RNA Interference Assays Research Articles

Molecular and functional characterization of MST2 in grass carp during bacterial infection

The regulation of host redox homeostasis is critically important in the immune response to pathogens. The “mammalian sterile 20-like” kinase 2 (MST2) has been shown to play a role in apoptosis, cell proliferation, and cancer; however, few studies have examined its ability to modulate redox homeostasis during innate immunity, especially in teleost fish. In this study, we cloned the MST2 gene of Ctenopharyngodon idella (CiMST2) and analyzed its tissue distribution. CiMST2 was present in most of the studied tissues, and it was most highly expressed in brain tissue. Expression patterns analysis revealed that MST2 mRNA and protein were significantly up-regulated under bacterial infection, suggesting that it is involved in the immune response. Bacterial stimulation significantly increased the level of antioxidases. To explore the interplay between CiMST2 and antioxidant regulation, we examined the effects of CiMST2 overexpression and conducted RNA interference assays in vitro. CiMST2 overexpression significantly increased the expression levels of nuclear factor E2-related factor 2 (Nrf2) and other antioxidases and vice versa, revealing that CiMST2 regulated host redox homeostasis via Nrf2-antioxidant responsive element (ARE) signaling. Overall, our findings provide a new perspective on the role of MST2 in innate immunity in teleosts as well as insights that will aid the prevention and control of disease in the grass carp farming industry.

Inherited duplications of PPP2R3B predispose to nevi and melanoma via a C21orf91-driven proliferative phenotype

PurposeMuch of the heredity of melanoma remains unexplained. We sought predisposing germline copy-number variants using a rare disease approach. MethodsWhole-genome copy-number findings in patients with melanoma predisposition syndrome congenital melanocytic nevus were extrapolated to a sporadic melanoma cohort. Functional effects of duplications in PPP2R3B were investigated using immunohistochemistry, transcriptomics, and stable inducible cellular models, themselves characterized using RNAseq, quantitative real-time polymerase chain reaction (qRT-PCR), reverse phase protein arrays, immunoblotting, RNA interference, immunocytochemistry, proliferation, and migration assays. ResultsWe identify here a previously unreported genetic susceptibility to melanoma and melanocytic nevi, familial duplications of gene PPP2R3B. This encodes PR70, a regulatory unit of critical phosphatase PP2A. Duplications increase expression of PR70 in human nevus, and increased expression in melanoma tissue correlates with survival via a nonimmunological mechanism. PPP2R3B overexpression induces pigment cell switching toward proliferation and away from migration. Importantly, this is independent of the known microphthalmia-associated transcription factor (MITF)-controlled switch, instead driven by C21orf91. Finally, C21orf91 is demonstrated to be downstream of MITF as well as PR70. ConclusionThis work confirms the power of a rare disease approach, identifying a previously unreported copy-number change predisposing to melanocytic neoplasia, and discovers C21orf91 as a potentially targetable hub in the control of phenotype switching.

CENPA is one of the potential key genes associated with the proliferation and prognosis of ovarian cancer based on integrated bioinformatics analysis and regulated by MYBL2.

BackgroundOvarian cancer (OV) is a highly lethal disease, and the fifth leading cause of all cancer-related deaths in women. The study aimed to identify potential key genes associated with the proliferation and prognosis of OV.MethodsDifferentially expressed genes (DEGs) between ovarian cancer and normal tissues were screened by the robust rank aggregation (RRA) method. The expression of CENPA and MYBL2 were examined in SKOV3 and A2780 ovarian cancer cell lines and tumor tissues by qRT-PCR and western blot. Small RNA interference assays, plasmid overexpression assays and EdU assays were used to validate the proliferative effect of the MYBL2-CENPA axis in ovarian cancer cell lines. The ChIP assay was used to verify the direct regulation of MYBL2 on CENPA.Results133 up-regulated genes and 158 down-regulated genes were identified, and the up-regulated genes mainly enrichment in cell cycle. The three up-regulated gene with DNA separation (CENPA, CENPF and CEP55) might be tightly correlated with proliferation and prognosis of OV. Knockdown CENPA expression inhibited the proliferation of A2780 and SKOV3 cells After the knockout of MYBL2, the expression of CENPA significantly decreased. MYBL2 directly binds to the promoter region of CENPA.ConclusionsThe MYBL2-CENPA pathway plays an important role in the proliferation of ovarian cancer cells, suggesting that this pathway may be a potential target for the treatment of ovarian cancer.

