Comprehensive single-cell analysis deciphered microenvironmental dynamics and immune regulator olfactomedin 4 in pathogenesis of gallbladder cancer.

OBJECTIVE: Elucidating complex ecosystems and molecular features of gallbladder cancer (GBC) and benign gallbladder diseases is pivotal to proactive cancer prevention and optimal therapeutic intervention. DESIGN: We performed single-cell transcriptome analysis on 230 737 cells from 15 GBCs, 4 cholecystitis samples, 3 gallbladder polyps, 5 gallbladder adenomas and 16 adjacent normal tissues. Findings were validated through large-scale histological assays, digital spatial profiler multiplexed immunofluorescence (GeoMx), etc. Further molecular mechanism was demonstrated with in vitro and in vivo studies. RESULTS: The cell atlas unveiled an altered immune landscape across different pathological states of gallbladder diseases. GBC featured a more suppressive immune microenvironment with distinct T-cell proliferation patterns and macrophage attributions in different GBC subtypes. Notably, mutual exclusivity between stromal and immune cells was identified and remarkable stromal ecosystem (SC) heterogeneity during GBC progression was unveiled. Specifically, SC1 demonstrated active interaction between Fibro-iCAF and Endo-Tip cells, correlating with poor prognosis. Moreover, epithelium genetic variations within adenocarcinoma (AC) indicated an evolutionary similarity between adenoma and AC. Importantly, our study identified elevated olfactomedin 4 (OLFM4) in epithelial cells as a central player in GBC progression. OLFM4 was related to T-cell malfunction and tumour-associated macrophage infiltration, leading to a worse prognosis in GBC. Further investigations revealed that OLFM4 upregulated programmed death-ligand 1 (PD-L1) expression through the MAPK-AP1 axis, facilitating tumour cell immune evasion. CONCLUSION: These findings offer a valuable resource for understanding the pathogenesis of gallbladder diseases and indicate OLFM4 as a potential biomarker and therapeutic target for GBC.

Rheumatoid arthritis reduces the risk of colorectal cancer through immune inflammation mediation.

There is a close relationship between immune-mediated inflammation and cancer, and there is still controversy over whether rheumatoid arthritis (RA) increases the risk of malignancy. We first used Mendelian randomization (MR) analysis to explore the potential causal relationship between RA and pan-cancer. And verify the effect of immune-mediated inflammation on cancer through intermediate MR analysis. Then we extracted the standardized incidence rate of malignancy in RA patients relative to the general population through large-scale meta-analysis. Finally, we performed pan-cancer analysis on the RA related genes obtained from MR analysis. And perform immune related analysis on key genes to reveal the association between RA and malignancy. The MR analysis demonstrated a negative correlation between RA and pan-cancer (p = 0.008). Autoimmune traits were the main mediating variable for the causal relationship between RA and pan-cancer. Based on the results of the meta-analysis, we validated that RA reduces the risk of developing colorectal cancer (SIR = 0.69, 95% CI 0.53-0.85). Pan-cancer analysis also showed that high expression of RA related genes was negatively correlated with colon adenocarcinoma. IL6R was the gene with the highest correlation among them, and its correlation with immune cells was higher in colorectal cancer than in other malignancy. Our MR study provides evidence that RA was associated with reduced risk of colorectal cancer. This effect is caused by immune-mediated inflammation, with IL6R being a key regulatory gene.

2D Ultrathin Titanium Nitride Nanosheets as Separator Coatings for Li-S Batteries.

Transition metal nitrides (TMNs) are affirmed to be an appealing candidate for boosting the performance of lithium-sulfur (Li-S) batteries due to their excellent conductivity, strong interaction with sulfur species, and the effective catalytic ability for conversion of polysulfides. However, the traditional bulk TMNs are difficult to achieve large active surface area and fast transport channels for electrons/ions simultaneously. Here, a 2D ultrathin geometry of titanium nitride (TiN) is realized by a facile topochemical conversion strategy, which can not only serve as an interconnected conductive platform but also expose abundant catalytic active sites. The ultrathin TiN nanosheets are coated on a commercial separator, serving as a multifunctional interlayer in Li-S batteries for hindering the polysulfide shuttle effect by strong capture and fast conversion of polysulfides, achieving a high initial capacity of 1357 mAh g-1 at 0.1 C and demonstrating a low capacity decay of only 0.046% per cycle over 1000 cycles at 1 C.

