scholarly journals xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells

2018 ◽  
Author(s):  
Avi Z. Rosenberg ◽  
Carrie Wright ◽  
Karen Fox-Talbot ◽  
Anandita Rajpurohit ◽  
Courtney Williams ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Small Rna ◽  
Mirna Expression ◽  
Low Cost ◽  
Expression Patterns ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Cell Type

AbstractAccurate, RNA-seq based, microRNA (miRNA) expression estimates from primary cells have recently been described. However, this in vitro data is mainly obtained from cell culture, which is known to alter cell maturity/differentiation status, significantly changing miRNA levels. What is needed is a robust method to obtain in vivo miRNA expression values directly from cells. We introduce expression microdissection miRNA small RNA sequencing (xMD-miRNA-seq), a method to isolate cells directly from formalin fixed paraffin-embedded (FFPE) tissues. xMD-miRNA-seq is a low-cost, high-throughput, immunohistochemistry-based method to capture any cell type of interest. As a proof-of-concept, we isolated colon epithelial cells from two specimens and performed low-input small RNA-seq. We generated up to 600,000 miRNA reads from the samples. Isolated epithelial cells, had abundant epithelial-enriched miRNA expression (miR-192; miR-194; miR-200b; miR-200c; miR-215; miR-375) and overall similar miRNA expression patterns to other epithelial cell populations (colonic enteroids and flow-isolated colon epithelium). xMD-derived epithelial cells were generally not contaminated by other adjacent cells of the colon as noted by t-SNE analysis. xMD-miRNA-seq allows for simple, economical, and efficient identification of cell-specific miRNA expression estimates. Further development will enhance rapid identification of cell-specific miRNA expression estimates in health and disease for nearly any cell type using archival FFPE material.

scholarly journals A Comparative Transcriptome Analysis of Human and Porcine Choroid Plexus Cells in Response to Streptococcus suis Serotype 2 Infection Points to a Role of Hypoxia

2021 ◽  
Vol 11 ◽  
Author(s):  
Alexa N. Lauer ◽  
Rene Scholtysik ◽  
Andreas Beineke ◽  
Christoph Georg Baums ◽  
Kristin Klose ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Inflammatory Response ◽  
Choroid Plexus ◽  
Cellular Proliferation ◽  
Inflammatory Responses ◽  
Streptococcus Suis ◽  
Gene Set Enrichment Analysis ◽  
Rna Seq

Streptococcus suis (S. suis) is an important opportunistic pathogen, which can cause septicemia and meningitis in pigs and humans. Previous in vivo observations in S. suis-infected pigs revealed lesions at the choroid plexus (CP). In vitro experiments with primary porcine CP epithelial cells (PCPEC) and human CP epithelial papilloma (HIBCPP) cells demonstrated that S. suis can invade and traverse the CP epithelium, and that the CP contributes to the inflammatory response via cytokine expression. Here, next generation sequencing (RNA-seq) was used to compare global transcriptome profiles of PCPEC and HIBCPP cells challenged with S. suis serotype (ST) 2 infected in vitro, and of pigs infected in vivo. Identified differentially expressed genes (DEGs) were, amongst others, involved in inflammatory responses and hypoxia. The RNA-seq data were validated via quantitative PCR of selected DEGs. Employing Gene Set Enrichment Analysis (GSEA), 18, 28, and 21 enriched hallmark gene sets (GSs) were identified for infected HIBCPP cells, PCPEC, and in the CP of pigs suffering from S. suis ST2 meningitis, respectively, of which eight GSs overlapped between the three different sample sets. The majority of these GSs are involved in cellular signaling and pathways, immune response, and development, including inflammatory response and hypoxia. In contrast, suppressed GSs observed during in vitro and in vivo S. suis ST2 infections included those, which were involved in cellular proliferation and metabolic processes. This study suggests that similar cellular processes occur in infected human and porcine CP epithelial cells, especially in terms of inflammatory response.

scholarly journals Small RNA Sequencing Reveals Differentially Expressed miRNAs in Necrotizing Enterocolitis in Rats

