Overexpression of MTFR1 promotes cancer progression and drug-resistance on cisplatin and is related to the immune microenvironment in lung adenocarcinoma

OBJECTIVE

The roles of MTFR1 in the drug resistance of lung adenocarcinoma (LAC) to cisplatin remain unexplored. In this study, the expression, clinical values and mechanisms of MTFR1 were explored, and the relationship between MTFR1 expression and immune microenvironment was investigated in LAC using bioinformatics analysis, cell experiments, and meta-analysis.

METHODS

MTFR1 expression and clinical values, and the relationship between MTFR1 expression and immunity were explored, through bioinformatics analysis. The effects of MTFR1 on the growth, migration and cisplatin sensitivity of LAC cells were identified using cell counting kit-8, wound healing and Transwell experiments. Additionally, the mechanisms of drug resistance of LAC cells involving MTFR1 were investigated using western blotting.

RESULTS

MTFR1 was elevated in LAC tissues. MTFR1 overexpression was associated with sex, age, primary therapy outcome, smoking, T stage, unfavourable prognosis and diagnostic value and considered an independent risk factor for an unfavourable prognosis in patients with LAC. MTFR1 co-expressed genes involved in the cell cycle, oocyte meiosis, DNA replication and others. Moreover, interfering with MTFR1 expression inhibited the proliferation, migration and invasion of A549 and A549/DDP cells and promoted cell sensitivity to cisplatin, which was related to the inhibition of p-AKT, p-P38 and p-ERK protein expression. MTFR1 overexpression was associated with stromal, immune and estimate scores along with natural killer cells, pDC, iDC and others in LAC.

CONCLUSIONS

MTFR1 overexpression was related to the unfavourable prognosis, diagnostic value and immunity in LAC. MTFR1 also participated in cell growth and migration and promoted the drug resistance of LAC cells to cisplatin via the p-AKT and p-ERK/P38 signalling pathways.

Comprehensive analysis of transcriptome-wide expression patterns and a circRNA/lncRNA-miRNA-mRNA network in the pathogenesis of cerebral ischemia in Rattus norvegicus

BACKGROUND

Although ischemic stroke exhibits a high prevalence in the elderly population, the involved genes and pathways are poorly understood. In this study, we proposed to identify differentially expressed genes (DEGs) and constructed a circular RAN (circRNA)/long noncoding RNA (lncRNA)/microRNA (miRNA)-mRNA network associated with the pathogenesis of ischemic stroke by using bioinformatics analysis.

METHODS

We constructed a rat model of middle cerebral artery occlusion (MCAO) and conducted total RNA and microRNA sequencing in brain specimens from MCAO and normal rats. Transcriptome-wide expression patterns were analyzed and DEGs were defined by applying Ballgown and a cut of log2-transformed fold-change (log2FC) ≥ 1 (or ≤ -1) with a P value < 0.05. We exploited Pearson correlation analysis to determine the association between the circRNA/lncRNA/mRNA network and miRNAs (P < 0.05 and corr ≤ -0.6), and the competing endogenous RNAs (ceRNA) interaction network was visualized with Cytoscape software and separated into subnetworks using the Molecular Complex Detection (MCODE) algorithm. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were implemented for the pathway analysis of DEGs.

RESULTS

Upregulated DEGs were significantly enhanced in positive regulation of cell migration, response to wounding, blood vessel morphogenesis, inflammatory response, and cell activation; Downregulated DEGs were associated with control of the modulation of chemical synaptic transmission, synapse organization, regulation of membrane potential, and regulation of ion transport. KEGG-pathway analysis showed that DEG-enhanced pathways were associated with the pathways of TNF signaling pathway, Fluid shear stress and atherosclerosis, NF-kappa B signaling pathway, Lipid and atherosclerosis, Human cytomegalovirus infection, Osteoclast differentiation, Chemokine signaling pathway, IL-17 signaling pathway, Viral protein interaction with cytokine and cytokine receptor, and Cytokine-cytokine receptor interaction. We uncovered several novel lncRNAs (lnc_00231, lnc_002239, lnc_004172; and a novel_circ0001704), five miRNAs (miR-200b-3p, miR-223-3p, miR-200c-3p, miR-3084a-3p, and miR-664-2-5p), and the top-10 mRNAs (upregulated mRNAs were Pdgfa, Il1b, Gdf15, Fosl1, and Cxcl2; downregulated mRNAs were Prkar2b, Olfm3, Lrrc73, Tmem38a, and Dlgap3) that were involved in ischemic stroke.

