scholarly journals Serum-Derived Neuronal Exosomal microRNAs as Stress-Related Biomarkers in an Atopic Dermatitis Model

Biomedicines ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 1764
Author(s):  
Minkyoung Sung ◽  
Soo-Eun Sung ◽  
Kyung-Ku Kang ◽  
Joo-Hee Choi ◽  
Sijoon Lee ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Next Generation Sequencing ◽  
Psychological Stress ◽  
Expression Patterns ◽  
Inflammatory Skin Disease ◽  
Significant Difference ◽  
As Stress ◽  
The Brain ◽  
Generation Sequencing ◽  
Over Time

Chronic allergic inflammatory skin disease—atopic dermatitis (AD)—is characterized by eczema, pruritus, xeroderma, and lichenification. Psychological stress is one cause of this disease; however, psychological stress will also result from the presence of AD symptoms. Previous studies have shown that psychological stress triggers neuroinflammation in the brain, where microRNAs (miRNAs) in the neuronal exosomes (nEVs) were analyzed to identify the composition of the miRNAs in the nEVs and how they were altered by AD. In this study, the AD model was induced by treatment with 2,4-dinitrochlorobenzene (DNCB). The expression patterns of neuroinflammation markers, such as brain-derived neurotrophic factor, cyclooxygenase-2, and glial fibrillary acidic protein, were subsequently evaluated over time. Among these groups, there was a significant difference in DNCB 14 days expression compared with the control; therefore, nEVs were isolated from serum and next-generation sequencing was performed. The results demonstrate that 9 miRNAs were upregulated and 16 were downregulated in the DNCB 14 days compared with the control. Previous studies have shown that some of these miRNAs are associated with stress and stress-induced depression, which suggests that the miRNAs in nEVs may also be stress-related biomarkers.

Utilizing next-generation sequencing to identify prey DNA in western North Atlantic grey seal Halichoerus grypus diet

2020 ◽  
Vol 655 ◽  
pp. 227-240
Author(s):  
KR Flanders ◽  
ZH Olson ◽  
KA Ono
Keyword(s):  
Next Generation Sequencing ◽  
Feeding Habits ◽  
Atlantic Menhaden ◽  
Halichoerus Grypus ◽  
Frequency Of Occurrence ◽  
Grey Seal ◽  
Next Generation ◽  
Significant Difference ◽  
Generation Sequencing ◽  
Seal Diet

Increasing grey seal Halichoerus grypus abundance in coastal New England is leading to social, political, economic, and ecological controversies. Central to these issues is the foraging ecology and diet composition of the seals. We studied grey seal feeding habits through next-generation sequencing of prey DNA using 16S amplicons from seal scat (n = 74) collected from a breeding colony on Monomoy Island in Massachusetts, USA, and report frequency of occurrence and relative read abundance. We also assigned seal sex to scat samples using a revised PCR assay. In contrast to current understanding of grey seal diet from hard parts and fatty acid analysis, we found no significant difference between male and female diet measured by alpha and beta diversity. Overall, we detected 24 prey groups, 18 of which resolved to species. Sand lance Ammodytes spp. were the most frequently consumed prey group, with a frequency of occurrence (FO) of 97.3%, consistent with previous studies, but Atlantic menhaden Brevoortia tyrannus, the second most frequently consumed species (FO = 60.8%), has not previously been documented in US grey seal diet. Our results suggest that a metabarcoding approach to seal food habits can yield important new ecological insights, but that traditional hard parts analysis does not underestimate consumption of Atlantic cod Gadus morhua (FO = 6.7%, Gadidae spp.) and salmon Salmo salar (FO = 0%), 2 particularly valuable species of concern.

scholarly journals Systematic Analysis of Transcriptomic Profile of Chondrocytes in Osteoarthritic Knee Using Next-Generation Sequencing and Bioinformatics

2018 ◽  
Vol 7 (12) ◽  
pp. 535 ◽  
Author(s):  
Yi-Jen Chen ◽  
Wei-An Chang ◽  
Ling-Yu Wu ◽  
Ya-Ling Hsu ◽  
Chia-Hsin Chen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Family Member ◽  
Subchondral Bone ◽  
Joint Pain ◽  
Expression Patterns ◽  
Cartilage Damage ◽  
Phenotypic Change ◽  
Next Generation ◽  
Arthritic Joint ◽  
Generation Sequencing

