Bioinformatics analysis and experimental validation of cuproptosis-related lncRNA LINC02154 in clear cell renal cell carcinoma.

BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is common in urinary system tumors. Cuproptosis is a non-apoptotic cell death pathway. Copper binds to fatty acylated mitochondrial proteins and activates various forms of cell death. LncRNA LINC02154 is significantly highly expressed in cells and tissues of many types of tumors, and the risk signature of LINC02154 in some tumors has been validated for effectiveness. METHODS: We constructed a risk prognostic signature by obtaining differentially expressed long noncoding RNAs (lncRNAs) associated with ccRCC outcomes and cuproptosis from The Cancer Genome Atlas (TCGA). We used TCGA to construct training and testing sets to analyze the risk signature and the impact of LINC02154, and we performed relevant survival analyses. Tumor mutational burdens were analyzed in different LINC02154 expression groups and risk score groups. We next analyzed the immune microenvironment of LINC20154. We performed LINC20154-related drug sensitivity analyses. We also investigated the cellular function of LINC02154 in the ACHN cell line and performed CCK-8 assay, EdU, wound-healing assay, and Transwell assay. The essential genes FDX1 and DLST of cuproptosis were detected by western blot. RESULTS: We demonstrated that LINC02154's impact on outcomes was statistically significant. We also demonstrated the association of different ages, genders, stages, and grades with LINC02154 and risk models. The results showed a significant difference in tumor mutation burden between the groups, which was closely related to clinical prognosis. We found differences in immune cells among groups with different levels of LINC02154 expression and significant differences in immune function, immunotherapeutic positive markers, and critical steps of the immune cycle. The sensitivity analysis showed that differential expression of LINC02154 discriminated between sensitivity to axitinib, doxorubicin, gemcitabine, pazopanib, sorafenib, sunitinib, and temsirolimus. This difference was also present in the high-risk group and low-risk group. We demonstrated that the proliferation and migration of t ACHN cells in the LINC02154 knockdown group were inhibited. The western blot results showed that the knockdown of LINC02154 significantly affected the expression of FDX1 and DLST, critical genes of cuproptosis. CONCLUSION: Finally, we demonstrated that LINC02154 and our constructed risk signature could predict outcomes and have potential clinical value.

Identification of fatty acid metabolism-based molecular subtypes and prognostic signature to predict immune landscape and guide clinical drug treatment in renal clear cell carcinoma.

Three subtypes of samples were generated based on genes involved in fatty acid metabolism in The Cancer Genome Atlas (TCGA)-RCC patients using a non-negative matrix factorization (NMF) algorithm. 32 co-expressed modules were identified using WCGNA. We constructed a four-gene signature in our training set using least absolute shrinkage selection operator regression analysis and verified it in our testing and overall sets. A relevant study analysis in clinical trials was conducted, which showed the model had good stability and potential application value for predicting outcomes. We analyzed the immune microenvironment using MCPcounter, CIBERSORT, quanTIseq, TIMER and ESTIMATE algorithms, and the result indicated risk was positively related to T cells, B-lineage, and fibroblasts and negatively correlated with monocytic lineage, myeloid dendritic cells, neutrophils, and endothelial cells, and CPT1B was positively related to T cells, CD8 + T cells, Cytotoxic lymphocytes and NK cells, and negatively correlated with myeloid dendritic cells, fibroblasts, endothelial cells. Tumor mutation burden was positively related to risk score and the expression of CPT1B using the R packages corrplot, circlize. Through the R package pRRophetic, drug sensitivity tests showed that the low-risk score group would benefit more from sunitinib and less from pazopanib, sorafenib, temsirolimus, gemcitabine and doxorubicin than the high-risk score group. We performed the relevant basic assay validation for CPT1B, and the proliferation ability of RCC cells was inhibited after the knockdown of protein expression of CPT1B. In conclusion, we established a four-gene model that can predict outcomes of RCC with potential applications in diagnosis and treatment.

Construction of a cuproptosis-associated lncRNA prognostic signature for bladder cancer and experimental validation of cuproptosis-related lncRNA UBE2Q1-AS1.

