Pan-Cancer Analysis of the LOX Family Reveals that LOX Affects Tumor Prognosis by Affecting Immune Infiltration.

The lysyl oxidase (LOX) gene family encodes for a group of copper-dependent enzymes that play a crucial role in the cross-linking of collagen and elastin fibers in the extracellular matrix (ECM). Dysregulation of LOX gene expression has been implicated in various pathological conditions, including cancer. Several studies have shown that the LOX gene family is involved in cancer progression and metastasis. The goal of this article is to conduct a comprehensive analysis of the LOX family's role in pan-cancer multiplexes. We utilized pan-cancer multi-omics sequencing data from TCGA to investigate the relationship between LOX family genes and tumors at four different levels: mutation, copy number variation, methylation, and gene expression. In addition, we also examined the relationship between LOX family genes and tumors at the cell line level using tumor cell line sequencing data from CCLE. Taking into account the impact of LOX family genes on lung cancer, we developed a LOX family lung cancer prognostic model to forecast the disease's prognosis. Our findings revealed that LOXL2 had the highest mutation frequency in tumors, while all four LOX family genes experienced some degree of copy number variation in diverse tumors. We observed that LOX, LOXL1 to LOXL3 were predominantly highly expressed in tumors including LUAD. The expression trends of LOX and LOXL1 to LOXL3 were consistent across tumor cell lines, but differed somewhat from LOXL4. Utilizing 25 LOX family-related genes, we constructed a LOX family prognostic model that performed well in predicting the prognosis of lung cancer. Through pan-cancer analysis, we gain further knowledge of the role of LOX family genes in different tumors, offering a novel pathway for future research into the relationship between LOX family genes and tumors.

IAGS: Inferring Ancestor Genome Structure under a Wide Range of Evolutionary Scenarios.

Significant improvements in genome sequencing and assembly technology have led to increasing numbers of high-quality genomes, revealing complex evolutionary scenarios such as multiple whole-genome duplication events, which hinders ancestral genome reconstruction via the currently available computational frameworks. Here, we present the Inferring Ancestor Genome Structure (IAGS) framework, a novel block/endpoint matching optimization strategy with single-cut-or-join distance, to allow ancestral genome reconstruction under both simple (single-copy ancestor) and complex (multicopy ancestor) scenarios. We evaluated IAGS with two simulated data sets and applied it to four different real evolutionary scenarios to demonstrate its performance and general applicability. IAGS is available at https://github.com/xjtu-omics/IAGS.

Analysis of the 2p-manifold population distribution in a diode-pumped metastable Ar laser.

The complex excited energy levels in the diode-pumped metastable Ar laser may induce harmful effects in laser cycling. Significantly, the influence of the population distribution in 2p energy levels on the laser performance is unclear yet. In this work, the absolute populations in all the 2p states were measured online by the simultaneous applications of tunable diode laser absorption spectroscopy and optical emission spectroscopy. The results showed that most atoms were populated to the 2p8, 2p9, and 2p10 levels while lasing, and the majority of the 2p9 population was efficiently transferred to the 2p10 level with the aid of helium, which was beneficial for the laser performance.

Osteoblast MR deficiency protects against adverse ventricular remodeling after myocardial infarction.

