© 2018 Functional Genomics Facility



Catalyzing Discoveries:

We are proud to catalyze research in the beautiful state of Colorado. Below is a (far from comprehensive) list of recent publications supported by the Functional Genomics Facility through reagents and expertise. Please cite the Functional Genomics Facility when appropriate, and let us know about your latest publications by emailing us at funcgenfac@colorado.edu. We'll be happy to advertise here your publications supported by the Facility.


Thank you all for your continued support!

A TDO2-AhR signaling axis facilitates anoikis resistance and metastasis in triple-negative breast cancer. - D'Amato NC, Rogers TJ, Gordon MA, Greene LI, Cochrane DR, Spoelstra NS, Nemkov TG, D'Alessandro A, Hansen KC, Richer JK.


Kinome RNAi Screens Reveal Synergistic Targeting of MTOR and FGFR1 Pathways for Treatment of Lung Cancer and HNSCC. - Singleton KR, Hinz TK, Kleczko EK, Marek LA, Kwak J, Harp T, Kim J, Tan AC, Heasley LE.


Hypoxia induces triglycerides accumulation in prostate cancer cells and extracellular vesicles supporting growth and invasiveness following reoxygenation. - Schlaepfer IR, Nambiar DK, Ramteke A, Kumar R, Dhar D, Agarwal C, Bergman B, Graner M, Maroni P, Singh RP, Agarwal R, Deep G.


An Inducible TGF-β2-TGFβR Pathway Modulates the Sensitivity of HNSCC Cells to Tyrosine Kinase Inhibitors Targeting Dominant Receptor Tyrosine Kinases. - Kleczko EK, Kim J, Keysar SB, Heasley LR, Eagles JR, Simon M, Marshall ME, Singleton KR, Jimeno A, Tan AC, Heasley LE.


C-terminal tensin-like protein mediates invasion of human lung cancer cells and is regulated by signal transducer and activator of transcription 3. - Bennett DT, Reece TB, Foley LS, Sjoberg A, Meng X, Fullerton DA, Weyant MJ.


HER2 activation results in β-catenin dependent changes in pulmonary epithelial permeability. - Finigan JH, Vasu VT, Thaikoottathil JV, Mishra R, Shatat MA, Mason RJ, Kern JA.


Inhibition of Lipid Oxidation Increases Glucose Metabolism and Enhances 2-Deoxy-2-[18F]Fluoro-D-Glucose Uptake in Prostate Cancer Mouse Xenografts. - Schlaepfer IR, Glodé LM, Hitz CA, Pac CT, Boyle KE, Maroni P, Deep G, Agarwal R, Lucia SM, Cramer SD, Serkova NJ, Eckel RH.


ATM regulates cell fate choice upon p53 activation by modulating mitochondrial turnover and ROS levels. - Sullivan KD, Palaniappan VV, Espinosa JM.


Lipid catabolism via CPT1 as a therapeutic target for prostate cancer. - Schlaepfer IR, Rider L, Rodrigues LU, Gijón MA, Pac CT, Romero L, Cimic A, Sirintrapun SJ, Glodé LM, Eckel RH, Cramer SD.


Progesterone downregulation of miR-141 contributes to expansion of stem-like breast cancer cells through maintenance of progesterone receptor and Stat5a. – Finlay-Schultz J, Cittelly DM, Hendricks P, Patel P, Kabos P, Jacobsen BM, Richer JK, Sartorius CA.


Intercellular adhesion molecule-1 mediates murine colon adenocarcinoma invasion. - Howard K, Lo KK, Ao L, Gamboni F, Edil BH, Schulick R, Barnett CC Jr.


STAT3 and HIF1α cooperatively activate HIF1 target genes in MDA-MB-231 and RCC4 cells. - Pawlus MR, Wang L, Hu CJ.


Autophagy controls the kinetics and extent of mitochondrial apoptosis by regulating PUMA levels. - Thorburn J, Andrysik Z, Staskiewicz L, Gump J, Maycotte P, Oberst A, Green DR, Espinosa JM, Thorburn A.


STAT3-mediated autophagy dependence identifies subtypes of breast cancer where autophagy inhibition can be efficacious. - Maycotte P, Gearheart CM, Barnard R, Aryal S, Mulcahy Levy JM, Fosmire SP, Hansen RJ, Morgan MJ, Porter CC, Gustafson DL, Thorburn A.


Autophagy variation within a cell population determines cell fate through selective degradation of Fap-1. -Gump JM, Staskiewicz L, Morgan MJ, Bamberg A, Riches DW, Thorburn A.