Introduction: Bladder cancer (BLCA) is the ninth most common malignancy worldwide and the fourth most common cancer in men. Copper levels are significantly altered in patients with thyroid, breast, lung, cervical, ovarian, pancreatic, oral, gastric, bladder, and prostate cancers. Outcomes can be predicted by constructing signatures using lncRNA-related genes associated with outcomes. Methods: We identified lncRNAs related to outcomes, those differentially expressed in bladder cancer, and cuproptosis-related lncRNAs from TCGA. We identified the intersection to obtain 12 genes and established a prognostic risk signature consisting of eight genes using LASSO-penalized multivariate Cox analysis. We constructed a training set, performed survival analysis on the high-and low-risk groups, and performed validation in the test and full sets. There existed a substantial contrast in the likelihood of survival among the cohorts of high and low risk. An in-depth analysis of the gene mutations associated with tumors was conducted to evaluate the risk of developing cancer. We also performed gene analysis on neoadjuvant chemotherapy. We conducted experimental validation on the key gene UBE2Q1-AS1 in our prognostic signature. Results: The risk signature we constructed shows significant differences between the high-risk group and the low-risk group. Univariate survival analysis of the eight genes in our signature showed that each gene distinguished between high- and low-risk groups. Sub-group analysis revealed that our risk score differed significantly in tumor stage, age, and gender. The analysis results of the tumor mutation burden (TMB) showed a significant difference in the TMB between the low- and high-risk groups, which had a direct impact on the outcomes. These findings highlight the importance of TMB as a potential prognostic marker in cancer detection and prevention. We analyzed the immune microenvironment and found significant differences in immune function, validation responses, immunotherapy-related positive markers, and critical steps in the tumor immunity cycle between the high- and low-risk groups. We found that the effect of anti-CTLA4 and PD-1 was higher in the high-risk group than in the low-risk group.Gene analysis of neoadjuvant chemotherapy revealed that the treatment effect in the high-risk group was better than in the low-risk group. The key gene UBE2Q1-AS1 in our prognostic signature can significantly influence the cell viability, migration, and proliferation of cancer cells. Discussion: We established a signature consisting of eight genes constructed from cuproptosis-related lncRNAs that have potential clinical applications for outcomes prediction, diagnosis, and treatment.

Genes associated with grey matter volume reduction in multiple sclerosis.

There is extensive grey matter volume (GMV) reduction in multiple sclerosis (MS), which may account for cognitive impairment in this disabling disorder. Although genome-wide association studies (GWASs) have identified hundreds of genes associated with MS, we know little about which genes associated with GMV reduction and cognitive decline in MS. In the present study, we aimed to uncover genes associated with GMV reduction in MS by performing cross-sample (1473 brain tissue samples) partial least squares regression between gene expression from 6 postmortem brains and case-control GMV difference of MS from a meta-analysis of 1391 patients and 1189 controls (discovery phase) and from the intergroup comparison between 69 patients and 70 controls (replication phase). We identified 623 genes whose brain spatial expression profiles were significantly associated with GMV reduction in MS. These genes showed significant enrichment for MS-related genes identified by GWAS; were functionally associated with ion channel, synaptic transmission, axon and neuron projection; and showed more significant cell type-specific expression in neurons than other cell types. More importantly, the identified genes showed significant enrichment for those genes with downregulated rather than upregulated expression in MS. The spatial distribution patterns of the expression of the identified genes showed more significant correlations with brain activation patterns of memory and language tasks. These findings indicate that grey matter atrophy in MS may be resulted from the joint effects of multiple genes that are associated with this disorder, especially genes with downregulated expression in MS.

Bridging the Gap Between Morphometric Similarity Mapping and Gene Transcription in Alzheimer's Disease.

Disruptions in brain connectivity have been widely reported in Alzheimer's disease (AD). Morphometric similarity (MS) mapping provides a new way of estimating structural connectivity by interregional correlation of T1WI- and DTI-derived parameters within individual brains. Here, we aimed to identify AD-related MS changing patterns and genes related to the changes and further explored the molecular and cellular mechanism underlying MS changes in AD. Both 3D-T1WI and DTI data of 106 AD patients and 106 well-matched healthy elderly individuals from the ADNI database were included in our study. Cortical regions with significantly decreased MS were found in the temporal and parietal cortex, increased MS was found in the frontal cortex and variant changes were found in the occipital cortex in AD patients. Mean MS in regions with significantly changed MS was positively or negatively associated with memory function. Negative MS-related genes were significantly downregulated in AD, specifically enriched in neurons, and participated in biological processes, with the most significant term being synaptic transmission. This study revealed AD-related cortical MS changes associated with memory function. Linking gene expression to cortical MS changes may provide a possible molecular and cellular substrate for MS abnormality and cognitive decline in AD.

