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JAXCC Significant Publications (from 2021-2023 RPPRs)
2023 RPPR
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
2022 RPPR
Farahmand S, Fernandez AI, Ahmed FS, Rimm DL, Chuang JH, Reisenbichler E, Zarringhalam K. Deep learning trained on hematoxylin and eosin tumor region of Interest predicts HER2 status and trastuzumab treatment response in HER2+ breast cancer. Mod Pathol. 2022 Jan;35(1):44-51. doi: 10.1038/s41379-021-00911-w. Epub 2021 Sep 7. PMID: 34493825.
Brohl AS, Sindiri S, Wei JS, Milewski D, Chou HC, Song YK, Wen X, Kumar J, Reardon HV, Mudunuri US, Collins JR, Nagaraj S, Gangalapudi V, Tyagi M, Zhu YJ, Masih KE, Yohe ME, Shern JF, Qi Y, Guha U, Catchpoole D, Orentas RJ, Kuznetsov IB, Llosa NJ, Ligon JA, Turpin BK, Leino DG, Iwata S, Andrulis IL, Wunder JS, Toledo SRC, Meltzer PS, Lau C, Teicher BA, Magnan H, Ladanyi M, Khan J. Immuno-transcriptomic profiling of extracranial pediatric solid malignancies. Cell Rep. 2021 Nov 23;37(8):110047. doi: 10.1016/j.celrep.2021.110047. PMID: 34818552; PMCID: PMC8642810.
Liu Y, Rosikiewicz W, Pan Z, Jillette N, Wang P, Taghbalout A, Foox J, Mason C, Carroll M, Cheng A, Li S. DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation. Genome Biol. 2021 Oct 18;22(1):295. doi: 10.1186/s13059-021-02510-z. PMID: 34663425; PMCID: PMC8524990.
Johnson KC, Anderson KJ, Courtois ET, Gujar AD, Barthel FP, Varn FS, Luo D, Seignon M, Yi E, Kim H, Estecio MRH, Zhao D, Tang M, Navin NE, Maurya R, Ngan CY, Verburg N, de Witt Hamer PC, Bulsara K, Samuels ML, Das S, Robson P, Verhaak RGW. Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response. Nat Genet. 2021 Oct;53(10):1456-1468. doi: 10.1038/s41588-021-00926-8. Epub 2021 Sep 30. PMID: 34594038; PMCID: PMC8570135.
Sun H, Cao S, Mashl RJ, Mo CK, Zaccaria S, Wendl MC, Davies SR, Bailey MH, Primeau TM, Hoog J, Mudd JL, Dean DA 2nd, Patidar R, Chen L, Wyczalkowski MA, Jayasinghe RG, Rodrigues FM, Terekhanova NV, Li Y, Lim KH, Wang-Gillam A, Van Tine BA, Ma CX, Aft R, Fuh KC, Schwarz JK, Zevallos JP, Puram SV, Dipersio JF; NCI PDXNet Consortium, Davis-Dusenbery B, Ellis MJ, Lewis MT, Davies MA, Herlyn M, Fang B, Roth JA, Welm AL, Welm BE, Meric-Bernstam F, Chen F, Fields RC, Li S, Govindan R, Doroshow JH, Moscow JA, Evrard YA, Chuang JH, Raphael BJ, Ding L. Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment. Nat Commun. 2021 Aug 24;12(1):5086. doi: 10.1038/s41467-021-25177-3. PMID: 34429404; PMCID: PMC8384880.
Na D, Chae J, Cho SY, Kang W, Lee A, Min S, Kang J, Kim MJ, Choi J, Lee W, Shin D, Min A, Kim YJ, Lee KH, Kim TY, Suh YS, Kong SH, Lee HJ, Kim WH, Park H, Im SA, Yang HK, Lee C, Kim JI. Predictive biomarkers for 5-fluorouracil and oxaliplatin-based chemotherapy in gastric cancers via profiling of patient-derived xenografts. Nat Commun. 2021 Aug 10;12(1):4840. doi: 10.1038/s41467-021-25122-4. PMID: 34376661; PMCID: PMC8355375.
