Chakravarty EF, Martyanov V, Fiorentino D, Wood TA, Haddon DJ, Jarrell JA, Utz PJ, Genovese MC, Whitfield ML, Chung L. A Pilot Randomized Placebo-Controlled study of Abatacept for the Treatment of Diffuse Cutaneous Systemic Sclerosis. Arthritis research & therapy. Forthcoming.
Taroni JN, Martyanov V, Wood TA, Choe S, Huang CC, Hirano I, Yang GY, Brenner D, Jung B, Carns M, Podluski S, Chang RW, Varga J, Whitfield ML, Hinchcliff M. Genome-wide gene expression analysis of systemic sclerosis esophageal biopsies identifies disease-specific molecular subsets. Arthritis research & therapy. Forthcoming.
Torres GM, Jarnagin HC, Park C, Yang H, Kosarek NN, Bhandari R, Wang CY, Kolling FW, Whitfield ML, Turk MJ, Liby KT, Pioli PA. CDDO-Methyl Ester Inhibits BRAF Inhibitor Resistance and Remodels the Myeloid Compartment in BRAF-mutant Melanoma. bioRxiv. 2023 Aug 3;. doi: 10.1101/2023.08.01.551524. PubMed PMID: 37577680; PubMed Central PMCID: PMC10418171.
Richmond JM, Patel D, Watanabe T, Chen HW, Martyanov V, Werner G, Garg M, Haddadi NS, Refat MA, Mahmoud BH, Wong LD, Dresser K, Deng A, Zhu JL, McAlpine W, Hosler GA, Feghali-Bostwick CA, Whitfield ML, Harris JE, Torok KS, Jacobe HT. CXCL9 Links Skin Inflammation and Fibrosis through CXCR3-Dependent Upregulation of Col1a1 in Fibroblasts. J Invest Dermatol. 2023 Jul;143(7):1138-1146.e12. doi: 10.1016/j.jid.2022.11.025. Epub 2023 Jan 25. PubMed PMID: 36708947.
Bhandari R, Yang H, Kosarek NN, Smith AE, Garlick JA, Hinchcliff M, Whitfield ML, Pioli PA. Human dermal fibroblast-derived exosomes induce macrophage activation in systemic sclerosis. Rheumatology (Oxford). 2023 Feb 6;62(SI):SI114-SI124. doi: 10.1093/rheumatology/keac453. PubMed PMID: 35946522; PubMed Central PMCID: PMC9910573.
Whitfield ML. Moving towards a molecular categorization of autoimmune disease. Nat Rev Rheumatol. 2021 Apr;17(4):193-194. doi: 10.1038/s41584-021-00589-z. PubMed PMID: 33654308.
Franks JM, Martyanov V, Wang Y, Wood TA, Pinckney A, Crofford LJ, Keyes-Elstein L, Furst DE, Goldmuntz E, Mayes MD, McSweeney P, Nash RA, Sullivan KM, Whitfield ML. Machine learning predicts stem cell transplant response in severe scleroderma. Ann Rheum Dis. 2020 Dec;79(12):1608-1615. doi: 10.1136/annrheumdis-2020-217033. Epub 2020 Sep 15. PubMed PMID: 32933919; PubMed Central PMCID: PMC8582621.
Bhandari R, Ball MS, Martyanov V, Popovich D, Schaafsma E, Han S, ElTanbouly M, Orzechowski NM, Carns M, Arroyo E, Aren K, Hinchcliff M, Whitfield ML, Pioli PA. Profibrotic Activation of Human Macrophages in Systemic Sclerosis. Arthritis Rheumatol. 2020 Jul;72(7):1160-1169. doi: 10.1002/art.41243. Epub 2020 May 31. PubMed PMID: 32134204; PubMed Central PMCID: PMC7329566.
Hinchcliff M, Toledo DM, Taroni JN, Wood TA, Franks JM, Ball MS, Hoffmann A, Amin SM, Tan AU, Tom K, Nesbeth Y, Lee J, Ma M, Aren K, Carns MA, Pioli PA, Whitfield ML. Mycophenolate Mofetil Treatment of Systemic Sclerosis Reduces Myeloid Cell Numbers and Attenuates the Inflammatory Gene Signature in Skin. J Invest Dermatol. 2018 Jun;138(6):1301-1310. doi: 10.1016/j.jid.2018.01.006. Epub 2018 Jan 31. PubMed PMID: 29391252; PubMed Central PMCID: PMC6590516.
Franks JM, Cai G, Whitfield ML. Feature specific quantile normalization enables cross-platform classification of molecular subtypes using gene expression data. Bioinformatics. 2018 Jun 1;34(11):1868-1874. doi: 10.1093/bioinformatics/bty026. PubMed PMID: 29360996; PubMed Central PMCID: PMC5972664.