Cell-Type-Specific Gene Modules Related to the Regional Homogeneity of Spontaneous Brain Activity and Their Associations With Common Brain Disorders.

Mapping gene expression profiles to neuroimaging phenotypes in the same anatomical space provides opportunities to discover molecular substrates for human brain functional properties. Here, we aimed to identify cell-type-specific gene modules associated with the regional homogeneity (ReHo) of spontaneous brain activity and their associations with brain disorders. Fourteen gene modules were consistently associated with ReHo in the three datasets, five of which showed cell-type-specific expression (one neuron-endothelial module, one neuron module, one astrocyte module and two microglial modules) in two independent cell series of the human cerebral cortex. The neuron-endothelial module was mainly enriched for transporter complexes, the neuron module for the synaptic membrane, the astrocyte module for amino acid metabolism, and microglial modules for leukocyte activation and ribose phosphate biosynthesis. In enrichment analyses of cell-type-specific modules for 10 common brain disorders, only the microglial module was significantly enriched for genes obtained from genome-wide association studies of multiple sclerosis (MS) and Alzheimer's disease (AD). The ReHo of spontaneous brain activity is associated with the gene expression profiles of neurons, astrocytes, microglia and endothelial cells. The microglia-related genes associated with MS and AD may provide possible molecular substrates for ReHo abnormality in both brain disorders.

ZNF804A rs1344706 interacts with COMT rs4680 to affect prefrontal volume in healthy adults.

The biological function of ZNF804A rs1344706, the first genome-wide supported risk variant of schizophrenia, remains largely unknown. Based on the upregulating effect of ZNF804A on the expression of COMT, we hypothesize that ZNF804A may affect grey matter volume (GMV) by interacting with COMT. Voxel-based morphometry was applied to analyze the main and interaction effects of ZNF804A rs1344706 and COMT rs4680 on brain GMV in 274 healthy young human subjects. The GMV of the left dorsolateral prefrontal cortex (DLPFC) showed a significant COMT rs4680 × ZNF804A rs1344706 interaction, manifesting as an inverted U-shape modulation by the presumed dopamine signaling. In COMT Met-allele carriers, the ZNF804A TG heterozygotes showed greater GMV in the left DLPFC than both GG and TT homozygotes. In COMT Val/Val homozygotes, however, the ZNF804A TG heterozygotes exhibited smaller GMV in the left DLPFC than GG homozygotes and comparable GMV with TT homozygotes. These findings suggest that ZNF804A affects the GMV of the prefrontal cortex by interacting with COMT, which may improve our understanding of neurobiological effect of ZNF804A and its association with schizophrenia.

Modulation of APOE and SORL1 genes on hippocampal functional connectivity in healthy young adults.

Apolipoprotein E (APOE) and sortilin-related receptor (SORL1) genes act on the same metabolic pathway and have been associated with Alzheimer's disease (AD) characterized by hippocampal impairment. Although the effects of APOE on hippocampal resting-state functional connectivity (rsFC) have been reported, the main effects of SORL1 and SORL1 × APOE interactions on hippocampal rsFC in healthy subjects remain largely unknown. Here, we systematically investigated the main effects of SORL1 rs2070045, and APOE, and their interaction effects on hippocampal rsFC in healthy young adults. The main effect of APOE showed that risk ε4 carriers had decreased positive hippocampal rsFC with the precuneus/posterior cingulate cortex and subgenual anterior cingulate cortex, and increased positive hippocampal rsFC with the sensorimotor cortex compared with non-ε4 carriers. The main effect of SORL1 showed that risk G-allele carriers had decreased positive rsFC between the hippocampus and middle temporal gyrus compared with TT carriers. No significant additive interaction was observed. Instead, significant SORL1 × APOE non-additive interaction was found in negative rsFC between the hippocampus and inferior frontal gyrus. Compared with subjects with TT genotype, SORL1 G-allele carriers had a stronger negative rsFC in APOE ε4 carriers, but a weaker negative rsFC in APOE non-ε4 carriers. These findings suggest that SORL1 and APOE genes modulate different hippocampal rsFCs and have a complex interaction. The SORL1- and APOE-dependent hippocampal connectivity changes may at least partly account for their association with AD.

Modulation effect of the SORL1 gene on functional connectivity density in healthy young adults.

