scholarly journals Curating clinically relevant transcripts for the interpretation of sequence variants

2018 ◽  
Author(s):  
Marina T. DiStefano ◽  
Sarah E. Hemphill ◽  
Brandon J. Cushman ◽  
Mark J. Bowser ◽  
Elizabeth Hynes ◽  
...  
Keyword(s):  
Critical Role ◽  
Tissue Expression ◽  
Variant Interpretation ◽  
Loss Of Function ◽  
Biologically Relevant ◽  
Multiple Transcripts ◽  
Uncertain Significance ◽  
Systematic Strategy ◽  
Exon Level ◽  
Single Transcript

AbstractVariant interpretation depends on accurate annotations using biologically relevant transcripts. We have developed a systematic strategy for designating primary transcripts, and applied it to 109 hearing loss-associated genes that were divided into 3 categories. Category 1 genes (n=38) had a single transcript, Category 2 genes (n=32) had multiple transcripts, but a single transcript was sufficient to represent all exons, and Category 3 genes (n=38) had multiple transcripts with unique exons. Transcripts were curated with respect to gene expression reported in the literature and the Genotype-Tissue Expression Project. In addition, high frequency loss of function variants in the Genome Aggregation Database, and disease-causing variants in ClinVar and the Human Gene Mutation Database across the 109 genes were queried. These data were used to classify exons as "clinically relevant", "uncertain significance", or "clinically insignificant". Interestingly, 7% of all exons, containing >124 "clinically significant" variants, were of “uncertain significance”. Finally, we used exon-level next generation sequencing quality metrics generated at two clinical labs, and identified a total of 43 technically challenging exons in 20 different genes that had inadequate coverage and/or homology issues which might lead to false variant calls. We have demonstrated that transcript analysis plays a critical role in accurate clinical variant interpretation.

scholarly journals Transcriptome analysis provides critical answers to the “variants of uncertain significance” conundrum

2022 ◽  
Author(s):  
Mackenzie Postel ◽  
Julie O. Culver ◽  
Charité Ricker ◽  
David Craig
Keyword(s):  
Transcriptome Analysis ◽  
Critical Role ◽  
European Ancestry ◽  
Biologically Relevant ◽  
Rna Analysis ◽  
Pathogenic Variants ◽  
Level Data ◽  
Splicing Variants ◽  
Uncertain Significance ◽  
Generation Sequencing

The vast volume of data that has been generated as a result of the next-generation sequencing revolution is overwhelming to sift through and interpret. Parsing functional vs. non-functional and benign vs. pathogenic variants continues to be a challenge. Out of three billion bases, the genomes of two given individuals will only differ by about 3 million variants (0.1%). Furthermore, only a small fraction of these are biologically-relevant and, of those that are functional, only a handful actually drive disease pathology. While whole genome and exome sequencing have transformed our collective understanding of the role that genetics plays in disease pathogenesis, there are certain conditions and populations for whom DNA-level data has failed to produce a molecular diagnosis. Patients of non-White race/non-European ancestry are disproportionately affected by “variants of unknown/uncertain significance” (VUS). This limits the scope of precision medicine for minority patients and perpetuates health disparities. VUS often include deep intronic and splicing variants which are difficult to interpret in DNA alone. RNA analysis is capable of illuminating the consequences of VUS thereby allowing for their reclassification as pathogenic vs. benign. Here we review the critical role, going forward, of transcriptome analysis for clarifying VUS in both neoplastic and non-neoplastic diseases.

scholarly journals ANK3 related neurodevelopmental disorders: expanding the spectrum of heterozygous loss-of-function variants

Neurogenetics ◽  
2021 ◽  
Author(s):  
Katja Kloth ◽  
Bernarda Lozic ◽  
Julia Tagoe ◽  
Mariëtte J. V. Hoffer ◽  
Amelie Van der Ven ◽  
...  
Keyword(s):  
Autosomal Recessive ◽  
Neuronal Development ◽  
Autosomal Dominant ◽  
Tissue Expression ◽  
Autism Spectrum ◽  
Loss Of Function ◽  
Ankyrin G ◽  
Phenotypic Spectrum ◽  
And Function ◽  
Neurodevelopmental Phenotype

