Small RNA Profiling in an HTLV-1-Infected Patient with Acute Adult T-Cell Leukemia-Lymphoma at Diagnosis and after Maintenance Therapy: A Case Study.

Small RNAs (sRNAs) are epigenetic regulators of essential biological processes associated with the development and progression of leukemias, including adult T-cell leukemia/lymphoma (ATLL) caused by human T-cell lymphotropic virus type 1 (HTLV-1), an oncogenic human retrovirus originally discovered in a patient with adult T-cell leukemia/lymphoma. Here, we describe the sRNA profile of a 30-year-old woman with ATLL at the time of diagnosis and after maintenance therapy with the aim of correlating expression levels with response to therapy.

Identification of miRnas with possible prognostic roles for HAM/TSP.

Human T-cell lymphotropic virus type 1 (HTLV-1)-associated myelopathy/tropic spastic paraparesis (HAM/TSP) is an insidiously progressive spinal cord disease for which there is no effective treatment. There is great interest in developing potential biomarkers to predict the pathogenesis of HAM/TSP disease. In this study, Illumina Massive Parallel Sequencing (MPS) technology was used to investigate the cellular global noncoding RNAome expression profile in HAM/TSP patients (n = 10), asymptomatic HTLV-1-infected carriers (ASP, n = 8), and a second group of healthy controls (n = 5). Various bioinformatics tools were used to align, annotate, and profile the sRNA-MPS reads. Among the 402 sRNAs detected, 251 were known and 50 were potentially novel sRNAs in the HAM and ASP groups compared with the HC group. Sixty-eight known sRNAs were significantly different between the ASP and HAM groups. Eighty-eight mature miRNAs were downregulated in subjects from HAM compared with ASP. Three of these miRs (hsa-miR-185-5p, 32-5p, and 192-5p) have the potential to be used as biomarkers for predicting the pathogenesis of HAM/TSP. The seven most deregulated miRs target genes have been associated with a variety of biological processes and molecular functions. The reactome pathways relevant to our findings provide a rich source of data and offer the opportunity to better understand sRNA regulation and function in HTLV-1 pathophysiology. To the best of our knowledge, this study is the first to demonstrate evaluates sRNAs in HTLV-1 patients with HAM/TSP.

A higher number of SARS-COV-2 infections in quilombola communities than in the local population in Brazil.

The historical and social vulnerability of quilombola communities in Brazil can make them especially fragile in the face of COVID-19, considering that several individuals have precarious health systems and inadequate access to water. This work aimed to characterize the frequency of SARS-COV-2 infections and the presence of IgM and IgG SARS-CoV-2 antibodies in quilombola populations and their relationship with the presence of risk factors or preexisting chronic diseases in the quilombola communities. We analyzed the sociodemographic and clinical characteristics, serological status, comorbidities, and symptoms of 1,994 individuals (478 males and 1,536 females) from 18 Brazilian municipalities in the State of Sergipe of quilombola communities, which were evaluated at different epidemiological weeks, starting at the 32nd (August 6th) and ending at the 40th (October 3rd) epidemiological week. More than 70% of studied families live in rural areas and they have an extreme poverty social status. Although we found a higher number of SARS-COV-2 infections in quilombola communities than in the local population, their SARS-CoV-2 reactivity and IgM and IgG positivity varied across the communities investigated. Arterial hypertension was the most risk factor, being found in 27.8% of the individuals (9.5% in stage 1, 10.8% in stage 2, and 7.5% in stage 3). The most common COVID-19 symptoms and comorbidities were headache, runny nose, flu, and dyslipidemia. However, most individuals were asymptomatic (79.9%). Our data indicate that mass testing must be incorporated into public policy to improve the health care system available to quilombola populations during a future pandemic or epidemic.

