Cornell University
University of California, Berkeley
Our research is in the novel area of Developmental Genomics and Regenerative Medicine with a focus on the molecular mechanisms controlling vertebral column development and an emphasis on early embryogenesis and embryonic stem cell commitment to specific differentiation pathways, but from a novel Systems Biology point of view. We use both mouse and zebrafish as model animals. In particular we are working on understanding the gene regulatory networks (GRNs) that govern normal embryonic development of the vertebral column and intervertebral disc (IVD). We are investigating the role of transcriptional regulators in the restriction of pluripotent embryonic stem cells into specific lineages that in turn comprise functional pre and postnatal vertebral elements with the goal of applying this knowledge to regenerative medicine using patient- specific induced pluripotent stem (iPS) cells and adult mesenchymal stem cells.
The incidence of lower back pain (LBP) is extraordinarily high and is a cause for societal and fiscal concern world wide. In the USA alone, LBP’s economic impact shows that it is the number one reason for people under 45 to restrict their life style, 2nd highest complaint seen by physician’s, 3rd leading cause for surgery and the 5th most common requirement for hospitalization. The economic impact of LBP is striking, and is in excess of the costs of coronary artery disease and the total costs of stroke, respiratory infection, rheumatoid disease and diabetes combined. Direct medical costs in the USA annually exceed USD $30 billion. Most often, LBP is due to degenerative changes in the disc, spinal disc herniation, trauma and fractures. Surgeons have an arsenal of procedures for repairing the damaged disc. The most common strategies provide pain relief, but fail to prevent further disc degeneration, or completely restore disc function. Thus these surgical procedures are less than ideal, as they do not prevent further degeneration of the impaired vertebral column.
Our current focus is on the Pax, Sox, Bapx and Runx GRNs in the commitment of cells to the chondro/osteoblast lineages which builds the fetal skeleton. Our goal here is to build a unified GRN for embryonic skeletal development as it pertains to the vertebral column and use this knowledge to direct iPS cells to fates of clinical significance and to provide a resource to reverse trauma and age-associated spinal degeneration. In particular the IVD. Our approach is multidisciplinary, collaborative, and technology-driven. We have been highly successful at developing novel experimental strategies that combine modern molecular genetic and transgenic approaches in mouse and zebrafish with the latest bioinformatic and genomic technologies such as comparative genomics, microarray, Ditag-Seq, ChIP-Seq, RNA-Seq and others. By applying these approaches in developing embryos, we show how relevant biological data can be generated to explain pleiotropic effects in organogenesis and finally by combining these approaches simultaneously with multiple interconnected genes, we have shown how a detailed network map can be elucidated for the developing vertebral column, reiterating the importance of building gene regulatory networks in complex processes.
In recent decades developmental biologists have been successful in determining some molecular level mechanisms controlling vertebral column development, such as the genes governing cell fate decisions, but have made comparatively little progress in other equally important areas such as patterning, morphogenesis, size control and regeneration. There is a major reason for this failure. These questions cannot be answered using the reductionist logic of one gene, one mutant, one phenotype, one function. Understanding these phenomena will require a more systems biological approach looking at multiple genes and their integrated activity in their native in vivo context using genomic approaches.