Immune-Omics Networks of CD27, PD1, and PDL1 in Non-Small Cell Lung Cancer.

Simple SummaryThere are currently no effective biomarkers to select chemotherapy, immunotherapy, and radiotherapy for treating lung cancer patients. This study identified genetic networks containing major immune-checkpoint inhibitors CD27, PD1, and PDL1, and their associated prognostic genes and proliferation genes in lung cancer tumors. A 5-gene prognostic model was developed and validated in extensive cohorts to select patients at a high risk for developing metastasis. CRISPR-Cas9 and RNA interference screening data were used in the selection of proliferation genes. These genes were associated with chemoresponse and radiotherapy response in lung cancer cell lines and patient tumors. This immune-omics network led to the discovery of repositioning drugs for improving lung cancer treatment.To date, there are no prognostic/predictive biomarkers to select chemotherapy, immunotherapy, and radiotherapy in individual non-small cell lung cancer (NSCLC) patients. Major immune-checkpoint inhibitors (ICIs) have more DNA copy number variations (CNV) than mutations in The Cancer Genome Atlas (TCGA) NSCLC tumors. Nevertheless, CNV-mediated dysregulated gene expression in NSCLC is not well understood. Integrated CNV and transcriptional profiles in NSCLC tumors (n = 371) were analyzed using Boolean implication networks for the identification of a multi-omics CD27, PD1, and PDL1 network, containing novel prognostic genes and proliferation genes. A 5-gene (EIF2AK3, F2RL3, FOSL1, SLC25A26, and SPP1) prognostic model was developed and validated for patient stratification (p < 0.02, Kaplan–Meier analyses) in NSCLC tumors (n = 1163). A total of 13 genes (COPA, CSE1L, EIF2B3, LSM3, MCM5, PMPCB, POLR1B, POLR2F, PSMC3, PSMD11, RPL32, RPS18, and SNRPE) had a significant impact on proliferation in 100% of the NSCLC cell lines in both CRISPR-Cas9 (n = 78) and RNA interference (RNAi) assays (n = 92). Multiple identified genes were associated with chemoresponse and radiotherapy response in NSCLC cell lines (n = 117) and patient tumors (n = 966). Repurposing drugs were discovered based on this immune-omics network to improve NSCLC treatment.

High value-added application of a renewable bioresource as acaricide: Investigation the mechanism of action of scoparone against Tetranychus cinnabarinus

IntroductionInvestigation into the action mechanisms of plant secondary metabolites against pests is a vital strategy for the development of novel promising biopesticides. Scoparone (isolated from Artemisia capillaris), a renewable plant-derived bioresource, displays potent acaricidal activities against mites, but its targets of action remain unclear. ObjectivesThis study aimed to systematically explore the potential molecular targets of scoparone against Tetranychus cinnabarinus and provide insights to guide the future application of scoparone as an agent for the management of agricultural mite pests worldwide. MethodsThe mechanism and potential targets of scoparone against mites were investigated using RNA-seq analysis; RNA interference (RNAi) assays; bioassays; and [Ca2+]i, pull-down and electrophysiological recording assays. ResultsRNA-seq analysis identified Ca2+ signalling pathway genes, specifically 5 calmodulin (CaM1–5) genes and 1 each of L-, T-, N-type voltage-gated Ca2+ channel (VGCC) genes, as candidate target genes for scoparone against mites. Furthermore, RNAi and electrophysiological data showed that the CaM1- and L-VGCC-mediated Ca2+ signalling pathways were activated by scoparone. Interestingly, by promoting the interaction between CaM1 and the IQ motif (a consensus CaM-binding domain of L-VGCC), CaM1 markedly enhanced the activating effect of scoparone on L-VGCC. Pull-down assays further demonstrated that CaM interacted with the IQ motif, triggering L-VGCC opening. Importantly, mutation of the IQ motif significantly weakened CaM1 binding and eliminated the CaM1-mediated enhancement of scoparone-induced L-VGCC activation, indicating that the effect of scoparone was dependent on the CaM1–IQ interaction. ConclusionThis study demonstrates, for the first time, that the acaricidal compound scoparone targets the interface between CaM1 and L-VGCC and activates the CaM-binding site, located in the IQ motif at the L-VGCC C-terminus. This work may contribute to the development of target-specific green acaricidal compounds based on L-VGCC.

