2024
Revsine M, Wang L, Forgues M, Behrens S, Craig AJ, Liu M, Tran B, Kelly M, Budhu A, Monge C, Xie C, Hernandez JM, Greten TF, Wang XW, Ma L. Lineage and ecology define liver tumor evolution in response to treatment. Cell Rep Med. 2024 Feb 20;5(2):101394. doi: 10.1016/j.xcrm.2024.101394. Epub 2024 Jan 26. PubMed PMID: 38280378; PubMed Central PMCID: PMC10897542.
Radtke AJ, Postovalova E, Varlamova A, Bagaev A, Sorokina M, Kudryashova O, Meerson M, Polyakova M, Galkin I, Svekolkin V, Isaev S, Wiebe D, Sharun A, Sarachakov A, Perelman G, Lozinsky Y, Yaniv Z, Lowekamp BC, Speranza E, Yao L, Pittaluga S, Shaffer AL 3rd, Jonigk D, Phelan JD, Davies-Hill T, Huang DW, Ovcharov P, Nomie K, Nuzhdina E, Kotlov N, Ataullakhanov R, Fowler N, Kelly M, Muppidi J, Davis JL, Hernandez JM, Wilson WH, Jaffe ES, Staudt LM, Roschewski M, Germain RN. Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients. Cancer Cell. 2024 Mar 11;42(3):444-463.e10. doi: 10.1016/j.ccell.2024.02.001. Epub 2024 Feb 29. PubMed PMID: 38428410; PubMed Central PMCID: PMC10966827.
Ohigashi I, White AJ, Yang MT, Fujimori S, Tanaka Y, Jacques A, Kiyonari H, Matsushita Y, Turan S, Kelly MC, Anderson G, Takahama Y. Developmental conversion of thymocyte-attracting cells into self-antigen-displaying cells in embryonic thymus medulla epithelium. Elife. 2024 Mar 11;12. doi: 10.7554/eLife.92552. PubMed PMID: 38466627; PubMed Central PMCID: PMC10928509.
Ushio A, Matsuda-Lennikov M, Kalle-Youngoue F, Shimizu A, Abdelmaksoud A, Kelly MC, Ishimaru N, Takahama Y. Functionally diverse thymic medullary epithelial cells interplay to direct central tolerance. Cell Rep. 2024 Apr 23;43(4):114072. doi: 10.1016/j.celrep.2024.114072. Epub 2024 Apr 5. PubMed PMID: 38581680; PubMed Central PMCID: PMC11079940.
Sui Y, Meyer TJ, Fennessey CM, Keele BF, Dadkhah K, Ma C, LaBranche CC, Breed MW, Kramer JA, Li J, Howe SE, Ferrari G, Williams LD, Cam M, Kelly MC, Shen X, Tomaras GD, Montefiori D, Greten TF, Miller CJ, Berzofsky JA. Innate protection against intrarectal SIV acquisition by a live SHIV vaccine. JCI Insight. 2024 May 21;9(12). doi: 10.1172/jci.insight.175800. PubMed PMID: 38912579; PubMed Central PMCID: PMC11383375.
Robinson W, Stone JK, Schischlik F, Gasmi B, Kelly MC, Seibert C, Dadkhah K, Gertz EM, Lee JS, Zhu K, Ma L, Wang XW, Sahinalp SC, Patro R, Leiserson MDM, Harris CC, Schäffer AA, Ruppin E. Identification of intracellular bacteria from multiple single-cell RNA-seq platforms using CSI-Microbes. Sci Adv. 2024 Jul 5;10(27):eadj7402. doi: 10.1126/sciadv.adj7402. Epub 2024 Jul 3. PubMed PMID: 38959321; PubMed Central PMCID: PMC11221508.
