Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells.

Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lead to mtDNA deletions accumulation are still unclear. Mitochondrial DNA deletion breakpoints preferentially occur at sequence motifs predicted to form G-quadruplexes (G4s), four-stranded nucleic acid structures that can fold in guanine-rich regions. Whether mtDNA G4s form in vivo and their potential implication for mtDNA instability is still under debate. In here, we developed new tools to map G4s in the mtDNA of living cells. We engineered a G4-binding protein targeted to the mitochondrial matrix of a human cell line and established the mtG4-ChIP method, enabling the determination of mtDNA G4s under different cellular conditions. Our results are indicative of transient mtDNA G4 formation in human cells. We demonstrate that mtDNA-specific replication stalling increases formation of G4s, particularly in the major arc. Moreover, elevated levels of G4 block the progression of the mtDNA replication fork and cause mtDNA loss. We conclude that stalling of the mtDNA replisome enhances mtDNA G4 occurrence, and that G4s not resolved in a timely manner can have a negative impact on mtDNA integrity.

Prenatal anxiety during the pandemic context is related to neurodevelopment of 6-month-old babies.

Prenatal anxiety and depression in pandemic context could introduce changes in the fetal developmental trajectories that, ultimately, could alter the adaptive behaviors of the offspring, potentially affecting, for example, general neurodevelopment. The sample consisted of 105 mother-child dyads, recruited between March and May 2020. The dyads were evaluated longitudinally, prenatally and postnatally (6 months). The Pandemic Impact Questionnaire, the State-Trait Anxiety Inventory, and the Beck-II Depression Inventory were used to assess indicators of maternal anxiety and depression, respectively. Regarding the babies, their mothers responded to Age and Stages: 3, which assesses different dimensions of early neurodevelopment, in addition to a closed questionnaire to identify sociodemographic and maternal and child health variables. A series of mediation models were tested to examine the association between prenatal psychopathology/negative experiences of the pandemic and neurodevelopment. The results indicated that the negative experiences of the pandemic were indirectly associated with the socio-individual and fine motor neurodevelopment of the offspring, through maternal anxiety symptoms, during the third trimester, which functioned as a mediator.  Conclusions: This study provides evidence on the mediating effects of maternal anxiety on infant neurodevelopment in contexts of early adversity. It is important to point out the need to implement public health policies that allow a timely evaluation of neurodevelopmental variables during early childhood, which can implement early interventions to reduce the risks associated with these deficits. What is Known: • Effects of maternal mental health have been reported, effects on child neurodevelopment, in motor, cognitive, linguistic and socio-emotional dimensions. • Contexts of early adversity have been associated with maternal mental health and offspring development. What is New: • The context of pandemic adversity caused by COVID-19 is associated with motor and socio-individual neurodevelopment, mediated by maternal prenatal anxiety.

High Glucose Promotes Inflammation and Weakens Placental Defenses against E. coli and S. agalactiae Infection: Protective Role of Insulin and Metformin.

Placentas from gestational diabetes mellitus (GDM) patients undergo significant metabolic and immunologic adaptations due to hyperglycemia, which results in an exacerbated synthesis of proinflammatory cytokines and an increased risk for infections. Insulin or metformin are clinically indicated for the treatment of GDM; however, there is limited information about the immunomodulatory activity of these drugs in the human placenta, especially in the context of maternal infections. Our objective was to study the role of insulin and metformin in the placental inflammatory response and innate defense against common etiopathological agents of pregnancy bacterial infections, such as E. coli and S. agalactiae, in a hyperglycemic environment. Term placental explants were cultivated with glucose (10 and 50 mM), insulin (50-500 nM) or metformin (125-500 µM) for 48 h, and then they were challenged with live bacteria (1 × 105 CFU/mL). We evaluated the inflammatory cytokine secretion, beta defensins production, bacterial count and bacterial tissue invasiveness after 4-8 h of infection. Our results showed that a GDM-associated hyperglycemic environment induced an inflammatory response and a decreased beta defensins synthesis unable to restrain bacterial infection. Notably, both insulin and metformin exerted anti-inflammatory effects under hyperglycemic infectious and non-infectious scenarios. Moreover, both drugs fortified placental barrier defenses, resulting in reduced E. coli counts, as well as decreased S. agalactiae and E. coli invasiveness of placental villous trees. Remarkably, the double challenge of high glucose and infection provoked a pathogen-specific attenuated placental inflammatory response in the hyperglycemic condition, mainly denoted by reduced TNF-α and IL-6 secretion after S. agalactiae infection and by IL-1ß after E. coli infection. Altogether, these results suggest that metabolically uncontrolled GDM mothers develop diverse immune placental alterations, which may help to explain their increased vulnerability to bacterial pathogens.

