Isolation and Analysis of Mitochondrial Small RNAs from Rat Liver Tissue and HepG2 Cells

Mitochondrial miR-12294-5p regulated copper-induced mitochondrial oxidative stress and mitochondrial quality control imbalance by targeted inhibition of CISD1 in chicken livers

Copper (Cu) is hazardous metal contaminant, which induced hepatotoxicity is closely related to mitochondrial disorder, but exact regulatory mechanism has not yet been revealed. Mitochondrial microRNAs (mitomiRs) are a novel and critical regulator of mitochondrial function and mitochondrial homeostasis. Hence, this study revealed the impact of Cu-exposure on mitomiR expression profiles in chicken livers, and further identified mitomiR-12294-5p and its target gene CISD1 as core regulators involved in Cu-induced hepatotoxicity. Additionally, our results showed that Cu-exposure induced mitochondrial oxidative damage, and mitochondrial quality control imbalance mediated by mitochondrial dynamics disturbances, mitochondrial biogenesis inhibition and abnormal mitophagy flux in chicken livers and primary chicken embryo hepatocytes (CEHs). Meaningfully, we discovered that inhibition of the expression of mitomiR-12294-5p effectively alleviated Cu-induced mitochondrial oxidative stress and mitochondrial quality control imbalance, while the up-regulation of mitomiR-12294-5p expression exacerbated Cu-induced mitochondrial damage. Simultaneously, the above Cu-induced mitochondrial damage can be effectively rescued by the overexpression of CISD1, while knockdown of CISD1 dramatically reverses the mitigating effect that inhibition of mitomiR-12294-5p expression on Cu-induced mitochondrial oxidative stress and mitochondrial quality control imbalance. Overall, these results suggested that mitomiR-12294-5p/CISD1 axis mediated mitochondrial damage is a novel molecular mechanism involved in regulating Cu-induced hepatotoxicity in chickens.

Exposure to zinc induces lysosomal-mitochondrial axis-mediated apoptosis in PK-15 cells

Zinc (Zn), a kind of metallic element, can cause poisonous effects on host physiology when its excess exposure. Lysosomes and mitochondria are the toxic targets of heavy metals, and the lysosomal-mitochondrial axis is also verified to take part in apoptosis, but the related underlying mechanisms in Zn-induced cytotoxicity remain undefined. Here, we identified that excess Zn could cause cell damage in PK-15 cells accompanied by the lysosomal and mitochondrial dysfunction, with the evidence by the elevated levels of cathepsin B/D (CTSB/CTSD) in cytoplasm and decrease of Lyso-Tracker Red signal, red fluorescence intensity of AO staining, mitochondrial complex enzyme activities and ATP production. Additionally, the number of Annexin V⁺/PI^--stained cells, apoptosis-related genes (Bax, Bid, Bak1, Caspase-9, and Caspase-3) and proteins levels of Bax, Bak1, Caspase-9, cleaved Caspase-3 and cytoplasmic Cyt C were signally elevated under Zn exposure, while the protein levels of Bcl2 and mitochondrial Cyt C were observably decreased. Importantly, Pepstatin A (the activity inhibitor of CTSD) and RNA interference of CTSD (si-CTSD) was used to reduce the release of lysosomal CTSD to the cytoplasm, which could signally alleviated Zn-induced mitochondrial damage and apoptosis. In summary, these results suggested that Zn could induced lysosomal and mitochondrial dysfunction in PK-15 cells, and the CTSD played an important role in Zn-induced lysosomal-mitochondrial axis-mediated apoptosis. Our results provided a new insight in Zn-induced toxicology, which for protecting the ecological environment and public health.

Mitochondrial miR-1285 regulates copper-induced mitochondrial dysfunction and mitophagy by impairing IDH2 in pig jejunal epithelial cells

Copper (Cu), a hazardous heavy metal, can lead to toxic effects on host physiology. Recently, specific mitochondria-localized miRNAs (mitomiRs) were shown to modulate mitochondrial function, but the underlying mechanisms remain undefined. Here, we identified mitomiR-1285 as an important molecule regulating mitochondrial dysfunction and mitophagy in jejunal epithelial cells under Cu exposure. Mitochondrial dysfunction and mitophagy were the important mechanisms of Cu-induced pathological damage in jejunal epithelial cells, which were accompanied by significant increase of mitomiR-1285 in vivo and in vitro. Knockdown of mitomiR-1285 significantly attenuated Cu-induced mitochondrial respiratory dysfunction, ATP deficiency, mitochondrial membrane potential reduction, mitochondrial reactive oxygen species accumulation, and mitophagy. Subsequently, bioinformatics analysis and luciferase reporter assay demonstrated that IDH2 was a direct target of mitomiR-1285. RNA interference of IDH2 dramatically reversed the effect that mitomiR-1285 knockdown relieved mitochondrial dysfunction and mitophagy induced by Cu, and the opposite effect was shown by overexpression of IDH2. Therefore, our results suggested that mitomiR-1285 aggravated Cu-induced mitochondrial dysfunction and mitophagy via suppressing IDH2 expression. These findings identified the important mechanistic connection between mitomiRs and mitochondrial metabolism under Cu exposure, providing a new insight into Cu toxicology.