Tian M, Wei JS, Cheuk AT, Milewski D, Zhang Z, Kim YY, Chou HC, Liu C, Badr S, Pope EG, Rahmy A, Wu JT, Kelly MC, Wen X, Khan J. CAR T-cells targeting FGFR4 and CD276 simultaneously show potent antitumor effect against childhood rhabdomyosarcoma. Nat Commun. 2024 Jul 23;15(1):6222. doi: 10.1038/s41467-024-50251-x. PubMed PMID: 39043633; PubMed Central PMCID: PMC11266617.
Nguyen HT, Li M, Vadakath R, Henke KA, Tran TC, Li H, Yamadi M, Darbha S, Yang Y, Kabat J, Albright AR, Centeno EG, Phelan JD, Roulland S, Huang DW, Kelly MC, Young RM, Pittaluga S, Difilippantonio S, Muppidi JR. Gα13 restricts nutrient driven proliferation in mucosal germinal centers. Nat Immunol. 2024 Sep;25(9):1718-1730. doi: 10.1038/s41590-024-01910-0. Epub 2024 Jul 18. PubMed PMID: 39025963; PubMed Central PMCID: PMC11362015.
2023
Sun M, Cao Y, Okada R, Reyes-González JM, Stack HG, Qin H, Li N, Seibert C, Kelly MC, Ruppin E, Ho M, Thiele CJ, Nguyen R. Preclinical optimization of a GPC2-targeting CAR T-cell therapy for neuroblastoma. J Immunother Cancer. 2023 Jan;11(1). doi: 10.1136/jitc-2022-005881. PubMed PMID: 36631162; PubMed Central PMCID: PMC9835961.
Golino JL, Wang X, Bian J, Ruf B, Kelly M, Karim BO, Cam MC, Xie C. Anti-Cancer Activity of Verteporfin in Cholangiocarcinoma. Cancers (Basel). 2023 Apr 25;15(9). doi: 10.3390/cancers15092454. PubMed PMID: 37173920; PubMed Central PMCID: PMC10177077.
Ishii K, Davies JS, Sinkoe AL, Nguyen KA, Norberg SM, McIntosh CP, Kadakia T, Serna C, Rae Z, Kelly MC, Hinrichs CS. Multi-tiered approach to detect autoimmune cross-reactivity of therapeutic T cell receptors. Sci Adv. 2023 Jul 28;9(30):eadg9845. doi: 10.1126/sciadv.adg9845. Epub 2023 Jul 26. PubMed PMID: 37494434; PubMed Central PMCID: PMC10371023.
Masih KE, Gardner RA, Chou HC, Abdelmaksoud A, Song YK, Mariani L, Gangalapudi V, Gryder BE, Wilson AL, Adebola SO, Stanton BZ, Wang C, Milewski D, Kim YY, Tian M, Cheuk AT, Wen X, Zhang Y, Altan-Bonnet G, Kelly MC, Wei JS, Bulyk ML, Jensen MC, Orentas RJ, Khan J. A stem cell epigenome is associated with primary nonresponse to CD19 CAR T cells in pediatric acute lymphoblastic leukemia. Blood Adv. 2023 Aug 8;7(15):4218-4232. doi: 10.1182/bloodadvances.2022008977. PubMed PMID: 36607839; PubMed Central PMCID: PMC10440404.
Ruf B, Bruhns M, Babaei S, Kedei N, Ma L, Revsine M, Benmebarek MR, Ma C, Heinrich B, Subramanyam V, Qi J, Wabitsch S, Green BL, Bauer KC, Myojin Y, Greten LT, McCallen JD, Huang P, Trehan R, Wang X, Nur A, Murphy Soika DQ, Pouzolles M, Evans CN, Chari R, Kleiner DE, Telford W, Dadkhah K, Ruchinskas A, Stovroff MK, Kang J, Oza K, Ruchirawat M, Kroemer A, Wang XW, Claassen M, Korangy F, Greten TF. Tumor-associated macrophages trigger MAIT cell dysfunction at the HCC invasive margin. Cell. 2023 Aug 17;186(17):3686-3705.e32. doi: 10.1016/j.cell.2023.07.026. PubMed PMID: 37595566; PubMed Central PMCID: PMC10461130.
