Faculty Opinions recommendation of A BAP1 synonymous mutation results in exon skipping, loss of function and worse patient prognosis.

Esophageal cancer is one of the most common types of cancer, and it has a poor prognosis. The molecular mechanisms of esophageal cancer progression remain largely unknown. In this study, we aimed to investigate the clinical significance and biological function of tumor necrosis factor receptor-associated factor 6 (TRAF6) in esophageal cancer. Expression of TRAF6 in esophageal cancer was examined, and its correlation with clinicopathological factors and patient prognosis was analyzed. A series of functional and mechanism assays were performed to further investigate the function and underlying mechanisms in esophageal cancer. Expression of TRAF6 was highly elevated in esophageal cancer tissues, and patients with high TRAF6 expression have a significantly shorter survival time than those with low TRAF6 expression. Furthermore, loss-of-function experiments showed that knockdown of TRAF6 significantly reduced the migration and invasion abilities of esophageal cancer cells. Moreover, the pro-oncogenic effects of TRAF6 in esophageal cancer were mediated by the upregulation of AEP and MMP2. Altogether, our data suggest that high expression of TRAF6 is significant for esophageal cancer progression, and TRAF6 indicates poor prognosis in esophageal cancer patients, which might be a novel prognostic biomarker or potential therapeutic target in esophageal cancer.

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Loss of Function of E-Cadherin in Embryonic Stem Cells and the Relevance to Models of Tumorigenesis

Journal of Oncology ◽

10.1155/2011/352616 ◽

2011 ◽

Vol 2011 ◽

pp. 1-19 ◽

Cited By ~ 28

Author(s):

Lisa Mohamet ◽

Kate Hawkins ◽

Christopher M. Ward

Keyword(s):

Stem Cells ◽

Growth Factor ◽

Epithelial Mesenchymal Transition ◽

Es Cells ◽

Embryonic Stem ◽

Loss Of Function ◽

Mesenchymal Transition ◽

Cell Metastasis ◽

Patient Prognosis ◽

E Cadherin

E-cadherin is the primary cell adhesion molecule within the epithelium, and loss of this protein is associated with a more aggressive tumour phenotype and poorer patient prognosis in many cancers. Loss of E-cadherin is a defining characteristic of epithelial-mesenchymal transition (EMT), a process associated with tumour cell metastasis. We have previously demonstrated an EMT event during embryonic stem (ES) cell differentiation, and that loss of E-cadherin in these cells results in altered growth factor response and changes in cell surface localisation of promigratory molecules. We discuss the implication of loss of E-cadherin in ES cells within the context of cancer stem cells and current models of tumorigenesis. We propose that aberrant E-cadherin expression is a critical contributing factor to neoplasia and the early stages of tumorigenesis in the absence of EMT by altering growth factor response of the cells, resulting in increased proliferation, decreased apoptosis, and acquisition of a stem cell-like phenotype.

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LncRNA-TUG1/EZH2 axis promotes cell proliferation, migration and the EMT phenotype formation through sponging miR-382

10.1101/123141 ◽

2017 ◽

Author(s):

Liang Zhao ◽

Hongwei Sun ◽

Hongru Kong ◽

Zongjing Chen ◽

Bicheng Chen ◽

...

Keyword(s):

