Deep whole-genome analysis of 494 hepatocellular carcinomas.

Over half of hepatocellular carcinoma (HCC) cases diagnosed worldwide are in China1-3. However, whole-genome analysis of hepatitis B virus (HBV)-associated HCC in Chinese individuals is limited4-8, with current analyses of HCC mainly from non-HBV-enriched populations9,10. Here we initiated the Chinese Liver Cancer Atlas (CLCA) project and performed deep whole-genome sequencing (average depth, 120×) of 494 HCC tumours. We identified 6 coding and 28 non-coding previously undescribed driver candidates. Five previously undescribed mutational signatures were found, including aristolochic-acid-associated indel and doublet base signatures, and a single-base-substitution signature that we termed SBS_H8. Pentanucleotide context analysis and experimental validation confirmed that SBS_H8 was distinct to the aristolochic-acid-associated SBS22. Notably, HBV integrations could take the form of extrachromosomal circular DNA, resulting in elevated copy numbers and gene expression. Our high-depth data also enabled us to characterize subclonal clustered alterations, including chromothripsis, chromoplexy and kataegis, suggesting that these catastrophic events could also occur in late stages of hepatocarcinogenesis. Pathway analysis of all classes of alterations further linked non-coding mutations to dysregulation of liver metabolism. Finally, we performed in vitro and in vivo assays to show that fibrinogen alpha chain (FGA), determined as both a candidate coding and non-coding driver, regulates HCC progression and metastasis. Our CLCA study depicts a detailed genomic landscape and evolutionary history of HCC in Chinese individuals, providing important clinical implications.

Prevalence, associated factors, and gene polymorphisms of obesity in Tibetan adults in Qinghai, China.

OBJECTIVES: To explore the prevalence and associated factors of obesity in Tibetan adults in Qinghai, China, and to determine the association between the FTO (rs1121980 and rs17817449) and MC4R gene (rs17782313 and rs12970134) polymorphisms with obesity. METHODS: A cross-sectional survey was conducted in 2015 in Qinghai to selected Tibetan adults aged 20 to 80 years. Prevalence of obesity (BMI ≥ 28 kg/m2) and overweight (BMI 24 ~ 27.9 kg/m2) were evaluated. Multivariable logistic models were used to determine the associated factors. Pair-matched subjects of obesity cases and normal-weight controls were selected for the gene polymorphism analyses. Conditional logistic models were used to assess the association between gene polymorphisms with obesity. Additive and multiplicative gene-environment interactions were tested. RESULTS: A total of 1741 Tibetan adults were enrolled. The age- and sex- standardized prevalence of obesity and overweight was 18.09% and 31.71%, respectively. Male sex, older age, heavy level of leisure-time exercise, current smoke, and heavy level of occupational physical activity were associated with both obesity and overweight. MC4R gene polymorphisms were associated with obesity in Tibetan adults. No significant gene-environment interaction was detected. CONCLUSION: The prevalence of obesity and overweight in Tibetan adults was high. Both environmental and genetic factors contributed to the obesity prevalent.

Multi-omics integrated circulating cell-free DNA genomic signatures enhanced the diagnostic performance of early-stage lung cancer and postoperative minimal residual disease.

BACKGROUND: Liquid biopsy is a promising non-invasive alternative for cancer screening and minimal residual disease (MRD) detection, although there are some concerns regarding its clinical applications. We aimed to develop an accurate detection platform based on liquid biopsy for both cancer screening and MRD detection in patients with lung cancer (LC), which is also applicable to clinical use. METHODS: We applied a modified whole-genome sequencing (WGS) -based High-performance Infrastructure For MultIomics (HIFI) method for LC screening and postoperative MRD detection by combining the hyper-co-methylated read approach and the circulating single-molecule amplification and resequencing technology (cSMART2.0). FINDINGS: For early screening of LC, the LC score model was constructed using the support vector machine, which showed sensitivity (51.8%) at high specificity (96.3%) and achieved an AUC of 0.912 in the validation set prospectively enrolled from multiple centers. The screening model achieved detection efficiency with an AUC of 0.906 in patients with lung adenocarcinoma and outperformed other clinical models in solid nodule cohort. When applied the HIFI model to real social population, a negative predictive value (NPV) of 99.92% was achieved in Chinese population. Additionally, the MRD detection rate improved significantly by combining results from WGS and cSMART2.0, with sensitivity of 73.7% at specificity of 97.3%. INTERPRETATION: In conclusion, the HIFI method is promising for diagnosis and postoperative monitoring of LC. FUNDING: This study was supported by CAMS Innovation Fund for Medical Sciences, Chinese Academy of Medical Sciences, National Natural Science Foundation of China, Beijing Natural Science Foundation and Peking University People's Hospital.