Maternal anxiety, exposure to the COVID-19 pandemic and socioemotional development of offspring.

The COVID-19 pandemic context may predispose mothers to increased maternal psychopathology, which may be associated with offspring socioemotional development. The aim of this study is to analyze the relationships between prenatal anxiety and depression and exposure to the COVID-19 pandemic with offspring socioemotional development, controlling for postnatal anxiety and depression. A total of 105 mother-child dyads were assessed in pre- and postnatal periods. Questionnaires were used to assess the impact of the pandemic, indicators of psychopathology, and the socioemotional development of the offspring. Results suggest that negative pandemic experiences are indirectly associated with offspring socioemotional development via prenatal maternal anxiety symptomatology and after controlling for postnatal anxiety and depression. These indicators predispose to emotional deficits and increase the risks of psychopathological and neurodevelopmental disorders. It is important to adopt health policies that provide timely assessment of development in early childhood to reduce the risks associated with these deficits.

PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data.

BACKGROUND: Processed pseudogenes (PΨgs) are disabled gene copies that are transcribed and may affect expression of paralogous genes. Moreover, their insertion in the genome can disrupt the structure or the regulatory region of a gene, affecting its expression level. These events have been identified as occurring mutations during cancer development, thus being able to identify PΨgs and their location will improve their impact on diagnostic testing, not only in cancer but also in inherited disorders. RESULTS: We have implemented PΨFinder (P-psy-finder), a tool that identifies PΨgs, annotates known ones and predicts their insertion site(s) in the genome. The tool screens alignment files and provides user-friendly summary reports and visualizations. To demonstrate its applicability, we scanned 218 DNA samples from patients screened for hereditary colorectal cancer. We detected 423 PΨgs distributed in 96% of the samples, comprising 7 different parent genes. Among these, we confirmed the well-known insertion site of the SMAD4-PΨg within the last intron of the SCAI gene in one sample. While for the ubiquitous CBX3-PΨg, present in 82.6% of the samples, we found it reversed inserted in the second intron of the C15ORF57 gene. CONCLUSIONS: PΨFinder is a tool that can automatically identify novel PΨgs from DNA sequencing data and determine their location in the genome with high sensitivity (95.92%). It generates high quality figures and tables that facilitate the interpretation of the results and can guide the experimental validation. PΨFinder is a complementary analysis to any mutational screening in the identification of disease-causing mutations within cancer and other diseases.

TC-hunter: identification of the insertion site of a transgenic gene within the host genome.

BACKGROUND: Transgenic animal models are crucial for the study of gene function and disease, and are widely utilized in basic biological research, agriculture and pharma industries. Since the current methods for generating transgenic animals result in the random integration of the transgene under study, the phenotype may be compromised due to disruption of known genes or regulatory regions. Unfortunately, most of the tools that predict transgene insertion sites from high-throughput data are not publicly available or not properly maintained. RESULTS: We implemented TC-hunter, Transgene-Construct hunter, an open tool that identifies transgene insertion sites and provides simple reports and visualization aids. It relies on common tools used in the analysis of high-throughput data and makes use of chimeric reads and discordant read pairs to identify and support the transgenic insertion site. To demonstrate its applicability, we applied TC-hunter to four transgenic mice samples harboring the human PPM1D gene, a model used in the study of malignant tumor development. We identified the transgenic insertion site in each sample and experimentally validated them with Touchdown-polymerase chain reaction followed by Sanger sequencing. CONCLUSIONS: TC-hunter is an accessible bioinformatics tool that can automatically identify transgene insertion sites from DNA sequencing data with high sensitivity (98%) and precision (92.45%). TC-hunter is a valuable tool that can aid in evaluating any potential phenotypic complications due to the random integration of the transgene and can be accessed at https://github.com/bcfgothenburg/SSF .

PALB2 germline mutations in a multi-gene panel testing cohort of 1905 breast-ovarian cancer patients in Argentina.