Inhibition of Wee1 sensitizes cancer cells to anti-metabolite chemotherapeutics independent of p53 functionality - Van Linden AA, Baturin D, Gardner L, Fosmire SP, Korch C, Reigan P, Porter CC.


Rapid and widespread suppression of self-renewal by microRNA-203 during epidermal differentiation - Jackson SJ, Zhang Z, Feng D, Flagg M, O'Loughlin E, Wang D, Stokes N, Fuchs E, Yi R.


A genetic screen identifies TCF3/E2A and TRIAP1 as pathway-specific regulators of the cellular response to p53 activation - Andrysik Z, Kim J, Tan AC (DT), Espinosa JM .


HIF1A employs CDK8-mediator to stimulate RNAPII elongation in response to hypoxia - Galbraith MD, Allen MA, Bensard CL, Wang X, Schwinn MK, Qin B, Long HW, Daniels DL, Hahn WC, Dowell RD, Espinosa JM.


The transcription factor SPDEF is required for E-cadherin expression in prostate cancer cells -

Pal M, Koul S, Koul HK.


Inhibition of cyclin-dependent kinase 6 suppresses cell proliferation and enhances radiation sensitivity in medulloblastoma cells - Whiteway SL, Harris PS, Venkataraman S, Alimova I, Birks DK, Donson AM, Foreman NK, Vibhakar R. J.


Claudins play a role in normal and tumor cell motility - Webb, P.G., Spillman, M.A., and Baumgartner, H.K.


A receptor tyrosine kinase network comprised of FGFRs, EGFR, ERBB2 and MET drives growth and survival of head and neck squamous carcinoma cell lines - Singleton KR, Kim J, Hinz TK, Marek LA, Casas-Selves M, Hatheway C, Tan AC, Degregori J, Heasley LE.


Human papillomavirus infection is inhibited by host autophagy in primary human keratinocytes - Griffin LM, Cicchini L, Pyeon D.

A DR4:tBID axis drives the p53 apoptotic response by promoting oligomerization of poised BAX - Henry RE, Andrysik Z, Paris R, Galbraith MD, Espinosa JM.


ATM and MET kinases are synthetic lethal with nongenotoxic activation of p53 - Sullivan KD, Padilla-Just N, Henry RE, Porter CC, Kim J, Tentler JJ, Eckhardt SG, Tan AC, DeGregori J, Espinosa JM.


ΔNp63α represses anti-proliferative genes via H2A.Z deposition - Gallant-Behm CL, Ramsey MR, Bensard CL, Nojek I, Tran J, Liu M, Ellisen LW, Espinosa JM.


Integrated genomic analyses identify WEE1 as a critical mediator of cell fate and a novel therapeutic target in acute myeloid leukemia - Porter CC, Kim J, Fosmire S, Gearheart CM, van Linden A, Baturin D, Zaberezhnyy V, Patel PR, Gao D, Tan AC, DeGregori J.


mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription - Brannan K, Kim H, Erickson B, Glover-Cutter K, Kim S, Fong N, Kiemele L, Hansen K, Davis R, Lykke-Andersen J, Bentley DL.


Progestin regulated miRNAs that mediate progesterone receptor action in breast cancer - Cochrane DR, Jacobsen BM, Connaghan KD, Howe EN, Bain DL, Richer JK.


Tankyrase and the canonical Wnt pathway protect lung cancer cells from EGFR inhibition - Casas-Selves M, Kim J, Zhang Z, Helfrich BA, Gao D, Porter CC, Scarborough HA, Bunn PA Jr, Chan DC, Tan AC, DeGregori J.


West Nile virus growth is independent of autophagy activation - Beatman E, Oyer R, Shives KD, Hedman K, Brault AC, Tyler KL, Beckham JD.





Trisomy 21 consistently activates the interferon response. Sullivan KD, Lewis HC, Hill AA, Pandey A, Jackson LP, Cabral JM, Smith KP, Liggett LA, Gomez EB, Galbraith MD, DeGregori J (MO/HEME), Espinosa JM (MO).  Elife 5: e16220, 2016.  PMID: 27472900 / PMC5012864


PRL-3 engages the focal adhesion pathway in triple-negative breast cancer cells to alter actin structure and substrate adhesion properties critical for cell migration and invasion. Gari HH, DeGala GD, Ray R, Lucia MS (DT), Lambert JR. Cancer Lett 380: 505-12, 2016.  PMID: 27452906 / PMC - In Process (NIHMS #871271)


Loss of the oncogenic phosphatase PRL-3 promotes a TNF-R1 feedback loop that mediates triple-negative breast cancer growth. Gari HH, DeGala GD, Lucia MS (DT), Lambert JR. Oncogenesis 5: e255, 2016.  PMID: 27526109 / PMC5007826


