GIInger predicts homologous recombination deficiency and patient response to PARPi treatment from shallow genomic profiles.

Homologous recombination deficiency (HRD) is a predictive biomarker for poly(ADP-ribose) polymerase 1 inhibitor (PARPi) sensitivity. Routine HRD testing relies on identifying BRCA mutations, but additional HRD-positive patients can be identified by measuring genomic instability (GI), a consequence of HRD. However, the cost and complexity of available solutions hamper GI testing. We introduce a deep learning framework, GIInger, that identifies GI from HRD-induced scarring observed in low-pass whole-genome sequencing data. GIInger seamlessly integrates into standard BRCA testing workflows and yields reproducible results concordant with a reference method in a multisite study of 327 ovarian cancer samples. Applied to a BRCA wild-type enriched subgroup of 195 PAOLA-1 clinical trial patients, GIInger identified HRD-positive patients who experienced significantly extended progression-free survival when treated with PARPi. GIInger is, therefore, a cost-effective and easy-to-implement method for accurately stratifying patients with ovarian cancer for first-line PARPi treatment.

Combined Aerobic and Strength Training Improves Dynamic Stability and can Prevent against Static Stability Decline in Postmenopausal Women: A Randomized Clinical Trial.

OBJECTIVE: To analyze the effect of combined training (CT) in postural control and gait parameters in postmenopausal women. METHODS: A parallel-group, randomized, control study was conducted with 16 weeks of combined training (n = 16) versus a non-training control group (n = 12) in postmenopausal women (aged 59.3 ± 8.0). Pre and postintervention assessments included postural control (using an AMTI force platform - Advanced Mechanical Technology, Inc., Watertown, MA, USA) and gait impairments (using baropodometry). In addition, the upper limb strength and abdominal tests, as well as aerobic capacity, assessed functional indicators. RESULTS: The CT intervention in postmenopausal women resulted in improved gait (stride length (p = 0.006); speed (p = 0.013); double support time (p = 0.045); and improved postural control (displacement area of postural sway in a normal base of support with eyes open (p = 0.006). Combined training increased functional indicators (abdominal - p = 0.031; aerobic capacity - p = 0.002). CONCLUSION: In conclusion, combined aerobic plus strength training effectively improved gait and balance control in older women. The postmenopausal women from the CT group walked faster and with bigger steps after the intervention than the control group. In addition, they presented decreased postural sway in standing and decreased the percentage of double support time while walking, which means improved static and dynamic balance control and functional indicators.

OBJETIVO: Analisar o efeito do treinamento combinado (TC) no controle postural e nos parâmetros da marcha em mulheres na pós-menopausa. MéTODOS: Foi realizado um estudo controlado randomizado de grupos paralelos com 16 semanas de treinamento combinado (n = 16) versus um grupo controle sem treinamento (n = 12) em mulheres na pós-menopausa (59,3 ± 8,0 anos). As avaliações pré e pós-intervenção incluíram controle postural (usando a plataforma de força AMTI) e deficiências da marcha (usando baropodometria). Além disso, os testes de força de membros superiors e abdominal, bem como a capacidade aeróbica, avaliaram indicadores funcionais. RESULTADOS: A intervenção do TC em mulheres na pós-menopausa resultou em melhora da marcha (comprimento da passada (p = 0,006), velocidade (p = 0,013), tempo de apoio duplo (p = 0,045) e controle postural aprimorado (área de deslocamento da oscilação postural em base de apoio normal com olhos abertos (p = 0,006). O TC aumentou os indicadores funcionais (abdominal - p = 0,031; capacidade aeróbia - p = 0,002). CONCLUSãO: Em conclusão, o TC de força e aeróbico melhorou efetivamente o controle da marcha e do equilíbrio em mulheres idosas. As mulheres na pós-menopausa do grupo CT caminharam mais rápido e com passos maiores após a intervenção do que o grupo controle. Além disso, elas apresentaram redução da oscilação postural em pé e do percentual de tempo de apoio duplo durante a caminhada, o que significa melhora no controle do equilíbrio estático e dinâmico e dos indicadores funcionais.