The phenotypic change of chondrocytes and the interplay between cartilage and subchondral bone in osteoarthritis (OA) has received much attention. Structural changes with nerve ingrowth and vascular penetration within OA cartilage may contribute to arthritic joint pain. The aim of this study was to identify differentially expressed genes and potential miRNA regulations in OA knee chondrocytes through next-generation sequencing and bioinformatics analysis. Results suggested the involvement of SMAD family member 3 (SMAD3) and Wnt family member 5A (WNT5A) in the growth of blood vessels and cell aggregation, representing features of cartilage damage in OA. Additionally, 26 dysregulated genes with potential miRNA–mRNA interactions were identified in OA knee chondrocytes. Myristoylated alanine rich protein kinase C substrate (MARCKS), epiregulin (EREG), leucine rich repeat containing 15 (LRRC15), and phosphodiesterase 3A (PDE3A) expression patterns were similar among related OA cartilage, subchondral bone and synovial tissue arrays in Gene Expression Omnibus database. The Ingenuity Pathway Analysis identified MARCKS to be associated with the outgrowth of neurite, and novel miRNA regulations were proposed to play critical roles in the pathogenesis of the altered OA knee joint microenvironment. The current findings suggest new perspectives in studying novel genes potentially contributing to arthritic joint pain in knee OA, which may assist in finding new targets for OA treatment.

scholarly journals MicroRNAs in Psychological Stress Reactions and Their Use as Stress-Associated Biomarkers, Especially in Human Saliva

2017 ◽  
Vol 2 (3) ◽  
pp. 1-15 ◽  
Author(s):  
Conrad Wiegand ◽  
Andreas Savelsbergh ◽  
Peter Heusser
Keyword(s):  
Psychological Stress ◽  
Human Saliva ◽  
Reaction Pathways ◽  
Stress Reactions ◽  
Cellular Processes ◽  
Noninvasive Biomarkers ◽  
As Stress ◽  
Acute Psychological Stress ◽  
The Brain ◽  
Reactive Processes

MicroRNAs (miRNAs) play a central role in the regulation of many cellular processes including physiological and psychological stress reaction pathways. Psychological stress is an important factor for the genesis and maintenance of many diseases. Several miRNAs have already been described to be involved in its regulation. The presence of miRNAs in all body fluids implies a widespread role in communication throughout the whole organism and together with their stability makes them formidable candidates as biomarkers. Alterations of stress-associated miRNA expression levels have been found in the brain and whole blood of humans and animals. In this paper, we review the participation of miRNAs in stress-reactive processes as well as their usability as salivary biomarkers of such processes. In conclusion, we suggest that salivary miRNAs may be useful as noninvasive biomarkers to assess epigenetic regulation processes of chronic or acute psychological stress reactions.

scholarly journals The genetic analysis of Chinese patients with clonal cytopenias using targeted next-generation sequencing

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Lijuan Zhang ◽  
YuYe Shi ◽  
Yue Chen ◽  
Shandong Tao ◽  
Wenting Shi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Myelodysplastic Syndromes ◽  
Rna Splicing ◽  
Myeloproliferative Neoplasms ◽  
Chinese Patients ◽  
Newly Diagnosed ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Significant Difference ◽  
Generation Sequencing

