Publications | Jacks Lab

Recent papers:

Goto N, Westcott PMK, Goto S, Imada S, Taylor MS, Eng G, Braverman J, Deshpande V, Jacks T, Agudo J, Yilmaz ÖH. SOX17 enables immune evasion of early colorectal adenomas and cancers. Nature. 2024;627(8004):636-645. doi:10.1038/s41586-024-07135-3. Epub 2024 Feb 18. PMID: 38418875.
Weng C, Yu F, Yang D, Poeschla M, Liggett LA, Jones MG, Qiu X, Wahlster L, Caulier A, Hussmann JA, Schnell A, Yost KE, Koblan L, Martin-Rufino JD, Min J, Hammond A, Ssozi D, Bueno R, Mallidi H, Kreso A, Escabi J, Rideout WM 3rd, Jacks T, Hormoz S, van Galen P, Weissman JS, Sankaran VG. Deciphering cell states and genealogies of human human hematopoesis. Nature. 2024 Mar; 627(8003):389-398. doi: 10.1038/s41586-024-07066-z. epub 2024 Jan 22. PMID:38253266.
Zhong Q, Tan EKW, Martin-Alonso C, Parisi T, Hao L, Kirkpatrick JD, Fadel T, Fleming HE, Jacks T, Bhatia SN. Inhalable point-of-care urinary diagnostic platform. Sci Adv. 2024 Jan 5;10(1):eadj9591. doi: 10.1126/sciadv.adj9591. Epub 2024 Jan 5. PMCID: PMC10776015.
Westcott PMK, Muyas F, Hauck H, Smith OC, Sacks NJ, Ely ZA, Jaeger AM, Rideout WM 3rd, Zhang D, Bhutkar A, Beytagh MC, Canner DA, Jaramillo GC, Bronson RT, Naranjo S, Jin A, Patten JJ, Cruz AM, Shanahan SL, Cortes-Ciriano I, Jacks T. Mismatch repair deficiency is not sufficient to elicit tumor immunogenicity. Nat Genet. 2023 Oct;55(10):1686-1695. doi: 10.1038/s41588-023-01499-4. Epub 2023 Sep 14. PMCID: PMC10562252.
Shiau C, Cao J, Gregory MT, Gong D, Yin X, Cho JW, Wang PL, Su J, Wang S, Reeves JW, Kim TK, Kim Y, Guo JA, Lester NA, Schurman N, Barth JL, Weissleder R, Jacks T, Qadan M, Hong TS, Wo JY, Roberts H, Beechem JM, Fernandez-Del Castillo C, Mino-Kenudson M, Ting DT, Hemberg M, Hwang WL. Therapy-associated remodeling of pancreatic cancer revealed by single-cell spatial trascriptomics and optimal transport analysis. bioRxiv. 2023 Jun 29:2023.06.28.546848. doi: 10.1101/2023.06.28.546848. Preprint. PMID: 37425692.
Ely ZA, Mathey-Andrews N, Naranjo S, Gould SI, Mercer KL, Newby GA, Cabana CM, Rideout WM 3rd, Jaramillo GC, Khirallah JM, Holland K, Randolph PB, Freed-Pastor WA, Davis JR, Kulstad Z, Westcott PMK, Lin L, Anzalone AV, Horton BL, Pattada NB, Shanahan SL, Ye Z, Spranger S, Xu Q, Sánchez-Rivera FJ, Liu DR, Jacks T. A prime editor mouse to model a broad spectrum of somatic mutations in vivo. Nat Biotechnol. 2024 March;42(3): 424-436. doi: 10.1038/s41587-023-01783-y. epub 2023 May 11. PMID: 37169967.