Identification of miRnas with possible prognostic roles for HAM/TSP

Human T-cell lymphotropic virus type 1 (HTLV-1)-associated myelopathy/tropic spastic paraparesis (HAM/TSP) is an insidiously progressive spinal cord disease for which there is no effective treatment. There is great interest in developing potential biomarkers to predict the pathogenesis of HAM/TSP disease. In this study, Illumina Massive Parallel Sequencing (MPS) technology was used to investigate the cellular global noncoding RNAome expression profile in HAM/TSP patients (n = 10), asymptomatic HTLV-1-infected carriers (ASP, n = 8), and a second group of healthy controls (n = 5). Various bioinformatics tools were used to align, annotate, and profile the sRNA-MPS reads. Among the 402 sRNAs detected, 251 were known and 50 were potentially novel sRNAs in the HAM and ASP groups compared with the HC group. Sixty-eight known sRNAs were significantly different between the ASP and HAM groups. Eighty-eight mature miRNAs were downregulated in subjects from HAM compared with ASP. Three of these miRs (hsa-miR-185-5p, 32-5p, and 192-5p) have the potential to be used as biomarkers for predicting the pathogenesis of HAM/TSP. The seven most deregulated miRs target genes have been associated with a variety of biological processes and molecular functions. The reactome pathways relevant to our findings provide a rich source of data and offer the opportunity to better understand sRNA regulation and function in HTLV-1 pathophysiology. To the best of our knowledge, this study is the first to demonstrate evaluates sRNAs in HTLV-1 patients with HAM/TSP.

Does In-Person Visiting Affect the Number of COVID-19 Cases in Prisons?

Even with the current advances that have been made in regard to COVID-19, such as a better understanding of the disease and the steady growth in the number of vaccinated individuals, it remains a challenge for humanity. Dealing with the disease in prison settings has been particularly difficult. This study sought to discover whether in-person visiting affected the number of cases of SARS-CoV-2 infection in the penitentiaries in the state of Sergipe (Brazil). We conducted a two-phase study (when visiting was suspended and after it recommenced) in seven penitentiaries in Sergipe using immunochromatography and nasopharyngeal swab testing to evaluate whether visiting affects the number of COVID-19 cases. In the first phase (n = 778), 57.6% of inmates reported risk factors and 32.5% were positive for COVID-19 (18.9% IgM, 24.2% IgG, 1% antigen). In the second phase, 19.6% tested positive (13.9% IgM, 7.9% IgG, 0.2% antigen). The occurrence of positive cases of COVID-19 and positive results (IgM and IgG) were significantly higher in the first phase. In the second phase, 56.7% of inmates had received visits and 18.7% were positive for COVID-19 (14% IgM, 7% IgG). Among those who had not received visits, 20.9% tested positive (13.8% IgM, 9.2% IgG, 0.5% antigen). There was no significant difference in positive cases/results between inmates that had and had not received visits. These findings suggest that, under the conditions assessed, visiting does not seem to affect the number of COVID-19 cases in prisons and reinforces the importance of sanitary measures to control dissemination.

Rapid diagnosis of COVID-19 in the first year of the pandemic: A systematic review.

BACKGROUND: COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global health threat and remains a challenge for modern medicine. Rapid and accurate diagnosis of COVID-19 is vital for proper disease and outbreak management. Our review aimed to analyze scientific articles published in the literature addressing the rapid tests available for COVID-19 diagnosis at the first year of the pandemic. METHODS: A systematic review was performed from October 22 to 27, 2020, searching data published in PubMed and Google Scholar databases, using subject headings or keywords related to point of care and rapid test diagnostic for SARS-CoV-2 and COVID-19. RESULTS: The first survey identified 403 articles, but only 23 met the defined criteria for the systematic analysis. The sensitivity and specificity parameters were assessed in 19 studies, and the data suggested that there was lower sensitivity in the period 1 to 7 days after the emergence of symptoms (∼38%) higher sensitivity at 8 to 14 days (∼90%), and the highest at 15 to 39 days (∼98%). Accuracy was reported in six studies, reporting values above 50%. Only three studies reported a possible cross-reaction. CONCLUSIONS: Our findings indicate that the rapid tests used in the first year of the pandemic were tested with a small number of samples and not adequately validated. And the studies that described them were conducted with little scientific rigor.

SARS-CoV-2 has been circulating in northeastern Brazil since February 2020: evidence for antibody detection in asymptomatic patients.

