scholarly journals Nanopore Sequencing Unveils Diverse Transcript Variants of the Epithelial Cell-Specific Transcription Factor Elf-3 in Human Malignancies

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 839
Author(s):  
Michaela A. Boti ◽  
Panagiotis G. Adamopoulos ◽  
Panagiotis Tsiakanikas ◽  
Andreas Scorilas
Keyword(s):  
Transcription Factor ◽  
Epithelial Cell ◽  
Wide Spectrum ◽  
Protein Isoforms ◽  
Alternative Transcript ◽  
Nanopore Sequencing ◽  
Transcript Variants ◽  
Mesenchymal To Epithelial Transition ◽  
Depth Analysis ◽  
Ets Family

The human E74-like ETS transcription factor 3 (Elf-3) is an epithelium-specific member of the ETS family, all members of which are characterized by a highly conserved DNA-binding domain. Elf-3 plays a crucial role in epithelial cell differentiation by participating in morphogenesis and terminal differentiation of the murine small intestinal epithelium, and also acts as an indispensable regulator of mesenchymal to epithelial transition, underlying its significant involvement in development and in pathological states, such as cancer. Although previous research works have deciphered the functional role of Elf-3 in normal physiology as well as in tumorigenesis, the present study highlights for the first time the wide spectrum of ELF3 mRNAs that are transcribed, providing an in-depth analysis of splicing events and exon/intron boundaries in a broad panel of human cell lines. The implementation of a versatile targeted nanopore sequencing approach led to the identification of 25 novel ELF3 mRNA transcript variants (ELF3 v.3–v.27) with new alternative splicing events, as well as two novel exons. Although the current study provides a qualitative transcriptional profile regarding ELF3, further studies must be conducted, so the biological function of all novel alternative transcript variants as well as the putative protein isoforms are elucidated.

scholarly journals Targeted Long-Read Sequencing Decodes the Transcriptional Atlas of the Founding RAS Gene Family Members

2021 ◽  
Vol 22 (24) ◽  
pp. 13298
Author(s):  
Panagiotis G. Adamopoulos ◽  
Panagiotis Tsiakanikas ◽  
Michaela A. Boti ◽  
Andreas Scorilas
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Protein Isoforms ◽  
Alternative Transcript ◽  
Transcriptional Level ◽  
Ras Gene ◽  
Ras Genes ◽  
Transcript Variants ◽  
Depth Analysis ◽  
Genes Encoding

The complicity of human RAS proteins in cancer is a well-documented fact, both due to the mutational hyperactivation of these GTPases and the overexpression of the genes encoding these proteins. Thus, it can be easily assumed that the study of RAS genes at the transcriptional and post-transcriptional level is of the utmost importance. Although previous research has shed some light on the basic mechanisms by which GTPases are involved in tumorigenesis, limited information is known regarding the transcriptional profile of the genes encoding these proteins. The present study highlights for the first time the wide spectrum of the mRNAs generated by the three most significant RAS genes (KRAS, NRAS and HRAS), providing an in-depth analysis of the splicing events and exon/intron boundaries. The implementation of a versatile, targeted nanopore-sequencing approach led to the identification of 39 novel RAS mRNA transcript variants and to the elucidation of their expression profiles in a broad panel of human cell lines. Although the present work unveiled multiple hidden aspects of the RAS gene family, further study is required to unravel the biological function of all the novel alternative transcript variants, as well as the putative protein isoforms.

scholarly journals 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 ◽  
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.

scholarly journals Glucocorticoid Receptor Activation Signals through Forkhead Transcription Factor 3a in Breast Cancer Cells

2006 ◽  
Vol 20 (10) ◽  
pp. 2304-2314 ◽  
Author(s):  
Wei Wu ◽  
Min Zou ◽  
Deanna R. Brickley ◽  
Travis Pew ◽  
Suzanne D. Conzen
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Transcription Factor ◽  
Epithelial Cell ◽  
Mammary Epithelial Cell ◽  
Breast Cancer Cells ◽  
Receptor Activation ◽  
Mammary Epithelial ◽  
Forkhead Transcription Factor ◽  
Igfbp 3

