scholarly journals Differential expression of cellular microRNAs in HPV-11 transfected cells. An analysis by three different array platforms and qRT-PCR

2010 ◽  
Vol 403 (3-4) ◽  
pp. 357-362 ◽  
Author(s):  
Anita Dreher ◽  
Maria Rossing ◽  
Bogumil Kaczkowski ◽  
Finn Cilius Nielsen ◽  
Bodil Norrild
2020 ◽  
Vol 63 (2) ◽  
pp. 303-313
Author(s):  
Li Li ◽  
Linli Zhang ◽  
Zhenghong Zhang ◽  
Nemat O. Keyhani ◽  
Qingwu Xin ◽  
...  

Abstract. Testicular transcriptomes were analyzed to characterize the differentially expressed genes between mulard and Pekin ducks, which will help establish gene expression datasets to assist in further determination of the mechanisms of genetic sterility in mulard ducks. Paraffin sections were made to compare the developmental differences in testis tissue between mulard and Pekin ducks. Comparative transcriptome sequencing of testis tissues was performed, and the expression of candidate genes was verified by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). In mulard ducks, spermatogonia and spermatocytes were arranged in a disordered manner, and no mature sperm were observed in the testis tissue. However, different stages of development of sperm were observed in seminiferous tubules in the testis tissue of Pekin ducks. A total of 43.84 Gb of clean reads were assembled into 193 535 UniGenes. Of these, 2131 transcripts exhibited differential expression (false discover rate <0.001 and fold change ≥2), including 997 upregulated and 1134 downregulated transcripts in mulard ducks as compared to those in Pekin duck testis tissues. Several upregulated genes were related to reproductive functions, including ryanodine receptor 2 (RYR2), calmodulin (CALM), argininosuccinate synthase and delta-1-pyrroline-5-carboxylate synthetase ALDH18A1 (P5CS). Downregulated transcripts included the testis-specific serine/threonine-protein kinase 3, aquaporin-7 (AQP7) and glycerol kinase GlpK (GK). The 10 related transcripts involved in the developmental biological process were identified by GO (Gene Ontology) annotation. The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways indicated that peroxisome proliferator-activated receptors (PPARs) and calcium signaling pathways were significantly (P<0.001) associated with normal testis physiology. The differential expression of select genes implicated in reproductive processes was verified by qRT-PCR, which was consistent with the expression trend of transcriptome sequencing (RNA-seq). Differentially expressed candidate genes RYR2, CALM, P5CS, AQP7 and GK were identified by transcriptional analysis in mulard and Pekin duck testes. These were important for the normal development of the male duck reproductive system. These data provide a framework for the further exploration of the molecular and genetic mechanisms of sterility in mulard ducks. Highlights. The mulard duck is an intergeneric sterile hybrid offspring resulting from mating between Muscovy and Pekin ducks. The transcriptomes of testis tissue from mulard and Pekin ducks were systematically characterized, and differentially expressed genes were screened, in order to gain insights into potential gonad gene expression mechanisms contributing to genetic sterility in mulard ducks.


Author(s):  
Jun-Young Shin ◽  
Jong-Ok Ji ◽  
Sang-Heon Choi ◽  
Da-Woon Choi ◽  
Ye-Jin An ◽  
...  

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Alexandra Kalmár ◽  
Zsófia Brigitta Nagy ◽  
Orsolya Galamb ◽  
István Csabai ◽  
András Bodor ◽  
...  

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.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 570-570
Author(s):  
Salomon Manier ◽  
Antonio Sacco ◽  
Patricia Maiso ◽  
Yong Zhang ◽  
Yang Liu ◽  
...  