Host-mediated RNAi for simultaneous silencing of different functional groups of genes in Meloidogyne incognita using fusion cassettes in Nicotiana tabacum.

This study establishes possibility of combinatorial silencing of more than one functional gene for their efficacy against root-knot nematode, M. incognita. Root-knot nematodes (RKN) of the genus Meloidogyne are the key important plant parasitic nematodes (PPNs) in agricultural and horticultural crops worldwide. Among RKNs, M. incognita is the most notorious that demand exploration of novel strategies for their management. Due to its sustainable and target-specific nature, RNA interference (RNAi) has gained unprecedented importance to combat RKNs. However, based on the available genomic information and interaction studies, it can be presumed that RKNs are dynamic and not dependent on single genes for accomplishing a particular function. Therefore, it becomes extremely important to consider silencing of more than one gene to establish any synergistic or additive effect on nematode parasitism. In this direction, we have combined three effectors specific to subventral gland cells of M. incognita, Mi-msp1, Mi-msp16, Mi-msp20 as fusion cassettes-1 and two FMRFamide-like peptides, Mi-flp14, Mi-flp18, and Mi-msp20 as fusion cassettes-2 to establish their possible utility for M. incognita management. In vitro RNAi assay in tomato and adzuki bean using these two fusion gene negatively altered nematode behavior in terms of reduced attraction, invasion, development, and reproduction. Subsequently, Nicotianatabacum plants were transformed with these two fusion gene hairpin RNA-expressing vectors (hpRNA), and characterized via PCR, qRT-PCR, and Southern blot hybridization. Production of siRNAs specific to Mi-flp18 and Mi-msp1 was also confirmed by Northern hybridization. Further, transgenic events expressing single copy insertions of hpRNA constructs of fusion 1 and fusion-2 conferred up to 85% reduction in M. incognita multiplication. Besides, expression quantification revealed a significant reduction in mRNA abundance of target genes (up to 1.8-fold) in M. incognita females extracted from transgenic plants, and provided additional evidence for successful gene silencing.

VX-765 ameliorates inflammation and extracellular matrix accumulation by inhibiting the NOX1/ROS/NF-κB pathway in diabetic nephropathy.

This study explores the potential role of a highly selective caspase-1 inhibitor, VX-765, on extracellular matrix (ECM) accumulation and inflammation in diabetic nephropathy (DN) and the underlying mechanisms. DN rats, induced via high-fat diet/streptozotocin, were used to assess the effects of VX-765. Parallel experiments were carried out on rat mesangial cell line HBZY-1 exposed to high glucose (HG) to reveal the molecular mechanism of VX-765 in preventing DN. Survival analysis, biochemical parameters and renal oxidative stress of rats were observed, and Western blotting and immunofluorescence were evaluated. In vitro, Nicotinamide adenine dinucleotide phosphate (NADPH) oxidases (NOX)1 silencing by RNA interference and quantitative real-time PCR (qPCR) assays were conducted in HBZY-1 cells exposed to HG levels. In vivo, VX-765 significantly reduced the increase in urine albumin excretion and ECM accumulation. The phosphorylation of nuclear factor kappa-B (NF-κB) and the expression of pro-inflammatory cytokines IL-1β, IL-6 and tumor necrosis factor (TNF)-α were significantly down-regulated. Furthermore, the generation of reactive oxygen species (ROS), phosphorylation of NF-κB and the expression of the NOX1 gene or protein were significantly decreased in HBZY-1 with VX-765 (5 μM) treatment in vitro. Our results demonstrated that VX-765 exerts favourable effects on DN via the simultaneous alleviation of systemic metabolic syndrome and down-regulating the renal NOX1/ROS/NF-κB pathway, suggesting that it has therapeutic potential for DN.

