Publications

Selected Publications

 

2024

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.(Pubmed)

2023

Oliveira G, Egloff AM, Afeyan AB, Wolff JO, Zeng Z, Chernock RD, Zhou L, Messier C, Lizotte P, Pfaff KL, Stromhaug K, Penter L, Haddad RI, Hanna GJ, Schoenfeld JD, Goguen LA, Annino DJ, Jo V, Oppelt P, Pipkorn P, Jackson R, Puram SV, Paniello RC, Rich JT, Webb J, Zevallos JP, Mansour M, Fu J, Dunn GP, Rodig SJ, Ley J, Morris LGT, Dunn L, Paweletz CP, Kallogjeri D, Piccirillo JF, Adkins DR, Wu CJ, Uppaluri R. Preexisting tumor-resident T cells with cytotoxic potential associate with response to neoadjuvant anti-PD-1 in head and neck cancer. Sci Immunol 2023. (Pubmed)

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. (Pubmed)

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. (Pubmed)

Zhang DKY, Adu-Berchie K, Iyer S, Liu Y, Cieri N, Brockman JM, Neuberg D, Wu CJ, Mooney DJ.  Enhancing CAR-T cell functionality in a patient-specific manner.  Nat Commun. 2023.(Pubmed)

Maurer K, Kim HT, Garrity HM, Liney D, Cutler CS, Antin JH, Koreth J, Ritz J, Shapiro RM, Romee R, Ho VT, Gooptu M, Soiffer RJ, Wu CJ, Nikiforow S. Lower Incidence of Chronic GVHD Observed after Transplantation with Cryopreserved Unrelated Allogeneic Stem Cells.  Blood Adv 2023.(Pubmed)

Penter L, Liu Y, Wolff JO, Yang L, Taing L, Jhaveri A, Southard J, Patel M, Cullen N, Pfaff KL, Cieri N, Oliveira G, Kim-Schulze S, Ranasinghe S, Leonard R, Robertson T, Morgan EA, Chen H, Song MH, Thurin M, Li S, Rodig SJ, Cibulskis C, Gabriel S, Bachireddy P, Ritz J, Streicher H, Neuberg D, Hodi FS, Gnjatic S, Davids MS, 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.(Pubmed)

Parry EM, Ten Hacken E, Wu CJ.  Richter syndrome: Novel insights into the biology of transformation.  Blood 2023. (Pubmed)

2022

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.(Pubmed)

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.(Pubmed)

Nagler A, Wu CJ.  The end of the beginning: Application of single cell sequencing to chronic lymphocytic leukemia (CLL).  Blood 2022.(Pubmed)

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.(Pubmed)

Knisbacher BA, Lin Z, Hahn CK, Nadeu F, Duran-Ferrer M, Stevenson KE, Tausch E, Delgado J, Barbera-Mourelle A, Taylor-Weiner A, Bousquets-Muñoz P, Diaz-Navarro A, Dunford A, Anand S, Kretzmer H, Gutierrez-Abril J, López-Tamargo S, Fernandes SM, Sun C, Sivina M, Rassenti LZ, Schneider C, Li S, Parida L, Meissner A, Aguet F, Burger JA, Wiestner A, Kipps TJ, Brown JR, Hallek M, Stewart C, Neuberg DS, Martín-Subero JI, Puente XS, Stilgenbauer S, Wu CJ, Campo E, Getz G.  Molecular map of chronic lymphocytic leukemia and its impact on outcome.  Nat Genet. 2022. (Pubmed)

Sellars MC, Wu CJ, Fritsch EF.  Cancer vaccines: Building a bridge over troubled waters.  Cell 2022.(Pubmed)

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. (Pubmed)

Robles-Oteiza C, Wu CJ.  Editorial overview: Vaccines: Reinvigorating therapeutic cancer vaccines.  Curr Opin Immunol. 2022. (Pubmed)

Gutierrez C, Vilas CK, Wu CJ, Al'Khafaji AM.  Functionalized Lineage Tracing Can Enable the Development of Homogenization-Based Therapeutic Strategies in Cancer.  Front Immunol. 2022.(Pubmed)

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.(Pubmed)

