Publications | Translational Immunogenomics Lab

Maurer K, Grabski IN, Houot R, Gohil SH, Miura S, Redd RA, Lyu H, Lu W, Arihara Y, Budka J, McDonough M, Ansuinelli M, Reynolds CG, Jacene H, Li S, Livak KJ, Ritz J, Miles B, Mattie M, Neuberg DS, Irizarry RA, Armand P, Wu CJ, Jacobson CA. Baseline Immune State and T-cell Clonal Kinetics are Associated with Durable Response to CAR-T Therapy in Large B-cell Lymphoma. Blood. 2024 Sep 6:blood.2024024381. doi: 10.1182/blood.2024024381. Epub ahead of print. PMID: 39241199.

Park C, Mani S, Beltran-Velez N, Maurer K, Huang T, Li S, Gohil S, Livak KJ, Knowles DA, Wu CJ, Azizi E. A Bayesian framework for inferring dynamic intercellular interactions from time-series single-cell data. Genome Res. 2024 Oct 11;34(9):1384-1396. doi: 10.1101/gr.279126.124. PMID: 39237300; PMCID: PMC11529839.

Penter L, Cieri N, Maurer K, Kwok M, Lyu H, Lu WS, Oliveira G, Gohil SH, Leshchiner I, Lareau CA, Ludwig LS, Neuberg DS, Kim HT, Li S, Bullinger L, Ritz J, Getz G, Garcia JS, Soiffer RJ, Livak KJ, Wu CJ. Tracking Rare Single Donor and Recipient Immune and Leukemia Cells after Allogeneic Hematopoietic Cell Transplantation Using Mitochondrial DNA Mutations. Blood Cancer Discov. 2024 Nov 1;5(6):442-459. doi: 10.1158/2643-3230.BCD-23-0138. PMID: 39236287; PMCID: PMC11528187.

Cieri N, Hookeri N, Stromhaug K, Li L, Keating J, Díaz-Fernández P, Gómez-García de Soria V, Stevens J, Kfuri-Rubens R, Shao Y, Kooshesh KA, Powell K, Ji H, Hernandez GM, Abelin J, Klaeger S, Forman C, Clauser KR, Sarkizova S, Braun DA, Penter L, Kim HT, Lane WJ, Oliveira G, Kean LS, Li S, Livak KJ, Carr SA, Keskin DB, Muñoz-Calleja C, Ho VT, Ritz J, Soiffer RJ, Neuberg D, Stewart C, Getz G, Wu CJ. Systematic identification of minor histocompatibility antigens predicts outcomes of allogeneic hematopoietic cell transplantation. Nat Biotechnol. 2024 Aug 21. doi: 10.1038/s41587-024-02348-3. Epub ahead of print. PMID: 39169264.

Truex NL, Mohapatra S, Melo M, Rodriguez J, Li N, Abraham W, Sementa D, Touti F, Keskin DB, Wu CJ, Irvine DJ, Gómez-Bombarelli R, Pentelute BL. Design of Cytotoxic T Cell Epitopes by Machine Learning of Human Degrons. ACS Cent Sci. 2024 Mar 6;10(4):793-802. doi: 10.1021/acscentsci.3c01544. PMID: 38680558; PMCID: PMC11046456.

Walker MA, Li S, Livak KJ, Karaa A, Wu CJ, Mootha VK. T cell activation contributes to purifying selection against the MELAS-associated m.3243A>G pathogenic variant in blood. J Inherit Metab Dis. 2024 Jul;47(4):757-765. doi: 10.1002/jimd.12726. Epub 2024 Mar 18. PMID: 38499449; PMCID: PMC11251844.

Zeng YC, Young OJ, Wintersinger CM, Anastassacos FM, MacDonald JI, Isinelli G, Dellacherie MO, Sobral M, Bai H, Graveline AR, Vernet A, Sanchez M, Mulligan K, Choi Y, Ferrante TC, Keskin DB, Fell GG, Neuberg D, Wu CJ, Mooney DJ, Kwon IC, Ryu JH, Shih WM. Fine tuning of CpG spatial distribution with DNA origami for improved cancer vaccination. Nat Nanotechnol. 2024 Jul;19(7):1055-1065. doi: 10.1038/s41565-024-01615-3. Epub 2024 Mar 15. PMID: 38491184.

