Xiuqian Mu MD, PhD
Xiuqian Mu
MD, PhD
Associate Professor
Jacobs School of Medicine & Biomedical Sciences
Specialty/Research Focus
Bioinformatics; Cell growth, differentiation and development; Gene Expression; Genomics and proteomics; Molecular genetics; Stem Cells; Transcription and Translation; Transgenic organisms; Vision science
Professional Summary:
We are interested in the fundamental mechanisms underlying the shift of cellular states from progenitors to fully functional mature cell types along individual cell lineages during development. We address this issue by studying cell fate specification and differentiation in the developing neural retina. Our efforts are on identifying key regulators, uncovering their roles in individual lineages, and understanding how they carry out these roles. One area of our research is focused on how transcription factors influence the epigenetic landscape along the retinal ganglion cell lineage. We have also begun to investigate how posttranscriptional control of gene expression affects retinal cell differentiation. We conduct our research using a combinatorial approach encompassing genetics, molecular biology, genomics, and bioinformatics. Most recently we are using single cell RNA-seq and single ATAC-seq technologies extensively to address the fundamental questions in retinal development.
Education and Training:
- PhD, Biochemistry and Molecular Biology, Peking Union Medical College (1994)
- MD, Medicine, Qingdao Medical College (1989)
Employment:
- Associate Professor (with tenure), Ophthalmology, University at Buffalo, School of Medicine and Biological Sciences (2015-present)
- Assistant Professor, Ophthalmology, University at Buffalo, School of Medicine and Biological Sciences (2008–2015)
- Assistant Professor, Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center (2003–2008)
- Instructor, Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center (2002–2003)
- Postdoctoral Associate, Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center (1999–2001)
- Postdoctoral Fellow, National Institutes of Health (1994–1999)
Research Expertise:
- Developmental biology: mouse retinal development, neural development, cell fate specification, cell differentiation
- Genomics: genomics, transcriptomics, epigenomics, single cell RNA-seq, single cell ATAC-seq
- Molecular biology: gene regulation, transcription factors, enhancers, epigenetics, post-transcriptional regulation
- Mouse genetics: genetically modified mice, gene targeting, CRISPR/cas9, genetic labeling
Research Centers:
- Ira G. Ross Eye Institute Research Center
- Center of Excellence in Bioinformatics and Life Sciences
UB 2020 Strategic Strengths:
- Molecular Recognition in Biological Systems and Bioinformatics
Grants and Sponsored Research:
- April 2020–March 2024
Regulation of mRNA decay in retinal development and maintenance
National Eye Institute
Role: Principal Investigator
$2,024,085 - September 2017–May 2022
Regulatory mechanisms for retinal ganglion cell genesis
National Institutes of Health
Role: Principal Investigator
$1,960,167 - June 2016–May 2018
Generation of retinal ganglion cells by direct reprograming
BrightFocus Foundation
Role: Principal Investigator
$150,000 - March 2011–February 2016
Interaction of Isl1 and Pou4f2 in retinal development
National Institutes of Health
Role: Principal Investigator
$1,950,000 - January 2013–December 2014
Function of Onecut transcription factors in retinal development and vision
SUNY Research Foundation
Role: Principal Investigator
$100,000 - January 2010–December 2013
Molecular mechanism for the formation of retinal ganglion cells
The Whitehall Foundation
Role: Principal Investigator
$225,000 - January 2009–December 2009
Math5 target genes in retinal ganglion cell formation
The Glaucoma Foundation
Role: Principal Investigator
$40,000 - July 2005–June 2007
Investigating retinal ganglion cell development using purified progenitor cells
The E. Matilda Ziegler Foundation for the Blind
Role: Principal Investigator
$210,000
Journal Articles:
- Wu F, Kaczynski TJ, Sethuramanujam S, Li R, Jain V, Slaughter M, Mu X. Two transcription factors, Pou4f2 and Isl1, are sufficient to specify the retinal ganglion cell fate.. Proc Natl Acad Sci U S A. 2015; 112(13).
- Wu F, Bard JE, Kann J, Yergeau D, Sapkota D, Ge Y, Hu Z, Wang J, Liu T, Mu X. Single cell transcriptomics reveals lineage trajectory of retinal ganglion cells in wild-type and Atoh7-null retinas. Nat Commun. 2021; 12(1).