Boosting Up Electrosynthesis of Urea with Nitrate and Carbon Dioxide via Synergistic Effect of Metallic Iron Cluster and Single-Atom.

Electrocatalytic conversion of nitrates and carbon dioxide to urea under ambient conditions shows promise as a potential substitute for traditional urea synthesis processes characterized by high consumption and pollution. In this study, a straightforward one-pot method is employed to prepare a highly efficient FeNC-Fe1N4 electrocatalyst, consisting of atomically dispersed Fe1N4 sites and metallic Fe clusters (FeNC) with particle size of 4-7 nm. The FeNC-Fe1N4 catalyst exhibits remarkable electrocatalytic activity for urea synthesis from nitrate anion (NO3 -) and carbon dioxide (CO2), achieving a urea production rate of 38.2 mmol gcat -1 h-1 at -0.9 V (vs RHE) and a Faradaic efficiency of 66.5% at -0.6 V (vs RHE). Both experimental and theoretical results conclusively demonstrate that metallic Fe clusters and Fe1N4 species provide active sites for the adsorption and activation of NO3 - and CO2, respectively, and the synergistic effect between Fe1N4 and metallic Fe clusters significantly enhances the electrochemical efficiency of urea synthesis. In all, this work contributes to the rational design and comprehensive synthesis of a dual-active site iron-based electrocatalyst, facilitating efficient and sustainable urea synthesis.

The Mutational, Prognostic, and Therapeutic Landscape of Neuroendocrine Neoplasms.

BACKGROUND: Neuroendocrine neoplasms (NENs) represent clinically and genetically heterogeneous malignancies, thus a comprehensive understanding of underlying molecular characteristics, prognostic signatures, and potential therapeutic targets is urgently needed. METHODS: Next-generation sequencing (NGS) and immunohistochemistry were applied to acquire genomic and immune profiles of NENs from 47 patients. RESULTS: Difference was distinguished based on differentiation grade and primary localization. Poorly differentiated neuroendocrine carcinomas (NECs) and well-differentiated neuroendocrine tumors (NETs) harbored distinct molecular features; we observed that tumor mutational burden (TMB) and tumor neoantigen burden (TNB) were significantly higher in NECs versus NETs. Notably, we identified a 7-gene panel (MLH3, NACA, NOTCH1, NPAP1, RANBP17, TSC2, and ZFHX4) as a novel prognostic signature in NENs; patients who carried mutations in any of the 7 genes exhibited significantly poorer survival. Furthermore, loss of heterozygosity (LOH) and germline homogeneity in human leukocyte antigen (HLA) are common in NENs, accounting for 39% and 36%, respectively. Notably, HLA LOH was an important prognostic biomarker for a subgroup of NEN patients. Finally, we analyzed clinically actionable targets in NENs, revealing that TMB high (TMB-H) or gene mutations in TP53, KRAS, and HRAS were the most frequently observed therapeutic indicators, which granted eligibility to immune checkpoint blockade (ICB) and targeted therapy. CONCLUSION: Our study revealed heterogeneity of NENs, and identified novel prognostic signatures and potential therapeutic targets, which directing improvements of clinical management for NEN patients in the foreseeable future.

Synthesis and Self-Assembly of Ultrathin Holey Graphdiyne Nanosheets for Oxygen Reduction Reaction.