Combined Aerobic and Strength Training Improves Dynamic Stability and can Prevent against Static Stability Decline in Postmenopausal Women: A Randomized Clinical Trial / O treinamento de força e aeróbio combinado melhora a estabilidade dinâmica e pode prevenir contra o declínio da estabilidade estática em mulheres na pósmenopausa: um ensaio clínico randomizado

Abstract Objective To analyze the effect of combined training (CT) in postural control and gait parameters in postmenopausal women. Methods A parallel-group, randomized, control study was conducted with 16 weeks of combined training (n = 16) versus a non-training control group (n = 12) in postmenopausal women (aged 59.3 ± 8.0). Pre and postintervention assessments included postural control (using an AMTI force platform - Advanced Mechanical Technology, Inc., Watertown, MA, USA) and gait impairments (using baropodometry). In addition, the upper limb strength and abdominal tests, as well as aerobic capacity, assessed functional indicators. Results The CT intervention in postmenopausal women resulted in improved gait (stride length (p = 0.006); speed (p = 0.013); double support time (p = 0.045); and improved postural control (displacement area of postural sway in a normal base of support with eyes open (p = 0.006). Combined training increased functional indicators (abdominal - p = 0.031; aerobic capacity - p = 0.002). Conclusion In conclusion, combined aerobic plus strength training effectively improved gait and balance control in older women. The postmenopausal women from the CT group walked faster and with bigger steps after the intervention than the control group. In addition, they presented decreased postural sway in standing and decreased the percentage of double support time while walking, which means improved static and dynamic balance control and functional indicators.

Resumo Objetivo Analisar o efeito do treinamento combinado (TC) no controle postural e nos parâmetros da marcha em mulheres na pós-menopausa. Métodos Foi realizado um estudo controlado randomizado de grupos paralelos com 16 semanas de treinamento combinado (n = 16) versus um grupo controle sem treinamento (n = 12) em mulheres na pós-menopausa (59,3 ± 8,0 anos). As avaliações pré e pós-intervenção incluíram controle postural (usando a plataforma de força AMTI) e deficiências da marcha (usando baropodometria). Além disso, os testes de força de membros superiors e abdominal, bem como a capacidade aeróbica, avaliaram indicadores funcionais. Resultados A intervenção do TC em mulheres na pós-menopausa resultou em melhora da marcha (comprimento da passada (p = 0,006), velocidade (p = 0,013), tempo de apoio duplo (p = 0,045) e controle postural aprimorado (área de deslocamento da oscilação postural em base de apoio normal com olhos abertos (p = 0,006). O TC aumentou os indicadores funcionais (abdominal - p = 0,031; capacidade aeróbia - p = 0,002). Conclusão Em conclusão, o TC de força e aeróbico melhorou efetivamente o controle da marcha e do equilíbrio em mulheres idosas. As mulheres na pós-menopausa do grupo CT caminharam mais rápido e com passos maiores após a intervenção do que o grupo controle. Além disso, elas apresentaram redução da oscilação postural em pé e do percentual de tempo de apoio duplo durante a caminhada, o que significa melhora no controle do equilíbrio estático e dinâmico e dos indicadores funcionais.

Improved NGS-based detection of microsatellite instability using tumor-only data.