Abstract Abstract 570 Background. MicroRNAs (miRNAs) play a pivotal role in tumorigenesis, due to their ability to target mRNAs involved in the regulation of cell proliferation, survival and differentiation. In particular, the Let-7 miRNA family members have been described to act as tumor suppressors, as demonstrated both in solid cancer and hematologic malignancies. However, the role of Let-7 in multiple myeloma (MM) has not been studied. Method. Circulating miRNA profiling has been performed in MM patients compared to healthy individuals using TaqMan human miRNA profiling, and validated by qRT-PCR. Exosomes were collected from both normal and MM peripheral blood, using ultracentrifugation; and further studied by using electron microscopy and immunogold labeling for the detection of CD63 and CD81. Exosomes were then evaluated for their miRNA content, by qRT-PCR. Gain- and loss-of functions studies were performed on MM cell lines (MM.1S; U266), using Let-7-mimic and Lin28B siRNA, respectively. Scramble probe-transfected cells were used as control. Cell proliferation and cell survival have been evaluated by using BrdU assay and MTT assay, respectively. Effects of Let-7 and Lin28B on signaling cascades have been evaluated by western blot. Results. We identified a MM specific signature characterized by down-regulation of miRNA-15a, −19b, −21, let-7b, let-7c and over-expression of miR-720 (P < 0.001). Circulating exosomes were studied at ultrastructural level showing positivity for CD81 and CD63, as demonstrated by immunogold labeling and electron microscopy. The same miRNA signature was found in the circulating exosomes, suggesting that circulating miRNAs may be transported by exosomes. The Let-7 family members were significantly decreased in peripheral blood of MM patient compared to healthy individuals, suggesting that Let-7 family could be down-regulated in MM cells. We then performed qRT-PCR in MM primary cells; and found that the Let-7 family is significantly down-regulated in MM primary cells, especially for Let-7b and c (5 fold change, P< 0.05). Over-expression of Let-7b and Let-7c in MM cells (U266; MM1S) transfected decreased cell proliferation. The RNA binding protein Lin28B is known to regulate the Let-7 family: we therefore performed Lin28-loss of function studies which led to up-regulation of the Let-7 family members, in MM transfected cells; and found that Lin28B-knockdown cells presented with reduced cell proliferation, supported by down-regulation of c-Myc and K-Ras, known to be Let-7-related targets. Conclusion. This data indicate that Let-7 miRNA family members play an important role in modulating MM biology, thus providing the basis for the development of new miRNA-based target therapies and biomarker in this disease. Disclosures: Ghobrial: Novartis: advisory board, advisory board Other; Millennium: Membership on an entity's Board of Directors or advisory committees; Onyx: Membership on an entity's Board of Directors or advisory committees; Bristol-Myers Squibb: advisory board, advisory board Other.


2009 ◽  
Vol 47 (11-12) ◽  
pp. 1116-1118 ◽  
Author(s):  
Olawole O. Obembe ◽  
Evert Jacobsen ◽  
Jean-Paul Vincken ◽  
Richard G.F. Visser

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. e14067-e14067
Author(s):  
Ofer Purim ◽  
Alina Weismann-Brenner ◽  
Michal Kushnir ◽  
Gila Lithwick-Yanai ◽  
Ranit T. Aharonov ◽  
...  

e14067 Background: To compare the microRNA (miRNA) profiles in the primary tumor of patients with recurrent and non-recurrent colon cancer. Methods: The study population included 110 patients, 51 (46%) with stage I and 59 (54%) with stage II disease, who underwent curative colectomies between 1995-2005 without adjuvant therapy and for whom reliable miR expression data was available. RNA was extracted from formalin-fixed paraffin-embedded tumor samples. Initial profiling, using microarrays, was done in order to identify potential biomarkers of recurrence. The miRNA expression was later verified by quantitative real-time polymerase chain reaction (qRT-PCR). Findings were compared between patients who had a recurrence within 36 months of surgery (bad prognosis group, n=23, 21%) and those who did not (good prognosis group, n=87, 79%) in the entire group and within each stage. Results: In stage I, none of the 903 miRNAs tested showed differential expression between patients with good prognosis compared with those with bad prognosis. In stage II, one miRNA, miR-29a, showed a clear differential expression between the groups (p=0.028). High expression of miR-29a was associated with a longer disease-free survival (DFS), on both univariate and multivariate analyses. Using miR-29a, the positive predictive value for non-recurrence was 94% (2 recurrences among 31 patients). The differential expression of miR-29a was verified by qRT-PCR, showing a similar impact of this miR on DFS. Conclusions: This study demonstrated a significant impact of miR-29a on the risk of recurrence in patients with stage II but not in patients with stage I colon cancer.