Chopp LB, Zhu X, Gao Y, Nie J, Singh J, Kumar P, Young KZ, Patel S, Li C, Balmaceno-Criss M, Vacchio MS, Wang MM, Livak F, Merchant JL, Wang L, Kelly MC, Zhu J, Bosselut R. Zfp281 and Zfp148 control CD4(+) T cell thymic development and T(H)2 functions. Sci Immunol. 2023 Nov 10;8(89):eadi9066. doi: 10.1126/sciimmunol.adi9066. Epub 2023 Nov 10. PubMed PMID: 37948511.
Golino JL, Bian J, Wang X, Fu J, Zhu XB, Yeo J, Kelly M, Escorcia FE, Cam M, Xie C. Single-cell RNA sequencing reveals cancer stem-like cells and dynamics in tumor microenvironment during cholangiocarcinoma progression. Front Cell Dev Biol. 2023;11:1250215. doi: 10.3389/fcell.2023.1250215. eCollection 2023. PubMed PMID: 38020927; PubMed Central PMCID: PMC10667919.
Malin J, Martinez-Ruiz GU, Zhao Y, Shissler SC, Cowan JE, Ding Y, Morales-Sanchez A, Ishikawa M, Lavaert M, Das A, Butcher D, Warner AC, Kallarakal M, Chen J, Kedei N, Kelly M, Brinster LR, Allman D, Bhandoola A. Expression of the transcription factor Klf6 by thymic epithelial cells is required for thymus development. Sci Adv. 2023 Nov 17;9(46):eadg8126. doi: 10.1126/sciadv.adg8126. Epub 2023 Nov 15. PubMed PMID: 37967174; PubMed Central PMCID: PMC10651122.
Craig AJ, Silveira MAD, Ma L, Revsine M, Wang L, Heinrich S, Rae Z, Ruchinskas A, Dadkhah K, Do W, Behrens S, Mehrabadi FR, Dominguez DA, Forgues M, Budhu A, Chaisaingmongkol J, Hernandez JM, Davis JL, Tran B, Marquardt JU, Ruchirawat M, Kelly M, Greten TF, Wang XW. Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing. Cell Rep. 2023 Nov 28;42(11):113446. doi: 10.1016/j.celrep.2023.113446. Epub 2023 Nov 18. PubMed PMID: 37980571; PubMed Central PMCID: PMC10750269.
Yossef R, Krishna S, Sindiri S, Lowery FJ, Copeland AR, Gartner JJ, Parkhurst MR, Parikh NB, Hitscherich KJ, Levi ST, Chatani PD, Zacharakis N, Levin N, Vale NR, Nah SK, Dinerman A, Hill VK, Ray S, Bera A, Levy L, Jia L, Kelly MC, Goff SL, Robbins PF, Rosenberg SA. Phenotypic signatures of circulating neoantigen-reactive CD8(+) T cells in patients with metastatic cancers. Cancer Cell. 2023 Dec 11;41(12):2154-2165.e5. doi: 10.1016/j.ccell.2023.11.005. Epub 2023 Nov 30. PubMed PMID: 38039963; PubMed Central PMCID: PMC10843665.
2022
Latt KZ, Heymann J, Jessee JH, Rosenberg AZ, Berthier CC, Arazi A, Eddy S, Yoshida T, Zhao Y, Chen V, Nelson GW, Cam M, Kumar P, Mehta M, Kelly MC, Kretzler M, Ray PE, Moxey-Mims M, Gorman GH, Lechner BL, Regunathan-Shenk R, Raj DS, Susztak K, Winkler CA, Kopp JB. Urine Single-Cell RNA Sequencing in Focal Segmental Glomerulosclerosis Reveals Inflammatory Signatures. Kidney Int Rep. 2022 Feb;7(2):289-304. doi: 10.1016/j.ekir.2021.11.005. eCollection 2022 Feb. PubMed PMID: 35155868; PubMed Central PMCID: PMC8821042.