Young K, Eudy E, Bell R, Loberg MA, Stearns T, Sharma D, Velten L, Haas S, Filippi MD, Trowbridge JJ. Decline in IGF1 in the bone marrow microenvironment initiates hematopoietic stem cell aging. Cell Stem Cell. 2021 Aug 5;28(8):1473-1482.e7. doi: 10.1016/j.stem.2021.03.017. Epub 2021 Apr 12. PMID: 33848471; PMCID: PMC8349778.
Trowbridge JJ, Starczynowski DT. Innate immune pathways and inflammation in hematopoietic aging, clonal hematopoiesis, and MDS. J Exp Med. 2021 Jul 5;218(7):e20201544. doi: 10.1084/jem.20201544. Epub 2021 Jun 15. PMID: 34129017; PMCID: PMC8210621.
Kocakavuk E, Anderson KJ, Varn FS, Johnson KC, Amin SB, Sulman EP, Lolkema MP, Barthel FP, Verhaak RGW. Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer. Nat Genet. 2021 Jul;53(7):1088-1096. doi: 10.1038/s41588-021-00874-3. Epub 2021 May 27. PMID: 34045764; PMCID: PMC8483261.
Dey M, Ayan B, Yurieva M, Unutmaz D, Ozbolat IT. Studying Tumor Angiogenesis and Cancer Invasion in a Three-Dimensional Vascularized Breast Cancer Micro-Environment. Adv Biol (Weinh). 2021 Jul;5(7):e2100090. doi: 10.1002/adbi.202100090. Epub 2021 Apr 15. PMID: 33857356; PMCID: PMC8574137.
Yu CI, Martinek J, Wu TC, Kim KI, George J, Ahmadzadeh E, Maser R, Marches F, Metang P, Authie P, Oliveira VKP, Wang VG, Chuang JH, Robson P, Banchereau J, Palucka K. Human KIT+ myeloid cells facilitate visceral metastasis by melanoma. J Exp Med. 2021 Jun 7;218(6):e20182163. doi: 10.1084/jem.20182163. PMID: 33857287; PMCID: PMC8056753.
Panday A, Willis NA, Elango R, Menghi F, Duffey EE, Liu ET, Scully R. FANCM regulates repair pathway choice at stalled replication forks. Mol Cell. 2021 Jun 3;81(11):2428-2444.e6. doi: 10.1016/j.molcel.2021.03.044. Epub 2021 Apr 20. PMID: 33882298; PMCID: PMC8180084.
Zhu Y, Gujar AD, Wong CH, Tjong H, Ngan CY, Gong L, Chen YA, Kim H, Liu J, Li M, Mil-Homens A, Maurya R, Kuhlberg C, Sun F, Yi E, deCarvalho AC, Ruan Y, Verhaak RGW, Wei CL. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Cancer Cell. 2021 May 10;39(5):694-707.e7. doi: 10.1016/j.ccell.2021.03.006. Epub 2021 Apr 8. PMID: 33836152; PMCID: PMC8119378.
Harrison DE, Strong R, Reifsnyder P, Kumar N, Fernandez E, Flurkey K, Javors MA, Lopez-Cruzan M, Macchiarini F, Nelson JF, Bitto A, Sindler AL, Cortopassi G, Kavanagh K, Leng L, Bucala R, Rosenthal N, Salmon A, Stearns TM, Bogue M, Miller RA. 17-a-estradiol late in life extends lifespan in aging UM-HET3 male mice; nicotinamide riboside and three other drugs do not affect lifespan in either sex. Aging Cell. 2021 May;20(5):e13328. doi: 10.1111/acel.13328. Epub 2021 Mar 31. PMID: 33788371; PMCID: PMC8135004.
Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science. 2021 Apr 2;372(6537):eabf7117. doi: 10.1126/science.abf7117. Epub 2021 Feb 25. PMID: 33632895; PMCID: PMC8026704.
