Neville Sanjana

Our lab develops technologies to understand how human genetic variants cause diseases of the nervous system and cancer. We use a multi-disciplinary approach, combining genome engineering, pooled genetic screens, bioinformatics, electrophysiology, and imaging, to dissect the inner workings of the human genome and its dysfunction in autism and tumor evolution.

We have capitalized on new technologies for large-scale DNA synthesis, gene editing and next-generation sequencing to develop pooled libraries of RNA-guided nucleases (e.g. CRISPR) for forward genetic screens (see figure below). By targeting all protein-coding genes in human/mouse genomes, we have identified novel genetic drivers of melanoma drug resistance, drivers of metastasis in vivo, and mechanisms used by tumors to evade immunotherapy.

Recently, we have developed pooled CRISPR libraries and gene editing approaches to target the noncoding genome. A major goal of our work is to understand the functional consequences of modifying noncoding elements in their native context and how they relate to existing hallmarks of noncoding function such as transcription factor binding, enhancer marks and physical genome structure. Previous/current projects include applications in cancer, neurodevelopmental disorders (using human stem cells and neurons) and hemoglobin regulation. We plan to continue expanding the genome engineering toolbox to further our understanding of the noncoding genome and its role in human health and disease.

To find out more about current projects and open positions in the Sanjana lab, please visit the lab webpage.

Institute for Systems Genetics, NYU Langone Medical School

Neurosciences Institute, NYU Langone Medical School

Core Faculty Member, New York Genome Center

Next Generation Leader, Paul Allen Institute for Brain Science

NIH/NHGRI Pathway to Independence Award (K99/R00)