2015 ◽  
Vol 35 (2) ◽  
pp. 663-675 ◽  
Author(s):  
Jingyun Li ◽  
Wei Long ◽  
Qian Li ◽  
Qing Zhou ◽  
Yu Wang ◽  
...  

Background: Recent studies suggest that long non-coding RNAs (lncRNAs) play crucial roles in human diseases. The function of lncRNAs in abnormal scar pathogenesis remains poorly understood. Methods: In this study, we examined the lncRNAs expression profiles among regressive and mature scars following caesarean sections. A total of 30,586 lncRNAs and 26,109 mRNAs were analyzed by microarrays (Human LncRNA Array v3.0, Arraystar, Inc.). Results: In total, we identified 1,871 lncRNAs and 817 mRNAs with differential expression between regressive and mature scar individuals (fold change≥3, p≤0.001). A set of differentially expressed lncRNA transcripts, in particular, lncRNA8975-1, AC097662.2 and RP11-586K2.1, were confirmed using qRT-PCR. Gene ontology and pathway analysis revealed that compared to mature scars, many processes over-represented in regressive scars are related to the immune system. Conclusion: Our results show significantly altered expression profiles of lncRNAs and mRNAs between regressive and mature scars. These transcripts are potential molecular targets for inhibiting abnormal scar formation following caesarean sections.


2011 ◽  
Vol 412 (1) ◽  
pp. 20-25 ◽  
Author(s):  
Anita Dreher ◽  
Maria Rossing ◽  
Bogumil Kaczkowski ◽  
Ditte K. Andersen ◽  
Therese Juhlin Larsen ◽  
...  

Reproduction ◽  
2010 ◽  
Vol 140 (3) ◽  
pp. 477-487 ◽  
Author(s):  
Kavarthapu Raghuveer ◽  
Balasubramanian Senthilkumaran

In vertebrates, sox9 is a transcription factor that plays a crucial role in testicular development and chondrogenesis. Here, we report cloning of isoforms of sox9 (sox9a and sox9b) from air-breathing catfish Clarias gariepinus, which undergoes an annual reproductive cycle. Tissue distribution pattern showed differential expression of sox9 duplicates, wherein both forms were highly expressed in brain and gonads. Furthermore, we observed a dimorphic expression pattern of sox9a and sox9b in both adult and developing gonads using RT-PCR, indicating that sox9a retained its function in testis while sox9b might have a new role to play in ovary. Changes in sox9 mRNA levels using real-time quantitative PCR (qRT-PCR) during the seasonal reproductive cycle revealed that sox9a transcript in testis was abundant during testicular recrudescence (during spermatogenesis), and its expression significantly decreased during spawning and post-spawning phases. Furthermore, treatments of human chorionic gonadotropin and 11-ketotestosterone in vitro up-regulated sox9a mRNA levels in the testicular slices at 12 and 24 h time points, suggesting that gonadotropins might stimulate sox9 expression. These results suggest that sox9 might have a plausible role in the entrainment of the testicular cycle. In contrast, during the ovarian cycle, sox9b mRNA levels gradually declined from preparatory to post-spawning phases. Immunohistochemical (IHC) data showed that, in testis, sox9 is detectable in Sertoli and spermatogonial cell types except spermatid/spermatozoa. In the ovary, it is localized in the ooplasm of primary and pre-vitellogenic oocytes. These results were further confirmed by whole-mount IHC and qRT-PCR.


PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0251713
Author(s):  
Frederik Helmprobst ◽  
Susanne Kneitz ◽  
Barbara Klotz ◽  
Magali Naville ◽  
Corentin Dechaud ◽  
...  

Malignant melanoma incidence is rising worldwide. Its treatment in an advanced state is difficult, and the prognosis of this severe disease is still very poor. One major source of these difficulties is the high rate of metastasis and increased genomic instability leading to a high mutation rate and the development of resistance against therapeutic approaches. Here we investigate as one source of genomic instability the contribution of activation of transposable elements (TEs) within the tumor. We used the well-established medaka melanoma model and RNA-sequencing to investigate the differential expression of TEs in wildtype and transgenic fish carrying melanoma. We constructed a medaka-specific TE sequence library and identified TE sequences that were specifically upregulated in tumors. Validation by qRT- PCR confirmed a specific upregulation of a LINE and an LTR element in malignant melanomas of transgenic fish.


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