Zfa is an expressed retroposon derived from an alternative transcript of the Zfx gene.

Alternative transcript cleavage and polyadenylation is linked to cancer cell transformation, proliferation and outcome. This has led researchers to develop methods to detect and bioinformatically analyse alternative polyadenylation as potential cancer biomarkers. If incorporated into standard prognostic measures such as gene expression and clinical parameters, these could advance cancer prognostic testing and possibly guide therapy. In this review, we focus on the existing methodologies, both experimental and computational, that have been applied to support the use of alternative polyadenylation as cancer biomarkers.

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Breast Cancer Patient Prognosis Is Determined by the Interplay between TP53 Mutation and Alternative Transcript Expression: Insights from TP53 Long Amplicon Digital PCR Assays

Cancers ◽

10.3390/cancers13071531 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1531

Author(s):

Annette Lasham ◽

Nicholas Knowlton ◽

Sunali Y. Mehta ◽

Antony W. Braithwaite ◽

Cristin G. Print

Keyword(s):

Breast Cancer ◽

Gene Locus ◽

Tp53 Mutation ◽

P53 Protein ◽

Tp53 Gene ◽

Digital Pcr ◽

Protein Isoforms ◽

Alternative Transcript ◽

Transcript Expression ◽

Splice Sites

The TP53 gene locus is capable of producing multiple RNA transcripts encoding the different p53 protein isoforms. We recently described multiplex long amplicon droplet digital PCR (ddPCR) assays to quantify seven of eight TP53 reference transcripts in human tumors. Here, we describe a new long amplicon ddPCR assay to quantify expression of the eighth TP53 reference transcript encoding ∆40p53α. We then applied these assays, alongside DNA sequencing of the TP53 gene locus, to tumors from a cohort of New Zealand (NZ) breast cancer patients. We found a high prevalence of mutations at TP53 splice sites in the NZ breast cancer cohort. Mutations at TP53 intron 4 splice sites were associated with overexpression of ∆133TP53 transcripts. Cox proportional hazards survival analysis showed that interplay between TP53 mutation status and expression of TP53 transcript variants was significantly associated with patient outcome, over and above standard clinical and pathological information. In particular, patients with no TP53 mutation and a low ratio of TP53 transcripts t2 to t1, which derive from alternative intron 1 acceptor splice sites, had a remarkably good outcome. We suggest that this type of analysis, integrating mutation and transcript expression, provides a step-change in our understanding of TP53 in cancer.

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Predictive value of survivin alternative transcript expression in locally advanced breast cancer patients treated with neoadjuvant chemotherapy

International Journal of Molecular Medicine ◽

10.3892/ijmm_00000129 ◽

1998 ◽

Author(s):

Lizard-Nacol

Keyword(s):

Breast Cancer ◽

Neoadjuvant Chemotherapy ◽

Advanced Breast Cancer ◽

Cancer Patients ◽

Predictive Value ◽

Locally Advanced Breast Cancer ◽

Locally Advanced ◽

Alternative Transcript ◽

Transcript Expression ◽

Breast Cancer Patients

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Alternative transcript imbalance underlying breast cancer susceptibility in a family carrying PALB2 c.3201+5G>T

Breast Cancer Research and Treatment ◽

10.1007/s10549-018-05094-8 ◽

2018 ◽

Vol 174 (2) ◽

pp. 543-550 ◽

Cited By ~ 4

Author(s):

Laura Duran-Lozano ◽

Gemma Montalban ◽

Sandra Bonache ◽

Alejandro Moles-Fernández ◽

Anna Tenés ◽

...

Keyword(s):

Breast Cancer ◽

Cancer Susceptibility ◽

Breast Cancer Susceptibility ◽

Alternative Transcript

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Comparison of ZFY and ZFX gene structure and analysis of alternative 3' untranslated regions of ZFY

Nucleic Acids Research ◽

10.1093/nar/19.10.2579 ◽

1991 ◽

Vol 19 (10) ◽

pp. 2579-2586 ◽

Cited By ~ 19

Author(s):

M. North ◽

C. Sargent ◽

J. O'Brien ◽

K. Taylor ◽

J. Wolfe ◽

...

