Publications

TIGL’s publications are listed according to their relevant technology platform.

Publications for single-cell immune profiling and TCR repertoire analysis

Li S, Sun J, Allesøe R, Datta K, Bao Y, Oliveira G, Forman J, Jin R, Olsen LR, Keskin DB, Shukla SA, Wu CJ, Livak KJ. RNase H-dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis. Nat Protoc Aug;14(8):2571-2594 (2019).

Li S, Livak KJ. Targeted TCR amplification from single-cell cDNA libraries. Methods Mol Bio 2019;1979:197-224 (2019).

Keskin DB, Anandappa AJ, Sun J, Tirosh I, Mathewson ND, Li S, Oliveira G, Giobbie-Hurder A, Felt K, Gjini E, Shukla SA, Hu Z, Li L, Le PM, Allesoe RL, Richman A, Kowalczyk M, Abdelrahman S, Geduldig JE, Charbonneau A, Pelton K, Iorgulescu JB, Elagina L, Zhang W, Olive O, McCluskey C, Olsen LR, Stevens J, Lane WJ, Salazar AM, Daley H, Wen PY, Chiocca EA, Harden M, Lennon N, Gabriel S, Getz G, Lander ES, Regev A, Ritz J, Neuberg D, Rodig SJ, Ligon KL, Suva, ML, Wucherpfennig K, Hacohen N, Fritsch EF, Livak KJ, Ott PA, Wu CJ, Reardon DA. Personal Neoantigen-Targeting Vaccination for Glioblastoma (GBM) Generates Intra-Tumoral T Cell Responses. Nature Jan;565(7738):234-239 (2019).

Wang L, Livak KJ, Wu CJ. High-dimension single-cell analysis applied to cancer. Mol Aspects Med 59, 70-84. Epub 2017 Aug 30 (2018).

Hu Z, Anandappa AJ, Sun J, Kim J, Leet DE, Bozym DJ, Chen C, Williams L, Shukla SA, Zhang W, Tabbaa D, Steelman S, Olive O, Livak KJ, Kishi H, Muraguchi A, Guleria I, Stevens J, Lane WJ, Burkhardt UE, Fritsch EF, Neuberg D, Ott PA, Keskin DB, Hacohen N, Wu CJ. A cloning and expression system to probe T cell receptor specificity and assess functional avidity to neoantigens. Blood Jan (2018).

Wang L, Fan J, Francis JM, Georghiou G, Herger S, Li S, Gambe R, Zhou CW, Yang C, Xiao S, Dal Cin P, Bowden M, Kotliar D, Shukla SA, Brown JR, Neuberg D, Alessi DR, Zhang C-Z, Kharchenko PC, Livak KJ, Wu CJ. Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia. Genome Res 27, 1300-1311 (2017).

Ott PA, Hu Z, Keskin DB, Shukla SA, Sun J, Bozym DJ, Zhang W, Luoma A, Giobbie-Hurder A, Peter L, Chen C, Olive O, Carter TA, Li S, Lieb DJ, Eisenhaure T, Gjini E, Stevens J, Lane WJ, Javeri I, Nellaiappan K, Salazar AM, Daley H, Seaman M, Buchbinder EI, Yoon CH, Harden M, Lennon N, Gabriel S, Rodig SJ, Barouch DH, Aster JC, Getz G, Wucherpfennig K, Neuberg D, Ritz J, Lander ES, Fritsch EF, Hacohen N, Wu CJ. An immunogenic personal neoantigen vaccine for patients with melanoma. Nature 547(7662), 217-221 (2017).

Wang L, Brooks AN, Fan J, Wan Y, Gambe R, Li S, Hergert S, Yin S, Freeman SS, Fan L, Seiler M, Buonamici S, Smith PG, Chau KF, Cibulskis CL, Zhang W, Rassenti LZ, Ghia EM, Kipps TJ, Fernandes S, Bloch DB, Kotliar D, Landau DA, Shukla SA, Aster JC, Reed R, DeLuca DS, Brown JR, Neuberg D, Getz G, Livak KJ, Meyerson MM, Kharchenko PV, Wu CJ. Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia. Cancer Cell 30, 750-763(2016). 

