STAB2: an updated spatio-temporal cell atlas of the human and mouse brain.

The brain is constituted of heterogeneous types of neuronal and non-neuronal cells, which are organized into distinct anatomical regions, and show precise regulation of gene expression during development, aging and function. In the current database release, STAB2 provides a systematic cellular map of the human and mouse brain by integrating recently published large-scale single-cell and single-nucleus RNA-sequencing datasets from diverse regions and across lifespan. We applied a hierarchical strategy of unsupervised clustering on the integrated single-cell transcriptomic datasets to precisely annotate the cell types and subtypes in the human and mouse brain. Currently, STAB2 includes 71 and 61 different cell subtypes defined in the human and mouse brain, respectively. It covers 63 subregions and 15 developmental stages of human brain, and 38 subregions and 30 developmental stages of mouse brain, generating a comprehensive atlas for exploring spatiotemporal transcriptomic dynamics in the mammalian brain. We also augmented web interfaces for querying and visualizing the gene expression in specific cell types. STAB2 is freely available at https://mai.fudan.edu.cn/stab2.

Third-generation PacBio sequencing to explore gut bacteria and gender in colorectal cancer.

BACKGROUND: Gut bacteria have an important influence on colorectal cancer (CRC). The differences of gut bacteria between genders have been the hot spots. OBJECTIVE: To analyze the relationship between gut bacteria and gender differences in patients with CRC. METHODS: A total of 212 patients with CRC and 212 healthy volunteers were recruited. The subjects' fecal samples were obtained, and the fecal microorganisms were analyzed by the third-generation sequencing PacBio. The composition of gut bacteria was analyzed. Linear discriminant analysis Effect Size (LEfSe) was used to analyze the differences in gut bacteria. Pearson coefficient was used to calculate the correlation between differential bacteria. CRC risk prediction models were used to rank the importance of effective differential bacteria. RESULTS: Escherichia flexneri and Phocaeicola vulgatus were the most frequent bacteria in both male and female CRC patients. Bacteroides, Verrucomicrobia and Akkermansiaceae were highly enriched in male CRC group, while Bacteroidetes, Phocaeicola and Tissierellales were highly enriched in female CRC group. Peptostreptococcus anaerobius and Phocaeicola vulgatus were important CRC related bacteria in males and females, respectively. Peptostreptococcus anaerobius was the most important characteristic bacterium of males (AUC = 0.951), and the sensitivity and specificity of the discovery set were 78.74 % and 93.98 %, respectively. Blautia stercoris was the most important characteristic bacterium of females (AUC = 0.966), and the sensitivity and specificity of the discovery set were 90.63 % and 90.63 %, respectively. CONCLUSION: Gut bacteria varied in different genders. Therefore, gender should be considered when gut bacteria are applied in the diagnose and prevention of CRC.

Analysis of clinical characteristics of mismatch repair status in colorectal cancer: a multicenter retrospective study.

BACKGROUND: Microsatellite instability (MSI) caused by DNA mismatch repair (MMR) deficiency is of great significance in the occurrence, diagnosis and treatment of colorectal cancer (CRC). AIM: This study aimed to analyze the relationship between mismatch repair status and clinical characteristics of CRC. METHODS: The histopathological results and clinical characteristics of 2029 patients who suffered from CRC and underwent surgery at two centers from 2018 to 2020 were determined. After screening the importance of clinical characteristics through machine learning algorithms, the patients were divided into deficient mismatch repair (dMMR) and proficient mismatch repair (pMMR) groups based on the immunohistochemistry results and the clinical feature data between the two groups were observed by statistical methods. RESULTS: The dMMR and pMMR groups had significant differences in histologic type, TNM stage, maximum tumor diameter, lymph node metastasis, differentiation grade, gross appearance, and vascular invasion. There were significant differences between the MLH1 groups in age, histologic type, TNM stage, lymph node metastasis, tumor location, and depth of invasion. The MSH2 groups were significantly different in age. The MSH6 groups had significant differences in age, histologic type, and TNM stage. There were significant differences between the PMS2 groups in lymph node metastasis and tumor location. CRC was dominated by MLH1 and PMS2 combined expression loss (41.77%). There was a positive correlation between MLH1 and MSH2 and between MSH6 and PMS2 as well. CONCLUSIONS: The proportion of mucinous adenocarcinoma, protruding type, and poor differentiation is relatively high in dMMR CRCs, but lymph node metastasis is rare. It is worth noting that the expression of MMR protein has different prognostic significance in different stages of CRC disease.