Integrated Multi-Omics Landscape of Liver Metastases.

BACKGROUND & AIMS: Lack of thorough knowledge about the complicated immune microenvironment (IM) within a variety of liver metastases (LMs) leads to inappropriate treatment and unsatisfactory prognosis. We aimed to characterize IM subtypes and investigate potential mechanisms in LMs. METHODS: Mass cytometry was applied to characterize immune landscape of a primary liver cancers and liver metastases cohort. Transcriptomic and whole-exome sequencing were used to explore potential mechanisms across distinct IM subtypes. Single-cell transcriptomic sequencing, multiplex fluorescent immunohistochemistry, cell culture, mouse model, Western blot, quantitative polymerase chain reaction, and immunohistochemistry were used for validation. RESULTS: Five IM subtypes were revealed in 100 LMs and 50 primary liver cancers. Patients featured terminally exhausted (IM1) or rare T-cell-inflamed (IM2 and IM3) immune characteristics showed worse outcome. Increased intratumor heterogeneity, enriched somatic TP53, KRAS, APC, and PIK3CA mutations and hyperactivated hypoxia signaling accounted for the formation of vicious subtypes. SLC2A1 promoted immune suppression and desert via increasing proportion of Spp1+ macrophages and their inhibitory interactions with T cells in liver metastatic lesions. Furthermore, SLC2A1 promoted immune escape and LM through inducing regulatory T cells, including regulatory T cells and LAG3+CD4+ T cells in primary colorectal cancer. CONCLUSIONS: The study provided integrated multi-omics landscape of LM, uncovering potential mechanisms for vicious IM subtypes and confirming the roles of SLC2A1 in regulating tumor microenvironment remodeling in both primary tumor and LM lesions.

Spatiotemporal genomic analysis reveals distinct molecular features in recurrent stage I non-small cell lung cancers.

Stage I non-small cell lung cancer (NSCLC) presents diverse outcomes. To identify molecular features leading to tumor recurrence in early-stage NSCLC, we perform multiregional whole-exome sequencing (WES), RNA sequencing, and plasma-targeted circulating tumor DNA (ctDNA) detection analysis between recurrent and recurrent-free stage I NSCLC patients (CHN-P cohort) who had undergone R0 resection with a median 5-year follow-up time. Integrated analysis indicates that the multidimensional clinical and genomic model can stratify the prognosis of stage I NSCLC in both CHN-P and EUR-T cohorts and correlates with positive pre-surgical deep next generation sequencing (NGS) ctDNA detection. Increased genomic instability related to DNA interstrand crosslinks and double-strand break repair processes is significantly associated with early tumor relapse. This study reveals important molecular insights into stage I NSCLC and may inform clinical postoperative treatment and follow-up strategies.

Whole exome sequencing in Chinese mucinous pulmonary adenocarcinoma uncovers specific genetic variations different from lung adenocarcinoma.