RATIONALE: Mineralocorticoid receptor (MR) antagonists have been clinically used to treat heart failure. However, the underlying cellular and molecular mechanisms remain incompletely understood. METHODS AND RESULTS: Using osteoblast MR knockout (MRobko) mouse in combination with myocardial infarction (MI) model, we demonstrated that MR deficiency in osteoblasts significantly improved cardiac function, promoted myocardial healing, as well as attenuated cardiac hypertrophy, fibrosis and inflammatory response after MI. Gene expression profiling using RNA sequencing revealed suppressed expression of osteocalcin (OCN) in calvaria from MRobko mice compared to littermate control (MRfl/fl) mice with or without MI. Plasma levels of undercarboxylated OCN (ucOCN) were also markedly decreased in MRobko mice compared to MRfl/fl mice. Administration of ucOCN abolished the protective effects of osteoblast MR deficiency on infarcted hearts. Mechanistically, ucOCN treatment promoted proliferation and inflammatory cytokine secretion in macrophages. Spironolactone, an MR antagonist, significantly inhibited the expression and secretion of OCN in post-MI mice. More importantly, spironolactone decreased plasma levels of ucOCN and inflammatory cytokines in heart failure patients. CONCLUSIONS: MR deficiency in osteoblasts alleviates pathological ventricular remodeling after MI, likely through its regulation on OCN. Spironolactone may work through osteoblast MR/OCN axis to exert its therapeutic effects on pathological ventricular remodeling and heart failure in mice and human patients.

Mineralocorticoid receptor deficiency in Treg cells ameliorates DSS-induced colitis in a gut microbiota-dependent manner.

Mineralocorticoid receptor (MR) is a classic nuclear receptor and an effective drug target in the cardiovascular system. The function of MR in immune cells such as macrophages and T cells has been increasingly appreciated. The aim of this study was to investigate the function of Treg MR in the process of inflammatory bowel disease (IBD). We treated Treg MR-deficient (MRflox/flox Foxp3YFP-Cre , KO) mice and control (Foxp3YFP-Cre , WT) mice with dextran sodium sulphate (DSS) to induce colitis and found that the severity of DSS-induced colitis was markedly alleviated in Treg MR-deficient mice, accompanied by reduced production of inflammatory cytokines, and relieved infiltration of monocytes, neutrophils and interferon γ+ T cells in colon lamina propria. Faecal microbiota of mice with colitis was analysed by 16S rRNA gene sequencing and the composition of gut microbiota was vastly changed in Treg MR-deficient mice. Furthermore, depletion of gut microbiota by antibiotics abolished the protective effects of Treg MR deficiency and resulted in similar severity of DSS-induced colitis in WT and KO mice. Faecal microbiota transplantation from KO mice attenuated DSS-induced colitis characterized by alleviated inflammatory infiltration compared to that from WT mice. Hence, our study demonstrates that Treg MR deficiency protects against DSS-induced colitis by attenuation of colonic inflammatory infiltration. Gut microbiota is both sufficient and necessary for Treg MR deficiency to exert the beneficial effects.

Periodontitis aggravates renal inflammatory response in a mouse model of renal fibrosis.

OBJECTIVES: To assess the effects of periodontitis on renal interstitial fibrosis in a mouse model. MATERIALS AND METHODS: Thirty C57BL/6 male mice were divided into control, periodontitis (PD), unilateral ureteral ligation (UUO) and PD+UUO groups. Unilateral ureteral ligation was performed 6 days after periodontitis. After 2 weeks, all mice were sacrificed, and samples were collected for the assessment of gene expression, immune cells, biochemical indicators and renal pathology. RESULTS: Expression of tumour necrosis factor-α, interleukin-1ß, and Ly6G in the kidneys in the PD+UUO group was significantly greater than in the UUO group. The percentage of CD11b+ Ly6G+ cells was significantly higher in the PD+UUO than in the UUO group. Fibrotic areas in the kidneys in the PD+UUO group were slightly, but not significantly, greater than those in the UUO group. Kidneys from the PD+UUO group showed markedly higher gene expression of matrix metalloproteinase-9, but not α-smooth muscle actin or collagen I, than those in the UUO group. There were no significant differences in blood urea nitrogen, serum creatinine and uric acid between the PD+UUO and UUO groups. CONCLUSIONS: Periodontitis increases the renal inflammatory response without showing a significant influence on renal interstitial fibrosis or renal function in the UUO mouse model.

Engineering SnO2 nanorods/ethylenediamine-modified graphene heterojunctions with selective adsorption and electronic structure modulation for ultrasensitive room-temperature NO2 detection.