Classification of Colorectal Cancer Subtypes Based on Endoplasmic Reticulum Stress.

INTRODUCTION: Endoplasmic reticulum stress (ERS) is associated with the occurrence and development of colorectal cancer (CRC). METHODS: One thousand nine CRC samples and 3 ERS gene sets from GEO database were used to screen and validate genes related to stage and prognosis of CRC. Twenty thousand five hundred thirty samples from the TCGA database validated the ERS genes related to prognosis. PPI network construction and coexpression analysis were used to investigate the correlation of genes. ConsensusClusterPlus analysis was used to classify CRC subtypes. Cox regression and the LASSO algorithm were used to screen ERS genes related to prognosis. HE staining, immunohistochemical staining, and RT-qPCR of 50 owner-central samples were used to verify the genes. The ERscore model was constructed based on the ERS genes related to prognosis. The nomogram model was used to verify that different subtypes of CRC patients have different prognosis. RESULTS: Fifty ERS differentially expressed genes related to CRC stage and 8 ERS model genes related to prognosis were screened. Three subtypes of CRC were classified based on the former 50 genes. The clinical characteristics were significantly different among the subtypes. The ERscore model was constructed based on the latter 8 genes, and its accuracy was verified by clinical samples. Finally, the nomogram was constructed based on ERscore, age, and CRC stage, and the accuracy of the nomogram prediction was verified. CONCLUSION: ERS-related genes can be used as classification criteria for CRC, and the related clinical characteristics of different CRC subtypes are different.

Mitochondria-associated endoplasmic reticulum membrane: Overview and inextricable link with cancer.

The mitochondrial-associated membrane (MAM) is a physical platform that facilitates communication between the endoplasmic reticulum (ER) and mitochondria. It is enriched with many proteins and enzymes and plays an important role in the regulation of several fundamental physiological processes, such as calcium (Ca2+ ) transfer, lipid synthesis, cellular autophagy and ER stress. Accumulating evidence suggests that oncogenes and suppressor genes are present at the ER-mitochondrial contact site, and their alterations can affect Ca2+ flux, lipid homeostasis, and the dysregulation of mitochondrial dynamics, thereby influencing the fate of cancer cells. Understanding the fundamental role of MAM-resident proteins in tumorigenesis could support the search for novel therapeutic targets in cancer. In this review, we summarize the basic structure of MAM and the core functions of MAM-resident proteins in tumorigenesis. In addition, we discuss the mechanisms by which natural compounds promote cancer cell apoptosis from the perspective of ER stress.

Pancreatic follicular dendritic cell sarcoma: a rare case report and systematic literature review of 7 cases.