Messemaker TC, Chadli L, Cai G, Goelela VS, Boonstra M, Dorjée AL, Andersen SN, Mikkers HMM, van 't Hof P, Mei H, Distler O, Draisma HHM, Johnson ME, Orzechowski NM, Simms RW, Toes REM, Aarbiou J, Huizinga TW, Whitfield ML, DeGroot J, de Vries-Bouwstra J, Kurreeman F. Antisense Long Non-Coding RNAs Are Deregulated in Skin Tissue of Patients with Systemic Sclerosis. J Invest Dermatol. 2018 Apr;138(4):826-835. doi: 10.1016/j.jid.2017.09.053. Epub 2017 Nov 24. PubMed PMID: 29179949.
Gordon JK, Martyanov V, Franks JM, Bernstein EJ, Szymonifka J, Magro C, Wildman HF, Wood TA, Whitfield ML, Spiera RF. Belimumab for the Treatment of Early Diffuse Systemic Sclerosis: Results of a Randomized, Double-Blind, Placebo-Controlled, Pilot Trial. Arthritis Rheumatol. 2018 Feb;70(2):308-316. doi: 10.1002/art.40358. Epub 2017 Dec 29. PubMed PMID: 29073351; PubMed Central PMCID: PMC6590997.
Martyanov V, Kim GJ, Hayes W, Du S, Ganguly BJ, Sy O, Lee SK, Bogatkevich GS, Schieven GL, Schiopu E, Marangoni RG, Goldin J, Whitfield ML, Varga J. Novel lung imaging biomarkers and skin gene expression subsetting in dasatinib treatment of systemic sclerosis-associated interstitial lung disease. PLoS One. 2017;12(11):e0187580. doi: 10.1371/journal.pone.0187580. eCollection 2017. PubMed PMID: 29121645; PubMed Central PMCID: PMC5679625.
Taroni JN, Mahoney JM, Whitfield ML. The mechanistic implications of gene expression studies in SSc: Insights from Systems Biology. Curr Treatm Opt Rheumatol. 2017 Sep;3(3):181-192. doi: 10.1007/s40674-017-0072-0. Epub 2017 Jul 29. PubMed PMID: 29520335; PubMed Central PMCID: PMC5837066.
Derrett-Smith EC, Martyanov V, Chighizola CB, Moinzadeh P, Campochiaro C, Khan K, Wood TA, Meroni PL, Abraham DJ, Ong VH, Lafyatis R, Whitfield ML, Denton CP. Limited cutaneous systemic sclerosis skin demonstrates distinct molecular subsets separated by a cardiovascular development gene expression signature. Arthritis Res Ther. 2017 Jul 4;19(1):156. doi: 10.1186/s13075-017-1360-7. PubMed PMID: 28676069; PubMed Central PMCID: PMC5496265.
Taroni JN, Martyanov V, Mahoney JM, Whitfield ML. A Functional Genomic Meta-Analysis of Clinical Trials in Systemic Sclerosis: Toward Precision Medicine and Combination Therapy. J Invest Dermatol. 2017 May;137(5):1033-1041. doi: 10.1016/j.jid.2016.12.007. Epub 2016 Dec 21. PubMed PMID: 28011145; PubMed Central PMCID: PMC8190797.
Cai G, Xiao F, Cheng C, Li Y, Amos CI, Whitfield ML. Population effect model identifies gene expression predictors of survival outcomes in lung adenocarcinoma for both Caucasian and Asian patients. PLoS One. 2017;12(4):e0175850. doi: 10.1371/journal.pone.0175850. eCollection 2017. PubMed PMID: 28426704; PubMed Central PMCID: PMC5398559.
Steinberg SM, Shabaneh TB, Zhang P, Martyanov V, Li Z, Malik BT, Wood TA, Boni A, Molodtsov A, Angeles CV, Curiel TJ, Whitfield ML, Turk MJ. Myeloid Cells That Impair Immunotherapy Are Restored in Melanomas with Acquired Resistance to BRAF Inhibitors. Cancer Res. 2017 Apr 1;77(7):1599-1610. doi: 10.1158/0008-5472.CAN-16-1755. Epub 2017 Feb 15. PubMed PMID: 28202513; PubMed Central PMCID: PMC5380540.
Taroni JN, Greene CS, Martyanov V, Wood TA, Christmann RB, Farber HW, Lafyatis RA, Denton CP, Hinchcliff ME, Pioli PA, Mahoney JM, Whitfield ML. A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis. Genome Med. 2017 Mar 23;9(1):27. doi: 10.1186/s13073-017-0417-1. PubMed PMID: 28330499; PubMed Central PMCID: PMC5363043.
Lofgren S, Hinchcliff M, Carns M, Wood T, Aren K, Arroyo E, Cheung P, Kuo A, Valenzuela A, Haemel A, Wolters PJ, Gordon J, Spiera R, Assassi S, Boin F, Chung L, Fiorentino D, Utz PJ, Whitfield ML, Khatri P. Integrated, multicohort analysis of systemic sclerosis identifies robust transcriptional signature of disease severity. JCI Insight. 2016 Dec 22;1(21):e89073. doi: 10.1172/jci.insight.89073. PubMed PMID: 28018971; PubMed Central PMCID: PMC5161207.
