RNA-binding protein QKI suppresses breast cancer via RASA1/MAPK signaling pathway

GAS5 regulated by FTO-mediated m6A modification suppresses cell proliferation via the IGF2BP2/QKI axis in breast cancer

BACKGROUND

The lncRNA growth arrest-specific 5 (GAS5) is involved in regulating breast cancer progression. In this study, we aimed to elucidate the function and mechanism of GAS5 in breast cancer.

METHODS

The expressions of GAS5, fat mass and obesity-associated protein (FTO), insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2), and Quaking (QKI) were assessed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and western blot. The m6A modification level of GAS5 was detected using m6A immunoprecipitation assay (MeRIP). The interaction between IGF2BP2 and GAS5 or QKI was detected using RNA immunoprecipitation assay (RIP) and dual luciferase reporter assay. Cell proliferation was measured using the Cell Counting Kit-8 (CCK-8) assay. The biological functions of the FTO/GAS5/IGF2BP2/QKI axis was assessed using the tumor xenograft assay.

RESULTS

LncRNA GAS5 expression decreased in breast cancer and was regulated by FTO-mediated m6A modification in an IGF2BP2-dependent manner, resulting in decreased GAS5 stability and expression. GAS5 recruited IGF2BP2 to target QKI and upregulated QKI expression in breast cancer cells. GAS5 suppressed breast cancer growth via IGF2BP2/QKI, and this inhibitory effect was modulated by FTO both in vitro and in vivo.

CONCLUSIONS

GAS5 regulated by FTO-mediated m6A modification represses the growth of breast cancer via the IGF2BP2/QKI pathway, suggesting that the FTO/GAS5/IGF2BP2/QKI pathway can be a potential target for breast cancer treatment.

Non-adherent culture method affects the proliferation and apoptosis of mesenchymal stem cells through inhibiting LINC00707 to promote RNF6-mediated QKI ubiquitination

Exploration of the molecular mechanisms of mesenchymal stem cell (MSC) growth has significant clinical benefits. Long non-coding RNAs (lncRNAs) have been reported to play vital roles in the regulation of the osteogenic differentiation of MSCs. However, the mechanism by which lncRNA affects the proliferation and apoptosis of MSCs is unclear. In this study, sequencing analysis revealed that LINC00707 was significantly decreased in non-adherent human MSCs (non-AC-hMSCs) compared to adherent human MSCs. Moreover, LINC00707 overexpression promoted non-AChMSC proliferation, cell cycle progression from the G0/G1 phase to the S phase and inhibited apoptosis, whereas LINC00707 silencing had the opposite effect. Furthermore, LINC00707 interacted directly with the quaking (QKI) protein and enhanced the E3 ubiquitin-protein ligase ring finger protein 6 (RNF6)-mediated ubiquitination of the QKI protein. Additionally, the overexpression of QKI rescued the promotive effects on proliferation and inhibitory effects on apoptosis in non-AC-hMSCs induced by the ectopic expression of LINC00707. Thus, LINC00707 contributes to the proliferation and apoptosis in non-AChMSCs by regulating the ubiquitination and degradation of the QKI protein.

Prognostic value and gene regulatory network of CMSS1 in hepatocellular carcinoma

BACKGROUND

Cms1 ribosomal small subunit homolog (CMSS1) is an RNA-binding protein that may play an important role in tumorigenesis and development.

OBJECTIVE

RNA-seq data from the GEPIA database and the UALCAN database were used to analyze the expression of CMSS1 in liver hepatocellular carcinoma (LIHC) and its relationship with the clinicopathological features of the patients.

METHODS

LinkedOmics was used to identify genes associated with CMSS1 expression and to identify miRNAs and transcription factors significantly associated with CMSS1 by GSEA.

RESULTS

The expression level of CMSS1 in hepatocellular carcinoma tissues was significantly higher than that in normal tissues. In addition, the expression level of CMSS1 in advanced tumors was significantly higher than that in early tumors. The expression level of CMSS1 was higher in TP53-mutated tumors than in non-TP53-mutated tumors. CMSS1 expression levels were strongly correlated with disease-free survival (DFS) and overall survival (OS) in patients with LIHC, and high CMSS1 expression predicted poorer OS (P< 0.01) and DFS (P< 0.01). Meanwhile, our results suggested that CMSS1 is associated with the composition of the immune microenvironment of LIHC.

