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In this Section

Thomas Lufkin
Professor and Bayard and Virginia Clarkson Endowed Chair in Biology

Department of Biology

155 Science Center

Clarkson University
PO Box 5805

Potsdam, NY 13699-5805

Web site

Phone: 315-268-6641


Ph.D. Cornell University (Molecular Biology and Virology)

A.B.  University of California, Berkeley (Cell Biology)

 Editorial Board Member

  • Frontiers in Stem Cell Treatments
  • BioMed Research International
  • Dataset papers in science
  • Frontiers in Bioengineering and Biotechnology

Courses Currently Taught

BY476/BY576 - Current Topics in Biology and Medicine
BY488/BY588 - Stem Cells and Regenerative Medicine

Research Interests

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.

Publications (last 5 years)

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 (2015). Tetratricopeptide Repeat Domain 9A Negatively Regulates Estrogen Receptor Alpha Activity. International Journal of Biological Sciences, 11(4): 434-447. 10.7150/ijbs.9311

Kraus, P., C.L. Winata and T. Lufkin (2015). BAC Transgenic zebrafish for transcriptional promoter and enhancer studies. Methods in Molecular Biology, 1227: 245-258. 10.1007/978-1-4939-1652-8_12

Kraus, P., V. Kocsis, C. Williams, B. Youngs and T. Lufkin (2015). 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, 37(8): 1573-1577. 10.1007/s10529-015-1833-1

Chatterjee, S., V. Sivakamasundari, P. Kraus, S.P. Yap, V. Kumar, S. Prabhakar and T. Lufkin (2015). Gene expression profiles of expressing FACS sorted cells from wildtype and null mouse embryos. Genomics Data, 5: 103-105. 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 (2014). Klf2 Is an Essential Factor that Sustains Ground State Pluripotency. Cell Stem Cell, 14(6): 864-872. 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, M.H. de Angelis, T. Lufkin and L.W. Stanton (2014). Pleiotropic Functions for Transcription Factor Zscan10. PLoS ONE, 9(8): e104568. 10.1371/journal.pone.0104568

Kraus, P., V. Sivakamasundari, X. Xing and T. Lufkin (2014). Generating mouse lines for lineage tracing and knockout studies. Methods in Molecular Biology, 1194: 37-62. 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 (2014). 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, 15(1): 1072. 10.1186/1471-2164-15-1072

Sng, J. and T. Lufkin (2013). Chapter 17: Advances in Stem Cell Therapies. Pluripotent Stem Cells. N. Lenka. Rijeka, InTech. 1: 375-396.

Sivakamasundari, V. and T. Lufkin (2013). Stemming The Degeneration: IVD Stem Cells And Stem Cell Regenerative Therapy For Degenerative Disc Disease. Advances in Stem Cells, Article ID 724547: 1-22. 10.5171/2013.724547

Sivakamasundari, V., P. Kraus, S. Jie and T. Lufkin (2013). Pax1(EGFP) : New wildtype and mutant EGFP mouse lines for molecular and fate mapping studies. Genesis: J of Genetics and Development, 51(6): 420-429. 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 (2013). In Vivo epigenomic profiling of germ cells reveals germ cell molecular signatures. Developmental Cell, 24(3): 324-333. 10.1016/j.devcel.2012.12.011

Kumar, V., M. Muratani, N.A. Rayan, P. Kraus, T. Lufkin, H.H. Ng and S. Prabhakar (2013). Uniform, optimal signal processing of mapped deep-sequencing data. Nature Biotechnology, 31(7): 615-622. 10.1038/nbt.2596

Kraus, P., V. Sivakamasundari, S.L. Lim, X. Xing, L. Lipovich and T. Lufkin (2013). Making sense of Dlx1 antisense RNA. Developmental Biology, 376: 224–235. 10.1016/j.ydbio.2013.01.035

Chatterjee, S., P. Kraus, V. Sivakamasundari, X. Xing, S.P. Yap, S. Jie and T. Lufkin (2013). A conditional mouse line for lineage tracing of Sox9 loss-of-function cells using enhanced green fluorescent protein. Biotechnology Letters, 35(12): 1991-1996. 10.1007/s10529-013-1303-6

Sng, J. and T. Lufkin (2012). Filling the Silent Void: Genetic Therapies for Hearing Impairment. Genetics Research International, 2012 Article ID 748698: 1-9 Epub 2012 Dec 2014. 10.1155/2012/748698