Keyword(s):

Gene Structure ◽

Untranslated Regions ◽

Zfx Gene

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Genomic structure and an alternative transcript of bovine mitochondrial glycerol-3-phosphate acyltransferase gene (GPAM)

Cytogenetic and Genome Research ◽

10.1159/000087517 ◽

2005 ◽

Vol 112 (1-2) ◽

pp. 82-89 ◽

Cited By ~ 8

Author(s):

R. Roy ◽

L. Ordovas ◽

S. Taourit ◽

P. Zaragoza ◽

A. Eggen ◽

...

Keyword(s):

Genomic Structure ◽

Alternative Transcript

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Expression of ZNF695 Transcript Variants in Childhood B-Cell Acute Lymphoblastic Leukemia

Genes ◽

10.3390/genes10090716 ◽

2019 ◽

Vol 10 (9) ◽

pp. 716 ◽

Cited By ~ 2

Author(s):

Rosa ◽

Villegas-Ruíz ◽

Caballero-Palacios ◽

Pérez-López ◽

Murata ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

B Cell ◽

Long Noncoding Rna ◽

Noncoding Rna ◽

Expression Profiles ◽

Lymphoblastic Leukemia ◽

Alternative Transcript ◽

Human Transcriptome ◽

Transcript Variants ◽

Cell Acute Lymphoblastic Leukemia

B-cell acute lymphoblastic leukemia is the most commonly diagnosed childhood malignancy worldwide; more than 50% of these cases are diagnosed in Mexico. Although the five-year survival rate is >80%, 30% of patients experience relapse with poor prognosis. Cancer-associated gene expression profiles have been identified in several malignancies, and some transcripts have been used to predict disease prognosis. The human transcriptome is incompletely elucidated; moreover, more than 80% of transcripts can be processed via alternative splicing (AS), which increases transcript and protein diversity. The human transcriptome is divided; coding RNA accounts for 2%, and the remaining 98% is noncoding RNA. Noncoding RNA can undergo AS, promoting the diversity of noncoding transcripts. We designed specific primers to amplify previously reported alternative transcript variants of ZNF695 and showed that six ZNF695 transcript variants are co-expressed in cancer cell lines. The amplicons were sequenced and identified. Additionally, we analyzed the expression of these six transcript variants in bone marrow from B-cell acute lymphoblastic leukemia patients and observed that ZNF695 transcript variants one and three were the predominant variants expressed in leukemia. Moreover, our results showed the co-expression of coding and long noncoding RNA. Finally, we observed that long noncoding RNA ZNF695 expression predicted survival rates.

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The carnitine acetyltransferase gene (CRAT): A characterization of porcine transcripts with insights into the 5’-end variants of mammalian transcripts and their possible sub-cellular localization

Cellular & Molecular Biology Letters ◽

10.2478/s11658-008-0036-3 ◽

2009 ◽

Vol 14 (1) ◽

Cited By ~ 2

Author(s):

Annie Robic ◽

Thomas Faraut ◽

Laurence Liaubet ◽

Denis Milan

Keyword(s):

Cellular Localization ◽

Energy Homeostasis ◽

Intron Retention ◽

Mammalian Species ◽

Alternative Transcript ◽

Carnitine Acetyltransferase ◽

Exon 2 ◽

Cellular Specificity ◽

Important Enzyme

AbstractCarnitine acetyltransferase (CRAT) is an important enzyme for energy homeostasis and fat metabolism. We characterized the predicted full length cDNA sequence of the porcine CRAT gene. Its structure is very similar to that in humans with respect to the size and organization of the 14 exons. We demonstrated the existence of a porcine alternative transcript resulting from a partial intron-retention at the 5’ end of exon 2. To perform a comparison of the 5’ end variants of the mammalian CRAT gene, we analyzed the Genbank data, and here we propose a new 5’ variant for dog, rat and mouse. In contrast to other mammals where this variant encodes a shorter protein (−21 aa in human, mouse and rat, and −14 aa in dog), the pig variant encodes for a longer protein (+18 aa). In all mammalian species, variant 1 has a high probability of a preferential mitochondrial sub-cellular localization. Nevertheless, it is not evident, in particular in porcine and dog species, that the second variant is associated with a different sub-cellular specificity.

