RÉSUMÉ
Spermatogonial stem cell (SSC) self-renewal and differentiation provide foundational support for long-term, steady-state spermatogenesis in mammals. Here, we have investigated the essential role of RNA exosome associated DIS3 ribonuclease in maintaining spermatogonial homeostasis and facilitating germ cell differentiation. We have established male germ-cell Dis3 conditional knockout (cKO) mice in which the first and subsequent waves of spermatogenesis are disrupted. This leads to a Sertoli cell-only phenotype and sterility in adult male mice. Bulk RNA-seq documents that Dis3 deficiency partially abolishes RNA degradation and causes significant increases in the abundance of transcripts. This also includes pervasively transcribed PROMoter uPstream Transcripts (PROMPTs), which accumulate robustly in Dis3 cKO testes. In addition, scRNA-seq analysis indicates that Dis3 deficiency in spermatogonia significantly disrupts RNA metabolism and gene expression, and impairs early germline cell development. Overall, we document that exosome-associated DIS3 ribonuclease plays crucial roles in maintaining early male germ cell lineage in mice.
Sujet(s)
Fécondité , Spermatogonies , Testicule , Animaux , Mâle , Souris , Différenciation cellulaire , Exosome multienzyme ribonuclease complex/métabolisme , Exosome multienzyme ribonuclease complex/génétique , Exosomes/métabolisme , Fécondité/génétique , Infertilité masculine/génétique , Souris knockout , Stabilité de l'ARN/génétique , Cellules de Sertoli/métabolisme , Spermatogenèse , Spermatogonies/métabolisme , Spermatogonies/cytologie , Testicule/métabolismeRÉSUMÉ
Thrombotic microangiopathy (TMA) in association with RNA exosome encoding mutations has only recently been recognized. Here, we present an infant (female) with an EXOSC5 mutation (c.230_232del p.Glu77del) associated with the clinical phenotype known as CABAC syndrome (cerebellar ataxia, brain abnormalities, and cardiac conduction defects), including pontocerebellar hypoplasia, who developed renal TMA. At the age of four months, she presented with signs of septic illness, after which she developed TMA. A stool culture showed rotavirus as a potential trigger. The patient received eculizumab once, alongside supportive treatment, while awaiting diagnostic analysis of TMA, including genetic complement analysis, all of which were negative. Eculizumab was withdrawn and the patient's TMA recovered quickly. A review of the literature identified an additional four patients (age < 1 year) who developed TMA after a viral trigger in the presence of mutations in EXOSC3. The recurrence of TMA in one of these patients with an EXOSC3 mutation while on eculizumab treatment underscores the apparent lack of responsiveness to C5 inhibition. In conclusion, mutations in genes influencing the RNA exosome, like EXOSC3 and EXOSC5, characterized by neurodevelopment and neurodegenerative disorders could potentially lead to TMA in the absence of complement dysregulation. Hence, these patients were likely non-responsive to eculizumab.
Sujet(s)
Exosome multienzyme ribonuclease complex , Mutation , Microangiopathies thrombotiques , Humains , Microangiopathies thrombotiques/génétique , Microangiopathies thrombotiques/étiologie , Femelle , Exosome multienzyme ribonuclease complex/génétique , Nourrisson , Protéines de liaison à l'ARN/génétique , Exosomes/génétique , Exosomes/métabolisme , Anticorps monoclonaux humanisés/usage thérapeutiqueRÉSUMÉ
The exosome multiprotein complex plays a critical role in RNA processing and degradation. This system governs the regulation of mRNA quality, degradation in the cytoplasm, the processing of short noncoding RNA, and the breakdown of RNA fragments. We determined two crystal structures of exosome components from Thermoplasma acidophilum (Taci): one with a resolution of 2.3 Å that reveals the central components (TaciRrp41 and TaciRrp42), and another with a resolution of 3.5 Å that displays the whole exosome (TaciRrp41, TaciRrp42, and TaciRrp4). The fundamental exosome structure revealed the presence of a heterodimeric complex consisting of TaciRrp41 and TaciRrp42. The structure comprises nine subunits, with TaciRrp41 and TaciRrp42 arranged in a circular configuration, while TaciRrp4 is located at the apex. The RNA degradation capabilities of the TaciRrp4:41:42 complex were verified by RNA degradation assays, consistent with prior findings in other archaeal exosomes. The resemblance between archaeal exosomes and bacterial PNPase suggests a common mechanism for RNA degradation. Despite sharing comparable topologies, the surface charge distributions of TaciRrp4 and other archaea structures are surprisingly distinct. Different RNA breakdown substrates may be responsible for this variation. These newfound structural findings enhance our comprehension of RNA processing and degradation in biological systems.
