Establishment of a new molecular subtyping and prognostic signature with m6A/m5C/m1A/m7G regulatory genes for hepatocellular carcinoma.

Background: RNA modification, including m6A, m5C, m1A, and m7G, participated in tumor progress. Therefore, the purpose of the present study was to explore the role of m6A/m5C/m1A/m7G regulatory genes in the prognosis and tumor microenvironment (TME) for hepatocellular carcinoma (HCC). Methods: 71 m6A/m5C/m1A/m7G regulatory genes expression for HCC was detected, differentially expressed genes were screened, and molecular forms were classified by unsupervised consensus clustering. Cox regression and the Least Absolute Shrinkage and Selection Operator (LASSO) analysis were applied to establish a prognostic signature. Time-dependent receiver operating characteristic (ROC) curves were evaluated for clinical effectiveness and accuracy of the prognostic hazard model. In cluster subtypes and risk models, the differences in prognosis, immune cell infiltration, immune checkpoint, immunotherapy, and drug sensitivity between different subtypes were evaluated. Results: HCC patients were classified into two clusters (cluster 1 and cluster 2) according to the expression of 71 m6A/m5C/m1A/m7G regulatory genes. Cluster 1 had a poor prognosis and different immune cell infiltration. Cluster 1 had higher immune checkpoint expression and TIDE score than cluster 2. Subsequently, we construct a five-gene prognostic model of m6A/m5C/m1A/m7G regulatory genes (YTHDF2, YTHDF1,YBX1, TRMT61A, TRMT10C). The Kaplan-Meier and ROC curve analysis showed that the prognostic signature exhibited good predictability. The risk score was considered an independent poor prognostic index. The high-risk group had higher immune checkpoint expression and higher TIDE scores. 5-Fluorouracil, docetaxel, doxorubicin, etoposide, gemcitabine, paclitaxel, sorafenib, and vinblastine were more suitable for high-risk patients. ECM receptor interaction, cell cycle, and Leishmania infection were enriched in the high-risk group. Conclusion: The clustering subgroups and prognostic model of m6A/m5C/m1A/m7G regulatory genes were linked with bad prognosis and TME for HCC, and had the potential to be a novel tool to evaluate the outcomes of HCC patients.

Upregulated CANT1 is correlated with poor prognosis in hepatocellular carcinoma.

BACKGROUND: CANT1, as calcium-activated protein nucleotidase 1, is a kind of phosphatase. It is overexpressed in some tumors and related to poor prognosis, but few studies explore its function and carcinogenic mechanism in hepatocellular carcinoma (HCC). METHODS: The expression of CANT1 mRNA and protein was analyzed by the Cancer Genome Atlas (TCGA) database and immunohistochemistry(IHC) staining. The relationship between CANT1 expression and clinicopathology was evaluated by various public databases. The receiver operating characteristic (ROC) curve was used to assess the diagnostic accuracy of CANT1 by the area under curve (AUC). Univariate, multivariate Cox regression and Kaplan-Meier curves were applied to evaluate the predictive value of CANT1 on the prognosis of HCC. Methsurv was used to analyze gene changes and DNA methylation, and its impact on prognosis. The enrichment analysis of DEGs associated with CANT1 revealed the biological process of CANT1 based on Gene Set Enrichment Analysis (GSEA). The relationship between immune cell infiltration level and CANT1 expression in HCC was investigated using the single-sample GSEA (ssGSEA) method and the Tumor Immune Estimation Resource (TIMER) database. Finally, the association between CANT1 and immune checkpoints and drug sensitivity was also analyzed. RESULTS: CANT1 was highly expressed in 22 cancers, including HCC, and CANT1 overexpression in HCC was confirmed by IHC. The expression of CANT1 was correlated with clinical features, such as histologic grade. Highly expressed CANT1 caused poor overall survival (OS) of HCC patients. Univariate and multivariate regression analysis suggested that CANT1 was an independent prognostic marker. Of the 31 DNA methylation at CpG sites, three CpG sites were associated with the prognosis of HCC. GSEA indicated that CANT1 was mainly involved in the cell cycle, DNA replication, and etc. Moreover, CANT1 expression was correlated with immune cell infiltration and independently associated with the prognosis of HCC patients. Finally, CANT1 expression was correlated with most immune checkpoints and drug sensitivity. CONCLUSION: CANT1 may be a latent oncogene of HCC, and associated with immune cells and immune checkpoints, which may assist in HCC treatment.

Quantifying the spatial spillover effects of non-pharmaceutical interventions on pandemic risk.