Qin X, Lam A, Zhang X, Sengupta S, Iorgulescu JB, Ni H, Das S, Rager M, Zhou Z, Zuo T, Meara GK, Floru AE, Kemet C, Veerapaneni D, Kashy D, Lin L, Lloyd K, Kwok L, Smith KS, Nagaraju RT, Meijers R, Ceol C, Liu CT, Alexandrescu S, Wu CJ, Keskin DB, George RE, Feng H. CKLF instigates a "cold" microenvironment to promote MYCN-mediated tumor aggressiveness. Sci Adv. 2024 Mar 15;10(11):eadh9547. doi: 10.1126/sciadv.adh9547. Epub 2024 Mar 15. PMID: 38489372; PMCID: PMC10942121.

Maurer K, Park CY, Mani S, Borji M, Penter L, Jin Y, Zhang JY, Shin C, Brenner JR, Southard J, Krishna S, Lu W, Lyu H, Abbondanza D, Mangum C, Olsen LR, Neuberg DS, Bachireddy P, Farhi SL, Li S, Livak KJ, Ritz J, Soiffer RJ, Wu CJ, Azizi E. Coordinated Immune Cell Networks in the Bone Marrow Microenvironment Define the Graft versus Leukemia Response with Adoptive Cellular Therapy. bioRxiv [Preprint]. 2024 Feb 12:2024.02.09.579677. doi: 10.1101/2024.02.09.579677. PMID: 38405900; PMCID: PMC10888840.

Cui A, Huang T, Li S, Ma A, Pérez JL, Sander C, Keskin DB, Wu CJ, Fraenkel E, Hacohen N. Dictionary of immune responses to cytokines at single-cell resolution. Nature. 2024 Jan;625(7994):377-384. doi: 10.1038/s41586-023-06816-9. Epub 2023 Dec 6. PMID: 38057668; PMCID: PMC10781646.

Yin S, Klaeger S, Chea VA, Carulli IP, Rachimi S, Black KE, Filbin M, Hariri LP, Knipe RS, Padera RF, Stevens JD, Lane WJ, Carr SA, Wu CJ, Kim EY, Keskin DB. Integrated Immunopeptidomic and Proteomic Analysis of COVID-19 lung biopsies. Front Immunol. 2023 Oct 20;14:1269335. doi: 10.3389/fimmu.2023.1269335. PMID: 37942334; PMCID: PMC10628763.

Parry EM, Lemvigh CK, Deng S, Dangle N, Ruthen N, Knisbacher BA, Broséus J, Hergalant S, Guièze R, Li S, Zhang W, Johnson C, Long JM, Yin S, Werner L, Anandappa A, Purroy N, Gohil S, Oliveira G, Bachireddy P, Shukla SA, Huang T, Khoury JD, Thakral B, Dickinson M, Tam C, Livak KJ, Getz G, Neuberg D, Feugier P, Kharchenko P, Wierda W, Olsen LR, Jain N, Wu CJ. ZNF683 marks a CD8⁺ T cell population associated with anti-tumor immunity following anti-PD-1 therapy for Richter syndrome. Cancer Cell. 2023 Oct 9;41(10):1803-1816.e8. doi: 10.1016/j.ccell.2023.08.013. Epub 2023 Sep 21. PMID: 37738974; PMCID: PMC10618915.

Truex NL, Mohapatra S, Melo M, Rodriguez J, Li N, Abraham W, Sementa D, Touti F, Keskin DB, Wu CJ, Irvine DJ, Gómez-Bombarelli R, Pentelute BL. Design of Cytotoxic T Cell Epitopes by Machine Learning of Human Degrons. bioRxiv [Preprint]. 2023 Sep 26:2023.08.22.554289. doi: 10.1101/2023.08.22.554289. Update in: ACS Cent Sci. 2024 Mar 06;10(4):793-802. doi: 10.1021/acscentsci.3c01544. PMID: 37662211; PMCID: PMC10473641.

Bachireddy P, Azizi E, Burdziak C, Nguyen VN, Ennis CS, Maurer K, Park CY, Choo ZN, Li S, Gohil SH, Ruthen NG, Ge Z, Keskin DB, Cieri N, Livak KJ, Kim HT, Neuberg DS, Soiffer RJ, Ritz J, Alyea EP, Pe'er D, Wu CJ. Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy. Cell Rep. 2023 Aug 29;42(8):113011. doi: 10.1016/j.celrep.2023.113011. Epub 2023 Aug 8. Erratum for: Cell Rep. 2021 Nov 9;37(6):109992. doi: 10.1016/j.celrep.2021.109992. PMID: 37556329; PMCID: PMC10618917.