Nuclear-Encoded lncRNA MALAT1 Epigenetically Controls Metabolic Reprogramming in HCC Cells through the Mitophagy Pathway

Mitochondrial dysfunction is a metabolic hallmark of cancer cells. In search of molecular factors involved in this dysregulation in hepatocellular carcinoma (HCC), we found that the nuclear-encoded long noncoding RNA (lncRNA) MALAT1 (metastasis-associated lung adenocarcinoma transcript 1) was aberrantly enriched in the mitochondria of hepatoma cells. Using RNA reverse transcription-associated trap sequencing (RAT-seq), we showed that MALAT1 interacted with multiple loci on mitochondrial DNA (mtDNA), including D-loop, COX2, ND3, and CYTB genes. MALAT1 knockdown induced alterations in the CpG methylation of mtDNA and in mitochondrial transcriptomes. This was associated with multiple abnormalities in mitochondrial function, including altered mitochondrial structure, low oxidative phosphorylation (OXPHOS), decreased ATP production, reduced mitophagy, decreased mtDNA copy number, and activation of mitochondrial apoptosis. These alterations in mitochondrial metabolism were associated with changes in tumor phenotype and in pathways involved in cell mitophagy, mitochondrial apoptosis, and epigenetic regulation. We further showed that the RNA-shuttling protein HuR and the mitochondria transmembrane protein MTCH2 mediated the transport of MALAT1 in this nuclear-mitochondrial crosstalk. This study provides the first evidence that the nuclear genome-encoded lncRNA MALAT1 functions as a critical epigenetic player in the regulation of mitochondrial metabolism of hepatoma cells, laying the foundation for further clarifying the roles of lncRNAs in tumor metabolic reprogramming.

The Regulatory Role of Mitochondrial MicroRNAs (MitomiRs) in Breast Cancer: Translational Implications Present and Future

Simple Summary

Mitochondrial microRNAs (mitomiRs) are an emerging field of study in a wide range of tumours including breast cancer. By targeting mitochondrial, or non-mitochondrial products, mitomiRs are able to regulate the functions of this organelle, thus controlling multiple carcinogenic processes. The knowledge of this system may provide a novel approach for targeted therapies, as potential biomarkers or helping in the diagnosis of such a complex malignancy.

Abstract

Breast cancer is the most prevalent and incident female neoplasm worldwide. Although survival rates have considerably improved, it is still the leading cause of cancer-related mortality in women. MicroRNAs are small non-coding RNA molecules that regulate the posttranscriptional expression of a wide variety of genes. Although it is usually located in the cytoplasm, several studies have detected a regulatory role of microRNAs in other cell compartments such as the nucleus or mitochondrion, known as “mitomiRs”. MitomiRs are essential modulators of mitochondrion tasks and their abnormal expression has been linked to the aetiology of several human diseases related to mitochondrial dysfunction, including breast cancer. This review aims to examine basic knowledge of the role of mitomiRs in breast cancer and discusses their prospects as biomarkers or therapeutic targets.

Improved Mammalian Mitochondrial RNA Isolation

Mitochondria have two sets of RNAs. One is encoded in mitochondrial genome, and the other that consists of imported RNAs within mitochondria and cytosolic RNAs associated with mitochondrial outer membrane is encoded in the nucleus. These mitochondrial RNAs play important roles in mitochondrion biosynthesis and signaling in and out of mitochondria. Isolation and analysis of mitochondrial RNAs can provide useful information on understanding the mitochondrial regulation of cellular processes. However, several ribonuclease activities have been found in mitochondria, which will degrade mitochondrial RNAs during the isolation process if they are not properly inactivated. Here, we describe an improved method to inactivate the ribonuclease activities prior to RNA extraction, and thus provide a reliable protocol to isolate mammalian mitochondrial RNAs for quantitative RT-PCR and other assays.

Transcriptome comparison between prenatal and postnatal Large White livers identifies differences in the expression level of genes related to metabolism and postnatal growth

The current study examined the liver transcriptomic profiles of the Large White different in developmental periods. It was performed on pigs of two developmental stages: 70-day fetus (P70) and 70-day piglets (D70). The objective of the study was to identify genes associated with Large White liver lipid metabolism, growth and development. We sequenced eight sRNA libraries of liver samples from four Large White at P70 and D70 respectively. We totally obtained 19,202 genes. 4916 of them were found to be differentially expressed (DEGs) (p < 0.05, fold change ≥ 1), of which 2502 were up-regulated and 2414 were down-regulated. GO enrichment and KEGG pathway analysis indicated that ACACA, ACADM, ACAA2 and HADH were simultaneously enriched in diverse pathways related to lipid metabolism, and so they were considered to be the promising candidate genes which could affect the porcine liver lipid metabolism. Notably, the gene insulin-like growth factor 1 (IGF1) which participated in somatotropic axis signaling was found to be up-regulated in D70 compared with P70. miRWalk and TargetScan softwares were used to screen the miRNAs which bound to the 3' untranslated region (3'UTR) of IGF1. After integration analysis with miRNAs sequencing data, miR-18b and miR-130b-3p were selected for further study. MiR-18b and miR-130b-3p were down-regulated in D70 compared with P70. Dual luciferase assays indicated that miR-18b and miR-130b-3p could obviously decrease (p < 0.05) the fluorescence activity of the group transfected with the wild-type vector of IGF1 3'UTR, while the relative luciferase activity of the group transfected with the mutant vector of IGF1 3'UTR did not change significantly. Taken together, it indicated that miR-18b and miR-130b-3p could target IGF1 directly.