ZFIN Lab: Cheng Lab

ZFIN ID: ZDB-LAB-970424-122

Cheng Lab

PI/Director:	Cheng, Keith C.
Contact Person:	Cheng, Keith C.
Email:	kcheng@psu.edu
URL:	http://www.pennstatehershey.org/web/pathology/keith-cheng
Address:	The Jake Gittlen Cancer Research Institute Hershey Medical Center Pennsylvania State University College of Medicine 500 University Drive Hershey, PA 17033 USA
Country:	United States
Phone:	(717) 531-4704
Fax:	(717) 531-5634
Line Designation:	kc

GENOMIC FEATURES ORIGINATING FROM THIS LAB

Show all 20 genomic features

STATEMENT OF RESEARCH INTERESTS

Our laboratory is using genetics to dissect vertebrate mechanisms of mutation and cell differentiation, using the zebrafish as a model system. We used parthenogenetic screens to generate genomic instabilty mutants using a mosaic eye screen and cell differentiation mutants using histological arrays (manuscripts in preparation). We hypothesize that some of our mutants will be tumor suppressor genes.

LAB MEMBERS

Sinha, Soniya Graduate Student	Thomas, Georgia Graduate Student	Hubley, Peggy Research Staff
Mest, Jason Research Staff	Rush, Lindsay Research Staff	Sabaliauskas, Nicole Research Staff
Wentz, Christina Research Staff	Lighty, Melissa Fish Facility Staff

ZEBRAFISH PUBLICATIONS OF LAB MEMBERS

Katz, S.R., Yakovlev, M.A., Vanselow, D.J., Ding, Y., Lin, A.Y., Parkinson, D.Y., Wang, Y., Canfield, V.A., Ang, K.C., Cheng, K.C. (2021) Whole-organism 3D quantitative characterization of zebrafish melanin by silver deposition micro-CT. eLIFE. 10:

Yang, H., Luan, Y., Liu, T., Lee, H.J., Fang, L., Wang, Y., Wang, X., Zhang, B., Jin, Q., Ang, K.C., Xing, X., Wang, J., Xu, J., Song, F., Sriranga, I., Khunsriraksakul, C., Salameh, T., Li, D., Choudhary, M.N.K., Topczewski, J., Wang, K., Gerhard, G.S., Hardison, R.C., Wang, T., Cheng, K.C., Yue, F. (2020) A map of cis-regulatory elements and 3D genome structures in zebrafish. Nature. 588(7837):337-343

Van Nuffel, S., Ang, K.C., Lin, A.Y., Cheng, K.C. (2020) Chemical Imaging of Retinal Pigment Epithelium in Frozen Sections of Zebrafish Larvae Using ToF-SIMS. Journal of the American Society for Mass Spectrometry. 32(1):255-261

Ding, Y., Vanselow, D.J., Yakovlev, M.A., Katz, S.R., Lin, A.Y., Clark, D.P., Vargas, P., Xin, X., Copper, J.E., Canfield, V.A., Ang, K.C., Wang, Y., Xiao, X., De Carlo, F., van Rossum, D.B., La Riviere, P., Cheng, K. (2019) Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography. eLIFE. 8:

Lin, A.Y., Ding, Y., Vanselow, D.J., Katz, S.R., Yakovlev, M.A., Clark, D.P., Mandrell, D., Copper, J.E., van Rossum, D.B., Cheng, K.C. (2018) Rigid Embedding of Fixed and Stained, Whole, Millimeter-Scale Specimens for Section-free 3D Histology by Micro-Computed Tomography. Journal of visualized experiments : JoVE. (140)

Copper, J.E., Budgeon, L.R., Foutz, C.A., van Rossum, D.B., Vanselow, D.J., Hubley, M.J., Clark, D.P., Mandrell, D.T., Cheng, K.C. (2017) Comparative analysis of fixation and embedding techniques for optimized histological preparation of zebrafish. Comparative biochemistry and physiology. Toxicology & pharmacology : CBP. 208:38-46

Xin, X., Clark, D., Ang, K.C., van Rossum, D.B., Copper, J., Xiao, X., La Riviere, P.J., Cheng, K.C. (2017) Synchrotron microCT imaging of soft tissue in juvenile zebrafish reveals retinotectal projections. Proceedings of SPIE--the International Society for Optical Engineering. 10060:

Ding, Y., Tavolara, T., Cheng, K. (2016) Automated Detection of Retinal Cell Nuclei in 3D Micro-CT Images of Zebrafish using Support Vector Machine Classification. Proceedings of SPIE--the International Society for Optical Engineering. 9791:

Cheng, K.C., Katz, S.R., Lin, A.Y., Xin, X., Ding, Y. (2016) Whole-Organism Cellular Pathology: A Systems Approach to Phenomics. Advances in genetics. 95:89-115

Thomas, G.K. (2015) A molecular and systems biology analysis of pleiotropic vertebrate phenotypes. Ph.D. Thesis. :218

