Protein truncating variants in mitochondrial-related nuclear genes and the risk of chronic liver disease.

BACKGROUND: Mitochondrial (MT) dysfunction is a hallmark of liver diseases. However, the effects of functional variants such as protein truncating variants (PTVs) in MT-related genes on the risk of liver diseases have not been extensively explored. METHODS: We extracted 60,928 PTVs across 2466 MT-related nucleus genes using whole-exome sequencing data obtained from 442,603 participants in the UK Biobank. We examined their associations with liver dysfunction that represented by the liver-related biomarkers and the risks of chronic liver diseases and liver-related mortality. RESULTS: 96.10% of the total participants carried at least one PTV. We identified 866 PTVs that were positively associated with liver dysfunction at the threshold of P value < 8.21e - 07. The coding genes of these PTVs were mainly enriched in pathways related to lipid, fatty acid, amino acid, and carbohydrate metabolisms. The 866 PTVs were presented in 1.07% (4721) of participants. Compared with participants who did not carry any of the PTVs, the carriers had a 5.33-fold (95% CI 4.15-6.85), 2.82-fold (1.69-4.72), and 4.41-fold (3.04-6.41) increased risk for fibrosis and cirrhosis of liver, liver cancer, and liver disease-related mortality, respectively. These adverse effects were consistent across subgroups based on age, sex, body mass index, smoking status, and presence of hypertension, diabetes, dyslipidemia, and metabolic syndrome. CONCLUSIONS: Our findings revealed a significant impact of PTVs in MT-related genes on liver disease risk, highlighting the importance of these variants in identifying populations at risk of liver diseases and facilitating early clinical interventions.

The Health Impact of MAFLD, a Novel Disease Cluster of NAFLD, Is Amplified by the Integrated Effect of Fatty Liver Disease-Related Genetic Variants.

BACKGROUND & AIMS: Metabolic dysfunction-associated fatty liver disease (MAFLD) is a newly proposed disease category that derived from non-alcoholic fatty liver disease. The impact of MAFLD on health events has not been investigated. METHODS: UK Biobank participants were diagnosed for whether MAFLD presented at baseline. Five genetic variants (PNPLA3 rs738409 C/G, TM6SF2 rs58542926 C/T, GCKR rs1260326 T/C, MBOAT7 rs641738 C/T, and HSD17B13 rs72613567 T/TA) were integrated into a genetic risk score (GRS). Cox proportional hazard model was used to examine the association of MAFLD with incident diseases. RESULTS: A total of 160 979 (38.0%, 95% confidence interval [CI] 37.9%, 38.2%) participants out of 423 252 were diagnosed as MAFLD. Compared with participants without MAFLD, MAFLD cases had multivariate adjusted hazard ratio (HR) for liver cancer of 1.59 (95% CI, 1.28, 1.98), cirrhosis of 2.77 (2.29, 3.36), other liver diseases of 2.09 (1.95, 2.24), cardiovascular diseases of 1.39 (1.34, 1.44), renal diseases of 1.56 (1.48, 1.65), and cancers of 1.07 (1.05, 1.10). The impact of MAFLD, especially on hepatic events, was amplified by high GRS, of which the genetic variations in PNPLA3, TM6SF2, and MBOAT7 play the principal roles. MAFLD case with normal body weight is also associated with an increased risk of hepatic outcomes, but the genetic factor seems do not influence the risk in this subpopulation. CONCLUSIONS: MAFLD is independently associated with an increased risk of both intrahepatic and extrahepatic events. Fatty liver disease related genetic variants amplify the effect of MAFLD on disease outcomes.

Evolutionary characteristics and immune mutation of hepatitis C virus genotype 1b among intravenous drug users in mainland, China.