Microsatellite instability (MSI) is a molecular signature of mismatch repair deficiency (dMMR), a predictive marker of immune checkpoint inhibitor therapy response. Despite its recognized pan-cancer value, most methods only support detection of this signature in colorectal cancer. In addition to the tissue-specific differences that impact the sensitivity of MSI detection in other tissues, the performance of most methods is also affected by patient ethnicity, tumor content, and other sample-specific properties. These limitations are particularly important when only tumor samples are available and restrict the performance and adoption of MSI testing. Here we introduce MSIdetect, a novel solution for NGS-based MSI detection. MSIdetect models the impact of indel burden and tumor content on read coverage at a set of homopolymer regions that we found are minimally impacted by sample-specific factors. We validated MSIdetect in 139 Formalin-Fixed Paraffin-Embedded (FFPE) clinical samples from colorectal and endometrial cancer as well as other more challenging tumor types, such as glioma or sebaceous adenoma or carcinoma. Based on analysis of these samples, MSIdetect displays 100% specificity and 96.3% sensitivity. Limit of detection analysis supports that MSIdetect is sensitive even in samples with relatively low tumor content and limited microsatellite instability. Finally, the results obtained using MSIdetect in tumor-only data correlate well (R=0.988) with what is obtained using tumor-normal matched pairs, demonstrating that the solution addresses the challenges posed by MSI detection from tumor-only data. The accuracy of MSI detection by MSIdetect in different cancer types coupled with the flexibility afforded by NGS-based testing will support the adoption of MSI testing in the clinical setting and increase the number of patients identified that are likely to benefit from immune checkpoint inhibitor therapy.

The activity of human enhancers is modulated by the splicing of their associated lncRNAs.

Pervasive enhancer transcription is at the origin of more than half of all long noncoding RNAs in humans. Transcription of enhancer-associated long noncoding RNAs (elncRNA) contribute to their cognate enhancer activity and gene expression regulation in cis. Recently, splicing of elncRNAs was shown to be associated with elevated enhancer activity. However, whether splicing of elncRNA transcripts is a mere consequence of accessibility at highly active enhancers or if elncRNA splicing directly impacts enhancer function, remains unanswered. We analysed genetically driven changes in elncRNA splicing, in humans, to address this outstanding question. We showed that splicing related motifs within multi-exonic elncRNAs evolved under selective constraints during human evolution, suggesting the processing of these transcripts is unlikely to have resulted from transcription across spurious splice sites. Using a genome-wide and unbiased approach, we used nucleotide variants as independent genetic factors to directly assess the causal relationship that underpin elncRNA splicing and their cognate enhancer activity. We found that the splicing of most elncRNAs is associated with changes in chromatin signatures at cognate enhancers and target mRNA expression. We provide evidence that efficient and conserved processing of enhancer-associated elncRNAs contributes to enhancer activity.

Analysis of Eukaryotic lincRNA Sequences Indicates Signatures of Hindered Translation Linked to Selection Pressure.

Long intergenic noncoding RNAs (lincRNAs) represent a large fraction of transcribed loci in eukaryotic genomes. Although classified as noncoding, most lincRNAs contain open reading frames (ORFs), and it remains unclear why cytoplasmic lincRNAs are not or very inefficiently translated. Here, we analyzed signatures of hindered translation in lincRNA sequences from five eukaryotes, covering a range of natural selection pressures. In fission yeast and Caenorhabditis elegans, that is, species under strong selection, we detected significantly shorter ORFs, a suboptimal sequence context around start codons for translation initiation, and trinucleotides ("codons") corresponding to less abundant tRNAs than for neutrally evolving control sequences, likely impeding translation elongation. For human, we detected signatures for cell-type-specific hindrance of lincRNA translation, in particular codons in abundant cytoplasmic lincRNAs corresponding to lower expressed tRNAs than control codons, in three out of five human cell lines. We verified that varying tRNA expression levels between cell lines are reflected in the amount of ribosomes bound to cytoplasmic lincRNAs in each cell line. We further propose that codons at ORF starts are particularly important for reducing ribosome-binding to cytoplasmic lincRNA ORFs. Altogether, our analyses indicate that in species under stronger selection lincRNAs evolved sequence features generally hindering translation and support cell-type-specific hindrance of translation efficiency in human lincRNAs. The sequence signatures we have identified may improve predicting peptide-coding and genuine noncoding lincRNAs in a cell type.

Recommendations for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples.