PURPOSE: PALB2 variants have been scarcely described in Argentinian and Latin-American reports. In this study, we describe molecular and clinical characteristics of PALB2 mutations found in multi-gene panels (MP) from breast-ovarian cancer (BOC) families in different institutions from Argentina. METHODS: We retrospectively identified PALB2 pathogenic (PV) and likely pathogenic (LPV) variants from a cohort of 1905 MP results, provided by one local lab (Heritas) and SITHER (Hereditary Tumor Information System) public database. All patients met hereditary BOC clinical criteria for testing, according to current guidelines. RESULTS: The frequency of PALB2 mutations is 2.78% (53/1905). Forty-eight (90.5%) are PV and five (9.5%) are LPV. Most of the 18 different mutations (89%) are nonsense and frameshift types and 2 variants are novel. One high-rate recurrent PV (Y551*) is present in 43% (23/53) of the unrelated index cases. From the 53 affected carriers, 94% have BC diagnosis with 14% of bilateral cases. BC phenotype is mainly invasive ductal (78%) with 62% of hormone-receptor positive and 22% of triple negative tumors. Self-reported ethnic background of the cohort is West European (66%) and native Latin-American (20%) which is representative of Buenos Aires and other big urban areas of the country. CONCLUSION: This is the first report describing molecular and clinical characteristics of PALB2 carriers in Argentina. Frequency of PALB2 PV in Argentinian HBOC families is higher than in other reported populations. Y551* is a recurrent mutation that seems to be responsible for almost 50% of PALB2 cases.

Comparison of online learning designs during the COVID-19 pandemic within bioinformatics courses in higher education.

MOTIVATION: Due to the worldwide COVID-19 pandemic, new strategies had to be adopted to move from classroom-based education to online education, in a very short time. The lack of time to set up these strategies, hindered a proper design of online instructions and delivery of knowledge. Bioinformatics-related training and other onsite practical education, tend to rely on extensive practice, where students and instructors have a face-to-face interaction to improve the learning outcome. For these courses to maintain their high quality when adapted as online courses, different designs need to be tested and the students' perceptions need to be heard. RESULTS: This study focuses on short bioinformatics-related courses for graduate students at the University of Gothenburg, Sweden, which were originally developed for onsite training. Once adapted as online courses, several modifications in their design were tested to obtain the best fitting learning strategy for the students. To improve the online learning experience, we propose a combination of: (i) short synchronized sessions, (ii) extended time for own and group practical work, (iii) recorded live lectures and (iv) increased opportunities for feedback in several formats. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Cardiomyopathy with lethal arrhythmias associated with inactivation of KLHL24.

Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiovascular disorder, yet the genetic cause of up to 50% of cases remains unknown. Here, we show that mutations in KLHL24 cause HCM in humans. Using genome-wide linkage analysis and exome sequencing, we identified homozygous mutations in KLHL24 in two consanguineous families with HCM. Of the 11 young affected adults identified, 3 died suddenly and 1 had a cardiac transplant due to heart failure. KLHL24 is a member of the Kelch-like protein family, which acts as substrate-specific adaptors to Cullin E3 ubiquitin ligases. Endomyocardial and skeletal muscle biopsies from affected individuals of both families demonstrated characteristic alterations, including accumulation of desmin intermediate filaments. Knock-down of the zebrafish homologue klhl24a results in heart defects similar to that described for other HCM-linked genes providing additional support for KLHL24 as a HCM-associated gene. Our findings reveal a crucial role for KLHL24 in cardiac development and function.

The social ecology of childhood and early life adversity.

An increasing prevalence of early childhood adversity has reached epidemic proportions, creating a public health crisis. Rather than focusing only on adverse childhood experiences (ACEs) as the main lens for understanding early childhood experiences, detailed assessments of a child's social ecology are required to assess "early life adversity." These should also include the role of positive experiences, social relationships, and resilience-promoting factors. Comprehensive assessments of a child's physical and social ecology not only require parent/caregiver surveys and clinical observations, but also include measurements of the child's physiology using biomarkers. We identify cortisol as a stress biomarker and posit that hair cortisol concentrations represent a summative and chronological record of children's exposure to adverse experiences and other contextual stressors. Future research should use a social-ecological approach to investigate the robust interactions among adverse conditions, protective factors, genetic and epigenetic influences, environmental exposures, and social policy, within the context of a child's developmental stages. These contribute to their physical health, psychiatric conditions, cognitive/executive, social, and psychological functions, lifestyle choices, and socioeconomic outcomes. Such studies must inform preventive measures, therapeutic interventions, advocacy efforts, social policy changes, and public awareness campaigns to address early life adversities and their enduring effects on human potential. IMPACT: Current research does not support the practice of using ACEs as the main lens for understanding early childhood experiences. The social ecology of early childhood provides a contextual framework for evaluating the long-term health consequences of early life adversity. Comprehensive assessments reinforced with physiological measures and/or selected biomarkers, such as hair cortisol concentrations to assess early life stress, may provide critical insights into the relationships between early adversity, stress axis regulation, and subsequent health outcomes.

