Publications

 

For the most updated listing of papers from the Bass Lab, check here:
http://www.ncbi.nlm.nih.gov/pubmed?term=(Adam%20Bass)%20NOT%20calgary


Stachler M, Taylor-Weiner A, Peng S, McKenna A, Agoston A, Odze RD, Davison JM, Nason KS, Loda M, Leschiner I, Stewart, S, Stojanov C, Seepo S, Lawrence MS, Ferrer Torres D, Lin J, Chang AC, Gabriel SB, Lander ES, Beer DG, Getz G, Carter SL, Bass AJ. Paired genomic sequencing of Barrett’s Esophagus and Esophageal Adenocarcinoma.  Nature Genetics, 2015 Sep;47(9):1047-55

Derks S, Nason KS, Liao X, Stachler MD, Liu KX, Liu JB, Sicinska E, Goldberg MS, Freeman GJ, Rodig SJ, Davison JM, Bass AJEpithelial PD-L2 expression marks Barrett’s Esophagus and Esophageal Adenocarcinoma.  Cancer Immunology Research.  In the press

Lin W, Watanabe H, Peng S, Francis JM, Kaplan N, Pedamallu CS, Ramachandran A, Agoston A, Bass AJ, Meyerson M.  Dynamic Epigenetic Regulation by Menin During Pancreatic Islet Tumor Formation.  Mol Cancer Res. 2014 Dec 23 (epub)

Kim J, Fox C, Peng S, Pusung M, Pectasides E, Mathee E, Hong YS, Do I, Jang J, Thorner AR, Van Hummelen P, Rustgi AK, Wong K, Zhou Z, Tang P, Kim KM, Lee J, Bass AJPre-existing alterations impact Trastuzumab sensitivity in ERBB2-amplified gastroesophageal adenocarcinoma.  Journal of Clinical Investigation, 2014 Dec 1;124(12):5145-58

Hong YS, Kim J, Pectasides E, Fox C, Hong SW, Ma Q, Wong GS, Peng S, Stachler MD, Thorner AR, Van Hummelen P, Bass AJ.  Src Mutation Induces Acquired Lapatinib Resistance in ERBB2-Amplified Human Gastroesophageal Adenocarcinoma Models.  PLOS One.  Oct 28;9(10):e109440

Kagawa, S., Natsuizaka, M., Whelan, K. A., Facompre, N., Naganuma, S., Ohashi, S., Kinugasa, H., Egloff, A. M., Basu, D., Gimotty, P. A., Klein-Szanto, A. J., Bass, A. J., Wong, K. K., Diehl, J. A., Rustgi, A. K. and Nakagawa, H. Cellular senescence checkpoint function determines differential Notch1-dependent oncogenic and tumor-suppressor activities. Oncogene. 2014; in press

Imamura, Y., Lochhead, P., Yamauchi, M., Kuchiba, A., Qian, Z. R., Liao, X., Nishihara, R., Jung, S., Wu, K., Nosho, K., Wang, Y. E., Peng, S., Bass, A. J., Haigis, K. M., Meyerhardt, J. A., Chan, A. T., Fuchs, C. S. and Ogino, S. Analyses of clinicopathological, molecular, and prognostic associations of KRAS codon 61 and codon 146 mutations in colorectal cancer: cohort study and literature review. Molecular cancer. 2014;13(1):135.

Cho, J.*, Bass, A. J.*, Lawrence, M. S., Cibulskis, K., Cho, A., Lee, S. N., Yamauchi, M., Wagle, N., Pochanard, P., Kim, N., Park, A. K., Won, J., Hur, H. S., Greulich, H., Ogino, S., Sougnez, C., Voet, D., Tabernero, J., Jimenez, J., Baselga, J., Gabriel, S. B., Lander, E. S., Getz, G., Eck, M. J., Park, W. Y. and Meyerson, M. Colon cancer-derived oncogenic EGFR G724S mutant identified by whole genome sequence analysis is dependent on asymmetric dimerization and sensitive to cetuximab. Molecular cancer. 2014;13(1):141.   (*co-first author)