Ever-increasing concerns over air quality and the newly emerged internet of things (IoT) for future environmental monitoring are stimulating the development of ultrasensitive room-temperature gas sensors, especially for nitrogen dioxide (NO2), one of the most harmful air pollution species released round-the-clock from power plants and vehicle exhausts. Herein, tin dioxide nanorods/ethylenediamine-modified reduced graphene oxide (SnO2/EDA-rGO) heterojunctions with selective adsorption and electronic structure modulation were engineered for highly sensitive and selective detection of NO2 at room temperature. The modified EDA groups not only enable selective adsorption to significantly enrich NO2 molecules around the interface but also realize a favorable modulation of SnO2/EDA-rGO electronic structure by increasing the Fermi level of rGO, through which the sensing performance of NO2 is synergistically enhanced. The response of the SnO2/EDA-rGO sensor toward 1 ppm NO2 reaches 282%, which exceeds the corresponding SnO2/rGO sensor by a factor of 2.8. It also exhibits a low detection limit down to 100 ppb, enhanced selectivity, and rapid response/recovery kinetics. This approach to designing a novel heterojunction with significantly enhanced chemical and electric effects may shed light on the future engineering of gas-sensing materials.

A Nomogram for Predicting Cancer-Specific Survival of Patients with Gastrointestinal Stromal Tumors.

BACKGROUND The aim of this study was to construct a nomogram to predict the prognosis of patients with gastrointestinal stromal tumor (GIST). MATERIAL AND METHODS We enrolled 4086 GIST patients listed in the SEER database from 1998 to 2015. They were separated to 2 groups: an experimental group (n=2862) and a verification group (n=1224). A nomogram was constructed by using statistically significant prognostic factors. RESULTS A nomogram that included age, sex, marital status, tumor location, grade, SEER stage, tumor size, and surgical management was developed. It can be used to predict overall survival (OS), while adding AJCC 7th TNM stage can predict cancer-specific survival (CSS). The C-index used to forecast OS and CSS nomograms was 0.778 (95% CI, 0.76-0.79) and 0.818 (95% CI, 0.80-0.84), respectively. CONCLUSIONS The nomogram can effectively predict 3- and 5-year CSS in patients with GIST, and its use can improve clinical practice.

Gaussian Belief Propagation for Solving Network Utility Maximization with Delivery Contracts.

Classical network utility maximization (NUM) models fail to capture network dynamics, which are of increasing importance for modeling network behaviors. In this paper, we consider the NUM with delivery contracts, which are constraints to the classical model to describe network dynamics. This paper investigates a method to distributively solve the given problem. We first transform the problem into an equivalent model of linear equations by dual decomposition theory, and then use Gaussian belief propagation algorithm to solve the equivalent issue distributively. The proposed algorithm has faster convergence speed than the existing first-order methods and distributed Newton method. Experimental results have demonstrated the effectiveness of our proposed approach.

Mineralocorticoid Receptor Deficiency in Macrophages Inhibits Atherosclerosis by Affecting Foam Cell Formation and Efferocytosis.

Mineralocorticoid receptor (MR) has been considered as a potential target for treating atherosclerosis. However, the cellular and molecular mechanisms are not completely understood. We aim to explore the functions and mechanisms of macrophage MR in atherosclerosis. Atherosclerosis-susceptible LDLRKO chimeric mice with bone marrow cells from floxed control mice or from myeloid MR knock-out (MRKO) mice were generated and fed with high cholesterol diet. Oil red O staining showed that MRKO decreased atherosclerotic lesion area in LDLRKO mice. In another mouse model of atherosclerosis, MRKO/APOEKO mice and floxed control/APOEKO mice were generated and treated with angiotensin II. Similarly, MRKO inhibited the atherosclerotic lesion area in APOEKO mice. Histological analysis showed that MRKO increased collagen coverage and decreased necrosis and macrophage accumulation in the lesions. In vitro results demonstrated that MRKO suppressed macrophage foam cell formation and up-regulated the expression of genes involved in cholesterol efflux. Furthermore, MRKO decreased accumulation of apoptotic cells and increased effective efferocytosis in atherosclerotic lesions. In vitro study further revealed that MRKO increased the phagocytic index of macrophages without affecting their apoptosis. In conclusion, MRKO reduces high cholesterol- or angiotensin II-induced atherosclerosis and favorably changes plaque composition, likely improving plaque stability. Mechanistically, MR deficiency suppresses macrophage foam cell formation and up-regulates expression of genes related to cholesterol efflux, as well as increases effective efferocytosis and phagocytic capacity of macrophages.