- Ge Y, Wu F, Cheng M, Bard J, Mu X. Two new genetically modified mouse alleles labeling distinct phases of retinal ganglion cell development by fluorescent proteins. Dev Dyn. 2020.
- Ramachandra Rao S, Skelton LA, Wu F, Onysk A, Spolnik G, Danikiewicz W, Butler MC, Stacks DA, Surmacz L, Mu X, Swiezewska E, Pittler SJ, Fliesler SJ. Retinal Degeneration Caused by Rod-Specific Dhdds Ablation Occurs without Concomitant Inhibition of Protein N-Glycosylation. iScience. 2020; 23(6).
- Toch M, Harris A, Schakman O, Kondratskaya E, Boulland JL, Dauguet N, Debrulle S, Baudouin C, Hidalgo-Figueroa M, Mu X, Gow A, Glover JC, Tissir F, Clotman F. Onecut-dependent Nkx6.2 transcription factor expression is required for proper formation and activity of spinal locomotor circuits. Sci Rep. 2020; 10(1).
- Zhang Q, Zagozewski J, Cheng S, Dixit R, Zhang S, de Melo J, Mu X, Klein WH, Brown NL, Wigle JT, Schuurmans C, Eisenstat DD. Regulation of Brn3b by DLX1 and DLX2 is required for retinal ganglion cell differentiation in the vertebrate retina. Development. 2017; 144(9).
- Gao Z, Mao CA, Pan P, Mu X, Klein WH. Transcriptome of Atoh7 retinal progenitor cells identifies new Atoh7-dependent regulatory genes for retinal ganglion cell formation. Dev Neurobiol. 2014; 74(11).
- Sapkota D, Chintala H, Wu F, Fliesler SJ, Hu Z, Mu X. Onecut1 and Onecut2 redundantly regulate early retinal cell fates during development. Proc Natl Acad Sci U S A. 2014; 111(39).
- Li R, Wu F, Ruonala R, Sapkota D, Hu Z, Mu X. Isl1 and Pou4f2 form a complex to regulate target genes in developing retinal ganglion cells. PLoS One. 2014; 9(3).
- Shi M, Kumar SR, Motajo O, Kretschmer F, Mu X, Badea TC. Genetic interactions between Brn3 transcription factors in retinal ganglion cell type specification. PLoS One. 2013; 8(10).
- Ehrman LA, Mu X, Waclaw RR, Yoshida Y, Vorhees CV, Klein WH, Campbell K. The LIM homeobox gene Isl1 is required for the correct development of the striatonigral pathway in the mouse. Proc Natl Acad Sci U S A. 2013; 110(42).
- Wu F, Li R, Umino Y, Kaczynski TJ, Sapkota D, Li S, Xiang M, Fliesler SJ, Sherry DM, Gannon M, Solessio E, Mu X. Onecut1 Is Essential for Horizontal Cell Genesis and Retinal Integrity. J Neurosci. 2013; 33(32).
- Wu F, Sapkota D, Li R, Mu X. Onecut 1 and Onecut 2 are potential regulators of mouse retinal development. J Comp Neurol. 2012; 520(5).
- Edwards MM, McLeod DS, Li R, Grebe R, Bhutto I, Mu X, Lutty GA. The deletion of Math5 disrupts retinal blood vessel and glial development in mice. Exp Eye Res. 2012; 96(1).
- Sapkota D, Wu F, Mu X. Focus on Molecules: Math5 and retinal ganglion cells. Exp Eye Res. 2011; 93(6).
- Kiyama T, Mao CA, Cho JH, Fu X, Pan P, Mu X, Klein WH. Overlapping spatiotemporal patterns of regulatory gene expression are required for neuronal progenitors to specify retinal ganglion cell fate. Vision Res. 2011; 51(2).
- Fu X, Kiyama T, Li R, Russell M, Klein WH, Mu X. Epitope-tagging Math5 and Pou4f2: new tools to study retinal ganglion cell development in the mouse. Dev Dyn. 2009; 238(9).
- Cho JH, Mu X, Wang SW, Klein WH. Retinal ganglion cell death and optic nerve degeneration by genetic ablation in adult mice. Exp Eye Res. 2009; 88(3).