CONCLUSIONS

Through bioinformatic network analysis, we identified the underlying molecular mechanisms and key central genes that may contribute to an inflammatory response after cerebral infarction.

[Identification and functional analysis of combined oxidative phosphorylation deficiency 28 gene mutation]

Objective: To report a case of combined oxidative phosphorylation deficiency 28 (COXPD28) in China, identified the pathogenic mutation and explored the pathogenic mechanism preliminarily. Methods: The clinical characteristics of a patient with COXPD28 were retrospectively analyzed and the pathogenic mutations were identified by mitochondrial gene sequencing and whole exome sequencing. The wild-type and mutant plasmids of pathogenic genes were constructed, and effect of mutation on protein expression by quantitative real-time PCR (qPCR) and Western blot were evaluated. Statistical methods mainly used one-way ANOVA and LSD test. Results: A 21 year old female patient presented with lactic acid poisoning due to repeated chest distress and wheezing since childhood. The sequencing of the whole exon group gene found that solute carrier family 25 member 26 (SLC25A26) gene had a compound heterozygous mutation (c.34G>C, p.A12P; c.197C>A, p.A66E), which was the first report in China. In vitro function test showed that the expression levels of SLC25A26 mRNA and S-adenosylmethionine carrier (SAMC) protein in cells transfected with SLC25A26 mutant plasmid were significantly lower than those transfected with wild type plasmid. The p.A66E mutant plasmid reduced the expression level of SLC25A26 mRNA and SAMC protein to 6% and 26% of wild type plasmids respectively (both P<0.001), while p.A12P mutant plasmid decreased to 62% and 82% of wild type plasmids respectively (P<0.001, P=0.044). When the double mutant (p.A66E+p.A12P) plasmids were co-transfected, the expression levels of SLC25A26 mRNA and SAMC protein decreased to 47% and 57% of the wild type plasmids, respectively (P<0.001, P=0.001). Conclusion: The pathogenic mutation gene of this patient with COXPD28 is SLC25A26 gene mutation (p.A66E, p.A12P), which causes the decrease of SLC25A26 expression level, mitochondrial oxidative phosphorylation dysfunction, and induces COXPD28.

Decreased APOC1 expression inhibited cancer progression and was associated with better prognosis and immune microenvironment in esophageal cancer

Several studies have demonstrated the involvement of apolipoprotein C1 (APOC1) in multiple cancers. However, the role of APOC1 in esophageal cancer (ESCA) has not been elucidated. Hence, we examined the expression of APOC1 in ESCA tissues acquired from The Cancer Genome Atlas (TCGA) database and clinical samples from our hospital. An investigation of the association of APOC1 with the clinicopathological characteristics, prognosis, and diagnosis of ESCA was carried out on the basis of survival, receiver operating characteristics, and correlation analyses. Gene ontology, KEGG analysis, and protein-protein interaction network showed that co-expressed APOC1 genes were involved in the functions, mechanisms, and action network. The effects of APOC1 expression on ESCA cells were explored using CCK-8, migration and invasion assays. The relationship between APOC1 expression and ESCA immune-infiltrating cells and cell markers were examined using correlation analysis. We found that APOC1 was overexpressed in TCGA ESCA tissues and the same was validated in clinical ESCA tissues, with the area under the curve for APOC1 being 0.887. Overexpression of APOC1 was associated with short overall survival, disease-specific survival, progression-free interval, T stage, pathological stage, body mass index, and histological grade. Inhibition of APOC1 expression significantly reduced the proliferation, migration, and invasion of ESCA cells. Furthermore, APOC1 expression positively correlated with the ESTIMATE, immune, and stromal scores in ESCA. Overexpression of APOC1 correlated with the tumor purity, B cells, T helper cells, natural killer cells, cytotoxic cells, and other immune cells. Moreover, APOC1 was involved in ESCA progression via T cell receptor, B cell receptor, and other immune signaling pathways. Thus, APOC1 overexpression is expected to be a biomarker for dismal prognosis and diagnosis of ESCA. Inhibition of APOC1 expression significantly reduced the proliferation, migration, and invasion of ESCA cells. Overexpression of APOC1 was associated with the immune microenvironment in ESCA. Thus, APOC1 may be an efficient biomarker for proper prognosis and diagnosis of ESCA.

