Publications

Longitudinal pathway analysis using structural information with case studies in early type 1 diabetes

Maria K Jaakkola et al.

Sci Rep. 2025 May 2;15(1):15393. doi: 10.1038/s41598-025-98492-0.

Pathway analysis is a frequent step in studies involving gene or protein expression data, but most of the available pathway methods are designed for simple case versus control studies of two sample groups without further complexity. The few available methods allowing the pathway analysis of more complex study designs cannot use pathway structures or handle the situation where the variable of interest is not defined for all samples. Such scenarios are common in longitudinal studies with so long...

Clonal hematopoiesis is associated with distinct rheumatoid arthritis phenotypes

Emil Hiitola et al.

Sci Adv. 2025 May 2;11(18):eadt9846. doi: 10.1126/sciadv.adt9846. Epub 2025 Apr 30.

Clonal hematopoiesis (CH) becomes more prevalent with aging and may influence inflammatory diseases by altering immune function. While CH of indeterminate potential (CHIP) promotes inflammation in nonmalignant conditions, its relationship with rheumatoid arthritis (RA) remains unknown. We analyzed CHIP mutations in RA using two population-level cohorts and patients with newly diagnosed RA. CHIP was associated with prevalent RA in 10,089 FINRISK study participants with whole-exome sequencing (OR,...

Evaluation of Integrin Glycovariants as Biomarkers of Metastasis, Invasion, and Therapy Stratification in Head and Neck Squamous Cell Carcinoma

Erica Routila et al.

Cancer Med. 2025 May;14(9):e70717. doi: 10.1002/cam4.70717.

CONCLUSIONS: We demonstrate that while integrin glycovariants are abundant in HNSCC tumors and ITGB1-WFL was associated with invasiveness, integrin glycovariants do not directly correlate with metastatic behavior. Further, serum ITGA2-UEA appeared as a potential radioresponse biomarker.

Novel Genetic Risk Variants Associated with Oral Tongue Squamous Cell Carcinoma

Rayan Nikkilä et al.

Head Neck Pathol. 2025 Apr 25;19(1):45. doi: 10.1007/s12105-025-01784-0.

CONCLUSION: The GWAS detected two novel genetic associations with OTSCC. Further research is needed to identify the genes at these loci that contribute to the molecular pathogenesis of OTSCC.

Histological tumor necrosis predicts decreased survival after neoadjuvant chemotherapy in head and neck squamous cell carcinoma

A R Koskenniemi et al.

Oral Oncol. 2025 Jun;165:107287. doi: 10.1016/j.oraloncology.2025.107287. Epub 2025 Apr 16.

CONCLUSIONS: Detection of tumor necrosis and AI-driven deep learning effectively predict neoadjuvant RT/CRT responses in HNSCC.

Heat shock factor 2 regulates oncogenic gamma-herpesvirus gene expression by remodeling the chromatin at the ORF50 and BZLF1 promoter

Lorenza Cutrone et al.

PLoS Pathog. 2025 Apr 17;21(4):e1013108. doi: 10.1371/journal.ppat.1013108. eCollection 2025 Apr.

The Human gamma-herpesviruses Kaposi's sarcoma herpesvirus (KSHV) and Epstein-Barr virus (EBV) are causally associated to a wide range of cancers. While the default infection program for these viruses is latent, sporadic lytic reactivation supports virus dissemination and oncogenesis. Despite its relevance, the repertoire of host factors governing the transition from latent to lytic phase is not yet complete, leaving much of this complex process unresolved. Here we show that heat shock factor 2...