The enigmatic RNase MRP of kinetoplastids.

The ribonucleoprotein RNase MRP is responsible for the processing of ribosomal RNA precursors. It is found in virtually all eukaryotes that have been examined. In the Euglenozoa, including the genera Euglena, Diplonema and kinetoplastids, MRP RNA and protein subunits have so far escaped detection using bioinformatic methods. However, we now demonstrate that the RNA component is widespread among the Euglenozoa and that these RNAs have secondary structures that conform to the structure of all other phylogenetic groups. In Euglena, we identified the same set of P/MRP protein subunits as in many other protists. However, we failed to identify any of these proteins in the kinetoplastids. This finding poses interesting questions regarding the structure and function of RNase MRP in these species.

Functional and genomic characterization of three novel cell lines derived from a metastatic gallbladder cancer tumor.

BACKGROUND: Gallbladder cancer (GBC) is the most common tumor of the biliary tract. The incidence of GBC shows a large geographic variability, being particularly frequent in Native American populations. In Chile, GBC represents the second cause of cancer-related death among women. We describe here the establishment of three novel cell lines derived from the ascitic fluid of a Chilean GBC patient, who presented 46% European, 36% Mapuche, 12% Aymara and 6% African ancestry. RESULTS: After immunocytochemical staining of the primary cell culture, we isolated and comprehensively characterized three independent clones (PUC-GBC1, PUC-GBC2 and PUC-GBC3) by short tandem repeat DNA profiling and RNA sequencing as well as karyotype, doubling time, chemosensitivity, in vitro migration capability and in vivo tumorigenicity assay. Primary culture cells showed high expression of CK7, CK19, CA 19-9, MUC1 and MUC16, and negative expression of mesothelial markers. The three isolated clones displayed an epithelial phenotype and an abnormal structure and number of chromosomes. RNA sequencing confirmed the increased expression of cytokeratin and mucin genes, and also of TP53 and ERBB2 with some differences among the three cells lines, and revealed a novel exonic mutation in NF1. The PUC-GBC3 clone was the most aggressive according to histopathological features and the tumorigenic capacity in NSG mice. CONCLUSIONS: The first cell lines established from a Chilean GBC patient represent a new model for studying GBC in patients of Native American descent.

Metformin use is associated with a lower risk of osteoporosis in adult women independent of type 2 diabetes mellitus and obesity. REDLINC IX study.

Metformin may decrease cell senescence, including bone; hence we aimed at evaluating the association between metformin use and osteoporosis. This was a cross-sectional study carried out in 1259 Latin American adult women aged 40 or more who were not on anti-osteoporotic drugs, were on metformin and had a bone densitometry performed. Of the whole sample, 40.3% reported being on metformin (at least 1 year), 30.2% had type 2 diabetes mellitus and 22.6% had osteoporosis. Median (interquartile range) body mass index (BMI) for the whole cohort was 27.7 (4.6) kg/m2 and 30.2% had type 2 diabetes mellitus. Current use of hormone therapy, calcium, and vitamin D corresponded respectively to 10.7%, 47.7%, and 43.1% of all surveyed women. A logistic regression model was used to analyze the association of osteoporosis with various covariates incorporated into the model such as age (OR: 1.07, 95% CI: 1.05-1.09), BMI (OR: 0.92, 95% CI: 0.89-0.96) and metformin use (OR: 0.44, 95% CI: 0.32-0.59). Metformin use, regardless of the presence of type 2 diabetes or obesity, was associated with a lower risk of osteoporosis in adult women. We propose that one explanation for this observation could be the effect of the drug over cellular senescence.

The sex-determination pattern in crocodilians: A systematic review of three decades of research.