INTRODUCTION: Pancreatic follicular dendritic cell sarcoma (FDCS) is an exceptionally rare and low-to-moderate malignancy, with only seven reported cases to date. Clinical diagnosis of FDCS is challenging due to the lack of distinct biological and radiographic features. CASE PRESENTATION: A 67-year-old woman presented to the hospital with a 4-day history of severe abdominal pain. Imaging studies (CT and MRI) revealed a large cystic mass located at the tail of the pancreas, which was suspected to be myeloid sarcoma (MS) based on EUS and CT-guided pancreatic puncture. Postoperative pathology and immunohistochemistry confirmed the diagnosis of pancreatic FDCS. After the diagnosis was confirmed, the patient received postoperative chemotherapy with the CHOP regimen. At 11 months of follow-up, there was no evidence of recurrence. Seven published cases have been reviewed to comprehensively summarize the clinical characteristics, diagnosis, and treatment options of FDCS. CONCLUSION: While imaging can be useful in detecting pancreatic FDCS, it should be interpreted with caution as it can be challenging to differentiate from other pancreatic tumors. Pathology and immunohistochemistry are considered the gold standard for diagnosis, with CD21, CD23, and CD35 being specific tumor cell markers. However, preoperative diagnosis of pancreatic FDCS remains difficult, and the pancreatic puncture may further increase the risk of misdiagnosis. The disease is highly prone to recurrence and metastasis, and surgery is the preferred method for both diagnosis and treatment of localized disease.

Long-term variation and evaluation of air quality across Hong Kong.

Study of Air Quality Objectives (AQOs) and long-term changes of air pollution plays a decisive role in formulating and refining pollution control strategies. In this study, 10-year variations of six major air pollutants were analyzed at seven monitoring sites in Hong Kong. The continuous decrease of annual averaged concentrations of NO2, SO2, CO, PM2.5 and PM10 and numbers of days with severe pollution conditions validated the efficiency of the series of air pollution control schemes implemented by the Hong Kong government. However, there is still a big gap to meet the ultimate targets described by the World Health Organization. Besides, the concentration of O3 at roadside and urban stations increased by 135% ± 25% and 37% ± 18% from 2011 to 2020, respectively, meanwhile the highest 8 hr averaged O3 concentration was observed as 294 µg/m3 at background station in 2020, which pointed out the increasing ozone pollution in Hong Kong. There was a great decrease in the annual times of air quality health index (AQHI) laying in "high", "very high" and "serious" categories from 2011 to 2020 with the decrease rate of 89.70%, 91.30% and 89.74% at roadside stations, and 79.03%, 95.98% and 72.73% at urban stations, respectively. Nevertheless, the number of days categorized as "high" or above at roadside station was twice more than that in the urban station during the past ten years. Thus, more policies and attentions should be given to the roadside air quality and its adverse health effect to pedestrians on street.

Structure-Based design of Marine-derived Meridianin C derivatives as glycogen synthase kinase 3ß inhibitors with improved oral bioavailability: From aminopyrimidyl-indoles to the sulfonyl analogues.

Glycogen synthase kinase 3ß (GSK-3ß) has become an attractive target for the treatment of diabetes. Compound I is an indole-based GSK-3ß inhibitor designed from the Meridianin C, a marine natural product (MNP) isolated from Aplidium meridianum. However, this compound has a moderate inhibitory activity toward GSK-3ß (IC50 = 24.4 µM), moderate glucose uptake (38%), and especially, a low oral bioavailability (F = 11.4%). In the present study, applying the structure-based design strategy, a series of derivatives modified on the indole moiety were synthesized based on the lead compound I, followed by evaluating their cytotoxic activity, antihyperglycemic activity, and kinase inhibitory activity. Among this series, compound 6x with a sulfonyl group displayed the highest glucose uptake (83.5%) in muscle L6 cells, showing much higher inhibitory activity against GSK-3ß (IC50 = 5.25 µM). Molecular docking indicated that compound 6x was properly inserted into the ATP-binding binding pocket of GSK-3ß with a higher docking score (-8.145 kcal/mol) compared with that of compound I (-6.950 kcal/mol), interpreting the higher kinase inhibitory activity toward GSK-3ß. Remarkably, compound 6x showed favorable drug-like properties, including significantly better oral bioavailability (F = 47.4%) and no two-week acute toxicity at a dose of 1 g/kg. Our findings suggest that these MNP-derived sulfonyl indole derivatives could be used as lead compounds for the development of anti-hyperglycemic drugs.

Role of long noncoding RNA taurine-upregulated gene 1 in cancers.

