Single-nucleus sequencing unveils heterogeneity in renal cell carcinomas microenvironment: Insights into pathogenic origins and treatment-responsive cellular subgroups

BACKGROUND

Different individuals with renal cell carcinoma (RCC) exhibit substantial heterogeneity in histomorphology, genetic alterations in the proteome, immune cell infiltration patterns, and clinical behavior.

OBJECTIVES

This study aims to use single-nucleus sequencing on ten samples (four normal, three clear cell renal cell carcinoma (ccRCC), and three chromophobe renal cell carcinoma (chRCC)) to uncover pathogenic origins and prognostic characteristics in patients with RCC.

METHODS

By using two algorithms, inferCNV and k-means, the study explores malignant cells and compares them with the normal group to reveal their origins. Furthermore, we explore the pathogenic factors at the gene level through Summary-data-based Mendelian Randomization and co-localization methods. Based on the relevant malignant markers, a total of 212 machine-learning combinations were compared to develop a prognostic signature with high precision and stability. Finally, the study correlates with clinical data to investigate which cell subtypes may impact patients' prognosis.

RESULTS & CONCLUSION

Two main origin tumor cells were identified: Proximal tubule cell B and Intercalated cell type A, which were highly differentiated in epithelial cells, and three gene loci were determined as potential pathogenic genes. The best malignant signature among the 212 prognostic models demonstrated high predictive power in ccRCC: (AUC: 0.920 (1-year), 0.920 (3-year) and 0.930 (5-year) in the training dataset; 0.756 (1-year), 0.828 (3-year), and 0.832 (5-year) in the testing dataset. In addition, we confirmed that LYVE1+ tissue-resident macrophage and TOX+ CD8 significantly impact the prognosis of ccRCC patients, while monocytes play a crucial role in the prognosis of chRCC patients.

Identifying endoplasmic reticulum stress-related genes as new diagnostic and prognostic biomarkers in clear cell renal cell carcinoma

Background

Clear cell renal cell carcinoma (ccRCC) is one of the most common cancers worldwide, and its incidence is increasing every year. Endoplasmic reticulum stress (ERS) caused by protein misfolding has broad and profound effects on the progression and metastasis of various cancers. Accumulating evidence suggests that ERS is closely related to the occurrence and progression of ccRCC. This study aimed to identify ERS-related genes for evaluating the prognosis of ccRCC.

Methods

Transcriptomic expression profiles were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), and clinical data were downloaded from the TCGA. First, the differentially expressed genes (DEGs) were analyzed using the limma package, and the DEGs related to ERS (ERS-DEGs) were identified from the GeneCards database. Second, a function and pathway enrichment analysis and a Gene Set Enrichment Analysis (GSEA) were performed. Third, a protein-protein interaction (PPI) network was constructed to identify the hub genes, and a gene-micro RNA (miRNA) network and gene-transcription factor (TF) network were established using the hub genes. Finally, a least absolute shrinkage and selection operator (LASSO) regression analysis was conducted to establish a diagnostic model, and a Cox analysis was used to analyze the correlations between the expression of the characteristic genes and the clinical characteristics.

Results

We identified 11 signature genes and established a diagnostic model. Further, the Cox analysis results revealed a correlation between the expression levels of the signature genes and the clinical characteristics. Ultimately, five signature genes (i.e., TNFSF13B, APOL1, COL5A3, and CDH5) were found to be associated with a poor prognosis.

Conclusions

This study suggests that TNFSF13B, APOL1, COL5A3, and CDH5 may have potential as prognostic biomarkers in ccRCC and may provide new evidence to support targeted therapy in ccRCC.

Neutrophil depletion reduces interstitial cajal-like cell injury and alleviates inflammation-induced motor dysfunction in guinea-pig gallbladder during acute cholecystitis

Objectives

Gallbladder interstitial Cajal-like cells (ICLCs) are known as some of the players in the complex motility mechanisms affecting gallbladder motility. This study aims to explore the mechanism of guinea-pig gallbladder motility disorders during Acute Cholecystitis (AC), focusing on the relationships between neutrophil alterations, gallbladder ICLCs, and smooth muscle contractility.