Gaglia G, Burger ML, Ritch CC, Rammos D, Dai Y, Crossland GE, Tavana SZ, Warchol S, Jaeger AM, Naranjo S, Coy S, Nirmal AJ, Krueger R, Lin JR, Pfister H, Sorger PK, Jacks T, Santagata S. Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma. Cancer Cell. 2023 May 8;41(5):871-886.e10. doi: 10.1016/j.ccell.2023.03.015. Epub 2023 Apr 13. PMID: 37059105.
Hill W, Lim EL, Weeden CE, Lee C, Augustine M, Chen K, Kuan FC, Marongiu F, Evans EJ Jr, Moore DA, Rodrigues FS, Pich O, Bakker B, Cha H, Myers R, van Maldegem F, Boumelha J, Veeriah S, Rowan A, Naceur-Lombardelli C, Karasaki T, Sivakumar M, De S, Caswell DR, Nagano A, Black JRM, Martínez-Ruiz C, Ryu MH, Huff RD, Li S, Favé MJ, Magness A, Suárez-Bonnet A, Priestnall SL, Lüchtenborg M, Lavelle K, Pethick J, Hardy S, McRonald FE, Lin MH, Troccoli CI, Ghosh M, Miller YE, Merrick DT, Keith RL, Al Bakir M, Bailey C, Hill MS, Saal LH, Chen Y, George AM, Abbosh C, Kanu N, Lee SH, McGranahan N, Berg CD, Sasieni P, Houlston R, Turnbull C, Lam S, Awadalla P, Grönroos E, Downward J, Jacks T, Carlsten C, Malanchi I, Hackshaw A, Litchfield K; TRACERx Consortium; DeGregori J, Jamal-Hanjani M, Swanton C. Lung Adenocarcinoma promotion by air pollutants. Nature. 2023 Apr;616(7955):159-167. doi: 10.1038/s41586-023-05874-3. Epub 2023 Apr 5. PMID: PMC7614604.
Warchol S, Krueger R, Nirmal AJ, Gaglia G, Jessup J, Ritch CC, Hoffer J, Muhlich J, Burger ML, Jacks T, Santagata S, Sorger PK, Pfister H.Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data. EEE Trans Vis Comput Graph. 2023 Jan;29(1):106-116. doi: 10.1109/TVCG.2022.3209378. Epub 2022 Dec 16. PMID: 36170403.
Amini AP, Kirkpatrick JD, Wang CS, Jaeger AM, Su S, Naranjo S, Zhong Q, Cabana CM, Jacks T, Bhatia SN. Multscale profiling of protease activity in cancer. Nat Commun. 2022 Oct 3;13(1):5745. doi: 10.1038/s41467-022-32988-5. PMID: 36192379.
Hwang WL, Jagadeesh KA, Guo JA, Hoffman HI, Yadollahpour P, Reeves JW, Mohan R, Drokhlyansky E, Van Wittenberghe N, Ashenberg O, Farhi SL, Schapiro D, Divakar P, Miller E, Zollinger DR, Eng G, Schenkel JM, Su J, Shiau C, Yu P, Freed-Pastor WA, Abbondanza D, Mehta A, Gould J, Lambden C, Porter CBM, Tsankov A, Dionne D, Waldman J, Cuoco MS, Nguyen L, Delorey T, Phillips D, Barth JL, Kem M, Rodrigues C, Ciprani D, Roldan J, Zelga P, Jorgji V, Chen JH, Ely Z, Zhao D, Fuhrman K, Fropf R, Beechem JM, Loeffler JS, Ryan DP, Weekes CD, Ferrone CR, Qadan M, Aryee MJ, Jain RK, Neuberg DS, Wo JY, Hong TS, Xavier R, Aguirre AJ, Rozenblatt-Rosen O, Mino-Kenudson M, Castillo CF, Liss AS, Ting DT, Jacks T, Regev A. Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment. Nature Genet. 2022 Aug 54(8):1178-1191.doi: 10.1038/s41588-022-01134-8. Epub 2022 Jul 28. PMID: PMC10290535.