Pancreatic Carcinoma ◽

Rna Binding ◽

Inverse Correlation ◽

Luciferase Reporter ◽

Clinical Samples ◽

Loss Of Function ◽

Expression Array ◽

Novel Treatments ◽

Patient Prognosis ◽

Phenotype Formation

AbstractPancreatic carcinoma (PC) is the one of the most common and malignant cancer in the world. Despite many effort have been made in recent years, the survival rate of PC still remains unsatisfied. Therefore, investigating the mechanisms underlying the progression of PC might facilitate the development of novel treatments that improve patient prognosis. LncRNA Taurine Up–regulated Gene 1 (TUG1) was initially identified as a transcript up - regulated by taurine, siRNA - based depletion of TUG1 suppresses mouse retinal development, and the abnormal expression of TUG1 has been reported in many cancers. However, the biological role and molecular mechanism of TUG1 in pancreatic carcinoma (PC) still needs to be further investigated. In the current study, the expression of TUG1 in the PC cell lines and tissues was measured by quantitative real-time PCR (qRT-PCR), and loss-of-function and gain-of-function approaches were applied to investigate the function of TUG1 in PC cell. Online database analysis tools showed that miR-382 could interact with TUG1 and we found an inverse correlation between TUG1 and miR-382 in PC specimens. Moreover, dual luciferase reporter assay, RNA-binding protein immunoprecipitation (RIP) and applied biotin-avidin pulldown system further provide evidence that TUG1 directly targeted miR-382 by binding with microRNA binding site harboring in the TUG1 sequence. Furthermore, gene expression array analysis using clinical samples and RT-qPCR proposed that EZH2 was a target of miR-382 in PC. Collectively, these findings revealed that TUG1 functions as an oncogenic lncRNA that promotes tumor progression at least partially through function as an endogenous ‘sponge’ by competing for miR-382 binding to regulate the miRNA target EZH2.

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A synonymous mutation in exon 39 of FBN1 causes exon skipping leading to Marfan syndrome

Genomics ◽

10.1016/j.ygeno.2020.06.024 ◽

2020 ◽

Vol 112 (6) ◽

pp. 3856-3861

Author(s):

Mingjie Li ◽

Xinxin Lu ◽

Jian Dong ◽

Zuwu Yao ◽

Yinlong Wu ◽

...

Keyword(s):

Marfan Syndrome ◽

Exon Skipping ◽

Synonymous Mutation

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Abstract 5672: Novel SCN5A Mutations and SNP in Patients with Brugada Syndrome

Circulation ◽

10.1161/circ.118.suppl_18.s_981-c ◽

2008 ◽

Vol 118 (suppl_18) ◽

Author(s):

Kazufumi Nakamura ◽

Daiji Miura ◽

Kaoru Kobayashi ◽

Mamoru Ouchida ◽

Kenji Shimizu ◽

...

Keyword(s):

Brugada Syndrome ◽

Direct Sequencing ◽

Single Point ◽

Point Mutations ◽

Exon Skipping ◽

Pcr Analysis ◽

Nucleotide Polymorphisms ◽

Loss Of Function ◽

Patch Clamp Technique ◽

Hek 293

Background: Sodium channel alpha 5 subunit (SCN5A) mutations are important genetic abnormalities of Brugada syndrome (BS). Here we report novel SCN5A mutations in patients with BS. Methods and Results: Genomic mutations in the SCN5A gene were analyzed by PCR and direct sequencing in 121 patients with BS (119 men and 2 women). Thirteen (11%) of the patients had SCN5A mutation and five (4%) of the patients had single nucleotide polymorphisms (SNP) associated with BS. Eleven patients had single point mutations, one patient had a deletion (1380 del N) and one patient had a mutation within the splicing junction (IVS21+1 g>a). The whole-cell patch clamp technique revealed that four novel mutations (F532C, R814Q, G833R, R878C) showed loss of function, and peak INa of a novel SNP (L1988R) transiently expressed in HEK 293 cells was significantly reduced (P<0.05). RT-PCR analysis revealed that the intronic mutation (IVS21+1 g>a) resulted in exon 21 deletion of SCN5A in cardiac biopsy specimens from the patient (Figure ). Conclusions: We detected five novel SCN5A mutations (1380 del N, F532C, R814Q, G833R, R878C) and a novel disease-associated SNP (L1988R) in patients with BS. We showed a novel analysis of splicing mutation (IVS21+1 g>a) that resulted in exon skipping in the heart.

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Zebrafish as a Model to Evaluate a CRISPR/Cas9-Based Exon Excision Approach as a Future Treatment Option for EYS-Associated Retinitis Pigmentosa

International Journal of Molecular Sciences ◽

10.3390/ijms22179154 ◽

2021 ◽

Vol 22 (17) ◽

pp. 9154

Author(s):

Renske Schellens ◽

Erik de Vrieze ◽

Pam Graave ◽

Sanne Broekman ◽

Kerstin Nagel-Wolfrum ◽

...