Lowery FJ, Krishna S, Yossef R, Parikh NB, Chatani PD, Zacharakis N, Parkhurst MR, Levin N, Sindiri S, Sachs A, Hitscherich KJ, Yu Z, Vale NR, Lu YC, Zheng Z, Jia L, Gartner JJ, Hill VK, Copeland AR, Nah SK, Masi RV, Gasmi B, Kivitz S, Paria BC, Florentin M, Kim SP, Hanada KI, Li YF, Ngo LT, Ray S, Shindorf ML, Levi ST, Shepherd R, Toy C, Parikh AY, Prickett TD, Kelly MC, Beyer R, Goff SL, Yang JC, Robbins PF, Rosenberg SA. Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers. Science. 2022 Feb 25;375(6583):877-884. doi: 10.1126/science.abl5447. Epub 2022 Feb 3. PubMed PMID: 35113651; PubMed Central PMCID: PMC8996692.
Nie J, Carpenter AC, Chopp LB, Chen T, Balmaceno-Criss M, Ciucci T, Xiao Q, Kelly MC, McGavern DB, Belkaid Y, Bosselut R. The transcription factor LRF promotes integrin β7 expression by and gut homing of CD8αα(+) intraepithelial lymphocyte precursors. Nat Immunol. 2022 Apr;23(4):594-604. doi: 10.1038/s41590-022-01161-x. Epub 2022 Mar 30. PubMed PMID: 35354951; PubMed Central PMCID: PMC9290758.
Hanada KI, Zhao C, Gil-Hoyos R, Gartner JJ, Chow-Parmer C, Lowery FJ, Krishna S, Prickett TD, Kivitz S, Parkhurst MR, Wong N, Rae Z, Kelly MC, Goff SL, Robbins PF, Rosenberg SA, Yang JC. A phenotypic signature that identifies neoantigen-reactive T cells in fresh human lung cancers. Cancer Cell. 2022 May 9;40(5):479-493.e6. doi: 10.1016/j.ccell.2022.03.012. Epub 2022 Apr 21. PubMed PMID: 35452604; PubMed Central PMCID: PMC9196205.
Andreatta M, Tjitropranoto A, Sherman Z, Kelly MC, Ciucci T, Carmona SJ. A CD4(+) T cell reference map delineates subtype-specific adaptation during acute and chronic viral infections. Elife. 2022 Jul 13;11. doi: 10.7554/eLife.76339. PubMed PMID: 35829695; PubMed Central PMCID: PMC9323004.
Tian M, Cheuk AT, Wei JS, Abdelmaksoud A, Chou HC, Milewski D, Kelly MC, Song YK, Dower CM, Li N, Qin H, Kim YY, Wu JT, Wen X, Benzaoui M, Masih KE, Wu X, Zhang Z, Badr S, Taylor N, Croix BS, Ho M, Khan J. An optimized bicistronic chimeric antigen receptor against GPC2 or CD276 overcomes heterogeneous expression in neuroblastoma. J Clin Invest. 2022 Aug 15;132(16). doi: 10.1172/JCI155621. PubMed PMID: 35852863; PubMed Central PMCID: PMC9374382.
Nguyen R, Zhang X, Sun M, Abbas S, Seibert C, Kelly MC, Shern JF, Thiele CJ. Anti-GD2 Antibodies Conjugated to IL15 and IL21 Mediate Potent Antitumor Cytotoxicity against Neuroblastoma. Clin Cancer Res. 2022 Sep 1;28(17):3785-3796. doi: 10.1158/1078-0432.CCR-22-0717. PubMed PMID: 35802683; PubMed Central PMCID: PMC9444978.
Zhang X, Lou HE, Gopalan V, Liu Z, Jafarah HM, Lei H, Jones P, Sayers CM, Yohe ME, Chittiboina P, Widemann BC, Thiele CJ, Kelly MC, Hannenhalli S, Shern JF. Single-cell sequencing reveals activation of core transcription factors in PRC2-deficient malignant peripheral nerve sheath tumor. Cell Rep. 2022 Sep 20;40(12):111363. doi: 10.1016/j.celrep.2022.111363. PubMed PMID: 36130486; PubMed Central PMCID: PMC9585487.
