28 Jun

Machine learning for ADA risk prediction

In collaboration with UCL, Charles University in Prague and the Karolinska Institute we have a poster at ISMB 2022 (Madison US) with the title “Using Metabolomic and Transcriptomic profiles to Predict Development of Anti- IFNβ Antibodies in people with Relapsing Remitting Multiple Sclerosis”.

Abstract

Anti-drug antibodies (ADA) reduces treatment efficacy in multiple sclerosis (MS) patients. Predisposing factors for ADA are poorly characterised, creating an unmet need for biomarkers to predict ADA and subsequent treatment failure. A multiomic approach was used to predict ADA development in interferon-beta (IFNβ) treated MS patients.
Serum was collected from MS patients, through the ABIRISK consortium, before and 3 months after IFNβ treatment. ADA status was determined after 12 months on IFNβ. Supervised machine learning, including logistic regression and sPLS-DA, were used to predict ADA status using metabolomic data (n=82), while transcriptomic profiles were examined in matched patients (n=11).
Before treatment, machine learning models classified patients with an accuracy ≈84%, while lipid metabolism gene counts clustered patients by ADA status, suggesting disrupted lipid metabolism amongst ADA+ patients. Strong correlations between these gene counts and metabolite concentrations were observed. Furthermore, ADA+ patients had distinct responses to IFNβ at month 3, showing differentially regulated metabolites and a down regulation of interferon signalling genes previously associated with response to IFNβ. This could predict ADA early in the treatment course.
Metabolomics and transcriptomics are promising tools for prediction of ADA in IFNβ treated MS patients and could provide novel insight into mechanisms of immunogenicity.

30 Oct

AI approaches in chronic inflammatory disease

Together with scientist from UCL, we have written a review article covering AI technologies in the field of chronic inflammatory disease. 

Machine Learning Techniques for Personalised Medicine Approaches in Immune-Mediated Chronic Inflammatory Diseases: Applications and Challenges. Peng J, Jury EC, Dönnes P, Ciurtin C. Front Pharmacol. 2021 Sep 30;12:720694. doi: 10.3389/fphar.2021.720694. eCollection 2021.

Pubmed

30 Sep

Covid-19 publications

Check out the latest Covid-19 related publications. SciCross main contributions in these projects has been the design of Sars-CoV-2 peptides used to study T-cell responses. 

An evaluation of a FluoroSpot assay as a diagnostic tool to determine SARS-CoV-2 specific T cell responses, PLoS One. 2021 Sep 30;16(9):e0258041, https://pubmed.ncbi.nlm.nih.gov/34591918/

Robust humoral and cellular immune responses and low risk for reinfection at least 8 months following asymptomatic to mild COVID-19, J Intern Med. 2021 Aug 30, https://pubmed.ncbi.nlm.nih.gov/34459525/

07 May

Covid-19 therapy

SciCross partners with scientists from Uppsala University, KTH and SciLifeLab in developing Covid-19 treatments in immune suppressed individuals. The project is called “An adaptable therapeutic technology platform to treat SARS-CoV infections in immune suppressed individuals” and has received funding from SciLifeLab and Knut and Alice Wallenberg Foundation (https://kaw.wallenberg.org/). SciCross focus will be on identifying parts in the SARS-CoV-2 genome that can elicit an immune response towards the virus. More details about the project will follow soon.

Structure of the SARS-CoV-2 spike glycoprotein, PDB:6VXX.
20 Dec

Early Christmas present

Great news before Christmas. SciCross is part of a project receiving funding from the Swedish Knowledge Foundation. The project title is “Biomedical AI-driven data analytics” (BIO-AID) and will start in 2020. The project will focus on how AI/Machine learning approaches can be designed and applied in Life Science. Coordinated by the University of Skövde, other project members include Merck, Takarabio, MultiD and TATAA Biocenter.

Read more at: https://www.mynewsdesk.com/se/his/pressreleases/miljonregn-oever-projekt-paa-hoegskolan-i-skoevde-2954981 (Swedish only)



31 May

Paper on adalimumab and infliximab anti-drug antibodies in rheumatoid arthritis patients

A recent paper originating from ABIRISK research has been made available online. The paper presents an analysis of retrospective data in European cohort of RA patients treated with adalimumab or infliximab.

The paper with title “Incidence and risk factors for adalimumab and infliximab anti-drug antibodies in rheumatoid arthritis: A European retrospective multicohort analysis” has been published in Seminars in Arthritis and Rheumatism:https://www.sciencedirect.com/science/article/pii/S0049017218301768