Cell cycle-related and expression-elevated protein in tumor overexpression is associated with proliferation behaviors and poor prognosis in non-small-cell lung cancer.

The cell cycle-related and expression-elevated protein in tumor (CREPT) is overexpressed in several human malignancies. However, the clinical relevance of CREPT expression and its biological role in non-small-cell lung cancer (NSCLC) remains unclear. In this study, we detected the expression of CREPT in both NSCLC tissues and cell lines by immunohistochemistry, Western blot analysis, and RT-PCR. The correlation between CREPT expression and clinicopathologic features was analyzed in 271 NSCLC patients. The prognostic value of CREPT expression was evaluated by Kaplan-Meier analysis and Cox regression analysis. CREPT was overexpressed in Calu-1 cell lines by using plasmid vector and its biological function was explored both in vitro and in vivo. We found that CREPT was significantly overexpressed in NSCLC compared with paired adjacent non-tumor tissues, and the expression level of CREPT was correlated with tumor differentiation, lymph node metastasis, and clinical stage. Kaplan-Meier analysis showed that the recurrence-free survival and overall survival of high CREPT expression groups were significantly shorter than those of the low CREPT expression group. Multivariate analysis identified that CREPT might be an independent biomarker for the prediction of NSCLC prognosis. Overexpression of CREPT increased cell proliferation and enhanced the migration and invasion ability of Calu-1 cells (a human NSCLC cell line with relative low CRPET expression) in vitro. Moreover, CREPT overexpression promoted tumor growth in a nude mice model. These results suggest that CREPT is closely relevant to the proliferation of NSCLC cells and it might be a potential prognostic marker in NSCLC patients.

A miR-124/ITGA3 axis contributes to colorectal cancer metastasis by regulating anoikis susceptibility.

Metastasis is the major cause for the death of patients with colorectal cancer (CRC). Anoikis resistance enhances the survival of cancer cells during systemic circulation, thereby facilitating secondary tumor formation in distant organs. miR-124 is a pleiotropically tumor suppressive small non-coding molecule. However, its role and mechanism in the regulation of cancer cell anoikis are still unknown. Here, we found that overexpression of miR-124 promotes anoikis of CRC cells in vitro and in vivo. In silico analysis and the experimental evidence supported that ITGA3 is a bona fide target of miR-124. Moreover, we identifies that ITGA3 plays a critical role in the regulation of anoikis sensitivity in CRC cells. Finally, our analysis in TCGA datasets demonstrates that high levels of ITGA3 are closely associated with poor prognosis in CRC patients. Collectively, we establish a functional link between miR-124 and anoikis susceptibility and provide that a miR-124/ITGA3 axis could be a potential target for the treatment of metastatic CRC.

Mineralocorticoid Receptor Deficiency in Macrophages Inhibits Neointimal Hyperplasia and Suppresses Macrophage Inflammation Through SGK1-AP1/NF-κB Pathways.