Mota I, Patrucco E, Mastini C, Mahadevan NR, Thai TC, Bergaggio E, Cheong TC, Leonardi G, Karaca-Atabay E, Campisi M, Poggio T, Menotti M, Ambrogio C, Longo DL, Klaeger S, Keshishian H, Sztupinszki ZM, Szallasi Z, Keskin DB, Duke-Cohan JS, Reinhold B, Carr SA, Wu CJ, Moynihan KD, Irvine DJ, Barbie DA, Reinherz EL, Voena C, Awad MM, Blasco RB, Chiarle R. ALK peptide vaccination restores the immunogenicity of ALK-rearranged non-small cell lung cancer. Nat Cancer. 2023 Jul;4(7):1016-1035. doi: 10.1038/s43018-023-00591-2. Epub 2023 Jul 10. PMID: 37430060.

Frost TC, Gartin AK, Liu M, Cheng J, Dharaneeswaran H, Keskin DB, Wu CJ, Giobbie-Hurder A, Thakuria M, DeCaprio JA. YAP1 and WWTR1 expression inversely correlates with neuroendocrine markers in Merkel cell carcinoma. J Clin Invest. 2023 Mar 1;133(5):e157171. doi: 10.1172/JCI157171. PMID: 36719743; PMCID: PMC9974098.

Penter L, Liu Y, Wolff JO, Yang L, Taing L, Jhaveri A, Southard J, Patel M, Cullen NM, Pfaff KL, Cieri N, Oliveira G, Kim-Schulze S, Ranasinghe S, Leonard R, Robertson T, Morgan EA, Chen HX, Song MH, Thurin M, Li S, Rodig SJ, Cibulskis C, Gabriel S, Bachireddy P, Ritz J, Streicher H, Neuberg DS, Hodi FS, Davids MS, Gnjatic S, Livak KJ, Altreuter J, Michor F, Soiffer RJ, Garcia JS, Wu CJ. Mechanisms of response and resistance to combined decitabine and ipilimumab for advanced myeloid disease. Blood. 2023 Apr 13;141(15):1817-1830. doi: 10.1182/blood.2022018246. PMID: 36706355; PMCID: PMC10122106.

Parry EM, Leshchiner I, Guièze R, Johnson C, Tausch E, Parikh SA, Lemvigh C, Broséus J, Hergalant S, Messer C, Utro F, Levovitz C, Rhrissorrakrai K, Li L, Rosebrock D, Yin S, Deng S, Slowik K, Jacobs R, Huang T, Li S, Fell G, Redd R, Lin Z, Knisbacher BA, Livitz D, Schneider C, Ruthen N, Elagina L, Taylor-Weiner A, Persaud B, Martinez A, Fernandes SM, Purroy N, Anandappa AJ, Ma J, Hess J, Rassenti LZ, Kipps TJ, Jain N, Wierda W, Cymbalista F, Feugier P, Kay NE, Livak KJ, Danysh BP, Stewart C, Neuberg D, Davids MS, Brown JR, Parida L, Stilgenbauer S, Getz G, Wu CJ. Evolutionary history of transformation from chronic lymphocytic leukemia to Richter syndrome. Nat Med. 2023 Jan;29(1):158-169. doi: 10.1038/s41591-022-02113-6. Epub 2023 Jan 9. PMID: 36624313; PMCID: PMC10155825.

ten Hacken E, Yin S, Redd R, Hernández Sánchez M, Clement K, Hoffmann GB, Regis FF, Witten E, Li S, Neuberg D, Pinello L, Livak KJ, Wu CJ. Loss-of-function lesions impact B-cell development and fitness but are insufficient to drive CLL in mouse models. Blood Adv. 2023 Aug 22;7(16):4514-4517. doi: 10.1182/bloodadvances.2022009135. PMID: 36477552; PMCID: PMC10425678.

Haradhvala NJ, Leick MB, Maurer K, Gohil SH, Larson RC, Yao N, Gallagher KME, Katsis K, Frigault MJ, Southard J, Li S, Kann MC, Silva H, Jan M, Rhrissorrakrai K, Utro F, Levovitz C, Jacobs RA, Slowik K, Danysh BP, Livak KJ, Parida L, Ferry J, Jacobson C, Wu CJ, Getz G, Maus MV. Distinct cellular dynamics associated with response to CAR-T therapy for refractory B cell lymphoma. Nat Med. 2022 Sep;28(9):1848-1859. doi: 10.1038/s41591-022-01959-0. Epub 2022 Sep 12. PMID: 36097221; PMCID: PMC9509487.