BACKGROUND: Non-pharmaceutical interventions (NPIs) implemented in one place can affect neighboring regions by influencing people's behavior. However, existing epidemic models for NPIs evaluation rarely consider such spatial spillover effects, which may lead to a biased assessment of policy effects. METHODS: Using the US state-level mobility and policy data from January 6 to August 2, 2020, we develop a quantitative framework that includes both a panel spatial econometric model and an S-SEIR (Spillover-Susceptible-Exposed-Infected-Recovered) model to quantify the spatial spillover effects of NPIs on human mobility and COVID-19 transmission. RESULTS: The spatial spillover effects of NPIs explain [Formula: see text] [[Formula: see text] credible interval: 52.8-[Formula: see text]] of national cumulative confirmed cases, suggesting that the presence of the spillover effect significantly enhances the NPI influence. Simulations based on the S-SEIR model further show that increasing interventions in only a few states with larger intrastate human mobility intensity significantly reduce the cases nationwide. These region-based interventions also can carry over to interstate lockdowns. CONCLUSIONS: Our study provides a framework for evaluating and comparing the effectiveness of different intervention strategies conditional on NPI spillovers, and calls for collaboration from different regions.

Clinicopathological Features of Hepatocellular Carcinoma with Metabolic Risk Factors.

Objective: This study aims to explore the pathological characteristics of metabolic-related hepatocellular carcinoma (HCC) and its correlation with metabolic factors. Methods: Fifty-one patients with liver cancer of unknown causes were enrolled. Biopsy of the liver and staining of the liver tissues with hematoxylin-eosin as well as special and immunohistochemical stains were performed. The histological subtypes of HCC were diagnosed based on the WHO Classification of Malignant Hepatocellular Tumors. The NAFLD activity score system was adopted for assessing the surrounding non-neoplastic liver tissues. Results: Of the total, 42 (82.4%) patients were diagnosed with HCC, 32 had metabolic risk factors, 20 patients met the diagnostic criteria of the metabolic-associated fatty liver disease (MAFLD)-related HCC, and 40.6% (13/32) had liver cirrhosis. The incidence of cirrhosis (p = 0.033) and diabetes mellitus type 2 (p = 0.036) in patients with MAFLD-related HCC was notably higher than that in HCC patients with only metabolic risk factors. Among the 32 HCC cases with metabolic risk factors, trabecular type was the most prevalent, followed by steatohepatitis type, scirrhous type, solid type, pseudoglandular type, clear-cell type, and macrotrabecular type. The degree of tumor cells' swelling and ballooning was found to be positively related to the degree of fibrosis in the surrounding liver tissues (p = 0.011) as well as the proportion of cirrhosis (p = 0.004). Moreover, the degree of fibrosis in the surrounding liver tissues showed a negative correlation with the levels of serum cholesterol (p = 0.002), low-density lipoprotein (p = 0.002), ApoA1 (p = 0.009), ApoB (p = 0.022), total protein (p = 0.015), WBC count (p = 0.006), and PLT count (p = 0.015). Conclusion: Pathological characteristics of the tumor and adjacent non-neoplastic liver tissues of HCC with metabolic risk factors were found to be correlated with metabolic abnormalities.

The m6A/m5C/m1A regulator genes signature reveals the prognosis and is related with immune microenvironment for hepatocellular carcinoma.

BACKGROUND: RNA methylation is a crucial in many biological functions, and its aberrant regulation is associated with cancer progression. N6-Methyladenosine (m6A), 5-Methylcytosine (m5C), N1-methyladenosine (m1A) are common modifications of RNA methylation. However, the effect of methylation of m6A/m5C/m1A in hepatocellular carcinoma (HCC) remains unclear. METHOD: The transcriptome datasets, clinic information, and mutational data of 48 m6A/m5C/m1A regulator genes were acquired from the TCGA database, and the prognostic hazard model was established by univariate and Least absolute shrinkage and selection operator (Lasso) regression. The multivariate regression was performed to determine whether the risk score was an independent prognostic indicator. Kaplan-Meier survival analysis and ROC curve analysis were used to evaluate the predictive ability of the risk model. Decision curve analysis（DCA）analysis was conducted to estimate the clinical utility of the risk model. We further analyzed the association between risk score and functional enrichment, tumor immune microenvironment, and somatic mutation. RESULT: The four-gene (YTHDF1, YBX1, TRMT10C, TRMT61A) risk signature was constructed. The high-risk group had shorter overall survival (OS) than the low-risk group. Univariate and multivariate regression analysis indicated that risk score was an independent prognostic indicator. Risk scores in male group, T3 + T4 group and Stage III + IV group were higher in female group, T1 + T2 group and stage I + II group. The AUC values for 1-, 2-, and 3-year OS in the TCGA dataset were 0.764, 0.693, and 0.689, respectively. DCA analysis showed that the risk score had a higher clinical net benefit in 1- and 2-year OS than other clinical features.The risk score was positively related to some immune cell infiltration and most immune checkpoints. CONCLUSION: We developed a novel m6A/m5C/m1A regulator genes' prognostic model, which could be applied as a latent prognostic tool for HCC and might guide the choice of immunotherapies.