Background: As a rare subtype of primary lung adenocarcinoma (LUAD), mucinous pulmonary adenocarcinoma (MPA) was considered a distinctive entity with unfavorable outcomes. Therefore, there is a great need for a better understanding of the genomic and immunological landscape of this rare tumor type, which would inform improved therapeutic strategies. Methods: A total of 96 patients histologically confirmed with MPA were recruited from Shandong Cancer Hospital and Institute (SCH). Single nucleotide variation (SNV), copy number variation (CNV), genomic instability, and immunological landscape insights into 96 MPA patients were identified using WES. Results: We demonstrated that MPAs had marked different genomic alterations and were more complex in genomic profiles than LUADs. Mutations in Tumor Protein 53 (TP53) and CYP7A Promoter-Binding Factor (CPF) pathways significantly shortened survival whereas mutations in Notch and Wnt pathways significantly prolonged survival in MPA. Besides, we demonstrated that mutations in immune-related genes influenced outcomes, with mutations in TP53, Ataxia Telangiectasia Mutated (ATM), Polymerase (DNA) Delta 1 (POLD1), and Epidermal Growth Factor Receptor (EGFR) correlated with worsened survival. Conclusions: We not only depicted the genetic and immunologic landscape of Chinese MPA but also reveal its distinction from LUAD in genomic and immune context. Our findings may provide opportunities for therapeutic susceptibility among Chinese MPA patients.

Intertumoural Heterogeneity and Branch Evolution of Synchronous Multiple Primary Lung Adenocarcinomas by Next-Generation Sequencing Analysis.

OBJECTIVES: Multiple primary lung cancers (MPLCs) are an increasingly well-known clinical phenomenon, but there is a lack of high-level evidence for their optimal clinical diagnosis and therapeutic approaches. Thus, we analysed genetic variation to determine the intertumoural heterogeneity and branch evolution of synchronous multiple primary lung adenocarcinomas. METHODS: We performed multiplex mutational sequencing on 93 synchronous multiple primary lung adenocarcinoma lesions from 42 patients who underwent surgical resection. RESULTS: The high discordance rate of mutation was 92.9% (n=39) between tumours in individual patients. EGFR, TP53 and KRAS mutations were detected in 57 (61.3%), 19 (20.4%) and 11 (11.8%) of the 93 tumours, respectively. 16 cases of multiple primary lung adenocarcinomas simultaneously harboured EGFR mutations and TP53 mutations. Matching mutations between paired tumours were observed in 1 (2.4%) patient for P20. The genotypes were all EGFR L858R mutations, but the pathological type of P20T1 was lepidic predominant, and P20T2 was adenocarcinoma in situ. In the phylogenetic tree, genetic variations were divided into trunk, shared and branch subtypes. Branch mutations accounted for 91.09% of variations in sMPLA, while the ratio of trunk (4.95%) and shared (3.96%) variations was significantly lower. CONCLUSIONS: Remarkable intertumoural heterogeneity and frequent branch mutations were found in synchronous multiple primary lung adenocarcinomas.

Prevalence and risk factors of refractive error in Qinghai, China: a cross-sectional study in Han and Tibetan adults in Xining and surrounding areas.

BACKGROUND: Our study aimed to explore the prevalence and risk factors of refractive error (RE) in Han and Tibetan population aged 50-79 years in Xining and surrounding areas in Qinghai Province on Qinghai-Tibet Plateau. METHODS: As part of the China National Health Survey, our cross-sectional study compared the age-adjusted prevalence of RE in Han and Tibetan older adults aged 50-79 years in Xining and surrounding areas. A multivariate logistic regression model was used to identify risk factors for myopia and hyperopia. RESULTS: Among 769 Han participants and 476 Tibetan participants, the age-adjusted prevalence of myopia (spherical equivalent (SE) < - 0.5D), hyperopia (SE > + 0.5D), high myopia (SE < -6.0D) and astigmatism (cylindrical equivalent > = 0.5D) is 28.56, 22.82, 2.80, and 69.38%. Han participants have higher age-adjusted prevalence of myopia (32.93% vs 21.64%, p < 0.001), high myopia (3.93% vs 1.02%, p = 0.001) and astigmatism (72.14% vs 64.94%, p = 0.021) compared to Tibetan participants. Being Tibetan is the protective factor of myopia compared to being Han (OR 0.58, 95%CI 0.42-0.79, p < 0.001). Older age (p = 0.032), longer time length in rural area (p = 0.048), undergraduate/graduate education level (p = 0.031), lighter active level (p = 0.007) and lower BMI (p = 0.015) are risk factors for myopia. Older age (all p < 0.001) and pterygium status of the same eye (p = 0.013) also increase the hyperopia risk. CONCLUSIONS: Our study found an overall prevalence of myopia of 28.56% in Xining and surrounding areas in adults older than 50 years. Han population has higher myopia risk than Tibetan population. More medical and social resources should be allocated to improve the vision and life quality of older adults.