The Risk Model Based on the Three Oxidative Stress-Related Genes Evaluates the Prognosis of LAC Patients

Background

Oxidative stress plays a role in carcinogenesis. This study explores the roles of oxidative stress-related genes (OSRGs) in lung adenocarcinoma (LAC). Besides, we construct a risk score model of OSRGs that evaluates the prognosis of LAC patients.

Methods

OSRGs were downloaded from the Gene Set Enrichment Analysis (GSEA) website. The expression levels of OSRGs were confirmed in LAC tissues of the TCGA database. GO and KEGG analyses were used to evaluate the roles and mechanisms of oxidative stress-related differentially expressed genes (DEGs). Survival, ROC, Cox analysis, and AIC method were used to screen the prognostic DEGs in LAC patients. Subsequently, we constructed a risk score model of OSRGs and a nomogram. Further, this work investigated the values of the risk score model in LAC progression and the relationship between the risk score model and immune infiltration.

Results

We discovered 163 oxidative stress-related DEGs in LAC, involving cellular response to oxidative stress and reactive oxygen species. Besides, the areas under the curve of CCNA2, CDC25C, ERO1A, CDK1, PLK1, ITGB4, and GJB2 were 0.970, 0.984, 0.984, 0.945, 0.984, 0.771, and 0.959, respectively. This indicates that these OSRGs have diagnosis values of LAC and are significantly related to the overall survival of LAC patients. ERO1A, CDC25C, and ITGB4 overexpressions were independent risk factors for the poor prognosis of LAC patients and were associated with risk scores in the risk model. High-risk score levels affected the poor prognosis of LAC patients. Notably, a high-risk score may be implicated in LAC progression via cell cycle, DNA replication, mismatch repair, and other mechanisms. Further, ERO1A, CDC25C, and ITGB4 expression levels were related to the immune infiltrating cells of LAC, including mast cells, NK cells, and CD8 T cells.

Conclusion

In summary, ERO1A, CDC25C, and ITGB4 of OSRGs are associated with poor prognosis of LAC patients. We confirmed that the risk model based on the ERO1A, CDC25C, and ITGB4 is expected to assess the prognosis of LAC patients.

Upregulated expression of MTFR2 as a novel biomarker predicts poor prognosis in hepatocellular carcinoma by bioinformatics analysis

Aim: The authors investigated the clinical role of MTFR2 in hepatocellular carcinoma (HCC) progression. Results: MTFR2 expression and methylation were abnormal in HCC tissues, and HCC patients with increased MTFR2 expression or methylation had poor or better overall survival, respectively. In addition, increased MTFR2 expression was correlated with age, grade, cancer stage and T stage. MTFR2 was an independent predictor of dismal prognosis in HCC patients. MTFR2 was involved in HCC progression by modulating the cell cycle, homologous recombination, DNA replication, p53 signaling pathway, etc. The ten hub genes were overexpressed in HCC tissues and were linked to cancer stage and dismal prognosis in HCC patients. Conclusion: MTFR2 could be a prospective biomarker of poor prognosis in individuals with HCC.