AbstractANK3 encodes multiple isoforms of ankyrin-G, resulting in variegated tissue expression and function, especially regarding its role in neuronal development. Based on the zygosity, location, and type, ANK3 variants result in different neurodevelopmental phenotypes. Autism spectrum disorder has been associated with heterozygous missense variants in ANK3, whereas a more severe neurodevelopmental phenotype is caused by isoform-dependent, autosomal-dominant, or autosomal-recessive loss-of-function variants. Here, we present four individuals affected by a variable neurodevelopmental phenotype harboring a heterozygous frameshift or nonsense variant affecting all ANK3 transcripts. Thus, we provide further evidence of an isoform-based phenotypic continuum underlying ANK3-associated pathologies and expand its phenotypic spectrum.

scholarly journals The fruitless gene affects female receptivity and species isolation

2020 ◽  
Vol 287 (1923) ◽  
pp. 20192765 ◽  
Author(s):  
Tabashir Chowdhury ◽  
Ryan M. Calhoun ◽  
Katrina Bruch ◽  
Amanda J. Moehring
Keyword(s):  
Mate Choice ◽  
Critical Role ◽  
Sensory Modality ◽  
Female Mate Choice ◽  
Neural Basis ◽  
Female Receptivity ◽  
Female Mate ◽  
Multiple Transcripts ◽  
Female Behaviour ◽  
Substrate Vibrations

Female mate rejection acts as a major selective force within species, and can serve as a reproductive barrier between species. In spite of its critical role in fitness and reproduction, surprisingly little is known about the genetic or neural basis of variation in female mate choice. Here, we identify fruitless as a gene affecting female receptivity within Drosophila melanogaster , as well as female Drosophila simulans rejection of male D. melanogaster . Of the multiple transcripts this gene produces, by far the most widely studied is the sex-specifically spliced transcript involved in the sex determination pathway. However, we find that female rejection behaviour is affected by a non-sex-specifically spliced fruitless transcript. This is the first implication of fruitless in female behaviour, and the first behavioural role identified for a fruitless non-sex-specifically spliced transcript. We found that this locus does not influence preferences via a single sensory modality, examining courtship song, antennal pheromone perception, or perception of substrate vibrations, and we conclude that fruitless influences mate choice via the integration of multiple signals or through another sensory modality.

scholarly journals Parkin interacting substrate zinc finger protein 746 is a pathological mediator in Parkinson’s disease

Brain ◽  
2019 ◽  
Vol 142 (8) ◽  
pp. 2380-2401 ◽  
Author(s):  
Saurav Brahmachari ◽  
Saebom Lee ◽  
Sangjune Kim ◽  
Changqing Yuan ◽  
Senthilkumar S Karuppagounder ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Critical Role ◽  
Trna Synthetase ◽  
Loss Of Function ◽  
Substrate Protein ◽  
Finger Protein ◽  
Sporadic Parkinson’S Disease

Abstract α-Synuclein misfolding and aggregation plays a major role in the pathogenesis of Parkinson’s disease. Although loss of function mutations in the ubiquitin ligase, parkin, cause autosomal recessive Parkinson’s disease, there is evidence that parkin is inactivated in sporadic Parkinson’s disease. Whether parkin inactivation is a driver of neurodegeneration in sporadic Parkinson’s disease or a mere spectator is unknown. Here we show that parkin in inactivated through c-Abelson kinase phosphorylation of parkin in three α-synuclein-induced models of neurodegeneration. This results in the accumulation of parkin interacting substrate protein (zinc finger protein 746) and aminoacyl tRNA synthetase complex interacting multifunctional protein 2 with increased parkin interacting substrate protein levels playing a critical role in α-synuclein-induced neurodegeneration, since knockout of parkin interacting substrate protein attenuates the degenerative process. Thus, accumulation of parkin interacting substrate protein links parkin inactivation and α-synuclein in a common pathogenic neurodegenerative pathway relevant to both sporadic and familial forms Parkinson’s disease. Thus, suppression of parkin interacting substrate protein could be a potential therapeutic strategy to halt the progression of Parkinson’s disease and related α-synucleinopathies.