Government Provides Vigorous Supports to the Improvement of Health Care in Qinghai Province, China.

Qinghai province is located in the northeastern part of the Tibetan Plateau, and is an underdeveloped province of inland China. Chinese government gives high priority to the improvement of the wellbeing of Qinghai people, and have provided great supports in aspects of policy, funding, and professional resource to the development of health care and medical system in Qinghai. Great progress has been made, and wellness of residents in Qinghai has been significantly improved. This article reviews the strategies and measures from central and provincial government in improving health care of Qinghai province under the leadership of the Communist Party of China.

Birth and death of Mx genes and the presence/absence of genes regulating Mx transcription are correlated with the diversity of anti-pathogenicity in vertebrate species.

Gene duplication and amino acid substitution are two types of genetic innovations of antiviral genes in inhibiting the emerging pathogens in different species. Mx proteins are well known for inhibiting negative-stranded RNA viruses and have evolved a number of paralogs or orthologs, showing distinct antiviral activities or capacities within or between species. The presence of upstream genes in the signaling pathway(s) that activates Mx genes (upstream regulators of Mx gene) also exhibits variety across species. The association between the evolution of Mx gene and their upstream regulators and the various antiviral capacities in host species has not been investigated. Herein, we traced the evolution of Mx gene and profiled the gene birth/death events on each branch of the 64 chordate species. We provided additional support that the diversity in gene member and amino acid changes in the different clades is correlated to their various antiviral activities of the species. We identified amino acid substitutions that may lead to the functional divergence between Mx paralogs in rodents. Although the copy number of the Mx gene is conserved in birds, infection by influenza A virus (IAV) results in diverse morbidity rates in different avian species. The evidences of gene interaction in the IAV-induced pathway and the genome analysis performed in this study indicated that the existence of the upstream regulators of Mx gene exhibits variation among different species, particularly in birds. The variation is related to the differences in the expression of Mx genes, resulting in the antiviral specificity and morbidity rates in avian species. We conclude that the antiviral capacity in host species is associated with the variations in the gene number of the Mx gene family and the existence of upstream regulators of Mx gene as well.

Comprehensive geriatric assessment of elderly highlanders in Qinghai, China I: activities of daily living, quality of life and metabolic syndrome.

AIM: To reveal the comparison of comprehensive geriatric functions of elderly highlanders in Qinghai Plateau in China among three different ethnic groups. METHODS: Activities of daily living (ADL), screening-based depression, quality of life (QOL) and checking-up of metabolic syndrome including community-based oral glucose tolerance test were assessed in 393 community-dwelling elderly subjects aged 60 years or more (247 Han elderly subjects, 49 Mongolian ones and 97 Tibetan ones). RESULTS: Tibetan elderly highlanders were more disabled in ADL, but had higher QOL than Han elderly ones in Qinghai Plateau. Blood pressure measurements, rate of hypertension and hemoglobin concentrations in Tibetan elderly highlanders were lower than Han ones. Rates of diabetes and impaired glucose tolerance in elderly highlanders were relatively lower than other Asian elderly lowlanders. CONCLUSION: Prevalence of metabolic syndrome in elderly highlanders in Qinghai was still not high, however, we should pay attention to its tendency related with socialglobalism in the near future. Further investigation on physiological adaptability to hypoxic environment and human ageing phenomena in a global context may open a new research frontier for ageing science.

Comprehensive geriatric assessment of elderly highlanders in Qinghai, China II: the association of polycythemia with lifestyle-related diseases among the three ethnicities.

