scholarly journals Comprehensive quantitative analysis of alternative splicing variants reveals the HNF1B mRNA splicing pattern in various tumour and non-tumour tissues

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Jan Hojny ◽  
Romana Michalkova ◽  
Eva Krkavcova ◽  
Quang Hiep Bui ◽  
Michaela Bartu ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Mrna Expression ◽  
Large Intestine ◽  
Digital Pcr ◽  
Splicing Pattern ◽  
Mrna Variants ◽  
Splicing Variants ◽  
Quantitative Changes ◽  
Nuclear Factor 1 ◽  
Regulatory Functions

AbstractHepatocyte nuclear factor-1-beta (HNF1B) is a transcription factor and putative biomarker of solid tumours. Recently, we have revealed a variety of HNF1B mRNA alternative splicing variants (ASVs) with unknown, but potentially regulatory, functions. The aim of our work was to quantify the most common variants and compare their expression in tumour and non-tumour tissues of the large intestine, prostate, and kidney. The HNF1B mRNA variants 3p, Δ7, Δ7–8, and Δ8 were expressed across all the analysed tissues in 28.2–33.5%, 1.5–2%, 0.8–1.7%, and 2.3–6.9% of overall HNF1B mRNA expression, respectively, and occurred individually or in combination. The quantitative changes of ASVs between tumour and non-tumour tissue were observed for the large intestine (3p, Δ7–8), prostate (3p), and kidney samples (Δ7). Decreased expression of the overall HNF1B mRNA in the large intestine and prostate cancer samples compared with the corresponding non-tumour samples was observed (p = 0.019 and p = 0.047, respectively). The decreased mRNA expression correlated with decreased protein expression in large intestine carcinomas (p < 0.001). The qualitative and quantitative pattern of the ASVs studied by droplet digital PCR was confirmed by next-generation sequencing, which suggests the significance of the NGS approach for further massive evaluation of the splicing patterns in a variety of genes.

scholarly journals Demonstration of a Melanoma-Specific CD44 Alternative Splicing Pattern That Remains Qualitatively Stable, but Shows Quantitative Changes during Tumour Progression

PLoS ONE ◽  
2013 ◽  
Vol 8 (1) ◽  
pp. e53883 ◽  
Author(s):  
Livia Raso-Barnett ◽  
Balazs Banky ◽  
Tamas Barbai ◽  
Peter Becsagh ◽  
Jozsef Timar ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Tumour Progression ◽  
Splicing Pattern ◽  
Quantitative Changes

scholarly journals Trans-acting Factors Required for Inclusion of Regulated Exons in the Ultrabithorax mRNAs of Drosophila melanogaster

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1517-1529 ◽  
Author(s):  
James M Burnette ◽  
Allyson R Hatton ◽  
A Javier Lopez
Keyword(s):  
Drosophila Melanogaster ◽  
Alternative Splicing ◽  
P Element ◽  
Splicing Factors ◽  
Loss Of Function ◽  
Large Collection ◽  
Splicing Pattern ◽  
Alternatively Spliced ◽  
Hypomorphic Alleles

Abstract Alternatively spliced Ultrabithorax mRNAs differ by the presence of internal exons mI and mII. Two approaches were used to identify trans-acting factors required for inclusion of these cassette exons. First, mutations in a set of genes implicated in the control of other alternative splicing decisions were tested for dominant effects on the Ubx alternative splicing pattern. To identify additional genes involved in regulation of Ubx splicing, a large collection of deficiencies was tested first for dominant enhancement of the haploinsufficient Ubx haltere phenotype and second for effects on the splicing pattern. Inclusion of the cassette exons in Ubx mRNAs was reduced strongly in heterozygotes for hypomorphic alleles of hrp48, which encodes a member of the hnRNP A/B family and is implicated in control of P-element splicing. Significant reductions of mI and mII inclusion were also observed in heterozygotes for loss-of-function alleles of virilizer, fl(2)d, and crooked neck. The products of virilizer and fl(2)d are also required for Sxl autoregulation at the level of splicing; crooked neck encodes a protein with structural similarities to yeast-splicing factors Prp39p and Prp42p. Deletion of at least five other loci caused significant reductions in the inclusion of mI and/or mII. Possible roles of identified factors are discussed in the context of the resplicing strategy for generation of alternative Ubx mRNAs.