Graphdiyne (GDY) is a fascinating graphene-like 2D carbon allotrope comprising sp and sp2 hybridized carbon atoms. However, GDY materials synthesized by solution-phase methods normally come as thick and porous films or amorphous powders with severely disordered stacking modes that obstruct macroscopic applications. Here, a facile and scalable synthesis of ultrathin holey graphdiyne (HGDY) nanosheets is reported via palladium/copper co-catalyzed homocoupling of 1,3,5-triethynylbenzene. The resulting freestanding 2D HGDY self-assembles into 3D foam-like networks which can in situ anchor clusters of palladium atoms on their surfaces. The Pd/HGDY hybrids exhibit high electrocatalytic activity and stability for the oxygen reduction reaction which outperforms that of Pt/C benchmark. Based on the ultrathin graphene-like sheets and their unique 3D interconnected macrostructures, Pd/HGDY holds great promise for practical electrochemical catalysis and energy-related applications.

Characterization of the tumor microenvironment and identification of spatially predictive biomarkers associated with beneficial neoadjuvant chemoradiotherapy in locally advanced rectal cancer.

Neoadjuvant chemoradiotherapy (nCRT) has become the standard treatment for patients with locally advanced rectal cancer (LARC). However, 20-40% of patients with LARC show little to no response to nCRT. Thus, comprehensively understanding the tumor microenvironment (TME), which might influence therapeutic efficacy, and identifying robust predictive biomarkers is urgently needed. Pre-treatment tumor biopsy specimens from patients with LARC were evaluated in detail through digital spatial profiling (DSP), public RNA sequencing datasets, and multiplex immunofluorescence (mIF). DSP analysis revealed distinct characteristics of the tumor stroma compared to the normal stroma and tumor compartments. We identified high levels of human leukocyte antigen-DR/major histocompatibility complex class II (HLA-DR/MHC-II) in the tumor compartment and B cells in the stroma as potential spatial predictors of nCRT efficacy in the Discovery cohort. Public datasets validated their predictive capacity for clinical outcomes. Using mIF in an independent nCRT cohort and/or the total cohort, we validated that a high density of HLA-DR/MHC-II+ cells in the tumor and CD20 + B cells in the stroma was associated with nCRT efficacy (all p ≤ 0.021). Spatial profiling successfully characterized the LARC TME and identified robust biomarkers with the potential to accurately predict nCRT response. These findings have important implications for individualized therapy.

Biochar benefits carbon off-setting in blue-green infrastructure soils - A lysimeter study.

Carbon sequestration with amendments in blue-green infrastructure soils could off-set anthropogenic greenhouse gas emissions to alleviate climate change. In this 3-year study, the effects of wheat straw and its biochar on carbon sequestration in an urban landscaping soil were investigated under realistic outdoor conditions using two large-scale lysimeters. Both amendments were carried out by incorporating pellets at 0-15 cm soil depth with an equivalent initial total carbon input of 2% of the dry soil weight. Soil carbon, carbon isotope ratios, dissolved carbon in leachates, CO2-C emissions, carbon fixed in above ground vegetation, soil water content, soil bulk electrical conductivity, and water infiltration rates, were then compared between the 2 lysimeters. After 3 years, we observed that, despite having a 17.2% lower vegetation growth, soil organic and inorganic carbon content was higher by 28.8% and 41.5%, respectively, in biochar as compared to wheat straw amended soil. Carbon isotope analysis confirmed the greater stability of the added carbon in the biochar amended soil. Water content was on average 23.2% and 13.0% in the straw pellet and biochar amended soil, respectively, whereas water infiltration rates were not significantly different between the two lysimeters. Overall, the incorporation of wheat straw biochar into soil could store an estimated 30 tonnes of carbon per hectare in city blue-green infrastructure spaces. Interviews involving institution stakeholders examined the feasibility of this biochar application. Stakeholders recognized the potential of biochar as an environment-friendly means for carbon offsetting, but were concerned about the practicality of biochar production and application into soil and increased maintenance work. Consequently, additional potential benefits of biochar for environmental management such as improving the quality of polluted run-off in stormwater treatment systems should be emphasized to make biochar an attractive proposition in sustainable urban development.

[Effect of aerobic exercise on AKT/GSK3ß mediated hepatocyte apoptosis in nonalcoholic fatty liver disease].