Materials and Methods

Forty-eight guinea pigs were randomly divided into four groups: normal, sham, common bile duct ligation (CBDL), and anti-PMN (anti-polymorphonuclear antibody treated +CBDL). Hematoxylin and eosin-stained slides from each gallbladder sample were examined for inflammation, and myeloperoxidase (MPO) activity was evaluated. The contractile response of gallbladder muscle to Ach, CCK-8, and KCl was registered by a tension transducer, and ultrastructure features of ICLCs were observed.

Results

Pretreatment with anti-PMN significantly reduced the circulating neutrophils by 80% and also considerably decreased the gallbladder MPO activity by 52.9% compared with the CBDL group (P<0.05). After adding Ach, CCK-8, and KCl, the contraction ability in CBDL and anti-PMN groups was lower than those of normal and sham groups (P<0.05), and they were increased substantially in the anti-PMN group compared with the CBDL group (P<0.05). Transmission electron microscopy confirmed that the cytoplasm of the neutrophils was full of granules, and neutrophils contacted closely with ICLCs. The ultrastructure of ICLCs in the anti-PMN group was less inflamed and the endoplasmic reticulum was mildly dilated, and cell processes also increased.

Conclusion

Anti-PMN could relieve the ultrastructure injury of ICLCs and alleviate gallbladder dysmotility during AC. Neutrophils may damage gallbladder ICLCs at first followed by dysmotility.

Bladder paraganglioma managed with transurethral holmium laser resection: A case report

RATIONALE

Bladder paraganglioma is characterized by headache, palpitations, hypertension, blurred vision, or sweating during voiding. Transurethral holmium laser resection is a safe and efficacious alternative method for the resection of bladder neoplasms.

PATIENT CONCERNS

A 24-year-old female had a 2-year history of intermittent headaches, palpitation, and sweating during micturition.

DIAGNOSIS

Physical examination revealed a rise in the patient's blood pressure to 180/90 mmHg after micturition. Laboratory examination found that the blood catecholamine metabolites were significantly increased. Abdominal ultrasound and computed tomography (CT) scan indicated a 37 mm × 31 mm paraganglioma situated at the right anterolateral wall of the bladder. A diagnosis of bladder paraganglioma was considered based on a comprehensive evaluation of the physical examination, laboratory examination, ultrasound and computerized tomography scan.

INTERVENTIONS

Preoperative oral administration of a nonselective α-adrenergic receptor antagonist (phenoxybenzamine, 10 mg three times a day,) accompanied by a high-sodium diet and generous fluid intake, was initiated 2 weeks before the surgery to stabilize intraoperative hemodynamics. As the patient was newly married and nulligravid, management with transurethral resection was considered superior to open or partial cystectomy and was selected as the treatment method.

OUTCOMES

Transurethral holmium resection of the bladder paraganglioma was successfully performed with blood loss less than 20 ml and well-controlled intraoperative blood pressure. The 1-year follow-up results demonstrated well-controlled symptoms. Cystoscopy and evaluation of blood catecholamine metabolites revealed no disease recurrence.

LESSONS

Transurethral holmium laser resection is a good alternative approach for the resection of bladder paraganglioma, given its advantages of safety and efficacy.

Pediatric allergic rhinitis with functional gastrointestinal disease: Associations with the intestinal microbiota and gastrointestinal peptides and therapeutic effects of interventions

Children are susceptible to allergic rhinitis (caused by external allergens) accompanied by functional gastrointestinal disease, which seriously affects physical and mental health. Antihistamines and nasal spray hormones are commonly used in clinical treatment, but these drugs often have unsatisfactory efficacy and result in high recurrence rates. Therefore, understanding the pathogenesis of allergic rhinitis with functional gastrointestinal disease and seeking safer treatment and prevention methods is essential. Herein, molecular ecology and immunoassays were used to analyze correlations between pediatric allergic rhinitis with functional gastrointestinal disease and both the intestinal microbiota and gastrointestinal peptide levels. Fifty healthy children (healthy group) and 80 children with allergic rhinitis with functional gastrointestinal disease (case group: evenly divided into a control group (conventional drug therapy) and an intervention group (conventional drug therapy + glutamine+probiotics)), were enrolled. Bifidobacterium and Lactobacillus counts and the gastrin and motilin levels were lower in the case group than in the healthy group, whereas Enterobacter, yeast, and Enterococcus counts and the somatostatin, serotonin, and vasoactive intestinal peptide levels were higher. Post treatment, intestinal microbiota indices, gastrointestinal peptide levels, and intestinal barrier function were better in the intervention group than in the control group (p < 0.05). The intervention group had a significantly higher total therapeutic response rate (95.00%) than the control group (77.50%). The intestinal microbiota was closely associated with gastrointestinal peptide levels. Treatment with glutamine and probiotics regulated these levels, re-established balance in the intestinal microbiota, and restored intestinal barrier function.

