Epigenetic approaches in direct correlation with assessment of critical genetic mutations in non-small cell lung cancer (NSCLC) are currently very intensive, as the epigenetic components underlying NSCLC development and progression have attained high recognition. In this level of research, established human NSCLC cell lines as well as experimental animals are widely used to detect novel biomarkers and pharmacological targets to treat NSCLC. The epigenetic background holds a great potential for the identification of epi-biomarkers for treatment response however, it is highly complex and requires precise definition as these phenomena are variable between NSCLC subtypes and systems origin. We engaged an in-depth characterization of non-coding (nc)RNAs prevalent in human
Abstract Treatment decision and response assessment in myelodysplastic syndromes (MDS) can be enhanced by the implementation of advanced diagnostic and prognostic assays for the detection of multiple molecular features. Higher-risk (HR) MDS, ineligible for allogeneic hematopoietic stem cell transplantation (alloHSCT), require prompt therapeutic interventions such as treatment with hypomethylating agents (HMAs) to restore normal DNA methylation levels, mainly of oncosuppressor genes and consequently to delay disease progression and increase overall survival (OS). However, response assessment to HMA treatment relies on conventional methods with limited capacity to uncover a wide spectrum of molecular events. We studied bone marrow aspirates from twenty-one HR MDS patients pre- and post-HMA treatment and seven healthy controls. Genomic DNA was analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) for 5’ methyl-cytosine (5mC), 5’ hydroxy-methyl cytosine (5hmC) levels detection, and global adenosine/thymidine ([dA]/[T]) ratio, to correlate differences during treatment course and at baseline state prior drug therapy. Results from methylation DNA sequencing (MeD-seq) from the same HR MDS cohort were also analyzed to identify targeted differentially methylated regions (DMRs). LC/MS-MS analysis revealed a significant hypomethylation status in responders (Rs) already established at baseline and a trend for further DNA methylation reduction post-HMA treatment. Non-responders (NRs) reached statistical significance for DNA hypomethylation only post-HMA treatment. MeD-seq confirmed results globally for both Rs and NRs and more specifically, identified DMRs associated with HMA treatment. Additionally, within statistically significant selected chromosomal bins, genes encoding for proteins and non-coding RNAs were highlighted with reversed methylation profiles between Rs and NRs. Dynamic DNA methylation changes in HR MDS patients undergoing HMA therapy demonstrated that response to treatment is associated only with few specific hypomethylated DMRs rather than presenting a global effect across genome. The 5hmC epigenetic mark was only rarely detected in Rs and NRs, in contrast to healthy controls. Global [dA]/[T] ratio was lower in both R and NR subgroups compared to controls suggesting high frequences of baseline transitions from 5mC to thymidine. Conclusively, LC-MS/MS methodology provided broad-based but rapid and cost-effective results on the molecular HR MDS background, potentially translatable into responsive phenotypes to HMA treatment.
Abstract The identification of succinct, universal fingerprints that enable the characterization of individual taxonomies can reveal insights into trait development and can have widespread applications in pathogen diagnostics, human healthcare, ecology and the characterization of biomes. Here, we investigated the existence of peptide k-mer sequences that are exclusively present in a specific taxonomy and absent in every other taxonomic level, termed taxonomic quasi-primes. By analyzing proteomes across 24,073 species, we identified quasi-prime peptides specific to superkingdoms, kingdoms, and phyla, uncovering their taxonomic distributions and functional relevance. These peptides exhibit remarkable sequence uniqueness at six- and seven-amino- acid lengths, offering insights into evolutionary divergence and lineage-specific adaptations. Moreover, we show that human quasi-prime loci are more prone to harboring pathogenic variants, underscoring their functional significance. This study introduces taxonomic quasi-primes and offers insights into their contributions to proteomic diversity, evolutionary pathways, and functional adaptations across the tree of life, while emphasizing their potential impact on human health and disease.
Abstract Background Patients with higher-risk (HR) myelodysplastic syndrome (MDS), ineligible for allogeneic hematopoietic stem cell transplantation (alloHSCT), require prompt therapeutic interventions, such as treatment with hypomethylating agents (HMAs) to restore normal DNA methylation patterns, mainly of oncosuppressor genes, and consequently to delay disease progression and increase overall survival (OS). However, response assessment to HMA treatment relies on conventional methods with limited capacity to uncover a wide spectrum of underlying molecular events. Methods We implemented liquid chromatography-tandem mass spectrometry (LC-MS/MS) to assess 5’ methyl-2’ deoxycytidine (5mdC), 5’ hydroxy-methyl-2’-deoxycytidine (5hmdC) levels and global adenosine/thymidine ([dA]/[T]) ratio in bone marrow aspirates from twenty-one HR MDS patients, pre- and post-HMA treatment. Additionally, targeted methylation analysis was performed by interpretation of NGS-methylation (MeD-seq) data obtained from the same patient cohort. Results LC/MS-MS analysis revealed a significant hypomethylation status in responders (Rs), already established at baseline and a trend for further DNA methylation reduction post-HMA treatment. Non-responders (NRs) reached statistical significance for DNA hypomethylation only post-HMA treatment. The 5hmdC epigenetic mark was approximately detected at 37.5–40% among NRs and Rs, implying the impairment of the natural active demethylation pathway, mediated by the ten-eleven (TET) 5mdC dioxygenases. R and NR subgroups displayed a [dA]/[T] ratio < 1 (0.727 − 0.633), supporting high frequences of 5mdC transition to thymidine. Response to treatment, according to whole genome MeD-seq data analysis, was associated with specific, scattered hypomethylated DMRs, rather than presenting a global effect across genome. MeD-seq analysis identified divergent epigenetic effects along chromosomes 7, 9, 12, 16, 18, 21, 22, X and Y. Within statistically significant selected chromosomal bins, genes encoding for proteins and non-coding RNAs with reversed methylation profiles between Rs and NRs, were highlighted. Conclusions Implementation of powerful analytical tools to identify the dynamic DNA methylation changes in HR MDS patients undergoing HMA therapy demonstrated that LC-MS/MS exerts high efficiency as a broad-based but rapid and cost-effective methodology (compared to MeD-seq) to decode different perspectives of the epigenetic background of HR MDS patients and possess discriminative efficacy of the response phenotype to HMA treatment.
