Recommended Readings: Denes Hnisz, Ph.D., October 12th

Special Lecture
Monday, October 12th, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Denes Hnisz, Ph.D.
Postdoctoral Fellow,
Whitehead Institute for Biomedical Research

Transcriptional Regulatory Mechanisms Defining Cell Identity

Recommended Readings

Dowen, J. M., Fan, Z. P., Hnisz, D., Ren, G., Abraham, B. J., Zhang, L. N., … & Young, R. A. (2014). Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Cell, 159(2), 374-387. doi:10.1016/j.cell.2014.09.030.

Hnisz, D., Abraham, B. J., Lee, T. I., Lau, A., Saint-André, V., Sigova, A. A., … & Young, R. A. (2013). Super-enhancers in the control of cell identity and disease. Cell, 155(4), 934-947. doi:10.1016/j.cell.2013.09.053.

Hnisz, D., Schuijers, J., Lin, C. Y., Weintraub, A. S., Abraham, B. J., Lee, T. I., … & Young, R. A. (2015). Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers. Molecular Cell, 58(2), 362-370. doi:10.1016/j.molcel.2015.02.014.

Whyte, W. A., Orlando, D. A., Hnisz, D., Abraham, B. J., Lin, C. Y., Kagey, M. H., … & Young, R. A. (2013). Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell, 153(2), 307-319. doi:10.1016/j.cell.2013.03.035.

Recommended Readings: Carl H. June, M.D., May 22nd

Friday Lecture Series
Friday, May 22, 2015
3:45 p.m., Caspary Auditorium

Carl H. June, M.D.
Director, Translational Research Program,
Abramson Family Cancer Research Institute
Richard W. Vague Professor in Immunotherapy,
Perelman School of Medicine,
University of Pennsylvania

Adoptive Cell Therapy with Engineered T Cells

Recommended Readings

Empirical Articles

Grupp, S. A., Kalos, M., Barrett, D., Aplenc, R., Porter, D. L., Rheingold, S. R., … & June, C. H. (2013). Chimeric antigen receptor–modified T cells for acute lymphoid leukemia. New England Journal of Medicine, 368(16), 1509-1518.  doi:10.1056/NEJMoa1215134

Kalos, M., Levine, B. L., Porter, D. L., Katz, S., Grupp, S. A., Bagg, A., & June, C. H. (2011). T cells with chimeric antigen receptors have potent antitumor effects and can establish memory in patients with advanced leukemia. Science Translational Medicine, 3(95), 95ra73-95ra73. doi:10.1126/scitranslmed.3002842

Porter, D. L., Levine, B. L., Kalos, M., Bagg, A., & June, C. H. (2011). Chimeric antigen receptor–modified T cells in chronic lymphoid leukemia. New England Journal of Medicine, 365(8), 725-733. doi:10.1056/NEJMoa1103849

Review Papers

June, C. H., Maus, M. V., Plesa, G., Johnson, L. A., Zhao, Y., Levine, B. L., … & Porter, D. L. (2014). Engineered T cells for cancer therapy. Cancer Immunology, Immunotherapy, 63(9), 969-975. doi:10.1007/s00262-014-1568-1

Maus, M. V., Fraietta, J. A., Levine, B. L., Kalos, M., Zhao, Y., & June, C. H. (2014). Adoptive immunotherapy for cancer or viruses. Annual Review of Immunology, 32, 189-225. doi:10.1146/annurev-immunol-032713-120136

Recommended Readings: Lingyin Li, Ph.D., February 25

Special Lecture
Wednesday, February 25, 2015
4:00 p.m., Carson Family Auditorium (CRC)

Lingyin Li, Ph.D.,
Merck Fellow of the Jane Coffins Child Memorial Fund,
Department of Systems Biology,
Harvard Medical School

Chemical Biology of Anti-Cancer Innate Immunity

Recommended Readings

Kim, S., Li, L., Maliga, Z., Yin, Q., Wu, H., & Mitchison, T. J. (2013). Anticancer flavonoids are mouse-selective STING agonists. ACS Chemical Biology, 8(7), 1396–1401. doi:10.1021/cb400264n

Li, L., Yin, Q., Kuss, P., Maliga, Z., Wu, H., & Mitchison, T. J. (2014). Hydrolysis of 2′3′-cGAMP by ENPP1 and design of nonhydrolyzable analogs. Nature Chemical Biology, 10(12), 1043–1048. doi:10.1038/nchembio.1661

Recommended Readings: Stephen Quake, Ph.D. November 12

Special Seminar Series
Wednesday, November 12, 2014,
4:00 p.m., Carson Family Auditorium (CRC)