Tsetskhladze, Z.R., Canfield, V.A., Ang, K.C., Wentzel, S.M., Reid, K.P., Berg, A.S., Johnson, S.L., Kawakami, K., and Cheng, K.C. (2012) Functional assessment of human coding mutations affecting skin pigmentation using zebrafish. PLoS One. 7(10):e47398

Cheng, K.C., Xin, X., Clark, D.P., and La Riviere, P. (2011) Whole-animal imaging, gene function, and the Zebrafish Phenome Project. Current opinion in genetics & development. 21(5):620-9

Canada, B.A., Thomas, G.K., Cheng, K.C., and Wang, J.Z. (2011) SHIRAZ: an automated histology image annotation system for zebrafish phenomics. Multimedia Tools and Applications. 51(2):401-440

Ekker, S.C., Parichy, D.M., and Cheng, K.C. (2008) Research implications of pigment biology in zebrafish. Zebrafish. 5(4):233-235

Aleström, P., Begemann, G., Carvan, M.J. 3rd, Cheng, K.C., Crosier, K., Crosier, P., Ekker, S., Huttenlocher, A., Kawakami, K., Kelly, G., Korzh, V., Lieschke, G., Mione, M., Neely, M.N., Neuhauss, S., and Trede, N.S. (2008) Views on four key questions about zebrafish research. Zebrafish. 5(1):9-24

Chen, H., Leung, T., Giger, K.E., Stauffer, A.M., Humbert, J.E., Sinha, S., Horstick, E.J., Hansen, C.A., and Robishaw, J.D. (2007) Expression of the G protein gammaT1 subunit during zebrafish development. Gene expression patterns : GEP. 7(5):574-583

Moore, J.L., Rush, L.M., Breneman, C., Mohideen, M.A., and Cheng, K.C. (2006) Zebrafish Genomic Instability Mutants and Cancer Susceptibility. Genetics. 174(2):585-600

Leung, T., Chen, H., Stauffer, A.M., Giger, K.E., Sinha, S., Horstick, E.J., Humbert, J.E., Hansen, C.A., and Robishaw, J.D. (2006) Zebrafish G protein γ2 is required for VEGF signaling during angiogenesis. Blood. 108(1):160-166

Sabaliauskas, N.A., Foutz, C.A., Mest, J.R., Budgeon, L.R., Sidor, AT, Gershenson, J.A., Joshi, S.B., and Cheng, K.C. (2006) High-throughput zebrafish histology. Methods (San Diego, Calif.). 39(3):246-254

Blasiole, B., Canfield, V.A., Vollrath, M.A., Huss, D., Mohideen, M.A., Dickman, J.D., Cheng, K.C., Fekete, D.M., and Levenson, R. (2006) Separate Na,K-ATPase genes are required for otolith formation and semicircular canal development in zebrafish. Developmental Biology. 294(1):148-160

Tang, J., Hu, G., Hanai, J.I., Yadlapalli, G., Lin, Y., Zhang, B., Galloway, J., Bahary, N., Sinha, S., Thisse, B., Thisse, C., Jin, J.P., Zon, L.I., and Sukhatme, V.P. (2006) A critical role for calponin 2 in vascular development. The Journal of biological chemistry. 281(10):6664-6672

Canada, B.A., Cheng, K.C., and Wang, J.Z. (2006) QCHARM: A Novel Computational and Scientific Visualization Framework for Facilitating Discovery and Improving Diagnostic Reliability in Medicine. AMIA Annual Symposium proceedings. :870

Lamason, R.L., Mohideen, M.A., Mest, J.R., Wong, A.C., Norton, H.L., Aros, M.C., Jurynec, M.J., Mao, X., Humphreville, V.R., Humbert, J.E., Sinha, S., Moore, J.L., Jagadeeswaran, P., Zhao, W., Ning, G., Makalowska, I., McKeigue, P.M., O'donnell, D., Kittles, R., Parra, E.J., Mangini, N.J., Grunwald, D.J., Shriver, M.D., Canfield, V.A., and Cheng, K.C. (2005) SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science (New York, N.Y.). 310(5755):1782-1786

Croushore, J.A., Blasiole, B., Riddle, R.C., Thisse, C., Thisse, B., Canfield, V.A., Robertson, G.P., Cheng, K.C., and Levenson, R. (2005) Ptena and ptenb genes play distinct roles in zebrafish embryogenesis. Developmental Dynamics : an official publication of the American Association of Anatomists. 234(4):911-921

Duffy, K.T., McAleer, M.F., Davidson, W.R., Kari, L., Kari, C., Liu, C.G., Farber, S.A., Cheng, K.C., Mest, J.R., Wickstrom, E., Dicker, A.P., and Rodeck, U. (2005) Coordinate control of cell cycle regulatory genes in zebrafish development tested by cyclin D1 knockdown with morpholino phosphorodiamidates and hydroxyprolyl-phosphono peptide nucleic acids. Nucleic acids research. 33(15):4914-4921