Burger JA,  Landau DA, Taylor-Weiner A, Bozic I, Zhang H, Sarosiek K, Wang L, Stewart C, Fan J, Hoellenriegel J, Sivina M, Dubuc AM, Fraser C, Han Y, Li SLivak KJ, Zou L, Wan Y, Konoplev S, Sougnez C, Brown JR, Abruzzo LV, Carter SL, Keating MJ, Davids MS, Wierda WG, Cibulskis K, Zenz T, Werner L, Dal Cin P, Kharchencko P, Neuberg D, Kantarjian H, Lander E, Gabriel S, O'Brien S, Letai A, Weitz D, Nowak MA, Getz G, Wu CJ. Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition. Nat Commun 7, 11589 (2016).

Landau DA, Clement K, Ziller MJ, Boyle P, Fan J, Gu H, Stevenson K, Sougnez C, Wang L, Li S, Kotliar D, Zhang W, Ghandi M, Garraway L, Fernandes SM, Livak KJ, Gabriel S, Gnirke A, Lander ES, Brown JR, Neuberg D, Kharchenko PV, Hacohen N, Getz G, Meissner A, Wu CJ. Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia. Cancer Cell 26(6), 813-825 (2014).

Recent meeting abstracts

Anandappa AJ, Keskin DB,  Hu Z, Sun J, Tirosh I, Mathewson ND, Shukla SALi S,  Olive O, Neuberg D, Fritsch EF, Livak KJ, Hacohen N, Ott PA, Reardon DA, Wu CJ. Detecting neoepitope-specific intra-tumoral T cell responses in a glioblastoma patient treated with personal neoantigen vaccine [abstract]. In: Journal of Immunology for American Association for Immunology Annual Meeting 2018.J Immunol May 1, 2018, 200 (1 Supplement) 181.11

Li S, Sun J, Anandappa A, Spiro O, Leshchiner I, Datta K, Bao Y, Hu Z, Hacohen N, Mathewson ND, Tirosh I, Wucherpfennig K, Regev A, Suva M, Keskin DB, Wu CJ, Livak KJNovel targeted single-cell TCR sequencing method used for analysis of a T cell infiltrate from a glioblastoma patient [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5387.

Publications for detection of antigen-specific immunity

Truex NL, Holden RL, Wang BY, Chen PG, Hanna S, Hu Z, Shetty K, Olive O, Neuberg D, Hacohen N, Keskin DB, Ott PA, Wu CJ, Pentelute BL. Automated Flow Synthesis of Tumor Neoantigen Peptides for Personalized ImmunotherapySci Rep. Jan 20;10(1):723 (2020).

Sarkizova S, Klaeger S, Le PM, Li LW, Oliveira G, Keshishian H, Hartigan CR, Zhang W, Braun DA, Ligon KL, Bachireddy P, Zervantonakis IK, Rosenbluth JM, Ouspenskaia T, Law T, Justesen S, Stevens J, Lane WJ, Eisenhaure T, Lan Zhang G, Clauser KR, Hacohen N, Carr SA, Wu CJKeskin DBA large peptidome dataset improves HLA class I eptiope prediction across most of the human populationNat Biotechnol. Feb;38(2):199-209. (2020).

Keskin DB, Anandappa AJ, Sun J, Tirosh I, Mathewson ND, Li S, Oliveira G, Giobbie-Hurder A, Felt K, Gjini E, Shukla SA, Hu Z, Li L, Le PM, Allesoe RL, Richman A, Kowalczyk M, Abdelrahman S, Geduldig JE, Charbonneau A, Pelton K, Iorgulescu JB, Elagina L, Zhang W, Olive O, McCluskey C, Olsen LR, Stevens J, Lane WJ, Salazar AM, Daley H, Wen PY, Chiocca EA, Harden M, Lennon N, Gabriel S, Getz G, Lander ES, Regev A, Ritz J, Neuberg D, Rodig SJ, Ligon KL, Suva, ML, Wucherpfennig K, Hacohen N, Fritsch EF, Livak KJ, Ott PA, Wu CJ, Reardon DA. Personal Neoantigen-Targeting Vaccination for Glioblastoma (GBM) Generates Intra-Tumoral T Cell Responses. Nature Jan;565(7738):234-239 (2019).

Hu Z, Anandappa AJ, Sun J, Kim J, Leet DE, Bozym DJ, Chen C, Williams L, Shukla SA, Zhang W, Tabbaa D, Steelman S, Olive O, Livak KJ, Kishi H, Muraguchi A, Guleria I, Stevens J, Lane WJ, Burkhardt UE, Fritsch EF, Neuberg D, Ott PA, Keskin DB, Hacohen N, Wu CJ. A cloning and expression system to probe T cell receptor specificity and assess functional avidity to neoantigens. Blood Jan (2018).