OBJECTIVES: Genotyping of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been instrumental in monitoring viral evolution and transmission during the pandemic. The quality of the sequence data obtained from these genotyping efforts depends on several factors, including the quantity/integrity of the input material, the technology, and laboratory-specific implementation. The current lack of guidelines for SARS-CoV-2 genotyping leads to inclusion of error-containing genome sequences in genomic epidemiology studies. We aimed to establish clear and broadly applicable recommendations for reliable virus genotyping. METHODS: We established and used a sequencing data analysis workflow that reliably identifies and removes technical artefacts; such artefacts can result in miscalls when using alternative pipelines to process clinical samples and synthetic viral genomes with an amplicon-based genotyping approach. We evaluated the impact of experimental factors, including viral load and sequencing depth, on correct sequence determination. RESULTS: We found that at least 1000 viral genomes are necessary to confidently detect variants in the SARS-CoV-2 genome at frequencies of ≥10%. The broad applicability of our recommendations was validated in over 200 clinical samples from six independent laboratories. The genotypes we determined for clinical isolates with sufficient quality cluster by sampling location and period. Our analysis also supports the rise in frequencies of 20A.EU1 and 20A.EU2, two recently reported European strains whose dissemination was facilitated by travel during the summer of 2020. CONCLUSIONS: We present much-needed recommendations for the reliable determination of SARS-CoV-2 genome sequences and demonstrate their broad applicability in a large cohort of clinical samples.

Translation is required for miRNA-dependent decay of endogenous transcripts.

Post-transcriptional repression of gene expression by miRNAs occurs through transcript destabilization or translation inhibition. mRNA decay is known to account for most miRNA-dependent repression. However, because transcript decay occurs co-translationally, whether target translation is a requirement for miRNA-dependent transcript destabilization remains unknown. To decouple these two molecular processes, we used cytosolic long noncoding RNAs (lncRNAs) as models for endogenous transcripts that are not translated. We show that, despite interacting with the miRNA-loaded RNA-induced silencing complex, the steady-state abundance and decay rates of these transcripts are minimally affected by miRNA loss. To further validate the apparent requirement of translation for miRNA-dependent decay, we fused two lncRNA candidates to the 3'-end of a protein-coding gene reporter and found this results in their miRNA-dependent destabilization. Further analysis revealed that the few natural lncRNAs whose levels are regulated by miRNAs in mESCs tend to associate with translating ribosomes, and possibly represent misannotated micropeptides, further substantiating the necessity of target translation for miRNA-dependent transcript decay. In summary, our analyses suggest that translation is required for miRNA-dependent transcript destabilization, and demonstrate that the levels of coding and noncoding transcripts are differently affected by miRNAs.

A circular RNA generated from an intron of the insulin gene controls insulin secretion.

Fine-tuning of insulin release from pancreatic ß-cells is essential to maintain blood glucose homeostasis. Here, we report that insulin secretion is regulated by a circular RNA containing the lariat sequence of the second intron of the insulin gene. Silencing of this intronic circular RNA in pancreatic islets leads to a decrease in the expression of key components of the secretory machinery of ß-cells, resulting in impaired glucose- or KCl-induced insulin release and calcium signaling. The effect of the circular RNA is exerted at the transcriptional level and involves an interaction with the RNA-binding protein TAR DNA-binding protein 43 kDa (TDP-43). The level of this circularized intron is reduced in the islets of rodent diabetes models and of type 2 diabetic patients, possibly explaining their impaired secretory capacity. The study of this and other circular RNAs helps understanding ß-cell dysfunction under diabetes conditions, and the etiology of this common metabolic disorder.

The Transcriptomic Response of the Murine Thyroid Gland to Iodide Overload and the Role of the Nrf2 Antioxidant System.