OBJECTIVE: To investigate the effect of aerobic exercise on AKT/GSK3ß pathway-mediated hepatocyte apoptosis in non-alcoholic fatty liver diseases(NAFLD). METHODS: A total of 30 6-week-old male C57BL/6J mice, and mice were fed adaptively for one week. The control group was fed with ordinary diet, and the model group and model exercise group were fed with high-fat diet until 18 weeks. At the 10th week of the experiment, the model exercise group received aerobic exercise intervention for 8 consecutive weeks until the end of the experiment at the 18th week. Automatic biochemical analyzer to detect serum total cholesterol(TC), triglycerides(TG), alanine aminotransferase(ALT), aspartate aminotransferase(AST), low-density lipoprotein(LDL-C) and high-density lipoprotein(HDL-C) levels. Liver pathological morphology was observed by staining with oil red O and HE. The expression changes of AKT, P-AKT~( Ser473), GSK3ß, P-GSK3ß~(Ser9) and Caspase-3 proteins were detected by western blot, and the apoptosis of hepatocytes was detected by in situ terminal transferase labeling(TUNEL). RESULTS: (1) After intervention, compared with control group, body weight, liver index, serum TC, TG, ALT, AST and LDL-C levels in model group were significantly increased(P<0.01 or P<0.05), while HDL-C level was significantly decreased(P<0.01). Compared with model group, body weight, liver index, serum TC, TG, ALT, AST and LDL-C levels in model exercise group were significantly decreased(P<0.01 or P<0.05), while HDL-C level was significantly increased(P<0.01). (2) Compared with the control group, hepatocyte steatosis and the number of lipid droplets in model group were significantly increased. Compared with the model group, the degree of hepatic adipose degeneration was significantly improved and the number of hepatic lipid droplets was significantly decreased in the model exercise group. (3) Compared with control group, the protein expression levels of P-AKT~(Ser473) and P-GSK3ß~(Ser9) in model group were significantly decreased(P<0.01 or P<0.05), the protein expression levels of Caspase-3 were significantly increased(P<0.05), and the number of hepatocyte apoptosis was significantly increased(P<0.05). Compared with model group, the expression of P-AKT~(Ser473) and P-GSK3ß~(Ser9) protein in model exercise group was significantly increased(P<0.01 or P<0.05), the expression of Caspase-3 protein was significantly decreased(P<0.05), and the number of hepatocyte apoptosis was significantly decreased(P<0.01). CONCLUSION: Aerobic exercise can effectively improve NAFLD, by activating AKT/GSK3ß pathway and increasing the expression of AKT/GSK3ß pathway related molecules, thereby reducing caspase-3 expression and hepatocyte apoptosis.

Palladium and Ruthenium Dual-Single-Atom Sites on Porous Ionic Polymers for Acetylene Dialkoxycarbonylation: Synergetic Effects Stabilize the Active Site and Increase CO Adsorption.

Heterogeneous single-metal-site catalysts usually suffer from poor stability, thereby limiting industrial applications. Dual Pd1 -Ru1 single-atom-sites supported on porous ionic polymers (Pd1 -Ru1 /PIPs) were constructed using a wetness impregnation method. The two isolated metal species in the form of a binuclear complex were immobilized on the cationic framework of PIPs through ionic bonds. Compared to the single Pd- or Ru-site catalyst, the dual single-atom system exhibits higher activity with 98 % acetylene conversion and near 100 % selectivity to dialkoxycarbonylation products, as well as better cycling stability for ten cycles without obvious decay. Based on DFT calculations, it was found that the single-Ru site exhibited a strong CO adsorption energy of -1.6 eV, leading to an increase in the local CO concentration of the catalyst. Notably, the Pd1 -Ru1 /PIPs catalyst had a much lower energy barrier of 2.49 eV compared to 3.87 eV of Pd1 /PIPs for the rate-determining step. The synergetic effect between neighboring single sites Pd1 and Ru1 not only enhanced the overall activity, but also stabilized PdII active sites. The discovery of synergetic effects between single sites can deepen our understanding of single-site catalysts at the molecular level.

