JAX Cancer Center Publications

2022 Significant Publications

 

1: Veiga DFT, Nesta A, Zhao Y, Deslattes Mays A, Huynh R, Rossi R, Wu TC, Palucka K, Anczukow O, Beck CR, Banchereau J. A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer. Sci Adv. 2022 Jan 21;8(3):eabg6711. doi: 10.1126/sciadv.abg6711. Epub 2022 Jan 19. PMID: 35044822; PMCID: PMC8769553.

 

2: Sargent JK, Warner MA, Low BE, Schott WH, Hoffert T, Coleman D, Woo XY, Sheridan T, Erattupuzha S, Henrich PP, Philip VM, Chuang JH, Wiles MV, Hasham MG. Genetically diverse mouse platform to xenograft cancer cells. Dis Model Mech. 2022 Sep 1;15(9):dmm049457. doi: 10.1242/dmm.049457. Epub 2022 Aug 29. PMID: 36037073; PMCID: PMC9459392.

 

3: Koc S, Lloyd MW, Grover JW, Xiao N, Seepo S, Subramanian SL, Ray M, Frech C, DiGiovanna J, Webster P, Neuhauser S, Srivastava A, Woo XY, Sanderson BJ, White B, Lott P, Dobrolecki LE, Dowst H; PDXNet Consortium; Evrard YA, Wallace TA, Moscow JA, Doroshow JH, Mitsiades N, Kaochar S, Pan CX, Chen MS, Carvajal- Carmona L, Welm AL, Welm BE, Lewis MT, Govindan R, Ding L, Li S, Herlyn M, Davies MA, Roth J, Meric-Bernstam F, Robinson PN, Bult CJ, Davis-Dusenbery B, Dean DA 2nd, Chuang JH. PDXNet portal: patient-derived Xenograft model, data, workflow and tool discovery. NAR Cancer. 2022 Apr 22;4(2):zcac014. doi:10.1093/narcan/zcac014. PMID: 35475145; PMCID: PMC9026194.

 

4: Rubinstein JC, Foroughi Pour A, Zhou J, Sheridan TB, White BS, Chuang JH. Deep learning image analysis quantifies tumor heterogeneity and identifies microsatellite instability in colon cancer. J Surg Oncol. 2022 Oct 17. doi:10.1002/jso.27118. Epub ahead of print. PMID: 36251352.

 

5: Zhang ZY, Ding Y, Ezhilarasan R, Lhakhang T, Wang Q, Yang J, Modrek AS, Zhang H, Tsirigos A, Futreal A, Draetta GF, Verhaak RGW, Sulman EP. Lineage-coupledclonal capture identifies clonal evolution mechanisms and vulnerabilities of BRAFV600E inhibition resistance in melanoma. Cell Discov. 2022 Oct 6;8(1):102. doi: 10.1038/s41421-022-00462-7. PMID: 36202798; PMCID: PMC9537441.

 

6: Dey M, Kim MH, Nagamine M, Karhan E, Kozhaya L, Dogan M, Unutmaz D, Ozbolat IT. Biofabrication of 3D breast cancer models for dissecting the cytotoxic response of human T cells expressing engineered MAIT cell receptors. Biofabrication. 2022 Sep 29;14(4):10.1088/1758-5090/ac925a. doi:10.1088/1758-5090/ac925a. PMID: 36108605; PMCID: PMC9556424.

 

7: Woo XY, Srivastava A, Mack PC, Graber JH, Sanderson BJ, Lloyd MW, Chen M, Domanskyi S, Gandour-Edwards R, Tsai RA, Keck J, Cheng M, Bundy M, Jocoy EL, Riess JW, Holland W, Grubb SC, Peterson JG, Stafford GA, Paisie C, Neuhauser SB, Karuturi RKM, George J, Simons AK, Chavaree M, Tepper CG, Goodwin N, Airhart SD, Lara PN, Openshaw TH, Liu ET, Gandara DR, Bult CJ. A Genomically and Clinically Annotated Patient-Derived Xenograft Resource for Preclinical Research in Non- Small Cell Lung Cancer. Cancer Res. 2022 Nov 15;82(22):4126-4138. doi:10.1158/0008-5472.CAN-22-0948. PMID: 36069866; PMCID: PMC9664138.

 

8: Foroughi Pour A, White BS, Park J, Sheridan TB, Chuang JH. Deep learning features encode interpretable morphologies within histological images. Sci Rep.2022 Jun 8;12(1):9428. doi: 10.1038/s41598-022-13541-2. PMID: 35676395; PMCID: PMC9177767.

