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Summary: Background: Much remains unknown regarding the associations of adversities in childhood and adulthood with incident cardiovascular diseases (CVD). We aimed to examine the independent and cumulative relations of adversities in childhood and adulthood with incident CVD and whether these associations can be mitigated by adopting a healthy lifestyle later in life. Methods: We included 136,073 men and women [38–72 years at baseline] free of diagnosed CVD at baseline who responded to surveys on adversities in childhood and adulthood in the United Kingdom Biobank prospective cohort. They were recruited between 2006 and 2010 and were followed-up until 28 January 2021. Adversities included physical abuse, emotional abuse, sexual abuse, emotional neglect, and physical neglect. Participants were categorised into four groups according to the exposure periods, which were no adversity, childhood adversity only, adulthood adversity only, and cumulative adversity (both childhood and adulthood). The primary outcomes included incident fatal and non-fatal CVD events. The modifiable lifestyle factors were smoking, physical activity, diet, sleeping, social or leisure activities, and friend or family visits. Findings: We identified 16,415 (10.71/1000 person-year) incident CVD during a median follow-up of 11.8 years. Compared with participants with no adversity, CVD incidence increased by 11% in those with childhood adversity only (adjusted hazard ratio [HR]: 1.11 [95% CI 1.06–1.17], p

Abstract Background Patients with repaired tetralogy of Fallot (rTOF) experience long-term chronic pulmonary valve regurgitation resulting in right ventricular (RV) dilatation. According to current guidelines, the evaluation of patients with rTOF for RV dilatation should be based on cardiac magnetic resonance (CMR). However, for many asymptomatic patients, routine CMR is not practical. Our study aims to identify screening methods for CMR based on echocardiographic data, with the goal of establishing a more practical and cheap method of screening for severity of RV dilatation in patients with asymptomatic rTOF. Methods Thirty two rTOF patients (mean age, 21(10.5) y, 21 males) with moderate to severe pulmonary regurgitation (PR) were prospectively recruited. Each patient received CMR and echocardiogram examination within 1 month prior to operation and collected clinical data, and then received echocardiogram examination at discharge and 3–6 months post-surgery. Results RV moderate-severe dilatation was defined as right ventricular end-diastolic volume index (RVEDVI) ≥ 160 ml/m2 or right ventricular end-systolic volume index (RVESVI) ≥ 80 ml/m2 in 15 of 32 patients (RVEDVI, 202.15[171.51, 252.56] ml/m2, RVESVI, 111.99 [96.28, 171.74] ml/m2). The other 17 (RVESDI, 130.19 [117.91, 139.35] ml/m2, RVESVI = 67.91 [63.35, 73.11] ml/m2) were defined as right ventricle mild dilatation, i.e., RVEDVI 2.35 were diagnosed with RV moderate-severe dilatation (AUC = 0,882; Sensitivity = 94.1%; Specificity = 77.3%). Conclusions RV moderate-severe dilatation is associated with worse preoperative cardiac function and short-term prognosis after PVR in rTOF patients with moderate to severe PR. The RV dilatation score is an effective screening method. When RV dilatation score > 2.35, the patient is indicated for further CMR examination and treatment.

The brick-and-mortar biomimetic structure Ti/Al3Ti metal-intermetallic laminate (BMS-MIL) composites were prepared by vacuum hot pressing. BMS-MIL composites with various Ti volume fractions from 45–71% were obtained by controlling the high-temperature diffusion time of Al–Ti. The phase composition of the BMS-MIL composites was analyzed, and the influence of Ti volume fraction on the microstructure was quantitatively characterized. Quasi-static compression and three-point bending tests were carried out to study the mechanical properties and fracture mechanism of the BMS-MIL composites. The results indicated that, in BMS-MIL composites, Al3Ti appears as polygonal platelets, and Ti fills the gaps between the platelets. With decreasing Ti volume fraction, the size of Al3Ti platelets increased, the number of platelets decreased, and the aspect ratio of platelets first increased and then decreased. The decrease of Ti volume fraction leads to the decrease of mechanical properties of composites. However, as a reasonable and efficient material design strategy, the brick-and-mortar structure ensured that the specific strength of the BMS-MIL composites with load perpendicular to the layer remained stable, with specific strength maintained between 345 and 353 kN m/kg. The compression properties with load parallel to the layer are significantly affected by the platelet's aspect ratio. The sample with 65% volume fraction Ti exhibited the optimal strength, specific strength, and failure strain when compressed parallel to the layer, with a strength of 1347.3 MPa, specific strength of 330.2 kN m/kg, and a failure strain of 6.32%.