We screened stored samples collected before COVID-19 had been reported in Brazil. 989 samples were tested for SAR-CoV-2 antibodies using two different methods; 16 (1.6%) were positive (7 (43.8%) IgM, 3 (18.8%) IgG and 6 (37.5%) IgG/IgM positive), suggesting SARS-CoV-2 had circulated before the first reported COVID-19 case in Brazil.

Global expression of noncoding RNome reveals dysregulation of small RNAs in patients with HTLV-1–associated adult T-cell leukemia: a pilot study

Background: Adult T cell lymphoma/leukemia (ATLL) is a peripheral T-cell neoplasm caused by human T-cell lymphotropic virus-1 (HTLV-1). Small RNAs (sRNAs), including microRNAs (miRNAs), play a pivotal role in the initiation and development of hematological malignancies and may represent potential therapeutic target molecules. However, little is known about how these molecules impact the pathogenesis of ATLL. In this study, we aimed to identify sRNA expression signatures associated with ATLL and to investigate their potential implication in the pathophysiology of the disease. Methods: Small-RNAseq analysis was performed in peripheral blood mononuclear cells from HTLV-1- associated ATLL (n = 10) in comparison to asymptomatic carriers (n = 8) and healthy controls (n = 5). Sequencing was carried out using the Illumina MiSeq platform, and the deregulation of selected miRNAs was validated by real-time PCR. Pathway analyses of most deregulated miRNA were performed and their global profiling was combined with transcriptome data in ATLL. Results: The sequencing identified specific sRNAs signatures associated with ATLL patients that target pathways relevant in ATLL, such as the transforming growth factor-(βTGF-β), Wnt, p53, apoptosis, and mitogen-activated protein kinase (MAPK) signaling cascades. Network analysis revealed several miRNAs regulating highly connected genes within the ATLL transcriptome. miR-451-3p was the most downregulated miRNA in active patients. Conclusions: Our findings shed light on the expression of specific sRNAs in HTLV-1 associated ATLL, which may represent promising candidates as biomarkers that help monitor the disease activity.

Seroprevalence of SARS-CoV-2 IgM and IgG antibodies in an asymptomatic population in Sergipe, Brazil.

OBJECTIVE: To estimate the prevalence of SARS-CoV-2 antibodies in an asymptomatic population in the state of Sergipe, Brazil.
. METHODS: This cross-sectional study with stratified sampling (sex and age) included serological immunofluorescent tests for IgM and IgG on samples from 3 046 asymptomatic individuals. Sample collection was performed in wet-markets of the 10 most populous cities of Sergipe, Brazil. Exclusion criteria included symptomatic individuals and health workers. The presence of comorbidities was registered.
. RESULTS: Of the 3 046 participants, 1 577 (51.8%) were female and 1 469 (48.2%) were male; the mean age was 39.76 (SD 16.83) years old. 2 921 tests were considered valid for IgM and 2 635 for IgG. Of the valid samples, 347 (11.9% [CI 10.7%-13.1%]) tested positive for IgM and 218 (8.3% [CI 7.2%-9.4%]) tested positive for IgG. Women over 40 had the highest prevalence for IgM (group C, p=0.006; group D p=0.04). The capital Aracaju displayed the highest prevalence for both antibodies; 83 (26.3% [CI 21.6%-31.6%]) tested positive for IgM and 35 (14.6% [CI 10.4%-19.7%]) for IgG. The most prevalent comorbidities were hypertension (64/123 individuals) and diabetes (29/123).
. CONCLUSIONS: A high prevalence of SARS-CoV-2 antibodies was found among asymptomatic persons in Sergipe. Women over 40 showed the highest rates. The capital, Aracaju, displayed the highest seroprevalence. Surveys like this one are important to understand how the virus spreads and to help authorities to plan measures to control it. Repeated serologic testing are required to track the progress of the epidemic.

