Background <5% of medulloblastoma patients survive following failure of contemporary radiation-based therapies. Understanding the molecular drivers of medulloblastoma relapse (rMB) will be essential to improve outcomes. Initial genome-wide investigations suggested significant genetic divergence of the relapsed disease. Methods We undertook large-scale integrated characterization of the molecular features of rMB - molecular subgroup, novel subtypes, copy number variation (CNV) and driver gene mutation. 119 rMBs were assessed in comparison with their paired diagnostic samples (n=107), alongside an independent reference cohort sampled at diagnosis (n=282). rMB events were investigated for association with outcome post-relapse in clinically-annotated patients (n=54). Results Significant genetic evolution occurred over disease-course; 40% of putative rMB drivers emerged at relapse and differed significantly between molecular subgroups. MBSHH Non-infant displayed significantly more chromosomal CNVs at relapse (TP53 mutation-associated). Relapsed MBGroup4 demonstrated the greatest genetic divergence, enriched for targetable (e.g. CDK amplifications) and novel (e.g. USH2A mutations) events. Importantly, many hallmark features of medulloblastoma were stable over time; novel subtypes (>90% of tumors) and established genetic drivers (e.g. SHH/WNT/P53 mutations; 60% of rMB events) were maintained from diagnosis. Critically, acquired and maintained rMB events converged on targetable pathways which were significantly enriched at relapse (e.g. DNA damage-signaling) and specific events (e.g. 3p loss) predicted survival post-relapse. Conclusions rMB is defined by the emergence of novel events and pathways, in concert with selective maintenance of established genetic drivers. Together, these define the actionable genetic landscape of rMB and provide a basis for improved clinical management and development of stratified therapeutics, across disease-course.

The development of tendinopathy is influenced by a variety of factors including age, gender, sex hormones and diabetes status. Cross platform comparative analysis of transcriptomic data elucidated the connections between these entities in the context of ageing. Tissue-engineered tendons differentiated from bone marrow derived mesenchymal stem cells from young (20–24 years) and old (54–70 years) donors were assayed using ribonucleic acid sequencing (RNA-seq). Extension of the experiment to microarray and RNA-seq data from tendon identified gender specific gene expression changes highlighting disparity with existing literature and published pathways. Separation of RNA-seq data by sex revealed underlying negative binomial distributions which increased statistical power. Sex specific de novo transcriptome assemblies generated fewer larger transcripts that contained miRNAs, lincRNAs and snoRNAs. The results identify that in old males decreased expression of CRABP2 leads to cell proliferation, whereas in old females it leads to cellular senescence. In conjunction with existing literature the results explain gender disparity in the development and types of degenerative diseases as well as highlighting a wide range of considerations for the analysis of transcriptomic data. Wider implications are that degenerative diseases may need to be treated differently in males and females because alternative mechanisms may be involved.

We characterize the subgroup‐dependent clinico‐molecular landscape of infant medulloblastoma, and also consider the importance of recently‐described subtypes of subgroups. We develop and validate subgroup‐specific survival models and proffer suggestions for the incorporation of subgroup/subtype information into future clinical decision making.

Cell senescence is a diverse phenotype and therapies often require combinatorial approaches. Here we have systematically collected transcriptomic data related to human fibroblasts to a total of 98 studies. We formed a database describing the relevant variables for each study which we have hosted online allowing users to filter the studies to select variables and genes of interest. Our own analysis of the database revealed 13 marker genes consistently downregulated in senescent cells compared to proliferating controls; however, we also found gene expression patterns that were highly specific and reliable for different senescence inducers, cell lines, and timepoint after induction, confirming several conclusions of existing studies based on single datasets, including differences in p53 and inflammatory signals between oncogene induced senescence (OIS) and DNA damage induced senescence (DDIS). We saw little evidence of an initial TGF-β-centric SASP, but we did find evidence of a decrease in Notch signalling. Contrary to some early observations, both p16 and p21 mRNA levels appeared to rise quickly, depending on senescence type, and persist for at least 8-11 days. We concluded that while universal biomarkers of senescence are difficult to identify, the conventional senescence markers follow predictable profiles and construction of a framework for studying senescence could lead to more reproducible data.

Skin ageing has been widely associated with the formation and presence of increasing quantities of senescent cells, the presence of which are thought to reduce cell renewal. This study aimed to identify key factors influencing fibroblast and skin aging using RNA-seq data. Key differences in study designs included known sources of biological differences (sex, age, ethnicity), experimental differences, and environmental factors known to accelerate skin ageing (smoking, UV exposure) as well as study specific batch effects which complicated the analysis. To overcome these complications samples were stratified by these factors and differential expression assessed using Salmon and CuffDiff. Stratification of female fibroblast and skin samples combined with female specific normalisation of transcriptomic and methylation data sets increased functional enrichment and consistency across studies. The results identify the importance of considering environmental factors known to increase the rate of ageing (smoking status of donors, and UV-exposure status of skin and fibroblast samples) both independently and in combination for the identification of key ageing signatures. The results identified that in old (> 65) female skin decreases in the expression of transmembrane ion transporters coincide with increased methylation of oxidoreductases, and consequently reductions in respiration. This was further evidenced in old fibroblasts from smokers which identified reductions ion homeostasis, and the transcription of mitochondrial tRNAs, that were accompanied by reduced mitochondrial fission, reduced lipid catabolism and reduced immune signalling. These changes occurred in combination with reductions in cell proliferation, adhesion, ECM organisation, cell movement, cytoskeleton organisation and circulatory system development. Middle and old aged skin without environmental stratification's identified decreased expression of transmembrane ion transporters occurred alongside reductions in keratinisation, reduced mitochondrial fission, and this was associated with reduced metabolism (specifically carbohydrates), and consequently a reduction in the production of lipids (phospholipids for membranes and others) occured, exacerbating ion homeostasis issues at a keratinocyte level. Interestingly in skin the combined impacts of UV-exposure, smoking and ageing yielded different results, increased expression of calcium homeostasis genes, cell adhesion molecules (integrins), structural membrane constituents (loricrin, mucins, keratins and collagens), increased cornification, as well as structural cytoskeletal molecules (KRTAPs). This occurred alongside increased expression of genes involved in skin peeling (kalikriens), proliferation and differentiation, glycosylation, oxidative stress, autophagy, lactose metabolism, and lipid catabolism. Aged UV-exposed skin from smokers is on the whole more fibrous, with cells showing significant cell membrane and cytoskeletal structural changes, similar to those seen in skin cancers. Interestingly in non-UV-exposed skin from smokers most of these processes were reduced, and in within age group comparisons of smokers they were also reduced, suggesting that smoking reduced skin development and regeneration. Female specific analysis of smokers from different age groups enrichment results identified additional factors relating to tissue development, cell adhesion, vasculature development, peptide cross-linking, calcium homeostasis, cancer and senescence, leading to age related declines skin structure and function. Interestingly many diseases and infections with overlapping molecular consequences, (ER Calcium stress, reduced protein targeting to membranes) including human cytomegalovirus and herpes simplex virus are identified by the age only analysis, suggesting that viral infections and ageing have similar molecular consequences for cells.