Abstract The ATR kinase, which coordinates cellular responses to DNA replication stress, is also essential for the proliferation of normal unstressed cells. Although its role in the replication stress response is well defined, the mechanisms by which ATR supports normal cell proliferation remain elusive. Here, we show that ATR is dispensable for the viability of G0-arrested naïve B cells. However, upon cytokine-induced proliferation, Atr-deficient B cells initiate DNA replication efficiently, but by mid-S phase they display dNTP depletion, fork stalling, and replication failure. Nonetheless, productive DNA replication and dNTP levels can be restored in Atr-deficient cells by suppressing origin firing, such as partial inhibition of CDC7 and CDK1 kinase activities. Together, these findings indicate that ATR supports the proliferation of normal unstressed cells by tempering the pace of origin firing during the early S phase to avoid exhaustion of dNTPs and importantly also other replication factors.

Glioblastoma is an immunologically cold tumour, with poor CD8 + T cell infiltration and enrichment in immunosuppressive tumour-associated myeloid cells. Here, the authors generate a bispecific lipid nanoparticle targeting CD47 and PD-L1, combined with a STING agonist, to promote anti-tumour immunity.

Immunotherapies have shown limited efficacy in patients with glioma. Here, based on an in vivo kinome knockout CRISPR screen, the authors show that checkpoint kinase 2 promotes CD8 T cell immune evasion and that its depletion or inhibition improve survival and response to PD1/PDL1 blockade in preclinical glioma models.

The brick-and-mortar structure of shell nacre allows for the simultaneous enhancement of strength and plasticity through the synergistic effect of multiple toughening mechanisms at different scales. In this work, a novel nacre-like brick-and-mortar structure Ti6Al4V/Al3Ti metal-intermetallic laminate (BMS-MIL) composite was successfully fabricated via vacuum hot pressing sintering method. The BMS-MIL composite is mainly composed of Al3Ti and Ti phases, with a small amount of Al2Ti and AlTi phases. Al3Ti is in the shape of polygonal platelet, and a 5–8 μm diffusion layer composed of Al2Ti and AlTi is distributed on the surface of the platelets. Ti6Al4V connects the platelets and is present in a continuous network frame structure. Compared with the layered structure Ti6Al4V/Al3Ti metal-intermetallic laminate (LS-MIL) composite, the fracture strain of BMS-MIL composite increases by 125.1% while maintaining high strength under load perpendicular to layer, and the compressive strength of BMS-MIL composite increases by 26.3% under load parallel to layer, respectively. Material isotropy in compressive properties has been significantly improved. In bending tests, the strength of the BMS-MIL composite is 1.9 times that of the LS-MIL composite. The brick-and-mortar structure’s excellent strengthening and toughening effect benefits from the enhancement of its crack constraint.

