Differential expression profiling of human milk derived exosomal MicroRNAs in HIV-1 infected Women from Nigeria
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE143039 | GEO | 2020/01/04
REPOSITORIES: GEO
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Project description:The breast milk plays a crucial role in shaping the initial intestinal microbiota and mucosal immunity of the infant. Interestingly, breastfeeding has proven to be protective against the early onset of immune-mediated diseases including type 1 diabetes (T1D). Studies have shown that exosomes from human breast milk (HM) are enriched in immune-modulating miRNAs suggesting that exosomal miRNAs transferred to the infant could play a critical role in the development of the infant’s immune system. In this study, we extracted exosome exosomal microRNAs (exomiRs) from breast milk of type 1 diabetic and healthy lactating mothers, in order to identify any differences in the exomiR content between the two groups
2019-08-01 | E-MTAB-7336 | biostudies-arrayexpress
Project description:Breast milk is the primary source of nutrition for newborns, and rich in immunological components. microRNAs (miRNAs), a well-defined group of non-coding small RNAs, are present in various body fluids (such as breast milk), which are selectively packaged inside the exosomes, a type of membrane vesicles, secreted by most cell types. These exosomal miRNAs could be actively delivered into recipient cells, and regulate target gene expression and recipient cell function. We present the lactation-related miRNA expression profiles in porcine milk exosomes across entire lactation period in pig industry (newborn to 28 days after birth) using deep sequencing technology. We found that the immune-related miRNAs are presented and enriched in breast milk exosomes, and generally resistant to relatively harsh conditions. Notably, these exosomal miRNAs exhibited the higher abundances in the colostrum (newborn to 3 days after birth) than that in the mature milk (7 to 28 days after birth), as well as in the serum of colostrum-feeding piglets compared with the only mature milk-feeding piglets. These immune-related miRNAs-loaded exosomes in breast milk may be transferred into the infant body via the digestive tract. These observations are prelude to the in-depth investigations of the essential roles of the breast milk in the development of the infant’s immune system. Eight small RNA libraries in porcine breast milk exosomes of six lactigenous stages (0, 3, 7, 14, 21 and 28 days after birth) from three female pigs were sequenced.
2012-09-17 | E-GEOD-36590 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to compare the small RNA expression profile in exosomes isolated from plasma samples from KSHV+/HIV- and KSHV+/HIV+ patients Methods: Total RNA was isolated from plasma exosomes obtained from Ugandan patients with different viral status. A small RNA fraction was gel purified and was used to make sequencing libraries. At least 14 million read sequences were obtained from each library. Non-redondant sequences were then aligned to genomic (hg19) and and mRNA sequence (hg19) using bowtie 2; sequences with perfect-match and 1bp mismatch alignments were retained for further analysis using DEseq2 Methods: Total RNA was isolated from plasma obtained from KSHV-infected patients with or without HIV co-infection. A small RNA fraction was gel purified and was used to make sequencing libraries. At least 14 million read sequences were obtained from each library. Non-redondant sequences were then aligned to genomic (hg19) and and mRNA sequence (hg19) using bowtie 2; sequences with perfect-match and 1bp mismatch alignments were retained for further analysis using DEseq2 Results:Plasma exosomes isolated from either KSHV-infected or KSHV/ HIV co-infected patients exposed to malaria are overwhelmingly populated with YRNAs instead of miRNAs Results: KSHV oral sheeding correlated with the detection of a pro-tumorigenic cellualr miRNA profile in plasma. KSHV plasma viremia is associated with the detec tion of KSHV encoded miRNA in plasma Conclusions: Ugandan patients exposed to Plasmodium falciparum show an unusual repertoire of small RNAs in plasma exosomes, as the exosomal RNA is mostly composed of small RNA from the YRNA biotype Conclusions: Our study represents the first detailed analysis of the small RNA biotypes present in plasma from KSHV infected and KSHV/HIV co-infected patients without clinical sign of KSHV associated malignancies.
