Alejandro Chavez, MD

Academic Appointments

  • Assistant Professor of Pathology & Cell Biology
Alejandro Chavez, MD

Email: ac4304@cumc.columbia.edu

Our research group strives to push the boundaries of genetic engineering by developing new methods with which to modify and regulate eukaryotic genomes. We apply these tools ourselves or through collaboration to gain fundamental biological insights with a particular focus towards understanding neurodegenerative diseases and cancer.

Our work employs a variety of techniques ranging from oligo chip synthesis and library-based screening to iPS cell differentiation and live-cell imaging. We utilize a variety of model systems ranging from yeast to human cell culture to assure that the technologies we generate are applicable to a broad swath of the scientific community.

Our team places a strong emphasis on mentoring, and values the opportunity to be able to train the next generation of budding scientists.

Departments and Divisions

  • Department of Pathology & Cell Biology

Areas of Expertise

  • Pathology - Anatomic & Clinical

Languages Spoken

  • Spanish

Education and Training

  • BA, 2004 Genetics and Molecular Biology, Northwestern University
  • MD, PhD, 2011 Cell and Molecular Biology, University of Pennsylvania - School of Medicine
  • Residency: 2014 Massachuetts General Hospital
  • Fellowship: 2017 Massachusettes General Hospital

Locations

  • 630 West 168th Street

    630 West 168th Street
    New York, NY 10032
    Phone:
    (212) 305-1150
  • CUIMC/Presbyterian Hospital and Vanderbilt Clinic

    622 West 168th Street
    New York, NY 10032

Provider Affiliations

  • NewYork-Presbyterian / Columbia University Irving Medical Center

This provider does not accept new patients

Lab Locations

  • 630 West 168th Street

    630 West 168th Street
    New York, NY 10032
  • CUIMC/Presbyterian Hospital and Vanderbilt Clinic

    622 West 168th Street
    New York, NY 10032

Contact Info

  • (212) 305-1150

Patents

Church, G.M., Vora, S., Chavez, A., Chen, J., Pruitt, B. 2017. Methods of Modulating Expression of Target Nucleic Acid Sequences in a Cell. U.S. Patent Application 62/470,538, filed March 13, 2017. Patent Pending

Guo, X., Kaas, C., and Chavez, A. 2016. Methods of genetically altering yeast to produce yeast variants. U.S. Patent Application 62/396,395, filed September 19, 2016. Patent Pending

Kaas, C., and Chavez, A. 2016. Methods for screening using barcoded libraries. U.S. Patent Application 62/358,878, filed July 6, 2016. Patent Pending

Guo, X., Chavez, A., Schubert, M., and Kelsic E. 2016. Library-scale engineering of metabolic pathways. U.S. Patent Application 62/348,438, filed June 10, 2016. Patent Pending

Esvelt, K.M., Min, J., Noble, C.M., Buchthal, J., Chavez, A. 2016. Methods to design and use gene drives. U.S. Patent Application 62/333,580, filed May 9, 2016. Patent Pending

Chavez, A. 2016. Mutant cas proteins. U.S. Patent Application 62/310,018, filed March 18, 2016. Patent Pending

Chavez, A., and Pruitt, B.W., 2015. Cas discrimination using tuned guide RNA. U.S. Patent Application 62/266,851, filed December 14, 2015. Patent Pending

Hu, J., and Chavez, A., 2015. Methods of making guide RNA. U.S. Patent Application 62/220,524, filed September 19, 2015. Patent Pending

Chavez, A., and Tuttle, M., 2015. Cas9 genome editing and transcriptional regulation. U.S. Patent Application 62/200,303, filed August 3, 2015. Patent Pending.

Chavez, A., Poelwijk F., and Church G.M., 2013. Mutant Cas9 proteins. U.S. Patent 9,074,199, granted July 7, 2015

Committees / Societies / Memberships

Member of Scientific Advisory Board, Addgene, Cambridge MA

Ad-hoc Reviewer for: Nature Communications, Nucleic Acid Research, ACS Synthetic Biology, Genome Biology

Research Interests

  • Cancer
  • COVID-19
  • Genome Engineering
  • Genomics
  • Neurodegeneration
  • Synthetic Biology

NIH Grants

  • IDENTIFYING ALS THERAPEUTICS THROUGH MULTIPLEXED DRUG DISCOVERY TECHNOLOGIES (Private)

    Sep 1 2019 - Aug 31 2022

    NOVEL TECHNOLOGIES AND THEIR APPLICATION TO NEURODEGENERATIVE DISEASES (Private)