Sujet(s)
Protéines d'archée , Exosomes , Thermoplasma , Thermoplasma/métabolisme , Exosomes/métabolisme , Exosomes/composition chimique , Cristallographie aux rayons X , Protéines d'archée/composition chimique , Protéines d'archée/métabolisme , Protéines d'archée/génétique , Modèles moléculaires , Sous-unités de protéines/composition chimique , Sous-unités de protéines/métabolisme , Exosome multienzyme ribonuclease complex/métabolisme , Exosome multienzyme ribonuclease complex/composition chimique , Stabilité de l'ARNRÉSUMÉ
The MYCN oncoprotein binds active promoters in a heterodimer with its partner protein MAX. MYCN also interacts with the nuclear exosome, a 3'-5' exoribonuclease complex, suggesting a function in RNA metabolism. Here, we show that MYCN forms stable high-molecular-weight complexes with the exosome and multiple RNA-binding proteins. MYCN binds RNA in vitro and in cells via a conserved sequence termed MYCBoxI. In cells, MYCN associates with thousands of intronic transcripts together with the ZCCHC8 subunit of the nuclear exosome targeting complex and enhances their processing. Perturbing exosome function results in global re-localization of MYCN from promoters to intronic RNAs. On chromatin, MYCN is then replaced by the MNT(MXD6) repressor protein, inhibiting MYCN-dependent transcription. RNA-binding-deficient alleles show that RNA-binding limits MYCN's ability to activate cell growth-related genes but is required for MYCN's ability to promote progression through S phase and enhance the stress resilience of neuroblastoma cells.
Sujet(s)
Protéine du proto-oncogène N-Myc , Protéines nucléaires , Protéines oncogènes , Protéines de liaison à l'ARN , Protéine du proto-oncogène N-Myc/métabolisme , Protéine du proto-oncogène N-Myc/génétique , Humains , Protéines de liaison à l'ARN/métabolisme , Protéines de liaison à l'ARN/génétique , Protéines nucléaires/métabolisme , Protéines nucléaires/génétique , Protéines oncogènes/métabolisme , Protéines oncogènes/génétique , Régions promotrices (génétique) , Lignée cellulaire tumorale , Neuroblastome/métabolisme , Neuroblastome/génétique , Neuroblastome/anatomopathologie , Exosomes/métabolisme , Exosomes/génétique , Introns , Liaison aux protéines , Noyau de la cellule/métabolisme , Exosome multienzyme ribonuclease complex/métabolisme , Exosome multienzyme ribonuclease complex/génétique , Régulation de l'expression des gènes tumoraux , ARN/métabolisme , ARN/génétique , Protéines de répression/métabolisme , Protéines de répression/génétique , Prolifération cellulaireRÉSUMÉ
How nuclear RNA homeostasis impacts cellular functions remains elusive. In this issue of Cell Stem Cell, Han et al.1 utilized a controllable protein degradation system targeting EXOSC2 to perturb RNA homeostasis in mouse pluripotent embryonic stem cells, revealing its vital role in orchestrating crucial nuclear events for cellular fitness.
Sujet(s)
Homéostasie , ARN nucléaire , Animaux , Souris , ARN nucléaire/métabolisme , ARN nucléaire/génétique , Exosome multienzyme ribonuclease complex/métabolisme , Exosome multienzyme ribonuclease complex/génétique , Noyau de la cellule/métabolisme , Cellules souches embryonnaires de souris/métabolisme , Cellules souches embryonnaires de souris/cytologie , Humains , Protéines de liaison à l'ARN/métabolisme , Protéines de liaison à l'ARN/génétique , ARN/métabolisme , Cellules souches pluripotentes/métabolisme , Cellules souches pluripotentes/cytologieRÉSUMÉ
Endometrial carcinoma (EC) is a common type of uterine cancer in developed countries, originating from the uterine epithelium. The incidence rate of EC in Taiwan has doubled from 2005. Cancer stem cells (CSCs) are a subpopulation of cancer cells that have high tumorigenicity and play a crucial role in the malignant processes of cancer. Targeting molecules associated with CSCs is essential for effective cancer treatments. This study delves into the role of Exosome component 5 (EXOSC5) in EC. Data from The Cancer Genome Atlas suggests a correlation between high EXOSC5 mRNA expression and unfavorable EC prognosis. EXOSC5 knockdown diminished EC-CSC self-renewal and reduced expression of key cancer stemness proteins, including c-MYC and SOX2. Intriguingly, this knockdown significantly curtailed tumorigenicity and CSC frequency in EC tumor spheres. A mechanistic examination revealed a reduction in netrin4 (NTN4) levels in EXOSC5-depleted EC cells. Moreover, NTN4 treatment amplified EC cell CSC activity and, when secreted, NTN4 partnered with integrin ß1, subsequently triggering the FAK/SRC axis to elevate c-MYC activity. A clear positive relation between EXOSC5 and NTN4 was evident in 93 EC tissues. In conclusion, EXOSC5 augments NTN4 expression, activating c-MYC via the integrin ß1/FAK/SRC pathway, offering potential avenues for EC diagnosis and treatment.