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.(Pubmed)

Pedersen CB, Dam SH, Barnkob MB, Leipold MD, Purroy N, Rassenti LZ, Kipps TJ, Nguyen J, Lederer JA, Gohil SH, Wu CJ, Olsen LR.  cyCombine allows for robust integration of single-cell cytometry datasets within and across technologies.  Nat Commun. 2022.(Pubmed)

2021

Bachireddy P, Azizi E, Burdziak C, Nguyen VN, Ennis C, Maurer K, Park CY, Choo Z-N, Li S, Gohil SH, Ruthen NG, Keskin D, 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 Reports 2021. (PubMed)

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. Nature Biotechnology 2021. (PubMed)

Zeng Z, Fu J, Cibulskis C, Jhaveri A, Gumbs C, Das B, Sanchez-Epiridion B, Janssens S, Taing L, Wang L, Wang J, Lindsay J, Vilimas T, Zhang J, Tokheim C, Das Sahu A, Jiang P, Yan C, Duose D, Cerami E, Chen L, Cohen D, Chen Q-R, Enos R, Huang X, Lee JJ, Liu Y. Neuberg D, Nguyen C, Patterson C, Sarkar S, Shukla S, Tang M, Tsuji J, Uduman M, Wang X, Weirarther J, Yu J, Yu J, Zhang J, Zhang J, Meerzaman D, Thurin M, Futreal PA, Karlovich C, Gabirel S, Wistuba I, Liu XS, Wu CJ.  Cross-site concordance evaluation of tumor DNA and RNA sequencing platforms for the CIMAC-CIDC network.  Clinical Cancer Research 2021. (PubMed)

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 K, 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 antitumor CD8+ T cells in melanoma.  Nature 2021. (PubMed)

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 L, Kipps TJ, Brown JR, Davids MS, Neuberg D, Livak KJ, Sankaran VG, Wu CJ.  Longitudinal single-cell dynamics of chromatin accessibility and mitochondrial mutations in chronic lymphocytic leukemia mirror disease history.  Cancer Discovery 2021. (PubMed)

Gutierrez C, Al’Khafaji AM, Brenner E, Johnson KE, Gohil SH, Lin Z, Knisbacher BA, Durret 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.  Multi-functional barcoding with ClonMapper enables high resolution study of clonal dynamics during tumor evolution and treatment.  Cancer Cell 2021.

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.  Co-evolving JAK2V617F+ relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case.  Blood Advances 2021. (PubMed)

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, Kin 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. (PubMed)

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. (PubMed)

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 L,  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 p.L162R in IKZF3 drives B cell neoplasia via transcriptional dysregulation.  Cancer Cell 2021. (PubMed)

2020

Kretzmer H, Biran Anat, Purroy N, Lemvigh C, Clement K, Gruber M, Gu H, Rassenti L, Mohammad AW, Lesnick C, Slager S, Braggio E, Shanafelt T, Kay NE, Wang L, Li S, Livak K, Neuberg D, Klages S, Timmermann B, Kipps, TJ, Campo E, Gnirke A, Wu CJ, Meissner A.  Pre-neoplastic alterations define CLL DNA methylome and persist through disease progression and therapy.  Blood Cancer Discovery 2020. (PubMed)

Hu Z, Leet DE, Allesoe RL, Li S, Oliveira G, Luoma AM, Liu J, Forman J, Huang T, Iorgulescu JB, Holden R, Sarkizova S, Gohil S, Redd R, 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 K, Fritsch EF, Keskin DB, Wu CJ, Ott PA.  Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in melanoma patients.  Nature Medicine 2020. (PubMed)

Braun D, Bakouny Z, Hirsch L, Flippot R, Van Allen E, Wu CJ, Choueiri T.  Beyond conventional immune checkpoint inhibition - novel immunotherapies for renal cell carcinoma. Nature Reviews Clinical Oncology 2021; Jan 12.  doi: 10.1038/s41571-020-00455-z. Online ahead of print.  PMID: 33437048. (PubMed)

ten Hacken E,  Clement K, Li S, Hernandez-Sanchez 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 Biology 2020; Oct 20;21(1):266.  doi: 10.1186/s13059-020-02174-1. (PubMed)