Shukla SA, Bachireddy P, Schilling B, Galonska C, Zhan Q, Bango C, Langer R, Lee PC, Gusenleitner D, Keskin DB, Babadi M, Mohammad A, Gnirke A, Clement K, Cartun ZJ, Van Allen EM, Miao D, Huang Y, Snyder A, Merghoub T, Wolchok JD, Garraway LA, Meissner A, Weber JS, Hacohen N, Neuberg D, Potts PR, Murphy GF, Lian CG, Schadendorf D, Hodi FS, Wu CJ. Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade. Cell 173(3), 624-633.e8 (2018).

Bae J, Hideshima T, Zhang GL, Zhou J, Keskin DB, Munshi NC, Anderson KC. Identification and characterization of HLA-A24 specific XBP1, CD138 (Syndecan-1), and CS1 (SLAMF7) peptides inducing antigens-specific memory cytotoxic T lymphocytes targeting multiple myeloma. Leukemia 32(3):752-764 (2018).

Yoshikawa A, Bi K, Keskin DB, Zhang G, Reinhold B, Reinherz EL. TCR-pMHC encounter differentially regulates transcriptomes of- tissue-resident CD8 T cells. Eur J Immunol 48(1):128-150 (2018).

Ott PA, Hu Z, Keskin DB, Shukla SA, Sun J, Bozym DJ, Zhang W, Luoma A, Giobbie-Hurder A, Peter L, Chen C, Olive O, Carter TA, Li S, Lieb DJ, Eisenhaure T, Gjini E, Stevens J, Lane WJ, Javeri I, Nellaiappan K, Salazar AM, Daley H, Seaman M, Buchbinder EI, Yoon CH, Harden M, Lennon N, Gabriel S, Rodig SJ, Barouch DH, Aster JC, Getz G, Wucherpfennig K, Neuberg D, Ritz J, Lander ES, Fritsch EF, Hacohen N, Wu CJ. An immunogenic personal neoantigen vaccine for patients with melanoma. Nature 547(7662), 217-221 (2017).

Abelin JG, Keskin DB, Sarkizova S, Hartigan CR, Zhang W, Sidney J, Stevens J, Lane W, Zhang GL, Eisenhaure TM, Clauser KR, Hacohen N, Rooney MS, Carr SA, Wu CJ. Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction. Immunity 46, 315–326 (2017).

Tabansky I, Messina MD, Bangeranye C, Goldstein J, Blitz-Shabbir KM, Machado S, Jeganathan V, Wright P, Najjar S, Cao Y, Sands W, Keskin DB, Stern JN. Advancing drug delivery systems for the treatment of multiple sclerosis. Immunol Res 63(1-3):58-69 (2015).

Keskin DB, Reinhold B, Zhang GL, Ivanov A, Karger B, Reinherz EL. Reply to van de Sandt and Rimmelzwann: Matching epitope display with functional avidity. Proc Natl Acad Sci U S A 112(19): E2418 (2015).

Bae J, Keskin DB, Cowens K, Hwee LA, Dranoff G, Munshi NC, Anderson KC. Lenalidomide polarizes Th1-specific Anti-tumor immune response and expands XBP1 antigen specific central memory CD3+CD8+ T cells against various tumors. J Leuk 3: 178 (2015).

Das DK, Feng Y, Mallis RJ, Li X, Keskin DB, Hussey RE, Brady SK, Jia-Huai W, Wagner G, Reinherz EL, Lang MJ. Force-dependent transition in the T cell receptor subunit allosterically regulates peptide discrimination and pMHC bond lifetime. Proc Natl Acad Sci U S A 112(5):1517-22 (2015).

Recent meeting abstracts

Keskin DB, Sarkizova S, Klaeger S, Letitia L, Le PM, Keshishian H, Hartigan CR, Zhang GL, Clauser K, Carr SA, Hacohen N, Wu CJ. Systematic profiling of HLA-C epitopes [abstract].Immunology for American Association for Immunology Annual Meeting 2018.

Keskin DB, Tirosh I, Anandappa A, Sun J, Mathewson ND, Shukla SA, Gjini E, Li S, Li L, Giobbie-Hurder A, Le PM, Hu Z, Zhang W, Olive O, McCluskey C, Daley H, Wen PY, Chiocca AE, Harden M, Lennon N. Gabriel S, Getz G, Neuberg D, Ritz J, Lander ES, Regev A, Wucherpfennig K, Suva M, Fritsch EF, Scott R, Ligon KL, Livak KJ, Hacohen N, Ott PA, Wu CJ, Reardon DA. Personal neoantigen-targeting vaccination generates neoepitope-specific T cell responses in tumors of patients with glioblastoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5631.