Abstract Background Efficient presentation of mutant peptide fragments by the human leukocyte antigen class I (HLA-I) genes is necessary for immune-mediated killing of cancer cells. According to recent reports, patient HLA-I genotypes can impact the efficacy of cancer immunotherapy, and the somatic loss of HLA-I heterozygosity has been established as a factor in immune evasion. While global deregulated expression of HLA-I has also been reported in different tumor types, the role of HLA-I allele-specific expression loss — that is, the preferential RNA expression loss of specific HLA-I alleles — has not been fully characterized in cancer. Methods Here, we use RNA and whole-exome sequencing data to quantify HLA-I allele-specific expression (ASE) in cancer using our novel method arcasHLA-quant. Results We show that HLA-I ASE loss in at least one of the three HLA-I genes is a pervasive phenomenon across TCGA tumor types. In pancreatic adenocarcinoma, tumor-specific HLA-I ASE loss is associated with decreased overall survival specifically in the basal-like subtype, a finding that we validated in an independent cohort through laser-capture microdissection. Additionally, we show that HLA-I ASE loss is associated with poor immunotherapy outcomes in metastatic melanoma through retrospective analyses. Conclusions Together, our results highlight the prevalence of HLA-I ASE loss and provide initial evidence of its clinical significance in cancer prognosis and immunotherapy treatment.

BackgroundPulmonary arterial end-diastolic forward flow (EDFF) following repaired tetralogy of Fallot (rTOF) is recognized as right ventricular (RV) restrictive physiology, which is closely related to poor prognosis. This study sought to review mid-term experience and investigate the risk factors of EDFF in the rTOF patients.MethodsFrom September 2016 to January 2019, 100 patients (age < 18 years old) who underwent complete tetralogy of Fallot (TOF) repair were enrolled and were divided into EDFF group (n = 52) and non-EDFF group (n = 48) based on the presence of postoperative EDFF. Elastic net analysis was performed for variable selection. Univariate and multivariate logistic analyses were used to analyze the correlation between risk factors and EDFF.ResultsEnd-diastolic forward flow group had lower systolic blood pressure (P = 0.037), diastolic blood pressure (P = 0.027), and higher vasoactive-inotrope score within 24 h after surgery (P = 0.022) than non-EDFF group. Transannular patch (TAP) was an independent predictor of postoperative EDFF [P = 0.029, OR: 2.585 (1.102∼6.061)]. Patients were followed up for a median of 2.6 years [interquartile range (IQR) 1.6] after the first TOF repair. During follow-up, the prevalence of the EDFF was lower in those with pulmonary valve (PV) reconstructions than that in those undergoing patch enlargement without PV reconstructions in the primary TOF repair (P < 0.001).ConclusionEnd-diastolic forward flow was associated with TAP. Patients with EDFF might have a transient hemodynamic instability in the early postoperative period. PV reconstructions in the TOF repair might reduce the incidence of EDFF in the mid-term follow-up.

Adipose tissue is a crucial regulator in maintaining cardiovascular homeostasis by secreting various bioactive products to mediate the physiological function of the cardiovascular system. Accumulating evidence shows that adipose tissue disorders contribute to several kinds of cardiovascular disease (CVD). Furthermore, the adipose tissue would present various biological effects depending on its tissue localization and metabolic statuses, deciding the individual cardiometabolic risk. Crosstalk between adipose and myocardial tissue is involved in the pathophysiological process of arrhythmogenic right ventricular cardiomyopathy (ARVC), cardiac fibrosis, heart failure, and myocardial infarction/atherosclerosis. The abnormal distribution of adipose tissue in the heart might yield direct and/or indirect effects on cardiac function. Moreover, mechanical transduction is critical for adipocytes in differentiation, proliferation, functional maturity, and homeostasis maintenance. Therefore, understanding the features of mechanotransduction pathways in the cellular ontogeny of adipose tissue is vital for underlining the development of adipocytes involved in cardiovascular disorders, which would preliminarily contribute positive implications on a novel therapeutic invention for cardiovascular diseases. In this review, we aim to clarify the role of mechanical stress in cardiac adipocyte homeostasis and its interplay with maintaining cardiac function.