The impacts of gene polymorphisms on methotrexate in Chinese psoriatic patients

BACKGROUND

Methotrexate (MTX) is the first-line treatment for psoriasis in China. The metabolic processes of MTX include various proteins and genes. Previous studies have shown that gene polymorphisms had significant impacts on the efficacy of MTX. However, the influence of gene polymorphisms has not been reported in the Chinese psoriatic patients.

OBJECTIVE

The aim of this study was to verify the impacts of candidate genes polymorphisms on the effectiveness of MTX in a Chinese psoriatic population.

METHODS

In this study, we enrolled 259 psoriasis patients from two clinical centres. Each of them received MTX treatment at 7.5-15 mg/week for at least 8 weeks. Patients were stratified as responders and non-responders according to whether the Psoriasis Area and Severity Index score declined more than 75% (PASI75). According to previous reports, 16 single nucleotide polymorphisms (SNPs) were selected and genotyped for each patient using the Sequenom platform. Fisher's exact test, the chi-square test, Mann-Whitney tests and ANOVA analyses were used for statistical analysis.

RESULTS

Among 259 patients, there were 182 males and 77 females, 63 patients with psoriatic arthritis and 196 patients without arthritis phenotype, and the age of all patients ranged from 19 to 70 years (49.7 ± 13.6). The baseline PASI value of patients was 13.8 ± 8.5, and 33.2% of patients achieved a PASI75 response after MTX treatment. Patients carrying the ATP-binding cassette subfamily B member 1 gene (ABCB1) rs1045642 TT genotype were associated with more severe psoriasis skin lesion (P = 0.032). Furthermore, the ABCB1 rs1045642 TT genotype was found to be more frequent in non-responders (P = 0.017), especially in moderate-to-severe patients (P = 0.002) and patients without psoriatic arthritis (P = 0.026) after MTX treatment.

CONCLUSION

We have demonstrated for the first time that polymorphism of the ABCB1 rs1045642 TT genotype is predictive of a worse clinical response of skin lesions to MTX therapy in a Chinese psoriatic population.

Method to retrieve aerosol extinction profiles and aerosol scattering phase functions with a modified CCD laser atmospheric detection system

Vertical distributions of ambient aerosols and their corresponding optical properties are crucial to the assessment of aerosol radiative effects. Traditionally, ambient aerosol phase function is assumed as a constant of input parameter in the retrieval of the vertical distribution of aerosol optical characteristics from remote sensing measurements (e.g. lidar or camera-laser based instruments). In this work, sensitivity studies revealed that using constant aerosol phase function assumptions in the algorithm would cause large uncertainties. Therefore, an improved retrieval method was established to simultaneously measure ambient aerosol scattering phase functions and aerosol scattering function profiles with a modified charge-coupled device-laser aerosol detection system (CLADS), which are then combined to yield vertical profiles of aerosol extinction coefficients. This method was applied and evaluated in a comprehensive field campaign in the North China Plain during January 2016. The algorithm showed robust performance and was able to capture temporal variations in ambient aerosol scattering phase functions and aerosol scattering function profiles. Aerosol extinction coefficients derived with simultaneously measured aerosol phase functions agreed well with in-situ measurements, indicating that uncertainties in the retrieval of aerosol extinction vertical profiles have been significantly reduced by using the proposed method with the modified CLADS. The advantage of this modified CLADS is that it can accomplish these aerosol measurements independent of other supplementary instruments. Benefiting from its low cost and high spatial resolution (∼1 m on average) in the boundary layer, this measurement system can play an important role in the research of aerosol vertical distributions and its impacts on environmental and climatic studies.