Lyons SM, Cunningham CH, Welch JD, Groh B, Guo AY, Wei B, Whitfield ML, Xiong Y, Marzluff WF. A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues. Nucleic Acids Res. 2016 Nov 2;44(19):9190-9205. doi: 10.1093/nar/gkw620. Epub 2016 Jul 8. PubMed PMID: 27402160; PubMed Central PMCID: PMC5100578.
Sargent JL, Li Z, Aliprantis AO, Greenblatt M, Lemaire R, Wu MH, Wei J, Taroni J, Harris A, Long KB, Burgwin C, Artlett CM, Blankenhorn EP, Lafyatis R, Varga J, Clark SH, Whitfield ML. Identification of Optimal Mouse Models of Systemic Sclerosis by Interspecies Comparative Genomics. Arthritis Rheumatol. 2016 Aug;68(8):2003-15. doi: 10.1002/art.39658. PubMed PMID: 26945694; PubMed Central PMCID: PMC5695038.
Johnson ME, Grassetti AV, Taroni JN, Lyons SM, Schweppe D, Gordon JK, Spiera RF, Lafyatis R, Anderson PJ, Gerber SA, Whitfield ML. Stress granules and RNA processing bodies are novel autoantibody targets in systemic sclerosis. Arthritis Res Ther. 2016 Jan 22;18:27. doi: 10.1186/s13075-016-0914-4. PubMed PMID: 26801089; PubMed Central PMCID: PMC4724133.
Martyanov V, Whitfield ML. Molecular stratification and precision medicine in systemic sclerosis from genomic and proteomic data. Curr Opin Rheumatol. 2016 Jan;28(1):83-8. doi: 10.1097/BOR.0000000000000237. Review. PubMed PMID: 26555452; PubMed Central PMCID: PMC4722537.
Iwamoto N, Vettori S, Maurer B, Brock M, Pachera E, Jüngel A, Calcagni M, Gay RE, Whitfield ML, Distler JH, Gay S, Distler O. Downregulation of miR-193b in systemic sclerosis regulates the proliferative vasculopathy by urokinase-type plasminogen activator expression. Ann Rheum Dis. 2016 Jan;75(1):303-10. doi: 10.1136/annrheumdis-2014-205326. Epub 2014 Nov 10. PubMed PMID: 25384965.
Brooks L 3rd, Lyons SM, Mahoney JM, Welch JD, Liu Z, Marzluff WF, Whitfield ML. A multiprotein occupancy map of the mRNP on the 3' end of histone mRNAs. RNA. 2015 Nov;21(11):1943-65. doi: 10.1261/rna.053389.115. Epub 2015 Sep 16. PubMed PMID: 26377992; PubMed Central PMCID: PMC4604434.
Rice LM, Ziemek J, Stratton EA, McLaughlin SR, Padilla CM, Mathes AL, Christmann RB, Stifano G, Browning JL, Whitfield ML, Spiera RF, Gordon JK, Simms RW, Zhang Y, Lafyatis R. A longitudinal biomarker for the extent of skin disease in patients with diffuse cutaneous systemic sclerosis. Arthritis Rheumatol. 2015 Nov;67(11):3004-15. doi: 10.1002/art.39287. PubMed PMID: 26240058; PubMed Central PMCID: PMC5522178.
Johnson ME, Pioli PA, Whitfield ML. Gene expression profiling offers insights into the role of innate immune signaling in SSc. Semin Immunopathol. 2015 Sep;37(5):501-9. doi: 10.1007/s00281-015-0512-6. Epub 2015 Jul 30. Review. PubMed PMID: 26223504; PubMed Central PMCID: PMC4722533.
Gordon JK, Martyanov V, Magro C, Wildman HF, Wood TA, Huang WT, Crow MK, Whitfield ML, Spiera RF. Nilotinib (Tasigna™) in the treatment of early diffuse systemic sclerosis: an open-label, pilot clinical trial. Arthritis Res Ther. 2015 Aug 18;17(1):213. doi: 10.1186/s13075-015-0721-3. PubMed PMID: 26283632; PubMed Central PMCID: PMC4538758.
Taroni JN, Martyanov V, Huang CC, Mahoney JM, Hirano I, Shetuni B, Yang GY, Brenner D, Jung B, Wood TA, Bhattacharyya S, Almagor O, Lee J, Sirajuddin A, Varga J, Chang RW, Whitfield ML, Hinchcliff M. Molecular characterization of systemic sclerosis esophageal pathology identifies inflammatory and proliferative signatures. Arthritis Res Ther. 2015 Jul 29;17:194. doi: 10.1186/s13075-015-0695-1. PubMed PMID: 26220546; PubMed Central PMCID: PMC4518531.
Rice LM, Padilla CM, McLaughlin SR, Mathes A, Ziemek J, Goummih S, Nakerakanti S, York M, Farina G, Whitfield ML, Spiera RF, Christmann RB, Gordon JK, Weinberg J, Simms RW, Lafyatis R. Fresolimumab treatment decreases biomarkers and improves clinical symptoms in systemic sclerosis patients. J Clin Invest. 2015 Jul 1;125(7):2795-807. doi: 10.1172/JCI77958. Epub 2015 Jun 22. PubMed PMID: 26098215; PubMed Central PMCID: PMC4563675.