Sidney Kimmel Scholar Award

Melanoma Research Foundation Young Investigator Award

Date of these PubMed search results: March 24 2020
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1. High-Throughput Screens of PAM-Flexible Cas9 Variants for Gene Knockout and Transcriptional Modulation.
   Cell Rep (2020 Mar 3) PMID: 32130891
   Legut M, Daniloski Z, Xue X, McKenzie D, Guo X, Wessels HH, Sanjana NE
2. Generation of a knock-in MAP2-tdTomato reporter human embryonic stem cell line with inducible expression of NEUROG2/1 (NYGCe001-A).
   Stem Cell Res (2019 Dec) PMC6919562 free full-text archive
   Lu C, Sanjana NE
3. Immunomagnetic cell sorting.
   Nat Biomed Eng (2019 Oct) PMID: 31548593
   Legut M, Sanjana NE
4. Multiscale Genome Engineering: Genome-Wide Screens and Targeted Approaches
   In: Jaenisch R, Zhang F, Gage F, editors. Multiscale Genome Engineering: Genome-Wide Screens and Targeted Approaches edition. Cham (CH): Springer; 2017 (2017) PMID: 31314449
   Sanjana NE
5. Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes.
   Cell Syst (2019 May 22) PMC6917527 free full-text archive
   Liu EM, Martinez‑Fundichely A, Diaz BJ, Aronson B, Cuykendall T, MacKay M, Dhingra P, Wong EWP, Chi P, Apostolou E, Sanjana NE, Khurana E
6. Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells.
   Nat Methods (2019 May) PMC6557128 free full-text archive
   Mimitou EP, Cheng A, Montalbano A, Hao S, Stoeckius M, Legut M, Roush T, Herrera A, Papalexi E, Ouyang Z, Satija R, Sanjana NE, Koralov SB, Smibert P
7. Overexpression of NEUROG2 and NEUROG1 in human embryonic stem cells produces a network of excitatory and inhibitory neurons.
   FASEB J (2019 Apr) PMC6436650 free full-text archive
   Lu C, Shi X, Allen A, Baez‑Nieto D, Nikish A, Sanjana NE, Pan JQ
8. Author Correction: Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening.
   Nat Protoc (2019 Jul) PMID: 30349047
   Joung J, Konermann S, Gootenberg JS, Abudayyeh OO, Platt RJ, Brigham MD, Sanjana NE, Zhang F
9. Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons.
   Nat Biomed Eng (2018 Jul) PMC6157920 free full-text archive
   Tekin H, Simmons S, Cummings B, Gao L, Adiconis X, Hession CC, Ghoshal A, Dionne D, Choudhury SR, Yesilyurt V, Sanjana NE, Shi X, Lu C, Heidenreich M, Pan JQ, Levin JZ, Zhang F
10. A genome-wide net to catch and understand cancer.
    Sci Transl Med (2018 Aug 8) PMC6180290 free full-text archive
    Sanjana NE
11. GFAP Mutations in Astrocytes Impair Oligodendrocyte Progenitor Proliferation and Myelination in an hiPSC Model of Alexander Disease.
    Cell Stem Cell (2018 Aug 2) PMC6230521 free full-text archive
    Li L, Tian E, Chen X, Chao J, Klein J, Qu Q, Sun G, Sun G, Huang Y, Warden CD, Ye P, Feng L, Li X, Cui Q, Sultan A, Douvaras P, Fossati V, Sanjana NE, Riggs AD, Shi Y
12. Two Angelman families with unusually advanced neurodevelopment carry a start codon variant in the most highly expressed UBE3A isoform.
    Am J Med Genet A (2018 Jul) PMC6117199 free full-text archive
    Sadhwani A, Sanjana NE, Willen JM, Calculator SN, Black ED, Bean LJH, Li H, Tan WH
13. Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments.
    Nat Protoc (2018 May) PMC6182299 free full-text archive
    Canver MC, Haeussler M, Bauer DE, Orkin SH, Sanjana NE, Shalem O, Yuan GC, Zhang F, Concordet JP, Pinello L
14. Target Discovery for Precision Medicine Using High-Throughput Genome Engineering.
    Adv Exp Med Biol (2017) PMID: 29130157
    Guo X, Chitale P, Sanjana NE
15. High-Throughput Approaches to Pinpoint Function within the Noncoding Genome.
    Mol Cell (2017 Oct 5) PMC5701515 free full-text archive
    Montalbano A, Canver MC, Sanjana NE
16. Erratum: Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood.
    Nature (2017 Sep 20) PMID: 28933431
    Joung J, Engreitz JM, Konermann S, Abudayyeh OO, Verdine VK, Aguet F, Gootenberg JS, Sanjana NE, Wright JB, Fulco CP, Tseng YY, Yoon CH, Boehm JS, Lander ES, Zhang F
17. GUIDES: sgRNA design for loss-of-function screens.
    Nat Methods (2017 Aug 31) PMC5870754 free full-text archive
    Meier JA, Zhang F, Sanjana NE
18. Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood.
    Nature (2017 Aug 17) PMC5706657 free full-text archive
    Joung J, Engreitz JM, Konermann S, Abudayyeh OO, Verdine VK, Aguet F, Gootenberg JS, Sanjana NE, Wright JB, Fulco CP, Tseng YY, Yoon CH, Boehm JS, Lander ES, Zhang F
19. Identification of essential genes for cancer immunotherapy.
    Nature (2017 Aug 31) PMC5870757 free full-text archive
    Patel SJ, Sanjana NE, Kishton RJ, Eidizadeh A, Vodnala SK, Cam M, Gartner JJ, Jia L, Steinberg SM, Yamamoto TN, Merchant AS, Mehta GU, Chichura A, Shalem O, Tran E, Eil R, Sukumar M, Guijarro EP, Day CP, Robbins P, Feldman S, Merlino G, Zhang F, Restifo NP
20. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening.
    Nat Protoc (2017 Apr) PMC5526071 free full-text archive
    Joung J, Konermann S, Gootenberg JS, Abudayyeh OO, Platt RJ, Brigham MD, Sanjana NE, Zhang F
21. Transcription control by the ENL YEATS domain in acute leukaemia.
