Aberrant Expression Profiles of lncRNAs and Their Associated Nearby Coding Genes in the Hippocampus of the SAMP8 Mouse Model with AD

MicroRNAs (miRNAs) can exhibit aberrant expression under different physiological and pathological conditions. Therefore, differentially expressed circulating miRNAs have been a focus of biomarker discovery research. However, the use of circulating miRNAs comes with challenges which may hinder the reliability for their clinical application. These include varied sample collection protocols, storage times/conditions, sample processing and analysis methods. This study focused on examining the effect of whole blood holding time on the stability of plasma miRNA expression profiles. Whole blood samples were collected from healthy pregnant women and were held at 4°C for 30 min, 2 h, 6 h or 24 h prior to processing for plasma isolation. Plasma RNA was extracted and the expression of 179 miRNAs were analyzed. Unsupervised principal component analysis demonstrated that whole blood holding time was a major source of variation in miRNA expression profiles with 53 of 179 miRNAs showing significant changes in expression. Levels of specific miRNAs previously reported to be associated with pregnancy-associated complications such as hsa-miR-150-5p, hsa-miR-191-5p, and hsa-miR-29a-3p, as well as commonly used endogenous miRNA controls, hsa-miR-16-5p, hsa-miR-25-3p, and hsa-miR-223-3p were significantly altered with increase in blood holding time. Current protocols for plasma-based miRNA profiling for diagnostics describe major differences in whole blood holding periods ranging from immediately after collection to 26 h after. Our results demonstrate holding time can have dramatic effects on analytical reliability and reproducibility. This highlights the importance of standardization of blood holding time prior to processing for plasma in order to minimize introduction of non-biological variance in miRNA profiles.

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The effect of CD26‐deficiency on dipeptidyl peptidase 8 and 9 expression profiles in a mouse model of Crohn's disease

Journal of Cellular Biochemistry ◽

10.1002/jcb.26867 ◽

2018 ◽

Vol 119 (8) ◽

pp. 6743-6755 ◽

Cited By ~ 1

Author(s):

Suncica Buljevic ◽

Dijana Detel ◽

Ester P. Pugel ◽

Jadranka Varljen

Keyword(s):

Crohn’S Disease ◽

Crohn's Disease ◽

Mouse Model ◽

Expression Profiles ◽

Dipeptidyl Peptidase

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Gene and protein expression profiles of JAK-STAT signalling pathway in the developing brain of the Ts1Cje down syndrome mouse model

International Journal of Neuroscience ◽

10.1080/00207454.2019.1580280 ◽

2019 ◽

Vol 129 (9) ◽

pp. 871-881 ◽

Cited By ~ 2

Author(s):

Han-Chung Lee ◽

Hadri Hadi Md Yusof ◽

Melody Pui-Yee Leong ◽

Shahidee Zainal Abidin ◽

Eryse Amira Seth ◽

...

Keyword(s):

Down Syndrome ◽

Mouse Model ◽

Protein Expression ◽

Expression Profiles ◽

Developing Brain ◽

Signalling Pathway ◽

Gene And Protein Expression ◽

Protein Expression Profiles

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P3-193: METFORMIN INCREASES PKC AND DECREASES APP AND TAU IN THE SAMP8 MOUSE MODEL OF ALZHEIMER'S DISEASE

Alzheimer s & Dementia ◽

10.1016/j.jalz.2018.06.1551 ◽

2006 ◽

Vol 14 (7S_Part_21) ◽

pp. P1141-P1141

Author(s):

John E. Morley ◽

Michael L. Niehoff ◽

Elizabeth C. Roesler ◽

Susan A. Farr

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Mouse Model ◽

Samp8 Mouse ◽

Model Of Alzheimer’S Disease

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Genome-wide expression profiling in colorectal cancer focusing on lncRNAs in the adenoma-carcinoma transition

BMC Cancer ◽

10.1186/s12885-019-6180-5 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 8

Author(s):

Alexandra Kalmár ◽

Zsófia Brigitta Nagy ◽

Orsolya Galamb ◽

István Csabai ◽

András Bodor ◽

...