Sng, J. and T. Lufkin (2012). Emerging stem cell therapies: treatment, safety, and biology. Stem Cells International, 2012: 521343. 10.1155/2012/521343

Sivakamasundari, V. and T. Lufkin (2012). Bridging the Gap: Understanding Embryonic Intervertebral Disc Development. Cell & Developmental Biology, 1(2). 10.4172/cdb.1000103

Sivakamasundari, V., H.Y. Chan, S.P. Yap, X. Xing, P. Kraus and T. Lufkin (2012). New Bapx1(Cre-EGFP) mouse lines for lineage tracing and conditional knockout studies. Genesis: J of Genetics and Development, 50(4): 375-383. 10.1002/dvg.20802

Lee, W.J., P. Kraus and T. Lufkin (2012). Endogenous tagging of the murine transcription factor Sox5 with hemaglutinin for functional studies. Transgenic Research, 21(2): 293-301. 10.1007/s11248-011-9531-9

Lee, M.Y. and T. Lufkin (2012). 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, 23(2): 69-77. 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 (2012). Mouse strain specific gene expression differences for Illumina microarray expression profiling in embryos. BMC Research Notes 5: 232. 10.1186/1756-0500-5-232

Chatterjee, S., V. Sivakamasundari, W.J. Lee, H.Y. Chan and T. Lufkin (2012). Making no bones about it: Transcription factors in vertebrate skeletogenesis and disease. Trends in Developmental Biology, 6: 45-52. 00000

Chatterjee, S. and T. Lufkin (2012). Regulatory Genomics: Insights from the Zebrafish. Current Topics in Genetics, 5: 1-10. 00000

Yap, S.P., X. Xing, P. Kraus, V. Sivakamasundari, H.Y. Chan and T. Lufkin (2011). Generation of mice with a novel conditional null allele of the Sox9 gene. Biotechnology Letters, 33(8): 1551-1558. 10.1007/s10529-011-0608-6

Wang, B., T. Lufkin and J.L. Rubenstein (2011). Dlx6 regulates molecular properties of the striatum and central nucleus of the amygdala. The Journal of Comparative Neurology, 519(12): 2320-2334. 10.1002/cne.22618

Phua, S.L., V. Sivakamasundari, Y. Shao, X. Cai, L.F. Zhang, T. Lufkin and M. Featherstone (2011). Nuclear Accumulation of an Uncapped RNA Produced by Drosha Cleavage of a Transcript Encoding miR-10b and HOXD4. PLoS ONE, 6(10): e25689. 10.1371/journal.pone.0025689

Ng, P. and T. Lufkin (2011). Ch. 16 - Building a Pluripotency Interaction Network for Embryonic Stem Cells. Embryonic Stem Cells - Basic Biology to Bioengineering. M. S. Kallos. Rijeka, InTech. 1: 305-320.

Ng, P. and T. Lufkin (2011). Embryonic Stem Cells: Protein-Interaction Networks. BioMolecular Concepts, 2(1-2): 13-25. 10.1515/bmc.2011.008

Lam, S.H., S.G. Lee, C.Y. Lin, J.S. Thomsen, P.Y. Fu, K.R. Murthy, H. Li, K.R. Govindarajan, L. Nick, G. Bourque, Z. Gong, T. Lufkin, E.T. Liu and S. Mathavan (2011). Molecular conservation of estrogen-response associated with cell cycle regulation, hormonal carcinogenesis and cancer in zebrafish and human cancer cell lines. BMC Medical Genomics, 4(1): 41. 10.1186/1755-8794-4-41

Cheong, C.Y. and T. Lufkin (2011). Alternative splicing in self-renewal of embryonic stem cells. Stem Cells International, In Special Issue on "Stem Cells and Nuclear Reprogramming": 560261. 10.4061/2011/560261

Cheong, C.Y., P.M. Lon Ng, R. Ponnampalam, H.H. Tsai, G. Bourque and T. Lufkin (2011). In silico tandem affinity purification refines an Oct4 interaction list. Stem Cell Research & Therapy, 2(3): 26. 10.1186/scrt67

Chatterjee, S. and T. Lufkin (2011). The Sounds of Silence: Mouse Models of Hearing Loss. Genetics Research International. 10.4061/2011/416450

Chatterjee, S. and T. Lufkin (2011). Fishing for function: zebrafish BAC transgenics for functional genomics. Molecular BioSystems, 7(8): 2345-2351. 10.1039/c1mb05116d