TCGA Consortium.* Comprehensive Molecular Characterization of Gastric Adenocarcinoma. Nature, in press.   (*Sole Corresponding Author)

Xu C, Fillmore CM, Koyama S, Wu H, Zhao Y, Chen Z, Herter-Sprie GS, Akbay EA, Tchaicha JH, Altabef A, Reibel JB, Walton Z, Ji H, Watanabe H, Janne PA, Castrillon DH, Rustgi AK, Bass AJ, Freeman GJ, Padera RF, Dranoff G, Hammerman PS, Kim CF, Wong KK. Loss of Lkb1 and Pten Leads to Lung Squamous Cell Carcinoma with Elevated PD-L1 Expression. Cancer Cell. 2014;25(5):590-604. doi: 10.1016/j.ccr.2014.03.033. PubMed PMID: 24794706.

Rampal R, Al-Shahrour F, Abdel-Wahab O, Patel J, Brunel JP, Mermel CH, Bass AJ, Pretz J, Ahn J, Hricik T, Kilpivaara O, Wadleigh M, Busque L, Gilliland DG, Golub TR, Ebert BL, Levine R. Integrated genomic analysis illustrates the central role of JAK-STAT pathway activation in myeloproliferative neoplasm pathogenesis. Blood. 2014. doi: 10.1182/blood-2014-02-554634. PubMed PMID: 24740812.

Dews M, Tan GS, Hultine S, Raman P, Choi J, Duperret EK, Lawler J, Bass A, Thomas-Tikhonenko A. Masking Epistasis Between MYC and TGF-beta Pathways in Antiangiogenesis-Mediated Colon Cancer Suppression. Journal of the National Cancer Institute. 2014. doi: 10.1093/jnci/dju043. PubMed PMID: 24627270

Bandla S, Peters JH, Ruff D, Chen SM, Li CY, Song K, Thoms K, Litle VR, Watson T, Chapurin N, Lada M, Pennathur A, Luketich JD, Peterson D, Dulak A, Lin L, Bass A, Beer DG, Godfrey TE, Zhou Z. Comparison of Cancer-Associated Genetic Abnormalities in Columnar-Lined Esophagus Tissues With and Without Goblet Cells. Annals of Surgery. 2014, in press

Watanabe H, Ma Q, Peng S, Adelmant G, Swain D, Song W, Fox C, Francis, JM, Pedamallu CS, DeLuca DS, Brooks AN, Wang S, Que J., Rustgi AK, Wong KK, Ligon KL, Liu, XS, Marto JA, Meyerson M, Bass AJSOX2-p63 interaction and genomic localization in squamous cell carcinoma.  Journal of Clinical Investigation, 2014 Apr 1;124(4):1636-45.

Hanna MC, Go C, Roden C, Jones RT, Pochanard P, Javed AY, Javed A, Mondal C, Palescandolo E, Van Hummelen P, Hatton C, Bass AJ, Chun SM, Na DC, Kim TI, Jang SJ, Osarogiagbon RU, Hahn WC, Meyerson M, Garraway LA, Macconaill LE.  Colorectal Cancers from Distinct Ancestral Populations Show Variations in BRAF Mutation Frequency.  PLoS One. 2013 Sep 16;8(9):e74950. doi: 10.1371/journal.pone.0074950

Sulahian, R.Sulahian R, Casey F, Shen J, Qian ZR, Shin H, Ogino S, Weir BA, Vazquez F, Liu XS, Hahn WC, Bass A, Chan V, Shivdasani RA.  An integrative analysis reveals functional targets of GATA6 transcriptional regulation in gastric cancer. Oncogene (2013).

Beauchamp EM, Woods BA, Dulak AM, Tan L, Xu C, Gray NS, Bass AJ, Wong KK, Meyerson M, Hammerman PS.. Acquired resistance to dasatinib in lung cancer cell lines conferred by DDR2 gatekeeper mutation and NF1 loss. Mol Cancer Ther (2013).