Bachireddy P, Ennis C, Nguyen VN, Clement K, Gohil SH, Shukla SA, Forman J, Barkas N, Freeman S, Bavli N, Elagina L, Leshchiner I, Mohammad AW, Rassenti LZ, Kipps TJ, Brown JR, Getz GA, 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 graft-versus-leukemia.  Science Translational Medicine 2020; Sep 16;12(561):eabb7661. doi: 10.1126/scitranslmed.abb7661. (PubMed)

Braun DA, Hou Y, Bakouny Z, Ficial M, Sant’ Angelo M, Forman J, Ross-Macdonald P, Berger AC, Jegede OA, Elagina L, Steinharter J, Sun M, Wind-Rotolo M, Pignon J-C, Cherniack AC, Lichtenstein L, Neuberg D, Catalano P, Freeman GJ, Sharpe AH, McDermott DF, Van Allen EM, Signoretti S, Wu CJ, Shukla SA, Choueiri TK.  Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma.  Nature Medicine 2020. (PubMed)

Penter L, Wu CJ.  Personal tumor antigens in blood malignancies: genomics-directed identification and targeting.  Journal of Clinical Investigations 2020; Jan 27. pii: 129209. doi: 10.1172/JCI129209. (PubMed)

Anandappa A, Wu CJ, Ott P.  Directing Traffic: How to effectively drive T cells into tumors.  Cancer Discovery 2020; Jan 23. doi: 10.1158/2159-8290.CD-19-0790. (PubMed)

2019

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, Eisenhauren T, Zhang GL, Clauserm KR, Hacohen N, Carr SA, Wu CJ, Keskin DB.  A large peptidome dataset improves HLA class I epitope prediction across most of the human population.  Nature Biotech 2020; Feb;38(2):199-209. doi: 10.1038/s41587-019-0322-9. Epub 2019 Dec 16. (PubMed)

Gutierrez C, Wu CJ.  Clonal dynamics in chronic lymphocytic leukemia.  Blood Advances 2019; Nov 26;3(22):3759-69. doi: 10.1182/bloodadvances.2019000367. (PubMed) 

Guièze R, Liu V, Rosebrock D, Jourdain AA, Hernández-Sánchez M, Martinez A, Sun J, Baranowski K, Thompson PA, Heo J-M, Cartun Z, Aygün O, Notarangelo G, Livitz D, Li S, Ten Hacken E, Davids, MS, Iorgelescu JB, Zhang W, Biran A, Fernandes SM, Brown JR, Lako A, Ciantra ZB, Keskin DB, Udeshi ND, Wierda WG, Livak KJ, Letai AG, Neuberg D, Harper JW, Carr SA, Piccioni F, Ott CJ, Leshchiner I, Johannessen CM, Doench J, Mootha VK, Getz G, Wu CJ.  Mitochondrial reprogramming underlies resistance to BCL-2 inhibition in lymphoid malignancies. Cancer Cell 2019; Oct 14;36(4):369-384.e13. doi: 10.1016/j.ccell.2019.08.005. (PubMed)

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. 2019 Aug;14(8):2571-2594. (PubMed)

Gruber M, Bozic I, Leshchiner I, Livitz D, Stevenson K, Rassenti L, Rosebrock D, Taylor-Weiner A, Olive O, Goyetche R, Fernandes SM, Sun J, Stewart C, Wong A, Cibulskis C, Zhang W, Reiter JG, Gerold JM, Gribben JG, Rai KR, Keating MJ, Brown JR, Neuberg D, Kipps TJ, Nowak MA, Getz G, Wu CJ. Growth dynamics in naturally progressing chronic lymphocytic leukaemia. Nature. 2019 Jun;570(7762):474-479. (PubMed)

Ott PA. Wu CJ.  Cancer vaccines: Steering T cells down the right path to eradicate tumors.  Cancer Discovery 2019; Mar 12. doi: 10.1158/2159-8290.CD-18-1357. (PubMed)