China is one of the countries with the heaviest burden of hepatitis C virus (HCV) worldwide, especially subtype 1b. To better control hepatitis C, insights into the characteristics of dynamic spread and genomic mutations are urgently needed. We retrieved sequences of HCV-1b NS5B among intravenous drug users (IDUs) and general people (Non-IDUs) in China from 2000 to 2011 in NCBI. Bayesian phylogenetic and phylogeographic analyses were used to evaluate the transmission dynamics of HCV-1b. Non-synonymous substitutions were detected to illustrate immune adaptation. Evolutionary history demonstrated that HCV-1b effective population size experienced a sharp increase in 1990. HCV-1b sequences among IDUs had a higher estimated evolutionary rate (5.7185 × 10-3  substitutions/site/year) than overall (7.7332 × 10-4 ). 105/136 (77.2%) of HCV-1b sequences clustered into 38 networks. The average non-synonymous HCV-1b immune epitopes among IDUs were 0.211, higher than non-IDUs, especially in the HLA-A*02 molecular recognition region. All of these posed significant challenges for the prevention and treatment of HCV. Heterogeneity and genetic linkages of HCV-1b suggest that evolutionary surveillance of HCV in cities in east-central China and among IDUs could not be neglected.

Environmental risk factors and genetic markers of Kaposi's sarcoma-associated herpesvirus infection among Uygur population in Xinjiang, China.

Kaposi sarcoma-associated herpesvirus (KSHV) is endemic in Xinjiang, China. Determinants of KSHV seropositivity among high-risk groups are not well understood. We seek to identify genetic and environmental predisposing factors for KSHV infection among Uygurs in this endemic region. A cross-sectional study was performed among the Uygur population in Xinjiang, China. KSHV-antibodies were detected using immunofluorescence assay (IFA) and human leukocyte antigen (HLA) alleles were genotyped. Univariate and multivariate logistic regression analyses were applied to explore the environmental and genetic risk factors of KSHV seropositivity. Finally, a total of 721 participants were included. The seroprevalence of KSHV was 24.1% among this population. Sweet-food preference (odds ratio [OR] 1.85, 95% confidence interval [CI] 1.03-3.34), and coronary heart disease (OR 1.91, 95%CI 1.24-2.94) were statistically correlated with KSHV infection. HLA-DQB1*06:09 were found to significantly increase the risk of KSHV infection under all 3 models (ORAllelic = 4.06; ORDominant = 3.27; and ORRecessive = 8.06). Six SNPs (SNP0260, SNP0361, SNP0797, SNP0852, SNP1159, and SNP1375) in the DQB1 and DRB1 region and haploid type GTCTAACTAATC in block 17 were statistically associated with KSHV infection. We demonstrated that genetic variations in HLA-DQB1/DRB1 and environmental risk factors were strongly associated with KSHV infection among this population.

Prevalence and correlates of Kaposi's sarcoma-associated herpesvirus and herpes simplex virus type 2 infections among adults: evidence from the NHANES III data.

BACKGROUND: Kaposi's sarcoma-associated herpes virus (KSHV) prevalence and risk factors exhibit considerable variations across populations in different geographic regions. Determinants and the transmission routes of KSHV infection are uncertain. We seek to identify the possible risk factors and the transmission routes of KSHV infection in non-endemic areas. METHODS: We collected annual cases and seroprevalence of KSHV and herpes simplex virus type 2 (HSV-2) from the NHANES III sampled individuals from the US general population (1988-1994). We included 13,179 and 10,720 individuals with available remaining serum samples of KSHV and HSV-2. Logistic regression was employed to explore potential risk factors for the seropositivity. RESULTS: The seroprevalence was 2.05% for KSHV infection and 31.03% for HSV2 infection among this population. All risk factors of sexual behaviors included were strongly associated with HSV-2 positive, however, only MSM had an approximately fivefold increased risk of KSHV infection (OR = 4.71; 95%CI 1.61 11.30). Mexican Americans (2.51%) and older (chi-squaretrend = - 6.71, P < 0.001) individuals had a higher risk of KSHV infection. After adjustment, individuals with higher level of education and economic status had lower KSHV infection. CONCLUSIONS: In non-endemic areas, KSHV transmission may be related to sexual activity in men, especially in male homosexuals. Higher education level and economic status are protective factors for KSHV infection.