Grugan KD, Vega ME, Wong GS, Diehl JA, Bass AJ, Wong KK, Nakagawa H, Rustgi AK.  A common p53 mutation (R175H) activates c-Met receptor tyrosine kinase to enhance tumor cell invasion.  Cancer Biol Ther.  2013.  18;14(9) epub ahead of print. s

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, Cortés 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, Getz G.  Mutational heterogeneity and the search for new cancer genes.  Nature.  2013 499(7457):214-8.

Dulak AM, Stojanov P, Peng, S, Lawrence MS, Fox C, Stewart, C, Bandla S, Imamura Y, Schumacher SE, Shefler E, Mckenna A, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Auclari D, Thompason K, Sougne C, Onofrio RC, Guiducci C, Beroukhim R, Zhou D, Lin L, Reddy R, Chang R, Landrenau R, Luketich JD, Pennathur A, Ogino S, Golub TR, Gabriel SB, Lander ES, Beer DG, Godfrey TG, Getz G, Bass AJExome and whole genome sequencing of esophageal adenocarcinoma identified recurrent driver events and mutational complexity.  Nature Genetics.  2013.  45(5):478-86.

The Cancer Genome Atlas Network.  Comprehensive Molecular Characterization of Human Colon and Rectal Cancer.  Nature  2012 Jul 18;487(7407):330-7

Dulak AM, Schumacher, S, van Lieshout J, Imamura Y, Fox C, Shim B, Ramos A, Saksena G, Baca S, Baselga S, Tabernero J, Barretina J, Enzinger P, Corso G, Roviello R, Lin L, Bandla S, Luketich J, Pennathur A, Meyerson M, Ogino S, Shivdasani RA, Beer DG, Godfrey TE, Beroukhim R, Bass AJGastrointestinal adenocarcinomas of the esophagus, stomach and colon exhibit distinct patterns of genome instability and oncogenesis.  Cancer Research. 2012: 72(17):4383-4393

Bandla S, Pennathur A, Luketich JD, Beer DG, Lin L, Bass AJ, Godfrey TE, Litle VR. Comparative genomics of esophageal adenocarcinoma and squamous cell carcinoma.
Ann Thorac Surg. 2012 Apr;93(4):1101-6. PMID: 22450065.

Habibollahi P, Figueiredo JL, Heidari P, Dulak AM, Imamura Y, Bass AJ, Ogino S, Chan AT, Mahmood U. Optical Imaging with a Cathepsin B Activated Probe for the Enhanced Detection of Esophageal Adenocarcinoma by Dual Channel Fluorescent Upper GI Endoscopy.
Theranostics. 2012;2(2):227-34. Epub 2012 Feb 16. PubMed PMID: 22400064;

Lin L, Bass AJ, Lockwood WW, Wang Z, Silvers AL, Thomas DG, Chang AC, Lin J, Orringer MB, Li W, Glover TW, Giordano TJ, Lam WL, Meyerson M, Beer DG. Activation of GATA binding protein 6 (GATA6) sustains oncogenic lineage-survival in esophageal adenocarcinoma.
Proc Natl Acad Sci U S A. 2012 Mar 13;109(11):4251-6. Epub 2012 Feb 28. PubMed PMID: 22375031

Hammerman PS, Sos ML, Ramos AH, Xu C, Dutt A, Zhou W, Brace LE, Woods BA, Lin W, Zhang J, Deng X, Lim SM, Heynck S, Peifer M, Simard JR, Lawrence MS, Onofrio RC, Salvesen HB, Seidel D, Zander T, Heuckmann JM, Soltermann A, Moch H, Koker M, Leenders F, Gabler F, Querings S, Ansén S, Brambilla E, Brambilla C, Lorimier P, Brustugun OT, Helland A, Petersen I, Clement JH, Groen H, Timens W, Sietsma H, Stoelben E, Wolf J, Beer DG, Tsao MS, Hanna M, Hatton C, Eck MJ, Janne PA, Johnson BE, Winckler W, Greulich H, Bass AJ, Cho J, Rauh D, Gray NS, Wong KK, Haura EB, Thomas RK, Meyerson M. Mutations in the DDR2 kinase gene identify a novel therapeutic target in squamous cell lung cancer.
Cancer Discov. 2011 Jun;1(1):78-89. PubMed PMID: 22328973.

Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, Ojesina AI, Jung J, Bass AJ, Tabernero J, Baselga J, Liu C, Shivdasani RA, Ogino S, Birren BW, Huttenhower C, Garrett WS, Meyerson M. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma.
Genome Res. 2012 Feb;22(2):292-8. Epub 2011 Oct 18. PubMed PMID: 22009990

Bass AJ, Lawrence MS, Brace LE, Ramos AH, Drier Y, Cibulskis K, Sougnez C, Voet D, Saksena G, Sivachenko A, Jing R, Parkin M, Pugh T, Verhaak RG, Stransky N, Boutin AT, Barretina J, Solit DB, Vakiani E, Shao W, Mishina Y, Warmuth M, Jimenez J, Chiang DY, Signoretti S, Kaelin WG, Spardy N, Hahn WC, Hoshida Y, Ogino S, Depinho RA, Chin L, Garraway LA, Fuchs CS, Baselga J, Tabernero J, Gabriel S, Lander ES, Getz G, Meyerson M. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion.
Nat Genet. 2011 Sep 4;43(10):964-8. doi: 10.1038/ng.936. PubMed PMID: 21892161.

Locasale JW, Grassian AR, Melman T, Lyssiotis CA, Mattaini KR, Bass AJ, Heffron G, Metallo CM, Muranen T, Sharfi H, Sasaki AT, Anastasiou D, Mullarky E, Vokes NI, Sasaki M, Beroukhim R, Stephanopoulos G, Ligon AH, Meyerson M, Richardson AL, Chin L, Wagner G, Asara JM, Brugge JS, Cantley LC, Vander Heiden MG. Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesis.
Nat Genet. 2011 Jul 31;43(9):869-74. doi: 10.1038/ng.890. PubMed PMID: 21804546.

Bass A. Impact of KRAS and BRAF gene mutations on targeted therapies in colorectal cancer.
J Clin Oncol. 2011 Jul 1;29(19):2728-9. Epub 2011 Jun 6. PubMed PMID: 21646605.

Wilbertz T, Wagner P, Petersen K, Stiedl AC, Scheble VJ, Maier S, Reischl M, Mikut R, Altorki NK, Moch H, Fend F, Staebler A, Bass AJ, Meyerson M, Rubin MA, Soltermann A, Lengerke C, Perner S. SOX2 gene amplification and protein overexpression are associated with better outcome in squamous cell lung cancer.
Mod Pathol. 2011 Jul;24(7):944-53. doi: 10.1038/modpathol. 2011.49. Epub 2011 Apr 1. PubMed PMID: 21460799.

Silvers AL, Lin L, Bass AJ, Chen G, Wang Z, Thomas DG, Lin J, Giordano TJ, Orringer MB, Beer DG, Chang AC. Decreased selenium-binding protein 1 in esophageal adenocarcinoma results from posttranscriptional and epigenetic regulation and affects chemosensitivity.
Clin Cancer Res. 2010 Apr 1;16(7):2009-21. Epub 2010 Mar 23. PubMed PMID: 20332323.

Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L, Greulich H, Reich M, Winckler W, Lawrence MS, Weir BA, Tanaka KE, Chiang DY, Bass AJ, Loo A, Hoffman C, Prensner J, Liefeld T, Gao Q, Yecies D, Signoretti S, Maher E, Kaye FJ, Sasaki H, Tepper JE, Fletcher JA, Tabernero J, Baselga J, Tsao MS, Demichelis F, Rubin MA, Janne PA, Daly MJ, Nucera C, Levine RL, Ebert BL, Gabriel S, Rustgi AK, Antonescu CR, Ladanyi M, Letai A, Garraway LA, Loda M, Beer DG, True LD, Okamoto A, Pomeroy SL, Singer S, Golub TR, Lander ES, Getz G, Sellers WR, Meyerson M. The landscape of somatic copy-number alteration across human cancers.
Nature. 2010 Feb 18;463(7283):899-905. PubMed PMID: 20164920.