Gohil S, Wu CJ.  Dissecting CLL through high dimensional single cell technologies.  Blood. 2019 Mar 28;133(13):1446-1456. doi: 10.1182/blood-2018-09-835389. Epub 2019 Feb 6. (PubMed) 

Yin S, Gambe RG, Sun J, Martinez AZ, Cartun ZJ, Regis FFD, Wan Y, Fan J, Brooks AN, Herman SEM, ten Hacken E, Taylor-Weiner A, Obeng EA, Cibulskis CL, Neuberg D, Campagna DR, Fleming MD, Ebert BL, Wiestner A, Leshchiner I, DeCaprio JA, Getz G, Reed R, Carrasco RD, Wu CJ*, Wang L*.  A murine model of chronic lymphocytic leukemia based on B cell-restricted expression of Sf3b1 mutation and Atm deletion.  Cancer Cell 2019; Feb 11;35(2):283-96.e5. doi: 10.1016/j.ccell.2018.12.013. (PubMed)

Keskin DB, Anandappa AJ, Sun J, Tirosh I, Mathewson ND, 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 2019 565:234-239. (PubMed) 

2018

ten Hacken E, Valentin R, Regis FFD, Sun J, Yin S, Werner L, Deng J, Gruber M, Wong J, Zheng M, Gill AL, Seiler M, Smith P, Thomas M, Buonamici S, Ghia EM, Kim E, Rassenti LZ, Burger JA, Kipps TJ, Meyerson ML, Bachireddy P, Wang L, Reed R, Neuberg D, Carrasco RD, Brooks AN, Letai A, Davids MS, Wu CJ.  Splicing modulation sensitizes chronic lymphocytic leukemia cells to venetoclax by remodeling mitochondrial apoptotic dependencies.  JCI Insight. 2018 Oct 4;3(19). pii: 121438. doi: 10.1172/jci.insight.121438 (PubMed)

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 2018. (Pubmed)

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 2018 Apr 19;173(3):624-633.e8. (PubMed) 

2017

Hu Z, Ott PA, Wu CJ.  Towards personalized, tumour-specific, therapeutic vaccines for cancer.  Nature Reviews Immunology 2018; Mar;18(3):168-182. doi: 10.1038/nri.2017.131. Epub 2017 Dec 11. (PubMed)

ten Hacken E, Guieze R, Wu CJ.  SnapShot: Chronic Lymphocytic Leukemia.  Cancer Cell 2017; Nov 13;32(5):716-716.e1. doi: 10.1016/j.ccell.2017.10.015. (PubMed)

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 A, 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 Melanoma Patients.  Nature 2017; Jul 13; 547:217-21. (PubMed)

Wang L, Fan J, Zhang C, Francis JM, Georghiou G, Hergert 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, Kharchenko PV, Livak KJ, Wu CJ.  Integrated single cell genetic and transcriptional analysis suggests novel private drivers of chronic lymphocytic leukemia.  Genome Research 2017;  Aug;27(8):1300-11. (PubMed)

Purroy N, Wu CJ. Coevolution of Leukemia and Host Immune Cells in Chronic Lymphocytic Leukemia. Cold Spring Harb Perspect Med 2017. (PubMed)

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 2017; Feb 21;46(2):315-26. (PubMed)

Kipps TJ, Stevenson FK, Wu CJ, Croce CM, Packham G, Wierda WG, O'Brien S, Gribben J, Rai K. Chronic lymphocytic leukaemia. Nat Rev Dis Primers 2017, Jan 19; 3:16096 (PubMed) (PDF)

 

2016

Wang L, Brooks AN, Fan J, Wan Y, Gambe R, Li S, Hergert S, Yin S, Freeman SS, Levin JZ, 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 2016, Nov 14; 30(5):750-763 (PubMed) (PDF)

Davids MS, Kim HT, Bachireddy P, Costello C, Liguori R, Savell A, Lukez AP, Avigan D, Chen YB, McSweeney P, LeBoeuf NR, Rooney MS, Bowden M, Zhou CW, Granter SR, Hornick JL, Rodig SJ, Hirakawa M, Severgnini M, Hodi FS, Wu CJ, Ho VT, Cutler C, Koreth J, Alyea EP, Antin JH, Armand P, Streicher H, Ball ED, Ritz J, Bashey A, Soiffer RJ, Leukemia LymphomaSocietyBloodCancerResearch. Ipilimumab for Patients with Relapse after Allogeneic Transplantation. N Engl J Med 2016, Jul 14; 375(2):143-53 (PubMed) (PDF)