CONCLUSIONS

The present study suggests that CMSS1 is a potential molecular marker for the diagnosis and prognostic of LIHC.

FOXP3-regulated lncRNA NONHSAT136151 promotes colorectal cancer progression by disrupting QKI interaction with target mRNAs

The role of lncRNAs in the pathogenesis of cancer, including colorectal cancer (CRC), has repeatedly been demonstrated. However, very few lncRNAs have been well annotated functionally. Our study identified a novel lncRNA upregulated in CRC, NONHSAT136151, which was correlated with clinical progression. In functional assays, NONHSAT136151 significantly enhanced CRC cell proliferation, migration and invasion. Mechanistically, NONHSAT136151 interacted with RNA-binding protein (RBP) QKI (Quaking) to interfere with QKI binding to target mRNAs and regulate their expression. As well, FOXP3 may be causally related to the dysregulation of NONHSAT136151 in CRC cells through its transcriptional activity. In conclusion, our findings identified a novel lncRNA regulated by FOXP3 participates in CRC progression through interacting with QKI, indicating a novel lncRNA-RBP interaction mechanism is involved in CRC pathogenesis.

RNA binding proteins in senescence: A potential common linker for age-related diseases?

Aging represents the major risk factor for the onset and/or progression of various disorders including neurodegenerative diseases, metabolic disorders, and bone-related defects. As the average age of the population is predicted to exponentially increase in the coming years, understanding the molecular mechanisms underlying the development of aging-related diseases and the discovery of new therapeutic approaches remain pivotal. Well-reported hallmarks of aging are cellular senescence, genome instability, autophagy impairment, mitochondria dysfunction, dysbiosis, telomere attrition, metabolic dysregulation, epigenetic alterations, low-grade chronic inflammation, stem cell exhaustion, altered cell-to-cell communication and impaired proteostasis. With few exceptions, however, many of the molecular players implicated within these processes as well as their role in disease development remain largely unknown. RNA binding proteins (RBPs) are known to regulate gene expression by dictating at post-transcriptional level the fate of nascent transcripts. Their activity ranges from directing primary mRNA maturation and trafficking to modulation of transcript stability and/or translation. Accumulating evidence has shown that RBPs are emerging as key regulators of aging and aging-related diseases, with the potential to become new diagnostic and therapeutic tools to prevent or delay aging processes. In this review, we summarize the role of RBPs in promoting cellular senescence and we highlight their dysregulation in the pathogenesis and progression of the main aging-related diseases, with the aim of encouraging further investigations that will help to better disclose this novel and captivating molecular scenario.

miR-31/QKI-5 axis facilitates cell cycle progression of non-small-cell lung cancer cells by interacting and regulating p21 and CDK4/6 expressions

BACKGROUND

RNA-binding protein Quaking-5 (QKI-5), a major isoform of QKIs, inhibits tumor progression in non-small cell lung cancer (NSCLC). However, the underlying molecular mechanisms of QKI-5 in the cell cycle of NSCLC are still largely unknown.

METHODS

MTT, flow cytometry, and colony formation assays were used to investigate cellular phenotypic changes. Mice xenograft model was used to evaluate the antitumor activities of QKI-5. Co-immunoprecipitation, RNA immunoprecipitation (RIP), and RIP sequencing were used to investigate protein-protein interaction and protein-mRNA interaction.

RESULTS

The QKI-5 expression was downregulated in NSCLC tissues compared with that in paired normal adjacent lung tissues. Overexpression of QKI-5 inhibited NSCLC cell proliferative and colony forming ability. In addition, QKI-5 induced cell cycle arrest at G0/G1 phase through upregulating p21^Waf1/Cip1 (p21) expression and downregulating cyclin D1, cyclin-dependent kinase 4 (CDK4), and CDK6 expressions. Further analyses showed that QKI-5 interacts with p21 protein and CDK4, CDK6 mRNAs, suggesting a critical function of QKI-5 in cell cycle regulation. In agreement with in vitro study, the mouse xenograft models validated tumor suppressive functions of QKI-5 in vivo through altering cell cycle G1-phase-associated proteins. Moreover, we demonstrated that QKI-5 is a direct target of miR-31. The QKI-5 expression was anticorrelated with the miR-31 expression in NSCLC patient samples.