Naranjo S, Cabana CM, LaFave LM, Romero R, Shanahan SL, Bhutkar A, Westcott PMK, Schenkel JM, Ghosh A, Liao LZ, Del Priore I, Yang D, Jacks T. Modeling diverse genetic subtypes of lung adenocarcinoma with a next-generation alveolar type 2 organoid platform. Genes Dev. 2022 Aug 1;36(15-16):936-949. doi: 10.1101/gad.349659.122. Epub 2022 Sep 29. PMID: 36175034,
Jaeger AM, Stopfer LE, Ahn R, Sanders EA, Sandel DA, Freed-Pastor WA, Rideout WM 3rd, Naranjo S, Fessenden T, Nguyen KB, Winter PS, Kohn RE, Westcott PMK, Schenkel JM, Shanahan SL, Shalek AK, Spranger S, White FM, Jacks T. Deciphering the immunopeptidome in vivo reveals new tumour antigens. Nature. 2022 Jul;607(7917):149-155. doi: 10.1038/s41586-022-04839-2. Epub 2022 Jun 15. PMID: PMC9945857.
Yang D, Jones MG, Naranjo S, Rideout WM 3rd, Min KHJ, Ho R, Wu W, Replogle JM, Page JL, Quinn JJ, Horns F, Qiu X, Chen MZ, Freed-Pastor WA, McGinnis CS, Patterson DM, Gartner ZJ, Chow ED, Bivona TG, Chan MM, Yosef N, Jacks T, Weissman JS. Lineage tracing reveals the phylodynamics, plasticity, and paths of tumor evolution. Cell. 2022 May 26;185(11):1905-1923.e25. doi: 10/1016/j.cell.2022.04.015. Epub 2022 May 5. PMID: PMC9452598 .
Shi DD, Guo JA, Hoffman HI, Su J, Mino-Kenudson M, Barth JL, Schenkel JM, Loeffler JS, Shih HA, Hong TS, Wo JY, Aguirre AJ, Jacks T, Zheng L, Wen PY, Wang TC, Hwang WL. Therapeutic avenues for cancer neuroscience: translational frontiers and clinical opportunities. Lancet Oncol. 2022 Feb;23(2):e62-e74. doi: 10.1016/s1470-2045(21)00596-9. PMID: PMC9516432. Review.
Patel RS, Romero R, Watson EV, Liang AC, Burger M, Westcott PMK, Mercer KL, Bronson RT, Wooten EC, Bhutkar A, Jacks T, Elledge SJ. A GATA4-regulated secretory program suppresses tumors through recruitment of cytotoxic CD8 T cells. Nature Comm. 2022 Jan 11;13(1):256. doi: 10.1038/s41467-021-27731-5. PMID: 35017504.
Zhao T, Chiang ZD, Morriss JW, LaFave LM, Murray EM, Del Priore I, Meli K, Lareau CA, Nadaf NM, Li J, Earl AS, Macosko EZ, Jacks T, Buenrostro JD, Chen F. Spatial genomics enables multi-modal study of clonal heterogeneity in tissues. Nature. 2022 Jan;601(7891):85-91. doi: 10.1038/s41586-021-04217-4. Epub 2021 Dec 15. PMID: 34912115.
Raghavan S, Winter PS, Navia AW, Williams HL, DenAdel A, Lowder KE, Galvez-Reyes J, Kalekar RL, Mulugeta N, Kapner KS, Raghavan MS, Borah AA, Liu N, Väyrynen SA, Costa AD, Ng RWS, Wang J, Hill EK, Ragon DY, Brais LK, Jaeger AM, Spurr LF, Li YY, Cherniack AD, Booker MA, Cohen EF, Tolstorukov MY, Wakiro I, Rotem A, Johnson BE, McFarland JM, Sicinska ET, Jacks TE, Sullivan RJ, Shapiro GI, Clancy TE, Perez K, Rubinson DA, Ng K, Cleary JM, Crawford L, Manalis SR, Nowak JA, Wolpin BM, Hahn WC, Aguirre AJ, Shalek AK. Microenvironment drives cell state, plasticity, and drug response in pancreatic cancer. Cell. 2021 Dec 9;184(25):6119-6137.e26. doi: 10.1016/j.cell.2021.11.017. PMID: 34890551.