scholarly journals AKT1-CREB stimulation of PDGFRα expression is pivotal for PTEN deficient tumor development

2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Xiaofeng Wan ◽  
Meng Zhou ◽  
Fuqiang Huang ◽  
Na Zhao ◽  
Xu Chen ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Human Cancer ◽  
Critical Role ◽  
Tumor Development ◽  
Growth Factor Receptor ◽  
Conditional Knockout ◽  
Loss Of Function ◽  
Akt Inhibitor ◽  
Human Cancer Cell Lines ◽  
Direct Binding

AbstractAs evidenced by the behavior of loss-of-function mutants of PTEN in the context of a gain-of-function mutation of AKT1, the PTEN-AKT1 signaling pathway plays a critical role in human cancers. In this study, we demonstrated that a deficiency in PTEN or activation of AKT1 potentiated the expression of platelet-derived growth factor receptor α (PDGFRα) based on studies on Pten−/− mouse embryonic fibroblasts, human cancer cell lines, the hepatic tissues of Pten conditional knockout mice, and human cancer tissues. Loss of PTEN enhanced PDGFRα expression via activation of the AKT1-CREB signaling cascade. CREB transactivated PDGFRα expression by direct binding of the promoter of the PDGFRα gene. Depletion of PDGFRα attenuated the tumorigenicity of Pten-null cells in nude mice. Moreover, the PI3K-AKT signaling pathway has been shown to positively correlate with PDGFRα expression in multiple cancers. Augmented PDGFRα was associated with poor survival of cancer patients. Lastly, combination treatment with the AKT inhibitor MK-2206 and the PDGFR inhibitor CP-673451 displayed synergistic anti-tumor effects. Therefore, activation of the AKT1-CREB-PDGFRα signaling pathway contributes to the tumor growth induced by PTEN deficiency and should be targeted for cancer treatment.

Abstract 82: Wnt11 Regulates Chamber Specific Neonatal Cardiomyocyte Proliferation During Perinatal Circulatory Transition

2017 ◽  
Vol 121 (suppl_1) ◽  
Author(s):  
Marlin Touma ◽  
Xuedong Kang ◽  
Fuying Gao ◽  
Yan Zhao ◽  
Reshma Biniwale ◽  
...  
Keyword(s):  
Heart Defects ◽  
Critical Role ◽  
Newborn Infants ◽  
R Package ◽  
Maturation Stage ◽  
Specific Gene ◽  
Mouse Heart ◽  
Cardiomyocyte Proliferation ◽  
Loss Of Function ◽  
Myocyte Proliferation