- Sapieha P, Sirinyan M, Hamel D, Zaniolo K, Joyal JS, Cho JH, Honoré JC, Kermorvant-Duchemin E, Varma DR, Tremblay S, Leduc M, Rihakova L, Hardy P, Klein WH, Mu X, Mamer O, Lachapelle P, Di Polo A, Beauséjour C, Andelfinger G, Mitchell G, Sennlaub F, Chemtob S. The succinate receptor GPR91 in neurons has a major role in retinal angiogenesis. Nat Med. 2008; 14(10).
- Mu X, Fu X, Beremand PD, Thomas TL, Klein WH. Gene regulation logic in retinal ganglion cell development: Isl1 defines a critical branch distinct from but overlapping with Pou4f2. Proc Natl Acad Sci U S A. 2008; 105(19).
- Burke RD, Angerer LM, Elphick MR, Humphrey GW, Yaguchi S, Kiyama T, Liang S, Mu X, Agca C, Klein WH, Brandhorst BP, Rowe M, Wilson K, Churcher AM, Taylor JS, Chen N, Murray G, Wang D, Mellott D, Olinski R, Hallböök F, Thorndyke MC. A genomic view of the sea urchin nervous system. Dev Biol. 2006; 300(1).
- Fu X, Sun H, Klein WH, Mu X. Beta-catenin is essential for lamination but not neurogenesis in mouse retinal development. Dev Biol. 2006; 299(2).
- Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevière AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R. The genome of the sea urchin Strongylocentrotus purpuratus. Science. 2006; 314(5801).
- Mu X, Fu X, Sun H, Beremand PD, Thomas TL, Klein WH. A gene network downstream of transcription factor Math5 regulates retinal progenitor cell competence and ganglion cell fate. Dev Biol. 2005; 280(2).
- Mu X, Fu X, Sun H, Liang S, Maeda H, Frishman LJ, Klein WH. Ganglion cells are required for normal progenitor- cell proliferation but not cell-fate determination or patterning in the developing mouse retina. Curr Biol. 2005; 15(6).
- Martin SE, Mu X, Klein WH. Identification of an N-terminal transcriptional activation domain within Brn3b/POU4f2. Differentiation. 2005; 73(1).
- Liang S, Zhao S, Mu X, Thomas T, Klein WH. Novel retinal genes discovered by mining the mouse embryonic RetinalExpress database. Mol Vis. 2004; 10.
- Mu X, Beremand PD, Zhao S, Pershad R, Sun H, Scarpa A, Liang S, Thomas TL, Klein WH. Discrete gene sets depend on POU domain transcription factor Brn3b/Brn-3.2/POU4f2 for their expression in the mouse embryonic retina. Development. 2004; 131(6).
- Mu X, Klein WH. A gene regulatory hierarchy for retinal ganglion cell specification and differentiation. Semin Cell Dev Biol. 2004; 15(1).
- Fortunel NO, Otu HH, Ng HH, Chen J, Mu X, Chevassut T, Li X, Joseph M, Bailey C, Hatzfeld JA, Hatzfeld A, Usta F, Vega VB, Long PM, Libermann TA, Lim B. Comment on " ‘Stemness‘: transcriptional profiling of embryonic and adult stem cells" and "a stem cell molecular signature". Science. 2003; 302(5644).
- Wang SW, Mu X, Bowers WJ, Klein WH. Retinal ganglion cell differentiation in cultured mouse retinal explants. Methods. 2002; 28(4).
- Wang SW, Mu X, Bowers WJ, Kim DS, Plas DJ, Crair MC, Federoff HJ, Gan L, Klein WH. Brn3b/Brn3c double knockout mice reveal an unsuspected role for Brn3c in retinal ganglion cell axon outgrowth. Development. 2002; 129(2).
- Mu X, Zhao S, Pershad R, Hsieh TF, Scarpa A, Wang SW, White RA, Beremand PD, Thomas TL, Gan L, Klein WH. Gene expression in the developing mouse retina by EST sequencing and microarray analysis. Nucleic Acids Res. 2001; 29(24).
- Mu X, Spanos SA, Shiloach J, Kimmel A. CRTF is a novel transcription factor that regulates multiple stages of Dictyostelium development. Development. 2001; 128(13).
- Mu X, Lee B, Louis JM, Kimmel AR. Sequence-specific protein interaction with a transcriptional enhancer involved in the autoregulated expression of cAMP receptor 1 in Dictyostelium. Development. 1998; 125(18).