Lee PC, Klaeger S, Le PM, Korthauer K, Cheng J, Ananthapadmanabhan V, Frost TC, Stevens JD, Wong AY, Iorgulescu JB, Tarren AY, Chea VA, Carulli IP, Lemvigh CK, Pedersen CB, Gartin AK, Sarkizova S, Wright KT, Li LW, Nomburg J, Li S, Huang T, Liu X, Pomerance L, Doherty LM, Apffel AM, Wallace LJ, Rachimi S, Felt KD, Wolff JO, Witten E, Zhang W, Neuberg D, Lane WJ, Zhang G, Olsen LR, Thakuria M, Rodig SJ, Clauser KR, Starrett GJ, Doench JG, Buhrlage SJ, Carr SA, DeCaprio JA, Wu CJ, Keskin DB. Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma. J Clin Invest. 2022 Jul 1;132(13):e151666. doi: 10.1172/JCI151666. PMID: 35775490; PMCID: PMC9246387.

Oliveira G, Stromhaug K, Cieri N, Iorgulescu JB, Klaeger S, Wolff JO, Rachimi S, Chea V, Krause K, Freeman SS, Zhang W, Li S, Braun DA, Neuberg D, Carr SA, Livak KJ, Frederick DT, Fritsch EF, Wind-Rotolo M, Hacohen N, Sade-Feldman M, Yoon CH, Keskin DB, Ott PA, Rodig SJ, Boland GM, Wu CJ. Landscape of helper and regulatory antitumour CD4⁺ T cells in melanoma. Nature. 2022 May;605(7910):532-538. doi: 10.1038/s41586-022-04682-5. Epub 2022 May 4. PMID: 35508657; PMCID: PMC9815755.

Liu M, Tayob N, Penter L, Sellars M, Tarren A, Chea V, Carulli I, Huang T, Li S, Cheng SC, Le P, Frackiewicz L, Fasse J, Qi C, Liu JF, Stover EH, Curtis J, Livak KJ, Neuberg D, Zhang G, Matulonis UA, Wu CJ, Keskin DB, Konstantinopoulos PA. Improved T-cell Immunity Following Neoadjuvant Chemotherapy in Ovarian Cancer. Clin Cancer Res. 2022 Aug 2;28(15):3356-3366. doi: 10.1158/1078-0432.CCR-21-2834. PMID: 35443043; PMCID: PMC9357177.

Purroy N, Tong YE, Lemvigh CK, Cieri N, Li S, Parry EM, Zhang W, Rassenti LZ, Kipps TJ, Slager SL, Kay NE, Lesnick C, Shanafelt TD, Ghia P, Scarfò L, Livak KJ, Kharchenko PV, Neuberg DS, Olsen LR, Fan J, Gohil SH, Wu CJ. Single-cell analysis reveals immune dysfunction from the earliest stages of CLL that can be reversed by ibrutinib. Blood. 2022 Apr 7;139(14):2252-2256. doi: 10.1182/blood.2021013926. PMID: 35020831; PMCID: PMC8990375.

Bachireddy P, Azizi E, Burdziak C, Nguyen VN, Ennis CS, Maurer K, Park CY, Choo ZN, Li S, Gohil SH, Ruthen NG, Ge Z, Keskin DB, Cieri N, Livak KJ, Kim HT, Neuberg DS, Soiffer RJ, Ritz J, Alyea EP, Pe'er D, Wu CJ. Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy. Cell Rep. 2021 Nov 9;37(6):109992. doi: 10.1016/j.celrep.2021.109992. Erratum in: Cell Rep. 2023 Aug 29;42(8):113011. doi: 10.1016/j.celrep.2023.113011. PMID: 34758319; PMCID: PMC9035342.

Ouspenskaia T, Law T, Clauser KR, Klaeger S, Sarkizova S, Aguet F, Li B, Christian E, Knisbacher BA, Le PM, Hartigan CR, Keshishian H, Apffel A, Oliveira G, Zhang W, Chen S, Chow YT, Ji Z, Jungreis I, Shukla SA, Justesen S, Bachireddy P, Kellis M, Getz G, Hacohen N, Keskin DB, Carr SA, Wu CJ, Regev A. Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer. Nat Biotechnol. 2022 Feb;40(2):209-217. doi: 10.1038/s41587-021-01021-3. Epub 2021 Oct 18. PMID: 34663921; PMCID: PMC10198624.