Westcott PMK, Sacks NJ, Schenkel JM, Ely ZA, Smith O, Hauck H, Jaeger AM, Zhang D, Backlund CM, Beytagh MC, Patten JJ, Elbashir R, Eng G, Irvine DJ, Yilmaz OH, Jacks T. Low neoantigen expression and poor T-cell priming underlie early immune escape in colorectal cancer. Nat Cancer. 2021 Oct;2(10):1071-1085. doi: 10.1038/s43018-021-00247-z. PMID:34738089.
Hamza B, Miller AB, Meier L, Stockslager M, Ng SR, King EM, Lin L, DeGouveia KL, Mulugeta N, Calistri NL, Strouf H, Bray C, Rodriguez F, Freed-Pastor WA, Chin CR, Jaramillo GC, Burger ML, Weinberg RA, Shalek AK, Jacks T, Manalis SR. Measuring kinietcs and metastatic propensity of CTCs by blood exchange between mice. Nat Commun. 2021 Sep 28;12(1):5680. doi: 10.1038/s41467-021-25917-5. PMID: 34584084.
Concepcion CP, Ma S, LaFave LM, Bhutkar A, Liu M, DeAngelo LP, Kim JY, Del Priore I, Schoenfeld AJ, Miller M, Kartha VK, Westcott PMK, Sanchez-Rivera FJ, Meli K, Gupta M, Bronson RT, Riely GJ, Rekhtman N, Rudin CM, Kim CF, Regev A, Buenrostro JD, Jacks T. SMARCA4 inactivation promotes lineage-specific transformation and early metatatic features in the lung. Cancer Discov. 2021 Sep 24:candisc.0248.2021. doi: 10.1158/2159-8290.CD-21-0248. Online ahead of print. PMID: 34561242.
Burger ML, Cruz AM, Crossland GE, Gaglia G, Ritch CC, Blatt SE, Bhutkar A, Canner D, Kienka T, Tavana SZ, Barandiaran AL, Garmilla A, Schenkel JM, Hillman M, de Los Rios Kobara I, Li A, Jaeger AM, Hwang WL, Westcott PMK, Manos MP, Holovatska MM, Hodi FS, Regev A, Santagata S, Jacks T. Antigen dominance hierarchies shape TCR1⁺ progenitor CD8 T cell phenotypes in tumors. Cell. 2021 Sep 16;184(19):4996-5014.e26. doi: 10.1016/j.cell.2021.08.020. PMID: 34534464.
Schenkel JM, Herbst RH, Canner D, Li A, Hillman M, Shanahan SL, Gibbons G, Smith OC, Kim JY, Westcott P, Hwang WL, Freed-Pastor WA, Eng G, Cuoco MS, Rogers P, Park JK, Burger ML, Rozenblatt-Rosen O, Cong L, Pauken KE, Regev A, Jacks T. Conventional type 1 dendric cells maintain a reservoir of proliferative tumor-antigen specific TCF-1⁺ CD8⁺ T cells in tumor-draining lumph nodes. Immunity. 2021 Sept 8:54(10):2338-2353.e6. doi: 10.1016/j.immuni.2021.08.026. PMID:34534439.
Genshaft AS, Ziegler CGK, Tzouanas CN, Mead BE, Jaeger AM, Navia AW, King RP, Mana MD, Huang S, Mitsialis V, Snapper SB, Yilmaz OH, Jacks T, Van Humbeck JF, Shalek AK. Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes. Nat Commun. 2021 Aug 17;12(1):5361. doi: 10.1038/s41467-021-25279-y. PMID: 34404785.