Sujet(s)
Tumeurs de l'endomètre , Antigènes CD29 , Humains , Femelle , Antigènes CD29/métabolisme , Transduction du signal/génétique , Tumeurs de l'endomètre/métabolisme , Cellules souches tumorales/métabolisme , Lignée cellulaire tumorale , Antigènes néoplasiques/métabolisme , Protéines de liaison à l'ARN/métabolisme , Exosome multienzyme ribonuclease complex/métabolisme , Nétrines/métabolismeRÉSUMÉ
The RNA exosome is a ribonuclease complex that mediates both RNA processing and degradation. This complex is evolutionarily conserved, ubiquitously expressed, and required for fundamental cellular functions, including rRNA processing. The RNA exosome plays roles in regulating gene expression and protecting the genome, including modulating the accumulation of RNA-DNA hybrids (R-loops). The function of the RNA exosome is facilitated by cofactors, such as the RNA helicase MTR4, which binds/remodels RNAs. Recently, missense mutations in RNA exosome subunit genes have been linked to neurological diseases. One possibility to explain why missense mutations in genes encoding RNA exosome subunits lead to neurological diseases is that the complex may interact with cell- or tissue-specific cofactors that are impacted by these changes. To begin addressing this question, we performed immunoprecipitation of the RNA exosome subunit, EXOSC3, in a neuronal cell line (N2A), followed by proteomic analyses to identify novel interactors. We identified the putative RNA helicase, DDX1, as an interactor. DDX1 plays roles in double-strand break repair, rRNA processing, and R-loop modulation. To explore the functional connections between EXOSC3 and DDX1, we examined the interaction following double-strand breaks and analyzed changes in R-loops in N2A cells depleted for EXOSC3 or DDX1 by DNA/RNA immunoprecipitation followed by sequencing. We find that EXOSC3 interaction with DDX1 is decreased in the presence of DNA damage and that loss of EXOSC3 or DDX1 alters R-loops. These results suggest EXOSC3 and DDX1 interact during events of cellular homeostasis and potentially suppress unscrupulous expression of genes promoting neuronal projection.
Sujet(s)
Exosomes , ARN , DEAD-box RNA helicases/génétique , DEAD-box RNA helicases/métabolisme , ADN/métabolisme , Exosome multienzyme ribonuclease complex/génétique , Exosome multienzyme ribonuclease complex/métabolisme , Exosomes/génétique , Exosomes/métabolisme , Protéomique , Structures en boucle R , ARN/métabolisme , RNA helicases/métabolisme , ARN nucléaire/métabolisme , Lignée cellulaire , Animaux , SourisRÉSUMÉ
Novel biomarkers and therapeutic strategies for prostate-cancer (PCa) are required to overcome its lethal progression. The dysregulation/implication of the RNA-Exosome-complex (REC; cellular machinery controlling the 3'-5'processing/degradation of most RNAs) in different cancer-types, including PCa, is poorly known. Herein, different cellular/molecular/preclinical approaches with human PCa-samples (tissues and/or plasma of 7 independent cohorts), and in-vitro/in-vivo PCa-models were used to comprehensively characterize the REC-profile and explore its role in PCa. Moreover, isoginkgetin (REC-inhibitor) effects were evaluated on PCa-cells. We demonstrated a specific dysregulation of the REC-components in PCa-tissues, identifying the Poly(A)-Binding-Protein-Nuclear 1 (PABPN1) factor as a critical regulator of major cancer hallmarks. PABPN1 is consistently overexpressed in different human PCa-cohorts and associated with poor-progression, invasion and metastasis. PABPN1 silencing decreased relevant cancer hallmarks in multiple PCa-models (proliferation/migration/tumourspheres/colonies, etc.) through the modulation of key cancer-related lncRNAs (PCA3/FALEC/DLEU2) and mRNAs (CDK2/CDK6/CDKN1A). Plasma PABPN1 levels were altered in patients with metastatic and tumour-relapse. Finally, pharmacological inhibition of REC-activity drastically inhibited PCa-cell aggressiveness. Altogether, the REC is drastically dysregulated in PCa, wherein this novel molecular event/mechanism, especially PABPN1 alteration, may be potentially exploited as a novel prognostic and therapeutic tool for PCa.