Combining a GSI and BCL-2 inhibitor to overcome melanoma's resistance to current treatments. Mukherjee N, Almeida A, Partyka KA, Lu Y, Schwan JV, Lambert K, Rogers M, Robinson WA (DT), Robinson SE, Applegate AJ, Amato CM, Luo Y, Fujita M (DT), Norris DA (DT), Shellman YG. Oncotarget 7: 84594-84607, 2016.  PMID: 27829238 / PMC5356684


An RNA matchmaker protein regulates the activity of the long noncoding RNA HOTAIR. Meredith EK, Balas MM, Sindy K, Haislop K, Johnson AM (MO). RNA 22: 995-1010, 2016.  PMID: 27146324 / PMC4911922


The NSL chromatin-modifying complex subunit KANSL2 regulates cancer stem-like properties in glioblastoma that contribute to tumorigenesis. Ferreyra Solari NE, Belforte FS, Canedo L, Videla-Richardson GA, Espinosa JM (MO), Rossi M, Serna E, Riudavets MA, Martinetto H, Sevlever G, Perez-Castro C. Cancer Res 76: 5383-94, 2016.  PMID: 27406830 / PMC5026635


GON4l drives cancer growth through a YY1-androgen receptor-CD24 axis. Agarwal N, Dancik GM, Goodspeed A, Costello JC (DT), Owens C, Duex JE, Theodorescu D (DT). Cancer Res 76: 5175-85, 2016.  PMID: 27312530 / PMC5010501


GON4L drives cancer growth through a YY1- androgen receptor-CD24 axis. - Agarwal N, Dancik GM, Goodspeed A, Costello JC, Owens C, Duex JE, Theodorescu D.


Use of a MCL-1 inhibitor alone to de-bulk melanoma and in combination to kill melanoma initiating cells. - Mukherjee N, Lu Y, Almeida A, Lambert K, Shiau CW, Su JC, Luo Y, Fujita M, Robinson WA, Robinson SE, Norris DA, Shellman YG.


Genome-wide functional genetic screen with the anticancer agent AMPI-109 identifies PRL-3 as an oncogenic driver in triple-negative breast cancers. - Gari HH, Gearheart CM, Fosmire S, DeGala GD, Fan Z, Torkko KC, Edgerton SM, Lucia MS, Ray R, Thor AD, Porter CC, Lambert JR.


RABIF/MSS4 is a Rab-stabilizing holdase chaperone required for GLUT4 exocytosis. Gulbranson DR, Davis EM, Demmitt BA, Ouyang Y, Ye Y, Yu H, Shen J. Proc Natl Acad Sci U S A. 2017 Sep 26;114(39):E8224-E8233. PMID: 28894007 PMCID: PMC5625932


Therapy-induced E-cadherin downregulation alters expression of programmed death ligand-1 in lung cancer cells. Suda K, Rozeboom L, Rivard CJ, Yu H, Ellison K, Melnick MAC, Hinz TK, Chan D, Heasley LE, Politi K, Mitsudomi T, Hirsch FR. Lung Cancer. 2017 Jul;109:1-8. PMID: 28577937


Hypoxia-Inducible Factor 1α Signaling Promotes Repair of the Alveolar Epithelium after Acute Lung Injury. McClendon J, Jansing NL, Redente EF, Gandjeva A, Ito Y, Colgan SP, Ahmad A, Riches DWH, Chapman HA, Mason RJ, Tuder RM, Zemans RL. Am J Pathol. 2017 Aug;187(8):1772-1786. PMID: 28618253 PMCID: PMC5530913


Cross talk between progesterone receptors and retinoic acid receptors in regulation of cytokeratin 5-positive breast cancer cells. Fettig LM, McGinn O, Finlay-Schultz J, LaBarbera DV, Nordeen SK, Sartorius CA. Oncogene advance online publication. PMID: 28692043


Identification of a core TP53 transcriptional program with highly distributed tumor suppressive activity. Andrysik Z, Galbraith MD, Guarnieri AL, Zaccara S, Sullivan KD, Pandey A, MacBeth M, Inga A, Espinosa JM (MO). Genome Res Oct 2017. PMID: 28904012 / PMC Journal - In process


A kinase-independent role for CDK19 in p53 response.  Audetat KA, Galbraith MD, Odell AT, Lee T, Pandey A, Espinosa JM (MO), Dowell RD, Taatjes DJ (MO). Mol Cell Biol, Epub ahead of print, 2017.  PMID: 28416637 / PMC Needed