Chakravarty EF, Martyanov V, Fiorentino D, Wood TA, Haddon DJ, Jarrell JA, Utz PJ, Genovese MC, Whitfield ML, Chung L. Gene expression changes reflect clinical response in a placebo-controlled randomized trial of abatacept in patients with diffuse cutaneous systemic sclerosis. Arthritis Res Ther. 2015 Jun 13;17(1):159. doi: 10.1186/s13075-015-0669-3. PubMed PMID: 26071192; PubMed Central PMCID: PMC4487200.
Marangoni RG, Korman BD, Wei J, Wood TA, Graham LV, Whitfield ML, Scherer PE, Tourtellotte WG, Varga J. Myofibroblasts in murine cutaneous fibrosis originate from adiponectin-positive intradermal progenitors. Arthritis Rheumatol. 2015 Apr;67(4):1062-73. doi: 10.1002/art.38990. PubMed PMID: 25504959; PubMed Central PMCID: PMC4472310.
Long KB, Li Z, Burgwin CM, Choe SG, Martyanov V, Sassi-Gaha S, Earl JP, Eutsey RA, Ahmed A, Ehrlich GD, Artlett CM, Whitfield ML, Blankenhorn EP. The Tsk2/+ mouse fibrotic phenotype is due to a gain-of-function mutation in the PIIINP segment of the Col3a1 gene. J Invest Dermatol. 2015 Mar;135(3):718-27. doi: 10.1038/jid.2014.455. Epub 2014 Oct 20. PubMed PMID: 25330296; PubMed Central PMCID: PMC4324084.
Johnson ME, Mahoney JM, Taroni J, Sargent JL, Marmarelis E, Wu MR, Varga J, Hinchcliff ME, Whitfield ML. Experimentally-derived fibroblast gene signatures identify molecular pathways associated with distinct subsets of systemic sclerosis patients in three independent cohorts. PLoS One. 2015;10(1):e0114017. doi: 10.1371/journal.pone.0114017. eCollection 2015. PubMed PMID: 25607805; PubMed Central PMCID: PMC4301872.
Mahoney JM, Taroni J, Martyanov V, Wood TA, Greene CS, Pioli PA, Hinchcliff ME, Whitfield ML. Systems level analysis of systemic sclerosis shows a network of immune and profibrotic pathways connected with genetic polymorphisms. PLoS Comput Biol. 2015 Jan;11(1):e1004005. doi: 10.1371/journal.pcbi.1004005. eCollection 2015 Jan. PubMed PMID: 25569146; PubMed Central PMCID: PMC4288710.
Whitfield ML. Systems biology in systemic sclerosis. In: Varga J, editor. Scleroderma: From Pathogenesis to Comprehensive Management London: Springer; 2015.
Whitfield ML, Hinchcliff M. Disease classification using molecular signatures. In: Varga J, editor. Scleroderma: From Pathogenesis to Comprehensive Management London: Springer; 2015. Chapter 8.
Arron ST, Dimon MT, Li Z, Johnson ME, Wood TA, Feeney L, Angeles JG, Lafyatis R, Whitfield ML. High Rhodotorula sequences in skin transcriptome of patients with diffuse systemic sclerosis. J Invest Dermatol. 2014 Aug;134(8):2138-2145. doi: 10.1038/jid.2014.127. Epub 2014 Mar 7. PubMed PMID: 24608988; PubMed Central PMCID: PMC4102619.
Whitfield ML. Editorial: plasma and B cell gene signatures: quantitative targeting and monitoring of B cell-depleting therapies in autoimmune diseases in the genomic era. Arthritis Rheumatol. 2014 Jan;66(1):10-4. doi: 10.1002/art.38192. PubMed PMID: 24431280.
Grant GD, Brooks L 3rd, Zhang X, Mahoney JM, Martyanov V, Wood TA, Sherlock G, Cheng C, Whitfield ML. Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors. Mol Biol Cell. 2013 Dec;24(23):3634-50. doi: 10.1091/mbc.E13-05-0264. Epub 2013 Oct 9. PubMed PMID: 24109597; PubMed Central PMCID: PMC3842991.
Hinchcliff M, Huang CC, Wood TA, Matthew Mahoney J, Martyanov V, Bhattacharyya S, Tamaki Z, Lee J, Carns M, Podlusky S, Sirajuddin A, Shah SJ, Chang RW, Lafyatis R, Varga J, Whitfield ML. Molecular signatures in skin associated with clinical improvement during mycophenolate treatment in systemic sclerosis. J Invest Dermatol. 2013 Aug;133(8):1979-89. doi: 10.1038/jid.2013.130. Epub 2013 Mar 14. PubMed PMID: 23677167; PubMed Central PMCID: PMC3714324.
Cheng C, Ung M, Grant GD, Whitfield ML. Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs. PLoS Comput Biol. 2013;9(7):e1003132. doi: 10.1371/journal.pcbi.1003132. Epub 2013 Jul 11. PubMed PMID: 23874175; PubMed Central PMCID: PMC3708869.