Amplicon-based next-generation sequencing of plasma cell-free DNA for detection of driver and resistance mutations in advanced non-small cell lung cancer

Background

Genomic analysis of plasma cell-free DNA is transforming lung cancer care; however, available assays are limited by cost, turnaround time, and imperfect accuracy. Here, we study amplicon-based plasma next-generation sequencing (NGS), rather than hybrid-capture-based plasma NGS, hypothesizing this would allow sensitive detection and monitoring of driver and resistance mutations in advanced non-small cell lung cancer (NSCLC).

Patients and methods

Plasma samples from patients with NSCLC and a known targetable genotype (EGFR, ALK/ROS1, and other rare genotypes) were collected while on therapy and analyzed blinded to tumor genotype. Plasma NGS was carried out using enhanced tagged amplicon sequencing of hotspots and coding regions from 36 genes, as well as intronic coverage for detection of ALK/ROS1 fusions. Diagnostic accuracy was compared with plasma droplet digital PCR (ddPCR) and tumor genotype.

Results

A total of 168 specimens from 46 patients were studied. Matched plasma NGS and ddPCR across 120 variants from 80 samples revealed high concordance of allelic fraction (R2 = 0.95). Pretreatment, sensitivity of plasma NGS for the detection of EGFR driver mutations was 100% (30/30), compared with 87% for ddPCR (26/30). A full spectrum of rare driver oncogenic mutations could be detected including sensitive detection of ALK/ROS1 fusions (8/9 detected, 89%). Studying 25 patients positive for EGFR T790M that developed resistance to osimertinib, 15 resistance mechanisms could be detected including tertiary EGFR mutations (C797S, Q791P) and mutations or amplifications of non-EGFR genes, some of which could be detected pretreatment or months before progression.

Conclusions

This blinded analysis demonstrates the ability of amplicon-based plasma NGS to detect a full range of targetable genotypes in NSCLC, including fusion genes, with high accuracy. The ability of plasma NGS to detect a range of preexisting and acquired resistance mechanisms highlights its potential value as an alternative to single mutation digital PCR-based plasma assays for personalizing treatment of TKI resistance in lung cancer.

LncRNA ZNF667-AS1 inhibits inflammatory response and promotes recovery of spinal cord injury via suppressing JAK-STAT pathway

OBJECTIVE

The aim of this study was to explore the role of lncRNA ZNF667-AS1 in the recovery of spinal cord injury (SCI), and to investigate its underlying mechanism.

MATERIALS AND METHODS

Mice were randomly assigned to the SCI group, the sham group and the lncRNA ZNF667-AS1 group, with 10 mice in each group. With Infinite Horizon device at a dose of 80 Kdyn, mice in the SCI group and the lncRNA ZNF667-AS1 group experienced SCI by an acute hit on the C5 spinous process. Before animal procedures, mice in the lncRNA ZNF667-AS1 group were additionally injected with overexpression lentivirus of lncRNA ZNF667-AS1. On the contrary, mice in the sham group only received laminectomy. After successful construction of the SCI model in mice, grip strength was accessed. LncRNA ZNF667-AS1 expression in spinal cord tissues before and after SCI was detected by quantitative Real Time-Polymerase Chain Reaction (qRT-PCR), respectively. Meanwhile, the protein expression levels of relative genes in Janus Kinase-signal transducer and activator of transcription (JAK-STAT) pathway were detected by Western blot.

RESULTS

Grip strength of forelimb in the SCI group recovered significantly slower than that of the sham group. With the prolongation of SCI, the expression of lncRNA ZNF667-AS1 was gradually decreased. However, the expression levels of JAK2, STAT3 and iNOS were upregulated in a time-dependent manner. In addition, mice in the lncRNA ZNF667-AS1 group presented remarkable grip strength recovery of forelimb after SCI.

CONCLUSIONS

LncRNA ZNF667-AS expression is gradually downregulated after SCI. Meanwhile, it inhibits the inflammatory response and promotes SCI recovery via suppressing the JAK-STAT pathway.