Molecular Characterization and Expression Analysis of a Novel Glutaredoxin 3 Gene in Pacific White Shrimp (Litopenaeus vannamei)

Glutaredoxins (Grxs), small heat-stable oxidoreductases, are key members of the thioredoxin (Trx) superfamily. Recently, an emerging subclass of Grxs with a cysteine residue in the active site was found in shrimps. However, molecular functions of Grx-related proteins in decapods were rarely reported. In this study, a novel full-length Grx 3 (LvGrx 3) complementary DNA (cDNA) was identified in Pacific white shrimp (Litopenaeus vannamei), which had a 975-bp open reading frame (ORF) encoding a polypeptide of 324 amino acids. The nucleic acid sequence of Pacific white shrimp glutaredoxin 3 (LvGrx 3) showed 99.59% identity with genomic DNA (gDNA) sequence and 63.49% coverage. Sequence alignment showed that the amino acid sequence of LvGrx 3 shared 97% identity with black tiger shrimp (Penaeus monodon) Grx 3 and 62% identity with amphipod (Hyalella azteca) Grx 3. LvGrx 3 showed higher expression in the intestine, gill, and hepatopancreas, and lower expression in epithelium and abdominal nerve. In response to ammonia-N stress, LvGrx 3 was significantly upregulated in both the hepatopancreas and gill, and the peak value appeared after 24 h exposure. After lipopolysaccharide (LPS) injection, expression levels of LvGrx 3 in the hepatopancreas were increased in the middle stage, and LvGrx 3 in gill was upregulated in the middle and later periods (24 and 48 h). These results indicate that LvGrx 3 can participate in immune responses against ammonia-N stress and pathogen infection. However, RNA interference (RNAi) assay showed that LvGrx 3 silencing in ammonia-N-challenged shrimp could significantly induce the gene expression of antioxidant enzymes and aggravate the oxidative damage of protein and lipid. These results suggest that LvGrx 3 is involved in regulating the antioxidant system and plays a vital role in defense responses against environmental stress.

Discovery of hydroxytyrosol as thioredoxin reductase 1 inhibitor to induce apoptosis and G1/S cell cycle arrest in human colorectal cancer cells via ROS generation.

Colorectal cancer (CRC) is one of the most common cancer types and a leading cause of cancer-associated mortality in China. Increased thioredoxin reductase 1 (TrxR1) levels have been previously identified as possible target for CRC. The present study revealed that the natural product hydroxytyrosol (HT), which exhibits a polyphenol scaffold, is a potent inhibitor of TrxR1. Inhibition of TrxR1 was indicated to result in accumulation of reactive oxygen species, inhibit proliferation and induce apoptosis and G1/S cell cycle arrest of CRC cells. Using a C-terminal mutant TrxR1 enzyme activity assay, TrxR1 RNA interference assay and HT binding model assay, the present study demonstrated the core character of the selenocysteine residue in the interaction between HT and TrxR1. HT can serve as polyphenol scaffold to develop novel TrxR1 inhibitors for CRC treatment in the future.

Transcriptomic Profiling of Apple Calli With a Focus on the Key Genes for ALA-Induced Anthocyanin Accumulation.

The red color is an attractive trait of fruit and determines its market acceptance. 5-Aminolevulinic acid (ALA), an eco-friendly plant growth regulator, has played a universal role in plant secondary metabolism regulation, particularly in flavonoid biosynthesis. It has been widely reported that ALA can up-regulate expression levels of several structural genes related to flavonoid metabolism and anthocyanin accumulation. However, the molecular mechanisms behind ALA-induced expression of these genes are complicated and still far from being completely understood. In this study, transcriptome analysis identified the differentially expressed genes (DEGs) associated with ALA-induced anthocyanin accumulation. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the flavonoid biosynthesis (ko00941) pathway was significantly enhanced in the ALA-treated apple calli at 24, 48, and 72 h after the treatment. Expression pattern revealed that ALA up-regulated the expression of the structural genes related to not only anthocyanin biosynthesis (MdCHS, MdCHI, MdF3’H, MdDFR, MdANS, and MdUFGT) but also anthocyanin transport (MdGST and MdMATE). Two R2R3-MYB transcription factors (MdMYB10 and MdMYB9), which are the known positive regulators of anthocyanin biosynthesis, were significantly induced by ALA. Gene overexpression and RNA interference assays demonstrated that MdMYB10 and MdMYB9 were involved in ALA-induced anthocyanin biosynthesis. Moreover, MdMYB10 and MdMYB9 might positively regulate the transcription of MdMATE8 by binding to the promoter region. These results indicate that MdMYB10 and MdMYB9 modulated structural gene expression of anthocyanin biosynthesis and transport in response to ALA-mediated apple calli coloration at the transcript level. We herein provide new details regarding transcriptional regulation of ALA-induced color development.