Comparison of immune cells and diagnostic markers between spondyloarthritis and rheumatoid arthritis by bioinformatics analysis.

BACKGROUND: Spondyloarthritis (SpA) and rheumatoid arthritis (RA) are chronic autoimmune diseases, but they are usually difficult to distinguish in the early stage of the diseases. The purpose of this study is to explore the differences of immune mechanism and diagnostic markers through bioinformatics analysis. METHODS: First, microarray datasets from patients with SpA, RA and normal controls were obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between groups were identified in R software. Functional and pathway enrichment of DEGs were analyzed by David database. Then, we screened the hub genes using Cytoscape plugin, and constructed the protein-protein interaction (PPI) network and heatmap of hub genes. After that, CIBERSORT was used to evaluate the differences and connections of immune cells in SpA and RA, and screened out diagnostic markers. Correlation analysis was used to analyze the relationship between immune cells and diagnostic markers. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) was used to verify the effectiveness of immunodiagnostic markers. RESULTS: We obtained three datasets, from which we can see that the functional enrichment of DEGs is mainly in cell chemotaxis, lymphocyte activation, primary immunodeficiency and other immune responses. The difference of immune cells between SpA, RA and normal control was concentrated in B, T lymphocytes cells, macrophages and dendritic cells. C19orf12 + S1PR3 is most associated with these immune cells and S1PR3 can be used as a diagnostic marker of this kind of immune diseases. In addition, MZB1 + XIST is closely related to T cells, NK cells and dendritic cells, and is expected to be used as a marker to distinguish the two diseases. CONCLUSION: Although the clinical manifestations of SpA and RA are similar, the pathogenesis is different. The screening of immune cells and diagnostic markers provides a more accurate target for the treatment of this kind of diseases.

Efficiency enhancement of organic light-emitting diodes via a self-assembled moth-eye nanopatterned hole-transporting layer.

A moth-eye nanopatterned hole-transporting layer (ME-HTL) is proposed to enhance the device efficiency of organic light-emitting diodes (OLEDs), which is fabricated via spontaneous phase separation during spin-coating between poly(N-vinylcarbazole) (PVK) and poly (9,9-dioctylfluorene) (PFO) induced by their surface energy difference. Meanwhile, film morphology characteristics confirm the conformal deposition of the following organic layers and metal electrode on the ME-HTL, indicating the extension of ME nanostructure over all layers in OLEDs. Finally, owning to the disruption of the internal waveguide light at the organic layer/anode interface and the suppression of surface plasmonic loss at organic layer/cathode interface, this device architecture obtained a current efficiency of 78.9 cd/A, with an enhancement factor of 40%. This approach takes the advantage of manufacturing compatibility on behalf of solution-process and thus can be a promising strategy to reduce the production cost of OLEDs.

Three-dimensional spiral motion of microparticles by a binary-phase logarithmic-spiral zone plate.

Acoustic vortex beams, which have both linear and angular momentum, can be used to make precise acoustic tweezers. Limited by the symmetry of a normal vortex beam, these tweezers are usually used for trapping or rotating particles in two dimensions. Here, the three-dimensional spiral motion of two soft particles of different sizes was realized using a vortex beam with a twisted focus, which was synthesized by a silicone binary-phase logarithmic-spiral zone plate. Numerical simulations and experimental measurements demonstrated that the beam had anisotropic focuses of crescent transverse intensity profiles and a screw phase dislocation with a singularity at the center. Experiments showed that a small particle (k0r ≈ 1.3) can follow the twisted intensity of the beam, but a large particle (k0r ≈ 4.7) spirals up away from the twisted field pattern. This is attributed to the dominant gradient force for the small particle, whereas the scattering effect induced a scattering force combined with a gradient force for the large particle. This focused twisted beam, which was generated with a structured silicone plate, and the three-dimensional spiral motion of microparticles, advance the development of simple, compact, and disposable acoustic devices for the precise and diverse manipulation of microparticles.

A deep learning approach for the fast generation of acoustic holograms.