Stephen Quake, Ph.D.
Lee Otterson Professor,
Bioengineering and Applied Physics,
Stanford University
Howard Hughes Medical Institute

Single Cell Genomics

Recommended Readings

Empirical Papers

Ashley, E. a, Butte, A. J., Wheeler, M. T., Chen, R., Klein, T. E., Dewey, F. E., … Altman, R. B. (2010). Clinical assessment incorporating a personal genome. Lancet, 375(9725), 1525–1535. doi:10.1016/S0140-6736(10)60452-7

Fan, H. C., Gu, W., Wang, J., Blumenfeld, Y. J., El-Sayed, Y. Y., & Quake, S. R. (2012). Non-invasive prenatal measurement of the fetal genome. Nature, 487(7407), 320–324. doi:10.1038/nature11251

Pushkarev, D., Neff, N. F., & Quake, S. R. (2009). Single-molecule sequencing of an individual human genome. Nature Biotechnology, 27(9), 847–850. doi:10.1038/nbt.1561

Wang, J., Fan, H. C., Behr, B., & Quake, S. R. (2012). Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm. Cell, 150(2), 402–412. doi:10.1016/j.cell.2012.06.030

Review Papers

Kalisky, T., Blainey, P., & Quake, S. R. (2011). Genomic analysis at the single-cell level. Annual Review of Genetics, 45, 431–445. doi:10.1146/annurev-genet-102209-163607

Melin, J., & Quake, S. R. (2007). Microfluidic large-scale integration: the evolution of design rules for biological automation. Annual Review of Biophysics and Biomolecular Structure, 36, 213–231. doi:10.1146/annurev.biophys.36.040306.132646

Recommended Readings: Elaine Fuchs, Ph.D. November 3

Monday Lecture Series
Monday, November 3, 2014
4:00 p.m., Carson Family Auditorium

Elaine Fuchs, Ph.D.
Rebecca C. Lancefield Professor and Head,
Laboratory of Mammalian Cell Biology and Development,
The Rockefeller University
Howard Hughes Medical Institute

Stem Cells in Silence, Action and Cancer

Recommended Readings

Empirical Articles

Blanpain, C., Lowry, W., & Geoghegan, A. (2004). Self-renewal, multipotency, and the existence of two cell populations within an epithelial stem cell niche. Cell, 118(5), 635–648. doi:10.1016/j.cell.2004.08.012

Lechler, T., & Fuchs, E. (2005). Asymmetric cell divisions promote stratification and differentiation of mammalian skin. Nature, 437(7056), 275–280. doi:10.1038/nature03922

Yi, R., Poy, M. N., Stoffel, M., & Fuchs, E. (2008). A skin microRNA promotes differentiation by repressing “stemness”. Nature, 452(7184), 225–9. doi:10.1038/nature06642

Review Papers

Fuchs, E., Tumbar, T., & Guasch, G. (2004). Socializing with the neighbors: stem cells and their niche. Cell, 116(6), 769–778. doi:10.1016/S0092-8674(04)00255-7

Hsu, Y.-C., Li, L., & Fuchs, E. (2014). Emerging interactions between skin stem cells and their niches. Nature Medicine, 20(8), 847–856. doi:10.1038/nm.3643

Recommended Readings: Craig B. Thompson, M.D. May 23

Friday Lecture Series
Friday, May 23, 2014
3:45 p.m., Caspary Auditorium

Craig B. Thompson, M.D.
President and CEO
Memorial Sloan Kettering Cancer Center

What Cancer Is Teaching Us about Cellular Metabolism

Recommended Readings:

Empirical Papers

Buzzai, M., Bauer, D. E., Jones, R. G., Deberardinis, R. J., Hatzivassiliou, G., Elstrom, R. L., & Thompson, C. B. (2005). The glucose dependence of Akt-transformed cells can be reversed by pharmacologic activation of fatty acid beta-oxidation. Oncogene, 24(26), 4165–4173. doi:10.1038/sj.onc.1208622

Lum, J. J., Bauer, D. E., Kong, M., Harris, M. H., Li, C., Lindsten, T., & Thompson, C. B. (2005). Growth factor regulation of autophagy and cell survival in the absence of apoptosis. Cell, 120(2), 237–248. doi:10.1016/j.cell.2004.11.046

Selak, M. a, Armour, S. M., MacKenzie, E. D., Boulahbel, H., Watson, D. G., Mansfield, K. D., … Gottlieb, E. (2005). Succinate links TCA cycle dysfunction to oncogenesis by inhibiting HIF-alpha prolyl hydroxylase. Cancer Cell, 7(1), 77–85. doi:10.1016/j.ccr.2004.11.022