DEPTOR suppresses the progression of esophageal squamous cell carcinoma and predicts poor prognosis

As a naturally occurring inhibitor of mTOR, accumulated evidence has suggested that DEPTOR plays a pivotal role in suppressing the progression of human malignances. However, the function of DEPTOR in the development of esophageal squamous cell carcinoma (ESCC) is still unclear. Here we report that the expression of DEPTOR is significantly reduced in tumor tissues derived from human patients with ESCC, and the downregulation of DEPTOR predicts a poor prognosis of ESCC patients. In addition, we found that the expression of DEPTOR negatively regulates the tumorigenic activities of ESCC cell lines (KYSE150, KYSE510 and KYSE190). Furthermore, ectopic DEPTOR expression caused a significant suppression of the cellular proliferation, migration and invasion of KYSE150 cells, which has the lowest expression level of DEPTOR in the three cell lines. Meanwhile, CRISPR/Cas9 mediated knockout of DEPTOR in KYSE-510 cells significantly promoted cellular proliferation, migration and invasion. In addition, in vivo assays further revealed that tumor growth was significantly inhibited in xenografts with ectopic DEPTOR expression as compared to untreated KYSE150 cells, and was markedly enhanced in DEPTOR knockout KYSE-510 cells. Biochemical studies revealed that overexpression of DEPTOR led to the suppression of AKT/mTOR pathway as evidenced by reduced phosphorylation of AKT, mTOR and downstream SGK1, indicating DEPTOR might control the progression of ESCC through AKT/mTOR signaling pathway. Thus, these findings, for the first time, demonstrated that DEPTOR inhibits the tumorigenesis of ESCC cells and might serve as a potential therapeutic target or prognostic marker for human patients with ESCC.

Pineal parenchymal tumours: minimum apparent diffusion coefficient in prediction of tumour grading

Retrospective assessment was performed of the minimum apparent diffusion coefficient (minADC) together with quantitative assessment of the histopathological features of resected tumour tissue and the Ki-67 labelling index (LI) for predicting pineal parenchymal tumour (PPT) grade. Magnetic resonance images of tumours from 26 male and female patients (mean age 27.7 years) with pathologically confirmed PPTs, comprising 10 pineocytomas (PCs), seven pineal parenchymal tumours of intermediate differentiation (PPTIDs) and nine pineoblastomas (PBs), were reviewed retrospectively. Using ADC maps derived from isotropic diffusion-weighted images, the minADC value of each tumour was determined postoperatively from several regions of interest defined in the tumour, excluding cystic, necrotic, haemorrhagic or calcified components. Surgical intervention was undertaken in all cases. The Ki-67 LI was measured in surgical specimens. Mean minADC and Ki-67 LI showed significant differences among PCs, PPTIDs and PBs, and minADC was negatively correlated with Ki-67 LI. It is concluded that the minADC of PPTs provide useful additional information when predicting tumour grading.

Value of Diffusion-Weighted Imaging in Grading Tumours Localized in the Fourth Ventricle Region by Visual and Quantitative Assessments

This study investigated visual and quantitative assessment of diffusion-weighted imaging (DWI) for grading tumours localized in the fourth ventricle region. Patients were diagnosed histopathologically and classified into two groups: those with high-grade (World Health Organization [WHO] grades III and IV) and those with low-grade tumours (benign, WHO grades I and II). DWI signal intensity was described using a five-point scale. Minimum apparent diffusion coefficient (ADC) values were obtained from areas with the lowest signal. The mean signal intensity was significantly higher in high-grade than in low-grade tumours. The mean minimum ADC value was significantly lower in high-grade than low-grade tumours. Marked hyperintensity had sensitivity, specificity, positive predictive value and negative predictive value of 89.7%, 100%, 100% and 94.2%, respectively, when used as a diagnostic tool for high-grade tumours compared with 96.6%, 97.9%, 96.6% and 97.9%, respectively, when using a minimum ADC of 0.9 × 10−3 mm2/s as a diagnostic marker. It was concluded that DWI is helpful in predicting the grades of tumours in the fourth ventricle region.