Cloning and RNAi-mediated three lethal genes that can be potentially used for Chilo suppressalis (Lepidoptera: Crambidae) management

RNA interference (RNAi) has gained attention in recent years as a viable pest control strategy. Here, RNAi assays were performed to screen the potential functionality of genes in Chilo suppressalis, a serious pest of rice, and to determine their potential for developing a highly targeted molecular control approach. Potential homologs of NADH dehydrogenase (ND), glycerol 3-phosphate dehydrogenase (GPDH) and male specific lethal 3 (MSL3) were cloned from C. suppressalis, and their spatiotemporal gene expression evaluated. The expression of all three genes was higher in the pupal and adult stages than the larval stages and largely higher in the larval head compared to other tissues. Newly hatched larvae exhibited high mortalities and suppressed growth when fed bacteria producing double-stranded RNAs (dsRNAs) corresponding to the three target genes. This study provides insights into the function of ND, GPDH and MSL3 during C. suppressalis larval development and suggests that all may be candidate gene targets for C. suppressalis pest management.

Molecular cloning, characterization and RNA interference assay of two toll-like receptors in giant freshwater prawn, Macrobrachium rosenbergii

Toll-like receptors are a family of conserved membrane receptors which are involved in the regulation of a series of innate immune responses in invertebrates and vertebrates. Two different types of Toll-like receptors from giant freshwater prawn (Macrobrachium rosenbergii), which were designated as MrToll1 and MrToll2, were cloned in the present study. The full-length cDNA of MrToll1 is 4234 bp in length, which includes a 3015-bp open reading frame (ORF) encoding a deduced protein of 1004 amino acids. The sequence of MrToll2 cDNA is 4383 bp in length containing a 2739-bp ORF which encodes 912 amino acid residues. The results from the multiple alignments of amino acid sequences and phylogenetic analysis indicated the two MrTolls identified in the present study should be classified as crustacean type-1 and type-2 Toll-like receptor, respectively. MrToll1 and MrToll2 were constitutively expressed in all the examined tissues, including gill, stomach, intestine, eyestalk, muscle, heart, ganglion, brain, hemocytes and hepatopancreas. RNA interference assay demonstrated that knockdown of MrToll1 with specific-siRNA significantly suppressed the expression of myeloid differentiation factor 88 (MyD88), anti-lipopolysaccharide factor (ALF), crustin and prophenoloxidase (proPO) and enhanced the expression level of MrToll2 in M. rosenbergii. Additionally, an obvious down-regulation of MyD88 and crustin expression was observed in MrToll2-silenced prawns. These findings suggest that MrToll1 and MrToll2 might play essential roles in the innate immunity of M. rosenbergii through regulating the expression of immune-related genes.

Mechanisms of DEET gustation in Drosophila

DEET is the most widely used active ingredient in insect repellents and offers protection against insect bites. We previously reported that DEET suppresses the feeding behavior of Drosophila, which is guided by gustatory receptors (GRs) in bitter-sensing gustatory receptor neurons. Here, we sought to identify new candidates using egg-laying assays. Upon screening all GR mutants, GR89a was identified as a potential DEET receptor. Gr89a mutants exhibited reduced oviposition avoidance, feeding avoidance, and electrophysiological responses compared to Gr32a, Gr33a, and Gr66a mutants. However, GR89a was found to modulate DEET avoidance, as demonstrated by genetic and RNA interference assays. Furthermore, we found that DEET ingestion severely affected larval and pupal development and survival, and therefore may act as an effective larvicide.