Chatterjee, S., G. Bourque and T. Lufkin (2011). Conserved and non-conserved enhancers direct tissue specific transcription in ancient germ layer specific developmental control genes. BMC Developmental Biology, 11: 63. 10.1186/1471-213X-11-63

Chan, H.Y., V. Sivakamasundari, X. Xing, P. Kraus, S.P. Yap, P. Ng, S.L. Lim and T. Lufkin (2011). Comparison of IRES and F2A-Based Locus-Specific Multicistronic Expression in Stable Mouse Lines. PLoS ONE, 6(12): e28885. 10.1371/journal.pone.0028885

Wang, Y., C.A. Dye, V. Sohal, J.E. Long, R.C. Estrada, T. Roztocil, T. Lufkin, K. Deisseroth, S.C. Baraban and J.L. Rubenstein (2010). Dlx5 and Dlx6 regulate the development of parvalbumin-expressing cortical interneurons. J Neuroscience, 30(15): 5334-5345.

Sheng, D., D. Qu, K.H. Kwok, S.S. Ng, A.Y. Lim, S.S. Aw, C.W. Lee, W.K. Sung, E.K. Tan, T. Lufkin, S. Jesuthasan, M. Sinnakaruppan and J. Liu (2010). Deletion of the WD40 domain of LRRK2 in Zebrafish causes Parkinsonism-like loss of neurons and locomotive defect. PLoS Genetics, 6(4): e1000914. 10.1371/journal.pgen.1000914

Kraus, P., G. Leong, V. Tan, X. Xing, J.W. Goh, S.P. Yap and T. Lufkin (2010). A more cost effective and rapid high percentage germ-line transmitting chimeric mouse generation procedure via microinjection of 2-cell, 4-cell, and 8-cell embryos with ES and iPS cells. Genesis: J of Genetics and Development, 48(6): 394-399. 10.1002/dvg.20627

Heng, J.C., B. Feng, J. Han, J. Jiang, P. Kraus, J.H. Ng, Y.L. Orlov, M. Huss, L. Yang, T. Lufkin, B. Lim and H.H. Ng (2010). The nuclear receptor Nr5a2 can replace Oct4 in the reprogramming of murine somatic cells to pluripotent cells. Cell Stem Cell, 6(2): 167-174. 10.1016/j.stem.2009.12.009

Han, J., P. Yuan, H. Yang, J. Zhang, B.S. Soh, P. Li, S.L. Lim, S. Cao, J. Tay, Y.L. Orlov, T. Lufkin, H.H. Ng, W.L. Tam and B. Lim (2010). Tbx3 improves the germ-line competency of induced pluripotent stem cells. Nature, 463(7284): 1096-1100. 10.1038/nature08735

Chia, N.Y., Y.S. Chan, B. Feng, X. Lu, Y.L. Orlov, D. Moreau, P. Kumar, L. Yang, J. Jiang, M.S. Lau, M. Huss, B.S. Soh, P. Kraus, P. Li, T. Lufkin, B. Lim, N.D. Clarke, F. Bard and H.H. Ng (2010). A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Nature, 468(7321): 316-320. 10.1038/nature09531

Cheong, C.Y. and T. Lufkin (2010). Transcriptional repression in ES cells. J Cell Biochem, 110(2): 288-293. 10.1002/jcb.22576

Chatterjee, S., L. Min, R.K. Karuturi and T. Lufkin (2010). The role of post-transcriptional RNA processing and plasmid vector sequences on transient transgene expression in zebrafish. Transgenic Research, 19(2): 299-304. 10.1007/s11248-009-9312-x

Chatterjee, S., P. Kraus and T. Lufkin (2010). A symphony of inner ear developmental control genes. BMC Genetics, 11: 68. 10.1186/1471-2156-11-68

Patents Issued

1. 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

2. U.S. Patent. 6031149. Genetically engineered mice containing alterations in the genes encoding retinoic acid receptor proteins. Issue Date: 2000-02-29

3. U.S. Patent. 6486381. Genetically engineered mice containing alterations in the genes encoding retinoic acid receptor proteins. Issue Date: 2002-11-2

4. U.S. Patent. 20090233986A1. Methods and compositions for using the Sax2 gene. Issue Date: 2009-09-17

5. U.S. Patent. 20110165570A1. Method Of Effecting De-Differentiation Of A Cell. Issue Date: 2011-07-07