OBJETIVO: estimar la prevalencia de anticuerpos dirigidos contra el SARS-CoV-2 en una población asintomática del estado de Sergipe, Brasil. MÉTODOS: estudio transversal con muestreo estratificado (por sexo y edad) que incluyó pruebas serológicas de inmunofluorescencia para IgM e IgG en muestras de 3 046 individuos asintomáticos. La recolección de muestras se realizó en los mercados húmedos de las 10 ciudades más pobladas de Sergipe, Brasil. Se excluyó a los individuos sintomáticos y a los trabajadores de la salud. Se registró la presencia de comorbilidades. RESULTADOS: De los 3 046 participantes, 1 577 (51,8%) eran mujeres y 1 469 (48,2%) varones; la edad promedio fue de 39,76 (SD 16,83) años. Se consideraron válidas 2 921 pruebas para la IgM y 2 635 para la IgG. De las muestras válidas, 347 (11,9% [CI 10,7%-13,1%]) resultaron positivas para IgM y 218 (8,3% [CI 7,2%-9,4%]) para IgG. Las mujeres mayores de 40 años tuvieron la mayor prevalencia de IgM (grupo C, p=0,006; grupo D, p=0,04). Aracaju, la capital del estado, mostró la mayor prevalencia para ambos anticuerpos; 83 (26,3% [CI 21,6%-31,6%]) resultaron positivas para IgM y 35 (14,6% [CI 10,4%-19,7%]) para IgG. Las comorbilidades más frecuentes fueron la hipertensión (64/123 individuos) y la diabetes (29/123). CONCLUSIONES: Se encontró una alta prevalencia de anticuerpos contra el SARS-CoV-2 en personas asintomáticas en Sergipe. Las mujeres mayores de 40 años mostraron las tasas más altas. La capital, Aracaju, mostró la mayor seroprevalencia. Las encuestas como esta son importantes para comprender cómo se propaga el virus y para ayudar a las autoridades a planificar medidas de control. Se requieren pruebas serológicas repetidas para dar seguimento al progreso de la epidemia.

Small RNA profiles of HTLV 1 asymptomatic carriers with monoclonal and polyclonal rearrangement of the T cell antigen receptor γ chain using massively parallel sequencing: A pilot study

In the present pilot study, massively parallel sequencing (MPS) technology was used to investigate cellular small RNA (sRNA) levels in the peripheral blood mononuclear cells (PBMCs) of human T­lymphotropic virus type I (HTLV­I) infected asymptomatic carriers with monoclonal (ASM) and polyclonal (ASP) T cell receptor (TCR) γ gene. Blood samples from 15 HTLV­I asymptomatic carriers (seven ASM and eight ASP) were tested for the clonal TCR­Î³ gene and submitted for sRNA library construction together with blood samples of five healthy controls (HCs) using Illumina sequencing platform. The sRNA­sequencing reads were aligned, annotated and profiled using various bioinformatics tools. Based on these results, possible markers were validated in the study samples by performing reverse transcription­quantitative (RT­q)PCR analysis. A total of 76 known sRNAs and 52 putative novel sRNAs were identified. Among them, 44 known and 34 potential novel sRNAs were differentially expressed in the ASM and ASP libraries compared with HCs. In addition, 10 known sRNAs were exclusively dysregulated in the ASM group and one (transfer RNA 65) was significantly upregulated in the ASP group. Homo sapiens (hsa) microRNA (miRNA/mir)­23a­3p, ­28­5p, hsa­let­7e­5p and hsa­mir­28­3p and ­361­5p were the most abundantly upregulated mature miRNAs and hsa­mir­363­3p, ­532­5p, ­106a­5p, ­25­3p and ­30e­5p were significantly downregulated miRNAs (P<0.05) with a >2­fold difference between the ASM and ASP groups compared with HCs. Based on these results, hsa­mir­23a­3p and ­363­3p were selected for additional validation. However, the quantification of these two miRNAs using RT­qPCR did not provide any significant differences. While the present study failed to identify predictive sRNA markers to distinguish between ASM and ASP, the MPS results revealed differential sRNA expression profiles in the PBMCs of HTLV­1 asymptomatic carriers (ASM and ASP) compared with HCs

Seroprevalence of SARS-CoV-2 IgM and IgG antibodies in an asymptomatic population in Sergipe, Brazil