Abstract Background Clonal hematopoiesis (CH) can be found in various myeloid neoplasms (MN), such as myelodysplastic syndromes (MDS), myelodysplastic syndromes/myeloproliferative neoplasms (MDS/MPN), also in pre-MDS conditions. Methods Cytogenetics is an independent prognostic factor in MDS, and fluorescence in-situ hybridization (FISH) can be used as an adjunct to karyotype analysis. In the past 5 years, only 35 of 100 newly diagnosed MDS and MDS/MPN patients were identified abnormalities, who underwent the FISH panel. In addition, we examined a cohort of 51 cytopenic patients suspected MDS or MDS/MPN with a 20-gene next generation sequencing (NGS), including 35 newly diagnosed MN patients and 16 clonal cytopenias of undetermined significance (CCUS) patients. Results Compared with the CCUS group, the MN group had higher male ratio (22/13 vs 10/6), cytogenetics abnormalities rate (41.4% vs 21.4%) and frequency of a series of mutations, such as ASXL1 (28.6% vs 25%), U2AF1 (25.7% vs 25%), RUNX1 (20% vs 0.0%); also, higher adverse mutations proportion (75% vs 85.2%), and double or multiple mutations (54.3% vs 43.75%). There were 7 MN patients and 4 CCUS patients who experienced cardio-cerebrovascular embolism events demonstrated a significant difference between the two groups (25% vs 20%). Ten of the 11 patients had somatic mutations, half had DNA methylation, while the other half had RNA splicing. Additionally, six patients had disease transformation, and four patients had mutated U2AF1, including two CCUS cases and two MDS-EB cases. Following up to January 2021, there was no significant difference in over survival between the CCUS and MN groups. Conclusion NGS facilitates the diagnosis of unexplained cytopenias. The monitoring and management of CCUS is necessary, also cardio-cerebrovascular embolism events in patients with CH need attention in the clinical practice.

scholarly journals Investigation of neglected protists Blastocystis sp. and Dientamoeba fragilis in immunocompetent and immunodeficient diarrheal patients using both conventional and molecular methods

2021 ◽  
Vol 15 (10) ◽  
pp. e0009779
Author(s):  
Fakhriddin Sarzhanov ◽  
Funda Dogruman-Al ◽  
Monica Santin ◽  
Jenny G. Maloney ◽  
Ayse Semra Gureser ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gastrointestinal Symptoms ◽  
Molecular Methods ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Next Generation ◽  
Dientamoeba Fragilis ◽  
Significant Difference ◽  
Generation Sequencing ◽  
Immunocompetent Patients

Introduction The clinical significance of Blastocystis sp. and Dientamoeba fragilis in patients with gastrointestinal symptoms is a controversial issue. Since the pathogenicity of these protists has not been fully elucidated, testing for these organisms is not routinely pursued by most laboratories and clinicians. Thus, the prevalence of these organisms and the subtypes of Blastocystis sp. in human patients in Turkey are not well characterized. This study aimed to determine the prevalence of Blastocystis sp. and D. fragilis in the diarrheic stool samples of immunodeficient and immunocompetent patients using conventional and molecular methods and to identify Blastocystis sp. subtypes using next generation sequencing. Material and methods Individual stool specimens were collected from 245 immunodeficient and 193 immunocompetent diarrheic patients between March 2017 and December 2019 at the Gazi University Training and Research Hospital in Ankara, Turkey. Samples were screened for Blastocystis sp. and D. fragilis by conventional and molecular methods. Molecular detection of both protists was achieved by separate qPCRs targeting a partial fragment of the SSU rRNA gene. Next generation sequencing was used to identify Blastocystis sp. subtypes. Results The prevalence of Blastocystis sp. and D. fragilis was 16.7% and 11.9%, respectively as measured by qPCR. The prevalence of Blastocystis sp. and D. fragilis was lower in immunodeficient patients (12.7% and 10.6%, respectively) compared to immunocompetent patients (21.8% and 13.5%, respectively). Five Blastocystis sp. subtypes were identified and the following subtype distribution was observed: ST3 54.4% (n = 37), ST2 16.2% (n = 11), ST1 4.4% (n = 3), ST6 2.9% (n = 2), ST4 1.5% (n = 1), ST2/ST3 11.8% (n = 8) and ST1/ST3 8.8% (n = 6). There was no statistically significant difference in the distribution of Blastocystis sp. subtypes between immunocompetent and immunodeficient patients. Conclusion and recommendation Our findings demonstrated that Blastocystis sp. and D. fragilis are commonly present in immunocompetent and immunodeficient patients with diarrhea. This study is the first to use next generation sequencing to address the presence of Blastocystis sp. mixed subtypes and intra-subtype variability in clinical samples in Turkey.

scholarly journals A case report of SMARCA4/BRG1-deficient non-small cell lung cancer with a spindle cell component found by next-generation sequencing of a brain metastasis