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Ren-qiang Yu ◽  
Min Wang ◽  
Shan-yu Jiang ◽  
Ying-hui Zhang ◽  
Xiao-yu Zhou ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Signaling Pathway ◽  
Rna Sequencing ◽  
Necrotizing Enterocolitis ◽  
Small Rna ◽  
Mirna Expression ◽  
Expression Patterns ◽  
Wnt Signaling Pathway ◽  
Differentially Expressed ◽  
Small Rna Sequencing

Necrotizing enterocolitis (NEC) is the leading cause of death due to gastrointestinal disease in preterm infants. The role of miRNAs in NEC is still unknown. The objective of this study was to identify differentially expressed (DE) miRNAs in rats with NEC and analyze their possible roles. In this study, a NEC rat model was established using Sprague-Dawley rat pups. Small RNA sequencing was used to analyze the miRNA expression profiles in the NEC and control rats. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out to identify target mRNAs for the DE miRNAs and to explore their potential roles. The DE miRNAs were verified by real-time quantitative PCR (RT-qPCR). The status of intestinal injury and the elevated levels of inflammatory cytokines in the NEC group confirmed that the NEC model was successfully established. The 16 miRNAs were found to be differentially expressed between the NEC group and the control group of rats. Bioinformatics analysis indicated that the parental genes of the DE miRNAs were predominantly implicated in the phosphorylation, cell migration, and protein phosphorylation processes. Moreover, the DE miRNAs were mainly found to be involved in the pathways of axon guidance, endocytosis, and focal adhesion, as well as in the Wnt signaling pathway, which is related to colitis. The expression patterns of the candidate miRNAs (rno-miR-27a-5p and rno-miR-187-3p), as assessed by RT-qPCR, were in accordance with the expression patterns obtained by miRNA-sequencing. The miRNA/mRNA/pathway network revealed that rno-miR-27a-5p and rno-miR-187-3p might be involved in NEC via the Wnt signaling pathway. We found an altered miRNA expression pattern in rats with NEC. We hypothesize that rno-miR-27a-5p and rno-miR-187-3p might mediate the NEC pathophysiological processes via the Wnt signaling pathway.

scholarly journals The microRNA miR-132 is a key regulator of lymphatic vascular remodelling

2021 ◽  
Author(s):  
Marc Achen ◽  
Valeria Arcucci ◽  
Musarat Ishaq ◽  
Sally Roufail ◽  
Kate Dredge ◽  
...  
Keyword(s):  
Growth Factors ◽  
Small Rna ◽  
Lymphatic Vessels ◽  
Tube Formation ◽  
Small Rna Sequencing ◽  
Lymphatic Endothelial Cells ◽  
Rna Molecules ◽  
Key Steps

Lymphangiogenesis (growth of new lymphatic vessels), and lymphatic remodelling more broadly, are important for disease progression in cancer, lymphedema and the pulmonary disease lymphangioleiomyomatosis. Multiple molecular pathways which signal for aspects of lymphangiogenesis are known but little is understood about their co-ordinate regulation in lymphatic endothelial cells (LECs). Small RNA molecules co-ordinately regulate complex biological processes, but knowledge about their involvement in lymphangiogenesis is limited. Here we used high-throughput small RNA sequencing of LECs to identify microRNAs (miRs) regulating lymphatic remodelling driven by the lymphangiogenic growth factors VEGF-C and VEGF-D. We identified miR-132 as up-regulated by both growth factors, and demonstrated that inhibiting miR-132 in LECs in vitro blocked cell proliferation and tube formation, key steps in lymphangiogenesis. We showed that miR-132 is expressed in human LECs in vivo in the lymphatics of human breast tumours expressing VEGF-D. Importantly, we demonstrated that inhibiting miR-132 in vivo blocked many aspects of lymphangiogenesis in mice. Finally, we identified mRNAs regulated by miR-132 in LECs, by sequencing after RNA-protein cross-linking and Argonaute immunoprecipitation, which demonstrated how miR-132 co-ordinately regulates signalling pathways in lymphangiogenesis. This study shows miR-132 is a critical regulator of lymphangiogenesis and a potential target for therapeutically manipulating lymphatic remodelling in disease.