Sujet(s)
Exosomes , Tumeurs de la prostate , Mâle , Humains , Exosome multienzyme ribonuclease complex , Exosomes/métabolisme , Lignée cellulaire tumorale , Régulation de l'expression des gènes tumoraux , Récidive tumorale locale , Tumeurs de la prostate/anatomopathologie , ARN messager , Protéine-1 de liaison au poly(A)/métabolismeRÉSUMÉ
Reduced oxygen availability (hypoxia) triggers adaptive cellular responses via hypoxia-inducible factor (HIF)-dependent transcriptional activation. Adaptation to hypoxia also involves transcription-independent processes like post-translational modifications; however, these mechanisms are poorly characterized. Investigating the involvement of protein SUMOylation in response to hypoxia, we discovered that hypoxia strongly decreases the SUMOylation of Exosome subunit 10 (EXOSC10), the catalytic subunit of the RNA exosome, in an HIF-independent manner. EXOSC10 is a multifunctional exoribonuclease enriched in the nucleolus that mediates the processing and degradation of various RNA species. We demonstrate that the ubiquitin-specific protease 36 (USP36) SUMOylates EXOSC10 and we reveal SUMO1/sentrin-specific peptidase 3 (SENP3) as the enzyme-mediating deSUMOylation of EXOSC10. Under hypoxia, EXOSC10 dissociates from USP36 and translocates from the nucleolus to the nucleoplasm concomitant with its deSUMOylation. Loss of EXOSC10 SUMOylation does not detectably affect rRNA maturation but affects the mRNA transcriptome by modulating the expression levels of hypoxia-related genes. Our data suggest that dynamic modulation of EXOSC10 SUMOylation and localization under hypoxia regulates the RNA degradation machinery to facilitate cellular adaptation to low oxygen conditions.
Sujet(s)
Exosomes , Transcriptome , Humains , Exosomes/métabolisme , Hypoxie/génétique , Hypoxie/métabolisme , Activation de la transcription , Oxygène/métabolisme , Sous-unité alpha du facteur-1 induit par l'hypoxie/métabolisme , Sumoylation , Exoribonucleases/génétique , Exoribonucleases/métabolisme , Exosome multienzyme ribonuclease complex/génétique , Exosome multienzyme ribonuclease complex/métabolisme , Cysteine endopeptidases/métabolisme , Ubiquitin thiolesterase/métabolismeRÉSUMÉ
Tissue regeneration mediated by mesenchymal stem cells (MSCs) is an ideal way to repair bone defects. RNA-binding proteins (RBPs) can affect cell function through post-transcriptional regulation. Exploring the role of RBPs in the process of osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) is helpful to find a key method to promote the osteogenic efficiency of BMSCs. By reviewing the literature, we obtained a differentially expressed mRNA dataset during the osteogenic differentiation of BMSCs and a human RBP dataset. A total of 82 differentially expressed RBPs in the osteogenic differentiation of BMSCs were screened by intersection of the two datasets. Functional analysis showed that the differentially expressed RBPs were mainly involved in RNA transcription, translation and degradation through the formation of spliceosomes and ribonucleoprotein complexes. The top 15 RBPs determined by degree score were FBL, NOP58, DDX10, RPL9, SNRPD3, NCL, IFIH1, RPL18A, NAT10, EXOSC5, ALYREF, PA2G4, EIF5B, SNRPD1 and EIF6. The results of this study demonstrate that the expression of many RBPs changed during osteogenic differentiation of BMSCs.
