1,721,152 research outputs found
Alternative splicing and cell survival: From tissue homeostasis to disease
No full textMost human genes encode multiple mRNA variants and protein products through alternative splicing of exons and introns during pre-mRNA processing. In this way, alternative splicing amplifies enormously the coding potential of the human genome and represents a powerful evolutionary resource. Nonetheless, the plasticity of its regulation is prone to errors and defective splicing underlies a large number of inherited and sporadic diseases, including cancer. One key cellular process affected by alternative splicing is the programmed cell death or apoptosis. Many apoptotic genes encode for splice variants having opposite roles in cell survival. This regulation modulates cell and tissue homeostasis and is implicated in both developmental and pathological processes. Furthermore, recent evidence has also unveiled splicing-mediated regulation of genes involved in autophagy, another essential process for tissue homeostasis. In this review, we highlight some of the best-known examples of alternative splicing events involved in cell survival. Emphasis is given to the role of this regulation in human cancer and in the response to chemotherapy, providing examples of how alternative splicing of apoptotic genes can be exploited therapeutically
Editorial: 365 days of progress in cancer genetics
Full text linkProgress in cancer research continues to advance rapidly, with significant developments in understanding the genetic basis of cancer, identification of new cancer-associated genes, and the development of targeted therapies based on genetic profiling. Advances are accelerating on many fronts due in large part to increased robustness of high throughput technologies and improvements in biospecimen acquisition and management. Notable key areas of progress in cancer genetics include cancer genomics, liquid biopsies, immunotherapy and biomarkers, precision medicine and cancer risk assessment.Progress in cancer research continues to advance rapidly, with significant developments in understanding the genetic basis of cancer, identification of new cancer-associated genes, and the development of targeted therapies based on genetic profiling. Advances are accelerating on many fronts due in large part to increased robustness of high throughput technologies and improvements in biospecimen acquisition and management. Notable key areas of progress in cancer genetics include cancer genomics, liquid biopsies, immunotherapy and biomarkers, precision medicine and cancer risk assessment
Dissecting a Hub for Immune Response: Modeling the Structure of MyD88
No full textImmune cells sense foreign organisms through the evolutionarily conserved family of Toll-like receptors. Signaling from these receptors relies on oligomerization of adaptor molecules. In this issue of Structure, Vynke et al. (2016) shed light on the dynamical structure of the homo- and hetero-dimerization domain of MyD88, the main adaptor utilized by Toll-like receptors
Timely-regulated intron retention as device to fine-tune protein expression
No full textA key step in pre-mRNA processing is represented by splicing, the multilayered process operated by the spliceosome that removes the intervening non-coding introns and ligates adjacent exons. Splicing is necessary to yield a mature, translatable mRNA and its dysregulation underlies many human pathologies.1 Notably, weak conservation of the sequences defining the exon-intron boundaries allows flexibility in the recognition of many exons by the spliceosome. As a consequence, alternative splicing (AS) of such variable exons generates multiple mRNAs, with potentially different coding properties and patterns of expression, from most mammalian genes.1 Retention of select introns into mature mRNAs represents a peculiar pattern of AS that is emerging as a regulatory mechanism for developmentally-modulated gene expression patterns.2 Granulocyte differentiation provided one of the first examples of intron retention (IR) program set in motion to regulate gene expression. Transcripts encoding for proteins no longer required for granulopoiesis, and potentially interfering with it, are eliminated by the nonsense-mediated (NMD) pathway through IR-mediated introduction of premature termination codons (PTCs).3 Similar coordinated and widespread dampening of specific set of genes through IR has been described for several differentiation programs or cellular