Keyword(s):

Retinitis Pigmentosa ◽

Single Molecule ◽

Therapeutic Potential ◽

Outer Nuclear Layer ◽

Exon Skipping ◽

Retinal Disease ◽

Loss Of Function ◽

Zebrafish Model ◽

Reading Frame ◽

Future Treatment

Retinitis pigmentosa (RP) is an inherited retinal disease (IRD) with an overall prevalence of 1 in 4000 individuals. Mutations in EYS (Eyes shut homolog) are among the most frequent causes of non-syndromic autosomal recessively inherited RP and act via a loss-of-function mechanism. In light of the recent successes for other IRDs, we investigated the therapeutic potential of exon skipping for EYS-associated RP. CRISPR/Cas9 was employed to generate zebrafish from which the region encompassing the orthologous exons 37-41 of human EYS (eys exons 40-44) was excised from the genome. The excision of these exons was predicted to maintain the open reading frame and to result in the removal of exactly one Laminin G and two EGF domains. Although the eysΔexon40-44 transcript was found at levels comparable to wild-type eys, and no unwanted off-target modifications were identified within the eys coding sequence after single-molecule sequencing, EysΔexon40-44 protein expression could not be detected. Visual motor response experiments revealed that eysΔexon40-44 larvae were visually impaired and histological analysis revealed a progressive degeneration of the retinal outer nuclear layer in these zebrafish. Altogether, the data obtained in our zebrafish model currently provide no indications for the skipping of EYS exons 37-41 as an effective future treatment strategy for EYS-associated RP.

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Sequencing the CaSR locus in Pakistani stone formers reveals a novel loss-of-function variant atypically associated with nephrolithiasis

BMC Medical Genomics ◽

10.1186/s12920-021-01116-5 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Ihsan Ullah ◽

Isabel Ottlewski ◽

Wasim Shehzad ◽

Amjad Riaz ◽

Sadaqat Ijaz ◽

...

Keyword(s):

Splice Variant ◽

Receptor Gene ◽

Exon Skipping ◽

Loss Of Function ◽

Calcium Sensing Receptor ◽

Calcium Sensing ◽

Stone Formers ◽

Unknown Significance ◽

Pakistani Families ◽

Calcium Sensing Receptor Gene

Abstract Background Nephrolithiasis (NL) affects 1 in 11 individuals worldwide and causes significant morbidity and cost. Common variants in the calcium sensing receptor gene (CaSR) have been associated with NL. Rare inactivating CaSR variants classically cause hyperparathyroidism, hypercalcemia and hypocalciuria. However, NL and familial hypercalciuria have been paradoxically associated with select inactivating CaSR variants in three kindreds from Europe and Australia. Methods To discover novel NL-associated CaSR variants from a geographically distinct cohort, 57 Pakistani families presenting with pediatric onset NL were recruited. The CaSR locus was analyzed by directed or exome sequencing. Results We detected a heterozygous and likely pathogenic splice variant (GRCh37 Chr3:122000958A>G; GRCh38 Chr3:12228211A>G; NM_000388:c.1609-2A>G) in CaSR in one family with recurrent calcium oxalate stones. This variant would be predicted to cause exon skipping and premature termination (p.Val537Metfs*49). Moreover, a splice variant of unknown significance in an alternative CaSR transcript (GRCh37 Chr3:122000929G>C; GRCh38 Chr3:122282082G >C NM_000388:c.1609-31G >C NM_001178065:c.1609-1G >C) was identified in two additional families. Conclusions Sequencing of the CaSR locus in Pakistani stone formers reveals a novel loss-of-function variant, expanding the connection between the CaSR locus and nephrolithiasis.

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Targeting NUFIP1 Suppresses Growth and Induces Senescence of Colorectal Cancer Cells

10.21203/rs.3.rs-130884/v1 ◽

2020 ◽

Author(s):

Aling Shen ◽

Meizhu Wu ◽

Liya Liu ◽

Youqin Chen ◽

Xiaoping Chen ◽

...