Targeting BET Proteins BRD2 and BRD3 in Combination with PI3K-AKT Inhibition as a Therapeutic Strategy for Ovarian Clear Cell Carcinoma.

Ovarian clear cell carcinoma (OCCC) is a rare, chemo-resistant subtype of ovarian cancer. To identify novel therapeutic targets and combination therapies for OCCC, we subjected a set of patient-derived ovarian cancer cell lines to arrayed high-throughput siRNA and drug screening. The results indicated OCCC cells are vulnerable to knockdown of epigenetic gene targets such as bromodomain and extra-terminal domain (BET) proteins BRD2 and BRD3. Subsequent RNA interference assays, as well as BET inhibitor treatments, validated these BET proteins as potential therapeutic targets. Because development of resistance to single targeted agents is common, we next performed sensitizer drug screens to identify potential combination therapies with the BET inhibitor CPI0610. Several PI3K or AKT inhibitors were among the top drug combinations identified and subsequent work showed CPI0610 synergized with alpelisib or MK2206 by inducing p53-independent apoptosis. We further verified synergy between CPI0610 and PI3K-AKT pathway inhibitors alpelisib, MK2206, or ipatasertib in tumor organoids obtained directly from patients with OCCC. These findings indicate further preclinical evaluation of BET inhibitors, alone or in combination with PI3K-AKT inhibitors for OCCC, is warranted.

Bioinformatics Analysis Reveals MicroRNA-193a-3p Regulates ACTG2 to Control Phenotype Switch in Human Vascular Smooth Muscle Cells.

Aortic dissection (AD) is among the most fatal cardiovascular diseases. However, the pathogenesis of AD remains poorly understood. This study aims to integrate the microRNAs (miRNA) and mRNA profiles and use bioinformatics analyses with techniques in molecular biology to delineate the potential mechanisms involved in the development of AD. We used the human miRNA and mRNA microarray datasets GSE98770, GSE52093, and GEO2R, Venn diagram analysis, gene ontology, and protein–protein interaction networks to identify target miRNAs and mRNAs involved in AD. RNA interference, western blotting, and luciferase reporter assays were performed to validate the candidate miRNAs and mRNAs in AD tissues and human vascular smooth muscle cells (VSMCs). Furthermore, we studied vascular smooth muscle contraction in AD. In silico analyses revealed that miR-193a-3p and ACTG2 were key players in the pathogenesis of AD. miR-193a-3p was upregulated in the AD tissues. We also found that biomarkers for the contractile phenotype in VSMCs were downregulated in AD tissues. Overexpression and depletion of miR-193a-3p enhanced and suppressed VSMC proliferation and migration, respectively. Dual luciferase reporter assays confirmed that ACTG2 was a target of miR-193a-3p. ACTG2 was also downregulated in human AD tissues and VMSCs overexpressing miR-193a-3p. Taken together, miR-193a-3p may be a novel regulator of phenotypic switching in VSMCs and the miR-193a-3p/ACTG2 axis may serve as a promising diagnostic biomarker and therapeutic candidate for AD.

A value-added application of eugenol as acaricidal agent: The mechanism of action and the safety evaluation