Lee J, Choi A, Cho SY, Jun Y, Na D, Lee A, Jang G, Kwon JY, Kim J, Lee S, Lee C. Genome-scale CRISPR screening identifies cell cycle and protein ubiquitination processes as druggable targets for erlotinib-resistant lung cancer. Mol Oncol. 2021 Feb;15(2):487-502. doi: 10.1002/1878-0261.12853. Epub 2020 Nov 28. PMID: 33188726; PMCID: PMC7858278.
Chen X, Ashoor H, Musich R, Wang J, Zhang M, Zhang C, Lu M, Li S. epihet for intra-tumoral epigenetic heterogeneity analysis and visualization. Sci Rep. 2021 Jan 11;11(1):376. doi: 10.1038/s41598-020-79627-x. PMID: 33432081; PMCID: PMC7801679.
Woo XY, Giordano J, Srivastava A, Zhao ZM, Lloyd MW, de Bruijn R, Suh YS, Patidar R, Chen L, Scherer S, Bailey MH, Yang CH, Cortes-Sanchez E, Xi Y, Wang J, Wickramasinghe J, Kossenkov AV, Rebecca VW, Sun H, Mashl RJ, Davies SR, Jeon R, Frech C, Randjelovic J, Rosains J, Galimi F, Bertotti A, Lafferty A, O'Farrell AC, Modave E, Lambrechts D, Ter Brugge P, Serra V, Marangoni E, El Botty R, Kim H, Kim JI, Yang HK, Lee C, Dean DA 2nd, Davis-Dusenbery B, Evrard YA, Doroshow JH, Welm AL, Welm BE, Lewis MT, Fang B, Roth JA, Meric-Bernstam F, Herlyn M, Davies MA, Ding L, Li S, Govindan R, Isella C, Moscow JA, Trusolino L, Byrne AT, Jonkers J, Bult CJ, Medico E, Chuang JH; PDXNET Consortium; EurOPDX Consortium. Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts. Nat Genet. 2021 Jan;53(1):86-99. doi: 10.1038/s41588-020-00750-6. Epub 2021 Jan 7. Erratum in: Nat Genet. 2021 May;53(5):761. PMID: 33414553; PMCID: PMC7808565.
Verma V, Jafarzadeh N, Boi S, Kundu S, Jiang Z, Fan Y, Lopez J, Nandre R, Zeng P, Alolaqi F, Ahmad S, Gaur P, Barry ST, Valge-Archer VE, Smith PD, Banchereau J, Mkrtichyan M, Youngblood B, Rodriguez PC, Gupta S, Khleif SN. MEK inhibition reprograms CD8+ T lymphocytes into memory stem cells with potent antitumor effects. Nat Immunol. 2021 Jan;22(1):53-66. doi: 10.1038/s41590-020-00818-9. Epub 2020 Nov 23. PMID: 33230330.
Robledo RF, Ciciotte SL, Graber JH, Zhao Y, Lambert AJ, Gwynn B, Maki NJ, Brindley EC, Hartman E, Blanc L, Peters LL. Differential effects of RASA3 mutations on hematopoiesis are profoundly influenced by genetic background and molecular variant. PLoS Genet. 2020 Dec 28;16(12):e1008857. doi: 10.1371/journal.pgen.1008857. PMID: 33370780; PMCID: PMC7793307.
Noorbakhsh J, Farahmand S, Foroughi Pour A, Namburi S, Caruana D, Rimm D, Soltanieh-Ha M, Zarringhalam K, Chuang JH. Deep learning-based cross-classifications reveal conserved spatial behaviors within tumor histological images. Nat Commun. 2020 Dec 11;11(1):6367. doi: 10.1038/s41467-020-20030-5. PMID: 33311458; PMCID: PMC7733499.