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 DA, Nowak MA, Getz G, Wu CJ. Clonal evolution in patients with chronic lymphocytic leukaemia developing resistance to BTK inhibition. Nat Commun 2016; 7:11589 (PubMed) (PDF)

2015

Landau DA, Tausch E, Taylor-Weiner AN, Stewart C, Reiter JG, Bahlo J, Kluth S, Bozic I, Lawrence M, Bottcher S, Carter SL, Cibulskis K, Mertens D, Sougnez CL, Rosenberg M, Hess JM, Edelmann J, Kless S, Kneba M, Ritgen M, Fink A, Fischer K, Gabriel S, Lander ES, Nowak MA, Dohner H, Hallek M, Neuberg D, Getz G, Stilgenbauer S and Wu CJ. Mutations driving CLL and their evolution in progression and relapse. Nature 2015, Oct 22; 526(7574):525-30 (PubMed) (PDF Part1)(PDF Part2)(PDF Part3)

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 and Getz G. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat Biotechnol 2015, Sep 15; 33(11):1152-1158 (PubMed) (PDF)

Guieze R, Wu CJ. Genomic and epigenomic heterogeneity in chronic lymphocytic leukemia. Blood 2015, Jul 23; 126(4):445-53 (PubMed) (PDF)

Bachireddy P, Burkhardt UE, Rajasagi M and Wu CJ. Haematological malignancies: at the forefront of immunotherapeutic innovation. Nat Rev Cancer 2015, Apr; 15(4):201-15 (PubMed) (PDF)

Rooney MS, Shukla SA, Wu CJ, Getz G and Hacohen N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell 2015, Jan 15; 160(1-2):48-61 (PubMed) (PDF)

2014

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 2014, Dec 8; 26(6):813-25 (PubMed) (PDF)

Wang L, Shalek AK, Lawrence M, Ding R, Gaublomme JT, Pochet N, Stojanov P, Sougnez C, Shukla SA, Stevenson KE, Zhang W, Wong J, Sievers QL, MacDonald BT, Vartanov AR, Goldstein NR, Neuberg D, He X, Lander E, Hacohen N, Regev A, Getz G, Brown JR, Park H and Wu CJ. Somatic mutation as a mechanism of Wnt/beta-catenin pathway activation in CLL. Blood 2014, Aug 14; 124(7):1089-98 (PubMed) (PDF)

Rajasagi M, Shukla SA, Fritsch EF, Keskin DB, DeLuca D, Carmona E, Zhang W, Sougnez C, Cibulskis K, Sidney J, Stevenson K, Ritz J, Neuberg D, Brusic V, Gabriel S, Lander ES, Getz G, Hacohen N and Wu CJ. Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia. Blood 2014, Jul 17; 124(3):453-62 (PubMed) (PDF) (supp PDF)

Fritsch EF, Rajasagi M, Ott PA, Brusic V, Hacohen N and Wu CJ. HLA-binding properties of tumor neoepitopes in humans. Cancer Immunol Res 2014, Jun; 2(6):522-9 (PubMed) (PDF)

Bachireddy P, Hainz U, Rooney M, Pozdnyakova O, Aldridge J, Zhang W, Liao X, Hodi FS, O'Connell K, Haining WN, Goldstein NR, Canning CM, Soiffer RJ, Ritz J, Hacohen N, Alyea EP 3rd, Kim HT and Wu CJ. Reversal of in situ T-cell exhaustion during effective human antileukemia responses to donor lymphocyte infusion. Blood 2014, Feb 27; 123(9):1412-21 (PubMed) (PDF)

