Intronic splicing of hyaluronan synthase 1 (HAS1): a biologically relevant indicator of poor outcome in multiple myeloma

Abstract In this study, we show that the hyaluronan synthase 1 (HAS1) gene undergoes aberrant intronic splicing in multiple myeloma (MM). In addition to HAS1 full length (HAS1FL), we identify 3 novel splice variants of HAS1, HAS1Va, HAS1Vb, and HAS1Vc, detected in patients with MM or monoclonal gammopathy of undetermined significance (MGUS). HAS1Vb and HAS1Vc undergo intronic splicing with creation of a premature stop codon. MM cells expressing one or more HAS1 variants synthesize extracellular and/or intracellular hyaluronan (HA). Expression of the HAS1Vb splice variant was significantly correlated with reduced survival (P = .001). Together, alternative HAS1 gene splicing, the correlations between HAS1 splicing and HA synthesis, and the correlations between HAS1 splicing and reduced survival of MM patients support the hypothesis that the family of HAS1 protein plays a significant role in disease progression. Further, expression of HAS1Vb, in conjunction with HAS1FL and/or other HAS1 variants, may lead to accumulation of intracellular HA molecules and an impact on receptor for HA-mediated motility (RHAMM)-mediated mitotic abnormalities in MM. This study highlights the potential importance of HAS1 and its alternative splicing in pathophysiology of MGUS and MM. (Blood. 2005;105: 4836-4844)

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Family’s History Based on the CDH1 Germline Variant (c.360delG) and a Suspected Hereditary Gastric Cancer Form

International Journal of Molecular Sciences ◽

10.3390/ijms21144904 ◽

2020 ◽

Vol 21 (14) ◽

pp. 4904

Author(s):

Laura Caggiari ◽

Mara Fornasarig ◽

Mariangela De Zorzi ◽

Renato Cannizzaro ◽

Agostino Steffan ◽

...

Keyword(s):

Gastric Cancer ◽

Cancer Susceptibility ◽

Stop Codon ◽

Case Reports ◽

Premature Stop Codon ◽

Diffuse Gastric Cancer ◽

Cancer Syndrome ◽

The Family ◽

Hereditary Gastric Cancer ◽

E Cadherin

Hereditary diffuse gastric cancer (HDGC) is a cancer susceptibility syndrome caused by germline pathogenic variant in CDH1, the gene encoding E-cadherin. The germline loss-of-function variants are the only proven cause of the cancer syndrome HDGC, occurring in approximately 10–18% of cases and representing a helpful tool in genetic counseling. The current case reports the family history based on a CDH1 gene variant, c.360delG, p.His121Thr in a suspected family for hereditary gastric cancer form. This frameshift deletion generates a premature stop codon at the amino acid 214, which leads to a truncated E-cadherin protein detecting it as a deleterious variant. The present study expands the mutational spectra of the family with the CDH1 variant. Our results highlight the clinical impact of the reported CDH1 variant running in gastric cancer families.

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Interferon lambda 4 expression is suppressed by the host during viral infection

Journal of Experimental Medicine ◽

10.1084/jem.20160437 ◽

2016 ◽

Vol 213 (12) ◽

pp. 2539-2552 ◽

Cited By ~ 28

Author(s):

MeeAe Hong ◽

Johannes Schwerk ◽

Chrissie Lim ◽

Alison Kell ◽

Abigail Jarret ◽

...

Keyword(s):