A unique magnetic resonance imaging feature of glioblastoma multiforme: the 'pseudopalisade' sign

This study was designed to investigate the unique magnetic resonance imaging (MRI) appearance of histopathologically-proven glioblastoma multiforme (GBM) with pseudopalisade necrosis and to assess its value for grading gliomas and providing a differential diagnosis. The study included 169 patients with intracranial masses who underwent surgery and had a proven histopathological diagnosis: 50 with GBM, 77 with gliomas (46 grade II and 31 grade III) and 42 with other intracranial masses (20 metastases, 14 lymphomas and eight abscesses). All patients underwent preoperative brain MRI including post-contrast T(1)-weighted imaging. The presence of the 'pseudopalisade' sign on post-contrast T(1)-weighted images was compared among the different types of brain mass. The frequency of the 'pseudopalisade' sign in GBMs (94.00%) was significantly higher than that seen in grade II and III gliomas (11.69%) and other intracranial masses (7.14%). The 'pseudopalisade' sign on post-contrast T(1)-weighted images was useful for grading gliomas and for differentiating GBM from other brain masses.

Identification of cytochrome P450 2E1 in rat brain

We have isolated cDNA fragments that were originated from P450 2E1 in rat brain by PCR analysis. Their size matched up to what we expected based on the reported sequence of rat liver P450 2E1 mRNA. Internal structure of the longest first-round PCR products were investigated by Southern blot analysis and "nested" PCR. Their results confirmed that PCR products actually originated from P450 2E1 mRNA in rat brain. RT-PCR was also carried out using P450 2E1 specific primers and the size of the product was exactly as we expected for P450 2E1. These experimental evidences should clarify the presence of P450 2E1 in rat brain.

Physiological indicators and susceptibility of plants to acidifying atmospheric pollution: a multivariate approach

Plant susceptibility to acidifying atmospheric pollution was investigated for a wide range of plant species under normal environmental conditions. Physiological and biochemical parameters were recorded for each plant species. Multivariate analysis using hierarchical clustering, principal component analysis ordination, as well as regression analysis were used to interpret the data. Analysis of the data separated plants into pioneer tree species, ruderal herbaceous species and climax, slow growing species. Pioneer and ruderal species showed higher potential for foliar nitrate assimilation coupled with higher base cation content and a tendency to a more neutral leaf pH than climax species. Acidic buffering capacities for leaf tissue from pioneer and ruderal species were higher than those of climax species. Nitrate assimilation produces hydroxyl ions, which in conjunction with high base cation content and more neutral leaf pH, provides better metabolic buffering and therefore make pioneer and ruderal species less susceptible to acidifying inputs. Climax species are less able to buffer against acidifying inputs and are subsequently more prone to acidifying air pollution damage.

Molecular cloning and sequencing of sulfated glycoprotein-2 cDNA from testis of mouse: implications of two different mRNAs of SGP-2

We cloned a mouse homolog of sulfated glycoprotein-2 (SGP-2) cDNA by screening a mouse testicular cDNA library and its nucleotide sequence was determined. The predicted amino acid sequence of the cDNA shares 93% identity with that of rat SGP-2. The nucleotide sequences of both cDNAs show extensive homology throughout the open reading frames and 3' untranslated regions. The 5' untranslated regions, however, share homology only up to 28 bp upstream from the start codons; the rest of sequences are quite different. DNA sequence homology search to mouse SGP-2 cDNA through the EMBL/GenBank database and a recent study on the genomic organization of rat TRPM-2 gene suggest a possibility that there are at least two different SGP-2 mRNAs as a result of alternative splicing and/or different promoter usage in mouse.