AIM: The objective of this study is to disclose the association of polycythemia with lifestyle-related diseases (hypertension, obesity and glucose intolerance) among the three ethnicities in Qinghai, China. METHODS: The subjects were 393 elderly people (247 Han, 97 Tibetan and 49 Mongolian) aged 60 years and more living in Qinghai (3000 m a.s.l.) in China. The associated factors with polycythemia were analyzed in the subjects. Excessive polycythemia was defined as hemoglobin concentration over 20 mg/dL. RESULTS: Polycythemia was associated with men, hypoxemia, obesity and high diastolic blood pressure (DBP) in the elderly in Qinghai. Male sex was associated with polycythemia in all ethnicities. Obesity was associated with Han and Tibetan men. Glucose intolerance and activities of daily living were not directly associated with polycythemia after adjustment for sex. There were 7.9% with excessive polycythemia. Independently-associated factors for excessive polycythemia were male sex, body mass index of 25 or more, SpO(2) of less than 85%, DBP of 85 mmHg or more and Han ethnicity (vs Tibetan) by multiple logistic regression. CONCLUSION: There was a close association of polycythemia with diastolic hypertension and obesity in lifestyle-related diseases in high-altitude elderly people. Han people had a higher hemoglobin concentration after adjustment of lifestyle-related diseases compared with Tibetan people. The difference of hemoglobin concentration may be due to Tibetans undergoing a much longer period of adaptation than Han people. Further study is needed to disclose the association between the difference of hypoxic adaptation, lifestyle-related diseases and chronic mountain sickness for their prevention.

Comprehensive geriatric assessment of elderly highlanders in Qinghai, China, III: oxidative stress and aging in Tibetan and Han elderly highlanders.

BACKGROUND: Although there are several factors which may contribute to oxidative stress at high altitude, little is known about the association between oxidative stress and aging in the community-dwelling elderly in the Tibetan Plateau. METHODS: Reactive oxygen species (ROS) and comprehensive geriatric functions were examined among 235 community-dwelling elderly subjects aged 60 years or more (146 Hans and 89 Tibetans). As a marker of ROS, the levels of reactive oxygen metabolites (ROM) were measured using the d-ROM test. RESULTS: The rate of dependence of basic activities of daily living (basic ADL) among Tibetan elderly highlanders was significantly higher than that among Han elderly highlanders. The d-ROM level was higher among the Tibetan elderly than those among the Han elderly (Tibetan 465.6 +/- 97.9 Carr U, Han 415.3 +/- 72.0 Carr U, P = 0.003). The ROM level was higher among women than those among men. Stepwise multiple regression analysis showed that being Tibetan, female, and oxygen saturation were independent predictors of increasing d-ROM level (Tibetan beta, 0.241; female beta, 0.206; oxygen saturation beta, 0.218). The high levels of ROM (d-ROM >500 Carr U) were significantly associated with dependence of basic ADL after adjustment for age, sex and ethnicity (odds ratio = 2.51, P = 0.028). CONCLUSION: The findings of this study imply the possibility that ROS is higher among Tibetan elderly highlanders than that of Han, which related to the geriatric items. Further studies are needed to show the impact of oxidative stress on the aging of highlanders.

Comprehensive geriatric assessment of elderly highlanders in Qinghai, China IV: comparison of food diversity and its relation to health of Han and Tibetan elderly.

AIM: To examine the association between food diversity and health status of Han and Tibetan elderly highlanders in Qinghai Plateau, China. METHODS: The study population consisted of 240 community-dwelling elderly subjects aged 60 years or more (176 Han elderly subjects, 64 Tibetan ones). Food diversity was determined using an 11-item Food Diversity Score Kyoto (FDSK-11). Subjects were interviewed on health status including activities of daily living (ADL), screening-based depression and quality of life (QOL). Blood chemical investigation was carried out in association with food diversity. RESULTS: ADL was significantly lower in both Han and Tibetan elderly with lower food diversity than those with higher diversity. In Han elderly with lower food diversity, QOL was significantly lower in the items of subjective sense of health, relationship with family and subjective happiness, but not significant in Tibetan elderly. A close association was found between lower food diversity and lower financial satisfaction in both Han and Tibetan subjects. No association was found between food diversity and age or body mass index. Higher food diversity was associated with lower blood glucose level in Han elderly subjects, but the opposite association was found in Tibetan ones. CONCLUSION: Food diversity was associated with ADL and QOL in highlanders in Qinghai, China. Food assessment is very important as a useful indicator to establish the actual condition of diet and its relation to health status of community-dwelling elderly as well as the change of economic background in the Qinghai highlands.