 

9: Tang-Schomer MD, Chandok H, Wu WB, Lau CC, Bookland MJ, George J. 3D patient- derived tumor models to recapitulate pediatric brain tumors In Vitro. Transl Oncol. 2022 Jun;20:101407. doi: 10.1016/j.tranon.2022.101407. Epub 2022 Apr 2. PMID: 35381525; PMCID: PMC8980497.

 

10: Guillen KP, Fujita M, Butterfield AJ, Scherer SD, Bailey MH, Chu Z, DeRose YS, Zhao L, Cortes-Sanchez E, Yang CH, Toner J, Wang G, Qiao Y, Huang X, Greenland JA, Vahrenkamp JM, Lum DH, Factor RE, Nelson EW, Matsen CB, Poretta JM, Rosenthal R, Beck AC, Buys SS, Vaklavas C, Ward JH, Jensen RL, Jones KB, Li Z, Oesterreich S, Dobrolecki LE, Pathi SS, Woo XY, Berrett KC, Wadsworth ME, Chuang JH, Lewis MT, Marth GT, Gertz J, Varley KE, Welm BE, Welm AL. A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology. Nat Cancer. 2022 Feb;3(2):232-250. doi: 10.1038/s43018-022-00337-6. Epub 2022 Feb 24. PMID: 35221336; PMCID: PMC8882468.

 

11: Menghi F, Banda K, Kumar P, Straub R, Dobrolecki L, Rodriguez IV, Yost SE, Chandok H, Radke MR, Somlo G, Yuan Y, Lewis MT, Swisher EM, Liu ET. Genomic and epigenomic BRCA alterations predict adaptive resistance and response to platinum-based therapy in patients with triple-negative breast and ovarian carcinomas. Sci Transl Med. 2022 Jul 6;14(652):eabn1926. doi: 0.1126/scitranslmed.abn1926. Epub 2022 Jul 6. PMID: 35857626; PMCID: PMC9585706.

 

12: Zhao X, Wang P, Diedrich JD, Smart B, Reyes N, Yoshimura S, Zhang J, Yang W, Barnett K, Xu B, Li Z, Huang X, Yu J, Crews K, Yeoh AEJ, Konopleva M, Wei CL,Pui CH, Savic D, Yang JJ. Epigenetic activation of the FLT3 gene by ZNF384 fusion confers a therapeutic susceptibility in acute lymphoblastic leukemia. Nat Commun. 2022 Sep 14;13(1):5401. doi: 10.1038/s41467-022-33143-w. PMID: 36104354; PMCID:PMC9474531.

 

13: Varn FS, Johnson KC, Martinek J, Huse JT, Nasrallah MP, Wesseling P, Cooper LAD, Malta TM, Wade TE, Sabedot TS, Brat D, Gould PV, Wöehrer A, Aldape K, Ismail A, Sivajothi SK, Barthel FP, Kim H, Kocakavuk E, Ahmed N, White K, Datta I, Moon HE, Pollock S, Goldfarb C, Lee GH, Garofano L, Anderson KJ, Nehar-Belaid D, Barnholtz-Sloan JS, Bakas S, Byrne AT, D'Angelo F, Gan HK, Khasraw M, Migliozzi S, Ormond DR, Paek SH, Van Meir EG, Walenkamp AME, Watts C, Weiss T, Weller M, Palucka K, Stead LF, Poisson LM, Noushmehr H, Iavarone A, Verhaak RGW; GLASS Consortium. Glioma progression is shaped by genetic evolution and microenvironment interactions. Cell. 2022 Jun 9;185(12):2184-2199.e16. doi:10.1016/j.cell.2022.04.038. Epub 2022 May 31. PMID: 35649412; PMCID: PMC9189056.

 

14: SanMiguel JM, Eudy E, Loberg MA, Miles LA, Stearns T, Mistry JJ, Rauh MJ, Levine RL, Trowbridge JJ. Cell origin-dependent cooperativity of mutant Dnmt3a and Npm1 in clonal hematopoiesis and myeloid malignancy. Blood Adv. 2022 Jun 28;6(12):3666-3677. doi: 10.1182/bloodadvances.2022006968. PMID: 35413095; PMCID: PMC9631557.