Anandappa AJ, Keskin DB,  Hu Z, Sun J, Tirosh I, Mathewson ND, Shukla SALi S,  Olive O, Neuberg D, Fritsch EF, Livak KJ, Hacohen N, Ott PA, Reardon DA, Wu CJ. Detecting neoepitope-specific intra-tumoral T cell responses in a glioblastoma patient treated with personal neoantigen vaccine [abstract]. In: Journal of Immunology for American Association for Immunology Annual Meeting 2018. J Immunol May 1, 2018, 200 (1 Supplement) 181.11

Publications for immunogenomic analysis

Braun DA, Ishii Y, Walsh AM, Van Allen EM, Wu CJShukla SA, Choueiri TK. Clinical validation of PBMR1 alterations as a marker of immune checkpoint inhbitor response in Renal Cell CarcinomaJAMA Oncol. (2019)

Mahoney KM, Shukla SA, Patsoukis N, Chaudhri A, Browne EP, Arazi A, Eisenhaure TM, Pendergraft WF 3rd, Hua P, Pham HC, Bu X, Zhu B, Hacohen N, Fritsch EF, Boussiotis VA, Wu CJ, Freeman GJ. A secreted PD-L1 splice variant that covalently dimerizes and mediates immunosuppressionCancer Immunol Immunother. Mar;68(3):421-432 (2019).

Keskin DB, Anandappa AJ, Sun J, Tirosh I, Mathewson ND, Li S, Oliveira G, Giobbie-Hurder A, Felt K, Gjini E, Shukla SA, Hu Z, Li L, Le PM, Allesoe RL, Richman A, Kowalczyk M, Abdelrahman S, Geduldig JE, Charbonneau A, Pelton K, Iorgulescu JB, Elagina L, Zhang W, Olive O, McCluskey C, Olsen LR, Stevens J, Lane WJ, Salazar AM, Daley H, Wen PY, Chiocca EA, Harden M, Lennon N, Gabriel S, Getz G, Lander ES, Regev A, Ritz J, Neuberg D, Rodig SJ, Ligon KL, Suva, ML, Wucherpfennig K, Hacohen N, Fritsch EF, Livak KJ, Ott PA, Wu CJ, Reardon DA. Personal Neoantigen-Targeting Vaccination for Glioblastoma (GBM) Generates Intra-Tumoral T Cell Responses. Nature Jan;565(7738):234-239 (2019).

Hu Z, Anandappa AJ, Sun J, Kim J, Leet DE, Bozym DJ, Chen C, Williams L, Shukla SA, Zhang W, Tabbaa D, Steelman S, Olive O, Livak KJ, Kishi H, Muraguchi A, Guleria I, Stevens J, Lane WJ, Burkhardt UE, Fritsch EF, Neuberg D, Ott PA, Keskin DB, Hacohen N, Wu CJ. A cloning and expression system to probe T cell receptor specificity and assess functional avidity to neoantigens. Blood Jan (2018).

Shukla SA, Bachireddy P, Schilling B, Galonska C, Zhan Q, Bango C, Langer R, Lee PC, Gusenleitner D, Keskin DB, Babadi M, Mohammad A, Gnirke A, Clement K, Cartun ZJ, Van Allen EM, Miao D, Huang Y, Snyder A, Merghoub T, Wolchok JD, Garraway LA, Meissner A, Weber JS, Hacohen N, Neuberg D, Potts PR, Murphy GF, Lian CG, Schadendorf D, Hodi FS, Wu CJ. Cancer-Germline Antigen Expression Discriminates Clinical Outcome to CTLA-4 Blockade. Cell 173(3), 624-633.e8 (2018).

Ott PA, Hu Z, Keskin DB, Shukla SA, Sun J, Bozym DJ, Zhang W, Luoma A, Giobbie-Hurder A, Peter L, Chen C, Olive O, Carter TA, Li S, Lieb DJ, Eisenhaure T, Gjini E, Stevens J, Lane WJ, Javeri I, Nellaiappan K, Salazar AM, Daley H, Seaman M, Buchbinder EI, Yoon CH, Harden M, Lennon N, Gabriel S, Rodig SJ, Barouch DH, Aster JC, Getz G, Wucherpfennig K, Neuberg D, Ritz J, Lander ES, Fritsch EF, Hacohen N, Wu CJ. An immunogenic personal neoantigen vaccine for patients with melanoma. Nature 547(7662), 217-221 (2017).