BACKGROUND: Thyroid follicular cells have physiologically high levels of reactive oxygen species because oxidation of iodide is essential for the iodination of thyroglobulin (Tg) during thyroid hormone synthesis. Thyroid follicles (the functional units of the thyroid) also utilize incompletely understood autoregulatory mechanisms to defend against exposure to excess iodide. To date, no transcriptomic studies have investigated these phenomena in vivo. Nuclear erythroid factor 2 like 2 (Nrf2 or Nfe2l2) is a transcription factor that regulates the expression of numerous antioxidant and other cytoprotective genes. We showed previously that the Nrf2 pathway regulates the antioxidant defense of follicular cells, as well as Tg transcription and Tg iodination. We, thus, hypothesized that Nrf2 might be involved in the transcriptional response to iodide overload. METHODS: C57BL6/J wild-type (WT) or Nrf2 knockout (KO) male mice were administered regular water or water supplemented with 0.05% sodium iodide for seven days. RNA from their thyroids was prepared for next-generation RNA sequencing (RNA-Seq). Gene expression changes were assessed and pathway analyses were performed on the sets of differentially expressed genes. RESULTS: Analysis of differentially expressed messenger RNAs (mRNAs) indicated that iodide overload upregulates inflammatory-, immune-, fibrosis- and oxidative stress-related pathways, including the Nrf2 pathway. Nrf2 KO mice showed a more pronounced inflammatory-autoimmune transcriptional response to iodide than WT mice. Compared to previously published datasets, the response patterns observed in WT mice had strong similarities with the patterns typical of Graves' disease and papillary thyroid carcinoma (PTC). Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) also responded to iodide overload, with the latter targeting mRNAs that participate mainly in inflammation pathways. CONCLUSIONS: Iodide overload induces the Nrf2 cytoprotective response and upregulates inflammatory, immune, and fibrosis pathways similar to autoimmune hyperthyroidism (Graves' disease) and PTC.

The Contribution of lincRNAs at the Interface between Cell Cycle Regulation and Cell State Maintenance.

Cell cycle progression is controlled by the interplay of established cell cycle regulators. Changes in these regulators' activity underpin differences in cell cycle kinetics between cell types. We investigated whether long intergenic noncoding RNAs (lincRNAs) contribute to embryonic stem cell cycle adaptations. Using single-cell RNA sequencing data for mouse embryonic stem cells (mESCs) staged as G1, S, or G2/M we found differentially expressed lincRNAs are enriched among cell cycle-regulated genes. These lincRNAs (CC-lincRNAs) are co-expressed with genes involved in cell cycle regulation. We tested the impact of two CC-lincRNA candidates and show using CRISPR activation that increasing their expression is associated with deregulated cell cycle progression. Interestingly, CC-lincRNAs are often differentially expressed between G1 and S, their promoters are enriched in pluripotency transcription factor (TF) binding sites, and their transcripts are frequently co-regulated with genes involved in the maintenance of pluripotency, suggesting a contribution of CC-lincRNAs to mESC cell cycle adaptations.

Publisher Correction: Loss-of-function of the long non-coding RNA A830019P07Rik in mice does not affect insulin expression and secretion.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Loss-of-function of the long non-coding RNA A830019P07Rik in mice does not affect insulin expression and secretion.

Long non-coding RNAs (lncRNAs) contribute to diverse cellular functions and the dysregulation of their expression or function can contribute to diseases, including diabetes. The contributions of lncRNAs to ß-cell development, function and survival has been extensively studied in vitro. However, very little is currently known on the in vivo roles of lncRNAs in the regulation of glucose and insulin homeostasis. Here we investigated the impact of loss-of-function in mice of the lncRNA A830019P07Rik, hereafter P07Rik, which was previously reported to be associated with reduced plasma insulin levels. Compared with wild-type littermates, male and female P07Rik mutant mice did not show any defect in glycaemia and plasma insulin levels in both fed and fasted state. Furthermore, P07Rik mutant mice displayed similar glucose and insulin levels in response to an intra-peritoneal glucose tolerance test. Ex vivo, islets from mutant P07Rik released similar amount of insulin in response to increased glucose concentration as wildtype littermates. In contrast with previous reports, our characterization of P07Rik mouse mutants revealed that loss of function of this lncRNA does not affect glucose and insulin homeostasis in mice.

A Protocol for Transcriptome-Wide Inference of RNA Metabolic Rates in Mouse Embryonic Stem Cells.