Prevalence of transmitted HIV-1 drug resistance among treatment-naive individuals in China, 2000-2016.

Human immunodeficiency virus (HIV) with transmitted drug-resistance (TDR) limits the therapeutic options available for treatment-naive HIV patients. This study aimed to further our understanding of the prevalence and transmission characteristics of HIV with TDR for the application of first-line antiretroviral regimens. A total of 6578 HIV-1 protease/reverse-transcriptase sequences from treatment-naive individuals in China between 2000 and 2016 were obtained from the Los Alamos HIV Sequence Database and were analyzed for TDR. Transmission networks were constructed to determine genetic relationships. The spreading routes of large TDR clusters were identified using a Bayesian phylogeographic framework. TDR mutations were detected in 274 (4.51%) individuals, with 1.40% associated with resistance to nucleoside reverse transcriptase inhibitors, 1.52% to non-nucleoside reverse transcriptase inhibitors, and 1.87% to protease inhibitors. The most frequent mutation was M46L (58, 0.89%), followed by K103N (36, 0.55%), M46I (36, 0.55%), and M184V (26, 0.40%). The prevalence of total TDR initially decreased between 2000 and 2010 (OR = 0.83, 95% CI 0.73-0.95) and then increased thereafter (OR = 1.50, 95% CI 1.13-1.97). The proportion of sequences in a cluster (clustering rate) among HIV isolates with TDR sequences was lower than that of sequences without TDR (40.5% vs. 48.8%, P = 0.023) and increased from 27.3% in 2005-2006 to 63.6% in 2015-2016 (P < 0.001). While most TDR mutations were associated with reduced relative transmission fitness, mutation M46I was associated with higher relative transmission fitness than the wild-type strain. This study identified a low-level prevalence of TDR HIV in China during the last two decades. However, the increasing TDR HIV rate since 2010, the persistent circulation of drug resistance mutations, and the expansion of self-sustaining drug resistance reservoirs may compromise the efficacy of antiretroviral therapy programs.

The trends in incidence of primary liver cancer caused by specific etiologies: Results from the Global Burden of Disease Study 2016 and implications for liver cancer prevention.

BACKGROUND & AIMS: Liver cancer is a common malignant neoplasm worldwide. The etiologies for liver cancer are diverse and the incidence trends of liver cancer caused by specific etiologies are rarely studied. We therefore aimed to determine the pattern of liver cancer incidence, as well as temporal trends. METHODS: We collected detailed information on liver cancer etiology between 1990-2016, derived from the Global Burden of Disease study in 2016. Estimated annual percentage changes (EAPCs) in liver cancer age standardized incidence rate (ASR), by sex, region, and etiology, were calculated to quantify the temporal trends in liver cancer ASR. RESULTS: Globally, incident cases of liver cancer increased 114.0% from 471,000 in 1990 to 1,007,800 in 2016. The overall ASR increased by an average 0.34% (95% CI 0.22%-0.45%) per year in this period. The ASR of liver cancer due to hepatitis B, hepatitis C, and other causes increased between 1990 and 2016. The corresponding EAPCs were 0.22 (95% CI 0.08-0.36), 0.57 (95% CI 0.48-0.66), and 0.51 (95% CI 0.41-0.62), respectively. The ASR of liver cancer due to reported alcohol use remained stable (EAPC = 0.10, 95% CI -0.06-0.25). This increasing pattern was heterogeneous across regions and countries. The most pronounced increases were generally observed in countries with a high socio-demographic index, including the Netherlands, the UK, and the USA. CONCLUSIONS: Liver cancer remains a major public health concern globally, though control of hepatitis B and C virus infections has contributed to the decreasing incidence in some regions. We observed an unfavorable trend in countries with a high socio-demographic index, suggesting that current prevention strategies should be reoriented, and much more targeted and specific strategies should be established in some countries to forestall the increase in liver cancer. LAY SUMMARY: Liver cancer is a common malignant neoplasm worldwide. The incidence patterns of liver cancer caused by different etiologies varied considerably across the world. In this study, we aim to determine the pattern of liver cancer incidence as well as the temporal trends, thereby facilitating the establishment of more tailored prevention strategies for liver cancer.

