stem cells, cancers, immune cells, neurons, embryo and development, and genetic diseases, in order to reveal the underlying molecular mechanisms and to explore the translational medical applications.

Selected Publications

  • Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, Marjani SL, Euskirchen G, Ma C, Lamotte RH, Park IH, Snyder MP, Mason CE, Weissman SM. (2013). Two methods for full-length RNA sequencing for low quantities of cells and single cells. Proc Natl Acad Sci U S A. 110(2):594-9. PMID: 23267071
  • Pan X, Urban AE, Dean P, Vincent S, Grubbert F, Hu Y, Snyder M, Weissman SM. (2008) A procedure for highly specific, hypersensitive and unbiased whole genome amplification. Proc Natl Acad Sci U S A. 105(40):15499-504. PMID: 18832167
  • Han L, Zi X, Garmire LX, Wu Y, Weissman SM, Pan X, Fan R. (2014) Co-detection and sequencing of genes and transcripts from the same single cells enabled by a microfluidics platform. Scientific Reports, 2014 Sep 26;4:6485. doi: 10.1038/srep06485. PMID: 25255798
  • Wang F, Pan X, Kalmbach K, Seth-Smith ML, Ye X, Antumes DM, Yin Y, Liu L, Keefe DL, Weissman SM. (2013) Robust measurement of telomere length in single cells. Proc Natl Acad Sci U S A. 110 (21): E1906–E1912. PMID: 23661059 (a corresponding author). It is shown in PNAS comments: New ruler for telomere length, May 10, 2013 by Sarah CP Williams; highlighted in “This week in PNAS - In this Issue”: May 21, 2013 by C.R.; and featured as “Telomere length measurement in single cells” by Hannah Stower published in Nature Reviews Genetics, 14, 444, (2013), doi:10.1038/nrg3529, June 18, 2013.
  • Guo S, Zi X, Schultz V, Cheng J, Zhong M, Koochaki S, Megyola CM, Pan X, Heydari K, Weissman SM, Gallagher PG, Krause DS, Fan R, Lu J. (2014) Non-stochastic reprogramming from a privileged somatic cell state. Cell, 156(4):649-62. PMID: 24486105.
  • Kim KY, Hysolli E, Tanaka Y, Wang B, Jung YW, Pan X, Weissman SM, and Park IH. (2014) X chromosome of female cells shows dynamic changes in status during human somatic cell reprogramming. Stem Cell Reports, 15;2(6):896-909. PMID: 24936474.
  • Han Lin, Huajun Wu, Haiying Zhu, Markus Riester, Kun-Yong Kim, Sadie Marjani, Ghia Euskirchen, Michael Snyder, In-Hyun Park, Sherman M. Weissman, Franziska Michor*, Rong Fan*, Xinghua Pan*, Single-cell genome-wide CpG methylation patterns based on enzymatic recognition and selective amplification (in submission)
  • Yang J, Seay M, Tanaka Y, Euskirchen G, Snyder M, Park I, Pan X*, Weissman SM*. Heterogeneity and cell cycle related changes in single cell transcriptomes of early hematopoietic precursors (in revision)

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