Chan, B., Sinha, S., Cho, D., Ramchandran, R., and Sukhatme, V.P. (2005) Critical roles of CD146 in zebrafish vascular development. Developmental Dynamics : an official publication of the American Association of Anatomists. 232(1):232-244

Gerhard, G.S., Malek, R.L., Keller, E., Murtha, J., and Cheng, K.C. (2004) Zebrafish, Killifish, Neither Fish, Both Fish?. The journals of gerontology. Series A, Biological sciences and medical sciences. 59(9):B873-B875

Moore, J.L., Gestl, E.E., and Cheng, K.C.. (2004) Mosaic eyes, genomic instability mutants, and cancer susceptibility. The Zebrafish: Cellular and Developmental Biology,2nd Ed. Methods Cell Biol.. 76:555-568

Cheng, K.C., Levenson, R., and Robishaw, J.D. (2003) Functional genomic dissection of multimeric protein families in zebrafish. Developmental Dynamics : an official publication of the American Association of Anatomists. 228(3):555-567

Mohideen, M.A., Beckwith, L.G., Tsao-Wu, G.S., Moore, J.L., Wong, A.C., Chinoy, M.R., and Cheng, K.C. (2003) Histology-based screen for zebrafish mutants with abnormal cell differentiation. Developmental Dynamics : an official publication of the American Association of Anatomists. 228(3):414-423

Sinha, S. (2003) An in-situ hybridization study of g-protein gamma subunits in the developing zebrafish. Master's Thesis. :88P

Gerhard, G.S. and Cheng, K.C. (2002) A call to fins! Zebrafish as a gerontological model. Aging Cell. 1(2):104-111

Gerhard, G., Kauffman, E., Wang, X., Stewart, R., Moore, J., Kasales, C., Demidenko, E., and Cheng, K. (2002) Life spans and senescent phenotypes in two strains of zebrafish (Danio rerio). Experimental gerontology. 37(8-9):1055-1068

Clarke, L.E., Cheng, K., Beckwith, L.G., Moore, J.L., Wang, X., and Boyer, P.J. (2002) Expression in adult zebrafish of antigens detected by immunomarkers commonly used in diagnostic pathology laboratories: Prelude to evaluation of spontaneously arising and induced neoplasms. Journal of neuropathology and experimental neurology. 61(5):112

Moore, J.L., Aros, M., Steudel, K.G., and Cheng, K.C. (2002) Fixation and decalcification of adult zebrafish for histological, immunocytochemical, and genotypic analysis. Biotechniques. 32(2):296-298

Rajarao, S.J., Canfield, V.A., Mohideen, M.A., Yan, Y.-L., Postlethwait, J.H., Cheng, K.C., and Levenson, R. (2001) The repertoire of Na,K-ATPase alpha and beta subunit genes expressed in the zebrafish, Danio rerio. Genome research. 11(7):1211-1220

Mohideen, M.A.P.K., Moore, J.L., and Cheng, K.C. (2000) Centromere-linked microsatellite markers for linkage groups 3, 4, 6, 7, 13, and 20 of zebrafish (Danio rerio). Genomics. 67(1):102-106

Beckwith, L.G., Moore, J.L., Tsao-Wu, G.S., Harshbarger, J.C., and Cheng, K.C. (2000) Ethylnitrosourea induces neoplasia in zebrafish (Danio rerio). Laboratory investigation; a journal of technical methods and pathology. 80(3):379-385

Tsao-Wu, G.S., Weber, C.H., Budgeon, L.R., and Cheng, K.C. (1998) Agarose-embedded tissue arrays for histologic and genetic analysis. Biotechniques. 25:614-618

Cheng, K.C. and Moore, J.L. (1997) Genetic dissection of vertebrate processes in zebrafish: A comparison of uniparental and two-generation screens. Biochemistry and cell biology = Biochimie et biologie cellulaire. 75:525-533

Gestl, E.E., Kauffman, E.J., Moore, J.L., and Cheng, K.C. (1997) New conditions for generation of gynogenetic half-tetrad embryos in the zebrafish (Danio rerio). The Journal of heredity. 88(1):76-79

Kauffman, E.J., Gestl, E.E., Kim, D.J., Walker, C., Hite, J.M., Yan, G., Rogan, P.K., Johnson, S.L., and Cheng, K.C. (1995) Microsatellite-centromere mapping in the zebrafish (Danio rerio). Genomics. 30:337-341

Gestl, E.E. and Cheng, K.C. (1995) A small zebrafish genetics facility. Zebrafish Science Monitor. 3:6-8

Ham, P.H. and Cheng, K.C. (1995) Construction of zebrafish spawning cages. Zebrafish Science Monitor. 3:5

Cheng, K.C., E.J. Kauffman, and E. Gestl (1993) Tidbits (nibbles) on raising zebrafish babies. Zebrafish Science Monitor. 2:3,6