Acoustic holographic techniques are crucial in diverse applications, such as three-dimensional holographic display and particle manipulation. However, conventional methods for computer-generated acoustics holography rely heavily on iterative optimization algorithms, which are time-consuming and particularly hinder their capacity of generating a dynamic hologram in real time. Here, a deep learning approach based on U-Net is proposed to rapidly generate an acoustic hologram with optimal amplitude and phase maps. It is demonstrated that, after being trained with adequate data that are numerically synthesized by the pseudo-inverse method, the proposed deep learning approach can generate both amplitude and phase maps for new target images with an improved overall reconstruction quality. Remarkably, after the offline cost is compensated by a lower online cost for the proposed DL approach, the hologram generation speed is significantly accelerated by the proposed deep learning approach as compared with the pseudo-inverse method, especially for complicated or dynamic images. With the hierarchical feature learning capability and the fast online computational speed, the proposed deep learning approach can serve as a smart platform for rapidly generating complete maps of holograms for the sophisticated or dynamical target images, leading to the new possibility of real-time acoustic-hologram-based applications.

TruNeo: an integrated pipeline improves personalized true tumor neoantigen identification.

BACKGROUND: Neoantigen-based personal vaccines and adoptive T cell immunotherapy have shown high efficacy as a cancer treatment in clinical trials. Algorithms for the accurate prediction of neoantigens have played a pivotal role in such studies. Some existing bioinformatics methods, such as MHCflurry and NetMHCpan, identify neoantigens mainly through the prediction of peptide-MHC binding affinity. However, the predictive accuracy of immunogenicity of these methods has been shown to be low. Thus, a ranking algorithm to select highly immunogenic neoantigens of patients is needed urgently in research and clinical practice. RESULTS: We develop TruNeo, an integrated computational pipeline to identify and select highly immunogenic neoantigens based on multiple biological processes. The performance of TruNeo and other algorithms were compared based on data from published literature as well as raw data from a lung cancer patient. Recall rate of immunogenic ones among the top 10-ranked neoantigens were compared based on the published combined data set. Recall rate of TruNeo was 52.63%, which was 2.5 times higher than that predicted by MHCflurry (21.05%), and 2 times higher than NetMHCpan 4 (26.32%). Furthermore, the positive rate of top 10-ranked neoantigens for the lung cancer patient were compared, showing a 50% positive rate identified by TruNeo, which was 2.5 times higher than that predicted by MHCflurry (20%). CONCLUSIONS: TruNeo, which considers multiple biological processes rather than peptide-MHC binding affinity prediction only, provides prioritization of candidate neoantigens with high immunogenicity for neoantigen-targeting personalized immunotherapies.

Identification of genomic alterations in oesophageal squamous cell cancer.

Oesophageal cancer is one of the most aggressive cancers and is the sixth leading cause of cancer death worldwide. Approximately 70% of global oesophageal cancer cases occur in China, with oesophageal squamous cell carcinoma (ESCC) being the histopathological form in the vast majority of cases (>90%). Currently, there are limited clinical approaches for the early diagnosis and treatment of ESCC, resulting in a 10% five-year survival rate for patients. However, the full repertoire of genomic events leading to the pathogenesis of ESCC remains unclear. Here we describe a comprehensive genomic analysis of 158 ESCC cases, as part of the International Cancer Genome Consortium research project. We conducted whole-genome sequencing in 17 ESCC cases and whole-exome sequencing in 71 cases, of which 53 cases, plus an additional 70 ESCC cases not used in the whole-genome and whole-exome sequencing, were subjected to array comparative genomic hybridization analysis. We identified eight significantly mutated genes, of which six are well known tumour-associated genes (TP53, RB1, CDKN2A, PIK3CA, NOTCH1, NFE2L2), and two have not previously been described in ESCC (ADAM29 and FAM135B). Notably, FAM135B is identified as a novel cancer-implicated gene as assayed for its ability to promote malignancy of ESCC cells. Additionally, MIR548K, a microRNA encoded in the amplified 11q13.3-13.4 region, is characterized as a novel oncogene, and functional assays demonstrate that MIR548K enhances malignant phenotypes of ESCC cells. Moreover, we have found that several important histone regulator genes (MLL2 (also called KMT2D), ASH1L, MLL3 (KMT2C), SETD1B, CREBBP and EP300) are frequently altered in ESCC. Pathway assessment reveals that somatic aberrations are mainly involved in the Wnt, cell cycle and Notch pathways. Genomic analyses suggest that ESCC and head and neck squamous cell carcinoma share some common pathogenic mechanisms, and ESCC development is associated with alcohol drinking. This study has explored novel biological markers and tumorigenic pathways that would greatly improve therapeutic strategies for ESCC.