2018-02-09 | GSE106238 | GEO
Project description:Human milk (HM) contains an array of regulatory biomolecules including miRNAs, the origin, properties, distribution and functional significance of which are still undetermined. In this study, we used the TaqMan OpenArray System to profile 681 human mature miRNAs in two fractions of HM (cells and lipids) collected from healthy mothers in month 2 of lactation (n=10). Comparisons were performed with maternal peripheral blood mononuclear cells (PBMCs) and plasma collected from the same individuals, as well as with a bovine- and a soy-based infant formulae. HM cells (292 miRNAs) and PBMCs (345 miRNAs) had higher miRNA content than HM lipids (242 miRNAs) and plasma (219 miRNAs), respectively (p<0.05). Despite the wide variation in miRNA profiles and expression between mothers, a strong association was found between HM cells and lipids within a mother, whilst PBMCs and plasma were distinctly different to the two milk fractions, with plasma displaying marked inter-individual variation. Considering the dominance of epithelial cells in mature milk of healthy women, these results suggest that HM cell and lipid miRNAs primarily originate from the mammary epithelium, whilst the maternal circulation may have a smaller contribution. Infant formulae contained very few human miRNA compared to HM. Our findings demonstrate that unlike infant formulae, human milk is a rich source of lactation-specific miRNA, which could be used as a biomarker of the performance and health status of the lactating gland. Given the recently identified stability and gene regulatory functions of food-derived miRNAs, HM miRNAs may contribute to infant protection and development.
2015-03-30 | GSE66358 | GEO
Project description:Despite clear evidence that exosomal microRNAs (miRNAs) are able to modulate the cellular microenvironment and that exosomal RNA cargo selection is often deregulated in pathological conditions, the mechanisms controlling specific RNA sorting into extracellular vescicles are still poorly understood. We identified here the RNA binding protein SYNCRIP (Synaptotagmin-binding Cytoplasmic RNA-Interacting Protein, also known as hnRNP-Q or NSAP1) as a component of the hepatocyte exosomal miRNA sorting machinery. SYNCRIP was found to bind directly a subset of miRNAs enriched in exosomes, sharing a common extra-seed sequence that we named hEXO motif. In vivo knock-down of SYNCRIP impaired microRNA sorting in exosomes and the hEXO motif was proven to play a role in the regulation of miRNA localization, as its embedment into a poorly exported miRNA enhanced its loading into exosomes. These results provide a new insight in the mechanisms of miRNA exosomal sorting process, that ca be exploited to further understand the role of these extracellular vescicles in cell-to-cell communications and the control of tissue micoenvironments.
2016-09-02 | E-MTAB-4502 | biostudies-arrayexpress
Project description:Breast milk is the primary source of nutrition for newborns, and rich in immunological components. microRNAs (miRNAs), a well-defined group of non-coding small RNAs, are present in various body fluids (such as breast milk), which are selectively packaged inside the exosomes, a type of membrane vesicles, secreted by most cell types. These exosomal miRNAs could be actively delivered into recipient cells, and regulate target gene expression and recipient cell function. We present the lactation-related miRNA expression profiles in porcine milk exosomes across entire lactation period in pig industry (newborn to 28 days after birth) using deep sequencing technology. We found that the immune-related miRNAs are presented and enriched in breast milk exosomes, and generally resistant to relatively harsh conditions. Notably, these exosomal miRNAs exhibited the higher abundances in the colostrum (newborn to 3 days after birth) than that in the mature milk (7 to 28 days after birth), as well as in the serum of colostrum-feeding piglets compared with the only mature milk-feeding piglets. These immune-related miRNAs-loaded exosomes in breast milk may be transferred into the infant body via the digestive tract. These observations are prelude to the in-depth investigations of the essential roles of the breast milk in the development of the infant’s immune system.