Background: Fetal to neonatal transition of heart involves major changes in cardiomyocytes (CMC) including proliferative capacity. However, the chamber specific CMC proliferation programs of remain poorly understood. Elucidating the mechanisms involved is critical to develop chamber specific therapies for newborn infants with single ventricle physiology and other congenital heart defects (CHDs). Methods: Transcriptomes of mouse left ventricle (LV) and right ventricle (RV) were analyzed by RNA-seq at postnatal days 0 (P0), P3 and P7. R package and Ingenuity suite were used for weighted gene co-expression network analysis (WGCNA) and gene ontology studies. Mechanistic analysis was conducted using gain and loss of function approaches. Results: Mouse neonatal cardiac transcriptome was mostly affected by developmental stage. WGCNA revealed 5 LV and 8 RV modules that were significantly correlated with maturation stage and highly preserved between both ventricles at P0 and P7. In contrast, P3 specific gene modules exhibited the largest chamber specific variations in cell signaling, involving proliferation in LV and Wnt signaling molecules, including Wnt11, in RV. Importantly, Wnt11 expression significantly decreased in cyanotic CHDs phenotypes and correlated with O2 saturation levels in hypoxemic infants with Tetralogy of Fallot (TOF). Notably, Perinatal hypoxia treatment in mice suppressed Wnt11 expression, induced CMC proliferation, downregulated Rb1 expression and enhanced Rb1 phosphorylation more robustly in RV vs. LV. Remarkably, Wnt11 inactivation was sufficient to induce myocyte proliferation in perinatal mouse heart and reduced Rb1 expression and phosphorylation in primary neonatal CMC. Importantly, downregulated Wnt11 in hypoxemic TOF infantile heart was also associated with Rb1 suppression and inversely correlated with proliferation marker Plk1 in human. Conclusion: Using integrated systems genomic and functional biology analyses of perinatal cardiac transcriptome, we revealed a previously uncharacterized function for Wnt11 in chamber specific growth and cyanotic CHD. Reduction of Wnt11 expression by hypoxia plays a critical role in neonatal CMC proliferation via modulating Rb1 expression and activity.

scholarly journals HMGB1 Promotes Systemic Lupus Erythematosus by Enhancing Macrophage Inflammatory Response

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Mudan Lu ◽  
Shanshan Yu ◽  
Wei Xu ◽  
Bo Gao ◽  
Sidong Xiong
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Inflammatory Response ◽  
Proinflammatory Cytokines ◽  
Lupus Erythematosus ◽  
Function Analysis ◽  
Critical Role ◽  
Loss Of Function ◽  
Systemic Lupus ◽  
Glycation End Products ◽  
Hmgb1 Expression

Background/Purpose. HMGB1, which may act as a proinflammatory mediator, has been proposed to contribute to the pathogenesis of multiple chronic inflammatory and autoimmune diseases including systemic lupus erythematosus (SLE); however, the precise mechanism of HMGB1 in the pathogenic process of SLE remains obscure.Method. The expression of HMGB1 was measured by ELISA and western blot. The ELISA was also applied to detect proinflammatory cytokines levels. Furthermore, nephritic pathology was evaluated by H&E staining of renal tissues.Results. In this study, we found that HMGB1 levels were significantly increased and correlated with SLE disease activity in both clinical patients and murine model. Furthermore, gain- and loss-of-function analysis showed that HMGB1 exacerbated the severity of SLE. Of note, the HMGB1 levels were found to be associated with the levels of proinflammatory cytokines such as TNF-αand IL-6 in SLE patients. Further study demonstrated that increased HMGB1 expression deteriorated the severity of SLE via enhancing macrophage inflammatory response. Moreover, we found that receptor of advanced glycation end products played a critical role in HMGB1-mediated macrophage inflammatory response.Conclusion. These findings suggested that HMGB1 might be a risk factor for SLE, and manipulation of HMGB1 signaling might provide a therapeutic strategy for SLE.

scholarly journals NR5A2 Is One of 12 Transcription Factors Predicting Prognosis in HNSCC and Regulates Cancer Cell Proliferation in a p53-Dependent Manner

2021 ◽  
Vol 11 ◽  
Author(s):  
Kun Zhang ◽  
Ming Xiao ◽  
Xin Jin ◽  
Hongyan Jiang
Keyword(s):  
Overall Survival ◽  
Survival Time ◽  
Cancer Progression ◽  
Risk Model ◽  
Critical Role ◽  
Disease Free Survival ◽  
Dependent Manner ◽  
Loss Of Function ◽  
Free Survival ◽  
Disease Free