The association between acrylamide (AA) and the development of cancer has been extensively discussed but the results remained controversial, especially in population studies. Large prospective epidemiological studies on the relationship of AA exposure with cancer mortality were still lacking. Therefore, we aimed to assess the association between AA biomarkers and cancer mortality in adult population from National Health and Nutrition Examination Survey (NHANES) 2003-2014. We followed 3717 participants for an average of 10.3 years. Cox regression models with multivariable adjustments were performed to determine the relationship of acrylamide hemoglobin adduct (HbAA) and glycidamide hemoglobin adduct (HbGA) with cancer mortality. Mediation analysis was conducted to demonstrate the mediated role of low-grade inflammation score (INFLA-score) in this correlation. Compared with the lowest quintile, participants with the highest quintile of HbAA, HbGA and HbAA+HbGA had increased cancer mortality risk, and the hazard ratios(HRs) were 2.07 (95%CI:1.04-4.14) for HbAA, 2.39 (95%CI:1.29-4.43) for HbGA and 2.48 (95%CI:1.28-4.80) for HbAA+HbGA, respectively. And there was a considerable non-linearity association between HbAA and cancer mortality (pfor non-linearity = 0.0139). We further found that increased INFLA-score significantly mediated 71.67% in the effect of HbGA exposure on increased cancer mortality risk. This study demonstrates that hemoglobin biomarkers of AA are positively associated with cancer mortality in adult American population and INFLA-score plays a mediated role in this process. Our findings can raise public awareness of environmental and dietary exposure to acrylamide and remind people to refrain from smoking or having acrylamide-rich foods.

Abstract Background Macrophages are the most common infiltrating immune cells in gliomas and play a wide variety of pro-tumor and anti-tumor roles. However, the different subpopulations of macrophages and their effects on the tumor microenvironment remain poorly understood. Methods We combined new and previously published single-cell RNA-seq data from 98,015 single cells from a total of 66 gliomas to profile 19,331 individual macrophages. Results Unsupervised clustering revealed a pro-tumor subpopulation of bone marrow-derived macrophages characterized by the scavenger receptor MARCO, which is almost exclusively found in IDH1-wild-type glioblastomas. Previous studies have implicated MARCO as an unfavorable marker in melanoma and non-small cell lung cancer; here, we find that bulk MARCO expression is associated with worse prognosis and mesenchymal subtype. Furthermore, MARCO expression is significantly altered over the course of treatment with anti-PD1 checkpoint inhibitors in a response-dependent manner, which we validate with immunofluorescence imaging. Conclusions These findings illustrate a novel macrophage subpopulation that drives tumor progression in glioblastomas and suggest potential therapeutic targets to prevent their recruitment.

Abstract Massive genome sequencing data have inspired new challenges in personalized treatments and facilitated oncological drug discovery. We present a comprehensive database, My Personal Mutanome (MPM), for accelerating the development of precision cancer medicine protocols. MPM contains 490,245 mutations from over 10,800 tumor exomes across 33 cancer types in The Cancer Genome Atlas mapped to 94,563 structure-resolved/predicted protein-protein interaction interfaces (“edgetic”) and 311,022 functional sites (“nodetic”), including ligand-protein binding sites and 8 types of protein posttranslational modifications. In total, 8884 survival results and 1,271,132 drug responses are obtained for these mapped interactions. MPM is available at https://mutanome.lerner.ccf.org .

Recurrent glioblastomas (rGBM) have dismal outcomes, but long-term survival has been observed in subsets of patients after immunotherapy. Here the authors report a positive association between low tumor mutation burden, inflammatory gene signatures, and survival after immunotherapy in rGBM patients.

Chemotherapy resistance in recurrent gliomas is a large hurdle for successful therapy. Here, the authors show that some recurrent gliomas harbour O-6-methylguanine-DNA methyltransferase (MGMT) genomic rearrangements, and in vitro and in vivo these contribute to temozolomide resistance.