2021 RPPR
Leclair NK, Brugiolo M, Urbanski L, Lawson SC, Thakar K, Yurieva M, George J, Hinson JT, Cheng A, Graveley BR, Anczuków O. Poison Exon Splicing Regulates a Coordinated Network of SR Protein Expression during Differentiation and Tumorigenesis. Mol Cell. 2020 Nov 19;80(4):648-665.e9. doi: 10.1016/j.molcel.2020.10.019. Epub 2020 Nov 10. PubMed [citation] PMID: 33176162, PMCID: PMC7680420
Li P, Lu M, Shi J, Gong Z, Hua L, Li Q, Lim B, Zhang XH, Chen X, Li S, Shultz LD, Ren G. Lung mesenchymal cells elicit lipid storage in neutrophils that fuel breast cancer lung metastasis. Nat Immunol. 2020 Nov;21(11):1444-1455. doi: 10.1038/s41590-020-0783-5. Epub 2020 Sep 21. PubMed [citation] PMID: 32958928, PMCID: PMC7584447
Li S, Chen X, Wang J, Meydan C, Glass JL, Shih AH, Delwel R, Levine RL, Mason CE, Melnick AM. Somatic Mutations Drive Specific, but Reversible, Epigenetic Heterogeneity States in AML. Cancer Discov. 2020 Dec;10(12):1934-1949. doi: 10.1158/2159-8290.CD-19-0897. Epub 2020 Sep 16. PubMed [citation] PMID: 32938585, PMCID: PMC7710625
Zhu JJ, Jillette N, Li XN, Cheng AW, Lau CC. C11orf95-RELA reprograms 3D epigenome in supratentorial ependymoma. Acta Neuropathol. 2020 Dec;140(6):951-960. doi: 10.1007/s00401-020-02225-8. Epub 2020 Sep 9. Erratum in: Acta Neuropathol. 2020 Oct 23;:. PubMed [citation] PMID: 32909151, PMCID: PMC7666583
Qi L, Kogiso M, Du Y, Zhang H, Braun FK, Huang Y, Teo WY, Lindsay H, Zhao S, Baxter P, Zhao X, Yu L, Liu Z, Zhang X, Su JM, Adesina A, Yang J, Chintagumpala M, Perlaky L, Tsz-Kwong Man C, Lau CC, Li XN. Impact of SCID mouse gender on tumorigenicity, xenograft growth and drug-response in a large panel of orthotopic PDX models of pediatric brain tumors. Cancer Lett. 2020 Nov 28;493:197-206. doi: 10.1016/j.canlet.2020.08.035. Epub 2020 Sep 3. Erratum in: Cancer Lett. 2020 Dec 23;:. PubMed [citation] PMID: 32891713
Li P, Lu M, Shi J, Hua L, Gong Z, Li Q, Shultz LD, Ren G. Dual roles of neutrophils in metastatic colonization are governed by the host NK cell status. Nat Commun. 2020 Sep 1;11(1):4387. doi: 10.1038/s41467-020-18125-0. PubMed [citation] PMID: 32873795, PMCID: PMC7463263
Kim H, Nguyen NP, Turner K, Wu S, Gujar AD, Luebeck J, Liu J, Deshpande V, Rajkumar U, Namburi S, Amin SB, Yi E, Menghi F, Schulte JH, Henssen AG, Chang HY, Beck CR, Mischel PS, Bafna V, Verhaak RGW. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat Genet. 2020 Sep;52(9):891-897. doi: 10.1038/s41588-020-0678-2. Epub 2020 Aug 17. PubMed [citation] PMID: 32807987, PMCID: PMC7484012
Ortmann D, Brown S, Czechanski A, Aydin S, Muraro D, Huang Y, Tomaz RA, Osnato A, Canu G, Wesley BT, Skelly DA, Stegle O, Choi T, Churchill GA, Baker CL, Rugg-Gunn PJ, Munger SC, Reinholdt LG, Vallier L. Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation. Cell Stem Cell. 2020 Sep 3;27(3):470-481.e6. doi: 10.1016/j.stem.2020.07.019. Epub 2020 Aug 13. PubMed [citation] PMID: 32795399, PMCID: PMC7487768