Social behavioral correlates of Kaposi sarcoma-associated herpesvirus infection among Han and Uygur populations in Xinjiang, China.

BACKGROUND: Kaposi sarcoma-associated herpesvirus (KSHV) is endemic in Xinjiang, China and its prevalence varies considerably across ethnic groups. The current study explored the prevalence and correlates of KSHV infection among Han and Uygur populations in Xinjiang. METHODS: A cross-sectional study, including 282 Han ethnicity and 312 Uygur, was conducted in Xinjiang, China. All participants underwent face to face questionnaire interview. Plasma samples were collected and screened for KSHV infection using immunofluorescence assay. Univariate and multivariate analyses were conducted to examine the correlates of KSHV seropositivity. RESULTS: The KSHV seroprevalence was 41.6% (95% confidence interval [CI], 37.6-45.6) overall and was higher in the Uygur group (59.9%; 95% CI, 54.3-65.4) than the Han group (21.3%; 95% CI, 16.6-26.5). A significant difference in the geometric mean titer (GMT) of the KSHV antibodies was detected between the Uygur and Han groups (158.2; interquartile range [IQR], 80-320 vs 89.1; IQR, 40-160; P < 0.001). After adjusting for potential confounders, Uygur ethnicity (odds ratios [OR], 5.96; 95% CI, 4.05-8.90), age greater than or equal to 50 years (OR, 1.84; 95% CI, 1.24-2.77), and preference for meat diet (OR, 2.15; 95% CI, 1.05-4.46) were significantly associated with increased odds of KSHV seropositivity. CONCLUSION: The study demonstrated high prevalence and correlates of KSHV infection in both Han and Uygur populations in Xinjiang, China. There is an urgent need for programmatic adaptation to address primary prevention interventions of KSHV infection in this endemic region.

Single extracellular vesicle surface protein-based blood assay identifies potential biomarkers for detection and screening of five cancers.

Extracellular vesicles (EVs) and EV proteins are promising biomarkers for cancer liquid biopsy. Herein, we designed a case-control study involving 100 controls and 100 patients with esophageal, stomach, colorectal, liver, or lung cancer to identify common and type-specific biomarkers of plasma-derived EV surface proteins for the five cancers. EV surface proteins were profiled using a sequencing-based proximity barcoding assay. In this study, five differentially expressed proteins (DEPs) and eight differentially expressed protein combinations (DEPCs) showed promising performance (area under curve, AUC > 0.900) in pan-cancer identification [e.g., TENM2 (AUC = 0.982), CD36 (AUC = 0.974), and CD36-ITGA1 (AUC = 0.971)]. Our classification model could properly discriminate between cancer patients and controls using DEPs (AUC = 0.981) or DEPCs (AUC = 0.965). When distinguishing one cancer from the other four, the accuracy of the classification model using DEPCs (85-92%) was higher than that using DEPs (78-84%). We validated the performance in an additional 14 cancer patients and 14 controls, and achieved an AUC value of 0.786 for DEPs and 0.622 for DEPCs, highlighting the necessity to recruit a larger cohort for further validation. When clustering EVs into subpopulations, we detected cluster-specific proteins highly expressed in immune-related tissues. In the context of colorectal cancer, we identified heterogeneous EV clusters enriched in cancer patients, correlating with tumor initiation and progression. These findings provide epidemiological and molecular evidence for the clinical application of EV proteins in cancer prediction, while also illuminating their functional roles in cancer physiopathology.

Host Genetic Factors, Comorbidities and the Risk of Severe COVID-19.