Smart identification of psoriasis by images using convolutional neural networks: a case study in China

BACKGROUND

Psoriasis is a chronic inflammatory skin disease, which holds a high incidence in China. However, professional dermatologists who can diagnose psoriasis early and correctly are insufficient in China, especially in the rural areas. A smart approach to identify psoriasis by pictures would be highly adaptable countrywide and could play a useful role in early diagnosis and regular treatment of psoriasis.

OBJECTIVES

Design and evaluation of a smart psoriasis identification system based on clinical images (without relying on a dermatoscope) that works effectively similar to a dermatologist.

METHODS

A set of deep learning models using convolutional neural networks (CNNs) was explored and compared in the system for automatic identification of psoriasis. The work was carried out on a standardized dermatological dataset with 8021 clinical images of 9 common disorders including psoriasis along with full electronic medical records of patients built over the last 9 years in China. A two-stage deep neural network was designed and developed to identify psoriasis. In the first stage, a multilabel classifier was trained to learn the visual patterns for each individual skin disease. In the second stage, the output of the first stage was utilized to distinguish psoriasis from other skin diseases.

RESULTS

The area under the curve (AUC) of the two-stage model reached 0.981 ± 0.015, which outperforms a single-stage model. And, the classifier showed superior performance (missed diagnosis rate: 0.03, misdiagnosis rate: 0.04) than 25 Chinese dermatologists (missed diagnosis rate: 0.19, misdiagnosis rate: 0.10) in the diagnosis of psoriasis on 100 clinical images.

CONCLUSIONS

Using clinical images to identify psoriasis is feasible and effective based on CNNs, which also builds a solid technical base for smart care of skin diseases especially psoriasis using mobile/tablet applications for teledermatology in China.

A microRNA expression signature as a predictor of survival for colon adenocarcinoma

Colon cancer is a major cause of cancer mortality worldwide and most colon cancers are adenocarcinoma. MicroRNA (miRNA) expression signature has been shown to be able to predict progression and prognosis of various cancers. The aim of our study was to explore a novel signature of microRNA expression for predicting survival of colon adenocarcinoma patients. By analyzing the miRNA expression profiles and clinical information of 329 colon adenocarcinoma patients derived from The Cancer Genome Atlas database. 129 miRNAs were identified to be expressed differentially between the cancer and adjacent tissues. Among them, 27 miRNAs were found to be associated with the corresponding clinical characteristics of the patients. Furthermore, 7 miRNAs (let-7a-2, mir-32, mir-181a-1, mir-197, mir-328, mir-505 and mir-652) were found to be significantly correlated with the patient survival. The risk established by the 7-miRNA signature we built was proved be an independent prognostic factor (Hazard ratio [HR] = 2.048; 95% CI = 1.144-3.664; p, 0.016). In summary, our study identified miRNAs correlated with progression and prognosis of colon adenocarcinoma and built a 7-microRNA expression signature for prediction of the survival of the patients with colon adenocarcinoma.

Cytotoxic effect of oxaloacetate on HepG2-human hepatic carcinoma cells via apoptosis and ROS accumulation

Oxaloacetate (OA) is one of the intermediates of the Krebs cycle. In addition to its role in energy production, OA may have other effects on the cell. We report here that OA could have a cell type dependent cytotoxic effect on the human hepatic carcinoma cell line HepG2 through induction of apoptosis and reactive oxygen species (ROS) accumulation. In our study, OA decreased the viability and colony formation of HepG2 cells and induced cell death. Caspase-3 activity was increased, the pro-apoptotic protein Bax was up-regulated, and the anti-apoptotic protein Bcl-2 was down-regulated in OA-treated HepG2 cells indicating that apoptosis through the intrinsic pathway was involved in the cell death. The ROS level in OA-treated HepG2 cells was increased. The anti-oxidant N-acetylcysteine (NAC) and glutathione (GSH) prevented the OA-induced decrease in cell but did not alter the enhanced apoptotic Bax/Bcl-2 mRNA ratio. These results suggest that the OA-induced apoptosis of HepG2 cell is not driven by oxidative damage and at least two distinct mechanisms, one mediated by ROS and one involving apoptosis, result in the cytotoxic effects of OA on HepG2 cells. These studies expand the biological functional repertoire of OA and provide a mechanism by which hepatocellular carcinoma may be targeted by OA.