Abstract Background Coronavirus Disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has now been confirmed worldwide. Yet, COVID-19 is strangely and tragically selective. Morbidity and mortality due to COVID19 rise dramatically with age and co-existing health conditions, including cancer and cardiovascular diseases. Human genetic factors may contribute to the extremely high transmissibility of SARS-CoV-2 and to the relentlessly progressive disease observed in a small but significant proportion of infected individuals, but these factors are largely unknown. Main body In this study, we investigated genetic susceptibility to COVID-19 by examining DNA polymorphisms in ACE2 and TMPRSS2 (two key host factors of SARS-CoV-2) from ~ 81,000 human genomes. We found unique genetic susceptibility across different populations in ACE2 and TMPRSS2. Specifically, ACE2 polymorphisms were found to be associated with cardiovascular and pulmonary conditions by altering the angiotensinogen-ACE2 interactions, such as p.Arg514Gly in the African/African-American population. Unique but prevalent polymorphisms (including p.Val160Met (rs12329760), an expression quantitative trait locus (eQTL)) in TMPRSS2, offer potential explanations for differential genetic susceptibility to COVID-19 as well as for risk factors, including those with cancer and the high-risk group of male patients. We further discussed that polymorphisms in ACE2 or TMPRSS2 could guide effective treatments (i.e., hydroxychloroquine and camostat) for COVID-19. Conclusion This study suggested that ACE2 or TMPRSS2 DNA polymorphisms were likely associated with genetic susceptibility of COVID-19, which calls for a human genetics initiative for fighting the COVID-19 pandemic.

An innovational self-reduction molecular-level-mixing method was proposed as a simplified manufacturing technique for the production of carbon nanotube copper matrix composites (CNT/Cu). Copper matrix composites reinforced with varying amounts of (0.1, 0.3, 0.5 and 0.7 wt%) carbon nanotubes were fabricated by using this method combined with hot-pressing sintering technology. The surface structure and elemental distribution during the preparation of CNT/Cu mixing powder were investigated. The microstructure and comprehensive properties of the CNT/Cu composites were examined by metallography, mechanical and electrical conductivity tests. The results revealed that the CNT/Cu could be produced by a high temperature reaction at 900 degrees under vacuum, during which the carbon atoms in the carbon nanotubes reduced the divalent copper on the surface to zero-valent copper monomers. The decrease in the ratio of D and G peaks on the Raman spectra indicated that the defective spots on the carbon nanotubes were wrapped and covered by the copper atoms after a self-reduction reaction. The prepared CNT/Cu powders were uniformly embedded in the grain boundaries of the copper matrix materials and effectively hindered the tensile fracture. The overall characteristics of the CNT/Cu composites steadily increased with increasing CNT until the maximum at 0.7 wt%. The performance was achieved with a hardness of 86.1 HV, an electrical conductivity of 81.8% IACS, and tensile strength of 227.5 MPa.

Atrial fibrillation is the most common form of cardiac arrhythmia. Atrial fibrosis is a significant feature of atrial fibrillation though its mechanism is not well understood. We searched the Gene Expression Omnibus database to compare mRNA expression patterns between atrial fibrillation and sinus rhythm samples; one hundred and forty eight differentially expressed genes were identified. Most of these genes were significantly enriched in the extracellular matrix organization process and collagen-activated tyrosine kinase receptor signaling pathway. To screen hub genes involved in atrial fibrosis, we constructed a protein-protein interaction network and found that three hub genes (SERPINE1/plasminogen activator inhibitor-1/PAI-1, TIMP Metallopeptidase Inhibitor 3/TIMP3 and decorin/DCN) play vital roles in atrial fibrosis, especially plasminogen activator inhibitor-1. Elevated plasminogen activator inhibitor-1 expression was positively correlated with the p53 signaling pathway. Plasminogen activator inhibitor-1 and p53 protein expression levels were verified in patients with sinus rhythm and atrial fibrillation by Western blot analysis. Compared with the sinus rhythm controls, p53 and plasminogen activator inhibitor-1 protein expressions were upregulated in the atrial tissues of patients with atrial fibrillation. p53 was also found to regulate plasminogen activator inhibitor-1 based on the results of cellular and molecular experiments. Thus, the p53/plasminogen activator inhibitor-1 signaling axis may participate in the pathophysiological processes of atrial fibrillation, and plasminogen activator inhibitor-1 may serve as a new therapeutic biomarker in atrial fibrillation.