    Nature (2017 Mar 9) PMC5497220 free full-text archive
    Erb MA, Scott TG, Li BE, Xie H, Paulk J, Seo HS, Souza A, Roberts JM, Dastjerdi S, Buckley DL, Sanjana NE, Shalem O, Nabet B, Zeid R, Offei‑Addo NK, Dhe‑Paganon S, Zhang F, Orkin SH, Winter GE, Bradner JE
22. Genome-Scale Networks Link Neurodegenerative Disease Genes to alpha-Synuclein through Specific Molecular Pathways.
    Cell Syst (2017 Feb 22) PMC5388136 free full-text archive
    Khurana V, Peng J, Chung CY, Auluck PK, Fanning S, Tardiff DF, Bartels T, Koeva M, Eichhorn SW, Benyamini H, Lou Y, Nutter‑Upham A, Baru V, Freyzon Y, Tuncbag N, Costanzo M, San Luis BJ, Schondorf DC, Barrasa MI, Ehsani S, Sanjana N, Zhong Q, Gasser T, Bartel DP, Vidal M, Deleidi M, Boone C, Fraenkel E, Berger B, Lindquist S
23. High-resolution interrogation of functional elements in the noncoding genome.
    Science (2016 Sep 30) PMC5144102 free full-text archive
    Sanjana NE, Wright J, Zheng K, Shalem O, Fontanillas P, Joung J, Cheng C, Regev A, Zhang F
24. CRISPR Screens to Discover Functional Noncoding Elements.
    Trends Genet (2016 Sep) PMC4992445 free full-text archive
    Wright JB, Sanjana NE
25. Microfluidic neurite guidance to study structure-function relationships in topologically-complex population-based neural networks.
    Sci Rep (2016 Jun 22) PMC4916598 free full-text archive
    Honegger T, Thielen MI, Feizi S, Sanjana NE, Voldman J
26. Genome-scale CRISPR pooled screens.
    Anal Biochem (2017 Sep 1) PMC5133192 free full-text archive
    Sanjana NE
27. GENOME ENGINEERING. The Genome Project-Write.
    Science (2016 Jul 8) PMID: 27256881
    Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof J, Maurano MT, Mitchell LA, Rine J, Rosser S, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L
28. Hypoxia as a therapy for mitochondrial disease.
    Science (2016 Apr 1) PMC4860742 free full-text archive
    Jain IH, Zazzeron L, Goli R, Alexa K, Schatzman‑Bone S, Dhillon H, Goldberger O, Peng J, Shalem O, Sanjana NE, Zhang F, Goessling W, Zapol WM, Mootha VK
29. Mice with Shank3 Mutations Associated with ASD and Schizophrenia Display Both Shared and Distinct Defects.
    Neuron (2016 Jan 6) PMC4754122 free full-text archive
    Zhou Y, Kaiser T, Monteiro P, Zhang X, Van der Goes MS, Wang D, Barak B, Zeng M, Li C, Lu C, Wells M, Amaya A, Nguyen S, Lewis M, Sanjana N, Zhou Y, Zhang M, Zhang F, Fu Z, Feng G
30. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis.
    Nature (2015 Nov 12) PMC4644101 free full-text archive
    Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, Maeda T, Yuan GC, Zhang F, Orkin SH, Bauer DE
31. A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.
    Cell (2015 Jul 30) PMC4522370 free full-text archive
    Parnas O, Jovanovic M, Eisenhaure TM, Herbst RH, Dixit A, Ye CJ, Przybylski D, Platt RJ, Tirosh I, Sanjana NE, Shalem O, Satija R, Raychowdhury R, Mertins P, Carr SA, Zhang F, Hacohen N, Regev A
32. High-throughput functional genomics using CRISPR-Cas9.
    Nat Rev Genet (2015 May) PMC4503232 free full-text archive
    Shalem O, Sanjana NE, Zhang F
33. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis.
    Cell (2015 Mar 12) PMC4380877 free full-text archive
    Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, Shi X, Scott DA, Song J, Pan JQ, Weissleder R, Lee H, Zhang F, Sharp PA
34. Rapid neurogenesis through transcriptional activation in human stem cells.
    Mol Syst Biol (2014 Nov 17) PMC4299601 free full-text archive
    Busskamp V, Lewis NE, Guye P, Ng AH, Shipman SL, Byrne SM, Sanjana NE, Murn J, Li Y, Li S, Stadler M, Weiss R, Church GM
35. Improved vectors and genome-wide libraries for CRISPR screening.
    Nat Methods (2014 Aug) PMC4486245 free full-text archive
    Sanjana NE, Shalem O, Zhang F
36. Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites.
    Cell Rep (2014 Jul 10) PMC4142486 free full-text archive
    Schwartz S, Mumbach MR, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter‑Ovanesyan D, Habib N, Cacchiarelli D, Sanjana NE, Freinkman E, Pacold ME, Satija R, Mikkelsen TS, Hacohen N, Zhang F, Carr SA, Lander ES, Regev A
37. Genome-scale CRISPR-Cas9 knockout screening in human cells.
    Science (2014 Jan 3) PMC4089965 free full-text archive
    Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelson T, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F
38. Activity-dependent A-to-I RNA editing in rat cortical neurons.
    Genetics (2012 Sep) PMC3430542 free full-text archive
    Sanjana NE, Levanon EY, Hueske EA, Ambrose JM, Li JB
39. A transcription activator-like effector toolbox for genome engineering.
    Nat Protoc (2012 Jan 5) PMC3684555 free full-text archive
    Sanjana NE, Cong L, Zhou Y, Cunniff MM, Feng G, Zhang F
40. The wanderlust of newborn neocortical interneurons.
    J Neurosci (2009 Jun 3) PMC6666492 free full-text archive
    Scott BB, Sanjana NE
41. A fast flexible ink-jet printing method for patterning dissociated neurons in culture.
    J Neurosci Methods (2004 Jul 30) PMID: 15183267
    Sanjana NE, Fuller SB