Genome-Wide Identification and Expression Analysis of the bHLH Transcription Factor Family and Its Response to Abiotic Stress in Mongolian Oak (Quercus mongolica).

The basic helix-loop-helix (bHLH) family, one of the largest families of transcription factors in plants, is extensively involved in the growth, development, and stress response of several woody plants. However, no systematic analysis of the bHLH gene family in Quercus mongolica has been reported. We characterize QmbHLH genes and identify the functions of QmbHLH proteins in Q. mongolica. We used bioinformatics approaches, qRT-PCR analysis, and RNA sequencing data to examine chromosomal distributions, gene structures, and conserved patterns, and identified 89 QmbHLH genes, which were divided into 21 subgroups based on the phylogenetic analysis of bHLH genes in Arabidopsis thaliana. Segmental replication played a more prominent role than tandem duplication in the expansion of the QmbHLH gene family. Based on patterns of tissue-specific expression, protein interactions, and cis-element analysis, QmbHLH genes may be extensively involved in the growth and development of Q. mongolica. In leaves, stems, and roots, 12 selected QmbHLH genes exhibited responsiveness to abiotic stresses (salt, cold, weak light, and drought). Our study facilitates follow-up functional investigations of the bHLH gene family in Q. mongolica and provides novel insights into bHLH superfamilies in woody plants.

Clinical pathology of primary central nervous system lymphoma in HIV-positive patients-a 41 Chinese patients retrospective study.

OBJECTIVES: The purpose of this study was to investigate the clinicopathological characteristics of primary central nervous system lymphoma (PCNSL). METHODS: We collected 41 PCNSL formalin-fixed, paraffin-embedded (FFPE) samples from human immunodeficiency virus (HIV)-positive patients and performed HE (haematoxylin-eosin) staining, immunohistochemistry (IHC) staining, in situ hybridization, fluorescence in situ hybridization (FISH). Real-time quantitative polymerase chain reaction (RT-qPCR) was performed in 9 cases of FFPE samples. Meanwhile, we analysed the clinical pathological significance of the results. RESULTS: Seven patients had diffuse large B-cell lymphoma (DLBCL) with germinal centre B-cell (GCB)-like DLBCL, 32 had activated B-cell (ABC)-like DLBCL, and 2 had Burkitt lymphoma (BL). GCB-like DLBCL patients were older at onset (P = 0.040).A lower CD4+ T-cell count and a decrease in cerebrospinal fluid (CSF) glucose content were more frequent in ABC-like DLBCL (P = 0.012, P = 0.006). Overexpression of P53 was more in ABC-like DLBCL (P = 0.041). 73.2 % cases were Epstein-Barr encoding region (EBER) positive, which was more likely in ABC-like DLBCL patients (P = 0.037). EBV DNA were detected in 5/7 EBER-negative DLBCL cases and none (0/2) of the BL cases. All the cases were negative for HHV8 staining. None of the 7 Double expressor lymphoma (DEL) cases had BCL2, BCL6, or c-MYC genetic rearrangements. CONCLUSIONS: HIV-related PCNSL showed unique clinical pathological significance. None of EBV detected in HIV-related BL and without HHV8 infectious are new sights in our single-center study of Chinese HIV-related PCNSL patients.

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Six Quercus mongolica plots with an area of 0.1 hm2 were thinned in 2018. A field survey was carried out in 2020 to examine the effects of different stand densities (high: 900 trees·hm-2; medium: 720 trees·hm-2; low: 600 trees·hm-2) on growth and regeneration of stands and understory species diversity of secondary Q. mongolica forests in Qingyuan, Liaoning Province. Due to the short interval after thinning, there was no significant difference in tree height and diameter at breast height under different densities. However, the crown symmetry index under low stand density was significantly higher than that of high stand density, indicating that crown growth was more sensitive to stand density than trunk growth. The abundance of seedlings was the highest in the medium density, and the basal diameter of the seedlings with the same height was significantly higher, and the seedling regeneration and growth at the medium density were much better than the other two densities. A total of 70 species were recorded, belonging to 41 families and 67 genera. Quercus mongolica, Lespedeza bicolor, Melampyrum roseum, and Potentilla freyniana were the dominant species of trees and herbs, respectively. Simpson index, Pielou index and Shannon index of shrub layer and herb layer were the highest at the medium density. It indicated that the stand density of 720 trees·hm-2 could help maintain the sustainable development of Q. mongolica secondary forest in the mountainous area of eastern Liaoning.