Keyword(s):

Colorectal Cancer ◽

Fruits And Vegetables ◽

Rna Binding ◽

Function Analysis ◽

Fragile X ◽

Disease Free Survival ◽

Loss Of Function ◽

Patient Prognosis

Abstract Background: NUFIP1 is an RNA-binding protein that interacts with fragile X mental retardation protein (FMRP) in the messenger ribonucleoprotein particle (mRNP). We previously showed that NUFIP1 was upregulated in colorectal cancer (CRC), but how the protein may contribute to the disease and patient prognosis is unknown. Methods: Here we combine database analysis, microarray, quantitative PCR, and immunohistochemistry of patients' samples to confirm our previous findings on NUFIP1 overexpression in CRC, and to reveal that increased expression of NUFIP1 in CRC tissues correlated with worse overall, recurrence-free, event-free and disease-free survival in patients, as well as with more advanced CRC clinicopathological stage. Results: Loss of function analysis demonstrated that NUFIP1 knockdown suppressed cell growth in vitro and in vivo, inhibited cell viability and survival, and induced cell cycle arrest and apoptosis in vitro. In addition, as a natural anticancer triterpene from various fruits and vegetables, ursolic acid (UA) treatment suppressed cell proliferation, down-regulated NUFIP1 protein expression, and further enhanced the effects of NUFIP1 knockdown in CRC cells in vitro. NUFIP1 knockdown up-regulated the expression of 136 proteins, down-regulated the expression of 41 proteins, and enriched multiple signaling pathways including the senescence-associated heterochromatin foci (SAHF) pathway. Furthermore, NUFIP1 knockdown enhanced the expression of senescence-associated-β-galactosidase (SA-β-gal), the SAHF markers HP1γ and trimethylation (H3k9me3), and the senescence-related protein HMGA2. Conclusion: Our findings suggest that NUFIP1 is overexpressed in CRC and correlates with disease progression and poor patient survival. NUFIP1 may exert oncogenic effects partly by altering senescence. UA may show potential to treat CRC by down-regulating NUFIP1.

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Identification and Functional Analysis of Mutations in the Hypocretin (Orexin) Genes of Narcoleptic Canines

Genome Research ◽

10.1101/gr.161001 ◽

2001 ◽

Vol 11 (4) ◽

pp. 531-539

Author(s):

Marcel Hungs ◽

Jun Fan ◽

Ling Lin ◽

Xiaoyan Lin ◽

Richard A. Maki ◽

...

Keyword(s):

Functional Analysis ◽

Novel Mutation ◽

Disease Onset ◽

Exon Skipping ◽

Single Amino Acid ◽

Membrane Localization ◽

Loss Of Function ◽

Hek 293 ◽

Sporadic Cases ◽

Multiplex Families

Narcolepsy is a sleep disorder affecting animals and humans. Exon skipping mutations of the Hypocretin/Orexin-receptor-2 (Hcrtr2) gene were identified as the cause of narcolepsy in Dobermans and Labradors. Preprohypocretin (Hcrt) knockout mice have symptoms similar to human and canine narcolepsy. In this study, 11 sporadic cases of canine narcolepsy and two additional multiplex families were investigated for possible Hcrt andHcrtr2 mutations. Sporadic cases have been shown to have more variable disease onset, increased disease severity, and undetectable Hypocretin-1 levels in cerebrospinal fluid. The canine Hcrtlocus was isolated and characterized for this project. Only one novel mutation was identified in these two loci. This alteration results in a single amino acid substitution (E54K) in the N-terminal region of the Hcrtr2 receptor and autosomal recessive transmission in a Dachshund family. Functional analysis of previously-described exon-skipping mutations and of the E54K substitution were also performed using HEK-293 cell lines transfected with wild-type and mutated constructs. Results indicate a truncated Hcrtr2 protein, an absence of proper membrane localization, and undetectable binding and signal transduction for exon-skipping mutated constructs. In contrast, the E54K abnormality was associated with proper membrane localization, loss of ligand binding, and dramatically diminished calcium mobilization on activation of the receptor. These results are consistent with a loss of function for all three mutations. The absence of mutation in sporadic cases also indicates genetic heterogeneity in canine narcolepsy, as reported previously in humans.

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