Tissue-Specific Differential Expression of Novel Genes and Long Intergenic Noncoding RNAs in Humans With Extreme Response to Evoked Endotoxemia

MALAT1 DEREPRESSES MIR-433-3P-MEDIATED RPTOR SUPPRESSION TO IMPAIR AUTOPHAGY AND DRIVE PYROPTOSIS IN ENDOTOXEMIA

ABSTRACT

Objective: Autophagy elevation in endotoxemia plays a protective role by negatively regulating the pyroptosis of vascular endothelial cells, but the molecular mechanisms are still poorly understood. The present study aimed to identify the mechanism underlying autophagy and pyroptosis in endotoxemia. Methods: Bioinformatics analysis and whole-gene transcriptome sequencing prediction were used to identify the endotoxemia-related lncRNA-miRNA-mRNA axis of interest. Human umbilical vein endothelial cells (HUVECs) were activated by lipopolysaccharide (LPS) to mimic the inflammatory environment encountered in endotoxemia. Autophagy and pyroptosis of LPS-treated HUVECs were assessed in response to the knockdown of MALAT1 (metastasis-associated lung adenocarcinoma transcript 1)/miR-433-3p (miRNA-433-3p)/RPTOR (regulatory-associated protein of mTOR). The binding affinity of MALAT1, miR-433-3p, and RPTOR was detected by RNA pull-down and luciferase activity assays. The endothelial cell-specific RPTOR knockout mice were developed and rendered septic using LPS induction to verify the role of RPTOR in autophagy, pyroptosis, and inflammatory response in vivo . Results: The in vitro experiments indicated that LPS could stimulate HUVECs to highly express RPTOR, and its knockdown enhanced cellular autophagy and restricted pyroptosis to curb inflammatory responses. Mechanically, MALAT1 is competitively bound to miR-433-3p to release RPTOR expression, thereby promoting pyroptosis and aggravating endotoxemia. In vivo experiments further confirmed that the knockdown of RPTOR activated autophagy and curtailed pyroptosis in septic mice. Conclusion: MALAT1 is highly expressed in endotoxemia. MALAT1 promotes RPTOR expression by competitively absorbing miR-433-3p, inhibits LPS-activated HUVEC cell autophagy, promotes cell death, enhances LPS-induced inflammatory activation of vascular endothelial cells, and ultimately promotes the progression of endotoxemia.

Exosomes from dysfunctional chondrocytes affect osteoarthritis in Sprague-Dawley rats through FTO-dependent regulation of PIK3R5 mRNA stability

Aims

Exosomes (exo) are involved in the progression of osteoarthritis (OA). This study aimed to investigate the function of dysfunctional chondrocyte-derived exo (DC-exo) on OA in rats and rat macrophages.

Methods

Rat-derived chondrocytes were isolated, and DCs induced with interleukin (IL)-1β were used for exo isolation. Rats with OA (n = 36) or macrophages were treated with DC-exo or phosphate-buffered saline (PBS). Macrophage polarization and autophagy, and degradation and chondrocyte activity of cartilage tissues, were examined. RNA sequencing was used to detect genes differentially expressed in DC-exo, followed by RNA pull-down and ribonucleoprotein immunoprecipitation (RIP). Long non-coding RNA osteoarthritis non-coding transcript (OANCT) and phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5) were depleted in DC-exo-treated macrophages and OA rats, in order to observe macrophage polarization and cartilage degradation. The PI3K/AKT/mammalian target of rapamycin (mTOR) pathway activity in cells and tissues was measured using western blot.

Results

DC-exo inhibited macrophage autophagy (p = 0.002) and promoted M1 macrophage polarization (p = 0.002). DC-exo at 20 μg/ml induced collagen degradation (p < 0.001) and inflammatory cell infiltration (p = 0.023) in rats. OANCT was elevated in DC (p < 0.001) and in cartilage tissues of OA patients (p < 0.001), and positively correlated with patients’ Kellgren-Lawrence grade (p < 0.001). PIK3R5 was increased in DC-exo-treated cartilage tissues (p < 0.001), and OANCT bound to fat mass and obesity-associated protein (FTO) (p < 0.001). FTO bound to PIK3R5 (p < 0.001) to inhibit the stability of PIK3R5 messenger RNA (mRNA) (p < 0.001) and disrupt the PI3K/AKT/mTOR pathway (p < 0.001).

Conclusion

Exosomal OANCT from DC could bind to FTO protein, thereby maintaining the mRNA stability of PIK3R5, further activating the PI3K/AKT/mTOR pathway to exacerbate OA.