    Sep 1 2017 - Aug 31 2022

    IDENTIFYING ALS THERAPEUTICS THROUGH MULTIPLEXED DRUG DISCOVERY TECHNOLOGIES (Federal Gov)

    Apr 1 2020 - Mar 31 2022

    IDENTIFYING ALS THERAPEUTICS THROUGH MULTIPLEXED DRUG DISCOVERY TECHNOLOGIES (Private)

    Apr 1 2020 - Mar 31 2022

    A MULTIMODAL ORAL NON-VIRAL CRISPR-CAS MEDICAL COUNTERMEASURE TO ENHANCE IONIZING RADIATION RESILIENCE AND SURVIVAL (Federal Gov)

    Jan 1 2019 - Mar 31 2022

    HIGH-THROUGHPUT DISEASE MODELING TO UNCOVER SHARED AND UNIQUE CHARACTERISTICS AMONG NEURODEGENERATIVE DISEASES (Federal Gov)

    Sep 15 2019 - Aug 31 2021

    A MULTIMODAL ORAL NON-VIRAL CRISPR-CAS MEDICAL COUNTERMEASURE TO ENHANCE IONIZING RADIATION RESILIENCE AND SURVIVAL (Federal Gov)

    Jan 1 2019 - Mar 31 2021

    A MULTIMODAL ORAL NON-VIRAL CRISPR-CAS MEDICAL COUNTERMEASURE TO ENHANCE IONIZING RADIATION RESILIENCE AND SURVIVAL (Federal Gov)

    Jan 1 2019 - Mar 31 2021

    SINGLE EXOSOME SEQUENCING (SESEQ) FOR REAL-TIME CANCER DIAGNOSTICS (Private)

    Jan 3 2019 - Dec 31 2020

Clinical Trials

COVID-19 STUDIES - Recruiting people who have recovered from COVID-19 (Coronavirus) to donate convalescent plasma.