Sujet(s)
Cellules souches mésenchymateuses , Ostéogenèse , Humains , Différenciation cellulaire , ARN , Protéines de liaison à l'ARN/génétique , Cellules de la moelle osseuse , Cellules cultivées , Antigènes néoplasiques , Exosome multienzyme ribonuclease complex , Protéines adaptatrices de la transduction du signal , DEAD-box RNA helicasesRÉSUMÉ
Exosome Complex Components 1 and 2 (EXOSC1 and 2) are two proteins in the RNA Exosome complex whose main function is 5' â 3' RNA degradation and processing. The RNA exosome complex is comprised of nine subunits that form two separate components: the S1/KH cap and the PH-core. EXOSC1 and 2 are both part of the S1/KH cap and are involved in binding nascent RNA. As part of a systemic characterization of early lethal alleles produced by the Knockout Mouse Project, we have examined Exosc1 and Exosc2 homozygous null (mutant) embryos to determine developmental and molecular phenotypes of embryos lacking their functions. Our studies reveal that Exosc1 null embryos implant and form an egg cylinder but are developmentally delayed and fail to initiate gastrulation by embryonic day 7.5. In contrast, Exosc2 null embryos are lethal during peri-implantation stages, and while they do form a morphologically normal blastocyst at E3.5, they cannot be recovered at post-implantation stages. We show the absence of stage-specific developmental and altered lineage-specification in both Exosc1 and Exosc2 mutant embryos and conclude that these genes are essential for the successful progression through early mammalian development.
Sujet(s)
Exosome multienzyme ribonuclease complex , Exosomes , Souris , Animaux , Souris knockout , Exosome multienzyme ribonuclease complex/métabolisme , Exosomes/génétique , Blastocyste/métabolisme , Implantation embryonnaire/génétique , Embryon de mammifère/métabolisme , MammifèresRÉSUMÉ
Mtr4 is an essential RNA helicase involved in nuclear RNA processing and degradation and is a member of the Ski2-like helicase family. Ski2-like helicases share a common core architecture that includes two RecA-like domains, a winged helix, and a helical bundle (HB) domain. In Mtr4, a short C-terminal tail immediately follows the HB domain and is positioned at the interface of the RecA-like domains. The tail ends with a SLYΦ sequence motif that is highly conserved in a subset of Ski2-like helicases. Here, we show that this sequence is critical for Mtr4 function. Mutations in the C-terminus result in decreased RNA unwinding activity. Mtr4 is a key activator of the RNA exosome complex, and mutations in the SLYΦ motif produce a slow growth phenotype when combined with a partial exosome defect in S. cerevisiae, suggesting an important role of the C-terminus of Mtr4 and the RNA exosome. We further demonstrate that C-terminal mutations impair RNA degradation activity by the major RNA exosome nuclease Rrp44 in vitro. These data demonstrate a role for the Mtr4 C-terminus in regulating helicase activity and coordinating Mtr4-exosome interactions.
Sujet(s)
Exosomes , Protéines de Saccharomyces cerevisiae , Exosomes/génétique , Exosomes/métabolisme , Saccharomyces cerevisiae/génétique , Saccharomyces cerevisiae/métabolisme , Protéines de Saccharomyces cerevisiae/métabolisme , Exosome multienzyme ribonuclease complex/génétique , Exosome multienzyme ribonuclease complex/composition chimique , Exosome multienzyme ribonuclease complex/métabolisme , DEAD-box RNA helicases/composition chimique , RNA helicases/composition chimique , Helicase/métabolismeRÉSUMÉ
Pontocerebellar hypoplasia (PCH) is a rare heterogeneous neurodegenerative disorder affecting the pons and cerebellum and is currently classified into 17 types (PCH1-PCH17). PCH1 is distinguishable from other types by the association of spinal motor neuron dysfunction. Based on the underlying genetic etiology, PCH1 is further classified into 6 different subtypes (PCH1 A-F). Of them, PCH type 1C is caused by pathogenic variants in EXOSC8 gene and so far, only four families have been described in the literature. In this study, we report a new patient with PCH1 who proved by whole-exome sequencing to harbor a novel homozygous missense variant in the splice region of EXOSC8 gene (c.238 G > A; p.Val80Ile). Studying mRNA of the patient confirmed that this variant results in skipping of exon 5 of the gene and early protein truncation. Our patient presented with the main clinical findings of PCH type 1C including psychomotor retardation, spasticity, spinal muscle atrophy, and respiratory problems. However, unlike most of the reported cases, he did not develop hearing or visual impairment and displayed a longer survival. In addition, our patient had dysmorphic facies, nystagmus, congenital esotropia and contractures which were infrequently described in patients with EXOSC8. Diaphragmatic hernia, dilated lateral ventricles, hypoplastic temporal lobes, and thinning of the brain stem were additional new findings noted in our patient. This study presents the fifth family with this extremely rare type of PCH and expands the associated clinical and brain imaging findings.