2013

Burkhardt UE, Hainz U, Stevenson K, Goldstein NR, Pasek M, Naito M, Wu D, Ho VT, Alonso A, Hammond NN, Wong J, Sievers QL, Brusic A, McDonough SM, Zeng W, Perrin A, Brown JR, Canning CM, Koreth J, Cutler C, Armand P, Neuberg D, Lee JS, Antin JH, Mulligan RC, Sasada T, Ritz J, Soiffer RJ, Dranoff G, Alyea EP and Wu CJ. Autologous CLL cell vaccination early after transplant induces leukemia-specific T cells. J Clin Invest 2013, Sep 3; 123(9):3756-65 (PubMed) (PDF)

Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortes ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Lee RS, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CW, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES and Getz G. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 2013, Jul 11; 499(7457):214-8 (PubMed) (PDF)

Landau DA, Carter SL, Stojanov P, McKenna A, Stevenson K, Lawrence MS, Sougnez C, Stewart C, Sivachenko A, Wang L, Wan Y, Zhang W, Shukla SA, Vartanov A, Fernandes SM, Saksena G, Cibulskis K, Tesar B, Gabriel S, Hacohen N, Meyerson M, Lander ES, Neuberg D, Brown JR, Getz G and Wu CJ. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell 2013, Feb 14; 152(4):714-26 (PubMed) (PDF)

Naito M, Hainz U, Burkhardt UE, Fu B, Ahove D, Stevenson KE, Rajasagi M, Zhu B, Alonso A, Witten E, Matsuoka K, Neuberg D, Duke-Cohan JS, Wu CJ and Freeman GJ. CD40L-Tri, a novel formulation of recombinant human CD40L that effectively activates B cells. Cancer Immunol Immunother 2013, Feb; 62(2):347-57 (PubMed) (PDF)

2012

Shalek AK, Gaublomme JT, Wang L, Yosef N, Chevrier N, Andersen MS, Robinson JT, Pochet N, Neuberg D, Gertner RS, Amit I, Brown JR, Hacohen N, Regev A, Wu CJ and Park H. Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia. Nano Lett 2012, Dec 12; 12(12):6498-504 (PubMed) (PDF)

Cai A, Keskin DB, DeLuca DS, Alonso A, Zhang W, Zhang GL, Hammond NN, Nardi V, Stone RM, Neuberg D, Sidney J, Brusic V and Wu CJ. Mutated BCR-ABL generates immunogenic T-cell epitopes in CML patients. Clin Cancer Res 2012, Oct 15; 18(20):5761-72 (PubMed) (PDF)

Brusic A, Hainz U, Wadleigh M, Neuberg D, Su M, Canning CM, Deangelo DJ, Stone RM, Lee JS, Mulligan RC, Ritz J, Dranoff G, Sasada T and Wu CJ. Detecting T-cell reactivity to whole cell vaccines: Proof of concept analysis of T-cell response to K562 cell antigens in CML patients. Oncoimmunology 2012, Oct 1; 1(7):1095-1103 (PubMed) (PDF)

Biernacki MA, Tai YT, Zhang GL, Alonso A, Zhang W, Prabhala R, Zhang L, Munshi N, Neuberg D, Soiffer RJ, Ritz J, Alyea EP, Brusic V, Anderson KC and Wu CJ. Novel myeloma-associated antigens revealed in the context of syngeneic hematopoietic stem cell transplantation. Blood 2012, Mar 29; 119(13):3142-50 (PubMed) (PDF)

2011

Wang L, Lawrence MS, Wan Y, Stojanov P, Sougnez C, Stevenson K, Werner L, Sivachenko A, DeLuca DS, Zhang L, Zhang W, Vartanov AR, Fernandes SM, Goldstein NR, Folco EG, Cibulskis K, Tesar B, Sievers QL, Shefler E, Gabriel S, Hacohen N, Reed R, Meyerson M, Golub TR, Lander ES, Neuberg D, Brown JR, Getz G and Wu CJ. SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med 2011, Dec 29; 365(26):2497-506 (PubMed) (PDF)

Lin Y, Zhang L, Cai AX, Lee M, Zhang W, Neuberg D, Canning CM, Soiffer RJ, Alyea EP, Ritz J, Hacohen N, Means TK and Wu CJ. Effective posttransplant antitumor immunity is associated with TLR-stimulating nucleic acid-immunoglobulin complexes in humans. J Clin Invest 2011, Apr; 121(4):1574-84 (PubMed) (PDF)