Publications

# denotes co-first author

^ denotes co-second author

* denotes co-senior author

  • Iketani, S., Forouhar, F., Liu, H., Hong, S.J., Lin, F-Y., Nair, M.S., Zask, A., Huang, Y., Xing, L., *Stockwell, B.R., *Chavez, A., *Ho, D.D. Lead compounds for the development of SARS-CoV-2 3CL protease inhibitors. Nature Communications. 2021; 12(1):2016
  • Resnick, S.J., Iketani, S., Hong, S.J., Zask, A., Liu, H., Kim, S., Melore, S., Nair, M.S., Huang, Y., Tay, N.E.S., Rovis, R., Yang, H.W., *Stockwell, B.R., *Ho, D.D., *Chavez, A.  A simplified cell-based assay to identify coronavirus 3CL protease inhibitors. Journal of Virology. 2021; JVI.02374-20 (online ahead of print)
  • Moghadam, F., LeGraw, R., Velazquez, J.J., Yeo, N.C., Xu, C., Park, J., Chavez, A., Ebrahimkhani, M.R., Kiani, S. Synthetic immunomodulation with a CRISPR super-repressor in vivo. Nature Cell Biology. 2020; 22:1143-1154
  • Labun, K., Guo, X., Chavez, A., Church, G., Gagnon, J.A., Valen, E., Accurate analysis of genuine CRISPR editing events with ampliCan. Genome research. 2019; 29:843-847
  • Nobel, C., Min, J., Olejarz, J., Buchthal, J., Chavez, A., Smidler, A.L., DeBenedictis, E.A., Church, G.M., Nowak, M.A., Esvelt, K.M. Daisy-chain gene drives for the alteration of local populations. PNAS. 2019; doi: 10.1073/pnas.1716358116
  • Xiong, K., Marquart, K.F., Karottki, K.J.C., Li, S., Shamie, I., Lee, J.S., Gerling, S., Yeo, N-C., Chavez, A., Lee, G.M., Lewis, N.E., Kildegaard, H.F. Reduced Apoptosis in Chinese Hamster Ovary Cells via Optimized CRISPR Interference. Biotechnology and Bioengineering. 2019; doi: 10.1002/bit.26969
  • Wensing, L., Sharma, J., Uthayakumar, D., Proteau, Y., Chavez, A., Shapiro, R.S. A CRISPR Interference Platform for Efficient Genetic Repression in Candida albicans. mSphere. 2019; 4: e00002-19
  • Halder, V., Porter, C.B.M., Chavez, A., Shapiro, R.S., Design, execution, and analysis of CRISPR-Cas9-based deletions and genetic interaction networks in the fungal pathogen Candida albicans. Nature Protocols. 2019; 14:955-975
  • #Nageshwaran, S., #Chavez, A., Yeo, N-C., Guo, X., Lance-Byrne, A., Tung, A., Collins, J.J., Church, G.M. CRISPR Guide RNA Cloning for Mammalian Systems. JoVE. 2018; 2:140
  • #Yeo, N-C., *#Chavez, A., Lance-Byrne, A., Chan, Y., Menn, D., Milanova, D., Kuo, C-C., Guo, X., Sharma, S., Tung, A., Cecchi, R.J., Tuttle, M., Pradhan, S., Lim, E.T., Davidsohn, N., Ebrahimkhani, M.R., Collins, J.J., Lewis, N.E., *Kiani, S., *Church, G.M. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nature Methods. 2018; 15:611-616
  • Clarke, R., Heler, R., MacDougall, M.S., Yeo, N-C., Chavez, A., Regan, M., Hanakahi, L., Church, G.M., Marraffini, L.A., Merrill, B.J. Enhanced Bacterial Immunity and Mammalian Genome Editing via RNA-Polymerase-Mediated Dislodging of Cas9 from Double-Strand DNA Breaks. Molecular Cell. 2018; 71:42-55.
  • #Guo, X., *#Chavez, A., #Tung, A., Chan, Y., Kaas, C., Yin, Y., Cecchi, R., Garnier, S.L., Kelsic, E.D., Schubert, M., DiCarlo, J.E., Collins, J.J., *Church, G.M., High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR–Cas9 in yeast. Nature Biotechnology. 2018; 36:540-546. PMC5990468
  • Chan, Y., Chan, Y.K., Goodman, D.B., Guo, X., Chavez, A., Lim, E.T., Church, G.M. Enabling multiplexed testing of pooled donor cells through whole-genome sequencing. Genome medicine. 2018; 10:31: PMC5909281
  • Bester, A.C., ^Lee, J.D., ^Chavez, A., Lee, Y-R., Nachmani, D., Vora, S., Victor, J., Sauvageau, M., Monteleone, E., Rinn, J.L., Provero, P., Church, G.M., Clohessy, J.G., Pandolfi, P.P. An Integrated Genome Wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance. Cell. 2018; 173:649-664.
  • *#Chavez, A., #Pruitt, B.W., Tuttle, M., Shapiro, R.S., Cecchi, R.J., Winston, J., Turczyk, B.M., Tung, M., Collins, J.J., and *Church, G.M. Precise Cas9 targeting enables genomic mutation prevention. PNAS. 2018; 115:3669-3673: PMCID: PMC5889643
  • #Shapiro, R.S., #Chavez, A., Porter, C.B.M., Hamblin, M., Kaas, C.S., DiCarlo, J.E., Zeng, G., Xu, X., Revtovich, A.V., Kirienko, N.V., Wang, Y., *Church, G.M., and *Collins, J.J. A CRISPR Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. Nature Microbiology. 2017; 3:73-82: PMCID: PMC5832965
  • Chari, R., Yeo, N.C., Chavez, A., Church, G.M. sgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity. ACS Synthetic Biology. 2017; 6:902-90: PMCID: PMC5793212