OBJECTIVE: Restenosis after percutaneous coronary intervention remains to be a serious medical problem. Although mineralocorticoid receptor (MR) has been implicated as a potential target for treating restenosis, the cellular and molecular mechanisms are largely unknown. This study aims to explore the functions of macrophage MR in neointimal hyperplasia and to delineate the molecular mechanisms. APPROACH AND RESULTS: Myeloid MR knockout (MMRKO) mice and controls were subjected to femoral artery injury. MMRKO reduced intima area and intima/media ratio, Ki67- and BrdU-positive vascular smooth muscle cells, expression of proinflammatory molecules, and macrophage accumulation in injured arteries. MMRKO macrophages migrated less in culture. MMRKO decreased Ki67- and BrdU-positive macrophages in injured arteries. MMRKO macrophages were less Ki67-positive in culture. Conditioned media from MMRKO macrophages induced less migration, Ki67 positivity, and proinflammatory gene expression of vascular smooth muscle cells. After lipopolysaccharide treatment, MMRKO macrophages had decreased p-cFos and p-cJun compared with control macrophages, suggesting suppressed activation of activator protein-1 (AP1). Nuclear factor-κB (NF-κB) pathway was also inhibited by MMRKO, manifested by decreased p-IκB kinase-ß and p-IκBα, increased IκBα expression, decreased nuclear translocation of p65 and p50, as welll as decreased phosphorylation and expression of p65. Finally, overexpression of serum-and-glucocorticoid-inducible-kinase-1 (SGK1) attenuated the effects of MR deficiency in macrophages. CONCLUSIONS: Selective deletion of MR in myeloid cells limits macrophage accumulation and vascular inflammation and, therefore, inhibits neointimal hyperplasia and vascular remodeling. Mechanistically, MR deficiency suppresses migration and proliferation of macrophages and leads to less vascular smooth muscle cell activation. At the molecular level, MR deficiency suppresses macrophage inflammatory response via SGK1-AP1/NF-κB pathways.

Usp2-69 overexpression slows down the progression of rat anti-Thy1.1 nephritis.

Mesangial proliferative glomerulonephritis is characterized by proliferation of mesangial cells (MCs) and transforming growth factor-ß (TGF-ß)-dependent stimulation of abnormal extracellular matrix (ECM) accumulation. We previously showed that Decorin--a leucine-rich proteoglycan inhibiting the progression of glomerulonephritis and glomerular sclerosis--can be degraded by the ubiquitin-proteasome pathway and deubiquitinated and stabilized by ubiquitin-specific processing protease 2-69(Usp2-69). Usp2-69 is highly expressed in the kidney and has been implicated in the regulation of cell proliferation and apoptosis. However, its role in mesangial proliferative glomerulonephritis remains unclear. Here, we explored the effect of Usp2-69 on MC proliferation and ECM deposition by transfecting Usp2-69 plasmid into rat anti-Thy1.1 nephritis model and into cultured MCs, as well as detected Usp2-69 and Decorin in rat anti-Thy1.1 nephritis model by western blot. Overexpressing Usp2-69 at the early stage, but not advanced stage, of anti-Thy1.1 nephritis alleviated cell proliferation and ECM deposition, which was shown by decreased Ki-67, Collagen IV and Fibronectin detected by immunohistochemistry. Overexpression also increased Decorin and decreased TGF-ß1 and Collagen IV both in vitro and in vivo. In conclusion, our findings suggest that Usp2-69 overexpression alleviates the progression of rat anti-Thy1.1 nephritis and, therefore, that exogenous plasmid injection via the renal artery enhanced by electrotransfer technology could be a promising avenue for glomerular disease research.

Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.

Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a "tipping point" mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.

Tropomyosin-related kinase B promotes distant metastasis of colorectal cancer through protein kinase B-mediated anoikis suppression and correlates with poor prognosis.