responses to external stimuli.2 Spermatogenesis, however, represents a remarkable exception. Spermatogenesis involves profound genetic and morphological changes that are necessary for the differentiation of the male germ cell into a motile, fertile spermatozoon. Although proper progression of spermatogenesis requires the timely regulated expression of specific factors for each phase, transcription is not always active during this process. Indeed, nuclear condensation in post-meiotic male germ cells leads to a progressive decline of their transcriptional activity, which ultimately halts in spermatozoa.4 We have recently shown that an orchestrated IR program activated during meiosis contributes to temporally regulate the expression of genes during spermatogenesis.5 IR generates stable transcripts which persist in the nucleus of meiotic spermatocytes for several days after their synthesis, whose splicing and translation is delayed until the post-meiotic phases of spermatogenesis.5 In this way, meiotic IR acts as a compensatory mechanism for the transcriptional inactivity of the terminal phases of germ cell differentiation. Of note, IR-regulated genes encode for proteins that are crucial for proper development and functionality of the spermatozoon, such as those involved in the maturation of the flagellum or in sperm-egg recognition. Interestingly, robust accumulation in the nucleus of stable intron-retaining transcripts was also observed during the cellular response to heat shock.6 This observation suggests that IR stabilizes precursor transcripts before the global inhibition of RNA transcription caused by heat, and that their delayed splicing may promote efficient recovery of gene expression at the end of the stress. Furthermore, a “positive” role for IR was described in neurons. Post-transcriptional splicing of intron-retaining transcripts during neuronal activation allowed rapid expression of proteins encoded by genes that are too long to be rapidly transcribed, processed and translated in response to transient external stimuli.7 Thus, regulation of IR is emerging as a mechanism that can compensate both deficiencies and inefficiencies of the transcriptional process in eukaryotic cells.5,7 Notably, common traits of spermatogenic and neuronal IR programs are the nuclear preservation of intron-retaining transcripts and their protection from nuclear mechanisms of RNA surveillance.5,7 Therefore, it might be of interest to understand whether common mechanisms underlying these features exist in germ cells and neurons, possibly relying on the activity of splicing factors that are selectively expressed in these cells, such as PTBP2 or the STAR protein SLM24.
Intron-retaining genes are expressed at higher levels than properly spliced genes in meiotic cells, and splicing of their weak introns is improved by reducing the transcriptional load through inhibition of the RNA polymerase II activity5 (Fig. 1). This finding suggests that an RNA synthetic activity exceeding the splicing capability of the cell represents the driver of the male meiotic IR program. Higher expression levels were also observed for heat shock-regulated intron-retaining genes and neuronal post-transcriptionally spliced pre-mRNAs.6,7 Thus, competition of introns for limiting splicing factors could represent a conserved mechanism controlling eukaryotic gene expression through developmentally and physiologically regulated IR. A crucial point in this regulatory mechanism is the combination of high transcriptional levels with intronic sequence features predisposing to poor splicing efficiency. It would be interesting to investigate whether these features have been evolutionary conserved in genes that play key roles in cellular processes characterized by transcriptional insufficiency.
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Figure 1.
Balance between transcriptional activity and splicing capability regulates intron-retention during germ cell differentiation. High transcriptional activity of meiotic spermatocytes (left panel) generates high levels of transcripts for intron-retaining genes (blue genes). Weak introns of these genes are not efficiently recognized by the spliceosome and their unspliced transcripts are consequently retained in the nucleus. The lower transcriptional activity of post-meiotic spermatids (right panel) then allows efficient splicing of such intron-retaining genes, whose transcripts are efficiently exported in the cytoplasm and translated into proteins.