CONCLUSION

Our results suggest that the miR-31/QKI-5/p21-CDK4-CDK6 axis might have critical functions in the progression of NSCLC, and targeting this axis could serve as a potential therapeutic strategy for NSCLC.

Imaging genetic association analysis of triple-negative breast cancer based on the integration of prior sample information

Triple-negative breast cancer (TNBC) is one of the more aggressive subtypes of breast cancer. The prognosis of TNBC patients remains low. Therefore, there is still a need to continue identifying novel biomarkers to improve the prognosis and treatment of TNBC patients. Research in recent years has shown that the effective use and integration of information in genomic data and image data will contribute to the prediction and prognosis of diseases. Considering that imaging genetics can deeply study the influence of microscopic genetic variation on disease phenotype, this paper proposes a sample prior information-induced multidimensional combined non-negative matrix factorization (SPID-MDJNMF) algorithm to integrate the Whole-slide image (WSI), mRNAs expression data, and miRNAs expression data. The algorithm effectively fuses high-dimensional data of three modalities through various constraints. In addition, this paper constructs an undirected graph between samples, uses an adjacency matrix to constrain the similarity, and embeds the clinical stage information of patients in the algorithm so that the algorithm can identify the co-expression patterns of samples with different labels. We performed univariate and multivariate Cox regression analysis on the mRNAs and miRNAs in the screened co-expression modules to construct a TNBC-related prognostic model. Finally, we constructed prognostic models for 2-mRNAs (IL12RB2 and CNIH2) and 2-miRNAs (miR-203a-3p and miR-148b-3p), respectively. The prognostic model can predict the survival time of TNBC patients with high accuracy. In conclusion, our proposed SPID-MDJNMF algorithm can efficiently integrate image and genomic data. Furthermore, we evaluated the prognostic value of mRNAs and miRNAs screened by the SPID-MDJNMF algorithm in TNBC, which may provide promising targets for the prognosis of TNBC patients.

Research progress on RNA−binding proteins in breast cancer

Breast cancer is the most common malignancy in women and has a high incidence rate and mortality. Abnormal regulation of gene expression plays an important role in breast cancer occurrence and development. RNA-binding proteins (RBPs) are one kind of the key regulators for gene expression. By interacting with RNA, RBPs are widely involved in RNA cutting, transport, editing, intracellular localization, and translation regulation. RBPs are important during breast cancer occurrence and progression by engaging in many aspects, like proliferation, migration, invasion, and stemness. Therefore, comprehensively understanding the role of RBPs in breast cancer progression can facilitate early diagnosis, timely treatment, and long-term survival and quality of life of breast cancer patients.

QKI deficiency in macrophages protects mice against JEV infection by regulating cell migration and antiviral response

Japanese encephalitis (JE) is a major reason to cause viral encephalitis, with 50% patients suffering from severe neuro-inflammation and permanent neural injury. Effective anti-viral treatment is urgently needed. Here, we found RNA binding protein quaking (QKI) was involved in the progression of JE by regulating migration and anti-viral response of macrophages. After JE virus (JEV) infection, QKI-deficient mice had lower viral loads in the brain and fewer neurological symptoms. In comparison with control mice, proinflammatory cytokines in the brain of QKI-deficient animals revealed distinct patterns, with lower levels of IL-6 (interleukin-6) and IFN-β (interferon-β) at the early stage but higher levels at the end of JE. Then we found infiltration of CCR2 positive ((C-C motif) receptor 2) peripheral macrophages and CCR2 expression on macrophages were inhibited in QKI-deficient mice, while the expression of CCR2 ligands was not changed. Bioinformatical analysis showed that a QRE (quaking response element) located on 3'UTR (untranslated region) of Ccr2. We further verified that QKI was able to interact with Ccr2 mRNA and regulate its degradation in vitro. Additionally, since the IFN-β production was increased in QKI-ablation mice after JEV infection, the anti-viral response was analyzed. Results in QKI-silenced N9 cells showed that the expression of RIG-I (retinoic acid-inducible gene-I) and TBK1 (TANK binding kinase 1) was increased, thus further inducing IRF3 (interferon regulatory factor 3) phosphorylation and interferon activation. Overall, these results revealed QKI mediated the anti-viral process via interfering migration of macrophages to CNS (central nervous system) and enhancing RIG-I/IRF3/IFN-β pathway to restrict virus dissemination.