Abstract Activation of the glucocorticoid receptor (GR) plays a critical role in the stress response of virtually all cell types. Despite recent advances in large-scale genomic and proteomic data acquisition, identification of physiologically relevant molecular events downstream of nuclear hormone receptor activation remains challenging. By analyzing gene expression changes 30 min after dexamethasone (Dex) treatment, we previously found that immediate induction of serum and glucocorticoid-regulated kinase-1 (SGK-1) expression is required for GR-mediated mammary epithelial cell survival signaling. We now report that activation of the GR mediates Forkhead transcription factor 3a (FOXO3a) phosphorylation and inactivation in mammary epithelial cells. GR-mediated induction of SGK-1 expression is required for FOXO3a inactivation; additional growth factor stimulation is not required. To further explore the gene expression changes that occur downstream of GR-mediated FOXO3a inactivation, we analyzed temporal gene expression data and selected GR-down-regulated genes containing core FOXO3a binding motifs in their proximal promoters. This approach revealed several previously unrecognized transcriptional target genes of FOXO3a, including IGF binding protein-3 (IGFBP-3). Endogenous IGFBP-3 expression was confirmed to be dependent on the GR-SGK-1-FOXO3a signaling pathway. Moreover, GR activation decreased FOXO3a-induced apoptosis in SK-BR-3 breast cancer cells. Collectively, our data suggest that GR-mediated FOXO3a inactivation is an important mechanism contributing to glucocorticoid-mediated mammary epithelial cell survival.

scholarly journals Characterization of NERF, a novel transcription factor related to the Ets factor ELF-1.

1996 ◽  
Vol 16 (9) ◽  
pp. 5091-5106 ◽  
Author(s):  
P Oettgen ◽  
Y Akbarali ◽  
J Boltax ◽  
J Best ◽  
C Kunsch ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Fetal Liver ◽  
Protein A ◽  
Related Factor ◽  
Gene Promoters ◽  
Human Spleen ◽  
Related Transcription Factor ◽  
Ets Family

We have cloned the gene for a novel Ets-related transcription factor, new Ets-related factor (NERF), from human spleen, fetal liver, and brain. Comparison of the deduced amino acid sequence of NERF with those of other members of the Ets family reveals that the level of homology to ELF-1, which is involved in the regulation of several T- and B-cell-specific genes, is highest. Homologies are clustered in the putative DNA binding domain in the middle of the protein, a basic domain just upstream of this domain, and several shorter stretches of homology towards the amino terminus. The presence of two predominant NERF transcripts in various fetal and adult human tissues is due to at least three alternative splice products, NERF-1a, NERF-1b, and NERF-2, which differ in their amino termini and their expression in different tissues. Only NERF-2 and ELF-1, and not NERF-1a and NERF-1b, function as transcriptional activators of the lyn and blk gene promoters, although all isoforms of NERF bind with affinities similar to those of ELF-1 to a variety of Ets binding sites in, among others, the blk, lck, lyn, mb-1, and immunoglobulin H genes and are expressed at similar levels. Since NERF and ELF-1 are coexpressed in B and T cells, both might be involved in the regulation of the same genes.

scholarly journals Investigation of Anti-Inflammatory Potential of N-Arylcinnamamide Derivatives

Molecules ◽  
2019 ◽  
Vol 24 (24) ◽  
pp. 4531 ◽  
Author(s):  
Jan Hošek ◽  
Jiří Kos ◽  
Tomáš Strhársky ◽  
Lucie Černá ◽  
Pavel Štarha ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Transcription Factor ◽  
Model Compound ◽  
Wide Spectrum ◽  
Reference Drug ◽  
X Ray ◽  
Inhibition Effect ◽  
Tnf Α ◽  
Anti Inflammatory ◽  
Bacteria And Fungi

A series of sixteen ring-substituted N-arylcinnamanilides, previously described as highly antimicrobially effective against a wide spectrum of bacteria and fungi, together with two new derivatives from this group were prepared and characterized. Moreover, the molecular structure of (2E)-N-(2-bromo-5-fluorophenyl)-3-phenylprop-2-enamide as a model compound was determined using single-crystal X-ray analysis. All the compounds were tested for their anti-inflammatory potential, and most tested compounds significantly attenuated the lipopolysaccharide-induced NF-κB activation and were more potent than the parental cinnamic acid. (2E)-N-[2-Chloro-5-(trifluoromethyl)phenyl]-3-phenylprop-2-enamide, (2E)-N-(2,6-dibromophenyl)- 3-phenylprop-2-enamide, and (2E)-N-(2,5-dichlorophenyl)-3-phenylprop-2-enamide demonstrated the highest inhibition effect on transcription factor NF-κB at the concentration of 2 µM and showed a similar effectiveness as the reference drug prednisone. Several compounds also decreased the level of TNF-α. Nevertheless, subsequent tests showed that the investigated compounds affect neither IκBα level nor MAPKs activity, which suggests that the N-arylcinnamanilides may have a different mode of action to prednisone. The modification of the C(2,5)ʹ or C(2,6)ʹ positions of the anilide core by rather lipophilic and bulky moieties seems to be preferable for the anti-inflammatory potential of these compounds.

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