IntroductionEugenol is a major component of essential oils of several plants, it exhibits significant antiparasitic and acaricidal activities, yet its molecular targets remain unknown. ObjectivesWe aimed to systematically investigate the mechanism of action and the potential targets of eugenol against P. cuniculi, and evaluate the safety for laying the theoretical foundation for clinical application as an acaricide. MethodsUsing RNA-Seq analysis, surface plasmon resonance analysis and RNA interference assay, the mode of action of eugenol against Psoroptes cuniculi was investigated. The effect on the mitochondrial membrane potential and complex I of PC12 cells and C6/36 cells was assayed to investigate the species specificity of eugenol in insects and mammals. Finally, a safety evaluation of eugenol in vivo was performed. ResultsEugenol inhibited complex I activity of the mitochondrial respiratory chain in the oxidative phosphorylation pathway by binding to NADH dehydrogenase chain 2 and resulted in the death of mites. The inhibition rates were 37.89% for 50 μg/mL and 60.26% for 100 μg/mL, respectively. Further experiments indicated that the difference in the complex I sequence between insects and mammals led to the different affinity of eugenol to specific peptide, resulting in species specificity. Eugenol exhibited significant inhibitory effects against the mitochondrial membrane potential and complex I in Aedes albopictus C6/36 cells but was not active in rat PC12 cells. Insect cells were particularly sensitive to eugenol. In contrast to the known inhibitor rotenone, eugenol had better safety and did not result in Parkinson’s disease or other diseases in rats. ConclusionThis is the first report on acaricidal eugenol targeting complex I of the mitochondrial respiratory chain. This work lays the foundation for the development of eugenol as an environmentally alternative acaricidal agent.

Transcriptional network modulated by the prognostic signature transcription factors and their long noncoding RNA partners in primary prostate cancer.

BackgroundTranscriptional regulators are seminal players in the onset and progression of prostate cancer. However, clarification of their underlying regulatory circuits and mechanisms demands considerable effort.MethodsIntegrated analyses were performed on genomic, transcriptomic, and clinicopathological profiles of primary prostate cancer and transcription factor-binding profiles, which included estimating transcription factor activity, identifying transcription factors of prognostic values, and discovering cis- and trans-regulations by long noncoding RNAs. Interactions between transcription factors and long noncoding RNAs were validated by RNA immunoprecipitation quantitative PCR. RNA interference assays were performed to explore roles of the selected transcription regulators.FindingsSixteen transcription factors, namely, ETS1, ARID4B, KLF12, GMEB1, HBP1, MXI1, MYC, MAX, PGR, BCL11A, AR, KLF4, SRF, HIF1A, EHF, and ATOH1, were jointly identified as a prognostic signature. Candidate long noncoding RNAs interplaying with the prognostic signature constituent transcription factors were further discovered. Their interactions were randomly checked, and many of them were experimentally proved. Transcription regulation by MYC and its long noncoding RNA partner AL590617.2 was further validated on their candidate targets. Moreover, the regulatory network governed by the transcription factors and their interacting long noncoding RNA partners is illustrated and stored in our LNCTRN database (https://navy.shinyapps.io/lnctrn).InterpretationThe prognostic signature constituent transcription factors and their interacting long noncoding RNAs may represent promising biomarkers and/or therapeutic targets for prostate cancer. Furthermore, the computational framework proposed in the present study can be utilized to explore critical transcriptional regulators in other types of cancer.FundingThis work was supported by National Natural Science Foundation of China and Fudan University.

MicroRNA-30/Cx43 axis contributes to podocyte injury by regulating ER stress in diabetic nephropathy.

BackgroundThe microRNA-30 family plays a critical role in the pathogenesis of podocyte injury. Cx43 plays an essential role in intercellular communication, which is essential for coordinated kidney function. This study was conducted to explore the function of microRNA-30s/Cx43 in podocyte injury in diabetic nephropathy (DN), both in vivo and in vitro.MethodsSD rats were given streptozotocin (STZ) injections to induce DN. Podocytes were incubated in the medium in the presence or absence of high glucose (HG). The effects of the microRNA-30/Cx43 axis on DN and its underlying mechanisms were investigated by TUNEL assay, PAS, immunohistochemical staining, immunofluorescence staining, Western blot, RT-qPCR, RNA interference, and luciferase reporter assay. Podocytes were transfected with microRNA-30 family mimics, microRNA-30 family inhibitors, Cx43 siRNA, and negative controls to detect the effect of the microRNA-30/Cx43 axis. MicroRNA-30 family mimic AAVs, and microRNA-30 family inhibitor AAVs applied to regulate microRNA-30 family expression in the kidneys of the STZ-induced DN model rats to reveal the underlying mechanisms of the microRNA-30/Cx43 axis in DN.ResultsMicroRNA-30 family member expression was downregulated in HG-treated podocytes and the glomeruli of STZ-induced DN rats. Luciferase reporter assays confirmed Cx43 is a directed target of microRNA-30s. The overexpression of microRNA-30 family members attenuated the HG-induced podocyte injury and protected against podocyte apoptosis and endoplasmic reticulum stress (ERS) both in vivo and in vitro. Also, silencing Cx43 expression eased podocyte apoptosis, injury, and ERS induced by a HG+microRNA-30 family inhibitor. Double-immunofluorescence staining assays proved the co-localization of caspase12 and Cx43.ConclusionsThe overexpression of microRNA-30 family members prevents HG-induced podocyte injury and attenuates ERS by modulating Cx43 expression. The microRNA-30/Cx43/ERS axis might be a potential therapeutic target to treat DN.