- U.S. Patent. 6030794. Genetically engineered mice and cell lines containing alterations in the genes encoding retinoic acid receptor and retinoid X receptor proteins. Issue Date: 2000-02-29
- U.S. Patent. 6031149. Genetically engineered mice containing alterations in the genes encoding retinoic acid receptor proteins. Issue Date: 2000-02-29
- U.S. Patent. 6486381. Genetically engineered mice containing alterations in the genes encoding retinoic acid receptor proteins. Issue Date: 2002-11-2
- U.S. Patent. 20090233986A1. Methods and compositions for using the Sax2 gene. Issue Date: 2009-09-17
- U.S. Patent. 20110165570A1. Method Of Effecting De-Differentiation Of A Cell. Issue Date: 2011-07-07
Complete List of Published Work at NCBI: https://www.ncbi.nlm.nih.gov/sites/myncbi/thomas.lufkin.1/bibliography/public/
Li, K., D. Kapper, B. Youngs, V. Kocsis, S. Mondal, P. Kraus, and T. Lufkin, Potential biomarkers of the mature intervertebral disc identified at the single cell level. J Anat, 2019. 234(1): p. 16-32. DOI: 10.1111/joa.12904
Li, K., D. Kapper, S. Mondal, T. Lufkin, and P. Kraus, Quantitative Single-Cell Transcript Assessment of Biomarkers Supports Cellular Heterogeneity in the Bovine IVD. Veterinary Sciences, 2019. 6(2): p. 1-19. DOI: 10.3390/vetsci6020042
Kraus, P., K. Li, D. Sipes, L. Varden, R. Yerden, A. Henderson, S. Sur, and T. Lufkin, Single-Cell Phenotyping of Complex Heterogeneous Tissue, in Handbook of Single Cell Technologies, T.S. Santra and F.-G. Tseng, Editors. 2019, Springer Singapore: Singapore. p. 1-17. DOI: 10.1007/978-981-10-4857-9_16-1. ISBN 978-981-10-4857-9
Sivakamasundari, V., P. Kraus, and T. Lufkin, Regulatory Functions of Pax1 and Pax9 in Mammalian Cells, in Gene Expression and Regulation in Mammalian Cells - Transcription Toward the Establishment of Novel Therapeutics, A. Sebata, Editor 2018, InTech: Rijeka. p. Ch. 9, 181-207. DOI: 10.5772/intechopen.71920. ISBN 978-953-51-3868-6
Kraus, P., R. Yerden, D. Sipes, S. Sur, and T. Lufkin, A quantitative and qualitative RNA expression profiling assay for cell culture with single cell resolution. Cytotechnology, 2018. 70(1): p. 185-192. DOI: 10.1007/s10616-017-0132-1
Kraus, P., V. Sivakamasundari, V. Olsen, V. Villeneuve, A. Hinds, and T. Lufkin, Klhl14 Antisense RNA is a Target of Key Skeletogenic Transcription Factors in the Developing Intervertebral Disc. Spine (Phila Pa 1976), 2018. DOI: 10.1097/BRS.0000000000002827
Sivakamasundari, V., P. Kraus, W. Sun, X. Hu, S.L. Lim, S. Prabhakar, and T. Lufkin, A developmental transcriptomic analysis of Pax1 and Pax9 in embryonic intervertebral disc development. Biol Open, 2017. 6(2): p. 187-199. DOI: 10.1242/bio.023218
Nusspaumer, G., S. Jaiswal, A. Barbero, R. Reinhardt, D. Ishay Ronen, A. Haumer, T. Lufkin, I. Martin, and R. Zeller, Ontogenic Identification and Analysis of Mesenchymal Stromal Cell Populations during Mouse Limb and Long Bone Development. Stem Cell Reports, 2017. 9(4): p. 1124-1138. DOI: 10.1016/j.stemcr.2017.08.007
Nichane, M., A. Javed, V. Sivakamasundari, M. Ganesan, L.T. Ang, P. Kraus, T. Lufkin, K.M. Loh, and B. Lim, Isolation and 3D expansion of multipotent Sox9(+) mouse lung progenitors. Nat Methods, 2017. 14(12): p. 1205-1212. DOI: 10.1038/nmeth.4498
Nichane, M., A. Javed, V. Sivakamasundari, M. Ganesan, L.T. Ang, P. Kraus, T. Lufkin, K.M. Loh, and B. Lim, 3D culture of multipotent Sox9+ mouse embryonic lung progenitors: Isolation, Expansion and Cryopreservation. Protocol Exchange, 2017. DOI: 10.1038/protex.2017.106