144 DOSAGE COMPENSATION AND X-LINKED GENE EXPRESSION IN BOVINE IN VIVO AND IN VITRO EMBRYOS

2016 ◽  
Vol 28 (2) ◽  
pp. 202 ◽  
Author(s):  
J. E. Duan ◽  
N. K. Jue ◽  
Z. Jiang ◽  
R. O'Neill ◽  
E. Wolf ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Dosage Compensation ◽  
Expression Patterns ◽  
Autosomal Gene ◽  
Rna Seq ◽  
X Gene ◽  
Diploid Cells

In human and mouse diploid cells and gametes, expression levels of X-linked genes are hypothesised to balance with those of autosomal genes (Ohno’s “dosage compensation”). Such a phenomenon, however, has not been systematically studied in cattle or compared between in vivo and in vitro embryos. Using RNA-seq data, we compared dosage compensation and expression differences of X-linked genes in bovine in vitro and in vivo oocytes and embryos. RNA-seq datasets GSE59186 and GSE52415 were non-uniquely (paralogs included) mapped to the bovine reference genome assembly UMD3.1 using tophat2. Cufflinks v1.0.3 was used to estimate fragments per kb of exon per million fragments (FPKM), which were then log2-transformed. In order to assess overall patterns of chromosomal gene expression without bias, statistical outliers were removed. A total of 12 928 X-linked transcripts were used to calculate the relative X to autosomal gene (A) expression (RXE): log2 (X expression) – log2 (A expression) for dosage compensation. Values ≥0 indicate dosage compensation (or X : A ratio ≥ 1); values <0 indicate incomplete dosage compensation; value = –1 indicates no dosage compensation (or X : A ratio = 0.5). Cuffdiff was used to identify differentially expressed genes between stages and the 2 datasets. Cuffnorm normalized FPKM for expression patterns, which were further clustered and graphed in R. Expression pattern distributions across regions on X were calculated by merging Cuffnorm output genes.attr_table to the expression pattern lists. The RXE values were higher than –1 in all embryonic stages studied, with in vitro embryos having higher RXE, suggesting some but incomplete dosage compensation and in vitro embryos exhibiting higher levels of X-gene expression. In vitro-produced immature oocytes and 4-cell embryos had RXE of 0, suggesting that both may be completely compensated. Additionally, embryos of the 2 sources exhibited significant differences in levels of X-gene expression at 4-cell to 8-cell and 16-cell to blastocyst stages. All expressed X-linked genes fell in 5 groups (patterns 1–5): increased, decreased, increased and then decreased, constant, decreased and then increased. Patterns 1 to 4 were seen in both datasets, whereas pattern 5 was only present in vitro, which may be why in vitro embryos had higher dosage of X. We further found that these expression patterns correlated with the genes’ proximity to the X inactivation centre (Xic: ~82 Mb): the highly dynamic patterns 3 and 5 were associated with proximity to Xic, supporting the notion that the Xist RNA spreads along the X through the Xic. In vivo and in vitro bovine oocytes and embryos have undergone some degree but incomplete dosage compensation. Expression of X-linked genes is correlated with their proximity to Xic. Globally, in vivo and in vitro embryos exhibit major differences in levels of X-gene expression.

scholarly journals Cell type-specific isolation and transcriptomic profiling informs glial pathology in human temporal lobe epilepsy

2020 ◽  
Author(s):  
Jessica Tome-Garcia ◽  
German Nudelman ◽  
Zarmeen Mussa ◽  
Elodia Caballero ◽  
Yan Jiang ◽  
...  
Keyword(s):  
Temporal Lobe Epilepsy ◽  
Temporal Lobe ◽  
Ex Vivo ◽  
Hybrid Population ◽  
Rna Seq ◽  
Cell Type ◽  
Fresh Frozen ◽  
Cell Type Specific