Ciampricotti M, Karakousi T, Richards AL Quintanal-Villalonga A, Karatza A, Caeser R, Costa EA, Allaj V, Manoj P, Spainhower KB, Kombak FE, Sanchez-Rivera FJ, Jaspers JE, Zavitsanou AM, Maddalo D, Ventura A, Rideout WM, Akama-Garren EH, Jacks T, Donoghue MTA, Sen T, Oliver TG, Poirier JT, Papagiannakopoulos T, Rudin CM. Rif-Mycl gene fusion drives tumorigenesis and metastasis in a mouse model of small cell lung cancer. Cancer Discov. 2021 Aug 3:candisc.0441.2021. doi: 10.1158/2159-8290.CD-21-0441. Online ahead of print. PMID: 34344693.
Freed-Pastor WA, Lambert LJ, Ely ZA, Pattada NB, Bhutkar A, Eng G, Mercer KL, Garcia AP, Lin L, Rideout WM 3rd, Hwang WL, Schenkel JM, Jaeger AM, Bronson RT, Westcott PMK, Hether TD, Divakar P, Reeves JW, Deshpande V, Delorey T, Phillips D, Yilmaz OH, Regev A, Jacks T. The CD155/TIGIT axis promotes and maintains immune evasion in neoantigen-expressing pancreatic cancer. Cancer Cell. 2021 Oct 11;39(10):1342-1360.e14. doi: 10.1016/j.ccell.2021.07.007. Epub 2021 Aug 5. PMID: 34358448.
Hajal C, Shin Y, Li L, Serrano JC, Jacks T, Kamm RD. The CCL2-CCR2 astrocyte-cancer cell axis in tumor extravasation at the brain. Sci Adv. 2021. June 23;7(26):eabg8139. doi: 10.1126/sciadv.abg8139. PMCID:34162553.
Del Priore I, Ma S, Strecker J, Jacks T, LaFave LM*, Buenrostro JD*. Protocol for single-cell ATAC-sequencing using combinatorial indexing. STAR Protocols. 2021. Jun 3;2(2):100583. doi: 10.1016/j.xpro.2021.100583. eCollection 2021 Jun 18. PMID: 34142101.
Lussier DM, Alspach E, Ward JP, Miceli AP, Runci D, White JM, Mpoy C, Arthur CD, Kohlmiller HN, Jacks T, Artyomov MN, Rogers BE, Schreiber RD. Radiation-induced neoantigens broaden the immunotherapeutic window of cancers with low mutational loads. Proc Natl Acad Sci U S A. 2021 Jun 15;118(24):e2102611118. doi: 10.1073/pnas.2102611118. PMID: 34099555.
Sánchez-Rivera FJ, Ryan J, Soto-Feliciano YM, Clare Beytagh M, Xuan L, Feldser DM, Hemann MT, Zamudio J, Dimitrova N, Letai A, Jacks T. Mitochondrial apoptotic priming is a key determinant of cell fate upon p53 restoration. Proc Natl Acad Sci U S A. 2021 Jun 8;118(23):e2019740118. doi: 10.1073/pnas.2019740118. PMID: 34074758.
Guo JA, Hoffman HI, Shroff SG, Chen P, Hwang PG, Kim DY, Kim DW, Cheng SW, Zhao D, Mahal BA, Alshalalfa M, Niemierko A, Wo JY, Loeffler JS, Fernandez-Del Castillo C, Jacks T, Aguirre AJ, Hong TS, Mino-Kenudson M, Hwang WL. Pan-Cancer Transcriptomic Predictors of Perineural Invasion Improve Occult Histopathologic Detection. Clin Cancer Res. 2021 May 15;27(10):2807-2815. doi: 10.1158/1078-0432.CCR-20-4382. Epub 2021 Feb 25. PMID: 33632928

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