Cervical cancer is primarily caused by persistent infection with high-risk human papillomavirus (hrHPV), which alters host RNA expression, including regulatory microRNAs (miRNAs). Because urine is emerging as a convenient biosource for cancer detection, we evaluated the feasibility of urinary miRNAs as non-invasive biomarkers for cervical cancer. We optimized miRNA isolation from whole urine and urine…

Malignant and non‐malignant cells within the tumor microenvironment (TME) actively secrete extracellular vesicles (EVs) that may mediate intercellular communication or enter the blood stream. Circulating EVs in Diffuse Large B‐Cell Lymphoma (DLBCL) patients are a promising source of liquid biopsy biomarkers; however, whether different cellular components of the TME preferentially secrete small (S‐) and/or large…

Tumour‐derived extracellular vesicles (TEVs) play a crucial role in cancer progression, metastasis and therapy resistance but their distinct profiles across different cancer stages and molecular subtypes remain underexplored. This study initially analysed TEVs from all CMS subtypes in colorectal cancer (CRC) cells and continued focusing on the epithelial (CMS2) and mesenchymal (CMS4) subtypes using six…

Multiple myeloma (MM) is a plasma cell neoplasm characterized by high inter- and intra-patient clonal heterogeneity, leading to high variability in therapeutic responses. Minimally invasive biomarkers that predict response may help personalize treatment decisions. IsoSeek, a single-nucleotide resolution small RNA sequencing method can profile thousands of microRNAs (miRNAs) and their variants (isomiRs) from patient plasma-purified…

The concept of a genome signature broadly refers to characteristic patterns in DNA sequences that enable the identification and comparison of species or individuals, often without requiring sequence alignment. Such signatures have applications ranging from forensic identification of individuals to cancer genomics. In comparative genomics and evolutionary biology, genome signatures typically rely on statistical properties…

The rapid evolution of SARS-CoV-2 during the pandemic was characterized by the fixation of a plethora of mutations, many of which enable the virus to evade host resistance, likely altering the virus’ genome compositional structure (i.e., the arrangement of compositional domains of varying lengths and nucleotide frequencies within the genome). To explore this hypothesis, we…

The rapid evolution of SARS-CoV-2 during the pandemic, driven by a plethora of mutations, many of which enable the virus to evade host resistance, has likely altered its genome’s compositional structure (i.e. the arrangement of compositional domains of varying lengths and nucleotide frequencies within the genome). To explore this hypothesis, we summarize the evolutionary effects…

Purpose Therapy resistance is a major clinical hurdle in bone cancer treatment and seems to be largely driven by poorly understood microenvironmental factors. Recent evidence suggests a critical role for a unique subpopulation of mesenchymal stem cells with inflammatory features (iMSC), though their origin and function remained unexplored. We demonstrate that cancer-secreted extracellular vesicles (EV)…

Small extracellular vesicles (sEVs) are heterogenous lipid membrane particles typically less than 200 nm in size and secreted by most cell types either constitutively or upon activation signals. sEVs isolated from biofluids contain RNAs, including small non-coding RNAs (ncRNAs), that can be either encapsulated within the EV lumen or bound to the EV surface. EV-associated…

Liquid biopsy-derived RNA sequencing (lbRNA-seq) exhibits significant promise for clinic-oriented cancer diagnostics due to its non-invasiveness and ease of repeatability. Despite substantial advancements, obstacles like technical artefacts and process standardisation impede seamless clinical integration. Alongside addressing technical aspects such as normalising fluctuating low-input material and establishing a standardised clinical workflow, the lack of result validation…

Viruses use miRNAs to enable efficient replication, control host defense mechanisms, and regulate latent infection. Herpes simplex virus 1 (HSV-1) expresses multiple miRNAs whose functions are largely unknown. The evolutionary conservation of many HSV-1 miRNAs in the closely related HSV-2 suggests their functional importance. miRNAs, similar to other transcripts, can undergo various post-transcriptional modifications that…

RNA-sequencing has become one of the most used high-throughput approaches to gain knowledge about the expression of all different RNA subpopulations. However, technical artifacts, either introduced during library preparation and/or data analysis, can influence the detected RNA expression levels. A critical step, especially in large and low input datasets or studies, is data normalization, which…

Simple Summary DNA structural biology deals with the understanding of DNA and three-dimensional chromatin structure, which can determine its function in the cell. The key structural properties of the DNA fiber, such as stability, flexibility, and susceptibility to damage, largely rely on the composition of the DNA sequence. Variations in the nucleotide sequence result in…

IsomiRs, sequence variants of mature microRNAs, are usually detected and quantified using high-throughput sequencing. Many examples of their biological relevance have been reported, but sequencing artifacts identified as artificial variants might bias biological inference and therefore need to be ideally avoided. We conducted a comprehensive evaluation of 10 different small RNA sequencing protocols, exploring both…

Transfer RNAs (tRNAs) are small adaptor RNAs essential for mRNA translation. Alterations in the cellular tRNA population can directly affect mRNA decoding rates and translational efficiency during cancer development and progression. To evaluate changes in the composition of the tRNA pool, multiple sequencing approaches have been developed to overcome reverse transcription blocks caused by the…

Wheat is one of the most important food sources on Earth. MicroRNAs (miRNA) play important roles in wheat productivity. To identify wheat miRNAs, we constructed and sequenced sRNA libraries from leaves and roots of two wheat cultivars (RAC875 and Kukri) with many different traits. Given that available miRNA wheat complement in the plant-specific database PmiREN…

Wheat is one of the most important food sources on Earth. MicroRNAs (miRNAs) play important roles in wheat productivity. To identify wheat miRNAs as well as their expression profiles under drought condition, we constructed and sequenced small RNA (sRNA) libraries from the leaves and roots of three wheat cultivars (Kukri, RAC875 and Excalibur) under water…

The current versions of the microRNA databases MiRgeneDB, miRBase, and PmiREN contain annotations for a total of 358 different species. Public repositories, however, host small RNA sequencing data for over 800 species. This discrepancy implies that microRNA research is also very active in species that neither have an available high-quality genome assembly nor annotations for…

Since the role of high-abundant, circulating RNA as liquid biopsy disease biomarker is increasingly recognized, optimized sequencing protocols for clinical implementation are required. We developed IsoSeek an unbiased small RNA sequencing method that diverges from prior protocols using 5N 5’and 3’randomized adapter ends as unique molecular identifiers (UMIs). With a synthetic reference miRNA pool and…

Extracellular Vesicle associated microRNAs (EV-miRNAs) can serve as minimallyinvasive therapy-response biomarkers, as shown with EDTA-plasma of patients with classic Hodgkin lymphoma. One drawback of EDTA-plasma as circulating EV source is the requirement for immediate processing (< 2 hours) of blood samples as dying cells still generate EVs ex-vivo, resulting in false positive contribution to the…