A chromosome-scale genome assembly of the Mongolian oak (Quercus mongolica).

Mongolian oak (Quercus mongolica Fisch.) is an ecologically and economically important white oak species native to and widespread in the temperate zone of East Asia. Here, we present a chromosome-scale reference genome assembly of Q. mongolica, a representative white oak species, by combining Illumina and PacBio data with Hi-C mapping technologies that is the first reference genome created for an Asian oak. Our results showed that the PacBio draft genome size was 809.84 Mb, with a BUSCO complete gene percentage of 92.71%. Hi-C scaffolding anchored 774.59 Mb contigs (95.65% of draft assembly) onto 12 pseudochromosomes. The contig N50 and scaffold N50 were 2.64 and 66.74 Mb, respectively. Of the 36,553 protein-coding genes predicted in the study, approximately 95% had functional annotations in public databases. A total of 435.34 Mb (53.75% of the genome) of repetitive sequences were predicted in the assembled genome. Genome evolution analysis showed that Q. mongolica is closely related to Q. robur from Europe, and they shared a common ancestor ~11.8 million years ago (Ma). Gene family evolution analysis of Q. mongolica revealed that the nucleotide-binding site (NBS)-encoding gene family related to disease resistance was significantly contracted, whereas the ECERIFERUM 1 (CER1) homologous genes related to cuticular wax biosynthesis was significantly expanded. This pioneering Asian oak genome resource represents an important supplement to the oak genomics community and will improve our understanding of Asian white oak biology and evolution.

Cytopathological analysis of bronchoalveolar lavage fluid in patients with and without HIV infection.

BACKGROUND: Human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) infection can lead to a broad spectrum of lung diseases, including infectious diseases and tumors. Recently, with the wide application of bronchoscopes and cytopathology of bronchoalveolar lavage fluid (BALF), the diagnostic efficiency of lung diseases has improved. The present study focuses on analyzing the cytopathologic characteristics of BALF in the diagnosis of HIV/AIDS-related lung disease and comparing the lung disease spectrum between HIV and HIV-uninfected patients. METHODS: BALF specimens were collected from 2211 patients. Using ThinPrep liquid-based technology, the cytologic smears were prepared by staining with Hematoxylin and Eosin (HE), Gomori's methenamine silver (GMS), and Periodic Acid Schiff (PAS), acid-fast and immunocytochemical (ICC) staining. Real-time PCR was used to detect cytomegalovirus (CMV) and Mycobacterium tuberculosis (M. tuberculosis) in the remaining BALF. PCR-reverse dot hybridization was used for mycobacterial species identification. RESULTS: From the 2211 BALF specimens, 1768 (79.96%) were specimens from HIV-infected patients, and 443 (20.04%) were speciments from HIV-uninfected patients. The HIV-infected patients with a median age of 38.5 ± 11.3 years were markedly younger than the HIV-uninfected patients (52.9 ± 14.9 years) (p < 0.01). We found that 1635 (92.5%) HIV-infected patients were males, showing a prominently higher proportion than those without HIV infection (71.1%) (p < 0.01). Meanwhile, 1045 specific lesions were found in 1768 HIV-infected patients (59.1%), including 1034 cases of infectious diseases and 11 neoplastic lesions, also exhibiting a distinctly higher proportion compared to the HIV-uninfected patients (12.2%) (p < 0.001). For the HIV-infected group, a distinctly higher proportion of single infection lesions (724/1768, 41%) was noted than the HIV-uninfected group (14/443, 3.2%) (p < 0.001). Among single infection lesions, the most common was Cytomegalovirus(CMV) infection (20.9%) for the HIV-infected group, followed by Pneumocystis jiroveci(PJ) (13.0%), Fungal (3.5%), and Mycobacterial infections (3.4%), of which M. tuberculosis infection accounted for 3.1%. Double infections (300/1768, 17.0%) and Triple infections (10/1768, 0.6%) were found only among the patients with HIV. The malignancies among HIV-infected patients included adenocarcinomas (0.22%), small cell carcinomas (0.2%), squamous cell carcinomas (0.1%), and diffuse large B-cell lymphoma (0.1%). HIV-infected patients exhibited a significantly lower incidence of neoplastic lesions (0.6% vs. 9.0%) than the HIV-uninfected patients (p < 0.001). CONCLUSIONS: There was a significant difference in the spectrum of lung diseases between HIV-infected and non-infected patients diagnosed by BALF cytopathology.