Ye, J., Mancuso, A., Tong, X., Ward, P. S., Fan, J., & Rabinowitz, J. D. (2012). Pyruvate kinase M2 promotes de novo serine synthesis to sustain mTORC1 activity and cell proliferation. Proceedings of the National Academy of Sciences, 109(18), 2–7. doi:10.1073/pnas.1204176109

Review Papers

DeBerardinis, R. J., Lum, J. J., Hatzivassiliou, G., & Thompson, C. B. (2008). The biology of cancer: metabolic reprogramming fuels cell growth and proliferation. Cell Metabolism, 7(1), 11–20. doi:10.1016/j.cmet.2007.10.002

Vander Heiden, M. G., Cantley, L. C., & Thompson, C. B. (2009). Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science, 324(5930), 1029–1033. doi:10.1126/science.1160809

Ward, P. S., & Thompson, C. B. (2012). Metabolic reprogramming: a cancer hallmark even Warburg did not anticipate. Cancer Cell, 21(3), 297–308. doi:10.1016/j.ccr.2012.02.014

Recommended Readings: Sangeeta Bhatia, M.D., Ph.D. May 12

Monday, May 12, 2014
4:00 p.m., Carson Family Auditorium

Sangeeta Bhatia, M.D., Ph.D.
John J. and Dorothy Wilson Professor of Health Sciences & Technology
Institute for Medical Engineering and Science
Director, Laboratory for Multiscale Regenerative Technologies
Massachusetts Institute of Technology
Investigator, Howard Hughes Medical Institute

Tiny Technologies for Studying Tissue Microenvironments

Recommended Readings:

Empirical Papers

Chen, A., & Thomas, D. (2011). Humanized mice with ectopic artificial liver tissues. Proceedings of the National Academy of Sciences, 108(29), 11842–11847. doi:10.1073/pnas.1101791108

Hui, E. E., & Bhatia, S. N. (2007). Micromechanical control of cell-cell interactions. Proceedings of the National Academy of Sciences, 104(14), 5722–5726. doi:10.1073/pnas.0608660104

Khetani, S. R., & Bhatia, S. N. (2008). Microscale culture of human liver cells for drug development. Nature Biotechnology, 26(1), 120–126. doi:10.1038/nbt1361

Review Papers

Underhill, G. H., Galie, P., Chen, C. S., & Bhatia, S. N. (2012). Bioengineering methods for analysis of cells in vitro. Annual Review of Cell and Developmental Biology, 28, 385–410. doi:10.1146/annurev-cellbio-101011-155709

Wong, I. Y., Bhatia, S. N., & Toner, M. (2013). Nanotechnology: emerging tools for biology and medicine. Genes & Development, 27(22), 2397–2408. doi:10.1101/gad.226837.113

Recommended Readings: Zena Werb, Ph.D.

Friday Lecture Series

Detlev Bronk Alumni Lecture

The Cellular Neighborhood: A Master Regulator from Development to Cancer

Zena Werb, Ph.D., professor and vice-chair, department of anatomy, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco

March 14, 2014

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Chou, J., Lin, J. H., Brenot, A., Kim, J. -., Provot, S., & Werb, Z. (2013). GATA3 suppresses metastasis and modulates the tumour microenvironment by regulating microRNA-29b expression. Nature Cell Biology, 15(2), 201-213

Chou, J., Shahi, P., & Werb, Z. (2013). MicroRNA-mediated regulation of the tumor microenvironment. Cell Cycle, 12(20), 3262-3271

Coussens, L. M., & Werb, Z. (2002). Inflammation and cancer. Nature, 420(6917), 860-867

Egeblad, M., Nakasone, E. S., & Werb, Z. (2010). Tumors as organs: Complex tissues that interface with the entire organism. Developmental Cell, 18(6), 884-901

Engelhardt, J. J., Boldajipour, B., Beemiller, P., Pandurangi, P., Sorensen, C., Werb, Z., . . . Krummel, M. F. (2012). Marginating dendritic cells of the tumor microenvironment cross-present tumor antigens and stably engage tumor-specific T cells. Cancer Cell, 21(3), 402-417

Heissig, B., Lund, L. R., Akiyama, H., Ohki, M., Morita, Y., Rømer, J., . . . Hattori, K. (2007). The plasminogen fibrinolytic pathway is required for hematopoietic regeneration. Cell Stem Cell, 1(6), 658-670

Ohki, M., Ohki, Y., Ishihara, M., Nishida, C., Tashiro, Y., Akiyama, H., . . . Hattori, K. (2010). Tissue type plasminogen activator regulates myeloid-cell dependent neoangiogenesis during tissue regeneration. Blood, 115(21), 4302-4312


Recommended Readings: Scott Lowe, Ph.D.