The pathophysiology of epilepsy underlies complex network dysfunction, the cell-type-specific contributions of which remain poorly defined in human disease. In this study, we developed a strategy that simultaneously isolates neuronal, astrocyte and oligodendroglial progenitor (OPC)-enriched nuclei from human fresh-frozen neocortex and applied it to characterize the distinct transcriptome of each cell type in temporal lobe epilepsy (TLE) surgical samples. Differential RNA-seq analysis revealed several dysregulated pathways in neurons, OPCs, and astrocytes, and disclosed an immature phenotype switch in TLE astrocytes. An independent single cell RNA-seq TLE dataset uncovered a hybrid population of cells aberrantly co-expressing canonical astrocyte and OPC-like progenitor markers (GFAP+OLIG2+ glia), which we corroborated in-situ in human TLE samples, and further demonstrated their emergence after chronic seizure injury in a mouse model of status epilepticus. In line with their immature signature, a subset of human TLE glia were also abnormally proliferative, both in-vivo and in-vitro. Generally, this analysis validates the utility of the proposed cell type-specific isolation strategy to study glia-specific changes ex vivo using fresh-frozen human samples, and specifically, it delineates an aberrant glial phenotype in human TLE specimens.

scholarly journals P057 CRL4DCAF2 promotes cell proliferation and limits the development of colitis

2021 ◽  
Vol 15 (Supplement_1) ◽  
pp. S163-S164
Author(s):  
C Wang ◽  
L Yao ◽  
Y Zhang ◽  
Q Cao
Keyword(s):  
Ulcerative Colitis ◽  
Epithelial Cells ◽  
Intestinal Inflammation ◽  
Intestinal Epithelial Cells ◽  
Sw480 Cell ◽  
Intestinal Epithelial ◽  
Rna Seq ◽  
Biopsy Specimens

Abstract Background Ulcerative colitis (UC) is an idiopathic intestinal inflammatory disease, which leads to chronic intestinal mucosal barrier damage. More and more evidences show that ubiquitination of proteins regulates the occurrence and development of intestinal inflammation. DCAF family proteins could form E3 ubiquitin ligase with CRL4-DDB1 to regulate cell growth, differentiation, apoptosis and other life activities. CRL4DCAF2 is a crucial regulator in cell cycle regulation, but there are few studies on its application in intestinal epithelium. This study aims to explore the specific mechanism of CRL4DCAF2 in regulating the proliferation and repairment of intestinal epithelial cells. Methods DSS - induced colitis in mice was used as the experimental model in vivo. HCT116 and SW480 cell lines were used as experimental models in vitro studies.The Cre-loxP system was used to construct a mouse model of intestinal epithelium-specific DCAF2 knockout. The intestinal mucosa biopsy specimens of 11 normal patients and 11 UC patients were collected. In addition, qRT-PCR, Western blot, RNA-seq and immunofluorescent staining were used to detect the expression levels of target genes in human colon biopsy specimens, mouse colon tissues, HCT116 or SW480 cells Results DCAF2 gene was highly expressed in the colon of mice. The occurrence and development of DSS-induced experimental colitis was accompanied by a significant down-regulation of DCAF2 protein expression in colon. DCAF2 mRNA level was significantly decreased in UC patients. Mouse with intestinal epithelial-specific knockout of DCAF2(i.e. DCAF2IEC-KO) suffered from embryonic death. Compared with wild-type adult C57BL/6J mice, DCAF2IEC-KD mouse showed more severe intestinal inflammation in DSS-induced colitis model. CCK-8 test, PI staining and EDU staining flow cytometry experiments showed that the proliferation of intestinal epithelial cells with DCAF2 overexpression was faster than that of the control (P &lt; 0.05) in HCT116 and SW480 cell lines, while in knockdown of DCAF2 models, the opposite results were obtained. Its effect may be related to the ubiquitination of p21. At the same time, MLN4924 in vivo and in vitro experiments further verified our experimental results. Combined with RNA-seq and Western blot, we also found that DCAF2 may reduce the symptoms of colitis by maintaining the stability of autophagy. Conclusion DCAF2 is low expressed in patients with ulcerative colitis, which may promote the activation and proliferation of intestinal epithelial cells. It could maintain autophagy stability, and restore intestinal barrier, thus alleviate the development of ulcerative colitis

scholarly journals 5′-tRF-GlyGCC: a tRNA-derived small RNA as a novel biomarker for colorectal cancer diagnosis

