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

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.

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

Genetics ◽

10.1093/genetics/151.4.1517 ◽

1999 ◽

Vol 151 (4) ◽

pp. 1517-1529 ◽

Cited By ~ 2

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.

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Alternative Splicing During the Chlamydomonasreinhardtii Cell Cycle

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401622 ◽

2020 ◽

Vol 10 (10) ◽

pp. 3797-3810

Author(s):

Manishi Pandey ◽

Gary D. Stormo ◽

Susan K. Dutcher

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Alternative Splicing ◽

Chlamydomonas Reinhardtii ◽

Intron Retention ◽

Exon Skipping ◽

Dark Phase ◽

Periodic Patterns ◽

Genome Wide ◽

Splicing Pattern

Genome-wide analysis of transcriptome data in Chlamydomonas reinhardtii shows periodic patterns in gene expression levels when cultures are grown under alternating light and dark cycles so that G1 of the cell cycle occurs in the light phase and S/M/G0 occurs during the dark phase. However, alternative splicing, a process that enables a greater protein diversity from a limited set of genes, remains largely unexplored by previous transcriptome based studies in C. reinhardtii. In this study, we used existing longitudinal RNA-seq data obtained during the light-dark cycle to investigate the changes in the alternative splicing pattern and found that 3277 genes (19.75% of 17,746 genes) undergo alternative splicing. These splicing events include Alternative 5′ (Alt 5′), Alternative 3′ (Alt 3′) and Exon skipping (ES) events that are referred as alternative site selection (ASS) events and Intron retention (IR) events. By clustering analysis, we identified a subset of events (26 ASS events and 10 IR events) that show periodic changes in the splicing pattern during the cell cycle. About two-thirds of these 36 genes either introduce a pre-termination codon (PTC) or introduce insertions or deletions into functional domains of the proteins, which implicate splicing in altering gene function. These findings suggest that alternative splicing is also regulated during the Chlamydomonas cell cycle, although not as extensively as changes in gene expression. The longitudinal changes in the alternative splicing pattern during the cell cycle captured by this study provides an important resource to investigate alternative splicing in genes of interest during the cell cycle in Chlamydomonas reinhardtii and other eukaryotes.

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Epithelial Splicing Regulator Protein 1 and Alternative Splicing in Somatotroph Adenomas

Endocrinology ◽

10.1210/en.2013-1051 ◽

2013 ◽

Vol 154 (9) ◽

pp. 3331-3343 ◽

Cited By ~ 5

Author(s):

Tove Lekva ◽

Jens Petter Berg ◽

Robert Lyle ◽

Ansgar Heck ◽

Geir Ringstad ◽

...

Keyword(s):

Alternative Splicing ◽

Epithelial Mesenchymal Transition ◽

Clinical Importance ◽

Somatostatin Analog ◽

Gh3 Cells ◽

Mesenchymal Transition ◽

Regulator Protein ◽

Splicing Pattern ◽

Splicing Regulator ◽

Granulation Pattern

Somatotroph adenomas secrete supraphysiological amounts of GH, causing acromegaly. We have previously hypothesized that epithelial mesenchymal transition (EMT) may play a central role in the progression of these adenomas and that epithelial splicing regulator 1 (ESRP1) may function prominently as a master regulator of the EMT process in pituitary adenomas causing acromegaly. To further elucidate the role of ESRP1 in somatotroph adenomas and in EMT progression, we used RNA sequencing (RNAseq) to sequence somatotroph adenomas characterized by high and low ESRP1 levels. Transcripts identified by RNAseq were analyzed in 65 somatotroph adenomas and in GH-producing pituitary rat cells with a specific knockdown of Esrp1. The clinical importance of the transcripts was further investigated by correlating mRNA expression levels with clinical indices of disease activity and treatment response. Many of the transcripts and isoforms identified by RNAseq and verified by quantitative PCR were involved in vesicle transport and calcium signaling and were associated with clinical outcomes. Silencing Esrp1 in GH3 cells resulted in changes of gene expression overlapping the data observed in human somatotroph adenomas and revealed a decreased granulation pattern and attenuated GH release. We observed an alternative splicing pattern for F-box and leucine-rich repeat protein 20, depending on the ESPR1 levels and on changes in circulating IGF-I levels after somatostatin analog treatment. Our study indicates that ESRP1 in somatotroph adenomas regulates transcripts that may be essential in the EMT progression and in the response to somatostatin analog treatment.

