Biology subjects

Medo, M.

Publications and source records attributed to Medo, M..

4 recordsLinked to original sources

bioRxiv2023

HPV and p53 status as precision determinants of head and neck cancer response to DNA-PKcs inhibition in combination with irradiation

Major risk factors of head and neck squamous cell carcinoma (HNSCC) are tobacco use and human papillomavirus (HPV). HPV E6 oncoprotein leads to the degradation of the p53 protein, whereas HPV-negative cancers are frequently associated with TP53 mutations. Peposertib is a potent and selective, orally administered small-molecule inhibitor of the catalytic subunit of the DNA-dependent kinase (DNA-PKcs), a key regulator of non-homologous end joining (NHEJ). NHEJ inhibition along with irradiation (IR)-induced DNA double-strand breaks has the potential to increase antitumor treatment efficacy. Here, we investigated the responses of HNSCC models with distinct HPV and p53 status to treatments with IR, DNA-PKcs inhibition, and their combination. We observed that IR-induced DNA damage combined with peposertib administration shortly before IR results in decreased cell viability and proliferation and causes DNA repair delay in all the studied HNSCC cell lines. However, our data confirm that the actual cell fate upon this treatment is strongly dependent on cellular p53/HPV status. Cells lacking functional p53 due to its degradation by HPV or due to the presence of a loss-of-function mutation are arrested in the G2 phase of the cell cycle and eliminated by apoptosis whereas p53-proficient HNSCC cell lines undergo senescence. Consequently, HPV+ cancer cell lines and xenografts display stronger and more durable responses and seem to benefit from the combined treatment more than p53-proficient HNSCCs. In conclusion, DNA-PKcs inhibitor peposertib should be further studied as a potential radiosensitizer for HNSCCs, taking into consideration the genetic background and the HPV status of a particular tumor.

cancer biology↗

bioRxiv2023

Replicability of bulk RNA-Seq differential expression and enrichment analysis results in cancer research

The high-dimensional and heterogeneous nature of transcriptomics data from RNA sequencing (RNA-Seq) experiments poses a challenge to routine down-stream analysis steps, such as differential expression analysis and enrichment analysis. Additionally, due to practical and financial constraints, RNA-Seq experiments are often limited to a small number of biological replicates; three replicates is a commonly employed minimum cohort size. In light of recent studies on the low replicability of preclinical cancer research, it is essential to understand how the combination of population heterogeneity and underpowered cohort sizes affects the replicability of RNA-Seq research. Using 7000 simulated RNA-Seq experiments based on real gene expression data from seven different cancer types, we find that the analysis results from underpowered experiments exhibit inflated effect sizes and are unlikely to replicate well. However, the ground-truth results obtained by analyzing large cohorts show that the precision of differentially expressed genes can be high even for small cohort sizes. The poor replicability of underpowered experiments is thus a direct consequence of their low recall (sensitivity). In other words, the low replicability of underpowered RNA-Seq cancer studies does not necessarily indicate a high prevalence of false positives. Instead, the results obtained from such studies are limited to small and mostly random subsets of a larger ground truth. We conclude with a set of practical recommendations to alleviate problems with underpowered RNA-Seq studies. Author SummaryTranscriptomics data from RNA sequencing (RNA-Seq) experiments are complex and challenging to analyze due to their high dimensionality and variability. These experiments often involve limited biological replicates due to practical and financial constraints. Recent concerns about the replicability of cancer research highlight the need to explore how this combination of limited cohort sizes and population heterogeneity impacts the reliability of RNA-Seq studies. To investigate these issues, we conducted 7000 simulated RNA-Seq experiments based on real gene expression data from seven different cancer types. We show that experiments with small cohort sizes tend to produce results with exaggerated effects that can be difficult to replicate. We further found that while underpowered studies with few replicates indeed lead to little-replicable results, the identified differentially expressed genes are reliable as shown by low rates of false positives. Each underpowered study thus discovers a small subset of the ground truth. Our study concludes with practical recommendations for RNA-Seq studies with small cohort sizes.

bioinformatics↗

bioRxiv2021

Tumour mutations in long noncoding RNAs that enhance cell fitness

Long noncoding RNAs (lncRNAs) can act as tumour suppressors or oncogenes to repress/promote tumour cell proliferation via RNA-dependent mechanisms. Recently, genome sequencing has identified elevated densities of tumour somatic single nucleotide variants (SNVs) in lncRNA genes. However, this has been attributed to phenotypically-neutral "passenger" processes, and the existence of positively-selected fitness-altering "driver" SNVs acting via lncRNAs has not been addressed. We developed and used ExInAtor2, an improved driver-discovery pipeline, to map pancancer and cancer-specific mutated lncRNAs across an extensive cohort of 2583 primary and 3527 metastatic tumours. The 54 resulting lncRNAs are mostly linked to cancer for the first time. Their significance is supported by a range of clinical and genomic evidence, and display oncogenic potential when experimentally expressed in matched tumour models. Our results revealed a striking SNV hotspot in the iconic NEAT1 oncogene, which was ascribed by previous studies to passenger processes. To directly evaluate the functional significance of NEAT1 SNVs, we used in cellulo mutagenesis to introduce tumour-like mutations in the gene and observed a consequent increase in cell proliferation in both transformed and normal backgrounds. Mechanistic analyses revealed that SNVs alter NEAT1 ribonucleoprotein assembly and boost subnuclear paraspeckles. This is the first experimental evidence that mutated lncRNAs can contribute to the pathological fitness of tumour cells.

genomics↗

bioRxiv2020

Altered patterning of interneuron progenitors in Down syndrome

Individuals with Down syndrome (DS, Ts21), the most common genetic cause of intellectual disability, have smaller brains that reflect fewer neurons at pre- and post-natal stages, implicating impaired neurogenesis during development. Our stereological analysis of adult DS cortex indicates a reduction of calretinin expressing interneurons. Using Ts21 human induced pluripotent stem cells (iPSCs) and isogenic controls, we find Ts21 progenitors generate fewer COUP-TFII+ progenitors with reduced proliferation. Single cell RNA-sequencing of Ts21 progenitors confirms the altered specification of progenitor subpopulations and identifies reduced WNT signaling. Activation of WNT signaling partially restores the COUP-TFII+ progenitor population in Ts21, suggesting that altered WNT signaling contributes to the defective development of cortical interneurons in DS.

developmental biology↗