Biochemical Characterization ◽

Splice Variants ◽

Stop Codon ◽

Association Studies ◽

Premature Stop Codon ◽

Genetic Association Studies ◽

Protein Isoforms ◽

Translation Efficiency ◽

Regulation Of Expression ◽

Protein Coding

Interferon (IFN) lambdas are critical antiviral effectors in hepatic and mucosal infections. Although IFNλ1, IFNλ2, and IFNλ3 act antiviral, genetic association studies have shown that expression of the recently discovered IFNL4 is detrimental to hepatitis C virus (HCV) infection through a yet unknown mechanism. Intriguingly, human IFNL4 harbors a genetic variant that introduces a premature stop codon. We performed a molecular and biochemical characterization of IFNλ4 to determine its role and regulation of expression. We found that IFNλ4 exhibits similar antiviral activity to IFNλ3 without negatively affecting antiviral IFN activity or cell survival. We show that humans deploy several mechanisms to limit expression of functional IFNλ4 through noncoding splice variants and nonfunctional protein isoforms. Furthermore, protein-coding IFNL4 mRNA are not loaded onto polyribosomes and lack a strong polyadenylation signal, resulting in poor translation efficiency. This study provides mechanistic evidence that humans suppress IFNλ4 expression, suggesting that immune function is dependent on other IFNL family members.

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A new mutation at exon 2 of hprt1 locus causing Lesch-Nyhan Syndrome.

Innovaciencia Facultad de Ciencias Exactas Físicas y Naturales ◽

10.15649/2346075x.362 ◽

2015 ◽

Vol 3 (1) ◽

pp. 18-21

Author(s):

Adriana María Gil Zapata ◽

Adriana Castillo Pico ◽

Leonor Gusmão ◽

António Amorim ◽

Fernando Rodríguez Sanabria

Keyword(s):

Genetic Counseling ◽

Inborn Error ◽

Stop Codon ◽

Premature Stop Codon ◽

Dna Fragments ◽

Hprt Gene ◽

New Mutation ◽

Exon 2 ◽

The Family ◽

Hypoxanthine Guanine Phosphoribosyl Transferase

Introduction: Lesch-Nyhan síndrome (LNS) is an X-linked recessive inborn error of metabolism, due to deficiency of the enzyme Hypoxanthine-guanine-phosphoribosyl transferase (HGPRT; EC.2.4.2.8) resulting in hyperuricemia, neurological and behavioural disturbances. In the present work, we report the results of the study of a Colombian family, where LNS was previously clinically and biochemically diagnosed. Material and Methods: The full HPRT gene, including 9 exons and 8 introns, was amplified on eight separate DNA fragments. Both strands, forward and reverse, of the amplified DNA fragments were analyzed and the obtained sequences were compared with those deposited at National Center for Biotechnology Information. Results and conclusions: Sequence analysis allowed the detection of new LNS causing mutation, an adenine deletion in exon 2 of HPRT1 gene resulting in a frameshift which determines a premature stop codon. This study, besides adding a new mutation to the already large spectrum of disease causing variation at HPRT, allows therefore providing genetic counseling for the family as well as prenatal diagnosis.

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Antisense Oligonucleotide-Mediated Splice Switching: Potential Therapeutic Approach for Cancer Mitigation

Cancers ◽

10.3390/cancers13215555 ◽

2021 ◽

Vol 13 (21) ◽

pp. 5555

Author(s):

Prithi Raguraman ◽

Akilandeswari Ashwini Balachandran ◽

Suxiang Chen ◽

Sarah D. Diermeier ◽

Rakesh N. Veedu

Keyword(s):

Cancer Progression ◽

Messenger Rna ◽

Splice Variants ◽

Stop Codon ◽

Mrna Level ◽

Premature Stop Codon ◽

Exon Skipping ◽

Protein Isoforms ◽

Delivery Strategies ◽

And Function

Splicing is an essential process wherein precursor messenger RNA (pre-mRNA) is reshaped into mature mRNA. In alternative splicing, exons of any pre-mRNA get rearranged to form mRNA variants and subsequently protein isoforms, which are distinct both by structure and function. On the other hand, aberrant splicing is the cause of many disorders, including cancer. In the past few decades, developments in the understanding of the underlying biological basis for cancer progression and therapeutic resistance have identified many oncogenes as well as carcinogenic splice variants of essential genes. These transcripts are involved in various cellular processes, such as apoptosis, cell signaling and proliferation. Strategies to inhibit these carcinogenic isoforms at the mRNA level are promising. Antisense oligonucleotides (AOs) have been developed to inhibit the production of alternatively spliced carcinogenic isoforms through splice modulation or mRNA degradation. AOs can also be used to induce splice switching, where the expression of an oncogenic protein can be inhibited by the induction of a premature stop codon. In general, AOs are modified chemically to increase their stability and binding affinity. One of the major concerns with AOs is efficient delivery. Strategies for the delivery of AOs are constantly being evolved to facilitate the entry of AOs into cells. In this review, the different chemical modifications employed and delivery strategies applied are discussed. In addition to that various AOs in clinical trials and their efficacy are discussed herein with a focus on six distinct studies that use AO-mediated exon skipping as a therapeutic strategy to combat cancer.