IR as a consequence of a transcriptional burst highlights the importance of maintaining a tight balance between transcription and splicing efficiency in eukaryotic cells. In line with this, the general increase in RNA synthesis elicited by oncogenic MYC was shown to render cancer cells more susceptible to spliceosome inhibition, which caused pervasive IR.8 Thus, while perturbing this balance augments vulnerability of proliferating cells, it appears to spare post-mitotic cells in which global IR regulation may have evolved as a fine-tuned differentiation/developmental program
The promoter associated non-coding RNA pncCCND1_B assembles a protein-RNA complex to regulate cyclin D1 transcription in Ewing sarcoma
No full textMost Ewing sarcomas are characterized by the in frame chromosomal translocation t(11;22), generating the EWS-FLI1 oncogene. EWS-FLI1 protein interacts with the RNA helicase DHX9 and affects transcription and processing of genes involved in neoplastic transformation, including CCND1 (the cyclin D1 gene), which contributes to cell cycle dysregulation in cancer. In this study, we found that CCND1 expression is significantly higher in Ewing sarcoma patients compared to other sarcomas and that the pncCCND1_B RNA, a previously uncharacterized CCND1 promoter-associated non-coding (pnc) transcript, is expressed in Ewing sarcoma cells. PncCCND1_B interacted with the RNA-binding protein Sam68 and repressed CCND1 expression. Notably, knockdown of Sam68 affected pncCCND1_B subcellular localization and cyclin D1 expression. Pharmacologic impairment of DHX9/EWS-FLI1 interaction promoted RNA-dependent association of Sam68 with DHX9 and recruitment of Sam68 to the CCND1 promoter, thus repressing it. Conversely, mitogenic stimulation of Ewing sarcoma cells with IGF-1 impaired Sam68/DHX9 interaction and positively regulated CCND1 expression. These studies uncover a fine-tuned modulation of the proto-oncogene CCND1 in Ewing sarcoma cells via alternative complexes formed by DHX9 with either EWS-FLI1 or pncCCND1_B-Sam68
Physiological and pathological roles of the transcriptional kinases CDK12 and CDK13 in the central nervous system
Full text linkThe cyclin-dependent kinases 12 (CDK12) and 13 (CDK13) govern several steps of gene expression, including transcription, RNA processing and translation. The main target of CDK12/13 is the serine 2 residue of the carboxy-terminal domain of RNA polymerase II (RNAPII), thus influencing the directionality, elongation rate and processivity of the enzyme. The CDK12/13-dependent regulation of RNAPII activity influences the expression of selected target genes with important functional roles in the proliferation and viability of all eukaryotic cells. Neuronal cells are particularly affected by the loss of CDK12/13, as result of the high dependency of neuronal genes on RNAPII processivity for their expression. Deregulation of CDK12/13 activity strongly affects brain physiology by influencing the stemness potential and differentiation properties of neuronal precursor cells. Moreover, mounting evidence also suggest the involvement of CDK12/13 in brain tumours. Herein, we discuss the functional role(s) of CDK12 and CDK13 in gene expression regulation and highlight similarities and differences between these highly homologous kinases, with particular attention to their impact on brain physiology and pathology. Lastly, we provide an overview of CDK12/13 inhibitors and of their efficacy in brain tumours and other neoplastic diseases
An impaired splicing program underlies differentiation defects in hSOD1G93A neural progenitor cells
No full textAmyotrophic lateral sclerosis (ALS) is an adult devastating neurodegenerative disease characterized by the loss of upper and lower motor neurons (MNs), resulting in progressive paralysis and death. Genetic animal models of ALS have highlighted dysregulation of synaptic structure and function as a pathogenic feature of ALS-onset and progression. Alternative pre-mRNA splicing (AS), which allows expansion of the coding power of genomes by generating multiple transcript isoforms from each gene, is widely associated with synapse formation and functional specification. Deciphering the link between aberrant splicing regulation and pathogenic features of ALS could pave the ground for novel therapeutic opportunities. Herein, we found that neural progenitor cells (NPCs) derived from the hSOD1(G93A) mouse model of ALS displayed increased proliferation and propensity to differentiate into neurons. In parallel, hSOD1(G93A) NPCs showed impaired splicing patterns in synaptic genes, which could contribute to the observed phenotype. Remarkably, master splicing regulators of the switch from stemness to neural differentiation are de-regulated in hSOD1(G93A) NPCs, thus impacting the differentiation program. Our data indicate that hSOD1(G93A) mutation impacts on neurogenesis by increasing the NPC pool in the developing mouse cortex and affecting their intrinsic properties, through the establishment of a specific splicing program