Penter L, Gohil SH, Huang T, Thrash EM, Schmidt D, Li S, Severgnini M, Neuberg D, Hodi FS, Livak KJ, Zeiser R, Bachireddy P, Wu CJ. Coevolving JAK2V617F+relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case. Blood Adv. 2021 Nov 23;5(22):4701-4709. doi: 10.1182/bloodadvances.2021004335. PMID: 34432868; PMCID: PMC8759138.

Klaeger S, Apffel A, Clauser KR, Sarkizova S, Oliveira G, Rachimi S, Le PM, Tarren A, Chea V, Abelin JG, Braun DA, Ott PA, Keshishian H, Hacohen N, Keskin DB, Wu CJ, Carr SA. Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples. Mol Cell Proteomics. 2021;20:100133. doi: 10.1016/j.mcpro.2021.100133. Epub 2021 Aug 12. PMID: 34391888; PMCID: PMC8724927.

Oliveira G, Stromhaug K, Klaeger S, Kula T, Frederick DT, Le PM, Forman J, Huang T, Li S, Zhang W, Xu Q, Cieri N, Clauser KR, Shukla SA, Neuberg D, Justesen S, MacBeath G, Carr SA, Fritsch EF, Hacohen N, Sade-Feldman M, Livak KJ, Boland GM, Ott PA, Keskin DB, Wu CJ. Phenotype, specificity and avidity of antitumour CD8⁺ T cells in melanoma. Nature. 2021 Aug;596(7870):119-125. doi: 10.1038/s41586-021-03704-y. Epub 2021 Jul 21. PMID: 34290406; PMCID: PMC9187974.

Penter L, Gohil SH, Lareau C, Ludwig LS, Parry EM, Huang T, Li S, Zhang W, Livitz D, Leshchiner I, Parida L, Getz G, Rassenti LZ, Kipps TJ, Brown JR, Davids MS, Neuberg DS, Livak KJ, Sankaran VG, Wu CJ. Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History. Cancer Discov. 2021 Dec 1;11(12):3048-3063. doi: 10.1158/2159-8290.CD-21-0276. PMID: 34112698; PMCID: PMC8660953.

Penter L, Zhang Y, Savell A, Huang T, Cieri N, Thrash EM, Kim-Schulze S, Jhaveri A, Fu J, Ranasinghe S, Li S, Zhang W, Hathaway ES, Nazzaro M, Kim HT, Chen H, Thurin M, Rodig SJ, Severgnini M, Cibulskis C, Gabriel S, Livak KJ, Cutler C, Antin JH, Nikiforow S, Koreth J, Ho VT, Armand P, Ritz J, Streicher H, Neuberg D, Hodi FS, Gnjatic S, Soiffer RJ, Liu XS, Davids MS, Bachireddy P, Wu CJ. Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation. Blood. 2021 Jun 10;137(23):3212-3217. doi: 10.1182/blood.2021010867. PMID: 33720354; PMCID: PMC8351891.

Braun DA, Street K, Burke KP, Cookmeyer DL, Denize T, Pedersen CB, Gohil SH, Schindler N, Pomerance L, Hirsch L, Bakouny Z, Hou Y, Forman J, Huang T, Li S, Cui A, Keskin DB, Steinharter J, Bouchard G, Sun M, Pimenta EM, Xu W, Mahoney KM, McGregor BA, Hirsch MS, Chang SL, Livak KJ, McDermott DF, Shukla SA, Olsen LR, Signoretti S, Sharpe AH, Irizarry RA, Choueiri TK, Wu CJ. Progressive immune dysfunction with advancing disease stage in renal cell carcinoma. Cancer Cell. 2021 May 10;39(5):632-648.e8. doi: 10.1016/j.ccell.2021.02.013. Epub 2021 Mar 11. PMID: 33711273; PMCID: PMC8138872.