The relative ease of mouse Embryonic Stem Cells (mESCs) culture and the potential of these cells to differentiate into any of the three primary germ layers: ectoderm, endoderm and mesoderm (pluripotency), makes them an ideal and frequently used ex vivo system to dissect how gene expression changes impact cell state and differentiation. These efforts are further supported by the large number of constitutive and inducible mESC mutants established with the aim of assessing the contributions of different pathways and genes to cell homeostasis and gene regulation. Gene product abundance is controlled by the modulation of the rates of RNA synthesis, processing, and degradation. The ability to determine the relative contribution of these different RNA metabolic rates to gene expression control using standard RNA-sequencing approaches, which only capture steady state abundance of transcripts, is limited. In contrast, metabolic labeling of RNA with 4-thiouridine (4sU) coupled with RNA-sequencing, allows simultaneous and reproducible inference of transcriptome wide synthesis, processing, and degradation rates. Here we describe, a detailed protocol for 4sU metabolic labeling in mESCs that requires short 4sU labeling times at low concentration and minimally impacts cellular homeostasis. This approach presents a versatile method for in-depth characterization of the gene regulatory strategies governing gene steady state abundance in mESC.

BAZ2A safeguards genome architecture of ground-state pluripotent stem cells.

Chromosomes have an intrinsic tendency to segregate into compartments, forming long-distance contacts between loci of similar chromatin states. How genome compartmentalization is regulated remains elusive. Here, comparison of mouse ground-state embryonic stem cells (ESCs) characterized by open and active chromatin, and advanced serum ESCs with a more closed and repressed genome, reveals distinct regulation of their genome organization due to differential dependency on BAZ2A/TIP5, a component of the chromatin remodeling complex NoRC. On ESC chromatin, BAZ2A interacts with SNF2H, DNA topoisomerase 2A (TOP2A) and cohesin. BAZ2A associates with chromatin sub-domains within the active A compartment, which intersect through long-range contacts. We found that ground-state chromatin selectively requires BAZ2A to limit the invasion of active domains into repressive compartments. BAZ2A depletion increases chromatin accessibility at B compartments. Furthermore, BAZ2A regulates H3K27me3 genome occupancy in a TOP2A-dependent manner. Finally, ground-state ESCs require BAZ2A for growth, differentiation, and correct expression of developmental genes. Our results uncover the propensity of open chromatin domains to invade repressive domains, which is counteracted by chromatin remodeling to establish genome partitioning and preserve cell identity.

Avaliação da percepção de dor em recém-nascidos por profissionais de saúde de unidade neonatal / Evaluation of pain perception in newborns by neonatal health professionals

Resumo Introdução A crescente utilização de recursos de terapia intensiva neonatal para manter a vida dos recém-nascidos enfermos pode gerar estímulos dolorosos, causando sofrimento a eles. Porém, nem sempre essa dor é percebida pelos profissionais envolvidos no cuidado, embora já exista um interesse crescente por parte deles nesse sentido. Objetivo Avaliar a percepção de dor do recém-nascido por profissionais de saúde que atuam em unidade neonatal. Método Pesquisa qualitativa do tipo exploratória, realizada em um hospital de referência em cuidado neonatal de uma capital do Nordeste. Foram realizadas entrevistas semiestruturadas com todos os profissionais que atuavam na Unidade de Terapia Intensiva Neonatal e/ou na Unidade de Cuidados Intermediários em cuidado direto com o recém-nascido. Utilizou-se da análise de conteúdo na modalidade temática, e os resultados foram agrupados em categorias. Resultados Foram realizadas 36 entrevistas. Os profissionais entrevistados reconheceram que a dor neonatal foi historicamente negligenciada e que hoje as evidências científicas comprovam sua existência. Foram identificadas carência na formação no tema e fragilidade na aplicação do conhecimento na prática. Conclusão Os profissionais têm conhecimento sobre a dor neonatal, entretanto quase não utilizam os parâmetros fisiológicos e possuem pouco conhecimento sobre a literatura científica atual. O principal desafio diz respeito à necessidade de uso sistemático de escalas que garantam a avaliação da dor.

