The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.

Metabolomics uses advanced analytical chemistry methods to analyze metabolites in biological samples. The most intensively studied samples are blood and its liquid components: plasma and serum. Armed with advanced equipment and progressive software solutions, the scientific community has shown that small molecules’ roles in living systems are not limited to traditional “building blocks” or “just fuel” for cellular energy. As a result, the conclusions based on studying the metabolome are finding practical reflection in molecular medicine and a better understanding of fundamental biochemical processes in living systems. This review is not a detailed protocol of metabolomic analysis. However, it should support the reader with information about the achievements in the whole process of metabolic exploration of human plasma and serum using mass spectrometry combined with gas chromatography.

Despite their astonishing biological diversity, surprisingly few shared traits connect all or nearly all living organisms. Aging, i.e., the progressive and irreversible decline in the function of multiple cells and tissues, is one of these fundamental features of all organisms, ranging from single-cell creatures to complex animals, alongside variability, adaptation, growth, healing, reproducibility, mobility, and, finally, death. Age is a key determinant for many pathologies, shaping the risks of incidence, severity, and treatment outcomes for cancer, neurodegeneration, heart failure, sarcopenia, atherosclerosis, osteoporosis, and many other diseases. In this review, we aim to systematically investigate the age-related features of the development of several diseases through the lens of multiomics: from genome instability and somatic mutations to pathway alterations and dysregulated metabolism.

Both biological and technical variations can discredit the reliability of obtained data in omics studies. In this technical note, we investigated the effect of prolonged cultivation of the HepG2 hepatoma cell line on its metabolomic profile. Using the GC × GC-MS approach, we determined the degree of metabolic variability across HepG2 cells cultured in uniform conditions for 0, 5, 10, 15, and 20 days. Post-processing of obtained data revealed substantial changes in relative abundances of 110 metabolites among HepG2 samples under investigation. Our findings have implications for interpreting metabolomic results obtained from immortal cells, especially in longitudinal studies. There are still plenty of unanswered questions regarding metabolomics variability and many potential areas for future targeted and panoramic research. However, we suggest that the metabolome of cell lines is unstable and may undergo significant transformation over time, even if the culture conditions remain the same. Considering metabolomics variability on a relatively long-term basis, careful experimentation with particular attention to control samples is required to ensure reproducibility and relevance of the research results when testing both fundamentally and practically significant hypotheses.

To represent the composition of small molecules circulating in HepG2 cells and the formation of the “core” of characteristic metabolites that often attract researchers’ attention, we conducted a meta-analysis of 56 datasets obtained through metabolomic profiling via mass spectrometry and NMR. We highlighted the 288 most commonly studied compounds of diverse chemical nature and analyzed metabolic processes involving these small molecules. Building a complete map of the metabolome of a cell, which encompasses the diversity of possible impacts on it, is a severe challenge for the scientific community, which is faced not only with natural limitations of experimental technologies, but also with the absence of transparent and widely accepted standards for processing and presenting the obtained metabolomic data. Formulating our research design, we aimed to reveal metabolites crucial to the Hepg2 cell line, regardless of all chemical and/or physical impact factors. Unfortunately, the existing paradigm of data policy leads to a streetlight effect. When analyzing and reporting only target metabolites of interest, the community ignores the changes in the metabolomic landscape that hide many molecular secrets.

The analysis of biological fluids plays a crucial role in biomarker discovery, disease diagnostics, and precision medicine. Dried sample carriers—such as dried blood spots, dried plasma, serum, saliva, tears, and urine—have emerged as powerful tools, offering advantages in sample collection, storage, and transport, particularly in remote and resource-limited settings. Recent advances in proteomic methodologies have expanded the potential of these dried matrices, yet challenges related to protein stability, sensitivity, and standardization persist. This review critically examines the current state of proteomic investigations using dried biological fluids. Furthermore, we compare proteomics’ progress in this field with other omics approaches, such as metabolomics, to contextualize its development and integration potential. While dried fluid proteomics is promising for non-invasive diagnostics and large-scale epidemiological studies, addressing technical limitations will be essential for its broader adoption in clinical and translational research.