Lazarian G, Yin S, Ten Hacken E, Sewastianik T, Uduman M, Font-Tello A, Gohil SH, Li S, Kim E, Joyal H, Billington L, Witten E, Zheng M, Huang T, Severgnini M, Lefebvre V, Rassenti LZ, Gutierrez C, Georgopoulos K, Ott CJ, Wang L, Kipps TJ, Burger JA, Livak KJ, Neuberg DS, Baran-Marszak F, Cymbalista F, Carrasco RD, Wu CJ. A hotspot mutation in transcription factor IKZF3 drives B cell neoplasia via transcriptional dysregulation. Cancer Cell. 2021 Mar 8;39(3):380-393.e8. doi: 10.1016/j.ccell.2021.02.003. PMID: 33689703; PMCID: PMC8034546.

Kretzmer H, Biran A, Purroy N, Lemvigh CK, Clement K, Gruber M, Gu H, Rassenti L, Mohammad AW, Lesnick C, Slager SL, Braggio E, Shanafelt TD, Kay NE, Fernandes SM, Brown JR, Wang L, Li S, Livak KJ, Neuberg DS, Klages S, Timmermann B, Kipps TJ, Campo E, Gnirke A, Wu CJ, Meissner A. Preneoplastic Alterations Define CLL DNA Methylome and Persist through Disease Progression and Therapy. Blood Cancer Discov. 2021 Jan;2(1):54-69. doi: 10.1158/2643-3230.BCD-19-0058. Epub 2020 Dec 3. PMID: 33604581; PMCID: PMC7888194.

Hu Z, Leet DE, Allesøe RL, Oliveira G, Li S, Luoma AM, Liu J, Forman J, Huang T, Iorgulescu JB, Holden R, Sarkizova S, Gohil SH, Redd RA, Sun J, Elagina L, Giobbie-Hurder A, Zhang W, Peter L, Ciantra Z, Rodig S, Olive O, Shetty K, Pyrdol J, Uduman M, Lee PC, Bachireddy P, Buchbinder EI, Yoon CH, Neuberg D, Pentelute BL, Hacohen N, Livak KJ, Shukla SA, Olsen LR, Barouch DH, Wucherpfennig KW, Fritsch EF, Keskin DB, Wu CJ, Ott PA. Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma. Nat Med. 2021 Mar;27(3):515-525. doi: 10.1038/s41591-020-01206-4. Epub 2021 Jan 21. PMID: 33479501; PMCID: PMC8273876.

Bachireddy P, Ennis C, Nguyen VN, Gohil SH, Clement K, Shukla SA, Forman J, Barkas N, Freeman S, Bavli N, Elagina L, Leshchiner I, Mohammad AW, Mathewson ND, Keskin DB, Rassenti LZ, Kipps TJ, Brown JR, Getz G, Ho VT, Gnirke A, Neuberg D, Soiffer RJ, Ritz J, Alyea EP, Kharchenko PV, Wu CJ. Distinct evolutionary paths in chronic lymphocytic leukemia during resistance to the graft-versus-leukemia effect. Sci Transl Med. 2020 Sep 16;12(561):eabb7661. doi: 10.1126/scitranslmed.abb7661. PMID: 32938797; PMCID: PMC7829680.

Kuai R, Singh PB, Sun X, Xu C, Najafabadi AH, Scheetz L, Yuan W, Xu Y, Hong H, Keskin DB, Wu CJ, Jain R, Schwendeman A, Moon JJ. Robust anti-tumor T cell response with efficient intratumoral infiltration by nanodisc cancer immunotherapy. Adv Ther (Weinh). 2020 Sep;3(9):2000094. doi: 10.1002/adtp.202000094. Epub 2020 Jun 23. PMID: 38317797; PMCID: PMC10843840.

Publications for single-cell immune profiling and TCR repertoire analysis

Penter L, Borji M, Nagler A, Lyu H, Lu WS, Cieri N, Maurer K, Oliveira G, Al'Khafaji AM, Garimella KV, Li S, Neuberg DS, Ritz J, Soiffer RJ, Garcia JS, Livak KJ, Wu CJ. Integrative genotyping of cancer and immune phenotypes by long-read sequencing. Nat Commun. 2024 Jan 2;15(1):32. doi: 10.1038/s41467-023-44137-7. PMID: 38167262; PMCID: PMC10762175.

Ten Hacken E, Gruber M, Hernández-Sánchez M, Hoffmann GB, Baranowski K, Redd RA, Clement K, Livak K, Wu CJ. Generation of mouse models carrying B cell restricted single or multiplexed loss-of-function mutations through CRISPR-Cas9 gene editing. STAR Protoc. 2023 Dec 15;4(4):102165. doi: 10.1016/j.xpro.2023.102165. Epub 2023 Sep 18. PMID: 37729058; PMCID: PMC10510057.