Abstract Background The increasing use of neonatal intensive care resources to maintain the lives of sick infants can generate painful stimuli and cause distress for them. However, this pain is not always perceived by the professionals involved in the care, although there is already an increasing interest on the part of the professionals involved in care. Objective To evaluate the perception of health professionals, who works in a neonatal unit related to newborn pain. Method Qualitative research of the exploratory type was carried out in a reference hospital in neonatal care of a capital of the Northeast. Semi-structured interviews were conducted with all professionals working in the Neonatal Intensive Care Unit and / or Intermediate Care Unit in direct care of the newborn. Content Analysis was used in the thematic modality and the results were grouped into categories. Results 36 interviews were conducted. The professionals interviewed acknowledged that neonatal pain was historically neglected and that scientific evidence today confirms its existence. It was identified lack in the training in the theme and fragility in the application of the knowledge in the practice. Conclusion The professionals have knowledge about neonatal pain; however they still use little physiological parameters and have little knowledge of current scientific literature. The main challenge is the need for systematic use of scales that guarantee the evaluation of pain.

Mixed secondary bacterial infection is associated with severe lesions of chromoblastomycosis in a neglected population from Brazil.

Chromoblastomycosis (CBM) is a chronic subcutaneous infection caused by melanotic fungi, affecting mainly rural workers in tropical and subtropical regions. Secondary bacterial infections (SBIs) in CBM lesions bring complications to the disease, but little is known about the agents involved. Fungal and bacterial identification and epidemiological profile of 50 patients with CBM were analyzed in this study. Bacteria were tested for susceptibility to antibacterial drugs. Fonseacea pedrosoi and Rhinocladiella aquaspersa were the fungal agents isolated. 88% of the patients presented SBI. Gram-positive bacteria coinfected mainly upper limbs, and Gram-negative bacteria were more isolated from lower limbs. Streptococcus pyogenes and mixed bacterial microbiota were associated with severe lesions. Staphylococcus aureus was associated with mixed infections and consequently with the severity of the infection. Resistance to ß-lactams and methicillin was detected. Our results emphasize the necessity of bacterial culture and susceptibility testing as part of routine monitoring CBM cases.

The long non-coding RNA Cerox1 is a post transcriptional regulator of mitochondrial complex I catalytic activity.

To generate energy efficiently, the cell is uniquely challenged to co-ordinate the abundance of electron transport chain protein subunits expressed from both nuclear and mitochondrial genomes. How an effective stoichiometry of this many constituent subunits is co-ordinated post-transcriptionally remains poorly understood. Here we show that Cerox1, an unusually abundant cytoplasmic long noncoding RNA (lncRNA), modulates the levels of mitochondrial complex I subunit transcripts in a manner that requires binding to microRNA-488-3p. Increased abundance of Cerox1 cooperatively elevates complex I subunit protein abundance and enzymatic activity, decreases reactive oxygen species production, and protects against the complex I inhibitor rotenone. Cerox1 function is conserved across placental mammals: human and mouse orthologues effectively modulate complex I enzymatic activity in mouse and human cells, respectively. Cerox1 is the first lncRNA demonstrated, to our knowledge, to regulate mitochondrial oxidative phosphorylation and, with miR-488-3p, represent novel targets for the modulation of complex I activity.

cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture.

Intergenic long noncoding RNAs (lincRNAs) are the largest class of transcripts in the human genome. Although many have recently been linked to complex human traits, the underlying mechanisms for most of these transcripts remain undetermined. We investigated the regulatory roles of a high-confidence and reproducible set of 69 trait-relevant lincRNAs (TR-lincRNAs) in human lymphoblastoid cells whose biological relevance is supported by their evolutionary conservation during recent human history and genetic interactions with other trait-associated loci. Their enrichment in enhancer-like chromatin signatures, interactions with nearby trait-relevant protein-coding loci, and preferential location at topologically associated domain (TAD) boundaries provide evidence that TR-lincRNAs likely regulate proximal trait-relevant gene expression in cis by modulating local chromosomal architecture. This is consistent with the positive and significant correlation found between TR-lincRNA abundance and intra-TAD DNA-DNA contacts. Our results provide insights into the molecular mode of action by which TR-lincRNAs contribute to complex human traits.