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A Second Promoter for the Human KCl Cotransporter 1 (KCC1) Gene Drives Differential Expression of a Variant Isoform in Sickle Versus Normal Reticulocytes.

Blood ◽

10.1182/blood.v104.11.3592.3592 ◽

2004 ◽

Vol 104 (11) ◽

pp. 3592-3592

Author(s):

Kathleen Anderson ◽

Scott C. Crable ◽

Suzan M. Hammond ◽

Clinton H. Joiner ◽

Patrick G. Gallagher

Keyword(s):

Promoter Activity ◽

Regulatory Elements ◽

Dominant Negative ◽

Jurkat Cells ◽

Pcr Analysis ◽

Luciferase Expression ◽

Alternative Transcript ◽

Red Cell ◽

Rt Pcr ◽

Tissue Samples

Abstract The K+Cl- cotransporter plays a significant role in the maintenance of red cell volume. During cellular maturation, this cotransporter actively moves K+ and Cl- out of the cell. The accompanying movement of water results in dehydration and shrinking of the red cell. Because KCl cotransporter activity is higher in sickle compared to normal reticulocytes, it has been considered a potential modifier gene for sickle cell disease. We have evidence for expression of three KCC genes in human reticulocytes and have investigated the promoter for KCC1. While the expression of the principal KCC1 transcript did not differ in SS compared to normal reticulocytes, we now describe an alternative transcript of the KCC1 gene emanating from a second promoter and exhibiting a restricted tissue distribution. Investigation of the EST databases revealed spliced ESTs corresponding to the use of four distinct N-terminal exons in the KCC1 gene, each reported multiple times in the dataset. Primers were developed for these 5′ regions (exon1, 1a, 1b, and 1c) and used in an RT-PCR reaction with human reticulocyte RNA. The exon1 form and the exon1b variant were expressed. When the relative levels of these forms were compared, expression of the exon1 transcript was unchanged, while significantly higher levels of the exon1b variant was evident in the AA reticulocyte RNA compared to numerous SS samples. In an analysis of seven other human tissue samples, the exon1b isoform was highly expressed in kidney, lung, and heart, while the KCC1ex1 transcript was expressed at a constant level in all tissues. Although the transcript for this variant could arise from the KCC1 promoter we have previously characterized, the pattern of expression suggested control from a second promoter. A 915bp region corresponding to −787 to +128 was isolated and cloned into a reporter construct to test for promoter activity. This clone was compared with KCC1 promoter constructs in transient transfection assays. The exon1b construct not only exhibited promoter activity by directing high levels of luciferase expression in K562 cells, it also demonstrated tissue-specificity with a low level of activity in Jurkat cells. This recapitulates the endogenous levels detected by RT-PCR analysis of these cell lines. The −787/+128 exon1b construct is also 3-fold more active than the ubiquitously expressed exon1 promoter. To identify the control elements for this promoter, we produced a series of deletion constructs; the smallest construct contained 181bp. No reduction in reporter gene activity was evident, indicating the major regulatory elements lie very close to this promoter. Since exon1 encodes 39aa and exon1b only 7aa, the use of this smaller first exon effectively produces an N-terminal truncation in the protein. Studies with the mouse KCC1 cDNA have demonstrated that proteins produced by an N-terminal truncation are not only inactive for K+Cl- cotransport, but also function as dominant negative regulators of a full-length KCC1 protein. High level expression of this variant in AA cells compared to SS cells would therefore be consistent with the low reported activity in the AA reticulocytes. Induction or modulation of the expression of the KCC1ex1b variant may be an key factor in the control of red cell hydration.