2012-09-17 | GSE36590 | GEO
Project description:Exososmes, potent intercellular communicators, are supposed to contribute to metastasis formation, which we confirmed for exosomes of the metastatic rat pancreatic adenocarcinoma line BSp73ASML that promote metastatic settlement in lymph nodes and lung of poorly metastatic BSp73ASML cells with a selective CD44v4-v7 (BSp73ASML-CD44vkd) knockdown. To define the molecular pathway(s), whereby exosomes contribute to premetastatic niche preparation, we profiled mRNA miRNA of BSp73ASMLwt and BSp73ASML-CD44vkd- exosomes and evaluated the impact on potential target cells. BSp73ASML exosomes are recovered in the draining lymph node after subcutaneous injection. In vitro, they preferentially bind and are taken-up by lymph node stroma cells (LnStr) and lung fibroblasts (LuFb) that were chosen as exosome targets. BSp73ASMLwt and BSp73ASML-CD44kd exosomes contain a restricted repertoire of mRNA and miRNA, hwere the lattter differe significantly between the two lines and even more pronounced, exosomes derived thereof with a not yet explored dominance of tumor-suppressor miRNA in ASML-CD44kd cells and exosomes. Both, exosomal mRNA and miRNA are recovered in target cells and exosome-uptake is accompanied by significant changes in gene expression. We didn't observe a correlation between exosomal mRNA and changes in target cell mRNA or proteins. Instead transferred miRNA significantly affected target cell mRNA translation as demonstrated for selected, most abundant ASML exosomal miRNA besides others, miR-494 known target MAL (myelin and lymphocytes protein)/cadherin17, and miR-542-3p which targets TRAF/cadherin17. Furthermore, MMP transcription suggested to accompany cadherin17 dwon-regulation was upregulated in miR-494 or miR542-3p transfected or exosome co-cultured LnStr. Taken together, tumor exosomes target in vivo non-transformed cells in premetastatic organs. Exosome uptake induced altered target celll gene expression is strongly promoted by exosomal miRNA where we demonstrate for the first time that exosomes/exosomal miRNA from a metastasizing tumor line can modulate stroma cells from premetastatic organs. Endothelial cells lines were treated with pancreatic adenocarcinoma (AS) derived exosomes or pancreatic adenocarcinoma derived exosomes expressing tetraspanin 8. Total RNA was isolated and used to perform the Agilent gene expression microarrays. In this assay a replicate of endothelial cell lines treated with ASTspan8 were also included. Moreover, total RNA from both base line expression of endothelial cells and rat endothelial fibroblasts were also used to perfrom gene expression microarrays. RNA isolated from Rat endothelial fibroblasts treated with the exosomes derived from rat pancreatic adenocarcinoma and exosomes derived from rat pancreatic adenocarcinoma expressing tetraspanin8 were individually used to perfrom gene expression microarrays. RNA isolated from exosomes derived from rat pancreatic adenocarcinoma cell lines expressing tetraspanin were used to peform gene expresiion to see the base line expression. Another replicate were also used. RNA isolated from base line or control of rat pancreatic adenocarcinoma wild type cells and also base line RNA isolated from rat pancreatic adenocarcinoma cells lines where CD44 was knock-down.
2012-06-12 | E-GEOD-38655 | biostudies-arrayexpress
Project description:Human milk (HM) is rich in miRNAs, which are thought to contribute to infant protection and development. We used deep sequencing to profile miRNAs in the cell and lipid fractions of HM obtained post-feeding from 10 lactating women in month 2, 4, and 6 postpartum. In both HM fractions, 1,195 mature known miRNAs were identified, which were positively associated with the cell (p=0.048) and lipid (p=0.010) content of HM. An additional 5,167 novel miRNA species were predicted, of which 235 were high-confidence miRNAs expressed in ≥3 samples with total reads of >20. HM cells contained more known miRNAs than HM lipids (1,136 and 835 respectively, p<0.001), with 146 of the common species upregulated in HM cells and 133 in HM lipids (p<0.05). Further, the profile of the novel miRNAs was very different between the two HM fractions, with the majority conserved in the cell fraction and being mother-specific. However, out of the 776 known miRNA species commonly present in the two HM fractions, 63.9% were similarly expressed (p>0.05), with great similarities in the profile of top 20 known miRNAs. These were largely similar also between the three lactation stages examined, as were the total miRNA concentration, and the number and overall expression of the known miRNAs commonly present in the two HM fractions (p>0.05). Yet, approximately a third of known miRNAs were differentially expressed during the first 6 months of lactation (p<0.05), with more pronounced miRNA upregulation seen in month 4. These findings indicate that although the total miRNA concentration of HM cells and lipids provided to the infant does not change in the first 6 months of lactation, the miRNA composition is somewhat altered, particularly in month 4 compared to months 2 and 6. This may reflect the remodeling of the gland in response to infant feeding patterns, which usually change after exclusive breastfeeding, and thus adaptation to infant needs.