Whole-Genome Sequencing Reveals Diverse Models of Structural Variations in Esophageal Squamous Cell Carcinoma.

Comprehensive identification of somatic structural variations (SVs) and understanding their mutational mechanisms in cancer might contribute to understanding biological differences and help to identify new therapeutic targets. Unfortunately, characterization of complex SVs across the whole genome and the mutational mechanisms underlying esophageal squamous cell carcinoma (ESCC) is largely unclear. To define a comprehensive catalog of somatic SVs, affected target genes, and their underlying mechanisms in ESCC, we re-analyzed whole-genome sequencing (WGS) data from 31 ESCCs using Meerkat algorithm to predict somatic SVs and Patchwork to determine copy-number changes. We found deletions and translocations with NHEJ and alt-EJ signature as the dominant SV types, and 16% of deletions were complex deletions. SVs frequently led to disruption of cancer-associated genes (e.g., CDKN2A and NOTCH1) with different mutational mechanisms. Moreover, chromothripsis, kataegis, and breakage-fusion-bridge (BFB) were identified as contributing to locally mis-arranged chromosomes that occurred in 55% of ESCCs. These genomic catastrophes led to amplification of oncogene through chromothripsis-derived double-minute chromosome formation (e.g., FGFR1 and LETM2) or BFB-affected chromosomes (e.g., CCND1, EGFR, ERBB2, MMPs, and MYC), with approximately 30% of ESCCs harboring BFB-derived CCND1 amplification. Furthermore, analyses of copy-number alterations reveal high frequency of whole-genome duplication (WGD) and recurrent focal amplification of CDCA7 that might act as a potential oncogene in ESCC. Our findings reveal molecular defects such as chromothripsis and BFB in malignant transformation of ESCCs and demonstrate diverse models of SVs-derived target genes in ESCCs. These genome-wide SV profiles and their underlying mechanisms provide preventive, diagnostic, and therapeutic implications for ESCCs.

MHC class II restricted neoantigen peptides predicted by clonal mutation analysis in lung adenocarcinoma patients: implications on prognostic immunological biomarker and vaccine design.

BACKGROUND: Mutant peptides presented by MHC (major histocompatibility complex) Class II in cancer are important targets for cancer immunotherapy. Both animal studies and clinical trials in cancer patients showed that CD4 T cells specific to tumor-derived mutant peptides are essential for the efficacy of immune checkpoint blockade therapy by PD1 antibody. RESULTS: In this study, we analyzed the next generation sequencing data of 147 lung adenocarcinoma patients from The Cancer Genome Atlas and predicted neoantigens presented by MHC Class I and Class II molecules. We found 18,175 expressed clonal somatic mutations, with an average of 124 per patient. The presentation of mutant peptides by an HLA(human leukocyte antigen) Class II molecule, HLA DRB1, were predicted by NetMHCIIpan3.1. 8804 neo-peptides, including 375 strong binders and 8429 weak binders were found. For HLA DRB1*01:01, 54 strong binders and 896 weak binders were found. The most commonly mutated genes with predicted neo-antigens are KRAS, TTN, RYR2, MUC16, TP53, USH2A, ZFHX4, KEAP1, STK11, FAT3, NAV3 and EGFR. CONCLUSIONS: Our results support the feasibility of discovering individualized HLA Class II presented mutant peptides as candidates for immunodiagnosis and immunotherapy of lung adenocarcinoma.