MacConaill LE, Campbell CD, Kehoe SM, Bass AJ, Hatton C, Niu L, Davis M, Yao K, Hanna M, Mondal C, Luongo L, Emery CM, Baker AC, Philips J, Goff DJ, Fiorentino M, Rubin MA, Polyak K, Chan J, Wang Y, Fletcher JA, Santagata S, Corso G, Roviello F, Shivdasani R, Kieran MW, Ligon KL, Stiles CD, Hahn WC, Meyerson ML, Garraway LA. Profiling critical cancer gene mutations in clinical tumor samples.
PLoS One. 2009 Nov 18;4(11):e7887. PubMed PMID: 19924296.

Bass AJ, Watanabe H, Mermel CH, Yu S, Perner S, Verhaak RG, Kim SY, Wardwell L, Tamayo P, Gat-Viks I, Ramos AH, Woo MS, Weir BA, Getz G, Beroukhim R, O’Kelly M, Dutt A, Rozenblatt-Rosen O, Dziunycz P, Komisarof J, Chirieac LR, Lafargue CJ, Scheble V, Wilbertz T, Ma C, Rao S, Nakagawa H, Stairs DB, Lin L, Giordano TJ, Wagner P, Minna JD, Gazdar AF, Zhu CQ, Brose MS, Cecconello I, Jr UR, Marie SK, Dahl O, Shivdasani RA, Tsao MS, Rubin MA, Wong KK, Regev A, Hahn WC, Beer DG, Rustgi AK, Meyerson M. SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas.
Nat Genet. 2009 Nov;41(11):1238-42. Epub 2009 Oct 4. PubMed PMID: 19801978.

Bass AJ, Meyerson M. Genome-wide association study in esophageal squamous cell carcinoma.
Gastroenterology. 2009 Nov;137(5):1573-6. Epub 2009 Sep 27. PubMed PMID: 19789091.

Ramos AH, Dutt A, Mermel C, Perner S, Cho J, Lafargue CJ, Johnson LA, Stiedl AC, Tanaka KE, Bass AJ, Barretina J, Weir BA, Beroukhim R, Thomas RK, Minna JD, Chirieac LR, Lindeman NI, Giordano T, Beer DG, Wagner P, Wistuba II, Rubin MA, Meyerson M. Amplification of chromosomal segment 4q12 in non-small cell lung cancer.
Cancer Biol Ther. 2009 Nov;8(21):2042-50. Epub 2009 Nov 7. PubMed PMID:  19755855.

Pomerantz MM, Ahmadiyeh N, Jia L, Herman P, Verzi MP, Doddapaneni H, Beckwith CA, Chan JA, Hills A, Davis M, Yao K, Kehoe SM, Lenz HJ, Haiman CA, Yan C, Henderson BE, Frenkel B, Barretina J, Bass A, Tabernero J, Baselga J, Regan MM, Manak JR, Shivdasani R, Coetzee GA, Freedman ML. The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer.
Nat Genet. 2009 Aug;41(8):882-4. Epub 2009 Jun 28. PubMed PMID: 19561607.

Kilpivaara O, Mukherjee S, Schram AM, Wadleigh M, Mullally A, Ebert BL, Bass A, Marubayashi S, Heguy A, Garcia Manero G, Kantarjian H, Offit K, Stone RM, Gilliland DG, Klein RJ, Levine RL. A germline JAK2 SNP is associated with predisposition to the development of JAK2(V617F)-positive myeloproliferative neoplasms.
Nat Genet. 2009 Apr;41(4):455-9. Epub 2009 Mar 15. PubMed PMID: 19287384.

Firestein R, Bass AJ, Kim SY, Dunn IF, Silver SJ, Guney I, Freed E, Ligon AH, Vena N, Ogino S, Chheda MG, Tamayo P, Finn S, Shrestha Y, Boehm JS, Jain S, Bojarski E, Mermel C, Barretina J, Chan JA, Baselga J, Tabernero J, Root DE, Fuchs CS, Loda M, Shivdasani RA, Meyerson M, Hahn WC. CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity. Nature. 2008 Sep 25;455(7212):547-51. Epub 2008 Sep 14. PubMed PMID: 18794900.