Long non-coding RNAs (lncRNAs) are a group of non-protein coding RNAs with a length of more than 200 bp. The lncRNA taurine up-regulated gene 1 (TUG1) is abnormally expressed in many human malignant cancers, where it acts as a competitive endogenous RNA (ceRNA), regulating gene expression by specifically sponging its corresponding microRNAs. In the present review, we summarised the current understanding of the role of lncRNA TUG1 in cancer cell proliferation, metastasis, angiogenesis, chemotherapeutic drug resistance, radiosensitivity, cell regulation, and cell glycolysis, as well as highlighting its potential application as a clinical biomarker or therapeutic target for malignant cancer. This review provides the basis for new research directions for lncRNA TUG1 in cancer prevention, diagnosis, and treatment.

Structural-Based Optimizations of the Marine-Originated Meridianin C as Glucose Uptake Agents by Inhibiting GSK-3ß.

Glycogen synthase kinase 3ß (GSK-3ß) is a widely investigated molecular target for numerous diseases, and inhibition of GSK-3ß activity has become an attractive approach for the treatment of diabetes. Meridianin C, an indole-based natural product isolated from marine Aplidium meridianum, has been reported as a potent GSK-3ß inhibitor. In the present study, applying the structural-based optimization strategy, the pyrimidine group of meridianin C was modified by introducing different substituents based on the 2-aminopyrimidines-substituted pyrazolo pyridazine scaffold. Among them, compounds B29 and B30 showed a much higher glucose uptake than meridianin C (<5%) and the positive compound 4-benzyl-2-methyl-1,2,4-thiadiazolidine-3,5-dione (TDZD-8, 16%), with no significant toxicity against HepG2 cells at the same time. Furthermore, they displayed good GSK-3ß inhibitory activities (IC50 = 5.85; 24.4 µM). These results suggest that these meridianin C analogues represent novel lead compounds with therapeutic potential for diabetes.

Immune-related genes in tumor-specific CD4+ and CD8+ T cells in colon cancer.

BACKGROUND: Immune escape is an immunological mechanism underlying tumorigenesis, and T cells play an important role in this process. In this study, immune-related genes were evaluated in tumor-infiltrating CD4+ and CD8+ T cells in colon cancer. METHODS: ESTIMATE was used to calculate stromal and immune scores for tumor datasets downloaded from The Cancer Genome Atlas-Colon Cancer (COAD). Differentially expressed genes (DEGs) between samples with high and low stromal and immune scores were screened, followed by a functional enrichment analysis of the overlapping DEGs. The DEGs related to CD4+ and the CD8+ T cells were then screened. Predicted miRNA-mRNA and lncRNA-miRNA pairs were used to construct a competing endogenous RNA (ceRNA) network. Furthermore, chemical-gene interactions were predicted for genes in the ceRNA network. Kaplan-Meier survival curves were also plotted. RESULTS: In total, 83 stromal-related DEGs (5 up-regulated and 78 down-regulated) and 1270 immune-related DEGs (807 up-regulated and 293 down-regulated genes) were detected. The 79 overlapping DEGs were enriched for 39 biological process terms. Furthermore, 79 CD4+ T cell-related genes and 8 CD8+ T cell-related genes, such as ELK3, were screened. Additionally, ADAD1 and DLG3, related to CD4+ T cells, were significantly associated with the prognosis of patients with colon cancer. The chr22-38_28785274-29,006,793.1-miR-106a-5p-DDHD1 and chr22-38_28785274-29,006,793.1-miR-4319-GRHL1 axes obtained from CD4+ and CD8+ T cell-related ceRNAs were identified as candidates for further studies. CONCLUSION: ELK3 is a candidate immune-related gene in colon cancer. The chr22-38_28785274-29,006,793.1-miR-106a-5p-DDHD1 and chr22-38_28785274-29,006,793.1-miR-4319-GRHL1 axes may be related to CD4+ and CD8+ T cell infiltration in colon cancer.