BACKGROUND: Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was varied in disease symptoms. We aim to explore the effect of host genetic factors and comorbidities on severe COVID-19 risk. METHODS: A total of 20,320 COVID-19 patients in the UK Biobank cohort were included. Genome-wide association analysis (GWAS) was used to identify host genetic factors in the progression of COVID-19 and a polygenic risk score (PRS) consisted of 86 SNPs was constructed to summarize genetic susceptibility. Colocalization analysis and Logistic regression model were used to assess the association of host genetic factors and comorbidities with COVID-19 severity. All cases were randomly split into training and validation set (1:1). Four algorithms were used to develop predictive models and predict COVID-19 severity. Demographic characteristics, comorbidities and PRS were included in the model to predict the risk of severe COVID-19. The area under the receiver operating characteristic curve (AUROC) was applied to assess the models' performance. RESULTS: We detected an association with rs73064425 at locus 3p21.31 reached the genome-wide level in GWAS (odds ratio: 1.55, 95% confidence interval: 1.36-1.78). Colocalization analysis found that two genes (SLC6A20 and LZTFL1) may affect the progression of COVID-19. In the predictive model, logistic regression models were selected due to simplicity and high performance. Predictive model consisting of demographic characteristics, comorbidities and genetic factors could precisely predict the patient's progression (AUROC = 82.1%, 95% CI 80.6-83.7%). Nearly 20% of severe COVID-19 events could be attributed to genetic risk. CONCLUSION: In this study, we identified two 3p21.31 genes as genetic susceptibility loci in patients with severe COVID-19. The predictive model includes demographic characteristics, comorbidities and genetic factors is useful to identify individuals who are predisposed to develop subsequent critical conditions among COVID-19 patients.

The effects of altered DNA damage repair genes on mutational processes and immune cell infiltration in esophageal squamous cell carcinoma.

BACKGROUND: Defects in DNA damage repair (DDR) pathways lead to genomic instability and oncogenesis. DDR deficiency is prevalent in esophageal squamous cell carcinoma (ESCC), but the effects of DDR alterations on mutational processes and tumor immune microenvironment in ECSS remain unclear. METHODS: Whole-exome and transcriptome sequencing data of 45 ESCC samples from Taizhou, China, were used to identify genomic variations, gene expression modulation in DDR pathways, and the abundance of tumor-infiltrating immune cells. Ninety-six ESCC cases from The Cancer Genome Atlas (TCGA) project were used for validation. RESULTS: A total of 57.8% (26/45) of the cases in the Taizhou data and 70.8% (68/96) of the cases in the TCGA data carried at least one functional impact DDR mutation. Mutations in the DDR pathways were associated with a high tumor mutation burden. Several DDR deficiency-related mutational signatures were discovered and were associated with immune cell infiltration, including T cells, monocytes, dendritic cells, and mast cells. The expression levels of two DDR genes, HFM1 and NEIL1, were downregulated in ESCC tumor tissues and had an independent effect on the infiltration of mast cells. In the Taizhou data, increased expression of HFM1 was associated with a poor prognosis, and the increased expression of NEIL1 was associated with a good outcome, but no reproducible correlation was observed in the TCGA data. CONCLUSION: This research demonstrated that DDR alterations could impact mutational processes and immune cell infiltration in ESCC. The suppression of HFM1 and NEIL1 could play a crucial role in ESCC progression and may also serve as prognostic markers.

The role of metabolites under the influence of genes and lifestyles in bone density changes.