Alternative splicing variants of carbonic anhydrase IX in human non-small cell lung cancer

Lung Cancer ◽  
2009 ◽  
Vol 64 (3) ◽  
pp. 271-276 ◽  
Author(s):  
Francesca Malentacchi ◽  
Lisa Simi ◽  
Caterina Nannelli ◽  
Matteo Andreani ◽  
Alberto Janni ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Alternative Splicing ◽  
Carbonic Anhydrase ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Small Cell ◽  
Carbonic Anhydrase Ix ◽  
Small Cell Lung ◽  
Splicing Variants

Effect of deoxynivalenol on the levels of toll-like receptors 2 and 9 and their mRNA expression in enterocytes in the porcine large intestine: a preliminary study

2017 ◽  
Vol 20 (2) ◽  
pp. 213-220 ◽  
Author(s):  
M. Dąbrowski ◽  
E. Jakimiuk ◽  
M. Gajęcka ◽  
M.T. Gajęcki ◽  
Ł. Zielonka
Keyword(s):  
Mrna Expression ◽  
Large Intestine ◽  
Control Group ◽  
Local Immune Response ◽  
Ascending Colon ◽  
Immune Disorders ◽  
The World ◽  
Preliminary Study ◽  
Experimental Group ◽  
Tlr2 Mrna

Abstract Deoxynivalenol (DON), one of the most prevalent mycotoxins in the world, and is capable of inducing immune disorders in humans and animals. The aim of this study was to determine the effect of feed contaminated with DON on the number of TLR2- and TLR9-positive cells and their mRNA expression in the porcine large intestine. The experiment was conducted on two equal groups of pigs (n=4). The experimental group (E) was administered feed contaminated with DON (1008 μg/kg of feed) for 6 weeks, and the control group (C) was administered non-contaminated feed over the same period of time. A decrease in the expression of TLR2 mRNA was noted in the cecum. The percentage of TLR9-positive enterocytes increased in the ascending colon and decreased in the cecum. The results of this study indicate that DON can modify the local immune response by changing the expression of TLRs.

ANALYSIS OF PROTEOGLYCAN GENE EXPRESSION IN CONNECTIVE TISSUES BY SEMI-QUANTITATIVE RT-PCR

2001 ◽  
Vol 05 (02) ◽  
pp. 79-88
Author(s):  
K. Dobra ◽  
A. Hjerpe
Keyword(s):  
Rt Pcr ◽  
Connective Tissues ◽  
Surrounding Matrix ◽  
Cell Proliferation And Differentiation ◽  
Extracellular Matrix Components ◽  
Proliferation And Differentiation ◽  
The Matrix ◽  
Quantitative Changes ◽  
Regulatory Functions ◽  
Multiple Samples

Proteoglycans (PGs) are cell-membrane and extracellular matrix components with a wide variety of different functions. In the matrix, they are mainly of structural importance, although some of them have been ascribed specific regulatory functions, such as in the assembly of collagen fibers. PGs on the cell surface act as essential modulators of specific ligand-binding reactions, involving interactions between adjacent cells and between cells and surrounding matrix. Through these interactions they participate in different processes, including cell proliferation and differentiation. Qualitative and quantitative changes in PG expression can therefore be associated with various physiological and pathological conditions. We have optimized the conditions for semi-quantitative evaluation of proteoglycan expression by RT-PCR reaction, using glyceraldehyde-3-phosphate dehydrogenase (GAPDH) as reference gene. The relative fluorescence of analyte to reference amplimers can — within certain limits — be used to estimate the amount of target RNA and allows direct comparison of multiple samples. The profile of PG expression obtained in this way can be used to extend our current understanding of the possible functions that can be associated with these complex molecules.

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