The sortilin-related receptor 1 (SORL1) gene has been associated with late-onset Alzheimer's disease (LOAD) and structural impairments in several ethnic populations. However, how this gene affects brain function properties remains unclear. We investigated associations of SORL1 rs2070045 with functional connectivity density (FCD) in healthy young adults. This single-nucleotide polymorphism was selected because it is the SORL1 variant that has been frequently associated with LOAD in several populations, including the Chinese Han population. A total of 275 healthy young Chinese Han subjects with successful genotyping and MRI examinations were included. The effect of SORL1 rs2070045 was explored using a voxel-wise FCD analysis. A significant effect of SORL1 rs2070045 on the FCD was found in the right inferior temporal gyrus. The risk G allele carriers of the rs2070045 exhibited a lower FCD than the protective TT carriers. This effect was independent of the status of apolipoprotein E. This study provides the first evidence that the SORL1 gene is associated with brain FCD differences in healthy young adults. In the genetic risk subjects, connectivity impairment already starts during young adulthood, which may predispose the risk allele carriers to be susceptible to LOAD after several decades.

Noise-based tube current reduction method with iterative reconstruction for reduction of radiation exposure in coronary CT angiography.

PURPOSE: To investigate the potential of noise-based tube current reduction method with iterative reconstruction to reduce radiation exposure while achieving consistent image quality in coronary CT angiography (CCTA). MATERIALS AND METHODS: 294 patients underwent CCTA on a 64-detector row CT equipped with iterative reconstruction. 102 patients with fixed tube current were assigned to Group 1, which was used to establish noise-based tube current modulation formulas, where tube current was modulated by the noise of test bolus image. 192 patients with noise-based tube current were randomly assigned to Group 2 and Group 3. Filtered back projection was applied for Group 2 and iterative reconstruction for Group 3. Qualitative image quality was assessed with a 5 point score. Image noise, signal intensity, volume CT dose index, and dose-length product were measured. RESULTS: The noise-based tube current modulation formulas were established through regression analysis using image noise measurements in Group 1. Image noise was precisely maintained at the target value of 35.00 HU with small interquartile ranges for Group 2 (34.17-35.08 HU) and Group 3 (34.34-35.03 HU), while it was from 28.41 to 36.49 HU for Group 1. All images in the three groups were acceptable for diagnosis. A relative 14% and 41% reduction in effective dose for Group 2 and Group 3 were observed compared with Group 1. CONCLUSION: Adequate image quality could be maintained at a desired and consistent noise level with overall 14% dose reduction using noise-based tube current reduction method. The use of iterative reconstruction further achieved approximately 40% reduction in effective dose.

Prospective ECG-triggered coronary CT angiography: clinical value of noise-based tube current reduction method with iterative reconstruction.

OBJECTIVES: To evaluate the clinical value of noise-based tube current reduction method with iterative reconstruction for obtaining consistent image quality with dose optimization in prospective electrocardiogram (ECG)-triggered coronary CT angiography (CCTA). MATERIALS AND METHODS: We performed a prospective randomized study evaluating 338 patients undergoing CCTA with prospective ECG-triggering. Patients were randomly assigned to fixed tube current with filtered back projection (Group 1, n = 113), noise-based tube current with filtered back projection (Group 2, n = 109) or with iterative reconstruction (Group 3, n = 116). Tube voltage was fixed at 120 kV. Qualitative image quality was rated on a 5-point scale (1 = impaired, to 5 = excellent, with 3-5 defined as diagnostic). Image noise and signal intensity were measured; signal-to-noise ratio was calculated; radiation dose parameters were recorded. Statistical analyses included one-way analysis of variance, chi-square test, Kruskal-Wallis test and multivariable linear regression. RESULTS: Image noise was maintained at the target value of 35HU with small interquartile range for Group 2 (35.00-35.03HU) and Group 3 (34.99-35.02HU), while from 28.73 to 37.87HU for Group 1. All images in the three groups were acceptable for diagnosis. A relative 20% and 51% reduction in effective dose for Group 2 (2.9 mSv) and Group 3 (1.8 mSv) were achieved compared with Group 1 (3.7 mSv). After adjustment for scan characteristics, iterative reconstruction was associated with 26% reduction in effective dose. CONCLUSION: Noise-based tube current reduction method with iterative reconstruction maintains image noise precisely at the desired level and achieves consistent image quality. Meanwhile, effective dose can be reduced by more than 50%.