2016-04-25 | GSE75726 | GEO
Project description:MicroRNAs (miRNAs) are intrinsic regulators in the various cellular processes, and their abnormalities are considered to be involved in the onset of human disorders, including cancer. Circulating miRNA is focused as new cancer biomarker however it is regarded that circulating RNA are released not only from tumor but also by various pathways. Recently, exosomes, small membrane vesicles, have been a major interest in cancer research field, because of their unique biological properties. Exosomes are secreted from various cells and the components (Lipids, mRNAs, miRNAs and proteins) reflect origin of the cells secreting them. Identification of exosomal miRNAs from cancer cells is expected to provide useful biomarkers of cancer. To identify specific exosomal miRNAs as candidate biomarkers for colorectal cancer, we compared exosomal miRNA profiles of 5 colon cancer cell lines with that of normal colon-derived epithelial cells, and isolated a subset of miRNAs as commonly-secreted miRNAs from colon cancer cells Endogenously expression of microRNAs were analyzed by Agilent Human miRNA V3 Microarray (G4470C) using total RNAs of human colon-derived FHC cells and human colon cancer cell lines (HCT116 cells and SW480 cells) at two independent experiments. Exosomal microRNAs were analyzed by microRNA microarray using total RNAs of exosomes from conditioned media of FHC cells, HCT116 cells, and SW480 cells at three independent experiments.As negative control of exosomal microRNAs in conditioned media, FBS-exosomal microRNAs were analyzed at four independent experiments. Exosomes were prepared by step-wise ultra-centrifugation methods. RNA was prepared by Trizol or Trizol-LS reagent (Invitrogen) and RNeasy mini spin column (Qiagen).
2014-04-01 | E-GEOD-39814 | biostudies-arrayexpress
Project description:Milk contains fats, carbohydrates, proteins, RNAs and enzymes, but also mRNA and microRNAs(miRNA), which plays an important role in neonatal innate and adaptive immunity. The following study investigates whether or not miRNA of exosome in milk is a vital pathway for miRNA of milk absorbing. Briefly, 280 pre-miRNAs and 326 mature miRNA were found. 37 exosomal miRNAs were upregulated (twice fold) compared to miRNAs found outside the exosomes. Among these miRNAs, ssc-miR-193a-3p’s expression was up regulated 1467.35 times, while ssc-miR-423-5p、ssc-miR-551a、ssc-miR-138、ssc-miR-1 and ssc-miR-124a were highly concentrated and upregulated from 13.58 to 30.06 times. Moreover, all of these miRNAs play essential roles in cell’s development and basic physiology processes in immune system. Following the analysis of target gene prediction and related signaling pathways, 9262 target genes showed to be mainly concentrated on three signaling pathway: metabolic pathways、pathways in cancer, and Phosphatidylinositol 3-kinase /Protein Kinase B(PI3K/Akt) signaling pathways. In addition, more than 20 miRNAs showed to be highly concentrated on exosomes, such as MECP2、GYS1、 LRRC8A、BCL9L、PHRF1 and ELOVL1, all closely related to immunity and engendering of gene. After performing in-depth research on miRNA’s localization, distribution and function related metabolism, we found that these exosome concentrated miRNA’s target genes were interrelated to development and basic cell functions, like metabolism and immunity. These results imply that miRNAs in breast milk can influence offspring via milk exosomes.
2017-12-05 | GSE107652 | GEO