Publications

OTUD6B-AS1 Might Be a Novel Regulator of Apoptosis in Systemic Sclerosis.
Takata M, Pachera E, Frank-Bertoncelj M, Kozlova A, Jungel A, Whitfield ML, Assassi S, Calcagni M, de Vries-Bouwstra J, Huizinga TW, Kurreeman F, Kania G, Distler O
Front Immunol. 2019;10:1100. doi: 10.3389/fimmu.2019.01100. Epub 2019 May 17.
PMID: 31156645

Senescence signature in skin biopsies from systemic sclerosis patients treated with senolytic therapy: potential predictor of clinical response?
Martyanov V, Whitfield ML, Varga J
Arthritis Rheumatol. 2019 May 21; doi: 10.1002/art.40934. Epub 2019 May 21.
PMID: 31112009

A Machine Learning Classifier for Assigning Individual Patients with Systemic Sclerosis to Intrinsic Molecular Subsets.
Franks JM, Martyanov V, Cai G, Wang Y, Li Z, Wood TA, Whitfield ML
Arthritis Rheumatol. 2019 Mar 28; doi: 10.1002/art.40898. Epub 2019 Mar 28.
PMID: 30920766

BioMethyl: An R package for Biological Interpretation of DNA Methylation Data.
Wang Y, Franks JM, Whitfield ML, Cheng C
Bioinformatics. 2019 Feb 25; pii: btz137. doi: 10.1093/bioinformatics/btz137. Epub 2019 Feb 25.
PMID: 30799505

Microbiome dysbiosis is associated with disease duration and increased inflammatory gene expression in systemic sclerosis skin.
Johnson ME, Franks JM, Cai G, Mehta BK, Wood TA, Archambault K, Pioli PA, Simms RW, Orzechowski N, Arron S, Whitfield ML
Arthritis Res Ther. 2019 Feb 6;21(1):49. doi: 10.1186/s13075-019-1816-z. Epub 2019 Feb 6.
PMID: 30728065

Lysyl oxidase enzymes mediate TGF-β1-induced fibrotic phenotypes in human skin-like tissues.
Huang M, Liu Z, Baugh L, DeFuria J, Maione A, Smith A, Kashpur O, Black Iii LD, Georgakoudi I, Whitfield ML, Garlick J
Lab Invest. 2019 Apr;99(4):514-527. doi: 10.1038/s41374-018-0159-8. Epub 2018 Dec 19.
PMID: 30568176

Patients with systemic sclerosis-associated pulmonary arterial hypertension express a genomic signature distinct from patients with interstitial lung disease.
Moll M, Christmann RB, Zhang Y, Whitfield ML, Wang YM, Rice L, Stratton E, Lafyatis R, Farber HW
J Scleroderma Relat Disord. 2018 Oct;3(3):242-248. doi: 10.1177/2397198318764780. Epub 2018 Mar 22.
PMID: 30498788

The mechanistic implications of gene expression studies in SSc: Insights from Systems Biology.
Taroni JN, Mahoney JM, Whitfield ML
Curr Treatm Opt Rheumatol. 2017 Sep;3(3):181-192. doi: 10.1007/s40674-017-0072-0. Epub 2017 Jul 29.
PMID: 29520335

Mycophenolate Mofetil Treatment of Systemic Sclerosis Reduces Myeloid Cell Numbers and Attenuates the Inflammatory Gene Signature in Skin.
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
J Invest Dermatol. 2018 Jun;138(6):1301-1310. doi: 10.1016/j.jid.2018.01.006. Epub 2018 Jan 31.
PMID: 29391252

Feature specific quantile normalization enables cross-platform classification of molecular subtypes using gene expression data.
Franks JM, Cai G, Whitfield ML
Bioinformatics. 2018 Jun 1;34(11):1868-1874. doi: 10.1093/bioinformatics/bty026.
PMID: 29360996

Antisense Long Non-Coding RNAs Are Deregulated in Skin Tissue of Patients with Systemic Sclerosis.
Messemaker TC, Chadli L, Cai G, Goelela VS, Boonstra M, Dorjee 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
J Invest Dermatol. 2018 Apr;138(4):826-835. doi: 10.1016/j.jid.2017.09.053. Epub 2017 Nov 24.
PMID: 29179949

Novel lung imaging biomarkers and skin gene expression subsetting in dasatinib treatment of systemic sclerosis-associated interstitial lung disease.
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
PLoS One. 2017;12(11):e0187580. doi: 10.1371/journal.pone.0187580. Epub 2017 Nov 9.
PMID: 29121645