Lenna S, Farina AG, Martyanov V, Christmann RB, Wood TA, Farber HW, Scorza R, Whitfield ML, Lafyatis R, Trojanowska M. Increased expression of endoplasmic reticulum stress and unfolded protein response genes in peripheral blood mononuclear cells from patients with limited cutaneous systemic sclerosis and pulmonary arterial hypertension. Arthritis Rheum. 2013 May;65(5):1357-66. doi: 10.1002/art.37891. PubMed PMID: 23400395; PubMed Central PMCID: PMC3636187.
Grant GD, Gamsby J, Martyanov V, Brooks L 3rd, George LK, Mahoney JM, Loros JJ, Dunlap JC, Whitfield ML. Live-cell monitoring of periodic gene expression in synchronous human cells identifies Forkhead genes involved in cell cycle control. Mol Biol Cell. 2012 Aug;23(16):3079-93. doi: 10.1091/mbc.E11-02-0170. Epub 2012 Jun 27. PubMed PMID: 22740631; PubMed Central PMCID: PMC3418304.
Wei J, Fang F, Lam AP, Sargent JL, Hamburg E, Hinchcliff ME, Gottardi CJ, Atit R, Whitfield ML, Varga J. Wnt/β-catenin signaling is hyperactivated in systemic sclerosis and induces Smad-dependent fibrotic responses in mesenchymal cells. Arthritis Rheum. 2012 Aug;64(8):2734-45. doi: 10.1002/art.34424. PubMed PMID: 22328118; PubMed Central PMCID: PMC3553791.
Lakota K, Wei J, Carns M, Hinchcliff M, Lee J, Whitfield ML, Sodin-Semrl S, Varga J. Levels of adiponectin, a marker for PPAR-gamma activity, correlate with skin fibrosis in systemic sclerosis: potential utility as biomarker?. Arthritis Res Ther. 2012 May 1;14(3):R102. doi: 10.1186/ar3827. PubMed PMID: 22548780; PubMed Central PMCID: PMC3446479.
Pendergrass SA, Lemaire R, Francis IP, Mahoney JM, Lafyatis R, Whitfield ML. Intrinsic gene expression subsets of diffuse cutaneous systemic sclerosis are stable in serial skin biopsies. J Invest Dermatol. 2012 May;132(5):1363-73. doi: 10.1038/jid.2011.472. Epub 2012 Feb 9. PubMed PMID: 22318389; PubMed Central PMCID: PMC3326181.
Greenblatt MB, Sargent JL, Farina G, Tsang K, Lafyatis R, Glimcher LH, Whitfield ML, Aliprantis AO. Interspecies comparison of human and murine scleroderma reveals IL-13 and CCL2 as disease subset-specific targets. Am J Pathol. 2012 Mar;180(3):1080-1094. doi: 10.1016/j.ajpath.2011.11.024. Epub 2012 Jan 11. PubMed PMID: 22245215; PubMed Central PMCID: PMC3349888.
Allen JA, Peterson A, Sufit R, Hinchcliff ME, Mahoney JM, Wood TA, Miller FW, Whitfield ML, Varga J. Post-epidemic eosinophilia-myalgia syndrome associated with L-tryptophan. Arthritis Rheum. 2011 Nov;63(11):3633-9. doi: 10.1002/art.30514. PubMed PMID: 21702023; PubMed Central PMCID: PMC3848710.
Bhattacharyya S, Sargent JL, Du P, Lin S, Tourtellotte WG, Takehara K, Whitfield ML, Varga J. Egr-1 induces a profibrotic injury/repair gene program associated with systemic sclerosis. PLoS One. 2011;6(9):e23082. doi: 10.1371/journal.pone.0023082. Epub 2011 Sep 13. PubMed PMID: 21931594; PubMed Central PMCID: PMC3172216.
Sargent JL, Whitfield ML. Capturing the heterogeneity in systemic sclerosis with genome-wide expression profiling. Expert Rev Clin Immunol. 2011 Jul;7(4):463-73. doi: 10.1586/eci.11.41. Review. PubMed PMID: 21790289; PubMed Central PMCID: PMC3178333.
Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, Horlings HM, Shah N, Umbricht C, Wang P, Wang Y, Kong B, Langerød A, Børresen-Dale AL, Kim SK, van de Vijver M, Sukumar S, Whitfield ML, Kellis M, Xiong Y, Wong DJ, Chang HY. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet. 2011 Jun 5;43(7):621-9. doi: 10.1038/ng.848. PubMed PMID: 21642992; PubMed Central PMCID: PMC3652667.
Christmann RB, Hayes E, Pendergrass S, Padilla C, Farina G, Affandi AJ, Whitfield ML, Farber HW, Lafyatis R. Interferon and alternative activation of monocyte/macrophages in systemic sclerosis-associated pulmonary arterial hypertension. Arthritis Rheum. 2011 Jun;63(6):1718-28. doi: 10.1002/art.30318. PubMed PMID: 21425123; PubMed Central PMCID: PMC4030759.
Whitfield ML, Lafyatis R. Disease classification using molecular signatures. In: Varga J, editor. Scleroderma: From Pathogenesis to Comprehensive Management London: Springer; 2011. Chapter 8.
