https://www.um.edu.mt/library/oar/handle/123456789/484 2026-04-16T14:59:22Z https://www.um.edu.mt/library/oar/handle/123456789/143490 Title: Gene amplifications associated with primary colorectal cancer tumours and matched lymph nodes Abstract: Colorectal cancer is among the most commonly diagnosed malignancies worldwide, with metastasis being the leading cause of mortality. CRC is a genetically heterogenous disease driven by a multitude of genomic alterations. Gene amplifications contribute to tumour progression, metastasis and therapy resistance by increasing the copy number of specific DNA sequences, thus leading to overexpression of genes that can alter signalling pathways, cell proliferation and survival. This study aimed to investigate gene amplifications in primary CRC tumours and matched metastatic lymph nodes to better understand their role in metastatic progression. While many studies focus on gene mutations in CRC, there is a relative lack of research on gene amplifications and their correlations with gene expression in matched tissue samples. Gene expression analysis of both the primary tumours and the matched metastatic lymph nodes was performed using the QuantiGene™ Plex assay, revealing high expression of several genes in the primary tumours, namely MET, GNAS, IGF2, TOP1, MTIF3, CDX2, MYC, MCL1 and KLF5. Four genes – MET, GNAS, IGF2 and TOP1 – were selected for analysis on matched lymph nodes with ddPCR using primer/probe sets designed in-house. IHC staining with FN1 was also done on a select number of cases to assess protein expression levels. Of interest, comparing the presence of amplifications with the gene expression in matched primary tumours, high IGF2 expression in the primary tumour was observed in the amplified samples. ddPCR analysis of CNVs in lymph nodes, resulted in amplification frequency of MET (58.3%), GNAS (45.8%), IGF2 (6.25%) and TOP1 (95.8%) in lymph nodes (n=48). Overall, correlation of gene expression and CNV was low and hence, these findings suggest that measuring both will give a more comprehensive understanding of metastatic progression. Study limitations included degradation over the years in the FFPE material used and a limited sample size, restricting the statistical power and limiting data analysis to visual interpretation via box plots. Despite these consstraints, this study establishes the basis for further studies, primarily the comparison of matched primary tumours and lymph nodes, including comparisons with matched invasion fronts and tumour buds, an emerging histological characteristic that is currently being investigated. Description: M.Sc.(Melit.) 2025-01-01T00:00:00Z https://www.um.edu.mt/library/oar/handle/123456789/142799 Title: Measuring the population attributable fraction and the potential impact fraction of dementia risk factors in Malta : a population based secondary data analysis Authors: Scerri, Anthony; Scerri, Charles Abstract: Background: The 2024 Lancet Commission report estimated that up to 45% of global dementia cases could be prevented by addressing modifiable risk factors. However, these estimates are based on international data and may not reflect national differences in risk factor prevalence or intervention feasibility. This study uses a population-based secondary data analysis to estimate both the population attributable fraction (PAF) and the potential impact fraction (PIF) for 14 dementia risk factors specific to the Maltese population.; Design and methods: Secondary data were used to estimate the prevalence of each risk factor from Maltese peer-reviewed studies or reputable international datasets where national data were unavailable. Unweighted PAFs were calculated using Levin’s formula and adjusted for overlap between risk factors. PIFs were derived by applying evidence-based relative risk reductions from published intervention studies for each weighted PAF, representing more realistic outcomes of targeted interventions.; Results: The weighted PAF for Malta was 40.47%, indicating the theoretical maximum proportion of preventable dementia cases if all risk factors were eliminated. The total PIF was 33.82%, reflecting the estimated reduction in dementia incidence if feasible interventions were implemented. The risk factors contributing most to preventable cases were high LDL cholesterol (6.15%), loneliness (4.29%), and untreated vision loss (4.25%).; Conclusions: Up to one-third of dementia cases in Malta could be reduced through population-level strategies targeting modifiable risk factors. These PIF estimates provide realistic, evidence-informed guidance for national dementia prevention planning and prioritisation. 2025-01-01T00:00:00Z https://www.um.edu.mt/library/oar/handle/123456789/142779 Title: Genomic locus tagged by lung function GWAS SNV rs12477314 (2q37. 3) acts as a regulatory region for a systemic inflammatory phenotype Authors: Grech, Godwin M.; Fawcett, Katherine A.; Hall, Robert J.; Grech, Godfrey; Ellul-Micallef, Roger; Hall, Ian P.; Fenech, Anthony G. Abstract: SNV rs12477314 (C>T; 1000G MAF = 0.14), which maps to an intergenic region on 2q37.3, is a genome-wide significant association signal for pulmonary function in genome-wide association study meta-analyses. Bioinformatic analysis revealed that the intergenic region in proximity to the sentinel SNV is enriched for histone methylation markers suggestive of active enhancer regions modifiable by DNA methylation. The aim of this study was to investigate the functionality of putative enhancer/s and their potential interaction with CpG islands in the genomic region tagged by rs12477314 and their relevance to lung disease, in particular COPD. Two independent CRISPR/Cas9n-targeted deletions of the putative enhancer/s were performed in an airway epithelial cell line (NCI-H460). Deletion clones were subjected to RNA-Seq, and differential expression gene (DEG) datasets were generated using the Cufflinks version 2.2.1 pipeline (p-FDR < 0.05). Biological pathway analysis was performed using Qiagen's Ingenuity Pathway Analysis. Associations with the blood proteome were explored in UK Biobank. Our results suggest that the deleted regions are co-acting enhancers regulating overlapping gene expression patterns. The DEG datasets from the two genomic deletions are enriched for similar canonical pathways, which may contribute to a pro-inflammatory phenotype. Pathway-based regulatory effects analysis of the two DEG datasets resulted in identifying potential downstream biological processes. There was overlap between the pathways identified in protein association datasets and the DEG datasets. Our results suggest that the genomic region tagged by SNV rs12477314 constitutes a regulatory region responsible for regulating biological pathways conducive to a systemic inflammatory phenotype. 2025-01-01T00:00:00Z https://www.um.edu.mt/library/oar/handle/123456789/141456 Title: The prevalence of tunnelled line-associated MRSA and MSSA bacteraemias in a Maltese haemodialysis patient cohort between 2017 and 2024 Authors: Farrugia, Elena; Sultana, George; De Silva, Peththawadu Thihan Daksitha; Azzopardi, Abigail; Lal, Athira; Farrugia, Emanuel; Borg, Michael Angelo; Scicluna, Elizabeth; Farrugia, Claire; Vassallo, Diana Abstract: Background and Aims: Sepsis is the second most common cause of death in haemodialysis patients and patients dialysing through tunnelled dialysis lines have a 2 to 3-fold increased risk of hospitalization for infection and death compared to patients dialysing through an arteriovenous fistula or graft. This is the first audit looking at the prevalence of catheter-related blood stream infections (CRBSI) in patients receiving haemodialysis via a tunnelled line in Malta. Our aims are to benchmark local data to UK renal registry data and to assess clinical outcomes. 2025-01-01T00:00:00Z