Systematic Investigation of mRNA N6-Methyladenosine Machinery in Primary Prostate Cancer

Background Appreciable findings have pointed out pivotal roles of N6-methyladenosine (m6A) machinery in cancer onset and progression. However, limited efforts have been directed towards relevant research in the prostate cancer area. Methods A PubMed search was conducted to acquire components of the mRNA m6A machinery. Multiomics integration was performed to systematically investigate the mRNA m6A machinery in primary prostate cancer. Furthermore, RNA interference assays of two prognostic m6A readers EIF3D and HNRNPA2B1 were conducted to explore m6A dependence of their functions in prostate cancer cell proliferation and migration. Results A total of 41 mRNA m6A regulators have been identified to date. A small degree of copy number aberrations and an extremely low frequency of somatic mutations were observed in the regulators across prostate tumors. Enrichment of CpG sites and extensive changes of DNA methylation in the m6A machinery were also found. Impact of copy number variation on m6A regulator expression was stronger than that of DNA methylation disturbance. Furthermore, our study identified a set of m6A regulators related to clinical features and/or survival which were largely m6A-binding proteins. The translation initiation factor subunit EIF3D and the splicing factor HNRNPA2B1 can be independent prognostic factors which may contribute to retardation and promotion of cancer progression, respectively, through affecting cancer-related processes such as cell cycle. Moreover, in vitro assays demonstrated that m6A impacted the EIF3D and HNRNPA2B1 roles in proliferation and migration of prostate cancer cells. Conclusions Our report systematically described molecular features of the mRNA m6A machinery and their potential roles in primary prostate cancer. Knowledge gained from this work may pave the way for further studies on the m6A system in prostate cancer.

The regulation of immune responses against white spot syndrome virus or Vibrio alginolyticus in toll-like receptors silenced giant freshwater prawn (Macrobrachium rosenbergii)

Toll-like receptors, which are a class of cell-surface proteins, have been regarded as the most important pattern recognition receptors in the innate immunity and play a vital role in multiple innate immune responses against pathogen invasion. The full-length cDNA of a novel Toll-like receptor (MrToll3) was identified from Macrobrachium rosenbergii in the current research. The nucleotide sequence of MrToll3 is 4481 bp long and contains a 3726-bp open reading frame encoding a putative protein of 1241 amino acids. MrToll3 was constitutively expressed in all the examined tissues, and high expression of MrToll3 was detected in gill, heart, and ganglion. The result of RNA interference assay revealed that silencing of MrToll1 remarkably suppressed the prophenoloxidase (proPO) expression and phenoloxidase (PO) activities while enhancing MrToll2 expression in the prawns. Furthermore, the expression of myeloid differentiation factor 88 (MyD88), anti-lipopolysaccharide factor (ALF) and crustin was remarkably down-regulated in the MrToll1-silenced prawns after white spot syndrome virus (WSSV) or Vibrio alginolyticus challenge. MrToll2-silenced prawns exhibited the significant decline of ALF and crustin expression post the pathogen challenges, and silencing of MrToll3 obviously improved the immune deficiency (IMD) expression during the whole RNA interference assay. Additionally, higher mortality was observed in MrToll1-or MrToll2-silenced prawns after V. alginolyticus challenge, and the MrToll1-silenced prawns also showed the obviously enhanced susceptibility to WSSV. These results suggested that MrToll1, 2, and 3 were involved in the innate immune responses against WSSV and V. alginolyticus in M. rosenbergii.