 

15: Jun Y, Suh YS, Park S, Lee J, Kim JI, Lee S, Lee WP, Anczuków O, Yang HK, Lee C. Comprehensive Analysis of Alternative Splicing in Gastric Cancer Identifies Epithelial-Mesenchymal Transition Subtypes Associated with Survival. Cancer Res. 2022 Feb 15;82(4):543-555. doi: 10.1158/0008-5472.CAN-21-2117. PMID: 34903603; PMCID: PMC9359730.

 

16: Yi E, Gujar AD, Guthrie M, Kim H, Zhao D, Johnson KC, Amin SB, Costa ML, Yu Q, Das S, Jillette N, Clow PA, Cheng AW, Verhaak RGW. Live-Cell Imaging Shows Uneven Segregation of Extrachromosomal DNA Elements and Transcriptionally Active Extrachromosomal DNA Hubs in Cancer. Cancer Discov. 2022 Feb;12(2):468-483. doi:10.1158/2159-8290.CD-21-1376. Epub 2021 Nov 24. PMID: 34819316; PMCID: PMC8831456.

 

17: Martinek J, Lin J, Kim KI, Wang VG, Wu TC, Chiorazzi M, Boruchov H, GulatiA, Seeniraj S, Sun L, Marches F, Robson P, Rongvaux A, Flavell RA, George J, Chuang JH, Banchereau J, Palucka K. Transcriptional profiling of macrophages in situ in metastatic melanoma reveals localization-dependent phenotypes and function. Cell Rep Med. 2022 May 17;3(5):100621. doi: 10.1016/j.xcrm.2022.100621. Epub 2022 Apr 27. PMID: 35584631; PMCID: PMC9133468.

 

18: Gong Z, Li Q, Shi J, Wei J, Li P, Chang CH, Shultz LD, Ren G. Lung fibroblasts facilitate pre-metastatic niche formation by remodeling the local immune microenvironment. Immunity. 2022 Aug 9;55(8):1483-1500.e9. doi: 10.1016/j.immuni.2022.07.001. Epub 2022 Jul 30. PMID: 35908547; PMCID: PMC9830653.

 

19: Taylor AM, Sun JM, Yu A, Voicu H, Shen J, Barkauskas DA, Triche TJ, Gastier-Foster JM, Man TK, Lau CC. Integrated DNA Copy Number and Expression Profiling Identifies IGF1R as a Prognostic Biomarker in Pediatric Osteosarcoma. Int J Mol Sci. 2022 Jul 21;23(14):8036. doi: 10.3390/ijms23148036. PMID: 35887382; PMCID:PMC9319262.

 

20: Jang G, Oh J, Jun E, Lee J, Kwon JY, Kim J, Lee SH, Kim SC, Cho SY, Lee C. Direct cell-to-cell transfer in stressed tumor microenvironment aggravates tumorigenic or metastatic potential in pancreatic cancer. NPJ Genom Med. 2022 Oct 27;7(1):63. doi: 10.1038/s41525-022-00333-w. PMID: 36302783; PMCID: PMC9613679.

 

21: Dogan M, Karhan E, Kozhaya L, Placek L, Chen X, Yigit M, Unutmaz D. Engineering Human MAIT Cells with Chimeric Antigen Receptors for Cancer Immunotherapy.J Immunol. 2022 Oct 15;209(8):1523-1531. doi:10.4049/jimmunol.2100856. Epub 2022 Sep 7. PMID: 36165183.

 

22: SanMiguel JM, Eudy E, Loberg MA, Young KA, Mistry JJ, Mujica KD, Schwartz LS, Stearns TM, Challen GA, Trowbridge JJ. Distinct Tumor Necrosis Factor Alpha Receptors Dictate Stem Cell Fitness versus Lineage Output in Dnmt3a-Mutant Clonal Hematopoiesis. Cancer Discov. 2022 Dec 2;12(12):2763-2773. doi: 10.1158/2159-8290.CD-22-0086. PMID: 36169447; PMCID: PMC9716249.

 

23: Voigt AY, Emiola A, Johnson JS, Fleming ES, Nguyen H, Zhou W, Tsai KY, Fink C, Oh J. Skin Microbiome Variation with Cancer Progression in Human Cutaneous Squamous Cell Carcinoma. J Invest Dermatol. 2022 Oct;142(10):2773-2782.e16. doi: 10.1016/j.jid.2022.03.017. Epub 2022 Apr 4. PMID: 35390349; PMCID: PMC9509417.