Katsumoto TR, Whitfield ML, Connolly MK. The pathogenesis of systemic sclerosis. Annu Rev Pathol. 2011;6:509-37. doi: 10.1146/annurev-pathol-011110-130312. Review. PubMed PMID: 21090968.
Wei J, Ghosh AK, Sargent JL, Komura K, Wu M, Huang QQ, Jain M, Whitfield ML, Feghali-Bostwick C, Varga J. PPARγ downregulation by TGFß in fibroblast and impaired expression and function in systemic sclerosis: a novel mechanism for progressive fibrogenesis. PLoS One. 2010 Nov 2;5(11):e13778. doi: 10.1371/journal.pone.0013778. PubMed PMID: 21072170; PubMed Central PMCID: PMC2970611.
Pendergrass SA, Hayes E, Farina G, Lemaire R, Farber HW, Whitfield ML, Lafyatis R. Limited systemic sclerosis patients with pulmonary arterial hypertension show biomarkers of inflammation and vascular injury. PLoS One. 2010 Aug 17;5(8):e12106. doi: 10.1371/journal.pone.0012106. PubMed PMID: 20808962; PubMed Central PMCID: PMC2923145.
Lemaire R, Farina G, Bayle J, Dimarzio M, Pendergrass SA, Milano A, Perbal B, Whitfield ML, Lafyatis R. Antagonistic effect of the matricellular signaling protein CCN3 on TGF-beta- and Wnt-mediated fibrillinogenesis in systemic sclerosis and Marfan syndrome. J Invest Dermatol. 2010 Jun;130(6):1514-23. doi: 10.1038/jid.2010.15. Epub 2010 Feb 25. PubMed PMID: 20182440; PubMed Central PMCID: PMC3071475.
Sargent JL, Milano A, Bhattacharyya S, Varga J, Connolly MK, Chang HY, Whitfield ML. A TGFbeta-responsive gene signature is associated with a subset of diffuse scleroderma with increased disease severity. J Invest Dermatol. 2010 Mar;130(3):694-705. doi: 10.1038/jid.2009.318. Epub 2009 Oct 8. PubMed PMID: 19812599; PubMed Central PMCID: PMC3867816.
Milks MW, Cripps JG, Lin H, Wang J, Robinson RT, Sargent JL, Whitfield ML, Gorham JD. The role of Ifng in alterations in liver gene expression in a mouse model of fulminant autoimmune hepatitis. Liver Int. 2009 Oct;29(9):1307-15. doi: 10.1111/j.1478-3231.2009.02028.x. Epub 2009 Apr 16. PubMed PMID: 19490417; PubMed Central PMCID: PMC3038248.
Chandriani S, Frengen E, Cowling VH, Pendergrass SA, Perou CM, Whitfield ML, Cole MD. A core MYC gene expression signature is prominent in basal-like breast cancer but only partially overlaps the core serum response. PLoS One. 2009 Aug 19;4(8):e6693. doi: 10.1371/journal.pone.0006693. PubMed PMID: 19690609; PubMed Central PMCID: PMC2723908.
MOLECULAR SIGNATURES FOR DIAGNOSING SCLERODERMA. United States US 2011/0190156 A1. 2009 July.
Varga J, Whitfield ML. Transforming growth factor-beta in systemic sclerosis (scleroderma). Front Biosci (Schol Ed). 2009 Jun 1;1(1):226-35. doi: 10.2741/s22. Review. PubMed PMID: 19482698.
Chung L, Fiorentino DF, Benbarak MJ, Adler AS, Mariano MM, Paniagua RT, Milano A, Connolly MK, Ratiner BD, Wiskocil RL, Whitfield ML, Chang HY, Robinson WH. Molecular framework for response to imatinib mesylate in systemic sclerosis. Arthritis Rheum. 2009 Feb;60(2):584-91. doi: 10.1002/art.24221. PubMed PMID: 19180499; PubMed Central PMCID: PMC2638060.
Beyrouthy MJ, Alexander KE, Baldwin A, Whitfield ML, Bass HW, McGee D, Hurt MM. Identification of G1-regulated genes in normally cycling human cells. PLoS One. 2008;3(12):e3943. doi: 10.1371/journal.pone.0003943. Epub 2008 Dec 15. PubMed PMID: 19079774; PubMed Central PMCID: PMC2600614.
Milano A, Pendergrass SA, Sargent JL, George LK, McCalmont TH, Connolly MK, Whitfield ML. Molecular subsets in the gene expression signatures of scleroderma skin. PLoS One. 2008 Jul 16;3(7):e2696. doi: 10.1371/journal.pone.0002696. PubMed PMID: 18648520; PubMed Central PMCID: PMC2481301.
Sargent JL, Milano A, Connolly MK, Whitfield ML. Scleroderma gene expression and pathway signatures. Curr Rheumatol Rep. 2008 Jul;10(3):205-11. doi: 10.1007/s11926-008-0034-5. Review. PubMed PMID: 18638428.