Sujet(s)
Maladies du cervelet , Mâle , Humains , Mutation , Maladies du cervelet/imagerie diagnostique , Maladies du cervelet/génétique , Maladies du cervelet/anatomopathologie , Cervelet/anatomopathologie , Exons/génétique , Protéines de liaison à l'ARN/génétique , Exosome multienzyme ribonuclease complex/génétiqueRÉSUMÉ
DIS3 gene mutations occur in approximately 10% of patients with multiple myeloma (MM); furthermore, DIS3 expression can be affected by monosomy 13 and del(13q), found in roughly 40% of MM cases. Despite the high incidence of DIS3 mutations and deletions, the biological significance of DIS3 and its contribution to MM pathogenesis remain poorly understood. In this study we investigated the functional role of DIS3 in MM, by exploiting a loss-of-function approach in human MM cell lines. We found that DIS3 knockdown inhibits proliferation in MM cell lines and largely affects cell cycle progression of MM plasma cells, ultimately inducing a significant increase in the percentage of cells in the G0/G1 phase and a decrease in the S and G2/M phases. DIS3 plays an important role not only in the control of the MM plasma cell cycle, but also in the centrosome duplication cycle, which are strictly co-regulated in physiological conditions in the G1 phase. Indeed, DIS3 silencing leads to the formation of supernumerary centrosomes accompanied by the assembly of multipolar spindles during mitosis. In MM, centrosome amplification is present in about a third of patients and may represent a mechanism leading to genomic instability. These findings strongly prompt further studies investigating the relevance of DIS3 in the centrosome duplication process. Indeed, a combination of DIS3 defects and deficient spindle-assembly checkpoint can allow cells to progress through the cell cycle without proper chromosome segregation, generating aneuploid cells which ultimately lead to the development of MM.
Sujet(s)
Myélome multiple , Humains , Myélome multiple/anatomopathologie , Centrosome/métabolisme , Centrosome/anatomopathologie , Mitose , Cycle cellulaire/génétique , Instabilité du génome , Exosome multienzyme ribonuclease complex/métabolismeRÉSUMÉ
OBJECTIVE: To explore the expression of Exosome Component 4ï¼EXOSC4ï¼ in the tissues of newly diagnosed patients with diffuse large B-cell lymphoma (DLBCL) and its clinical significance. METHODS: The expression of EXOSC4 protein in the tissues of 181 newly diagnosed DLBCL patients was analyzed by immunohistochemical staining. Clinical data were collected. The correlation between EXOSC4 protein expression in the tissues of newly diagnosed DLBCL patients and clinical features were analyzed and its prognostic significance. RESULTS: The positive rate of EXOSC4 protein expression was 68.51% in the tissues of 181 newly diagnosed DLBCL patients. These patients were divided into two groups, with 44 cases in high expression group and 137 cases in low expression group. There were no significant differences in age, gender, B symptoms, serum lactate dehydrogenase (LDH) level, Eastern Cooperative Oncology Group (ECOG) score, Ann Arbor stage, extranodal disease, International Prognostic Index (IPI) score, National Comprehensive Cancer Network IPI (NCCN-IPI) score, and cell origin between the two groups (P>0.05). Cox multivariate regression analysis showed that high EXOSC4 protein expression in tissues was an independent poor prognostic factor for OS and PFS in newly diagnosed DLBCL patients (all P<0.05). K-M survival analysis showed that newly diagnosed DLBCL patients with high EXOSC4 protein expression had significantly shorter overall survival (OS) and progression free survival (PFS) than those patients with low EXOSC4 protein expression (all P<0.05). CONCLUSION: High EXOSC4 protein expression in tissues of newly diagnosed DLBCL patients is an independent poor prognostic factor for survival.
Sujet(s)
Exosome multienzyme ribonuclease complex , Lymphome B diffus à grandes cellules , Humains , Pertinence clinique , Lymphome B diffus à grandes cellules/diagnostic , Lymphome B diffus à grandes cellules/anatomopathologie , Pronostic , Études rétrospectives , Exosome multienzyme ribonuclease complex/génétiqueRÉSUMÉ
The eukaryotic THO complex coordinates the assembly of so-called messenger RNA-ribonucleoprotein particles (mRNPs), a process that involves cotranscriptional coating of nascent mRNAs with proteins. Once formed, mRNPs undergo a quality control step that marks them either for active transport to the cytoplasm, or Rrp6/RNA exosome-mediated degradation in the nucleus. However, the mechanism behind the quality control of nascent mRNPs is still unclear. We investigated the cotranscriptional quality control of mRNPs in budding yeast by expressing the bacterial Rho helicase, which globally perturbs yeast mRNP formation. We examined the genome-wide binding profiles of the THO complex subunits Tho2, Thp2, Hpr1, and Mft1 upon perturbation of the mRNP biogenesis, and found that Tho2 plays two roles. In addition to its function as a subunit of the THO complex, upon perturbation of mRNP biogenesis Tho2 targets Rrp6 to chromatin via its carboxy-terminal domain. Interestingly, other THO subunits are not enriched on chromatin upon perturbation of mRNP biogenesis and are not necessary for localizing Rrp6 at its target loci. Our study highlights the potential role of Tho2 in cotranscriptional mRNP quality control, which is independent of other THO subunits. Considering that both the THO complex and the RNA exosome are evolutionarily highly conserved, our findings are likely relevant for mRNP surveillance in mammals.