2010

Marina O, Hainz U, Biernacki MA, Zhang W, Cai A, Duke-Cohan JS, Liu F, Brusic V, Neuberg D, Kutok JL, Alyea EP, Canning CM, Soiffer RJ, Ritz J and Wu CJ. Serologic markers of effective tumor immunity against chronic lymphocytic leukemia include nonmutated B-cell antigens. Cancer Res 2010, Feb 15; 70(4):1344-55 (PubMed) (PDF)

Zhang W, Choi J, Zeng W, Rogers SA, Alyea EP, Rheinwald JG, Canning CM, Brusic V, Sasada T, Reinherz EL, Ritz J, Soiffer RJ and Wu CJ. Graft-versus-leukemia antigen CML66 elicits coordinated B-cell and T-cell immunity after donor lymphocyte infusion. Clin Cancer Res 2010, May 15; 16(10):2729-39 (PubMed) (PDF)

Biernacki MA, Marina O, Zhang W, Liu F, Bruns I, Cai A, Neuberg D, Canning CM, Alyea EP, Soiffer RJ, Brusic V, Ritz J and Wu CJ. Efficacious immune therapy in chronic myelogenous leukemia (CML) recognizes antigens that are expressed on CML progenitor cells. Cancer Res 2010, Feb 1; 70(3):906-15 (PubMed) (PDF)

 

Reviews, chapters, monographs, and editorials (selected)

Fritsch EF, Burkhardt UE, Hacohen N, Wu CJ. Personal neoantigen cancer vaccines: a road not fully paved.  Cancer Immunology Research 2020 (in press).

Bozic I, Wu CJ. Delineating the evolutionary dynamics of cancer from theory to reality.  Nature Cancer 2020; 1:580–588 (2020)https://doi.org/10.1038/s43018-020-0079-6

Fritsch EF, Hacohen N and Wu CJ. Personal neoantigen cancer vaccines: The momentum builds. Oncoimmunology 2014; 3:e29311 (PubMed) (PDF)

Gruber M and Wu CJ. Evolving understanding of the CLL genome. Semin Hematol 2014, Jul; 51(3):177-87 (PubMed) (PDF)

Bachireddy P, Wu CJ. Understanding anti-leukemia responses to donor lymphocyte infusion. OncoImmunology 2014, Feb; 3:e28187 (PDF)

Landau DA, Carter SL, Getz G and Wu CJ. Clonal evolution in hematological malignancies and therapeutic implications. Leukemia 2014, Jan; 28(1):34-43 (PubMed) (PDF)

Burkhardt UE and Wu CJ. Boosting leukemia-specific T cell responses in patients following stem cell transplantation. Oncoimmunology 2013, Nov 1; 2(11):e26587 (PubMed) (PDF)

Wan Y and Wu CJ. SF3B1 mutations in chronic lymphocytic leukemia. Blood 2013, Jun 6; 121(23):4627-34 (PubMed) (PDF)

Landau DA and Wu CJ. Chronic lymphocytic leukemia: molecular heterogeneity revealed by high-throughput genomics. Genome Med 2013; 5(5):47 (PubMed) (PDF)

Hacohen N, Fritsch EF, Carter TA, Lander ES and Wu CJ. Getting personal with neoantigen-based therapeutic cancer vaccines. Cancer Immunol Res 2013, Jul; 1(1):11-5 (PubMed) (PDF)

Brusic A and Wu CJ. Enhancing graft-versus-leukemia after transplant: the rise of anti-cancer vaccines. Front Biosci (Landmark Ed) 2012; 17:635-55 (PubMed) (PDF)

Chapman M, Warren EH 3rd, and Wu CJ. Applications of next-generation sequencing to blood and marrow transplantation. Biol Blood Marrow Transplant 2012, Jan; 18(1 Suppl):S151-60 (PubMed) (PDF)

Wu CJ. CLL clonal heterogeneity: an ecology of competing subpopulations. Blood 2012, Nov 15; 120(20):4117-8 (PubMed) (PDF)