Head and neck squamous cell carcinoma (HNSCC) rank seventh among the most common type of malignant tumor worldwide. Various evidences suggest that transcriptional factors (TFs) play a critical role in modulating cancer progression. However, the prognostic value of TFs in HNSCC remains unclear. Here, we identified a risk model based on a 12-TF signature to predict recurrence-free survival (RFS) in patients with HNSCC. We further analyzed the ability of the 12-TF to predict the disease-free survival time and overall survival time in HNSCC, and found that only NR5A2 down-regulation was strongly associated with shortened overall survival and disease-free survival time in HNSCC. Moreover, we systemically studied the role of NR5A2 in HNSCC and found that NR5A2 regulated HNSCC cell growth in a TP53 status-dependent manner. In p53 proficient cells, NR5A2 knockdown increased the expression of TP53 and activated the p53 pathway to enhance cancer cells proliferation. In contrast, NR5A2 silencing suppressed the growth of HNSCC cells with p53 loss/deletion by inhibiting the glycolysis process. Therefore, our results suggested that NR5A2 may serve as a promising therapeutic target in HNSCC harboring loss-of-function TP53 mutations.

scholarly journals Overview of the Development and Use of Akt Inhibitors in Prostate Cancer

2021 ◽  
Vol 11 (1) ◽  
pp. 160
Author(s):  
Anis Gasmi ◽  
Guilhem Roubaud ◽  
Charles Dariane ◽  
Eric Barret ◽  
Jean-Baptiste Beauval ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Clinical Trials ◽  
Phase Ii ◽  
Critical Role ◽  
Castration Resistant Prostate Cancer ◽  
Loss Of Function ◽  
Pten Loss ◽  
Castration Resistant ◽  
Recent Phase ◽  
Phase Ii And Iii

Deregulation of the PI3K-Akt-mTOR pathway plays a critical role in the development and progression of many cancers. In prostate cancer, evidence suggests that it is mainly driven by PTEN loss of function. For many years, the development of selective Akt inhibitors has been challenging. In recent phase II and III clinical trials, Ipatasertib and Capivasertib associated with androgen deprivation therapies showed promising outcomes in patients with metastatic castration-resistant prostate cancer and PTEN-loss. Ongoing trials are currently assessing several Akt inhibitors in prostate cancer with different combinations, at different stages of the disease.

scholarly journals UBE3A-mediated PTPA ubiquitination and degradation regulate PP2A activity and dendritic spine morphology

2019 ◽  
Vol 116 (25) ◽  
pp. 12500-12505 ◽  
Author(s):  
Jie Wang ◽  
Sen-Sen Lou ◽  
Tingting Wang ◽  
Rong-Jie Wu ◽  
Guangying Li ◽  
...  
Keyword(s):  
Ubiquitin Ligase ◽  
Dendritic Spine ◽  
Isotope Labeling ◽  
Neurodevelopmental Disorder ◽  
Critical Role ◽  
Motor Impairment ◽  
Autism Spectrum ◽  
Loss Of Function ◽  
Pp2a Activity

Deficiency in the E3 ubiquitin ligase UBE3A leads to the neurodevelopmental disorder Angelman syndrome (AS), while additional dosage of UBE3A is linked to autism spectrum disorder. The mechanisms underlying the downstream effects of UBE3A gain or loss of function in these neurodevelopmental disorders are still not well understood, and effective treatments are lacking. Here, using stable-isotope labeling of amino acids in mammals and ubiquitination assays, we identify PTPA, an activator of protein phosphatase 2A (PP2A), as a bona fide ubiquitin ligase substrate of UBE3A. Maternal loss of Ube3a (Ube3am−/p+) increased PTPA level, promoted PP2A holoenzyme assembly, and elevated PP2A activity, while maternal 15q11–13 duplication containing Ube3a down-regulated PTPA level and lowered PP2A activity. Reducing PTPA level in vivo restored the defects in dendritic spine maturation in Ube3am−/p+ mice. Moreover, pharmacological inhibition of PP2A activity with the small molecule LB-100 alleviated both reduction in excitatory synaptic transmission and motor impairment in Ube3am−/p+ mice. Together, our results implicate a critical role of UBE3A-PTPA-PP2A signaling in the pathogenesis of UBE3A-related disorders and suggest that PP2A-based drugs could be potential therapeutic candidates for treatment of UBE3A-related disorders.

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