Young K, Loberg MA, Eudy E, Schwartz LS, Mujica KD, Trowbridge JJ. Heritable genetic background alters survival and phenotype of Mll-AF9-induced leukemias. Exp Hematol. 2020 Sep;89:61-67.e3. doi: 0.1016/j.exphem.2020.07.012. Epub 2020 Aug 6. PubMed [citation] PMID: 32768438, PMCID: PMC7508790
Oldrini B, Vaquero-Siguero N, Mu Q, Kroon P, Zhang Y, Galán-Ganga M, Bao Z, Wang Z, Liu H, Sa JK, Zhao J, Kim H, Rodriguez-Perales S, Nam DH, Verhaak RGW, Rabadan R, Jiang T, Wang J, Squatrito M. MGMT genomic rearrangements contribute to chemotherapy resistance in gliomas. Nat Commun. 2020 Aug 4;11(1):3883. doi: 10.1038/s41467-020-17717-0. PubMed [citation] PMID: 32753598, PMCID: PMC7403430
Nehar-Belaid D, Hong S, Marches R, Chen G, Bolisetty M, Baisch J, Walters L, Punaro M, Rossi RJ, Chung CH, Huynh RP, Singh P, Flynn WF, Tabanor-Gayle JA, Kuchipudi N, Mejias A, Collet MA, Lucido AL, Palucka K, Robson P, Lakshminarayanan S, Ramilo O, et al. Mapping systemic lupus erythematosus heterogeneity at the single-cell level. Nat Immunol. 2020 Sep;21(9):1094-1106. doi: 10.1038/s41590-020-0743-0. Epub 2020 Aug 3. PubMed [citation] PMID: 32747814, PMCID: PMC7442743
Rosikiewicz W, Chen X, Dominguez PM, Ghamlouch H, Aoufouchi S, Bernard OA, Melnick A, Li S. TET2 deficiency reprograms the germinal center B cell epigenome and silences genes linked to lymphomagenesis. Sci Adv. 2020 Jun 17;6(25):eaay5872. doi: 10.1126/sciadv.aay5872. eCollection 2020 Jun. PubMed [citation] PMID: 32596441, PMCID: PMC7299612
Nasrallah R, Imianowski CJ, Bossini-Castillo L, Grant FM, Dogan M, Placek L, Kozhaya L, Kuo P, Sadiyah F, Whiteside SK, Mumbach MR, Glinos D, Vardaka P, Whyte CE, Lozano T, Fujita T, Fujii H, Liston A, Andrews S, Cozzani A, Yang J, Mitra S, et al. A distal enhancer at risk locus 11q13.5 promotes suppression of colitis by T(reg) cells. Nature. 2020 Jul;583(7816):447-452. doi: 10.1038/s41586-020-2296-7. Epub 2020 May 13. PubMed [citation] PMID: 32499651
Wang P, Tang Z, Lee B, Zhu JJ, Cai L, Szalaj P, Tian SZ, Zheng M, Plewczynski D, Ruan X, Liu ET, Wei CL, Ruan Y. Chromatin topology reorganization and transcription repression by PML-RARα in acute promyeloid leukemia. Genome Biol. 2020 May 11;21(1):110. doi: 10.1186/s13059-020-02030-2. PubMed [citation] PMID: 32393309, PMCID: PMC7212609
Ramirez D, Kohar V, Lu M. Toward Modeling Context-Specific EMT Regulatory Networks Using Temporal Single Cell RNA-Seq Data. Front Mol Biosci. 2020 Apr 23;7:54. doi: 10.3389/fmolb.2020.00054. eCollection 2020. PubMed [citation] PMID: 32391378, PMCID: PMC7190801
Zhang Z, Zhou C, Li X, Barnes SD, Deng S, Hoover E, Chen CC, Lee YS, Zhang Y, Wang C, Metang LA, Wu C, Tirado CR, Johnson NA, Wongvipat J, Navrazhina K, Cao Z, Choi D, Huang CH, Linton E, Chen X, Liang Y, et al. Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation. Cancer Cell. 2020 Apr 13;37(4):584-598.e11. doi: 10.1016/j.ccell.2020.03.001. Epub 2020 Mar 26. PubMed [citation] PMID: 32220301, PMCID: PMC7292228
