Dr Elisabetta Sciacca, PhD, MEng, BEng

Profile

Elisabetta Sciacca is a biomedical data scientist with major focus on applied statistics for RNA-sequencing data. 
She is part of  the bioinformatics team led by Dr. Myles Lewis at Experimental Medicine and Rheumatology, engaged in the MATURA consortium and the 3TR project.

Her work at EMR focuses on the development and validation of transcriptomic-based models for classifying and predicting treatment response in rheumatoid arthritis and other autoimmune disesases. She is author of 'DEGGs', a novel network-based R package able to detect differential, functionally relevant gene-gene interactions between subgroups of patients for personalised/stratified medicine. The tool makes use of robust linear modelling incorporating interaction terms to statistically evaluate the predictability of those gene-gene pairs that are significantly associated with phenotipical features (e.g. response to treatment). The tool can be also used as feature selection method in machine learning pipelines. 

Elisabetta is also interested in data visualisation of big clinical data and dissemination of results through interactive data web portals. She is major author of an R shiny-based website to allow exploration of RNA-sequencing data on blood and salivary gland biopsies from the TRACTISS cohort. This portal provide in-depth interrogation of the data by allowing researchers to directly compare salivary gland and blood genes in Sjogren's syndrome and see how gene expression correlates with clinical features and response to therapy.

Research

Publications

Published with EMR

Sciacca, E., Alaimo, S., Silluzio, G., Ferro, A., Latora, V., Pitzalis, C., ... & Lewis, M. J. (2023). DEGGs: an R package with shiny app for the identification of differentially expressed gene–gene interactions in high-throughput sequencing data. Bioinformatics, 39(4), btad192.

Mauro, D., Manou-Stathopoulou, S., Rivellese, F., Sciacca, E., Goldmann, K., Tsang, V., ... & Lewis, M. J. (2023). UBE2L3 regulates TLR7-induced B cell autoreactivity in Systemic Lupus Erythematosus. Journal of Autoimmunity, 136, 103023.

Rivellese, F., Surace, A. E., Goldmann, K., Sciacca, E., Çubuk, C., Giorli, G., ... & Pitzalis, C. (2022). Rituximab versus tocilizumab in rheumatoid arthritis: synovial biopsy-based biomarker analysis of the phase 4 R4RA randomized trial. Nature medicine, 28(6), 1256-1268.

Sciacca, E., Surace, A. E., Alaimo, S., Pulvirenti, A., Rivellese, F., Goldmann, K., ... & Lewis, M. J. (2022). Network analysis of synovial RNA sequencing identifies gene-gene interactions predictive of response in rheumatoid arthritis. Arthritis Research & Therapy, 24(1), 1-14.

Pontarini, E., Sciacca, E., Grigoriadou, S., Rivellese, F., Lucchesi, D., Fossati-Jimack, L., ... & Bombardieri, M. (2021). NKp30 receptor upregulation in salivary glands of Sjögren’s syndrome characterizes ectopic lymphoid structures and is restricted by rituximab treatment. Frontiers in immunology, 12, 706737.

Pontarini, E., Chowdhury, F., Sciacca, E., Grigoriadou, S., Murray-Brown, W., Rivellese, F., ... & Bombardieri, M. (2022). POS0145 CLINICAL RESPONSE TO RITUXIMAB IS ASSOCIATED WITH PREVENTION OF B-CELL DRIVEN SALIVARY GLAND INFLAMMATION AND EPITHELIAL RESTORATION AS REVEALED BY MOLECULAR PATHOLOGY: RESULTS FROM THE TRACTISS TRIAL IN PRIMARY SJOGREN’S SYNDROME.

Rivellese, F., Cubuk, C., Surace, A., Goldmann, K., Sciacca, E., Giorli, G., ... & Pitzalis, C. (2022). OP0085 CELL LINEAGE-SPECIFIC TRANSCRIPT DECONVOLUTION OF SYNOVIAL BIOPSIES FROM THE R4RA TRIAL IDENTIFIES CELL POPULATIONS ASSOCIATED WITH RESPONSE TO RITUXIMAB AND TOCILIZUMAB.

Nerviani, A., Boutet, M. A., Ghirardi, G. M., Goldmann, K., Sciacca, E., Rivellese, F., ... & Pitzalis, C. (2022). POS0441 IN-DEPTH ANALYSIS OF Axl AND MerTK EXPRESSION PATTERNS AND REGULATION BY BIOLOGIC TREATMENTS IN RHEUMATOID ARTHRITIS.

Surace, A., Sciacca, E., Goldmann, K., Rivellese, F., Cubuk, C., Giorli, G., ... & Pitzalis, C. (2022). OP0077 SYNOVIAL RNA-SEQ ANALYSIS OF THE R4RA TRIAL IDENTIFIES SIGNATURES OF TREATMENT RESISTANCE AND REFRACTORY STATE IN RHEUMATOID ARTHRITIS.

Pontarini, E., Chowdhury, F., Sciacca, E., Grigoriadou, S., Rivellese, F., Lucchesi, D., ... & Bombardieri, M. (2021). OP0136 Rituximab Prevents the Progression of B-Cell Driven Inflammatory Infiltrate in the Minor Salivary Glands of Primary Sjogren’s Syndrome by Downregulating Immunological Pathways Key in Ectopic Germinal Centre Organization: Results From the Tractiss Trial.

Sciacca, E., Alaimo, S., Pulvirenti, A., Latora, V., Humby, F., Ferro, A., ... & Pitzalis, C. (2020). P22 Micro-RNA enriched pathway impact analysis applied to synovial RNA-seq in early rheumatoid arthritis identifies response prediction pathways. Rheumatology, 59(Supplement_2), keaa111-021.

Rivellese, F., Humby, F., Ribera, G. L., Nerviani, A., Sciacca, E., Giorli, G., ... & Pitzalis, C. (2020). OP0217 INVOLVEMENT OF LARGE JOINTS AT DISEASE PRESENTATION IS ASSOCIATED WITH DIVERSE HISTOPATHOLOGICAL FEATURES AND CLINICAL OUTCOMES IN EARLY RHEUMATOID ARTHRITIS.