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An Alternative Transcript of the PANE1 Gene Encodes a Minor Histocompatibility Antigen That Is Selectively Expressed in Resting CD19+ Cells and B-CLL.

Blood ◽

10.1182/blood.v106.11.2957.2957 ◽

2005 ◽

Vol 106 (11) ◽

pp. 2957-2957

Author(s):

Anthony G. Brickner ◽

Jeffrey K. Mito ◽

Xin Feng ◽

Tetsuya Nishida ◽

Liane Fairfull ◽

...

Keyword(s):

Peripheral Blood ◽

Mononuclear Cells ◽

Small Sample ◽

Histocompatibility Antigen ◽

Dermal Fibroblasts ◽

Alternative Transcript ◽

Minor Histocompatibility Antigen ◽

Cd8 Cells ◽

Cytotoxicity Assays ◽

Low Levels

Abstract We recently identified an HLA-A3-restricted minor histocompatibility antigen (mHAg) encoded by an alternative transcript (transcript k) of the PANE1 gene within an exon unique from all other PANE1 transcripts. Differential CTL recognition of mHAg+ and mHAg− cells is due to a single nucleotide polymorphism that replaces an arginine codon (CGA) with a translation termination codon (TGA). Cytotoxicity assays revealed robust recognition of HLA-A3+ EBV-LCL, minimal recognition of unfractionated peripheral blood mononuclear cells and PHA-stimulated T-cell blasts (PHA-T), and no recognition of dermal fibroblasts. To determine whether the restricted tissue distribution of the mHAg correlated with transcript k expression, we developed a real-time quantitative PCR assay to specifically detect transcript k. In normal tissues, expression was highest in spleen, low in all other tissues examined, and undetectable in dermal fibroblasts. Analysis of resting and activated peripheral blood cell fractions revealed very high expression levels in resting CD19+ cells, intermediate levels in EBV-LCL and resting CD4+ and CD8+ cells, and very low levels in activated CD19+ cells as well as resting and activated mononuclear cells, CD14+ cells, and activated CD4+ and CD8+ cells. EBV-LCL from mHAg− TGA homozygotes express significantly lower transcript k levels (p=0.043; Student’s t test) than mHAg+ EBV-LCL, suggesting the possibility of nonsense-mediated decay. The preferential expression of transcript k in normal resting CD19+ cells prompted us to investigate expression in malignant CD19+ cells. In a small sample of CD19+ acute lymphoblastic leukemia cells, we observed low-level expression comparable to that of activated normal CD19+ cells. In contrast, we observed high-level expression in CD19+ B-CLL cells comparable to or greater than that of normal resting CD19+ cells, and far greater than the levels in any other cell type tested. CTL cytotoxicity assays of a subset of HLA-A3+, mHAg+ B-CLLs revealed that they uniformly presented the mHAg encoded by PANE1 transcript k. Our finding that transcript k was selectively expressed in resting CD19+ cells and CD19+ B-CLL contradicted a previous report (Bierie et al., Gene Expression Patterns4:389, 2004) that the longest PANE1 transcript (transcript c) is preferentially expressed in activated lymphoid cells. We therefore evaluated transcript c expression in the same panel of samples, and confirmed that it was selectively expressed in activated CD19+ cells, with very low levels in resting CD19+ and primary B-CLL cells. Thus, PANE1 transcripts k and c display reciprocal expression in resting and activated CD19+ cells and primary CD19+ B-CLL cells. To determine if activation of CD19+ cells would increase expression of transcript c and decrease expression of transcript k, we evaluated the effect of CD40L stimulation in 6 primary B-CLL samples. In all samples tested, CD40L stimulation led to a profound decrease in transcript k expression, and a significant increase in transcript c expression. These studies suggest distinct roles for different PANE1 isoforms in resting versus activated CD19+ cells, and identify PANE1 as a potential therapeutic target in B-CLL.

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