Purpose: Osteoporosis is a complex bone disease influenced by numerous factors. Previous studies have found that some metabolites are related to bone mineral density (BMD). However, the associations between metabolites and BMD under the influence of genes and lifestyle have not been fully investigated. Methods: We analyzed the effect of metabolites on BMD under the synergistic effect of genes and lifestyle, using the data of 797 participants aged 55-65 years from the Taizhou Imaging Study. The cumulative sum method was used to calculate the polygenic risk score of SNPs, and the healthful plant-based diet index was used to summarize food intake. The effect of metabolites on BMD changes under the influence of genes and lifestyle was analyzed through interaction analysis and mediation analysis. Results: Nineteen metabolites were found significantly different in the osteoporosis, osteopenia, and normal BMD groups. We found two high-density lipoprotein (HDL) subfractions were positively associated with osteopenia, and six very-low-density lipoprotein subfractions were negatively associated with osteopenia or osteoporosis, after adjusting for lifestyles and genetic factors. Tea drinking habits, alcohol consumption, smoking, and polygenic risk score changed BMD by affecting metabolites. Conclusion: With the increased level of HDL subfractions, the risk of bone loss in the population will increase; the risk of bone loss decreases with the increased level of very-low-density lipoprotein subfractions. Genetic factors and lifestyles can modify the effects of metabolites on BMD. Our results show evidence for the precise prevention of osteoporosis.

Investigating the Association Between Seven Sleep Traits and Nonalcoholic Fatty Liver Disease: Observational and Mendelian Randomization Study.

Background and Aim: Aberrant sleep parameters are associated with the risk of nonalcoholic fatty liver disease (NAFLD). However, existing information is inconsistent among studies and involves reverse causation. Therefore, we aimed to investigate the observational associations and causations between sleep traits and NAFLD. Methods: We performed multivariable regression to assess observational associations of seven sleep traits (sleep duration, easiness of getting up in the morning, chronotype, nap during day, snoring, insomnia, and narcolepsy), and NAFLD in the UK Biobank (1,029 NAFLD). The Cox proportional hazards model was applied to derive hazard ratios and 95% confidence intervals (CIs). Furthermore, a bidirectional two-sample Mendelian randomization (MR) approach was used to explore the causal relationships between sleep traits and NAFLD. Results: In the multivariable regression model adjusted for potential confounders, getting up in the morning not at all easy (HR, 1.51; 95% CI, 1.27-1.78) and usually insomnia (HR, 1.46; 95% CI, 1.21-1.75) were associated with the risk of NAFLD. Furthermore, the easiness of getting up in the morning and insomnia showed a dose-response association with NAFLD (Ptrend <0.05). MR analysis found consistent causal effects of NAFLD on easiness of getting up in the morning (OR, 0.995; 95% CI, 0.990-0.999; p = 0.033) and insomnia (OR, 1.006; 95% CI, 1.001-1.011; p = 0.024). These results were robust to weak instrument bias, pleiotropy, and heterogeneity. Conclusions: Findings showed consistent evidence of observational analyses and MR analyses that trouble getting up in the morning and insomnia were associated with an increased risk of NAFLD. Bidirectional MR demonstrated causal effects of NAFLD on sleep traits.

Genetic predisposition, lifestyle risk, and obesity associate with the progression of nonalcoholic fatty liver disease.

BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is prevalent worldwide. We aim to identify the factors promoting NAFLD progression. METHODS: UK Biobank study participants were diagnosed for whether NAFLD presented at baseline. Cox regression model was used to examine the association of risk factors with incident diseases (significant liver diseases [SLDs], type 2 diabetes [T2D], cardiovascular diseases [CVDs], chronic kidney diseases [CKDs], and cancers) among NAFLD cases. RESULTS: Of 78 283 individuals, 35 159 (44.9%) were females, and the mean (SD) age was 57.56 (7.90) years. Compared with participants had both low genetic and lifestyle risk, individuals with both high genetic and lifestyle risk had a hazard ratio of 1.64 (95% CI 1.32-2.03) for SLDs, 1.16 (1.08-1.24) for T2D, 1.25 (1.13-1.37) for CVDs, 1.33 (1.18-1.49) for CKDs, and 1.13 (1.05-1.22) for cancers. Compared with participants who were non-obese and had low genetic risk, those with obesity and high genetic risk had an 75% (95% CI 38-123%), 147% (128-167%), 46% (33-61%), and 76% (56-99%) increased risk for developing SLDs, T2D, CVDs, and CKDs, respectively. The population-attributable fractions suggested that lifestyle risk and obesity contributed more to the progression of NAFLD than genetic risk. CONCLUSION: Adhering to a healthy lifestyle and avoiding obesity are important to prevent NAFLD progression.