Sujet(s)
Chromatine , Protéines de Saccharomyces cerevisiae , Chromatine/génétique , Chromatine/métabolisme , Exosome multienzyme ribonuclease complex/génétique , Exosome multienzyme ribonuclease complex/métabolisme , Ribonucléoprotéines/génétique , Ribonucléoprotéines/métabolisme , Saccharomyces cerevisiae/génétique , Saccharomyces cerevisiae/métabolisme , Protéines de Saccharomyces cerevisiae/métabolismeRÉSUMÉ
Long, noncoding RNAs (lncRNAs) are indispensable for normal cell physiology and, consequently, are tightly regulated in human cells. Yet, unlike mRNA, substantially less is known about the mechanisms for lncRNA degradation. It is important to delineate the regulatory control of lncRNA degradation, particularly for lncRNA telomeric repeat-containing RNA (TERRA), as the TERRA-telomere R-loops dictate cell cycle progression and genomic stability. We now report that the exosome complex component Exosc9 degrades lncRNA TERRA in human mammary epithelial cells. Heterochromatin protein 1 alpha (HP1α) recruits Exosc9 to the telomeres; specifically, the SUMO-modified form of HP1α supports interaction with Exosc9 and, as previously reported, lncRNA TERRA. The telomeric enrichment of Exosc9 is cell cycle-dependent and consistent with the loss of telomeric TERRA in the S/G2 phase. Elevated Exosc9 is frequently observed and drives the growth of endocrine therapy-resistant (ET-R) HR+ breast cancer (BCa) cells. Specifically, the knockdown of Exosc9 inversely impacts telomeric R-loops and the integrity of the chromosome ends of ET-R cells. Consistently, Exosc9 levels dictate DNA damage and the sensitivity of ET-R BCa cells to PARP inhibitors. In this regard, Exosc9 may serve as a promising biomarker for predicting the response to PARP inhibitors as a targeted monotherapy for ET-R HR+ BCa.
Sujet(s)
Tumeurs du sein , Exosome multienzyme ribonuclease complex , ARN long non codant , Protéines de liaison à l'ARN , Femelle , Humains , Tumeurs du sein/traitement médicamenteux , Tumeurs du sein/génétique , Homologue-5 de la protéine chromobox , Inhibiteurs de poly(ADP-ribose) polymérases , ARN long non codant/génétique , ARN long non codant/métabolisme , Télomère/génétique , Télomère/métabolisme , Exosome multienzyme ribonuclease complex/génétique , Protéines de liaison à l'ARN/génétiqueRÉSUMÉ
BACKGROUND: The unfolding protein response is a critical biological process implicated in a variety of physiological functions and disease states across eukaryotes. Despite its significance, the role and underlying mechanisms of the response in the context of ischemic stroke remain elusive. Hence, this study endeavors to shed light on the mechanisms and role of the unfolding protein response in the context of ischemic stroke. METHODS: In this study, mRNA expression patterns were extracted from the GSE58294 and GSE16561 datasets in the GEO database. The screening and validation of protein response-related biomarkers in stroke patients, as well as the analysis of the immune effects of the pathway, were carried out. To identify the key genes in the unfolded protein response, we constructed diagnostic models using both random forest and support vector machine-recursive feature elimination methods. The internal validation was performed using a bootstrapping approach based on a random sample of 1,000 iterations. Lastly, the target gene was validated by RT-PCR using clinical samples. We utilized two algorithms, CIBERSORT and MCPcounter, to investigate the relationship between the model genes and immune cells. Additionally, we performed uniform clustering of ischemic stroke samples based on expression of genes related to the UPR pathway and analyzed the relationship between different clusters and clinical traits. The weighted gene co-expression network analysis was conducted to identify the core genes in various clusters, followed by enrichment analysis and protein profiling for the hub genes from different clusters. RESULTS: Our differential analysis revealed 44 genes related to the UPR pathway to be statistically significant. The integration of both machine learning algorithms resulted in the identification of 7 key genes, namely ATF6, EXOSC5, EEF2, LSM4, NOLC1, BANF1, and DNAJC3. These genes served as the foundation for a diagnostic model, with an area under the curve of 0.972. Following 1000 