Keyword(s):

Colorectal Cancer ◽

Differential Expression ◽

Colorectal Adenoma ◽

Expression Profiles ◽

Expression Patterns ◽

Aberrant Expression ◽

Array Data ◽

Lncrna Expression ◽

Qrt Pcr ◽

Mrna Targets

Abstract Background Long non-coding RNAs (lncRNAs) play a fundamental role in colorectal cancer (CRC) development, however, lncRNA expression profiles in CRC and its precancerous stages remain to be explored. We aimed to study whole genomic lncRNA expression patterns in colorectal adenoma–carcinoma transition and to analyze the underlying functional interactions of aberrantly expressed lncRNAs. Methods LncRNA expression levels of colonic biopsy samples (20 CRCs, 20 adenomas (Ad), 20 healthy controls (N)) were analyzed with Human Transcriptome Array (HTA) 2.0. Expression of a subset of candidates was verified by qRT-PCR and in situ hybridization (ISH) analyses. Furthermore, in silico validation was performed on an independent HTA 2.0, on HGU133Plus 2.0 array data and on the TCGA COAD dataset. MiRNA targets of lncRNAs were predicted with miRCODE and lncBase v2 algorithms and miRNA expression was analyzed on miRNA3.0 Array data. MiRNA-mRNA target prediction was performed using miRWALK and c-Met protein levels were analyzed by immunohistochemistry. Comprehensive lncRNA-mRNA-miRNA co-expression pattern analysis was also performed. Results Based on our HTA results, a subset of literature-based CRC-associated lncRNAs showed remarkable expression changes already in precancerous colonic lesions. In both Ad vs. normal and CRC vs. normal comparisons 16 lncRNAs, including downregulated LINC02023, MEG8, AC092834.1, and upregulated CCAT1, CASC19 were identified showing differential expression during early carcinogenesis that persisted until CRC formation (FDR-adjusted p < 0.05). The intersection of CRC vs. N and CRC vs. Ad comparisons defines lncRNAs characteristic of malignancy in colonic tumors, where significant downregulation of LINC01752 and overexpression of UCA1 and PCAT1 were found. Two candidates with the greatest increase in expression in the adenoma-carcinoma transition were further confirmed by qRT-PCR (UCA1, CCAT1) and by ISH (UCA1). In line with aberrant expression of certain lncRNAs in tumors, the expression of miRNA and mRNA targets showed systematic alterations. For example, UCA1 upregulation in CRC samples occurred in parallel with hsa-miR-1 downregulation, accompanied by c-Met target mRNA overexpression (p < 0.05). Conclusion The defined lncRNA sets may have a regulatory role in the colorectal adenoma-carcinoma transition. A subset of CRC-associated lncRNAs showed significantly differential expression in precancerous samples, raising the possibility of developing adenoma-specific markers for early detection of colonic lesions.

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MicroRNA-99b predicts clinical outcome of osteosarcoma and suppresses tumor cell proliferation, migration and invasion

Diagnostic Pathology ◽

10.1186/s13000-019-0889-y ◽

2019 ◽

Vol 14 (1) ◽

Cited By ~ 1

Author(s):

Xin Shi ◽

Xingfa Guan

Keyword(s):

Cell Proliferation ◽

Cell Lines ◽

Prognostic Value ◽

Cox Regression ◽

Expression Profiles ◽

Migration And Invasion ◽

Aberrant Expression ◽

Cox Regression Analysis ◽

Normal Tissues

Abstract Background Osteosarcoma (OS) is a malignancy predominantly occurred in children and adolescents. Numerous microRNAs are involved in the pathogenesis of various cancers. This study aimed to investigate the expression profiles of miR-99b and its prognostic value in OS patients, and further analyze the biological function of miR-99b in the tumor progression by using OS cells. Methods Expression of miR-99b was measured using quantitative real-time PCR. Kaplan-Meier survival curves and Cox regression analysis were performed to evaluate the prognostic value of miR-99b. OS cell lines were used to investigate the effects of miR-99b on cell proliferation, migration and invasion. Results A significant decreased expression of miR-99b was observed in the OS tissues and cell lines respectively compared with the normal tissues and cells. Aberrant expression of miR-99b was associated with the patients’ metastasis and TNM stage, and could be used to predict the prognosis of OS. The expression of miR-99b was regulated in vitro by cell transfection, and we found that the overexpression of miR-99b led to suppressed cell proliferation, migration and invasion, whereas the knockdown of miR-99b resulted in the opposite results. Conclusions In one word, the aberrantly expressed miR-99b serves a prognostic biomarker for OS patients. OS cell proliferation, migration and invasion can be inhibited by the overexpression of miR-99b, suggesting that the methods to increase miR-99b expression may be novel therapeutic strategies in OS.

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