  • Rock, J.M., Hopkins, F.F., Chavez, A., Diallo, M., Gerrick, E.R., Prichard, J.R., Church, G.M., Rubin, E.J., Sassetti, C.M., Schnappinger, D., and Fortune, S.M. Programmable transcriptional repression in mycobacteria using an orthogonal CRISPR interference platform. Nature Microbiology. 2016; 2:16274: PMCID: PMC5302332
  • #Chavez, A., #Tuttle, M., Pruitt, B.W., Ewen-Campen, B., Chari, R., Ter-Ovanesyan, D., Haque, S.J., Cecchi, R.J., Kowal, E.J., Buchthal, J., Housden, B.E., Perrimon, N., Collins, J.J., and Church, G. Comparison of Cas9 activators in multiple species. Nature Methods. 2016; 13:563-567: PMCID: PMC4927356
  • #Kiani, S., #Chavez, A., Tuttle, M., Hall, R.N., Chari, R., Ter-Ovanesyan, D., Qian, J., Pruitt, B.W., Beal, J., Vora, S., Buchthal, J., Kowal, E.J., Ebrahimkhani, M.R., Collins, J.J., Weiss, R., Church., G. Cas9 gRNA engineering for genome editing, activation and repression. Nature Methods. 2015; 12:1051-1054: PMCID: PMC4666719
  • #DiCarlo, J.E., #Chavez, A., Dietz, S.L., Esvelt, K.M., Church, G.M. Safeguarding CRISPR-Cas9 gene drives in yeast. Nature Biotechnology. 2015; 33:1250-1255: PMCID: PMC4675690
  • #Chavez, A., #Scheiman, J., #Vora, S., Pruitt, B.W., Tuttle, M., P R Iyer, E., Lin, S., Kiani, S., Guzman, C. D., Wiegand, D.J., Ter-Ovanesyan, D., Braff, J.L., Davidsohn, N., Housden, B.E., Perrimon, N., Weiss, R., Aach, J., Collins, J.J., and Church, G.M. Highly efficient Cas9-mediated transcriptional programming. Nature Methods. 2015; 12:326-328: PMCID: PMC4393883
  • Jaiswal, S., Fontanillas, P., Flannick, J., Manning, A., Grauman, P. V., Mar, B. G., Lindsley, R. C., Mermel, C. H., Burtt, N., Chavez, A., Higgins, J. M., Moltchanov, V., Kuo, F. C., Kluk, M. J., Henderson, B., Kinnunen, L., Koistinen, H. A., Ladenvall, C., Getz, G., Correa, A., Banahan, B. F., Gabriel, S., Kathiresan, S., Stringham, H. M., McCarthy, M. I., Boehnke, M., Tuomilehto, J., Haiman, C., Groop, L., Atzmon, G., Wilson, J. G., Neuberg, D., Altshuler, D., and Ebert, B. L. Age-related clonal hematopoiesis associated with adverse outcomes. N. Engl. J. Med. 2014; 371:2488–2498: PMCID: PMC4306669
  • #Glineburg M.R., #Chavez A., Agrawal V., Brill S.J., Johnson F.B. Resolution by unassisted Top3 points to template switch recombination intermediates during DNA replication. J Biol Chem. 2013; 288:33193-33204: PMCID: PMC3829166
  • Platt, J. M., Ryvkin, P., Wanat, J. J., Donahue, G., Ricketts, M. D., Barrett, S. P., Waters, H. J., Song, S., Chavez, A., Abdallah, K. O., Master, S. R., Wang, L. S., and Johnson, F. B. Rap1 relocalization contributes to the chromatin-mediated gene expression profile and pace of cell senescence. Genes & Development. 2013; 27:1406-1420: PMCID: PMC3701195
  • Chi, A.W-S., Chavez, A., Xu, L., Weber, B.N., Shestova, O., Schaffer, A., Wertheim, G., Pear, W.S., Izon, D., Bhandoola, A. Identification of Flt3+CD150– myeloid progenitors in adult mouse bone marrow that harbor T lymphoid developmental potential. Blood. 2011; 118:2723-2732: PMCID: PMC3172791
  • Weber, B.N., Chi, A.W., Chavez, A., Yashiro-Ohtani, Y., Yang, Q., Shestova, O., Bhandoola,
  • A. A critical role for TCF-1 in T-lineage specification and differentiation. Nature. 2011; 476:63-68: PMCID: PMC3156435
  • Chavez, A., Agrawal, V., Johnson, F.B. Homologous recombination-dependent rescue of Smc5/6 deficiency. J Biol Chem.  2011; 286:5119-5125: PMCID: PMC3037623
  • Chavez, A., George, V., Agrawal, V., Johnson, F.B. Sumoylation and the structural maintenance of chromosomes (Smc) 5/6 complex slow senescence through recombination intermediate resolution. J Biol Chem. 2010; 285:11922-11930: PMCID: PMC2852929
  • Kozak, M.L., Chavez, A., Dang, W., Berger, S.L., Ashok, A., Guo, X., Johnson, F.B. Inactivation of the Sas2 histone acetyltransferase delays senescence driven by telomere dysfunction. EMBO J. 2009; 29:158-70: PMCID: PMC2808364
  • Lee, J.Y., Mogen, J.L., Chavez, A., Johnson F.B. Sgs1 RecQ helicase inhibits survival of Saccharomyces cerevisiae cells lacking telomerase and homologous recombination. J Biol Chem. 2008; 283:29847-29858: PMCID: PMC2573055
  • Turaga, R.V., Massip, L., Chavez, A., Johnson F.B., Lebel M. Werner and Bloom Syndrome proteins prevent DNA breaks upon chromatin structure alteration. Aging Cell. 2007; 6:471-81
  • Nollen, E.A., Garcia, S.M., van Haaften, G., Kim, S., Chavez, A., Morimoto, R.I., Plasterk, R.H. Genome-wide RNA interference screen identifies previously undescribed regulators of polyglutamine aggregation.  PNAS. 2004; 101:6403-6408: PMCID: PMC404057