Sex in crocodilians is not determined by chromosomes, but by egg incubation temperature, where different temperatures produce different clutch sex ratios. Two patterns have been proposed to describe these changes in sex ratios: a 100% female proportion at low and high temperatures with male predominance at intermediate ones (FMF) or a simpler pattern with a single female-to-male transition (FM). Over the last three decades, researchers have provided empirical information to support either of these two patterns in different species; however, no consensus has been reached partly because data have not been analysed as a whole. Here, we aimed at gathering the existing data on these patterns to provide models of temperature-dependent sex determination in those crocodilians studied so far. Potentially relevant publications were searched on Web of Knowledge, Scopus, Scielo and Science Direct. Studies that reported results on the sexual identity of crocodilian hatchlings obtained from constant temperature incubation treatments were considered. Using statistical models varying in their underlying assumptions, we evaluated which sex-determination pattern was best supported for the studied crocodilians and constructed species-specific and latitude-specific models. Based on the 8,458 sexed hatchlings studied throughout 31 studies, we show that the evidence supports a shared FMF pattern in all the crocodilian species for which enough data are available. We find that such pattern changes between species and at different latitudes. These results suggest a lability of the FMF crocodilian sex-determination pattern, a key feature under the present climate change scenario.

The P-type ATPase CtpG preferentially transports Cd2+ across the Mycobacterium tuberculosis plasma membrane.

P1B-type ATPases are involved in heavy metal transport across the plasma membrane. Some Mycobacterium tuberculosis P-type ATPases are induced during infection, suggesting that this type of transporter could play a critical role in mycobacterial survival. To date, the ion specificity of M. tuberculosis heavy metal-transporting P1B-ATPases is not well understood. In this work, we observed that, although divalent heavy metal cations such as Cu2+, Co2+, Ni2+, Zn2+ Cd2+ and Pb2+ stimulate the ATPase activity of the putative P1B-type ATPase CtpG in the plasma membrane, whole cells of M. smegmatis expressing CtpG only tolerate high levels of Cd2+ and Cu2+. As indicator of the catalytic constant, Michaelis-Menten kinetics showed that CtpG embedded in the mycobacterial cell membrane has a V max/K m ratio 7.4-fold higher for Cd2+ than for Cu2+ ions. Thus, although CtpG can accept different substrates in vitro, this P-type ATPase transports Cd2+ more efficiently than other heavy metal cations across the mycobacterial plasma membrane.

Effect of Nitrogen Compounds on Shrimp Litopenaeus vannamei: Histological Alterations of the Antennal Gland.

Two experimental modules with different stocking densities (M1 = 70 and M2 = 120 shrimp m-2) were examined weekly during 72-day culture cycle at low-salinity water (1.9 g L-1) and zero-water exchange to examine the effects of water quality deterioration on the antennal gland (AG) of shrimp. Results showed survival rates of 87.7% and 11.9% in M1 and M2, respectively. Water temperature, pH, dissolved oxygen, and chlorophyll a were not significantly different between modules but the concentrations of the nitrogen compounds were significantly different between modules with the exception of nitrite-N, showing a higher histological alteration index in M2 (32 ± 10) than M1 (22 ± 0) with a strong correlation with the nitrogen compounds. During the last weeks was evidenced in M1 inflammation and hemocytic and hemolymph infiltration, while in M2, melanization, hemocytic melanized nodules and cells with kariorrexis.

Loss of the Mediator subunit Med20 affects transcription of tRNA and other non-coding RNA genes in fission yeast.

Mediator is a co-regulator of RNA polymerase II (Pol II), transducing signals from regulatory elements and transcription factors to the general transcription machinery at the promoter. We here demonstrate that Med20 influences ribosomal protein expression in fission yeast. In addition, loss of Med20 leads to an accumulation of aberrant, readthrough tRNA transcripts. These transcripts are polyadenylated and targeted for degradation by the exosome. Similarly, other non-coding RNA molecules, such as snRNA, snoRNA and rRNA, are also enriched in the polyadenylate preparations in the absence of Med20. We suggest that fission yeast Mediator takes part in a regulatory pathway that affects Pol III-dependent transcripts.

Regulation of DNA replication at the end of the mitochondrial D-loop involves the helicase TWINKLE and a conserved sequence element.