MYC up-regulation confers resistance to everolimus and establishes vulnerability to cyclin dependent kinase inhibitors in pancreatic neuroendocrine neoplasms cells
No full textIntroduction Dysregulation of the mTORC1-dependent pathways in pancreatic neuroendocrine neoplasms (PanNENs) underlies the introduction of the mTORC1 inhibitor everolimus as treatment of advanced progressive PanNENs. Although everolimus significantly increases progression free survival, most patients acquire secondary resistance to the drug. This study aimed at identifying mechanisms involved in acquisition of resistance to everolimus. Methods BON-1 and everolimus-resistant (ER) BON-1 cells were used as in vitro system of sensitivity and acquired resistance. Transcriptome changes occurring in BON-1 and ER-BON-1 were investigated by RNA sequencing and validated by quantitative PCR analysis. RNA extracted from patients' biopsies was used to validate MYC up-regulation. Drug screening and functional assays were performed using ER-BON-1 cells. Cell cycle progression was evaluated by FACS analysis. Results Our results show that MYC overexpression is a key event in the development of secondary resistance to everolimus in PanNENs cell lines and in metastatic lesions from NEN patients. MYC knock-down restored ER-BON-1 sensitivity to everolimus. Pharmacological inhibition of MYC mediated by the cyclin-dependent kinase inhibitor Dinaciclib strongly reduced viability of ER-BON-1. Dinaciclib synergized with everolimus and inhibited ER-BON-1 cell cycle progression. Discussion Our findings suggest that MYC up-regulation drives the development of secondary resistance to everolimus in PanNENs and that its inhibition is an exploitable vulnerability. Indeed, our results indicate that combined treatments with cyclin-dependent kinase and mTOR inhibitors may counteract secondary resistance to everolimus in PanNENs and may pave the ground for new therapeutic regimens for these tumors
Combined treatment with the histone deacetylase inhibitor LBH589 and a splice-switch antisense oligonucleotide enhances SMN2 splicing and SMN expression in Spinal Muscular Atrophy cells
Full text linkSpinal muscular atrophy (SMA) is a motor neuron disease caused by loss of function mutations in the Survival Motor Neuron 1 (SMN1) gene and reduced expression of the SMN protein, leading to spinal motor neuron death, muscle weakness and atrophy. Although humans harbour the highly homologousSMN2 gene, its defective splicingregulation yields a truncated and unstable SMN protein. The first therapy for SMA was recently approved by the Food and Drug Administration and consists of an an -tisense oligonucleotide (Nusinersen) renderingSMN2 functional and thus improving patients’ motor activity and quality of life. Nevertheless, not all patients equally re -spond to this therapy and the long-term tolerability and safety of Nusinersen are still unknown. Herein, in vivo splicing assays indicated that the HDAC inhibitor LBH589is particularly efficient in rescuing the SMN2 splicing defect in SMA fibroblasts and SMA type-I mice-derived neural stem cells. Western blot analyses showed that LBH589 also causes a significant increase in SMN protein expression in SMA cells. Moreover chromatin immunoprecipitation analyses revealed that LBH589 treatment induces widespread H4 acetylation of the entire SMN2 locus and selectively favors the inclusion of the disease-linked exon 7 in SMN2 mature mRNA. The combined treatment of SMA cells with sub-optimal doses of LBH589 and of an antisense oligo-nucleotide that mimic Nusinersen (ASO_ISSN1) elicits additive effects on SMN2 splic-ing and SMN protein expression. These findings suggest that HDAC inhibitors can potentiate the activity of Nusinersen and support the notion that ‘SMN-plus’ com -binatorial therapeutic approaches might represent an enhanced opportunity in the scenario of SMA therapy.KEYWORD
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