An increasing amount of evidence demonstrated that the neurotrophic receptor tropomyosin-related kinase B (TrkB) plays a critical role in the development and progression of multiple types of cancer. However, its underlying mechanism in distant metastasis through the circulatory and lymphatic systems in colorectal cancer (CRC) is still unclear. Here we showed that downregulation of TrkB using short hairpin RNA obviously increased anoikis (detachment-induced apoptosis resulting from loss of cell-matrix interactions) sensitivity of CRC cells in vitro. Furthermore, using tail vein injection model, we confirmed that silencing TrkB significantly inhibited metastasis of CRC cells in vivo. Conversely, overexpression of TrkB obviously protected CRC cells from anoikis in vitro. Both loss- and gain-of-functional experiments indicated that TrkB could be a functional molecule in anti-anoikis of CRC cells. Mechanistically, we found that protein kinase B (PKB, also known as Akt) signaling pathway was a functional link in TrkB-induced anoikis suppression in CRC cells. Phosphorylation levels of Akt are closely related with the expression pattern of TrkB in CRC cells and inhibition of Akt activation robustly induces anoikis of CRC cells in vitro. In addition, our clinical investigation showed that high TrkB expression levels in CRC patients were associated with lymph node metastasis, distant metastasis and unfavourable prognosis. Thus, based on our results, this study suggests that an important function of TrkB is to protect CRC cells from anoikis in the circulatory and lymphatic systems, and that TrkB could be a promising candidate in CRC therapy, especially in the inhibition of cancer metastasis.

Aquaporin 3 and 8 are down-regulated in TNBS-induced rat colitis.

Aquaporins (AQPs) plays an important role in transcellular water movement, but the AQPs expression profile has not been demonstrated in 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitis which closely mimics human Crohn's disease (CD) histopathologically. To solve the problem, 30 female Sprague-Dawley (SD) rats were randomly divided into a model group (n=18), an ethanol control group (n=6) and a normal control group (n=6). On day 1, the rats in the model group received TNBS+50% ethanol via the rectum, while the ethanol control rats received an equal volume of 50% ethanol and the normal control rats did not receive any treatment. All rats were sacrificed on day 7, and ileum, proximal colon and distal colon specimens were obtained to examine the alteration in AQP3 and AQP8 using real-time polymerase chain reaction, Western blot analysis and immunohistochemistry. As a result, exposure to TNBS+ethanol resulted in a marked decrease in both the mRNA and protein expression of AQP3 and AQP8, with the exception of AQP8 protein which was negative in the distal colon in all three groups. These reductions in AQP3 and AQP8 were accompanied by an increase in intestinal inflammation and injury. The results obtained here implied that both AQP3 and AQP8 may be involved in the pathogenesis of inflammatory bowel disease.

MOEA/D with adaptive weight adjustment.

Recently, MOEA/D (multi-objective evolutionary algorithm based on decomposition) has achieved great success in the field of evolutionary multi-objective optimization and has attracted a lot of attention. It decomposes a multi-objective optimization problem (MOP) into a set of scalar subproblems using uniformly distributed aggregation weight vectors and provides an excellent general algorithmic framework of evolutionary multi-objective optimization. Generally, the uniformity of weight vectors in MOEA/D can ensure the diversity of the Pareto optimal solutions, however, it cannot work as well when the target MOP has a complex Pareto front (PF; i.e., discontinuous PF or PF with sharp peak or low tail). To remedy this, we propose an improved MOEA/D with adaptive weight vector adjustment (MOEA/D-AWA). According to the analysis of the geometric relationship between the weight vectors and the optimal solutions under the Chebyshev decomposition scheme, a new weight vector initialization method and an adaptive weight vector adjustment strategy are introduced in MOEA/D-AWA. The weights are adjusted periodically so that the weights of subproblems can be redistributed adaptively to obtain better uniformity of solutions. Meanwhile, computing efforts devoted to subproblems with duplicate optimal solution can be saved. Moreover, an external elite population is introduced to help adding new subproblems into real sparse regions rather than pseudo sparse regions of the complex PF, that is, discontinuous regions of the PF. MOEA/D-AWA has been compared with four state of the art MOEAs, namely the original MOEA/D, Adaptive-MOEA/D, [Formula: see text]-MOEA/D, and NSGA-II on 10 widely used test problems, two newly constructed complex problems, and two many-objective problems. Experimental results indicate that MOEA/D-AWA outperforms the benchmark algorithms in terms of the IGD metric, particularly when the PF of the MOP is complex.