Increasing prevalence of NAFLD/NASH among children, adolescents and young adults from 1990 to 2017: a population-based observational study.

OBJECTIVE: To describe the prevalence and variations of non-alcoholic fatty liver disease/non-alcoholic steatohepatitis (NAFLD/NASH) among children and adolescents (CADs) and young adults (YADs). DESIGN: A population-based observational study. SETTING: Annual cases and prevalence of NAFLD/NASH from 1990 to 2017, by sex, region and country were collected from the Global Burden of Disease database. MAIN OUTCOME MEASURES: The estimated annual percentage change, which was calculated by a regression line, was used to quantify the temporal trends in NAFLD/NASH burden among young people at the global, regional and national levels. RESULTS: Globally, NAFLD/NASH incidence increased from 19.34 million in 1990 to 29.49 million in 2017 among CADs, with an annual increase of 1.35%. Additionally, in YADs, the number of cases and NAFLD/NASH prevalence significantly increased during this period, independent of sex and region. The greatest NAFLD/NASH increase was in North Africa and the Middle East. Almost all countries showed an increasing trend from 1990 to 2017, with the most pronounced increase observed in the developed regions. CONCLUSIONS: The epidemiology of NAFLD/NASH in young people has changed considerably over the last three decades. Both the prevalence and number of cases have increased irrespective of sex, age and region. This phenomenon can result in a predictable increase in chronic liver disease burden in the near future. Understanding the prevalence of NAFLD/NASH and its variations is of paramount importance to develop strategies to implement public health policy.

Prognostic value of immune-related genes and immune cell infiltration analysis in the tumor microenvironment of head and neck squamous cell carcinoma.

BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is one of the few malignant tumors that respond well to immunotherapy. We aimed to investigate the immune-related genes and immune cell infiltration of HNSCC and construct a predictive model for its prognosis. METHODS: We calculated the stromal/immune scores of patients with HNSCC from The Cancer Genome Atlas using the Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data algorithm and investigated the relationship between the scores and patients' prognosis. Three machine learning algorithms (LASSO, Random Forest, and Rbsurv) were performed to screen key immune-related genes and constructed a predictive model. The immune cell infiltrating was calculated by the Tumor Immune Estimation Resource algorithm. RESULTS: The stromal and immune scores significantly correlated with prognosis. A 6-gene signature was selected and displayed a robust predictive effect. The expressions of key genes were associated with immune infiltrating. GSE65858 validated the results. CONCLUSION: Our study comprehensively analyzed the tumor microenvironment of HNSCC and constructed a robust predictive model, providing a basis for further investigation of therapy.

Evolutionary characteristics and genetic transmission patterns of predominant HIV-1 subtypes among men who have sex with men in China.