Penter L, Ten Hacken E, Southard J, Lareau CA, Ludwig LS, Li S, Neuberg DS, Livak KJ, Wu CJ. Mitochondrial DNA Mutations as Natural Barcodes for Lineage Tracing of Murine Tumor Models. Cancer Res. 2023 Mar 2;83(5):667-672. doi: 10.1158/0008-5472.CAN-22-0275. PMID: 36469010; PMCID: PMC9988704.

Ten Hacken E, Sewastianik T, Yin S, Hoffmann GB, Gruber M, Clement K, Penter L, Redd RA, Ruthen N, Hergalant S, Sholokhova A, Fell G, Parry EM, Broséus J, Guieze R, Lucas F, Hernández-Sánchez M, Baranowski K, Southard J, Joyal H, Billington L, Regis FFD, Witten E, Uduman M, Knisbacher BA, Li S, Lyu H, Vaisitti T, Deaglio S, Inghirami G, Feugier P, Stilgenbauer S, Tausch E, Davids MS, Getz G, Livak KJ, Bozic I, Neuberg DS, Carrasco RD, Wu CJ. In Vivo Modeling of CLL Transformation to Richter Syndrome Reveals Convergent Evolutionary Paths and Therapeutic Vulnerabilities. Blood Cancer Discov. 2023 Mar 1;4(2):150-169. doi: 10.1158/2643-3230.BCD-22-0082. PMID: 36468984; PMCID: PMC9975769.

Liu S, Iorgulescu JB, Li S, Borji M, Barrera-Lopez IA, Shanmugam V, Lyu H, Morriss JW, Garcia ZN, Murray E, Reardon DA, Yoon CH, Braun DA, Livak KJ, Wu CJ, Chen F. Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response. Immunity. 2022 Oct 11;55(10):1940-1952.e5. doi: 10.1016/j.immuni.2022.09.002. PMID: 36223726; PMCID: PMC9745674.

Song L, Ouyang Z, Cohen D, Cao Y, Altreuter J, Bai G, Hu X, Livak KJ, Li H, Tang M, Li B, Liu XS. Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies. Cancer Immunol Res. 2022 Jul 1;10(7):788-799. doi: 10.1158/2326-6066.CIR-21-0965. PMID: 35605261; PMCID: PMC9299271.

Gutierrez C, Al'Khafaji AM, Brenner E, Johnson KE, Gohil SH, Lin Z, Knisbacher BA, Durrett RE, Li S, Parvin S, Biran A, Zhang W, Rassenti L, Kipps TJ, Livak KJ, Neuberg D, Letai A, Getz G, Wu CJ, Brock A. Multifunctional barcoding with ClonMapper enables high-resolution study of clonal dynamics during tumor evolution and treatment. Nat Cancer. 2021 Jul;2(7):758-772. doi: 10.1038/s43018-021-00222-8. Epub 2021 Jul 12. PMID: 34939038; PMCID: PMC8691751.

Gohil SH, Iorgulescu JB, Braun DA, Keskin DB, Livak KJ. Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy. Nat Rev Clin Oncol. 2021 Apr;18(4):244-256. doi: 10.1038/s41571-020-00449-x. Epub 2020 Dec 4. PMID: 33277626; PMCID: PMC8415132.

Ten Hacken E, Clement K, Li S, Hernández-Sánchez M, Redd R, Wang S, Ruff D, Gruber M, Baranowski K, Jacob J, Flynn J, Jones KW, Neuberg D, Livak KJ, Pinello L, Wu CJ. High throughput single-cell detection of multiplex CRISPR-edited gene modifications. Genome Biol. 2020 Oct 20;21(1):266. doi: 10.1186/s13059-020-02174-1. PMID: 33081820; PMCID: PMC7574538.

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. R Nase 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 S, Livak 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).

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 Immunotherapy. Sci 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 CJ, Keskin DB. A large peptidome dataset improves HLA class I eptiope prediction across most of the human population. Nat 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).

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 SA, Li 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 CJ, Shukla SA, Choueiri TK. Clinical validation of PBMR1 alterations as a marker of immune checkpoint inhbitor response in Renal Cell Carcinoma. JAMA 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 immunosuppression. Cancer Immunol Immunother. Mar;68(3):421-432 (2019).

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).