Quantifying COVID-19 importation risk in a dynamic network of domestic cities and international countries.

Since its outbreak in December 2019, the novel coronavirus 2019 (COVID-19) has spread to 191 countries and caused millions of deaths. Many countries have experienced multiple epidemic waves and faced containment pressures from both domestic and international transmission. In this study, we conduct a multiscale geographic analysis of the spread of COVID-19 in a policy-influenced dynamic network to quantify COVID-19 importation risk under different policy scenarios using evidence from China. Our spatial dynamic panel data (SDPD) model explicitly distinguishes the effects of travel flows from the effects of transmissibility within cities, across cities, and across national borders. We find that within-city transmission was the dominant transmission mechanism in China at the beginning of the outbreak and that all domestic transmission mechanisms were muted or significantly weakened before importation posed a threat. We identify effective containment policies by matching the change points of domestic and importation transmissibility parameters to the timing of various interventions. Our simulations suggest that importation risk is limited when domestic transmission is under control, but that cumulative cases would have been almost 13 times higher if domestic transmissibility had resurged to its precontainment level after importation and 32 times higher if domestic transmissibility had remained at its precontainment level since the outbreak. Our findings provide practical insights into infectious disease containment and call for collaborative and coordinated global suppression efforts.

Association between idiopathic intracranial hypertension and sigmoid sinus dehiscence/diverticulum with pulsatile tinnitus: a retrospective imaging study.

INTRODUCTION: The mechanism of occurrence of sigmoid sinus dehiscence/diverticulum (SSDD) in pulsatile tinnitus (PT) patients remains under debate. Its association with idiopathic intracranial hypertension (IIH) lacks evidence, which is important for therapeutic planning and improving the clinical outcome. This study aimed to evaluate the association between SSDD and IIH by comparing the prevalence of several established imaging features of IIH between PT patients with SSDD and healthy volunteers. METHODS: Thirty-three unilateral PT patients with SSDD identified on CT images and 33 age- and sex-matched healthy volunteers underwent T1-weighted volumetric magnetic resonance imaging (MRI). The optic nerve, pituitary gland, transverse sinus, and ventricles were assessed. The prevalence of established IIH imaging features was compared between the two groups. Furthermore, the PT patients were divided into two subgroups: PT patients with dehiscence only and PT patients with diverticulum. The same statistical analysis was performed on each pathophysiologic entity respectively. RESULTS: The PT patients with SSDD showed a significantly higher prevalence of empty sella (P < 0.001), flattened posterior sclera (P = 0.001), vertical tortuosity of the optic nerve (P = 0.001), protrusion of the optic nerve (P = 0.006), transverse sinus stenosis (P = 0.011), and distension of the optic nerve sheath (P = 0.000). There were no significant differences between the PT and control groups in the maximum widths of the third and fourth ventricles and the lateral ventricle size. In contrast to controls, the imaging findings persisted in both of pathophysiologic entities, except for transverse sinus stenosis. CONCLUSIONS: Several IIH imaging features occur more frequently in PT patients with SSDD than in healthy individuals, which suggests a potential correlation between SSDD with PT and IIH.

Detection of serum p53 antibodies from Chinese patients with papillary thyroid carcinoma using phage-SP-ELISA: correlation with clinical parameters.

The goal of the present study was to investigate whether p53 antibodies (Abs) could be a relevant marker for papillary thyroid carcinoma (PTC). Three types of enzyme-linked immunosorbent assay (ELISA) methods were developed for the detection of p53 Abs, including p53-ELISA, phage-SS-ELISA, and phage-SP-ELISA. A total of 304 patients, including 117 cases with thyroid adenoma and 187 PTC patients, were enrolled in this study. Expression of p53 protein and mutation in BRAF gene were evaluated in paraffin-embedded tissue from 44 patients with PTC, in order to elucidate their correlations with the presence of p53 Abs. Compared with p53-ELISA and phage-SS-ELISA, phage-SP-ELISA presented the highest detection efficiency of p53 Abs in patients with PTC, and a combination of these three ELISA systems could make the detection of p53 Abs more sensitive than using each of the individual ELISA methods. Furthermore, p53 Abs was positively associated with clinical stage (P = 0.044), node metastasis (P = 0.010), and p53 protein accumulation (P = 0.019). These results indicate that serum p53 Abs could be a useful marker for PTC.