Evaluation of NF1 and RASA1 gene expression in endometriosis

Background

Endometrios affecting 6-10% of women of reproductive ages around the globe. Important pathways, including the MAPK and PI3K / Akt pathways, have been identified in the disease. The NF1 and RASA1 genes inactivate Ras by their own GTPase activity and controlled the high activity of these pathways.

Objective

In this study, we measured NF1 and RASA1 gene expression in the endometrial tissues of patients (eutopic and ectopic tissues) compared to the control samples.

Materials and methods

In our study, tissue samples were collected from 15 patients with endometriosis and 15 healthy women. We used quantitative polymerase chain reaction (qRT-PCR) to measure the NF1 and RASA1 gene expression levels in these samples.

Results

We observed a significant decrease in the expression level of the NF1 gene in both eutopic and ectopic samples of endometriosis patients compared to control samples, while the expression of the RASA1 gene was significantly reduced only in ectopic tissues.

The Estrogen Receptor α Signaling Pathway Controls Alternative Splicing in the Absence of Ligands in Breast Cancer Cells

Background: The transcriptional activity of estrogen receptor α (ERα) in breast cancer (BC) is extensively characterized. Our group has previously shown that ERα controls the expression of a number of genes in its unliganded form (apoERα), among which a large group of RNA-binding proteins (RBPs) encode genes, suggesting its role in the control of co- and post-transcriptional events. Methods: apoERα-mediated RNA processing events were characterized by the analysis of transcript usage and alternative splicing changes in an RNA-sequencing dataset from MCF-7 cells after siRNA-induced ERα downregulation. Results: ApoERα depletion induced an expression change of 681 RBPs, including 84 splicing factors involved in translation, ribonucleoprotein complex assembly, and 3′end processing. ApoERα depletion results in 758 isoform switching events with effects on 3′end length and the splicing of alternative cassette exons. The functional enrichment of these events shows that post-transcriptional regulation is part of the mechanisms by which apoERα controls epithelial-to-mesenchymal transition and BC cell proliferation. In primary BCs, the inclusion levels of the experimentally identified alternatively spliced exons are associated with overall and disease-free survival. Conclusion: Our data supports the role of apoERα in maintaining the luminal phenotype of BC cells by extensively regulating gene expression at the alternative splicing level.

ARHGEF19 promotes the growth of breast cancer in vitro and in vivo by the MAPK pathway

OBJECTIVE

To assess the expression of ARHGEF19 in human breast cancer, investigate its role in breast cancer, and clarify the mechanism.

METHODS

Bioinformatics analysis, immunoblot, quantitative PCR, and immunohistochemical (IHC) assays were performed to assess ARHGEF19 expression in breast cancer. CCK-8 and Edu assays were conducted to reveal its role in breast cancer cell proliferation. Flow cytometry (FCM) assays and immunoblot were performed to confirm its effects on breast cancer apoptosis. Immunoblot was also performed to clarify the mechanism. Finally, tumor growth assays were aimed to confirm the role of ARHGEF19 in mice.

RESULTS

We observed that ARHGEF19 was highly expressed in human breast cancer. ARHGEF19 promoted breast cancer cell growth in vitro, and suppressed apoptosis. In addition, we found that ARHGEF19 could activate the MAPK pathway in breast cancer cells. Our findings further confirmed that ARHGEF19 contributed to breast cancer growth in mice.

CONCLUSION

We observed that ARHGEF19 promoted the growth of breast cancer in vitro and in vivo via MAPK pathway, and presume it could serve as a breast cancer therapeutic target.