Emmons J, Townley-Tilson WH, Deleault KM, Skinner SJ, Gross RH, Whitfield ML, Brooks SA. Identification of TTP mRNA targets in human dendritic cells reveals TTP as a critical regulator of dendritic cell maturation. RNA. 2008 May;14(5):888-902. doi: 10.1261/rna.748408. Epub 2008 Mar 26. PubMed PMID: 18367721; PubMed Central PMCID: PMC2327351.
Andrew AS, Jewell DA, Mason RA, Whitfield ML, Moore JH, Karagas MR. Drinking-water arsenic exposure modulates gene expression in human lymphocytes from a U.S. population. Environ Health Perspect. 2008 Apr;116(4):524-31. doi: 10.1289/ehp.10861. PubMed PMID: 18414638; PubMed Central PMCID: PMC2290973.
Pendergrass SA, Whitfield ML, Gardner H. Understanding systemic sclerosis through gene expression profiling. Curr Opin Rheumatol. 2007 Nov;19(6):561-7. doi: 10.1097/BOR.0b013e3282f00375. Review. PubMed PMID: 17917536.
Townley-Tilson WH, Pendergrass SA, Marzluff WF, Whitfield ML. Genome-wide analysis of mRNAs bound to the histone stem-loop binding protein. RNA. 2006 Oct;12(10):1853-67. doi: 10.1261/rna.76006. Epub 2006 Aug 24. PubMed PMID: 16931877; PubMed Central PMCID: PMC1581977.
Cowling VH, Chandriani S, Whitfield ML, Cole MD. A conserved Myc protein domain, MBIV, regulates DNA binding, apoptosis, transformation, and G2 arrest. Mol Cell Biol. 2006 Jun;26(11):4226-39. doi: 10.1128/MCB.01959-05. PubMed PMID: 16705173; PubMed Central PMCID: PMC1489101.
Whitfield ML, George LK, Grant GD, Perou CM. Common markers of proliferation. Nat Rev Cancer. 2006 Feb;6(2):99-106. doi: 10.1038/nrc1802. Review. PubMed PMID: 16491069.
Jones SB, DePrimo SE, Whitfield ML, Brooks JD. Resveratrol-induced gene expression profiles in human prostate cancer cells. Cancer Epidemiol Biomarkers Prev. 2005 Mar;14(3):596-604. doi: 10.1158/1055-9965.EPI-04-0398. PubMed PMID: 15767336; PubMed Central PMCID: PMC3889115.
Whitfield ML, Kaygun H, Erkmann JA, Townley-Tilson WH, Dominski Z, Marzluff WF. SLBP is associated with histone mRNA on polyribosomes as a component of the histone mRNP. Nucleic Acids Res. 2004;32(16):4833-42. doi: 10.1093/nar/gkh798. Print 2004. PubMed PMID: 15358832; PubMed Central PMCID: PMC519100.
Murray JI, Whitfield ML, Trinklein ND, Myers RM, Brown PO, Botstein D. Diverse and specific gene expression responses to stresses in cultured human cells. Mol Biol Cell. 2004 May;15(5):2361-74. doi: 10.1091/mbc.e03-11-0799. Epub 2004 Mar 5. PubMed PMID: 15004229; PubMed Central PMCID: PMC404029.
Novoradovskaya N, Whitfield ML, Basehore LS, Novoradovsky A, Pesich R, Usary J, Karaca M, Wong WK, Aprelikova O, Fero M, Perou CM, Botstein D, Braman J. Universal Reference RNA as a standard for microarray experiments. BMC Genomics. 2004 Mar 9;5(1):20. doi: 10.1186/1471-2164-5-20. PubMed PMID: 15113400; PubMed Central PMCID: PMC394318.
Zhao H, Whitfield ML, Xu T, Botstein D, Brooks JD. Diverse effects of methylseleninic acid on the transcriptional program of human prostate cancer cells. Mol Biol Cell. 2004 Feb;15(2):506-19. doi: 10.1091/mbc.e03-07-0501. Epub 2003 Nov 14. PubMed PMID: 14617803; PubMed Central PMCID: PMC329225.
Whitfield ML, Finlay DR, Murray JI, Troyanskaya OG, Chi JT, Pergamenschikov A, McCalmont TH, Brown PO, Botstein D, Connolly MK. Systemic and cell type-specific gene expression patterns in scleroderma skin. Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12319-24. doi: 10.1073/pnas.1635114100. Epub 2003 Oct 6. PubMed PMID: 14530402; PubMed Central PMCID: PMC218756.
Allard P, Champigny MJ, Skoggard S, Erkmann JA, Whitfield ML, Marzluff WF, Clarke HJ. Stem-loop binding protein accumulates during oocyte maturation and is not cell-cycle-regulated in the early mouse embryo. J Cell Sci. 2002 Dec 1;115(Pt 23):4577-86. doi: 10.1242/jcs.00132. PubMed PMID: 12415002; PubMed Central PMCID: PMC5115915.
Zhao H, Hastie T, Whitfield ML, Børresen-Dale AL, Jeffrey SS. Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis. BMC Genomics. 2002 Oct 30;3(1):31. doi: 10.1186/1471-2164-3-31. Epub 2002 Oct 30. PubMed PMID: 12445333; PubMed Central PMCID: PMC137577.