Lee, W.J., S. Chatterjee, S.P. Yap, S.L. Lim, X. Xing, P. Kraus, W. Sun, X. Hu, V. Sivakamasundari, H.Y. Chan, P.R. Kolatkar, S. Prabhakar, and T. Lufkin, An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos. Biomed Res Int, 2017. 2017: p. 8932583. DOI: 10.1155/2017/8932583
Kraus, P., R. Yerden, V. Kocsis, and T. Lufkin, RNA in situ hybridization characterization of non-enzymatic derived bovine intervertebral disc cell lineages suggests progenitor cell potential. Acta Histochemistry, 2017. 119(2): p. 150-160. DOI: 10.1016/j.acthis.2016.12.004
Kraus, P. and T. Lufkin, Implications for a Stem Cell Regenerative Medicine Based Approach to Human Intervertebral Disk Degeneration. Front Cell Dev Biol, 2017. 5: p. 17. DOI: 10.3389/fcell.2017.00017
Lim, L.W., S. Shrestha, Y.Z. Or, S.Z. Tan, H.H. Chung, Y. Sun, C.L. Lim, S. Khairuddin, T. Lufkin, and V.C. Lin, Tetratricopeptide repeat domain 9A modulates anxiety-like behavior in female mice. Sci Rep, 2016. 6: p. 37568. DOI: 10.1038/srep37568
Kumar, V., N.A. Rayan, M. Muratani, S. Lim, B. Elanggovan, X. Lixia, T. Lu, H. Makhija, J. Poschmann, T. Lufkin, H.H. Ng, and S. Prabhakar, Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters. Genome Research, 2016. 26(5): p. 612-23. DOI: 10.1101/gr.201038.115
Kraus, P. and T. Lufkin, Bovine annulus fibrosus cell lines isolated from intervertebral discs. Genomics Data, 2016. 10: p. 83-89. DOI: 10.1016/j.gdata.2016.09.012
Chatterjee, S., P. Kraus, V. Sivakamasundari, S.P. Yap, V. Kumar, S. Prabhakar, and T. Lufkin, Genome wide binding (ChIP-Seq) of murine Bapx1 and Sox9 proteins in vivo and in vitro. Genomics Data, 2016. 10: p. 51-59. DOI: 10.1016/j.gdata.2016.09.002
Shrestha, S., Y. Sun, T. Lufkin, P. Kraus, Y. Or, Y.A. Garcia, N. Guy, P. Ramos, M.B. Cox, F. Tay, and V.C. Lin, Tetratricopeptide Repeat Domain 9A Negatively Regulates Estrogen Receptor Alpha Activity. International Journal of Biological Sciences, 2015. 11(4): p. 434-47. DOI: 10.7150/ijbs.9311
Kraus, P., C.L. Winata, and T. Lufkin, BAC Transgenic zebrafish for transcriptional promoter and enhancer studies. Methods Mol Biol, 2015. 1227: p. 245-58. DOI: 10.1007/978-1-4939-1652-8_12
Kraus, P., V. Kocsis, C. Williams, B. Youngs, and T. Lufkin, Plate in situ hybridization (PISH) as a time and cost effective RNA expression assay to study phenotypic heterogeneity in a population of cultured murine cells at single cell resolution. Biotechnology Letters, 2015. 37(8): p. 1573-1577. DOI: 10.1007/s10529-015-1833-1
Chatterjee, S., V. Sivakamasundari, P. Kraus, S.P. Yap, V. Kumar, S. Prabhakar, and T. Lufkin, Gene expression profiles of expressing FACS sorted cells from wildtype and null mouse embryos. Genomics Data, 2015. 5: p. 103-105. DOI: 10.1016/j.gdata.2015.05.031
Yeo, J.C., J. Jiang, Z.Y. Tan, G.R. Yim, J.H. Ng, J. Goke, P. Kraus, H. Liang, K.A. Gonzales, H.C. Chong, C.P. Tan, Y.S. Lim, N.S. Tan, T. Lufkin, and H.H. Ng, Klf2 Is an Essential Factor that Sustains Ground State Pluripotency. Cell Stem Cell, 2014. 14(6): p. 864-872. DOI: 10.1016/j.stem.2014.04.015
Kraus, P., S. V, H.B. Yu, X. Xing, S.L. Lim, T. Adler, J.A. Pimentel, L. Becker, A. Bohla, L. Garrett, W. Hans, S.M. Holter, E. Janas, K. Moreth, C. Prehn, O. Puk, B. Rathkolb, J. Rozman, J. Adamski, R. Bekeredjian, D.H. Busch, J. Graw, M. Klingenspor, T. Klopstock, F. Neff, M. Ollert, T. Stoeger, A.O. Yildrim, O. Eickelberg, E. Wolf, W. Wurst, H. Fuchs, V. Gailus-Durner, M.H. de Angelis, T. Lufkin, and L.W. Stanton, Pleiotropic Functions for Transcription Factor Zscan10. PLoS ONE, 2014. 9(8): p. e104568. DOI: 10.1371/journal.pone.0104568
Kraus, P., V. Sivakamasundari, X. Xing, and T. Lufkin, Generating mouse lines for lineage tracing and knockout studies. Methods Mol Biol, 2014. 1194: p. 37-62. DOI: 10.1007/978-1-4939-1215-5_3