Biological significance of piRNA in liver cancer: a review.

Liver cancer is one of the most common and deadly cancers in the world. In recent years, non-coding RNA has been a hot topic in liver cancer research. piRNAs (PIWI-interacting RNAs) are a new type of small non-coding RNA, which are formed by the PIWI proteins interacting with RNA. The latest research shows that piRNA and PIWI proteins are abnormally expressed in various cancers, including pancreatic, colorectal, breast, etc. piRNA plays an important regulatory role in liver cancer. In this review, we discuss the biological function of piRNAs and new progress in the development of liver cancer, and new targets and ideas for piRNA and PIWI proteins in the diagnosis and treatment of liver cancer.

Nutrition and metabolism status alteration in advanced hepatocellular carcinoma patients treated with anti-PD-1 immunotherapy.

PURPOSE: The aim of this study was to evaluate the nutrition and metabolism status alteration during immunotherapy in advanced hepatocellular carcinoma (HCC) patients. METHODS: Patients with advanced HCC who participated in the clinical trials of single-agent anti-PD-1 immunotherapy or sorafenib were retrospectively included. We analyzed self-comparison of the nutritional and metabolic indices of patients in the anti-PD-1 and sorafenib treatment group. We conducted mutual-comparison of the mentioned indices between the disease progression group and disease control group among anti-PD-1 treatment patients. We further analyzed those indices with statistical differences by partial correlation and survival analysis. RESULTS: Both self-comparison before and after treatment in the anti-PD-1 group and mutual-comparison of disease progression and the control group showed significant differences in multiple indices, but we did not observe significant differences in the sorafenib group. Strikingly, albumin (ALB)/prognostic nutritional index (PNI, calculated by serum albumin and lymphocyte count) decreased distinctly in the immunotherapy disease progression group patients. However, changes in ALB/PNI were not significant in disease progression patients from the sorafenib group or in the disease control patients with immunotherapy. Partial correlation analysis suggested that ALB and PNI were positively correlated with the efficacy of immunotherapy. Furthermore, survival analysis showed that the median progression-free survival and median overall survival of patients in the ALB/PNI decreased group were significantly shorter than those of patients from the ALB/PNI increased group. CONCLUSION: Anti-PD-1 immunotherapy might alter the nutritional and metabolic status in advanced HCC patients. We also should pay attention to the nutritional and metabolic status of patients when drug resistance is detected.

Follow on-based optimization of the biphenyl-DAPYs as HIV-1 nonnucleoside reverse transcriptase inhibitors against the wild-type and mutant strains.

The present work follows our preliminary discovery of biphenyl diarylpyrimidines (DAPYs) as HIV-1 nonnucleoside reverse transcriptase inhibitors. Further structural optimization of biphenyl-DAPYs led to the identification of a new series of biphenyl-substituted thiophene[3,2-d]pyrimidine analogues by a scaffold-hopping strategy. Biological evaluation of this series showed that these compounds possessed up to single-digit nanomolar potency (EC50 = 7.8-526.2 nM) and prominently low toxicity (CC50 = 18.5-280.8 µM) against wild-type (WT) HIV-1-infected cells. Furthermore, the results also demonstrated that compounds 29-32 exhibited high, broad-spectrum antiviral effects against clinically observed HIV-1 mutants. Specifically, compound 30, which had the highest selectivity index (SI = 16094) and the best anti-reverse transcriptase ability (IC50 = 39 nM), displayed marked inhibitory activity (EC50 = 13.5, 9.4, 17.0, 52.0, and 58.2 nM) against WT, K103N, E138K, L100I, Y181C mutants and moderate activity against double mutants. This study provides important avenues for the further design of HIV-1 inhibitors.

Secreted frizzled-related protein 1 (SFRP1) gene methylation changes in the human lung adenocarcinoma cells treated with L-securinine.