Androgen receptor supports an anchorage-independent, cancer stem cell-like population in triple-negative breast cancer. Barton VN, Christenson JL, Gordon MA, Greene LI, Rogers TJ, Butterfield K, Babbs B, Spoelstra NS, D'Amato NC, Elias A (DT), Richer JK (MO).   Cancer Res, Epub ahead of print, 2017.  PMID: 28512248


A genome-wide loss-of-function screen identifies SLC26A2 as a novel mediator of trail resistance. Dimberg LY, Towers CG, Behbakht K (DT), Hotz TJ, Kim J, Fosmire S, Porter CC, Tan AC (DT), Thorburn A (CCB), Ford HL (CCB).  Mol Cancer Res 15: 382-394, 2017.  PMID: 28108622 / PMC5380511


Lipid catabolism inhibition sensitizes prostate cancer cells to antiandrogen blockade. Flaig TW (DT), Salzmann-Sullivan M, Su LJ, Zhang Z, Joshi M, Gijon MA, Kim J, Arcaroli JJ, Van Bokhoven A, Lucia MS (DT), La Rosa FG, Schlaepfer IR (CCB). Oncotarget, Epub ahead of print, 2017.  PMID: 28473655 / PMC Needed


CD147: a small molecule transporter ancillary protein at the crossroad of multiple hallmarks of cancer and metabolic reprogramming. Kendrick AA, Schafer J, Dzieciatkowska M, Nemkov T, D'Alessandro A, Neelakantan D, Ford HL (CCB), Pearson CG (CCB), Weekes CD (DT), Hansen KC (CCB), Eisenmesser EZ (MO).  Oncotarget 8: 6742-6762, 2017.  PMID: 28039486 / PMC5341751


Therapeutic targeting of MLL degradation pathways in MLL-rearranged leukemia. Liang K, Volk AG, Haug JS, Marshall SA, Woodfin AR, Bartom ET, Gilmore JM, Florens L, Washburn MP, Sullivan KD, Espinosa JM (MO), Cannova J, Zhang J, Smith ER, Crispino JD, Shilatifard A. Cell 168: 59-72 e13, 2017.  PMID: 28065413 / PMC5351781


MiR-193b, downregulated in Ewing Sarcoma, targets the ErbB4 oncogene to inhibit anchorage-independent growth. Moore C, Parrish JK, Jedlicka P (MO). PLoS One 12: e0178028, 2017.  PMID: 28542597 / PMC5436853


Autophagy inhibition overcomes multiple mechanisms of resistance to BRAF inhibition in brain tumors. Mulcahy Levy JM (CCB), Zahedi S, Griesinger AM, Morin A, Davies KD, Aisner DL (LHN), Kleinschmidt-DeMasters BK, Fitzwalter BE, Goodall ML, Thorburn J, Amani V, Donson AM, Birks DK, Mirsky DM, Hankinson TC (CPC), Handler MH, Green AL (CCB), Vibhakar R (CCB), Foreman NK (DT), Thorburn A (CCB). Elife 6: e19671 DOI: 10.7554/eLife.19671, 2017.  PMID: 28094001 / PMC5241115


AZ1366: An inhibitor of tankyrase and the canonical Wnt pathway that limits the persistence of non-small cell lung cancer cells following EGFR inhibition. Scarborough HA, Helfrich BA, Casas-Selves M, Schuller A, Grosskurth SE, Kim J, Tan AC (DT), Chan DC, Zhang Z, Zaberezhnyy V, Bunn PA (LHN), DeGregori J (MO/HEME). Clin Cancer Res 23: 1531-1541, 2017.  PMID: 27663586 / PMC5354947


The histone demethylase KDM3A, and its downstream target MCAM, promote Ewing sarcoma cell migration and metastasis. Sechler M, Parrish JK, Birks DK, Jedlicka P (MO). Oncogene, Epub ahead of print, 2017.  PMID: 28319067 / PMC - In Process (NIHMS #849669)


Non-cell-autonomous Effects of Autophagy Inhibition in Tumor Cells Promote Growth of Drug-resistant Cells. Thorburn J, Staskiewicz L, Goodall ML, Dimberg L, Frankel AE, Ford HL (CCB), Thorburn A (CCB). Mol Pharmacol 91: 58-64, 2017.  PMID: 27974637 / PMC5198514


EGFR mediates responses to small molecule drugs targeting oncogenic fusion kinases. Vaishnavi A, Schubert L, Rix U, Marek LA, Le AT, Keysar S, Glogowska MJ, Smith MA, Kako SL, Sumi NJ, Davies KD, Ware KE, Varella-Garcia M (LHN), Haura EB, Jimeno A (CCB/LHN/DT), Heasley LE (LHN), Aisner DL (LHN), Doebele RC (LHN). Cancer Res, Epub ahead of print, 2017.  PMID: 28428274 / PMC Needed