Friday Lecture Series

Cancer Initiation and Maintenance Genes

Scott Lowe, Ph.D., chair, Geoffrey Beene Cancer Research Center,

Memorial Sloan Kettering Cancer Center;

investigator, Howard Hughes Medical Institute

January 3, 2014

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Readings

Chicas, A., Kapoor, A., Wang, X., Aksoy, O., Evertts, A. G., Zhang, M. Q., . . . Lowe, S. W. (2012). H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence. Proceedings of the National Academy of Sciences of the United States of America, 109(23), 8971-8976

Dow, L. E., & Lowe, S. W. (2012). Life in the fast lane: Mammalian disease models in the genomics era. Cell, 148(6), 1099-1109

Premsrirut, P. K., Dow, L. E., Kim, S. Y., Camiolo, M., Malone, C. D., Miething, C., . . . Lowe, S. W. (2011). A rapid and scalable system for studying gene function in mice using conditional RNA interference. Cell, 145(1), 145-158

Sawey, E., Chanrion, M., Cai, C., Wu, G., Zhang, J., Zender, L., . . . Powers, S. (2011). Identification of a therapeutic strategy targeting amplified FGF19 in liver cancer by oncogenomic screening. Cancer Cell, 19(3), 347-358

Xue, W., Kitzing, T., Roessler, S., Zuber, J., Krasnitz, A., Schultz, N., . . . Lowe, S. W. (2012). A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proceedings of the National Academy of Sciences of the United States of America, 109(21), 8212-8217

Zuber, J., Rappaport, A. R., Luo, W., Wang, E., Chen, C., Vaseva, A. V., . . . Lowe, S. W. (2011). An integrated approach to dissecting oncogene addiction implicates a myb-coordinated self-renewal program as essential for leukemia maintenance. Genes and Development, 25(15), 1628-1640


Recommended Readings: Leonard Zon, M.D.

Monday, November 4, 2013
4:00 p.m., Carson Family Auditorium

Leonard Zon, M.D.
Director of the Stem Cell Program at Children’s Hospital Boston
Grousbeck Professor of Pediatric Medicine, Harvard Medical School
Investigator, Howard Hughes Medical Institute

Pathways that Stimulate Stem Cell Development and Self-Renewal

Recommended Readings:

Review Papers

De Jong, J. L. O., & Zon, L. I. (2005). Use of the zebrafish system to study primitive and definitive hematopoiesis. Annual Review of Genetics, 39, 481–501. doi:10.1146/annurev.genet.39.073003.095931

Orkin, S. H., & Zon, L. I. (2008). Hematopoiesis: an evolving paradigm for stem cell biologyCell132(4), 631–644. doi:10.1016/j.cell.2008.01.025

White, R., Rose, K., & Zon, L. (2013). Zebrafish cancer: the state of the art and the path forward. Nature Reviews Cancer, 13(9), 624–636. doi:10.1038/nrc3589

Zon, L. I. (2008). Intrinsic and extrinsic control of haematopoietic stem-cell self-renewal. Nature, 453(7193), 306–313. doi:10.1038/nature07038

Empirical Articles

Goessling, W., North, T. E., Loewer, S., Lord, A. M., Lee, S., Stoick-Cooper, C. L., … Zon, L. I. (2009). Genetic interaction of PGE2 and Wnt signaling regulates developmental specification of stem cells and regeneration. Cell, 136(6), 1136–1147. doi:10.1016/j.cell.2009.01.015

Lengerke, C., Schmitt, S., Bowman, T. V, Jang, I. H., Maouche-Chretien, L., McKinney-Freeman, S., … Daley, G. Q. (2008). BMP and Wnt specify hematopoietic fate by activation of the Cdx-Hox pathway. Cell Stem Cell, 2(1), 72–82. doi:10.1016/j.stem.2007.10.022

North, T. E., Goessling, W., Peeters, M., Li, P., Ceol, C., Lord, A. M., … Zon, L. I. (2009). Hematopoietic stem cell development is dependent on blood flow. Cell, 137(4), 736–748. doi:10.1016/j.cell.2009.04.023

North, T. E., Goessling, W., Walkley, C. R., Lengerke, C., Kopani, K. R., Lord, A. M., … Zon, L. I. (2007). Prostaglandin E2 regulates vertebrate haematopoietic stem cell homeostasis. Nature, 447(7147), 1007–1011. doi:10.1038/nature05883