2020 ◽  
Author(s):  
Hiroko Ikeda ◽  
Takashi Sone ◽  
Kazuo Kasahara ◽  
Satoko Nakada ◽  
Kaori Yoshimura ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Next Generation Sequencing ◽  
Spindle Cell ◽  
Small Cell ◽  
Pathological Examination ◽  
Next Generation ◽  
Small Cell Lung ◽  
Immunohistochemical Examination ◽  
The Brain ◽  
Generation Sequencing

Abstract Background: Several studies of different cancers have revealed mutations in switch/sucrose non-fermenting (SWI/SNF) complex genes. Brahma-related gene 1 (BRG1), which is encoded by SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 4 (SMARCA4), is a member of this complex. SMARCA4/BRG-1-deficient non-small cell lung carcinoma (NSCLC) has been considered a subset of lung cancer that has distinct clinical, pathological, and molecular characteristics, which implies its relationship with SMARCA4/BRG1-deficient thoracic sarcoma. Case presentation: We experienced a case of SMARCA4/BRG1-deficient lung cancer in a 40-year-old female patient with a history of smoking. Magnetic resonance imaging revealed a large mass in the right lung apex with an extension to the extrapulmonary region and cerebral metastasis. Histological analysis showed poorly differentiated carcinoma with spindle cell components. She was diagnosed with NSCLC (stage IV) at that point. An EGFR mutation and ALK and ROS1 rearrangement were not detected, and then treated with chemoradiotherapy. Overall, the tumors were resistant to chemotherapy, and therefore, after 2 years, the brain tumor was excised for histological and molecular analysis. Histologically, the brain mass was an undifferentiated tumor with round cells and glandular components. The mutation in SMARCA4 in the brain specimen was identified by next-generation sequencing. Immunohistochemical examination revealed a complete loss of BRG1. SMARCA4/BRG1-deficient thoracic sarcoma had been raised as a differential diagnosis, collectively, she was diagnosed with SMARCA4/BRG1-deficient NSCLC considering for the result of positivity for cytokeratin AE1/AE3 and claudin-4, and negativity for Sal-like protein 4, CD34, and SRY-box 2 by immunohistochemical examination. Regrettably, a definitive diagnosis required approximately 2 years. She is alive with disease at 30 months after the presentation. Conclusions: The diagnosis of SMARCA4/BRG1-deficient NSCLC is frequently difficult because of no specific morphology and necessity of discrimination from SMARCA4/BRG1-deficient thoracic sarcoma, which is the practical reason this disease is sometimes missed. Immunohistochemistry for BRG1 should be encouraged for the pathological examination of NSCLC with any histology for the prompt and precise diagnosis of SMARCA4/BRG1-deficient NSCLC.

scholarly journals Megakaryocytes differentially sort mRNAs for matrix metalloproteinases and their inhibitors into platelets: a mechanism for regulating synthetic events

Blood ◽  
2011 ◽  
Vol 118 (7) ◽  
pp. 1903-1911 ◽  
Author(s):  
Luca Cecchetti ◽  
Neal D. Tolley ◽  
Noemi Michetti ◽  
Loredana Bury ◽  
Andrew S. Weyrich ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Matrix Metalloproteinases ◽  
Mrna Expression ◽  
Vascular Remodeling ◽  
Differentially Express ◽  
Expression Patterns ◽  
Critical Role ◽  
Rna Seq ◽  
Next Generation ◽  
Generation Sequencing

Abstract Megakaryocytes transfer a diverse and functional transcriptome to platelets during the final stages of thrombopoiesis. In platelets, these transcripts reflect the expression of their corresponding proteins and, in some cases, serve as a template for translation. It is not known, however, if megakaryocytes differentially sort mRNAs into platelets. Given their critical role in vascular remodeling and inflammation, we determined whether megakaryocytes selectively dispense transcripts for matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs) into platelets. Next-generation sequencing (RNA-Seq) revealed that megakaryocytes express mRNA for 10 of the 24 human MMP family members. mRNA for all of these MMPs are present in platelets with the exception of MMP-2, 14, and 15. Megakaryocytes and platelets also express mRNA for TIMPs 1-3, but not TIMP-4. mRNA expression patterns predicted the presence and, in most cases, the abundance of each corresponding protein. Nonetheless, exceptions were observed: MMP-2 protein is present in platelets but not its transcript. In contrast, quiescent platelets express TIMP-2 mRNA but only traces of TIMP-2 protein. In response to activating signals, however, platelets synthesize significant amounts of TIMP-2 protein. These results demonstrate that megakaryocytes differentially express mRNAs for MMPs and TIMPs and selectively transfer a subset of these into platelets. Among the platelet messages, TIMP-2 serves as a template for signal-dependent translation.