Tumor-specific genomic alterations allow systematic identification of genetic interactions that promote tumorigenesis and tumor vulnerabilities, offering novel strategies for development of targeted therapies for individual patients. We develop an Individualized Network-based Co-Mutation (INCM) methodology by inspecting over 2.5 million nonsynonymous somatic mutations derived from 6,789 tumor exomes across 14 cancer types from The Cancer Genome Atlas. Our INCM analysis reveals a higher genetic interaction burden on the significantly mutated genes, experimentally validated cancer genes, chromosome regulatory factors, and DNA damage repair genes, as compared to human pan-cancer essential genes identified by CRISPR-Cas9 screenings on 324 cancer cell lines. We find that genes involved in the cancer type-specific genetic subnetworks identified by INCM are significantly enriched in established cancer pathways, and the INCM-inferred putative genetic interactions are correlated with patient survival. By analyzing drug pharmacogenomics profiles from the Genomics of Drug Sensitivity in Cancer database, we show that the network-predicted putative genetic interactions (e.g., BRCA2-TP53) are significantly correlated with sensitivity/resistance of multiple therapeutic agents. We experimentally validated that afatinib has the strongest cytotoxic activity on BT474 (IC50 = 55.5 nM, BRCA2 and TP53 co-mutant) compared to MCF7 (IC50 = 7.7 μM, both BRCA2 and TP53 wild type) and MDA-MB-231 (IC50 = 7.9 μM, BRCA2 wild type but TP53 mutant). Finally, drug-target network analysis reveals several potential druggable genetic interactions by targeting tumor vulnerabilities. This study offers a powerful network-based methodology for identification of candidate therapeutic pathways that target tumor vulnerabilities and prioritization of potential pharmacogenomics biomarkers for development of personalized cancer medicine.

Abstract Background Genome–phenome studies have identified thousands of variants that are statistically associated with disease or traits; however, their functional roles are largely unclear. A comprehensive investigation of regulatory mechanisms and the gene regulatory networks between phenome-wide association study (PheWAS) and genome-wide association study (GWAS) is needed to identify novel regulatory variants contributing to risk for human diseases. Methods In this study, we developed an integrative functional genomics framework that maps 215,107 significant single nucleotide polymorphism (SNP) traits generated from the PheWAS Catalog and 28,870 genome-wide significant SNP traits collected from the GWAS Catalog into a global human genome regulatory map via incorporating various functional annotation data, including transcription factor (TF)-based motifs, promoters, enhancers, and expression quantitative trait loci (eQTLs) generated from four major functional genomics databases: FANTOM5, ENCODE, NIH Roadmap, and Genotype-Tissue Expression (GTEx). In addition, we performed a tissue-specific regulatory circuit analysis through the integration of the identified regulatory variants and tissue-specific gene expression profiles in 7051 samples across 32 tissues from GTEx. Results We found that the disease-associated loci in both the PheWAS and GWAS Catalogs were significantly enriched with functional SNPs. The integration of functional annotations significantly improved the power of detecting novel associations in PheWAS, through which we found a number of functional associations with strong regulatory evidence in the PheWAS Catalog. Finally, we constructed tissue-specific regulatory circuits for several complex traits: mental diseases, autoimmune diseases, and cancer, via exploring tissue-specific TF-promoter/enhancer-target gene interaction networks. We uncovered several promising tissue-specific regulatory TFs or genes for Alzheimer’s disease (e.g. ZIC1 and STX1B) and asthma (e.g. CSF3 and IL1RL1). Conclusions This study offers powerful tools for exploring the functional consequences of variants generated from genome–phenome association studies in terms of their mechanisms on affecting multiple complex diseases and traits.