[ABSTRACT]. Objective. To estimate the prevalence of SARS-CoV-2 antibodies in an asymptomatic population in the state of Sergipe, Brazil. Methods. This cross-sectional study with stratified sampling (sex and age) included serological immunofluorescent tests for IgM and IgG on samples from 3 046 asymptomatic individuals. Sample collection was performed in wet-markets of the 10 most populous cities of Sergipe, Brazil. Exclusion criteria included symptomatic individuals and health workers. The presence of comorbidities was registered. Results. Of the 3 046 participants, 1 577 (51.8%) were female and 1 469 (48.2%) were male; the mean age was 39.76 (SD 16.83) years old. 2 921 tests were considered valid for IgM and 2 635 for IgG. Of the valid samples, 347 (11.9% [CI 10.7%–13.1%]) tested positive for IgM and 218 (8.3% [CI 7.2%–9.4%]) tested positive for IgG. Women over 40 had the highest prevalence for IgM (group C, p=0.006; group D p=0.04). The capital Aracaju displayed the highest prevalence for both antibodies; 83 (26.3% [CI 21.6%-31.6%]) tested positive for IgM and 35 (14.6% [CI 10.4%-19.7%]) for IgG. The most prevalent comorbidities were hypertension (64/123 individuals) and diabetes (29/123). Conclusions. A high prevalence of SARS-CoV-2 antibodies was found among asymptomatic persons in Sergipe. Women over 40 showed the highest rates. The capital, Aracaju, displayed the highest seroprevalence. Surveys like this one are important to understand how the virus spreads and to help authorities to plan measures to control it. Repeated serologic testing are required to track the progress of the epidemic.

[RESUMEN]. Objetivo. Estimar la prevalencia de anticuerpos dirigidos contra el SARS-CoV-2 en una población asintomática del estado de Sergipe, Brasil. Métodos. Estudio transversal con muestreo estratificado (por sexo y edad) que incluyó pruebas serológicas de inmunofluorescencia para IgM e IgG en muestras de 3 046 individuos asintomáticos. La recolección de muestras se realizó en los mercados húmedos de las 10 ciudades más pobladas de Sergipe, Brasil. Se excluyó a los individuos sintomáticos y a los trabajadores de la salud. Se registró la presencia de comorbilidades. Resultados. De los 3 046 participantes, 1 577 (51,8%) eran mujeres y 1 469 (48,2%) varones; la edad promedio fue de 39,76 (SD 16,83) años. Se consideraron válidas 2 921 pruebas para la IgM y 2 635 para la IgG. De las muestras válidas, 347 (11,9% [CI 10,7%-13,1%]) resultaron positivas para IgM y 218 (8,3% [CI 7,2%-9,4%]) para IgG. Las mujeres mayores de 40 años tuvieron la mayor prevalencia de IgM (grupo C, p=0,006; grupo D, p=0,04). Aracaju, la capital del estado, mostró la mayor prevalencia para ambos anticuerpos; 83 (26,3% [CI 21,6%-31,6%]) resultaron positivas para IgM y 35 (14,6% [CI 10,4%-19,7%]) para IgG. Las comorbilidades más frecuentes fueron la hipertensión (64/123 individuos) y la diabetes (29/123). Conclusiones. Se encontró una alta prevalencia de anticuerpos contra el SARS-CoV-2 en personas asintomáticas en Sergipe. Las mujeres mayores de 40 años mostraron las tasas más altas. La capital, Aracaju, mostró la mayor seroprevalencia. Las encuestas como esta son importantes para comprender cómo se propaga el virus y para ayudar a las autoridades a planificar medidas de control. Se requieren pruebas serológicas repetidas para dar seguimento al progreso de la epidemia.