Evrard YA, Srivastava A, Randjelovic J, Doroshow JH, Dean DA 2nd, Morris JS, Chuang JH; NCI PDXNet Consortium.. Systematic Establishment of Robustness and Standards in Patient-Derived Xenograft xperiments and Analysis. Cancer Res. 2020 Jun 1;80(11):2286-2297. doi: 10.1158/0008-5472.CAN-19-3101. Epub 2020 Mar 9. PubMed [citation] PMID: 32152150, PMCID: PMC7272270
Ashoor H, Chen X, Rosikiewicz W, Wang J, Cheng A, Wang P, Ruan Y, Li S. Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data. Nat Commun. 2020 Mar 3;11(1):1173. doi: 10.1038/s41467-020-14974-x. PubMed [citation] PMID: 32127534, PMCID: PMC7054322
Ngan CY, Wong CH, Tjong H, Wang W, Goldfeder RL, Choi C, He H, Gong L, Lin J, Urban B, Chow J, Li M, Lim J, Philip V, Murray SA, Wang H, Wei CL. Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development. Nat Genet. 2020 Mar;52(3):264-272. doi: 10.1038/s41588-020-0581-x. Epub 2020 Feb 24. PubMed [citation] PMID: 32094912
Márquez EJ, Chung CH, Marches R, Rossi RJ, Nehar-Belaid D, Eroglu A, Mellert DJ, Kuchel GA, Banchereau J, Ucar D. Sexual-dimorphism in human immune system aging. Nat Commun. 2020 Feb 6;11(1):751. doi: 10.1038/s41467-020-14396-9. PubMed [citation] PMID: 32029736, PMCID: PMC7005316
Akdemir KC, Le VT, Chandran S, Li Y, Verhaak RG, Beroukhim R, Campbell PJ, Chin L, Dixon JR, Futreal PA; PCAWG Structural Variation Working Group.; PCAWG Consortium.. Disruption of chromatin folding omains by somatic genomic rearrangements in human cancer. Nat Genet. 2020 Mar;52(3):294-305. doi: 10.1038/s41588-019-0564-y. Epub 2020 Feb 5. PubMed [citation] PMID: 32024999, PMCID: PMC7058537
Zhou W, Spoto M, Hardy R, Guan C, Fleming E, Larson PJ, Brown JS, Oh J. Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin. Cell. 2020 Feb 6;180(3):454-470.e18. doi: 10.1016/j.cell.2020.01.006. Epub 2020 Jan 30. PubMed [citation] PMID: 32004459, PMCID: PMC7192218
Chen Y, Nakanishi M, Bautista EJ, Qendro V, Sodergren E, Rosenberg DW, Weinstock GM. Colon Cancer Prevention with Walnuts: A Longitudinal Study in Mice from the Perspective of a Gut Enterotype-like Cluster. Cancer Prev Res (Phila). 2020 Jan;13(1):15-24. doi: 10.1158/1940-6207.CAPR-19-0273. Epub 2019 Dec 9. PubMed [citation] PMID: 31818852
Draaisma K, Chatzipli A, Taphoorn M, Kerkhof M, Weyerbrock A, Sanson M, Hoeben A, Lukacova S, Lombardi G, Leenstra S, Hanse M, Fleischeuer R, Watts C, McAbee J, Angelopoulos N, Gorlia T, olfinopoulos V, Kros JM, Verhaak RGW, Bours V, van den Bent MJ, McDermott U, et al. Molecular Evolution of IDH Wild-Type Glioblastomas Treated With Standard of Care Affects Survival and Design of Precision Medicine Trials: A Report From the EORTC 1542 Study. J Clin Oncol. 2020 Jan 1;38(1):81-99. doi: 10.1200/JCO.19.00367. Epub 2019 Nov 19. PubMed [citation] PMID: 31743054
Nan X, Wang J, Cheng H, Yin Z, Sheng J, Qiu B, Lau CC, Yustein JT, Zhao H, Wong STC. Imatinib revives the therapeutic potential of metformin on ewing sarcoma by attenuating tumor hypoxic response and inhibiting convergent signaling pathways. Cancer Lett. 2020 Jan 28;469:195-206. doi: 10.1016/j.canlet.2019.10.034. Epub 2019 Oct 28. PubMed [citation] PMID: 31672491, PMCID: PMC6905085