Cite this article: Bone Joint Res 2022;11(9):652–668.

Screening a novel signature and predicting the immune landscape of metastatic osteosarcoma in children via immune-related lncRNAs

BACKGROUND

The immune microenvironment plays an essential role in osteosarcoma (OSs); however, differences in immune-related long non-coding ribonucleic acids (irlncRNAs) in children with localized OSs and metastatic OSs have not yet been investigated.

METHODS

The clinical data and the transcriptome of OSs were obtained from the Therapeutically Applicable Research to Generate Effective Treatments (TARGET) database, and the immune-related genes were derived from the imported dataset. The correlations between immune-related genes and lncRNAs were examined. Next, the differential expressions of the irlncRNA pairs (IRLPs) in localized OSs and distant metastatic OSs were analyzed, and a prognostic model was constructed based on the significant differentially expressed IRLPs. We also analyzed the association between the IRLPs' signature risk score and the infiltration of the immune cells. Finally, we investigated the correlation between risk score and drug resistance.

RESULTS

Thirty upregulated and 22 downregulated lncRNAs were identified in the localized and metastatic OSs samples. Univariate and multivariate cox regression analyses were undertaken to select 6 lncRNA pairs to establish the prognostic signature, the model was valuable in predicting OSs prognosis. Further, the expression of the finally selected irlncRNAs indicated that VPS9D1-AS1 (P=0.031), AP003086.2 (P=0.041), AL031847.1 (P=0.008), AL020997.3 (P=0.020), AC011444.1 (P=0.025), and AC006449.2 (P=0.003) were significantly upregulated in metastasis patients, but USP27X-AS1 (P=0.046), AL008721.2 (P=0.005), AC002091.1 (P=0.033), and AL118558.4 (P=0.049) were significantly overexpressed in localized patients. The overexpression of AC002091.1 (P=0.038) and AL118558.4 (P=0.004) resulted in better overall survival, but the upregulation of AC011444.1 (P=0.045), AL031847.1 (P=0.020), VPS9D1-AS1 (P=0.039), and AC006449.2 (0.006) led to a poor outcome. Differences in immune cell infiltration indicated that metastatic patients and localized have significant difference of 4 (CD4) T cells (P=0.006), monocytes (P=0.029), activated mast cells (P=0.018), and neutrophils (P=0.026), and a high abundance of activated dendritic cells (P=0.010) and activated mast cells (P=0.049) resulted in poor prognosis. Patients in the high-risk-score group were resistant to axitinib, but sensitive to dasatinib, bortezomib, and cisplatin.

CONCLUSIONS

In the present study, IRLPs were used to construct a novel and practical model for predicting the prognosis of localized and metastatic OSs in children.

Nonconserved Long Intergenic Noncoding RNAs Associate With Complex Cardiometabolic Disease Traits

OBJECTIVE

Transcriptome profiling of human tissues has revealed thousands of long intergenic noncoding RNAs (lincRNAs) at loci identified through large-scale genome-wide studies for complex cardiometabolic traits. This raises the question of whether genetic variation at nonconserved lincRNAs has any systematic association with complex disease, and if so, how different this pattern is from conserved lincRNAs. We evaluated whether the associations between nonconserved lincRNAs and 8 complex cardiometabolic traits resemble or differ from the pattern of association for conserved lincRNAs. Approach and Results: Our investigation of over 7000 lincRNA annotations from GENCODE Release 33-GRCh38.p13 for complex trait genetic associations leveraged several large, established meta-analyses genome-wide association study summary data resources, including GIANT (Genetic Investigation of Anthropometric Traits), UK Biobank, GLGC (Global Lipids Genetics Consortium), Cardiogram (Coronary Artery Disease Genome Wide Replication and Meta-Analysis), and DIAGRAM (Diabetes Genetics Replication and Meta-Analysis)/DIAMANTE (Diabetes Meta-Analysis of Trans-Ethnic Association Studies). These analyses revealed that (1) nonconserved lincRNAs associate with a range of cardiometabolic traits at a rate that is generally consistent with conserved lincRNAs; (2) these findings persist across different definitions of conservation; and (3) overall across all cardiometabolic traits, approximately one-third of genome-wide association study-associated lincRNAs are nonconserved, and this increases to about two-thirds using a more stringent definition of conservation.

CONCLUSIONS

These findings suggest that the traditional notion of conservation driving prioritization for functional and translational follow-up of complex cardiometabolic genomic discoveries may need to be revised in the context of the abundance of nonconserved long noncoding RNAs in the human genome and their apparent predilection to associate with complex cardiometabolic traits.