The relationship between anti-tumoral immunity and cancer progression is complex. Recently, immune editing has emerged as a model to explain the interplay between the immune system and the selection of genetic alterations in cancer. In this model, the immune system selects cancer cells that grow as these are fit to escape immune surveillance during tumor development. Gliomas and glioblastoma, the most aggressive and most common of all primary malignant brain tumors are genetically heterogeneous, are relatively less antigenic, and are less responsive to immunotherapy than other cancers. In this review, we provide an overview of the relationship between glioma´s immune suppressive features, anti-tumoral immunity and cancer genomics. In this context, we provide a critical discussion of evidence suggestive of immune editing in this disease and discuss possible alternative explanations for these findings.

Viruses require host cellular factors for successful replication. A comprehensive systems-level investigation of the virus-host interactome is critical for understanding the roles of host factors with the end goal of discovering new druggable antiviral targets. Gene-trap insertional mutagenesis is a high-throughput forward genetics approach to randomly disrupt (trap) host genes and discover host genes that are essential for viral replication, but not for host cell survival. In this study, we used libraries of randomly mutagenized cells to discover cellular genes that are essential for the replication of 10 distinct cytotoxic mammalian viruses, 1 gram-negative bacterium, and 5 toxins. We herein reported 712 candidate cellular genes, characterizing distinct topological network and evolutionary signatures, and occupying central hubs in the human interactome. Cell cycle phase-specific network analysis showed that host cell cycle programs played critical roles during viral replication (e.g. MYC and TAF4 regulating G0/1 phase). Moreover, the viral perturbation of host cellular networks reflected disease etiology in that host genes (e.g. CTCF, RHOA, and CDKN1B) identified were frequently essential and significantly associated with Mendelian and orphan diseases, or somatic mutations in cancer. Computational drug repositioning framework via incorporating drug-gene signatures from the Connectivity Map into the virus-host interactome identified 110 putative druggable antiviral targets and prioritized several existing drugs (e.g. ajmaline) that may be potential for antiviral indication (e.g. anti-Ebola). In summary, this work provides a powerful methodology with a tight integration of gene-trap insertional mutagenesis testing and systems biology to identify new antiviral targets and drugs for the development of broadly acting and targeted clinical antiviral therapeutics.

Cancer development and progression result from somatic evolution by an accumulation of genomic alterations. The effects of those alterations on the fitness of somatic cells lead to evolutionary adaptations such as increased cell proliferation, angiogenesis, and altered anticancer drug responses. However, there are few general mathematical models to quantitatively examine how perturbations of a single gene shape subsequent evolution of the cancer genome. In this study, we proposed the gene gravity model to study the evolution of cancer genomes by incorporating the genome-wide transcription and somatic mutation profiles of ~3,000 tumors across 9 cancer types from The Cancer Genome Atlas into a broad gene network. We found that somatic mutations of a cancer driver gene may drive cancer genome evolution by inducing mutations in other genes. This functional consequence is often generated by the combined effect of genetic and epigenetic (e.g., chromatin regulation) alterations. By quantifying cancer genome evolution using the gene gravity model, we identified six putative cancer genes (AHNAK, COL11A1, DDX3X, FAT4, STAG2, and SYNE1). The tumor genomes harboring the nonsynonymous somatic mutations in these genes had a higher mutation density at the genome level compared to the wild-type groups. Furthermore, we provided statistical evidence that hypermutation of cancer driver genes on inactive X chromosomes is a general feature in female cancer genomes. In summary, this study sheds light on the functional consequences and evolutionary characteristics of somatic mutations during tumorigenesis by propelling adaptive cancer genome evolution, which would provide new perspectives for cancer research and therapeutics.