Single-cell profiling of response to neoadjuvant chemo-immunotherapy in surgically resectable esophageal squamous cell carcinoma.

BACKGROUND: The efficacy of neoadjuvant chemo-immunotherapy (NAT) in esophageal squamous cell carcinoma (ESCC) is challenged by the intricate interplay within the tumor microenvironment (TME). Unveiling the immune landscape of ESCC in the context of NAT could shed light on heterogeneity and optimize therapeutic strategies for patients. METHODS: We analyzed single cells from 22 baseline and 24 post-NAT treatment samples of stage II/III ESCC patients to explore the association between the immune landscape and pathological response to neoadjuvant anti-PD-1 combination therapy, including pathological complete response (pCR), major pathological response (MPR), and incomplete pathological response (IPR). RESULTS: Single-cell profiling identified 14 major cell subsets of cancer, immune, and stromal cells. Trajectory analysis unveiled an interesting link between cancer cell differentiation and pathological response to NAT. ESCC tumors enriched with less differentiated cancer cells exhibited a potentially favorable pathological response to NAT, while tumors enriched with clusters of more differentiated cancer cells may resist treatment. Deconvolution of transcriptomes in pre-treatment tumors identified gene signatures in response to NAT contributed by specific immune cell populations. Upregulated genes associated with better pathological responses in CD8 + effector T cells primarily involved interferon-gamma (IFNγ) signaling, neutrophil degranulation, and negative regulation of the T cell apoptotic process, whereas downregulated genes were dominated by those in the immune response-activating cell surface receptor signaling pathway. Natural killer cells in pre-treatment tumors from pCR patients showed a similar upregulation of gene expression in response to IFNγ but a downregulation of genes in the neutrophil-mediated immunity pathways. A decreased cellular contexture of regulatory T cells in ESCC TME indicated a potentially favorable pathological response to NAT. Cell-cell communication analysis revealed extensive interactions between CCL5 and its receptor CCR5 in various immune cells of baseline pCR tumors. Immune checkpoint interaction pairs, including CTLA4-CD86, TIGIT-PVR, LGALS9-HAVCR2, and TNFSF4-TNFRSF4, might serve as additional therapeutic targets for ICI therapy in ESCC. CONCLUSIONS: This pioneering study unveiled an intriguing association between cancer cell differentiation and pathological response in esophageal cancer patients, revealing distinct subgroups of tumors for which neoadjuvant chemo-immunotherapy might be effective. We also delineated the immune landscape of ESCC tumors in the context of clinical response to NAT, which provides clinical insights for better understanding how patients respond to the treatment and further identifying novel therapeutic targets for ESCC patients in the future.

Continuous Encoding for Overlapping Community Detection in Attributed Network.

Detecting overlapping communities of an attribute network is a ubiquitous yet very difficult task, which can be modeled as a discrete optimization problem. Besides the topological structure of the network, node attributes and node overlapping aggravate the difficulty of community detection significantly. In this article, we propose a novel continuous encoding method to convert the discrete-natured detection problem to a continuous one by associating each edge and node attribute in the network with a continuous variable. Based on the encoding, we propose to solve the converted continuous problem by a multiobjective evolutionary algorithm (MOEA) based on decomposition. To find the overlapping nodes, a heuristic based on double-decoding is proposed, which is only with linear complexity. Furthermore, a postprocess community merging method in consideration of node attributes is developed to enhance the homogeneity of nodes in the detected communities. Various synthetic and real-world networks are used to verify the effectiveness of the proposed approach. The experimental results show that the proposed approach performs significantly better than a variety of evolutionary and nonevolutionary methods on most of the benchmark networks.