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Yingmin Wu ◽  
Xiangling Yang ◽  
Guanmin Jiang ◽  
Haisheng Zhang ◽  
Lichen Ge ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Small Rna ◽  
Expression Profiles ◽  
Diagnostic Value ◽  
Carbohydrate Antigen ◽  
Small Rna Sequencing ◽  
In Vivo Models ◽  
Diagnostic Values

Abstract Background tRNA-derived small RNAs (tDRs), which are widely distributed in human tissues including blood and urine, play an important role in the progression of cancer. However, the expression of tDRs in colorectal cancer (CRC) plasma and their potential diagnostic values have not been systematically explored. Methods The expression profiles of tDRs in plasma of CRC and health controls (HCs) are investigated by small RNA sequencing. The level and diagnostic value of 5′-tRF-GlyGCC are evaluated by quantitative PCR in plasma samples from 105 CRC patients and 90 HCs. The mechanisms responsible for biogenesis of 5′-tRF-GlyGCC are checked by in vitro and in vivo models. Results 5′-tRF-GlyGCC is dramatically increased in plasma of CRC patients compared to that of HCs. The area under curve (AUC) for 5′-tRF-GlyGCC in CRC group is 0.882. The combination of carcinoembryonic antigen (CEA) and carbohydrate antigen 199 (CA199) with 5′-tRF-GlyGCC improves the AUC to 0.926. Consistently, the expression levels of 5′-tRF-GlyGCC in CRC cells and xenograft tissues are significantly greater than that in their corresponding controls. Blood cells co-cultured with CRC cells or mice xenografted with CRC tumors show increased levels of 5′-tRF-GlyGCC. In addition, we find that the increased expression of 5′-tRF-GlyGCC is dependent on the upregulation of AlkB homolog 3 (ALKBH3), a tRNA demethylase which can promote tRNA cleaving to generate tDRs. Conclusions The level of 5′-tRF-GlyGCC in plasma is a promising diagnostic biomarker for CRC diagnosis.

scholarly journals Identification of the Lineage Markers and Inhibition of DAB2 in In Vitro Fertilized Porcine Embryos

2020 ◽  
Vol 21 (19) ◽  
pp. 7275
Author(s):  
Jong-Nam Oh ◽  
Mingyun Lee ◽  
Gyung Cheol Choe ◽  
Dong-Kyung Lee ◽  
Kwang-Hwan Choi ◽  
...  
Keyword(s):  
Low Cost ◽  
Expression Patterns ◽  
Mouse Embryos ◽  
Marker Genes ◽  
Lineage Specification ◽  
Marker Proteins ◽  
Lineage Markers ◽  
Human And Mouse

Specification of embryonic lineages is an important question in the field of early development. Numerous studies analyzed the expression patterns of the candidate transcripts and proteins in humans and mice and clearly determined the markers of each lineage. To overcome the limitations of human and mouse embryos, the expression of the marker transcripts in each cell has been investigated using in vivo embryos in pigs. In vitro produced embryos are more accessible, can be rapidly processed with low cost. Therefore, we analyzed the characteristics of lineage markers and the effects of the DAB2 gene (trophectoderm marker) in in vitro fertilized porcine embryos. We investigated the expression levels of the marker genes during embryonic stages and distribution of the marker proteins was assayed in day 7 blastocysts. Then, the shRNA vectors were injected into the fertilized embryos and the differences in the marker transcripts were analyzed. Marker transcripts showed diverse patterns of expression, and each embryonic lineage could be identified with localization of marker proteins. In DAB2-shRNA vectors injected embryos, HNF4A and PDGFRA were upregulated. DAB2 protein level was lower in shRNA-injected embryos without significant differences. Our results will contribute to understanding of the mechanisms of embryonic lineage specification in pigs.