Small RNA profiles of HTLV-1 asymptomatic carriers with monoclonal and polyclonal rearrangement of the t-cell antigen receptor γ-chain using massively parallel sequencing: a pilot study

In the present pilot study, massively parallel sequencing (MPS) technology was used to investigate cellular small RNA (sRNA) levels in the peripheral blood mononuclear cells (PBMCs) of human T‑lymphotropic virus type I (HTLV‑I) infected asymptomatic carriers with monoclonal (ASM) and polyclonal (ASP) T cell receptor (TCR) γ gene. Blood samples from 15 HTLV‑I asymptomatic carriers (seven ASM and eight ASP) were tested for the clonal TCR‑γ gene and submitted for sRNA library construction together with blood samples of five healthy controls (HCs) using Illumina sequencing platform. The sRNA‑sequencing reads were aligned, annotated and profiled using various bioinformatics tools. Based on these results, possible markers were validated in the study samples by performing reverse transcription‑quantitative (RT‑q)PCR analysis. A total of 76 known sRNAs and 52 putative novel sRNAs were identified. Among them, 44 known and 34 potential novel sRNAs were differentially expressed in the ASM and ASP libraries compared with HCs. In addition, 10 known sRNAs were exclusively dysregulated in the ASM group and one (transfer RNA 65) was significantly upregulated in the ASP group. Homo sapiens (hsa) microRNA (miRNA/mir)‑23a‑3p, ‑28‑5p, hsa‑let‑7e‑5p and hsa‑mir‑28‑3p and ‑361‑5p were the most abundantly upregulated mature miRNAs and hsa‑mir‑363‑3p, ‑532‑5p, ‑106a‑5p, ‑25‑3p and ‑30e‑5p were significantly downregulated miRNAs (P<0.05) with a >2‑fold difference between the ASM and ASP groups compared with HCs. Based on these results, hsa‑mir‑23a‑3p and ‑363‑3p were selected for additional validation. However, the quantification of these two miRNAs using RT‑qPCR did not provide any significant differences. While the present study failed to identify predictive sRNA markers to distinguish between ASM and ASP, the MPS results revealed differential sRNA expression profiles in the PBMCs of HTLV‑1 asymptomatic carriers (ASM and ASP) compared with HCs.

Data on global expression of non-coding RNome in mice gastrocnemius muscle exposed to jararhagin, snake venom metalloproteinase.

This article describes the data on the global expression profile of small RNA (smRNAs) molecules in mice gastrocnemius muscle exposed to jararhagin, snake venom metalloproteinase. The data include smRNAs in mice gastrocnemius muscle challenged with Jararhagin (Jar; n=4) in the right paw or phosphate-buffered saline (PBS; control; n=4) in the left paw. smRNA-Seq libraries were generated after 24 h of exposure to PBS or jararhagin. The expression profiles of smRNAs including microRNA and snoRNA were compared between both groups. The sequencing data from both groups have been uploaded to Zenodo http://dx.doi.org/10.5281/zenodo.56492.

Prognostic impact of MYCN, DDX1, TrkA, and TrkC gene transcripts expression in neuroblastoma.

BACKGROUND: The aims of this study were to define the mRNA expression profiles of MYCN, DDX1, TrkA, and TrkC in biopsy tumor samples from 64 Brazilian patients with neuroblastomas of different risk stages and to correlate altered expression with prognostic values. PROCEDURE: Patients were retrospectively classified into low- (n = 11), intermediate- (n = 18), and high-risk (n = 35) groups using standard criteria. The mRNA levels of the above genes were measured by quantitative real-time polymerase chain reaction. Univariate analyses were performed and survival curves were plotted by the Kaplan-Meier method. RESULTS: Of the 64 patients, 53% were female and 62.5% were older than 18 months. The 5-year overall survival (OS) for the entire cohort was 40.3%, with inferior median OS in patients identified in the intermediate- and high-risk groups. A significant difference in OS with respect to TrkA mRNA expression was found for the high-risk group vs. either the low- or intermediate-risk groups (P < 0.01, log rank test). Within the intermediate-risk group, neuroblastoma patients with positive TrkA mRNA expression had better clinical outcomes than patients with no TrkA transcript expression (P = 0.004). Another difference in OS was only found between the intermediate- and high-risk groups (P < 0.027, log rank test). No significant correlation of mRNA expression and survival outcome could be detected for the MYCN, DDX1. CONCLUSIONS: Positive expression of TrkA mRNA may be a clinically useful addition to the current risk classification system, allowing the identification of NB tumors with favorable prognosis.