Whitfield ML, Sherlock G, Saldanha AJ, Murray JI, Ball CA, Alexander KE, Matese JC, Perou CM, Hurt MM, Brown PO, Botstein D. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell. 2002 Jun;13(6):1977-2000. doi: 10.1091/mbc.02-02-0030. PubMed PMID: 12058064; PubMed Central PMCID: PMC117619.
Richardson RT, Batova IN, Widgren EE, Zheng LX, Whitfield M, Marzluff WF, O'Rand MG. Characterization of the histone H1-binding protein, NASP, as a cell cycle-regulated somatic protein. J Biol Chem. 2000 Sep 29;275(39):30378-86. doi: 10.1074/jbc.M003781200. PubMed PMID: 10893414.
Whitfield ML, Zheng LX, Baldwin A, Ohta T, Hurt MM, Marzluff WF. Stem-loop binding protein, the protein that binds the 3' end of histone mRNA, is cell cycle regulated by both translational and posttranslational mechanisms. Mol Cell Biol. 2000 Jun;20(12):4188-98. doi: 10.1128/MCB.20.12.4188-4198.2000. PubMed PMID: 10825184; PubMed Central PMCID: PMC85788.
Marzluff WF, Whitfield ML, Dominski Z, Wang ZF. Identification of the Protein That Interacts with the 3' End of Histone mRNA.. In: Richter JD, editor. mRNA Formation and Function New York: Academic Press; 1997. p.163-193.
Wang ZF, Whitfield ML, Ingledue TC 3rd, Dominski Z, Marzluff WF. The protein that binds the 3' end of histone mRNA: a novel RNA-binding protein required for histone pre-mRNA processing. Genes Dev. 1996 Dec 1;10(23):3028-40. doi: 10.1101/gad.10.23.3028. PubMed PMID: 8957003.
Dominski Z, Sumerel J, Hanson RJ, Whitfield ML, Marzluff WF. The polyribosomal protein bound to the 3' end of histone mRNA can function in histone pre-mRNA processing. Nucleic Acids Symp Ser. 1995;(33):234-6. PubMed PMID: 8643381.
Grant GD, Parker JJ, Whitfield ML. Identification of FOXM1 targets in a genome-wide analysis of periodic gene expression. American Society for Cell Biology; 2007; c00.
Chung L, Fiorentino DF, Benbarak MJ, Adler AS, Mariano MM, Panigua RT, Milano A, Connolly MK, Ratiner BD, Wiskocil RL, Whitfield ML, Chang HY, Robinson WH. Molecular Framework for Response to Imatinib in Systemic Sclerosis. American College of Rheumatology Annual Meeting; 2008; c00.
Sargent JL, Milano A, Bhattacharyya S, Varga J, Chang HY, Connolly MK, Whitfield ML. A transforming growth factor-b (TGFb)-responsive gene signature predicts more severe skin disease and occurrence of interstitial lung disease (ILD) in diffuse cutaneous systemic sclerosis (dcSSc). American College of Rheumatology Annual Meeting; 2007; c00.
George LK, Whitfield ML. Identification of a novel cell cycle-regulated gene involved in maintaining spindle bipolarity. American Society for Cell Biology; 2007; c00.
Sargent JL, Aliprantis AO, Lemaire R, Lafyatis R, Glimcher L, Whitfield ML. Microarray Analysis of Murine cGVHD as an Animal Model for Human Systemic Sclerosis. 10th International Workshop on Scleroderma Research; 2008; c00.
Ghosh A, Wu M, Melichian D, Sargent JL, Milano A, Connolly MK, Whitfield ML, Varga J. Novel Function of PPAR-g: Endogenous Anti-fibrotic that Ameliorates Murine Scleroderma and May be Defective in Systemic Sclerosis (SSc). American College of Rheumatology Annual Meeting; 2007; c00.
Pendergrass SA, Lemaire R, Lafyatis RA, Whitfield ML. Reproducible And Stable Gene Expression Subsets In Serial Skin Biopsies Taken From Patients Treated In An Open-label Trial Of Rituximab. American College of Rheumatology Annual Meeting; 2008; c00.
Wei J, Leng E, Sargent JL, Whitfield ML, Lam A, Gottardi C, Varga J. Profibrotic Wnt Signaling in Human Mesenchymal Cells: Implications for Scleroderma. American College of Rheumatology Annual Meeting; 2009; c00.
Milano A, Pendergrass SA, Sargent JL, Dou X, Connolly MK, Whitfield ML. Molecular subtypes of systemic sclerosis (SSc) from gene expression signatures. American College of Rheumatology Annual Meeting; 2007; c00.
Sargent JL, Aliprantis AO, Greenblatt MB, Wu M, Farina GA, Lemaire R, Glimcher LH, Clark SH, Varga J, Lafyatis R, Whitfield ML. Distinct Deregulated Pathways Underlie the Molecular Subsets of Scleroderma and Are Recapitulated in Animal Models. American College of Rheumatology Annual Meeting; 2009; c00.