CBIO-14. SINGLE CELL RNA SEQUENCING ANALYSIS OF HUMAN GLIOBLASTOMA STEM-LIKE CELL CULTURES AND XENOGRAFT TUMORS

2021 ◽  
Vol 23 (Supplement_6) ◽  
pp. vi30-vi30
Author(s):  
Sonali Arora ◽  
Anca Mihalas ◽  
John Bassett ◽  
Anoop Patel ◽  
Patrick Paddison
Keyword(s):  
Single Cell ◽  
Developmental Trajectories ◽  
Expression Patterns ◽  
Experimental Models ◽  
Tumor Formation ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Human Glioblastoma

Abstract Single cell RNA-seq (scRNA-seq) studies for glioma have yielded critical insight into intratumoral heterogeneity and developmental gene expression patterns for primary gliomas. One key conclusion from these studies is that each tumor represents a complex, yet maligned, neuro-developmental ecosystem, harboring diverse cell types, which presumably contribute to tumor growth and homeostasis in specific ways (e.g., vascular mimicry, immune evasion, recreating NSC niches, neural injury responses, etc.). Here, to better understand experimental models of human glioblastoma (GB), we performed single cell RNA-seq analysis of human GB stem-like cells (GSCs) of distinct tumor subtypes (mesenchymal and proneural) during their in vitro culture in serum-free conditions and also during tumor formation in immunocompromised mice. This analysis revealed surprising differences between in vitro and in vivo grown GSCs. Among our results, we find that in vivo mesenchymal GSCs are capable of transitioning to proneural-like states, while proneural GSCs are capable of transitioning to mesenchymal states. We characterize cycling cells based on expression of and G2/M and S phase makers, estimate RNA velocity, and examine different developmental trajectories arising in vitro and in vivo. We also compare and discuss different analysis pipelines for scRNA-seq data.

scholarly journals ZRANB1 Drives Hepatocellular Carcinoma Progression through SP1-LOXL2 Axis

2021 ◽  
Author(s):  
Peiyi Xie ◽  
Qing Li ◽  
Qing Chao ◽  
Jiayu Fang ◽  
Jing Xie ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Molecular Mechanisms ◽  
Lysyl Oxidase ◽  
Expression Patterns ◽  
Rna Seq ◽  
Loss Of Function ◽  
Close Relationship ◽  
Hcc Cells

Abstract BackgroundDeubiquitinase (DUB) zinc finger RANBP2-type containing 1 (ZRANB1/TRABID) has been reported to have a close relationship with cancers. However, its underlying role and molecular mechanisms in hepatocellular carcinoma (HCC) remain elusive. MethodsGene and protein expression of ZRANB1 in HCC tissues were determined by qRT-PCR, western blot and immunohistochemistry. A series of gain- and loss-of-function assays were used to investigated the role of ZRANB1 in HCC cells progression. Moreover, RNA-seq were used to identify the downstream targets of ZRANB1 in HCC cells. The interaction between ZRANB1 and SP1 was examined through co-IP experiment and in vitro ubiquitination assay.ResultsZRANB1 was highly expressed in HCC tissues and ZRANB1 can regulate HCC cell growth and metastasis in vitro and in vivo. Through RNA-seq, we identified that Lysyl oxidase-like 2 (LOXL2) was the most significantly downregulated gene after ZRANB1 knockdown. Furthermore, the scatter plots indicated a significant positive correlation between ZRANB1 and LOXL2 expression in clinical HCC specimens. Additionally, LOXL2 was essential for ZRANB1-mediated HCC growth and metastasis. More importantly, specificity protein 1 (SP1) was critical in ZRANB1-mediated regulation of LOXL2 expression. Mechanistically, ZRANB1 bound with SP1 directly and stabilized the SP1 protein by deubiquitinating it. The expression patterns of ZRANB1, SP1 and LOXL2 were evaluated in HCC patients. ConclusionZRANB1 overexpression facilitates the carcinogenesis of HCC through stabilizing and upregulating SP1 to promote LOXL2 expression, suggesting ZRANB1 can be novel prognostic biomarker for HCC treatment.

Sign in / Sign up

Export Citation Format

Share Document