rounds of internal validation via randomized sampling, the model was confirmed to exhibit high levels of both specificity and sensitivity. Furthermore, the expression of these genes was found to be linked with the infiltration of immune cells such as neutrophils and CD8 T cells. The cluster analysis of ischemic stroke samples revealed three distinct groups, each with differential expression of most genes related to the UPR pathway, immune cell infiltration, and inflammatory factor secretion. The weighted gene co-expression network analysis showed that all three clusters were associated with the unfolded protein response, as evidenced by gene enrichment analysis and the protein landscape of each cluster. The results showed that the expression of the target gene in blood was consistent with the previous analysis. CONCLUSION: The study of the relationship between UPR and ischemic stroke can help to better understand the underlying mechanisms of the disease and provide new targets for therapeutic intervention. For example, targeting the UPR pathway by blocking excessive autophagy or inducing moderate UPR could potentially reduce tissue injury and promote cell survival after ischemic stroke. In addition, the results of this study suggest that the use of UPR gene expression levels as biomarkers could improve the accuracy of early diagnosis and prognosis of ischemic stroke, leading to more personalized treatment strategies. Overall, this study highlights the importance of the UPR pathway in the pathology of ischemic stroke and provides a foundation for future studies in this field.
Sujet(s)
Accident vasculaire cérébral ischémique , Accident vasculaire cérébral , Humains , Accident vasculaire cérébral/génétique , Algorithmes , Forêts aléatoires , Marqueurs biologiques , Antigènes néoplasiques , Protéines de liaison à l'ARN , Exosome multienzyme ribonuclease complexRÉSUMÉ
Pervasive transcription of the human genome generates an abundance of RNAs that must be processed and degraded. The nuclear RNA exosome is the main RNA degradation machinery in the nucleus. However, nuclear exosome must be recruited to its substrates by targeting complexes, such as NEXT or PAXT. By proteomic analysis, we identify additional subunits of PAXT, including many orthologs of MTREC found in S. pombe. In particular, we show that polyA polymerase gamma (PAPγ) associates with PAXT. Genome-wide mapping of the binding sites of ZFC3H1, RBM27 and PAPγ shows that PAXT is recruited to the TSS of hundreds of genes. Loss of ZFC3H1 abolishes recruitment of PAXT subunits including PAPγ to TSSs and concomitantly increases the abundance of PROMPTs at the same sites. Moreover, PAPγ, as well as MTR4 and ZFC3H1, is implicated in the polyadenylation of PROMPTs. Our results thus provide key insights into the direct targeting of PROMPT ncRNAs by PAXT at their genomic sites.
Sujet(s)
Exosome multienzyme ribonuclease complex , Exosomes , ARN non traduit , Humains , Exosome multienzyme ribonuclease complex/génétique , Exosome multienzyme ribonuclease complex/métabolisme , Exosomes/génétique , Exosomes/métabolisme , Protéomique , ARN/métabolisme , Stabilité de l'ARN/génétique , ARN non traduit/métabolisme , Polynucleotide adenylyltransferase/métabolismeRÉSUMÉ
The Ski2-Ski3-Ski8 (Ski238) helicase complex directs cytoplasmic mRNAs toward the nucleolytic exosome complex for degradation. In yeast, the interaction between Ski238 and exosome requires the adaptor protein Ski7. We determined different cryo-EM structures of the Ski238 complex depicting the transition from a rigid autoinhibited closed conformation to a flexible active open conformation in which the Ski2 helicase module has detached from the rest of Ski238. The open conformation favors the interaction of the Ski3 subunit with exosome-bound Ski7, leading to the recruitment of the exosome. In the Ski238-Ski7-exosome holocomplex, the Ski2 helicase module binds the exosome cap, enabling the RNA to traverse from the helicase through the internal exosome channel to the Rrp44 exoribonuclease. Our study pinpoints how conformational changes within the Ski238 complex regulate exosome recruitment for RNA degradation. We also reveal the remarkable conservation of helicase-exosome RNA channeling mechanisms throughout eukaryotic nuclear and cytoplasmic exosome complexes.