The majority of mitochondrial DNA replication events are terminated prematurely. The nascent DNA remains stably associated with the template, forming a triple-stranded displacement loop (D-loop) structure. However, the function of the D-loop region of the mitochondrial genome remains poorly understood. Using a comparative genomics approach we here identify two closely related 15 nt sequence motifs of the D-loop, strongly conserved among vertebrates. One motif is at the D-loop 5'-end and is part of the conserved sequence block 1 (CSB1). The other motif, here denoted coreTAS, is at the D-loop 3'-end. Both these sequences may prevent transcription across the D-loop region, since light and heavy strand transcription is terminated at CSB1 and coreTAS, respectively. Interestingly, the replication of the nascent D-loop strand, occurring in a direction opposite to that of heavy strand transcription, is also terminated at coreTAS, suggesting that coreTAS is involved in termination of both transcription and replication. Finally, we demonstrate that the loading of the helicase TWINKLE at coreTAS is reversible, implying that this site is a crucial component of a switch between D-loop formation and full-length mitochondrial DNA replication.

[Potentially traumatic events and post-traumatic symptomatology in high school students]. / Eventos potencialmente traumáticos y sintomatología postraumática en estudiantes de preparatoria.

OBJECTIVE: Describe the occurrence of potentially traumatic events (PTE) in high-school students, measure subthreshold post-traumatic symptomatology in those who still experience PTE repercussions and associate the symptomatology with sociodemographic and PTE characteristics. MATERIALS AND METHODS: Analytic transversal study carried out in a convenience sample of one thousand students from three high schools in the State of Mexico. The Scale for Post Traumatic Stress in University Students was applied. The presence of symptoms, their frequency and their association with explanatory variables was assessed by means of logistic and quantile logistic regression models, respectively. RESULTS: 80% reported PTE. Of this, 79% still experienced current repercussions and almost a half presented symptomatology. Gender, number of events, and PTE characteristics (perceived and grave symptoms) were associated. CONCLUSIONS: Results suggest to intervene early to reduce the risk of developing a disorder.

OBJETIVO: Describir la ocurrencia de eventos potencialmente traumáticos (EPT) en estudiantes de preparatoria, medir la sintomatología postraumática subumbral en quienes aún sufren repercusiones de un EPT y asociar la sintomatología con variables sociodemográficas y características del EPT. MATERIAL Y MÉTODOS: Estudio transversal analítico realizado en un muestra por conveniencia de 1000 estudiantes de tres preparatorias del Estado de México. Se aplicó la Escala para Estrés Postraumático en Universitarios Mexicanos. Se evaluó la presencia de síntomas y su frecuencia; la asociación con variables explicativas se realizó con modelos de regresión logística y cuantílica, respectivamente. RESULTADOS: 80% reportó un EPT. De éstos, 79% aún sufría repercusiones actuales y casi la mitad de ellos presentó sintomatología. El sexo, número de eventos y características del EPT (cambios percibidos y gravedad) se encontraron asociados. CONCLUSIONES: Los resultados sugieren intervenir tempranamente para disminuir el riesgo de desarrollar un trastorno.

Small RNA deep sequencing discriminates subsets of extracellular vesicles released by melanoma cells--Evidence of unique microRNA cargos.

Melanoma cells release different types of extracellular vesicles (EVs) into the extracellular milieu that are involved with communication and signaling in the tumor microenvironment. Subsets of EVs include exosomes, microvesicles, and apoptotic bodies that carry protein and genetic (RNA) cargos. To define the contribution of the RNA cargo of melanoma cell derived EVs we performed small RNA sequencing to identify different small RNAs in the EV subsets. Using validated centrifugation protocols, we separated these EV subsets released by the melanoma cell line MML-1, and performed RNA sequencing with the Ion Torrent platform. Various, but different, non-coding RNAs were detected in the EV subsets, including microRNA, mitochondrial associated tRNA, small nucleolar RNA, small nuclear RNA, Ro associated Y-RNA, vault RNA and Y-RNA. We identified in total 1041 miRNAs in cells and EV subsets. Hierarchical clustering showed enrichment of specific miRNAs in exosomes, including hsa-miR-214-3p, hsa-miR-199a-3p and hsa-miR-155-5p, all being associated with melanoma progression. Comparison of exosomal miRNAs with miRNAs in clinical melanoma samples indicate that multiple miRNAs in exosomes also are expressed specifically in melanoma tissues, but not in benign naevi. This study shows for the first time the presence of distinct small RNAs in subsets of EVs released by melanoma cells, with significant similarities to clinical melanoma tissue, and provides unique insights into the contribution of EV associated extracellular RNA in cancer.