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Incomplete Segregation of MSH6 Frameshift Variants with Phenotype of Lynch Syndrome

10.20944/preprints201704.0027.v1 ◽

2017 ◽

Author(s):

Raffaella Liccardo ◽

Marina De Rosa ◽

Giovanni Battista Rossi ◽

Nicola Carlomagno ◽

Paola Izzo ◽

...

Keyword(s):

Lynch Syndrome ◽

In Silico ◽

Stop Codon ◽

Direct Sequencing ◽

Premature Stop Codon ◽

In Silico Analysis ◽

Frameshift Deletion ◽

The Family ◽

Novel Variants ◽

Repair Genes

Background: Lynch syndrome, the most frequent form of hereditary colorectal cancer and involves mutations in mismatch repair genes. The aim of this study was to identify mutations in MSH6 from 97 subjects negative for mutations in MLH1 and MSH2. Methods: By direct sequencing, we identified 27 MSH6 variants, of which, nine were novel. To verify the pathogenicity of these novel variants we performed in silico and segregation analyses. Results: Three novel variants were predicted by in silico analysis as damaging mutations and segregated with the disease phenotype. While, a novel frameshift deletion variant that was predicted to yield a premature stop codon, did not segregate with the LS phenotype in 3 of 4 cases in the family. Interestingly, another frame-shift variant identified in this study, already described in the literature, also did not segregate with the LS phenotype in 1 of 2 affected subjects in the family. In all affected subjects of both families, no mutation was detected in other MMR genes. Therefore, it is expected that within these families other genetic factors contribute to the disease either alone or in combination with MSH6 variants. Conclusion: We conclude that caution should be exercised in counseling for MSH6-associated LS family members.

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A Frameshift Variant in KIAA0825 Causes Postaxial Polydactyly

Molecular Syndromology ◽

10.1159/000512062 ◽

2020 ◽

pp. 1-5

Author(s):

Muhammad Bilal ◽

Wasim Ahmad

Keyword(s):

Stop Codon ◽

Premature Stop Codon ◽

Causative Gene ◽

Pakistani Population ◽

Postaxial Polydactyly ◽

The Family ◽

Novel Variant ◽

Limb Malformations ◽

Polymorphic Microsatellite ◽

Autosomal Recessive Manner

Postaxial polydactyly (PAP) is characterized by counterproductive 5th digit (pinky finger) duplication on hands and/or feet which often leads to functional complications. To date, at least 11 genes involved in causing various types of nonsyndromic polydactylies have been reported. In the present study, a consanguineous family of Sindhi origin with a segregating nonsyndromic form of PAP in an autosomal recessive manner was clinically and genetically evaluated. Genotyping, using polymorphic microsatellite markers, established linkage in the family on chromosome 5q15 harboring the <i>KIAA0825</i> gene (MIM 617266). Sequence analysis of the gene revealed a novel frameshift variant leading to a premature stop codon [c.143delG, p.(Cys48Serfs*28)]. This is only the 4th novel variant in the <i>KIAA0825</i> gene that leads to PAP type A10 (PAPA10) (MIM 618498). Identification of variants in the PAP causative gene will support the diagnosis of patients with limb malformations in the Pakistani population.

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Case Report: A Novel Variant c.2262+3A>T of the SCN5A Gene Results in Intron Retention Associated With Incessant Ventricular Tachycardias

Frontiers in Medicine ◽

10.3389/fmed.2021.659119 ◽

2021 ◽

Vol 8 ◽

Author(s):

Jie Yin ◽

Jia Zhou ◽

Jinlong Chen ◽

Ting Xu ◽

Zhongman Zhang ◽

...