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Expression and alternative splicing pattern of human telomerase reverse transcriptase in human lung cancer cells

International Journal of Oncology ◽

10.3892/ijo.24.4.925 ◽

2004 ◽

Cited By ~ 2

Author(s):

Masachika Fujiwara ◽

Hiroshi Kamma ◽

Wenwen Wu ◽

Makoto Hamasaki ◽

Setsuko Kaneko ◽

...

Keyword(s):

Lung Cancer ◽

Alternative Splicing ◽

Cancer Cells ◽

Human Lung ◽

Human Lung Cancer ◽

Telomerase Reverse Transcriptase ◽

Human Telomerase Reverse Transcriptase ◽

Splicing Pattern ◽

Human Lung Cancer Cells ◽

Human Telomerase

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Genome-Wide Profiling of Prognostic Alternative Splicing Pattern in Pancreatic Cancer

Frontiers in Oncology ◽

10.3389/fonc.2019.00773 ◽

2019 ◽

Vol 9 ◽

Cited By ~ 4

Author(s):

Min Yu ◽

Weifeng Hong ◽

Shiye Ruan ◽

Renguo Guan ◽

Lei Tu ◽

...

Keyword(s):

Pancreatic Cancer ◽

Alternative Splicing ◽

Genome Wide ◽

Splicing Pattern

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Multiple variants and a differential splicing pattern of kinectin in human hepatocellular carcinoma

Biochemistry and Cell Biology ◽

10.1139/o04-003 ◽

2004 ◽

Vol 82 (2) ◽

pp. 321-327 ◽

Cited By ~ 11

Author(s):

Hong-Cheng Wang ◽

Yan-Rong Su ◽

Ke-Jun Han ◽

Xue-Wen Pang ◽

Ji-Run Peng ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Alternative Splicing ◽

Tissue Sample ◽

Cdna Expression Library ◽

Serological Analysis ◽

Expression Library ◽

Humoral Immune ◽

Cdna Expression ◽

Splicing Pattern ◽

Alternatively Spliced

To extend the search for hepatocellular carcinoma (HCC) associated antigens with immunogenicity for clinical applications, we constructed a cDNA expression library using resected human HCC tissue sample and screened it by serological analysis of recombinant cDNA expression library (SEREX) with autologous and allogeneic sera. A total of 24 distinct antigens were isolated and kinectin was the antigen most frequently identified. We found that kinectin was alternatively spliced at four sites and obtained all eight theoretical forms of variant, six by SEREX and two by RT-PCR, from the different splicing combinations of the last three sites. In addition, the splicing patterns of four sites were analyzed. Variant containing D2 was overexpressed in cancerous tissues and this alteration may be tumor associated. The four splicing sites, the variants generated by alternative splicing, and the humoral immune response in HCC patients, may help to analyze the role of kinectin in human HCC cell biology.Key words: alternative splicing, antibody response, hepatocellular carcinoma, kinectin, serological analysis of recombinant cDNA expression library (SEREX).

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Targeted RNA-Seq profiling of splicing pattern in the DMD gene: exons are mostly constitutively spliced in human skeletal muscle

Scientific Reports ◽

10.1038/srep39094 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 13

Author(s):

Anne-Laure Bougé ◽

Eva Murauer ◽

Emmanuelle Beyne ◽

Julie Miro ◽

Jessica Varilh ◽

...

Keyword(s):

Skeletal Muscle ◽

Alternative Splicing ◽

Cdna Sequence ◽

454 Sequencing ◽

Exon Skipping ◽

Rna Seq ◽

Splicing Pattern ◽

Alternative Splicing Events ◽

Diagnostic Research ◽

Dmd Gene

Abstract We have analysed the splicing pattern of the human Duchenne Muscular Dystrophy (DMD) transcript in normal skeletal muscle. To achieve depth of coverage required for the analysis of this lowly expressed gene in muscle, we designed a targeted RNA-Seq procedure that combines amplification of the full-length 11.3 kb DMD cDNA sequence and 454 sequencing technology. A high and uniform coverage of the cDNA sequence was obtained that allowed to draw up a reliable inventory of the physiological alternative splicing events in the muscular DMD transcript. In contrast to previous assumptions, we evidenced that most of the 79 DMD exons are constitutively spliced in skeletal muscle. Only a limited number of 12 alternative splicing events were identified, all present at a very low level. These include previously known exon skipping events but also newly described pseudoexon inclusions and alternative 3′ splice sites, of which one is the first functional NAGNAG splice site reported in the DMD gene. This study provides the first RNA-Seq-based reference of DMD splicing pattern in skeletal muscle and reports on an experimental procedure well suited to detect condition-specific differences in this low abundance transcript that may prove useful for diagnostic, research or RNA-based therapeutic applications.

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