scholarly journals Validation of Next-Generation Sequencing and Array Comparative Genomic Hybridization for Diagnosis and Screening of Reciprocal and Robertsonian Translocations in Human Blastocysts

2020 ◽  
Author(s):  
Shengrong Du ◽  
Yun-Hong Lin ◽  
Yan Sun ◽  
Qing-Fen Chen ◽  
Zhi-Qing Huang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Comparative Genomic Hybridization ◽  
Array Comparative Genomic Hybridization ◽  
Cell Mass ◽  
Comparative Genomic ◽  
Next Generation ◽  
Genomic Hybridization ◽  
Robertsonian Translocations ◽  
Significant Difference ◽  
Generation Sequencing

Abstract Background: Advances in biotechnology, especially next-generation sequencing (NGS) and array comparative genomic hybridization (aCGH) approaches, have improved preimplantation genetic screening; however, these methods have not been directly compared. This study was carried out to identify the more promising method for screening reciprocal and Robertsonian translocations. Here, blastocysts from carriers with reciprocal and Robertsonian translocations were retrospectively evaluated and results from preimplantation genetic testing in 272 blastocytes were analysed for parental unbalanced translocations using aCGH and NGS. Results: There was no significant difference in the no embryo-transfer rate between aCGH and NGS. Among 59 blastocysts screened in the aCGH group, 32.76% were normal embryos and 67.24% were abnormal embryos, including 36.21% embryos with a translocation, 17.24% with no translocation, and 15.52% with combined abnormalities. Similar results were obtained from the 214 blastocysts tested in the NGS group. In women <35-years, more normal blastocysts were identified in the NGS group compared to the aCGH group. There was a higher rate of euploidy among blastocysts with higher quality grades in the NGS group than in the aCGH group for the trophectoderm (43.51% vs 29.41%) and inner cell mass (59.11% vs 25.00%). Conclusion: Equivalent clinical findings were observed for aCGH and NGS for parental reciprocal chromosomal translocations. However, NGS has the potential to overcome the inherent limitations of aCGH, including the detection of mosaicism and smaller partial gains/losses, thereby providing improvements in the detection of euploid blastocysts, along with enhanced reliability and sensitivity.

scholarly journals Psychological Stress of Parents of Children With Atopic Dermatitis: The Korea National Health and Nutrition Examination Survey

2021 ◽  
Author(s):  
Hyun Ji Lee ◽  
Gyu-Na Lee ◽  
Ji Hyun Lee ◽  
Ju Hee Han ◽  
Kyungdo Han ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Psychological Stress ◽  
National Health ◽  
Suicide Ideation ◽  
Skin Condition ◽  
Family Quality Of Life ◽  
Nutrition Examination Survey ◽  
Cross Sectional ◽  
Health And Nutrition ◽  
Significant Difference

Abstract Background: Atopic dermatitis (AD) is a chronically relapsing inflammatory skin condition that has profound impacts on patient and family quality of life.Objectives: To investigate the psychological stress of parents of children with AD in Korea using data from the Korean National Health and Nutrition Examination Survey (KNHANES).Methods: The cross-sectional study included parents of 8,575 participants under age 19 (970 with AD and 5,733 without AD) from the 2009–2012 KNHANES. Self-perception of stress, depressed mood, suicidal ideation, and diagnosis of depression by a physician were assessed for determination of psychological distress. Results: After adjusting for age, gender, education level, occupation, and marital status, logistic regression analyses indicated that mothers of children with AD showed higher frequency of stress perception (adjusted odds ratio [aOR] 1.458 [95% confidence interval (CI), 1.223-1.739], p < 0.0001) and suicide ideation (aOR 1.403 [95% CI 1.099-1.791], p = 0.0066) than those without AD. In contrast, fathers of children with AD did not show a significant difference compared to those of children without AD.Conclusions: Understanding the psychological stress of parents of children with AD is important for clinicians as evaluation, management, and support for parents, especially mothers, of children with AD are required.

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