Keyword(s):

Cardiac Electrophysiology ◽

Splice Variants ◽

Stop Codon ◽

Clinical Manifestations ◽

Premature Stop Codon ◽

Splice Donor Site ◽

Molecular Defect ◽

Truncated Protein ◽

Mutant Transcript ◽

Ventricular Tachycardias

Objective: Voltage-gated sodium channel Nav1.5 encoded by the SCN5A gene plays crucial roles in cardiac electrophysiology. Previous genetic studies have shown that mutations in SCN5A are associated with multiple inherited cardiac arrhythmias. Here, we investigated the molecular defect in a Chinese boy with clinical manifestations of arrhythmias.Methods: Gene variations were screened using whole-exome sequencing and validated by direct Sanger sequencing. A minigene assay and reverse transcription PCR (RT-PCR) were performed to confirm the effects of splice variants in vitro. Western blot analysis was carried out to determine whether the c.2262+3A>T variant produced a truncated protein.Results: By genetic analysis, we identified a novel splice variant c.2262+3A>T in SCN5A gene in a Chinese boy with incessant ventricular tachycardias (VT). This variant was predicted to activate a new cryptic splice donor site and was identified by in silico analysis. The variant retained 79 bp at the 5′ end of intron 14 in the mature mRNA. Furthermore, the mutant transcript that created a premature stop codon at 818 amino acids [p.(R818*)] could be produced as a truncated protein.Conclusion: We verified the pathogenic effect of splicing variant c.2262+3A>T, which disturbed the normal mRNA splicing and caused a truncated protein, suggesting that splice variants play an important role in the molecular basis of early onset incessant ventricular tachycardias, and careful molecular profiling of these patients will be essential for future effective personalized treatment options.

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Ectopic Transcript Analysis Indicates that Allelic Exclusion is an Important Cause of Type I Protein C Deficiency in Patients with Nonsense and Frameshift Mutations in the PROC Gene

Thrombosis and Haemostasis ◽

10.1055/s-0038-1650386 ◽

1996 ◽

Vol 75 (06) ◽

pp. 870-876 ◽

Cited By ~ 4

Author(s):

José Manuel Soria ◽

Lutz-Peter Berg ◽

Jordi Fontcuberta ◽

Vijay V Kakkar ◽

Xavier Estivill ◽

...

Keyword(s):

Splice Site ◽

Protein C ◽

Stop Codon ◽

Premature Stop Codon ◽

Allelic Exclusion ◽

Polymorphism Analysis ◽

Type I ◽

Protein C Deficiency ◽

Nonsense Mutations ◽

Stop Codons

SummaryNonsense mutations, deletions and splice site mutations are a common cause of type I protein C deficiency. Either directly or indirectly by altering the reading frame, these' lesions generate or may generate premature stop codons and could therefore be expected to result in premature termination of translation. In this study, the possibility that such mutations could instead exert their pathological effects at an earlier stage in the expression pathway, through “allelic exclusion” at the RNA level, was investigated. Protein C (PROC) mRNA was analysed in seven Spanish type I protein C deficient patients heterozygous for two nonsense mutations, a 7bp deletion, a 2bp insertion and three splice site mutations. Ectopic RNA transcripts from patient and control lymphocytes were analysed by RT-PCR and direct sequencing of amplified PROC cDNA fragments. The nonsense mutations and the deletion were absent from the cDNAs indicating that only mRNA derived from the normal allele had been expressed. Similarly for the splice site mutations, only normal PROC cDNAs were obtained. In one case, exclusion of the mutated allele could be confirmed by polymorphism analysis. In contrast to these six mutations, the 2 bp insertion was not associated with loss of mRNA from the mutated allele. In this case, cDNA analysis revealed the absence of 19 bases from the PROC mRNA consistent with the generation and utilization of a cryptic splice site 3’ to the site of mutation, which would result in a frameshift and a premature stop codon. It is concluded that allelic exclusion is a common causative mechanism in those cases of type I protein C deficiency which result from mutations that introduce premature stop codons

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