Nanduri R, Furusawa T, Lobanov A, He B, Xie C, Dadkhah K, Kelly MC, Gavrilova O, Gonzalez FJ, Bustin M. Epigenetic regulation of white adipose tissue plasticity and energy metabolism by nucleosome binding HMGN proteins. Nat Commun. 2022 Nov 26;13(1):7303. doi: 10.1038/s41467-022-34964-5. PubMed PMID: 36435799; PubMed Central PMCID: PMC9701217.
Ma L, Heinrich S, Wang L, Keggenhoff FL, Khatib S, Forgues M, Kelly M, Hewitt SM, Saif A, Hernandez JM, Mabry D, Kloeckner R, Greten TF, Chaisaingmongkol J, Ruchirawat M, Marquardt JU, Wang XW. Multiregional single-cell dissection of tumor and immune cells reveals stable lock-and-key features in liver cancer. Nat Commun. 2022 Dec 7;13(1):7533. doi: 10.1038/s41467-022-35291-5. PubMed PMID: 36476645; PubMed Central PMCID: PMC9729309.
2021
Ohigashi I, Frantzeskakis M, Jacques A, Fujimori S, Ushio A, Yamashita F, Ishimaru N, Yin D, Cam M, Kelly MC, Awasthi P, Takada K, Takahama Y. The thymoproteasome hardwires the TCR repertoire of CD8+ T cells in the cortex independent of negative selection. J Exp Med. 2021 Apr 5;218(4). doi: 10.1084/jem.20201904. PubMed PMID: 33555295; PubMed Central PMCID: PMC7873839.
Kaczanowska S, Beury DW, Gopalan V, Tycko AK, Qin H, Clements ME, Drake J, Nwanze C, Murgai M, Rae Z, Ju W, Alexander KA, Kline J, Contreras CF, Wessel KM, Patel S, Hannenhalli S, Kelly MC, Kaplan RN. Genetically engineered myeloid cells rebalance the core immune suppression program in metastasis. Cell. 2021 Apr 15;184(8):2033-2052.e21. doi: 10.1016/j.cell.2021.02.048. Epub 2021 Mar 24. PubMed PMID: 33765443; PubMed Central PMCID: PMC8344805.
Shaffer AL 3rd, Phelan JD, Wang JQ, Huang D, Wright GW, Kasbekar M, Choi J, Young RM, Webster DE, Yang Y, Zhao H, Yu X, Xu W, Roulland S, Ceribelli M, Zhang X, Wilson KM, Chen L, McKnight C, Klumpp-Thomas C, Thomas CJ, Häupl B, Oellerich T, Rae Z, Kelly MC, Ahn IE, Sun C, Gaglione EM, Wilson WH, Wiestner A, Staudt LM. Overcoming Acquired Epigenetic Resistance to BTK Inhibitors. Blood Cancer Discov. 2021 Nov;2(6):630-647. doi: 10.1158/2643-3230.BCD-21-0063. eCollection 2021 Nov. PubMed PMID: 34778802; PubMed Central PMCID: PMC8580621.
Ma L, Wang L, Khatib SA, Chang CW, Heinrich S, Dominguez DA, Forgues M, Candia J, Hernandez MO, Kelly M, Zhao Y, Tran B, Hernandez JM, Davis JL, Kleiner DE, Wood BJ, Greten TF, Wang XW. Single-cell atlas of tumor cell evolution in response to therapy in hepatocellular carcinoma and intrahepatic cholangiocarcinoma. J Hepatol. 2021 Dec;75(6):1397-1408. doi: 10.1016/j.jhep.2021.06.028. Epub 2021 Jun 30. PubMed PMID: 34216724; PubMed Central PMCID: PMC8604764.