Belimumab for the Treatment of Early Diffuse Systemic Sclerosis: Results of a Randomized, Double-Blind, Placebo-Controlled, Pilot Trial.
Gordon JK, Martyanov V, Franks JM, Bernstein EJ, Szymonifka J, Magro C, Wildman HF, Wood TA, Whitfield ML, Spiera RF
Arthritis Rheumatol. 2018 Feb;70(2):308-316. doi: 10.1002/art.40358. Epub 2017 Dec 29.
PMID: 29073351

Limited cutaneous systemic sclerosis skin demonstrates distinct molecular subsets separated by a cardiovascular development gene expression signature.
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
Arthritis Res Ther. 2017 Jul 4;19(1):156. doi: 10.1186/s13075-017-1360-7. Epub 2017 Jul 4.
PMID: 28676069

Population effect model identifies gene expression predictors of survival outcomes in lung adenocarcinoma for both Caucasian and Asian patients.
Cai G, Xiao F, Cheng C, Li Y, Amos CI, Whitfield ML
PLoS One. 2017;12(4):e0175850. doi: 10.1371/journal.pone.0175850. Epub 2017 Apr 20.
PMID: 28426704

A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis.
Taroni JN, Greene CS, Martyanov V, Wood TA, Christmann RB, Farber HW, Lafyatis RA, Denton CP, Hinchcliff ME, Pioli PA, Mahoney JM, Whitfield ML
Genome Med. 2017 Mar 23;9(1):27. doi: 10.1186/s13073-017-0417-1. Epub 2017 Mar 23.
PMID: 28330499

Myeloid Cells That Impair Immunotherapy Are Restored in Melanomas with Acquired Resistance to BRAF Inhibitors.
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
Cancer Res. 2017 Apr 1;77(7):1599-1610. doi: 10.1158/0008-5472.CAN-16-1755. Epub 2017 Feb 15.
PMID: 28202513

Integrated, multicohort analysis of systemic sclerosis identifies robust transcriptional signature of disease severity.
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
JCI Insight. 2016 Dec 22;1(21):e89073. doi: 10.1172/jci.insight.89073. Epub 2016 Dec 22.
PMID: 28018971

A Functional Genomic Meta-Analysis of Clinical Trials in Systemic Sclerosis: Toward Precision Medicine and Combination Therapy.
Taroni JN, Martyanov V, Mahoney JM, Whitfield ML
J Invest Dermatol. 2017 May;137(5):1033-1041. doi: 10.1016/j.jid.2016.12.007. Epub 2016 Dec 21.
PMID: 28011145

A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues.
Lyons SM, Cunningham CH, Welch JD, Groh B, Guo AY, Wei B, Whitfield ML, Xiong Y, Marzluff WF
Nucleic Acids Res. 2016 Nov 2;44(19):9190-9205. Epub 2016 Jul 8.
PMID: 27402160

Identification of Optimal Mouse Models of Systemic Sclerosis by Interspecies Comparative Genomics.
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
Arthritis Rheumatol. 2016 Aug;68(8):2003-15. doi: 10.1002/art.39658.
PMID: 26945694

Stress granules and RNA processing bodies are novel autoantibody targets in systemic sclerosis.
Johnson ME, Grassetti AV, Taroni JN, Lyons SM, Schweppe D, Gordon JK, Spiera RF, Lafyatis R, Anderson PJ, Gerber SA, Whitfield ML
Arthritis Res Ther. 2016 Jan 22;18:27. doi: 10.1186/s13075-016-0914-4. Epub 2016 Jan 22.
PMID: 26801089

Molecular stratification and precision medicine in systemic sclerosis from genomic and proteomic data.
Martyanov V, Whitfield ML
Curr Opin Rheumatol. 2016 Jan;28(1):83-8. doi: 10.1097/BOR.0000000000000237.
PMID: 26555452

A multiprotein occupancy map of the mRNP on the 3' end of histone mRNAs.
Brooks L 3rd, Lyons SM, Mahoney JM, Welch JD, Liu Z, Marzluff WF, Whitfield ML
RNA. 2015 Nov;21(11):1943-65. doi: 10.1261/rna.053389.115. Epub 2015 Sep 16.
PMID: 26377992

Nilotinib (Tasigna™) in the treatment of early diffuse systemic sclerosis: an open-label, pilot clinical trial.
Gordon JK, Martyanov V, Magro C, Wildman HF, Wood TA, Huang WT, Crow MK, Whitfield ML, Spiera RF
Arthritis Res Ther. 2015 Aug 18;17:213. doi: 10.1186/s13075-015-0721-3. Epub 2015 Aug 18.
PMID: 26283632