OBJECTIVES: Men who have sex with men (MSM) represent one of the major risk groups for HIV-1 infection in China, and the predominant subtypes among this population has changed over the last two decades. The objective of this study was to determine the evolutionary characteristics and transmission patterns of the dominant HIV-1 strains in the Chinese MSM population. METHODS: A total of 4980 published HIV-1 pol gene sequences from MSM in China were retrieved and comprehensive evolutionary and transmission analyses were then conducted. Bayesian coalescent-based methods and selection pressure analyses were used to reconstruct the time-scale and demographic history and to estimate other evolutionary parameters. Transmission patterns were characterized using network analyses. RESULTS: There were 2546 (51.12%) CRF01_AE, 1263 (25.36%) CRF07_BC, and 623 (12.51%) subtype B, accounting for 88.99% of the total sequences. From 2000 to 2016, the prevalence of CRF01_AE was stable, comprising nearly half of all sequences over time (58.33-45.38%, p=0.071). CRF07_BC increased slightly from 13.3% to 22.49% (p<0.001), while subtype B decreased dramatically from 41.67% to 9.04% (p<0.001). Demographic reconstruction showed that the greatest expansion of the HIV epidemic occurred between 1999 and 2005. CRF01_AE had a higher estimated evolutionary rate (2.97×10-3 substitutions/site/year) and exhibited more sites under positive selection (25/351 codons) compared to the other subtypes. Network analyses showed that CRF07_BC (68.29%, 84/123) had a higher proportion of cross-region networks than CRF01_AE (49.1%, 174/354) and subtype B (36.46%, 35/96) (p<0.001). CONCLUSIONS: The predominant subtypes of HIV-1 in Chinese MSM have different evolutionary characteristics and transmission patterns, which poses a significant challenge to HIV treatment and disease prevention.

Future of cancer incidence in Shanghai, China: Predicting the burden upon the ageing population.

AIM: The age-specific cancer patterns have changed significantly over the last few decades in urban Shanghai. Predicting the cancer incidence in an ageing population can help to anticipate future resource needs, evaluate primary prevention strategies, and inform further research studies. MATERIALS AND METHODS: Annual cancer cases and population data from 1988 to 2013 were collected from Shanghai Cancer Registry. A Bayesian age-period-cohort model was applied to project the future cancer incidence with demographical changes from 2014 to 2025. RESULTS: From 1988 through 2013, the urban population aged < 65 years decreased by 19.5%, while the population aged ≥ 65 years increased by 58.4%. In the same period, cancer cases increased by 66.0% (from 8315 to 13,806) and 88.6% (from 7448 to 14,048) in these two populations, respectively. From 2014-2025, the population size is expected to decrease by an additional 29.6% in people aged < 65 years, while it will increase by an additional 68.3% in people aged ≥ 65 years. Correspondingly, the model predicts an 87.5% and 143.4% increase in cancer cases for these two populations, respectively. The most pronounced increase was found in thyroid cancer in both sexes, followed by prostate, kidney, and colon cancer in men. In women, lung, kidney, and cervical cancer in women was expected to increase. CONCLUSIONS: The number of cancer cases in urban Shanghai, especially in older people, is expected to significantly increase in the next decade. Particular strategies targeting the elderly are required to combat the cancers.

Disparities in Cancer Incidence among Chinese Population versus Migrants to Developed Regions: A Population-Based Comparative Study.

BACKGROUND: The incidence of cancer was determined by genetic and environmental factors and varied across the world. The discrepancies in cancer profile among Chinese people living in different regions remained obscure. METHODS: Chinese people living in urban Shanghai, Hong Kong, Taiwan, Macau, Singapore, and Los Angeles were included in this study. The cancer case data and population data were collected from either the Cancer Incidence in Five Continents Plus database or the regional cancer registry. A rate model was applied to examine the regional differences in cancer risk with Shanghai set as the reference. RESULTS: From 1983 to 2013, the cancer profiles in most regions were changed. Significant differences in cancer incidence, by sex, period, and age, were detected across regions. The most pronounced disparities were found between Shanghai people and American Chinese in Los Angeles. For cancer site, the most significant differences were detected in prostate, gastrointestinal, gynecologic, oral cavity and pharynx, and brain and central nervous system (CNS) cancers. Specifically, Shanghai was significantly higher in stomach, liver, esophageal, pancreatic, and brain and CNS cancers, while lower in colon, prostate, breast, cervical, and oral cavity and pharynx cancers compared with the other five populations. CONCLUSIONS: Cancer profile was distinct across Chinese populations, which shared a similar genetic background but lived in different regions. The disparities indicate that cancer development was majorly determined by environmental factors, and suggests that region-tailored cancer prevention strategies were warranted. IMPACT: The cancer patterns in populations sharing the same genetic background were significantly influenced by different living conditions.