George S, Miao D, Demetri GD, Adeegbe D, Rodig SJ, Shukla S, Lipschitz M, Amin-Mansour A, Raut CP, Carter SL, Hammerman P, Freeman GJ, Wu CJ, Ott PA, Wong KK, Van Allen EM. Loss of PTEN Is Associated with Resistance to Anti-PD-1 Checkpoint Blockade Therapy in Metastatic Uterine Leiomyosarcoma. Immunity 46(2):197-204 (2017).

Shukla SA, Howitt BE, Wu CJ, Konstantinopoulos PA. Gynecol Oncol Rep 19: 42-45. Predicted neoantigen load in non-hypermutated endometrial cancers: Correlation with outcome and tumor-specific genomic alterations. Gynecol Oncol Rep 19: 42-45 (2016).

Giannakis M, Mu XJ, Shukla SA, Qian ZR, Cohen O, Nishihara R, Bahl S, Cao Y, Amin-Mansour A, Yamauchi M, Sukawa Y, Stewart C, Rosenberg M, Mima K, Inamura K, Nosho K, Nowak JA, Lawrence MS, Giovannucci EL, Chan AT, Ng K, Meyerhardt JA, Van Allen EM, Getz G, Gabriel SB, Lander ES, Wu CJ, Fuchs CS, Ogino S, Garraway LA. Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. Cell Rep 17(4):1206. (2016).

Li B, Li T, Pignon JC, Wang B, Wang J, Shukla SA, Dou R, Chen Q, Hodi FS, Choueiri TK, Wu CJ, Hacohen N, Signoretti S, Liu JS, Liu XS. Landscape of tumor-infiltrating T cell repertoire of human cancers. Nat Genet 48(7):725-32 (2016). doi: 10.1038/ng.3581.

Campbell JD, Alexandrov A, Kim J, Wala J, Berger AH, Pedamallu CS, Shukla SA, Guo G, Brooks AN, Murray BA, Imielinski M, Hu X, Ling S, Akbani R, Rosenberg M, Cibulskis C, Ramachandran A, Collisson EA, Kwiatkowski DJ, Lawrence MS, Weinstein JN, Verhaak RG, Wu CJ, Hammerman PS, Cherniack AD, Getz Cancer Genome Atlas Research Network, Artyomov MN, Schreiber R, Govindan R, Meyerson M. Distinct patterns of somatic genome alterations  in lung adenocarcinomas and squamous cell carcinomas. Nat Genet 48(6):607-16 (2016).

Strickland KC, Howitt BE, Shukla SA, Rodig S, Ritterhouse LL, Liu JF, Garber JE, Chowdhury D, Wu CJ, D'Andrea AD, Matulonis UA, Konstantinopoulos PA.  Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer. Oncotarget 7(12):13587-98 (2016).

Howitt BE, Shukla SA, Sholl LM, Ritterhouse LL, Watkins JC, Rodig S, Stover E, Strickland KC, D'Andrea AD, Wu CJ, Matulonis UA, Konstantinopoulos PA. POLE-mutated and MSI endometrial cancers are associated with elevated neoantigen load, increased number of tumor-infiltrating lymphocytes and higher expression of PD-1/PD-L1. JAMA oncology 1(9):1319-23 (2015).

Shukla SA, Rooney MS, Rajasagi M, Tiao G, Dixon PM, Lawrence MS, Stevens J, Lane WJ, Dellagatta JL, Steelman S, Sougnez C, Cibulskis K, Kiezun A, Hacohen N, Brusic V, Wu CJ, Getz G. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat Biotechnol 33, 1152-1158 (2015).

Rooney MS, Shukla SA, Wu CJ, Getz G and Hacohen N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell 160(1-2):48-61 (2015).

Van Allen EM, Miao D, Schilling B, Shukla SA, Blank C, Zimmer L, Sucker A, Hillen U, Foppen MHG, Goldinger SM, Utikal J, Hassel JC, Weide B, Kaehler KC, Loquai C, Mohr P, Gutzmer R, Dummer R, Gabriel S, Wu CJ, Schadendorf D, Garraway LA. Genomic correlates of response to ipilimumab in metastatic melanoma. Science 350(6257):207-11. (2015).