Lung cancer remains the leading cause of cancer-related death worldwide. It is important to explore the biomarkers of diagnosis and prognosis in lung cancer. To evaluate the cytotoxicity of L-securinine and the expression and methylation of secreted frizzled-related proteins (SFRPs) genes in the human lung adenocarcinoma cells, cell counting kit-8 (CCK-8) assay was used to assess the proliferation of lung adenocarcinoma cells treated with L-securinine. Quantitative real-time PCR (qRT-PCR) and bisulfite sequencing PCR were used to detect the expression and the DNA methylation of SFRPs genes, respectively. L-securinine inhibited the proliferation of lung adenocarcinoma cells and induced the upregulation of SFRP1 gene expression and the methylation changes at CpG sites in the SFRP1 promoter region. L-securinine was a potential agent in the treatment of lung cancer by upregulation of SFRP1 gene expression and changing the SFRP1 gene methylation.

Novel amide-functionalized chloramphenicol base bifunctional organocatalysts for enantioselective alcoholysis of meso-cyclic anhydrides.

A family of novel chloramphenicol base-amide organocatalysts possessing a NH functionality at C-1 position as monodentate hydrogen bond donor were developed and evaluated for enantioselective organocatalytic alcoholysis of meso-cyclic anhydrides. These structural diversified organocatalysts were found to induce high enantioselectivity in alcoholysis of anhydrides and was successfully applied to the asymmetric synthesis of (S)-GABOB.

Tongue images and tongue coating microbiome in patients with colorectal cancer.

BACKGROUND: Tongue diagnosis, as a unique method of traditional Chinese medicine (TCM), discriminates physiological functions and pathological conditions by observing the changes of the tongue coating. AIMS: To evaluate the differences of tongue images and tongue coating microbiome between patients with colorectal cancer and healthy people. METHODS: The tongue diagnostic information acquisition system was used to photograph the tongue images and analyze the thickness of the tongue coatings in patients with colorectal cancer and healthy people. The next-generation sequencing technology was used to determine the V2-V4 hypervariable region of 16S rDNA to investigate the microbial community structure and diversity on the tongue coating. RESULTS: The tongue coatings in patients with colorectal cancer were obvious thickening compared with tongue images in healthy people. The microbial community structure on the tongue coating was different between patients with colorectal cancer and healthy people. CONCLUSION: Tongue diagnosis may provide important leads towards novel microbiome-related diagnostic tools and tongue coating microbiome may be a novel biomarker for characterizing patient with colorectal cancer.

Antiproliferative activity and apoptosis-inducing mechanism of L-securinine on human breast cancer MCF-7 cells.

Natural products have been discovered to be valuable sources of antitumor drugs. L-Securinine is a natural product extracted from the leaves or roots of Securinega suffruticosa Pall Rehd. The current study was done to investigate the molecular mechanisms of antitumor effects of L-securinine. The inhibitory activities of L-securinine on human breast cancer MCF-7 cells were studied in vitro by a Cell Counting Kit-8(cck8) assay. Flow cytometry was used to analyze the apoptotic ratio and cell cycle distribution of control and treated MCF-7 cells with L-Securinine. Real-time quantitative PCR was conducted to evaluate expression levels of apoptosis related genes P53, Bax, Bcl-2, Mtor, P70s6k. L-Securinine exhibited remarkable antiproliferation activities on MCF-7 cells in dose- and time-dependent manner (24, 48 and 72 h of incubation). A 48 h exposure to L-securinine at a concentration ranging from 0 to 40 microM resulted in a significant increase in apoptotic ratio. At both low and high concentrations, L-securinine preferably perturbed the cell cycle in MCF-7 cells by arrest of G1 phase. These results were further confirmed by the increased expression of bax, p53 and the decreased expression of bcl-2, mtor, p70s6k in a dose-dependent manner. In summary, these findings suggest that L-securinine has an anti-tumor effect against MCF-7 cells and could be further exploited as a potential lead in antitumor drug development.