Chatterjee, S., V. Sivakamasundari, S.P. Yap, P. Kraus, V. Kumar, X. Xing, S.L. Lim, J. Sng, S. Prabhakar, and T. Lufkin, In vivo genome-wide analysis of multiple tissues identifies gene regulatory networks, novel functions and downstream regulatory genes for Bapx1 and its co-regulation with Sox9 in the mammalian vertebral column. BMC Genomics, 2014. 15(1): p. 1072. DOI: 10.1186/1471-2164-15-1072
Sng, J. and T. Lufkin, Chapter 17: Advances in Stem Cell Therapies, in Pluripotent Stem Cells, N. Lenka, Editor 2013, InTech: Rijeka. p. 375-396. DOI: 10.5772/55061. ISBN 978-953-51-1192-4
Sivakamasundari, V. and T. Lufkin, Stemming The Degeneration: IVD Stem Cells And Stem Cell Regenerative Therapy For Degenerative Disc Disease. Advances in Stem Cells, 2013. Article ID 724547: p. 1-22. DOI: 10.5171/2013.724547
Sivakamasundari, V., P. Kraus, S. Jie, and T. Lufkin, Pax1(EGFP) : New wildtype and mutant EGFP mouse lines for molecular and fate mapping studies. Genesis: J of Genetics and Development, 2013. 51(6): p. 420-9. DOI: 10.1002/dvg.22379
Ng, J.H., V. Kumar, M. Muratani, P. Kraus, J.C. Yeo, L.P. Yaw, K. Xue, T. Lufkin, S. Prabhakar, and H.H. Ng, In Vivo epigenomic profiling of germ cells reveals germ cell molecular signatures. Developmental Cell, 2013. 24(3): p. 324-33. DOI: 10.1016/j.devcel.2012.12.011
Kumar, V., M. Muratani, N.A. Rayan, P. Kraus, T. Lufkin, H.H. Ng, and S. Prabhakar, Uniform, optimal signal processing of mapped deep-sequencing data. Nature Biotechnology, 2013. 31(7): p. 615-22. DOI: 10.1038/nbt.2596
Kraus, P., V. Sivakamasundari, S.L. Lim, X. Xing, L. Lipovich, and T. Lufkin, Making sense of Dlx1 antisense RNA. Developmental Biology, 2013. 376: p. 224–235. DOI: 10.1016/j.ydbio.2013.01.035
Chatterjee, S., P. Kraus, V. Sivakamasundari, X. Xing, S.P. Yap, S. Jie, and T. Lufkin, A conditional mouse line for lineage tracing of Sox9 loss-of-function cells using enhanced green fluorescent protein. Biotechnology Letters, 2013. 35(12): p. 1991-6. DOI: 10.1007/s10529-013-1303-6
Sng, J. and T. Lufkin, Filling the Silent Void: Genetic Therapies for Hearing Impairment. Genetics Research International, 2012. 2012 Article ID 748698: p. 1-9 Epub 2012 Dec 4. DOI: 10.1155/2012/748698
Sng, J. and T. Lufkin, Emerging stem cell therapies: treatment, safety, and biology. Stem Cells International, 2012. 2012: p. 521343. DOI: 10.1155/2012/521343
Sivakamasundari, V. and T. Lufkin, Bridging the Gap: Understanding Embryonic Intervertebral Disc Development. Cell & Developmental Biology, 2012. 1(2): p. 1-7. DOI: 10.4172/cdb.1000103
Sivakamasundari, V., H.Y. Chan, S.P. Yap, X. Xing, P. Kraus, and T. Lufkin, New Bapx1(Cre-EGFP) mouse lines for lineage tracing and conditional knockout studies. Genesis: J of Genetics and Development, 2012. 50(4): p. 375-83. DOI: 10.1002/dvg.20802
Lee, W.J., P. Kraus, and T. Lufkin, Endogenous tagging of the murine transcription factor Sox5 with hemaglutinin for functional studies. Transgenic Research, 2012. 21(2): p. 293-301. DOI: 10.1007/s11248-011-9531-9
Lee, M.Y. and T. Lufkin, Development of the “Three-step MACS”: a novel strategy for isolating rare cell populations in the absence of known cell surface markers from complex animal tissue. J Biomolecular Techniques, 2012. 23(2): p. 69-77. DOI: 10.7171/jbt.12-2302-003
Kraus, P., X. Xing, S.L. Lim, M.E. Fun, V. Sivakamasundari, S.P. Yap, H. Lee, R.K. Karuturi, and T. Lufkin, Mouse strain specific gene expression differences for Illumina microarray expression profiling in embryos. BMC Research Notes 2012. 5: p. 232. DOI: 10.1186/1756-0500-5-232
Chatterjee, S., V. Sivakamasundari, W.J. Lee, H.Y. Chan, and T. Lufkin, Making no bones about it: Transcription factors in vertebrate skeletogenesis and disease. Trends in Developmental Biology, 2012. 6: p. 45-52. DOI: 00000
Chatterjee, S. and T. Lufkin, Regulatory Genomics: Insights from the Zebrafish. Current Topics in Genetics, 2012. 5: p. 1-10. DOI: 00000