Ciucci T, Vacchio MS, Chen T, Nie J, Chopp LB, McGavern DB, Kelly MC, Bosselut R. Dependence on Bcl6 and Blimp1 drive distinct differentiation of murine memory and follicular helper CD4+ T cells. J Exp Med. 2022 Jan 3;219(1). doi: 10.1084/jem.20202343. Epub 2021 Nov 18. PubMed PMID: 34792530; PubMed Central PMCID: PMC8605495.
2020
Kim D, Kobayashi T, Voisin B, Jo JH, Sakamoto K, Jin SP, Kelly M, Pasieka HB, Naff JL, Meyerle JH, Ikpeama ID, Fahle GA, Davis FP, Rosenzweig SD, Alejo JC, Pittaluga S, Kong HH, Freeman AF, Nagao K. Targeted therapy guided by single-cell transcriptomic analysis in drug-induced hypersensitivity syndrome: a case report. Nat Med. 2020 Feb;26(2):236-243. doi: 10.1038/s41591-019-0733-7. Epub 2020 Jan 20. PubMed PMID: 31959990; PubMed Central PMCID: PMC7105105.
Krishna S, Lowery FJ, Copeland AR, Bahadiroglu E, Mukherjee R, Jia L, Anibal JT, Sachs A, Adebola SO, Gurusamy D, Yu Z, Hill V, Gartner JJ, Li YF, Parkhurst M, Paria B, Kvistborg P, Kelly MC, Goff SL, Altan-Bonnet G, Robbins PF, Rosenberg SA. Stem-like CD8 T cells mediate response of adoptive cell immunotherapy against human cancer. Science. 2020 Dec 11;370(6522):1328-1334. doi: 10.1126/science.abb9847. PubMed PMID: 33303615; PubMed Central PMCID: PMC8883579.
Chopp LB, Gopalan V, Ciucci T, Ruchinskas A, Rae Z, Lagarde M, Gao Y, Li C, Bosticardo M, Pala F, Livak F, Kelly MC, Hannenhalli S, Bosselut R. An Integrated Epigenomic and Transcriptomic Map of Mouse and Human αβ T Cell Development. Immunity. 2020 Dec 15;53(6):1182-1201.e8. doi: 10.1016/j.immuni.2020.10.024. Epub 2020 Nov 25. PubMed PMID: 33242395; PubMed Central PMCID: PMC8641659.
Yu G, Butler MK, Abdelmaksoud A, Pang Y, Su YT, Rae Z, Dadkhah K, Kelly MC, Song YK, Wei JS, Terabe M, Atony R, Mentges K, Theeler BJ, Penas-Prado M, Butman J, Camphausen K, Zaghloul KA, Nduom E, Quezado M, Aldape K, Armstrong TS, Gilbert MR, Gulley JL, Khan J, Wu J. Case Report: Single-Cell Transcriptomic Analysis of an Anaplastic Oligodendroglioma Post Immunotherapy. Front Oncol. 2020;10:601452. doi: 10.3389/fonc.2020.601452. eCollection 2020. PubMed PMID: 33520712; PubMed Central PMCID: PMC7841290.
2019
Ma L, Hernandez MO, Zhao Y, Mehta M, Tran B, Kelly M, Rae Z, Hernandez JM, Davis JL, Martin SP, Kleiner DE, Hewitt SM, Ylaya K, Wood BJ, Greten TF, Wang XW. Tumor Cell Biodiversity Drives Microenvironmental Reprogramming in Liver Cancer. Cancer Cell. 2019 Oct 14;36(4):418-430.e6. doi: 10.1016/j.ccell.2019.08.007. Epub 2019 Oct 3. PubMed PMID: 31588021; PubMed Central PMCID: PMC6801104.
Cowan JE, Malin J, Zhao Y, Seedhom MO, Harly C, Ohigashi I, Kelly M, Takahama Y, Yewdell JW, Cam M, Bhandoola A. Myc controls a distinct transcriptional program in fetal thymic epithelial cells that determines thymus growth. Nat Commun. 2019 Dec 2;10(1):5498. doi: 10.1038/s41467-019-13465-y. PubMed PMID: 31792212; PubMed Central PMCID: