[Research progress in methylation modification in tooth root development]

Methylation modification is one of the most common epigenetic modification regulation in eukaryotes, including histone methylation, DNA methylation, RNA methylation, etc., which plays an important regulatory role in physiological processes and pathologic occurrence and development. Tooth root development is carried out by both epithelial and mesenchymal cells and involves a variety of cell-molecular interactions. In recent years, a large number of studies have found that methylation plays a key role in the regulation of tooth root development and expands the mechanism network of tooth root development. In this paper, we review the role and mechanism of methylation modification during root development.

The Molecular Characteristics and Therapeutic Implications of O-Glycan Synthesis in Pancreatic Cancer by Integrating Transcriptome and Single-Cell Data

BACKGROUND

Glycans constitute the primary components of proteins that regulate key carcinogenic processes in cancer progression. This study investigated the significance of O-glycan synthesis in the pathogenesis, outcome, and therapy of pancreatic cancer (PC).

METHODS

Transcriptomic data and clinical prognostic information of PC were acquired via TCGA and GEO databases. CSA database was used to obtain single-cell data of PC. The O-glycan biosynthesis signaling pathway and its related genes were acquired via the MSigDB platform. The nonnegative matrix factorization (NMF) clustering was utilized to construct the O-glycan biosynthesis-associated molecular subtypes in PC. The LASSO and Cox regression were utilized to build the prognostic prediction model. We utilized real-time quantitative PCR (qRT-PCR) to verify the expressed levels of model genes. Single-cell analysis was utilized to investigate the levels of target genes and O-glycan biosynthesis signaling pathway in the PC tumour microenvironment.

RESULTS

We obtained 30 genes related to O-glycan biosynthesis, among which 15 were associated with the prognosis of PC. All PC samples were grouped into two distinct molecular subtypes associated with O-glycan biosynthesis: OGRGcluster C1 and OGRGcluster C2, and compared to OGRGcluster C1. PCs in OGRGcluster C2 had a more advanced clinical stage and pathological grade, worse prognosis, and more active O-glycan biosynthesis function. Immune analysis indicated that naïve B cell, CD8+ T cell, memory-activated CD4+ T cell, and monocytes displayed remarkably higher infiltration levels in OGRGcluster C1 while resting NK cell, macrophages M0, resting dendritic cell, activated dendritic cell, and neutrophils exhibited markedly higher infiltration levels in OGRGcluster C2. OGRGcluster C1 exhibited higher sensitivities to drugs, such as cisplatin, irinotecan, KRAS(G12C) inhibitor-12, oxaliplatin, paclitaxel, and sorafenib. Besides, we built the O-glycan biosynthesis-related prognostic model (including SPRR1B, COL17A1, and ECT2) with a good prediction performance. SPRR1B, COL17A1, and ECT2 were remarkably highly expressed in PC tissues and linked to a poor outcome. Single-cell analysis revealed that Oglycan biosynthesis was observed only in PC, and consistent with this, the target genes were significantly enriched in PC.

CONCLUSION

We first constructed molecular subtypes and prognostic models related to O-glycan biosynthesis in PC. It is clear that O-glycan biosynthesis is related to the development, prognosis, immune microenvironment, and treatment of PC. This provides new strategies for stratification, diagnosis, and treatment of PC patients.

Deciphering drug resistance in gastric cancer: Potential mechanisms and future perspectives

Gastric cancer (GC) is a malignant tumor that originates from the epithelium of the gastric mucosa. The latest global cancer statistics show that GC ranks fifth in incidence and fourth in mortality among all cancers, posing a serious threat to public health. While early-stage GC is primarily treated through surgery, chemotherapy is the frontline option for advanced cases. Currently, commonly used chemotherapy regimens include FOLFOX (oxaliplatin + leucovorin + 5-fluorouracil) and XELOX (oxaliplatin + capecitabine). However, with the widespread use of chemotherapy, an increasing number of cases of drug resistance have emerged. This article primarily explores the potential mechanisms of chemotherapy resistance in GC patients from five perspectives: cell death, tumor microenvironment, non-coding RNA, epigenetics, and epithelial-mesenchymal transition. Additionally, it proposes feasibility strategies to overcome drug resistance from four angles: cancer stem cells, tumor microenvironment, natural products, and combined therapy. The hope is that this article will provide guidance for researchers in the field and bring hope to more GC patients.

Measurements of All-Particle Energy Spectrum and Mean Logarithmic Mass of Cosmic Rays from 0.3 to 30 PeV with LHAASO-KM2A

We present the measurements of all-particle energy spectrum and mean logarithmic mass of cosmic rays in the energy range of 0.3-30 PeV using data collected from LHAASO-KM2A between September 2021 and December 2022, which is based on a nearly composition-independent energy reconstruction method, achieving unprecedented accuracy. Our analysis reveals the position of the knee at 3.67±0.05±0.15  PeV. Below the knee, the spectral index is found to be -2.7413±0.0004±0.0050, while above the knee, it is -3.128±0.005±0.027, with the sharpness of the transition measured with a statistical error of 2%. The mean logarithmic mass of cosmic rays is almost heavier than helium in the whole measured energy range. It decreases from 1.7 at 0.3 PeV to 1.3 at 3 PeV, representing a 24% decline following a power law with an index of -0.1200±0.0003±0.0341. This is equivalent to an increase in abundance of light components. Above the knee, the mean logarithmic mass exhibits a power law trend towards heavier components, which is reversal to the behavior observed in the all-particle energy spectrum. Additionally, the knee position and the change in power-law index are approximately the same. These findings suggest that the knee observed in the all-particle spectrum corresponds to the knee of the light component, rather than the medium-heavy components.

[Comparative study of percutaneous transfacet screw and pedicle screw in oblique lumbar interbody fusion for the treatment of single-level lumbar spinal stenosis]

Objective: To conduct a comparative study of radiological and clinical outcomes between percutaneous transfacet screw (TFS) and pedicle screw (BPS) in oblique lateral lumbar interbody fusion (OLIF) for single-level lumbar spinal stenosis. Methods: A retrospective cohort study. Patients who underwent OLIF with TFS or BPS for the treatment of single-level lumbar spinal stenosis at Beijing Jishuitan Hospital from January 2019 to June 2022 were retrospectively analyzed. Radiological parameters and clinical indicators were compared between the two groups. Radiological parameters included preoperative, immediate postoperative (within 5 days), and 1-year postoperative measurements of disc height and segmental lordosis angle, as well as interbody fusion status at 1 year postoperatively. Clinical indicators included operative time, blood loss, length of hospital stay, complications, and Oswestry Disability Index (ODI), visual analogue scale (VAS) scores for back pain, and leg pain before and 1 year after surgery. Results: Four male and 10 female patients with an average age of (61.0±11.2) years underwent OLIF with TFS, while 9 male and 12 female patients underwent OLIF with BPS, with a mean age of (60.9±6.7) years. There was no statistically significant difference in preoperative disc height between the TFS and BPS groups (P>0.05). The immediate postoperative disc height was (12.9±2.1) mm and it was (10.4±1.7) mm at 1-year follow-up in the TFS group; in the BPS group, it was (12.9±2.1) mm immediately postoperatively and (11.9±2.1) mm at 1-year follow-up; there was statistically significant difference between the two groups at 1-year follow-up (P=0.037). The segmental lordosis angle showed no significant differences within each group or between the two groups at preoperative, immediate postoperative, or 1-year postoperative follow-up (all P>0.05). At 1-year postoperative follow-up, the fusion rates was 92.9%(13/14) in the TFS group and 95.2%(20/21) in the BPS group, with no statistically significant difference between the two groups (P>0.05). The TFS group had a significantly shorter operative time and less blood loss compared to the BPS group [(164.3±33.9) minutes vs (191.7±31.8) minutes and (74.3±46.9) ml vs (124.8±54.0) ml, respectively] (both P<0.05). Both groups showed significant improvement in ODI and VAS scores at 1 year postoperatively compared to those preoperatively, but with no statistically significant difference was found between the groups (both P>0.05). Conclusions: OLIF with TFS fixation can effectively restore disc height and alleviate back and leg pain in patients with single-level lumbar spinal stenosis. Compared to the OLIF with BPS procedure, OLIF with TFS has shorter operative time and less blood loss.

Combination of bulk RNA sequencing and scRNA sequencing uncover the molecular characteristics of MAPK signaling in kidney renal clear cell carcinoma

The MAPK signaling pathway significantly impacts cancer progression and resistance; however, its functions remain incompletely assessed across various cancers, particularly in kidney renal clear cell carcinoma (KIRC). Therefore, there is an urgent need for comprehensive pan-cancer investigations of MAPK signaling, particularly within the context of KIRC. In this research, we obtained TCGA pan-cancer multi-omics data and conducted a comprehensive analysis of the genomic and transcriptomic characteristics of the MAPK signaling pathway. For in-depth investigation in KIRC, status of MAPK pathway was quantitatively estimated by ssGSEA and Ward algorithm was utilized for cluster analysis. Molecular characteristics and clinical prognoses of KIRC patients with distinct MAPK activities were comprehensively explored using a series of bioinformatics algorithms. Subsequently, a combination of LASSO and COX regression analyses were utilized sequentially to construct a MAPK-related signature to help identify the risk level of each sample. Patients in the C1 subtype exhibited relatively higher levels of MAPK signaling activity, which were associated with abundant immune cell infiltration and favorable clinical outcomes. Single-cell RNA sequencing (scRNA-seq) analysis of KIRC samples identified seven distinct cell types, and endothelial cells in tumor tissues had obviously higher MAPK scores than normal tissues. The immunohistochemistry results indicated the reduced expression levels of PAPSS1, MAP3K11, and SPRED1 in KIRC samples. In conclusion, our study represents the first integration of bulk RNA sequencing and single-cell RNA sequencing to elucidate the molecular characteristics of MAPK signaling in KIRC, providing a solid foundation for precision oncology.

A review on tissue-needle interaction and path planning models for bevel tip type flexible needle minimal intervention

A flexible needle has emerged as a crucial clinical technique in contemporary medical practices, particularly for minimally invasive interventions. Its applicability spans diverse surgical domains such as brachytherapy, cardiovascular surgery, neurosurgery and others. Notably, flexible needles find utility in biopsies requiring deep skin penetration to access infected areas. Despite its minimally invasive advantages, the precise guidance of the needle to its intended target, while avoiding damage to bones, blood vessels, organs and tissues, remains a significant challenge for researchers. Consequently, extensive research has been dedicated to enhancing the steering and accuracy of flexible needles. Here, we aim to elucidate the recent advancements, trends and perspectives in flexible needle steering models and path planning over the last 15 years. The discussed models encompass various types, including symmetric-tip needles, curved-tip needles, tendon-actuated needles, programmable needles and the innovative fracture-directed waterjet needles. Moreover, the paper offers a comprehensive analysis, comparing the trajectories followed by these needle models to attain the desired target with minimal tissue damage. By delving into these aspects, the paper contributes to a deeper understanding of the current landscape of flexible needle technology and guides future research directions in this dynamic field.

Integrative transcriptome and single-cell sequencing technology analysis of the potential therapeutic benefits of oleanolic acid in liver injury and liver cancer

BACKGROUND

Oleanolic acid has important hepatoprotective effects and inhibits liver tissue carcinogenesis. The aim of this study was to investigate the mechanism of action of oleanolic acid in inhibiting liver injury and liver cancer.

METHOD

In this study, we applied differential gene analysis and gene enrichment analysis to identify the targets of oleanolic acid for the treatment of liver injury. And this study also applied Cibersort and GSVA methods to investigate the targets of oleanolic acid in liver injury. Based on oleanolic acid targets, we explored the major targets and further explored the role of the major targets in liver cancer. This study used the oncoPredict and the TIDE algorithm to predict the effect of oleanolic acid on drug resistance. Finally, the binding effect of oleanolic acid to relevant targets was explored using molecular docking techniques.

RESULT

In this study, oleanolic acid was found to inhibit liver injury and promote liver regeneration mainly by promoting elevated expression of HMOX1. Oleanolic acid can inhibit oxidative stress and promotes Ferroptosis in liver injury. In liver cancer, we identified that the main target of oleanolic acid is HMOX1 and HDAC1. And we determined that HMOX1 promotes Ferroptosis in liver cancer. This reduced the sensitivity of liver cancer to targeted therapies and immunotherapy. Molecular docking showed high binding of oleanolic acid to HDAC1 and HMOX1.

CONCLUSIONS

Oleanolic acid is an antioxidant by promoting high expression of HMOX1 and promotes the development of Ferroptosis in liver cancer and liver injury.

Low-density lipoprotein receptor promotes crosstalk between cell stemness and tumor immune microenvironment in breast cancer: a large data-based multi-omics study

BACKGROUND

Tumor cells with stemness in breast cancer might facilitate the immune microenvironment's suppression process and led to anti-tumor immune effects. The primary objective of this study was to identify potential targets to disrupt the communication between cancer cell stemness and the immune microenvironment.

METHODS

In this study, we initially isolated tumor cells with varying degrees of stemness using a spheroid formation assay. Subsequently, we employed RNA-seq and proteomic analyses to identify genes associated with stemness through gene trend analysis. These stemness-related genes were then subjected to pan-cancer analysis to elucidate their functional roles in a broader spectrum of cancer types. RNA-seq data of 3132 patients with breast cancer with clinical data were obtained from public databases. Using the identified stemness genes, we constructed two distinct stemness subtypes, denoted as C1 and C2. We subsequently conducted a comprehensive analysis of the differences between these subtypes using pathway enrichment methodology and immune infiltration algorithms. Furthermore, we identified key immune-related stemness genes by employing lasso regression analysis and a Cox survival regression model. We conducted in vitro experiments to ascertain the regulatory impact of the key gene on cell stemness. Additionally, we utilized immune infiltration analysis and pan-cancer analysis to delineate the functions attributed to this key gene. Lastly, single-cell RNA sequencing (scRNA-seq) was employed to conduct a more comprehensive examination of the key gene's role within the microenvironment.

RESULTS

In our study, we initially identified a set of 65 stemness-related genes in breast cancer cells displaying varying stemness capabilities. Subsequently, through survival analysis, we pinpointed 41 of these stemness genes that held prognostic significance. We observed that the C2 subtype exhibited a higher stemness capacity compared to the C1 subtype and displayed a more aggressive malignancy profile. Further analysis using Lasso-Cox algorithm identified LDLR as a pivotal immune-related stemness gene. It became evident that LDLR played a crucial role in shaping the immune microenvironment. In vitro experiments demonstrated that LDLR regulated the cell stemness of breast cancer. Immune infiltration analysis and pan-cancer analysis determined that LDLR inhibited the proliferation of immune cells and might promote tumor cell progression. Lastly, in our scRNA-seq analysis, we discovered that LDLR exhibited associations with stemness marker genes within breast cancer tissues. Moreover, LDLR demonstrated higher expression levels in tumor cells compared to immune cells, further emphasizing its relevance in the context of breast cancer.

CONCLUSION

LDLR is an important immune stemness gene that regulates cell stemness and enhances the crosstalk between breast cancer cancer cell stemness and tumor immune microenvironment.

A Nucleotide Metabolism-Related Gene Signature for Risk Stratification and Prognosis Prediction in Hepatocellular Carcinoma Based on an Integrated Transcriptomics and Metabolomics Approach

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality worldwide. The in-depth study of genes and metabolites related to nucleotide metabolism will provide new ideas for predicting the prognosis of HCC patients. This study integrated the transcriptome data of different cancer types to explore the characteristics and significance of nucleotide metabolism-related genes (NMGRs) in different cancer types. Then, we constructed a new HCC classifier and prognosis model based on HCC samples from TCGA and GEO, and detected the gene expression level in the model through molecular biology experiments. Finally, nucleotide metabolism-related products in serum of HCC patients were examined using untargeted metabolomics. A total of 97 NMRGs were obtained based on bioinformatics techniques. In addition, a clinical model that could accurately predict the prognostic outcome of HCC was constructed, which contained 11 NMRGs. The results of PCR experiments showed that the expression levels of these genes were basically consistent with the predicted trends. Meanwhile, the results of untargeted metabolomics also proved that there was a significant nucleotide metabolism disorder in the development of HCC. Our results provide a promising insight into nucleotide metabolism in HCC, as well as a tailored prognostic and chemotherapy sensitivity prediction tool for patients.

Identification and characterization of interferon-γ signaling-based personalized heterogeneity and therapeutic strategies in patients with pancreatic cancer

Background

Interferon-γ (IFN-γ) is a key cytokine with diverse biological functions, including antiviral defense, antitumor activity, immune regulation, and modulation of cellular processes. Nonetheless, its role in pancreatic cancer (PC) therapy remains debated. Therefore, it is worthwhile to explore the role of Interferon-γ related genes (IFN-γGs) in the progression of PC development.

Methodology

Transcriptomic data from 930 PC were sourced from TCGA, GEO, ICGC, and ArrayExpress, and 93 IFN-γGs were obtained from the MSigDB. We researched the characteristics of IFN-γGs in pan-cancer. Subsequently, the cohort of 930 PC was stratified into two distinct subgroups using the NMF algorithm. We then examined disparities in the activation of cancer-associated pathways within these subpopulations through GSVA analysis. We scrutinized immune infiltration in both subsets and probed classical molecular target drug sensitivity variations. Finally, we devised and validated a novel IFN-γ related prediction model using LASSO and Cox regression analyses. Furthermore, we conducted RT-qPCR and immunohistochemistry assays to validate the expression of seven target genes included in the prediction model.

Results

We demonstrated the CNV, SNV, methylation, expression levels, and prognostic characteristics of IFN-γGs in pan-cancers. Notably, Cluster 2 demonstrated superior prognostic outcomes and heightened immune cell infiltration compared to Clusters 1. We also assessed the IC50 values of classical molecular targeted drugs to establish links between IFN-γGs expression levels and drug responsiveness. Additionally, by applying our prediction model, we segregated PC patients into high-risk and low-risk groups, identifying potential benefits of cisplatin, docetaxel, pazopanib, midostaurin, epothilone.B, thapsigargin, bryostatin.1, and AICAR for high-risk PC patients, and metformin, roscovitine, salubrinal, and cyclopamine for those in the low-risk group. The expression levels of these model genes were further verified through HPA website data and qRT-PCR assays in PC cell lines and tissues.

Conclusion

This study unveils IFN-γGs related molecular subsets in pancreatic cancer for the first time, shedding light on the pivotal role of IFN-γGs in the progression of PC. Furthermore, we establish an IFN-γGs related prognostic model for predicting the survival of PC, offering a theoretical foundation for exploring the precise mechanisms of IFN-γGs in PC.

Measurement of Ultra-High-Energy Diffuse Gamma-Ray Emission of the Galactic Plane from 10 TeV to 1 PeV with LHAASO-KM2A

The diffuse Galactic γ-ray emission, mainly produced via interactions between cosmic rays and the interstellar medium and/or radiation field, is a very important probe of the distribution, propagation, and interaction of cosmic rays in the Milky Way. In this Letter, we report the measurements of diffuse γ rays from the Galactic plane between 10 TeV and 1 PeV energies, with the square kilometer array of the Large High Altitude Air Shower Observatory (LHAASO). Diffuse emissions from the inner (15°10  TeV). The energy spectrum in the inner Galaxy regions can be described by a power-law function with an index of -2.99±0.04, which is different from the curved spectrum as expected from hadronic interactions between locally measured cosmic rays and the line-of-sight integrated gas content. Furthermore, the measured flux is higher by a factor of ∼3 than the prediction. A similar spectrum with an index of -2.99±0.07 is found in the outer Galaxy region, and the absolute flux for 10≲E≲60  TeV is again higher than the prediction for hadronic cosmic ray interactions. The latitude distributions of the diffuse emission are consistent with the gas distribution, while the longitude distributions show clear deviation from the gas distribution. The LHAASO measurements imply that either additional emission sources exist or cosmic ray intensities have spatial variations.

Heritable epigenetic modification of BpPIN1 is associated with leaf shapes in Betula pendula

The new variety Betula pendula 'Dalecarlica', selected from Betula pendula, shows high ornamental value owing to its lobed leaf shape. In this study, to identify the genetic components of leaf shape formation, we performed bulked segregant analysis and molecular marker-based fine mapping to identify the causal gene responsible for lobed leaves in B. pendula 'Dalecarlica'. The most significant variations associated with leaf shape were identified within the gene BpPIN1 encoding a member of the PIN-FORMED family, responsible for the auxin efflux carrier. We further confirmed the hypomethylation at the promoter region promoting the expression level of BpPIN1, which causes stronger and longer veins and lobed leaf shape in B. pendula 'Dalecarlica'. These results indicated that DNA methylation at the BpPIN1 promoter region is associated with leaf shapes in B. pendula. Our findings revealed an epigenetic mechanism of BpPIN1 in the regulation of leaf shape in Betula  Linn. (birch), which could help in the molecular breeding of ornamental traits.

Serum human epidermal growth factor receptor-2 extracellular domain, carcinoma embryonic antigen and carbohydrate antigen 15-3 combined detection in early diagnosis of breast cancer

The multi-markers combined detection can make up for the deficiency of single marker detection and significantly increase the positive detection rates of tumors. This study aimed to assess the performance of serum HER-2 extracellular domain (HER-2/neu ECD), carcinoembryonic antigen (CEA), and cancer antigen 15-3 (CA15-3) in early screening and auxiliary diagnosis of breast cancer. The HER-2, CEA, and CA15-3 serum levels were measured in 164 healthy volunteers, 111 patients with benign nodules (BN), 123 with early breast cancer (EBC), and 25 with advanced breast cancer. In distinguishing health and EBC, the sensitivity and specificity of joint detection of HER-2, CEA, and CA15-3 were 96.75% and 96.95%, respectively; the accuracy was up to 96.19%, and the AUC was 0.994. In the cohort for distinguishing BN from EBC, serum HER-2, CEA, and CA15-3 sensitivities were 77.03%, 75.27%, and 48.65%, respectively. Combined with three markers, the sensitivity was increased to 84.46%, the AUC was 0.834. All in all, through the combined detection of serum HER-2, CEA and CA15-3 levels in healthy volunteers, BN and EBC, our study found that this method can significantly improve the diagnosis level of breast cancer, suggesting that the three markers panel can be used as an effective tool to improve the early screening level, early diagnosis, and clinical intervention of breast cancer.

[Prognostic significance and immune cell infiltration analysis of differentially expressed genes in malignant pleural mesothelioma]

Objective: To explore and analyze differential expressed genes in malignant pleural mesothelioma (MPM) by bioinformatics method, and to study their prognostic value in MPM and their potential role in immunotherapy. Methods: In January 2022, the dataset GSE51024 was downloaded from the GEO database, and MPM (55 cases) and normal tissue (41 cases) samples were obtained. Using R software and HMDD and miRNet database, MPM-related differential genes were screened and co-expressed genes were identified. Co-expressed genes were enriched and functionally annotated, and protein-protein interaction (PPI) networks were constructed and key genes were identified using the STRING database and Cytoscape software. TRRUST and GEPIA databases were used to predict transcription factors of key genes and to analyze prognosis and survival. The correlation between key genes and the degree of infiltration of immune cells was analyzed using TIMER. Results: A total of 435 co-expressed genes were obtained, which were mainly concentrated in the extracellular matrix tissue and the signaling pathways of cell adhesion molecules. Combined with PPI and TRRUST database, seven key MPM prognostic genes were identified. Among them, cyclin 20 (CDC20) , cell cycle checkpoint kinase 1 (CHEK1) , enhancer of Zeste homolog 2 (EZH2) , ribonucleotide reductase subunit M2 (RRM2) , topoisomerase 2A (TOP2A) , ubiquitin like plant homeodomain and ring finger domain 1 (UHRF1) were significantly up-regulated in MPM, while cyclin A1 (CCNA1) was significantly down-regulated. The expressions of CCNA1, CDC20, CHEK1, EZH2, RRM2, TOP2A and UHRF1 genes were significantly associated with MPM overall survival (P<0.05) . The expressions of CDC20, CHEK1, EZH2, RRM2 and TOP2A genes were positively correlated with B cells and dendritic cells (P<0.05) , and negatively correlated with neutrophils (P<0.05) . Conclusion: CCNA1, CDC20, CHEK1, EZH2, RRM2, TOP2A and UHRF1 may be potential prognostic markers in MPM patients, and their expressions may be related to MPM tumor immunity.

Integrated single-cell and bulk RNA sequencing revealed the molecular characteristics and prognostic roles of neutrophils in pancreatic cancer

Pancreatic cancer, one of the most prevalent tumors of the digestive system, has a dismal prognosis. Cancer of the pancreas is distinguished by an inflammatory tumor microenvironment rich in fibroblasts and different immune cells. Neutrophils are important immune cells that infiltrate the microenvironment of pancreatic cancer tumors. The purpose of this work was to examine the complex mechanism by which neutrophils influence the carcinogenesis and development of pancreatic cancer and to construct a survival prediction model based on neutrophil marker genes. We incorporated the GSE111672 dataset, comprising RNA expression data from 27,000 cells obtained from 3 patients with PC, and conducted single-cell data analysis. Thorough investigation of pancreatic cancer single-cell RNA sequencing data found 350 neutrophil marker genes. Using The Cancer Genome Atlas (TCGA), GSE28735, GSE62452, GSE57495, and GSE85916 datasets to gather pancreatic cancer tissue transcriptome data, and consistent clustering was used to identify two categories for analyzing the influence of neutrophils on pancreatic cancer. Using the Random Forest algorithm and Cox regression analysis, a survival prediction model for pancreatic cancer was developed, the model showed independent performance for survival prognosis, clinic pathological features, immune infiltration, and drug sensitivity. Multivariate Cox analysis findings revealed that the risk scores derived from predictive models is independent prognostic markers for pancreatic patients. In conclusion, based on neutrophil marker genes, this research created a molecular typing and prognostic grading system for pancreatic cancer, this system was very accurate in predicting the prognosis, tumor immune microenvironment status, and pharmacological treatment responsiveness of pancreatic cancer patients.

Molecular characteristics and therapeutic implications of Toll-like receptor signaling pathway in melanoma

Melanoma is a malignant tumor of melanocytes and is often considered immunogenic cancer. Toll-like receptor-related genes are expressed differently in most types of cancer, depending on the immune microenvironment inside cancer, and the key function of Toll-like receptors (TLRs) for melanoma has not been fully elucidated. Based on multi-omics data from TCGA and GEO databases, we first performed pan-cancer analysis on TLR, including CNV, SNV, and mRNA changes in TLR-related genes in multiple human cancers, as well as patient prognosis characterization. Then, we divided melanoma patients into three subgroups (clusters 1, 2, and 3) according to the expression of the TLR pathway, and explored the correlation between TLR pathway and melanoma prognosis, immune infiltration, metabolic reprogramming, and oncogene expression characteristics. Finally, through univariate Cox regression analysis and LASSO algorithm, we selected six TLR-related genes to construct a survival prognostic model, divided melanoma patients into the training set, internal validation set 1, internal validation set 2, and external validation set for multiple validations, and discussed the correlation between model genes and clinical features of melanoma patients. In conclusion, we constructed a prognostic survival model based on TLR-related genes that precisely and independently demonstrated the potential to assess the prognosis and immune traits of melanoma patients, which is critical for patients' survival.

The psychology and policy of overcoming economic inequality

Recent arguments claim that behavioral science has focused - to its detriment - on the individual over the system when construing behavioral interventions. In this commentary, we argue that tackling economic inequality using both framings in tandem is invaluable. By studying individuals who have overcome inequality, "positive deviants," and the system limitations they navigate, we offer potentially greater policy solutions.

A prospective prognostic signature for pancreatic adenocarcinoma based on ubiquitination-related mRNA-lncRNA with experimental validation in vitro and vivo

Ubiquitination-related genes (URGs) exerted a crucial part in a variety of human disease disorders; however, their association with pancreatic adenocarcinoma (PAAD) had yet to be clearly described. We aimed to comprehensively characterize the contributions of URGs in PAAD through in silico analysis and experimental validation, and then identified a robust mRNA-lncRNA-based molecular prognostic panel for patients with PAAD using bulk RNA-sequencing and single-cell RNA-sequencing data. Initially, we collected the multi-omics data from TCGA platform to depict a comprehensive landscape of URGs in pan-cancer. Furthermore, we were accurate to PAAD for in-depth analysis. Significant differences of the activation of ubiquitination pathways and the expression of URGs were detected between normal and malignant cells. Unsupervised hierarchical clustering determined two PAAD subtypes with distinct clinical outcomes, ubiquitination pathway activities, immune microenvironment, and functional annotation characteristics. The expression profiles of ubiquitination-associated mRNAs and lncRNAs in the training and validation datasets were utilized to develop and verify a novel ubiquitination-related mRNA-lncRNA prognostic panel, which had a satisfied prediction efficiency. Our ubiquitination-associated model could function as an effective prognostic index and outperformed four other recognized panels in evaluating PAAD patients' survival status. Tumor immune microenvironment, mutation burden, and chemotherapy response were intensively explored to demonstrate the underlying mechanism of prognostic difference according to our panel. Our findings also revealed that FTI-277, a farnesyltransferase inhibitor, had a better curative effect in high-risk patients, while MK-2206, an Akt allosteric inhibitor, had a superior therapeutic effect in low-risk patients. The real-time PCR results uncovered the RNA expression of AC005062.1 in all the three PAAD cell lines was elevated several thousandfold. In conclusion, our URGs-based classification panel could be triumphantly served as a prediction tool for survival evaluation in patients with PAAD, and the genes in this panel could be developed as a potential target in PAAD therapy.

Image-guided prostate biopsy robots: A review

At present, the incidence of prostate cancer (PCa) in men is increasing year by year. So, the early diagnosis of PCa is of great significance. Transrectal ultrasonography (TRUS)-guided biopsy is a common method for diagnosing PCa. The biopsy process is performed manually by urologists but the diagnostic rate is only 20%-30% and its reliability and accuracy can no longer meet clinical needs. The image-guided prostate biopsy robot has the advantages of a high degree of automation, does not rely on the skills and experience of operators, reduces the work intensity and operation time of urologists and so on. Capable of delivering biopsy needles to pre-defined biopsy locations with minimal needle placement errors, it makes up for the shortcomings of traditional free-hand biopsy and improves the reliability and accuracy of biopsy. The integration of medical imaging technology and the robotic system is an important means for accurate tumor location, biopsy puncture path planning and visualization. This paper mainly reviews image-guided prostate biopsy robots. According to the existing literature, guidance modalities are divided into magnetic resonance imaging (MRI), ultrasound (US) and fusion image. First, the robot structure research by different guided methods is the main line and the actuators and material research of these guided modalities is the auxiliary line to introduce and compare. Second, the robot image-guided localization technology is discussed. Finally, the image-guided prostate biopsy robot is summarized and suggestions for future development are provided.

The persistence of cognitive biases in financial decisions across economic groups

While economic inequality continues to rise within countries, efforts to address it have been largely ineffective, particularly those involving behavioral approaches. It is often implied but not tested that choice patterns among low-income individuals may be a factor impeding behavioral interventions aimed at improving upward economic mobility. To test this, we assessed rates of ten cognitive biases across nearly 5000 participants from 27 countries. Our analyses were primarily focused on 1458 individuals that were either low-income adults or individuals who grew up in disadvantaged households but had above-average financial well-being as adults, known as positive deviants. Using discrete and complex models, we find evidence of no differences within or between groups or countries. We therefore conclude that choices impeded by cognitive biases alone cannot explain why some individuals do not experience upward economic mobility. Policies must combine both behavioral and structural interventions to improve financial well-being across populations.

A tera-electron volt afterglow from a narrow jet in an extremely bright gamma-ray burst

Some gamma-ray bursts (GRBs) have a tera-electron volt (TeV) afterglow, but the early onset of this has not been observed. We report observations with the Large High Altitude Air Shower Observatory of the bright GRB 221009A, which serendipitously occurred within the instrument field of view. More than 64,000 photons >0.2 TeV were detected within the first 3000 seconds. The TeV flux began several minutes after the GRB trigger, then rose to a peak about 10 seconds later. This was followed by a decay phase, which became more rapid ~650 seconds after the peak. We interpret the emission using a model of a relativistic jet with half-opening angle ~0.8°. This is consistent with the core of a structured jet and could explain the high isotropic energy of this GRB.

Mass Measurement of Upper fp-Shell N=Z-2 and N=Z-1 Nuclei and the Importance of Three-Nucleon Force along the N=Z Line

Using a novel method of isochronous mass spectrometry, the masses of ^{62}Ge, ^{64}As, ^{66}Se, and ^{70}Kr are measured for the first time, and the masses of ^{58}Zn, ^{61}Ga, ^{63}Ge, ^{65}As, ^{67}Se, ^{71}Kr, and ^{75}Sr are redetermined with improved accuracy. The new masses allow us to derive residual proton-neutron interactions (δV_{pn}) in the N=Z nuclei, which are found to decrease (increase) with increasing mass A for even-even (odd-odd) nuclei beyond Z=28. This bifurcation of δV_{pn} cannot be reproduced by the available mass models, nor is it consistent with expectations of a pseudo-SU(4) symmetry restoration in the fp shell. We performed ab initio calculations with a chiral three-nucleon force (3NF) included, which indicate the enhancement of the T=1 pn pairing over the T=0 pn pairing in this mass region, leading to the opposite evolving trends of δV_{pn} in even-even and odd-odd nuclei.

Determination and characterization of molecular heterogeneity and precision medicine strategies of patients with pancreatic cancer and pancreatic neuroendocrine tumor based on oxidative stress and mitochondrial dysfunction-related genes

Background

Mitochondria are significant both for cellular energy production and reactive oxygen/nitrogen species formation. However, the significant functions of mitochondrial genes related to oxidative stress (MTGs-OS) in pancreatic cancer (PC) and pancreatic neuroendocrine tumor (PNET) are yet to be investigated integrally. Therefore, in pan-cancer, particularly PC and PNET, a thorough assessment of the MTGs-OS is required.

Methods

Expression patterns, prognostic significance, mutation data, methylation rates, and pathway-regulation interactions were studied to comprehensively elucidate the involvement of MTGs-OS in pan-cancer. Next, we separated the 930 PC and 226 PNET patients into 3 clusters according to MTGs-OS expression and MTGs-OS scores. LASSO regression analysis was utilized to construct a novel prognostic model for PC. qRT-PCR(Quantitative real-time PCR) experiments were performed to verify the expression levels of model genes.

Results

The subtype associated with the poorest prognosis and lowerest MTGs-OS scores was Cluster 3, which could demonstrate the vital function of MTGs-OS for the pathophysiological processes of PC. The three clusters displayed distinct variations in the expression of conventional cancer-associated genes and the infiltration of immune cells. Similar molecular heterogeneity was observed in patients with PNET. PNET patients with S1 and S2 subtypes also showed distinct MTGs-OS scores. Given the important function of MTGs-OS in PC, a novel and robust MTGs-related prognostic signature (MTGs-RPS) was established and identified for predicting clinical outcomes for PC accurately. Patients with PC were separated into the training, internal validation, and external validation datasets at random; the expression profile of MTGs-OS was used to classify patients into high-risk (poor prognosis) or low-risk (good prognosis) categories. The variations in the tumor immune microenvironment may account for the better prognoses observed in high-risk individuals relative to low-risk ones.

Conclusions

Overall, our study for the first time identified and validated eleven MTGs-OS remarkably linked to the progression of PC and PNET, and elaborated the biological function and prognostic value of MTGs-OS. Most importantly, we established a novel protocol for the prognostic evaluation and individualized treatment for patients with PC.

The combined signatures of the tumour microenvironment and nucleotide metabolism-related genes provide a prognostic and therapeutic biomarker for gastric cancer

The tumour microenvironment (TME) is vital to tumour development and influences the immunotherapy response. Abnormal nucleotide metabolism (NM) not only promotes tumour cell proliferation but also inhibits immune responses in the TME. Therefore, this study aimed to determine whether the combined signatures of NM and the TME could better predict the prognosis and treatment response in gastric cancer (GC). 97 NM-related genes and 22 TME cells were evaluated in TCGA-STAD samples, and predictive NM and TME characteristics were determined. Subsequent correlation analysis and single-cell data analysis illustrated a link between NM scores and TME cells. Thereafter, NM and TME characteristics were combined to construct an NM-TME classifier. Patients in the NMlow/TMEhigh group exhibited better clinical outcomes and treatment responses, which could be attributed to the differences in immune cell infiltration, immune checkpoint genes, tumour somatic mutations, immunophenoscore, immunotherapy response rate and proteomap. Additionally, the NMhigh/TMElow group benefited more from Imatinib, Midostaurin and Linsitinib, while patients in the NMlow/TMEhigh group benefited more from Paclitaxel, Methotrexate and Camptothecin. Finally, a highly reliable nomogram was developed. In conclusion, the NM-TME classifier demonstrated a pretreatment predictive value for prognosis and therapeutic responses, which may offer novel strategies for strategizing patients with optimal therapies.

Identification of novel characteristic biomarkers and immune infiltration profile for the anaplastic thyroid cancer via machine learning algorithms

PURPOSE

Anaplastic thyroid cancer (ATC) is a rare and lethal malignant cancer. In recent years, the application of molecular-driven targeted therapy and immunotherapy has markedly improved the prognosis of ATC. This study aimed to identify characteristic genes for ATC diagnosis and revealed the role of ATC characteristic genes in drug sensitivity and immune cell infiltration.

METHODS

We downloaded ATC RNA-sequencing data from the GEO database. Following the combination and normalization of the dataset, we first divided the combined datasets into the training cohort and the validation cohort. We identified differentially expressed genes (DEGs) in ATC by differential expression analysis in the training cohort. We used two machine learning algorithms, least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE) to identify ATC characteristic genes. The CIBERSORT algorithm was performed to calculate the abundance of various immune cells in ATC. Finally, we validated the expression of ATC characteristic genes by quantitative RT-PCR (RT-qPCR) in ATC cell lines and immunohistochemistry (IHC).

RESULTS

A total of 425 DEGs were identified in the training cohort, including 240 upregulated genes and 185 downregulated genes. Four ATC characteristic genes (ADM, PXDN, MMP1, and TFF3) were identified, and their diagnostic value was validated in the validation cohort (AUC in ROC analysis > 0.75). We established a practical gene expression-based nomogram to accurately predict the probability of ATC. We also found that ATC characteristic biomarkers are associated with the tumor immune microenvironment and drug sensitivity.

CONCLUSION

ADM, PXDN, MMP1, and TFF3 might serve as potential ATC diagnostic biomarkers and may be helpful for ATC molecular targeted therapy and immunotherapy.

[Study on the related factors of antiviral treatment in previously reported hepatitis C patients based on the Andersen model]

Objective: To understand the basic characteristics of previously reported patients with hepatitis C and analyze the related factors affecting their antiviral treatment. Methods: A convenient sampling method was adopted. Patients who had been previously diagnosed with hepatitis C in the Wenshan Prefecture of Yunnan Province and Xuzhou City of Jiangsu Province were contacted by telephone for an interview study. The Andersen health service utilization behavior model and related literature were used to design the research framework for antiviral treatment in previously reported hepatitis C patients. A step-by-step multivariate regression analysis was used in previously reported hepatitis C patients treated with antiviral therapy. Results: A total of 483 hepatitis C patients, aged 51.73 ± 12.06 years, were investigated. The proportion of male, agricultural occupants who were registered permanent residents, farmers and migrant workers was 65.24%, 67.49%, and 58.18%, respectively. Han ethnicity (70.81%), married (77.02%), and junior high school and below educational level (82.61%) were the main ones. Multivariate logistic regression analysis results showed that married patients with hepatitis C (OR = 3.19, 95% CI: 1.93-5.25, compared with unmarried, divorced, and widowed patients) with high school education or above (OR = 2.54, 95% CI: 1.54-4.20, compared with patients with junior high school education or below) were more likely to receive antiviral treatment in the predisposition module. Patients with severe self-perceived hepatitis C in the need factor module (compared with patients with mild self-perceived disease, OR = 3.36, 95% CI: 2.09-5.40) were more likely to receive treatment. In the competency module, the family's per capita monthly income was more than 1,000 yuan (compared with patients with per capita monthly income below 1,000 yuan, OR = 1.59, 95% CI: 1.02-2.47), and the patients had a high level of awareness of hepatitis C knowledge (compared with patients with a low level of knowledge, OR = 1.54, 95% CI: 1.01-2.35), and the family members who knew the patient's infection status (compared with patients with an unknown infection status, OR = 4.59, 95% CI: 2.24-9.39) were more likely to receive antiviral treatment. Conclusion: Different income, educational, and marital statuses are related to antiviral treatment behavior in hepatitis C patients. Family support of hepatitis C patients receiving hepatitis C-related knowledge and their families knowing the infection status is more important in promoting the antiviral treatment of patients, suggesting that in the future, we should further strengthen the hepatitis C knowledge of hepatitis C patients, especially the family support of hepatitis C patients' families in treatment.

Comprehensive Characterization of RNA-Binding Proteins in Colon Adenocarcinoma Identifies a Novel Prognostic Signature for Predicting Clinical Outcomes and Immunotherapy Responses Based on Machine Learning

BACKGROUND

RNA-binding proteins (RBPs) are crucial factors that function in the posttranscriptional modification process and are significant in cancer.

OBJECTIVE

This research aimed for a multigene signature to predict the prognosis and immunotherapy response of patients with colon adenocarcinoma (COAD) based on the expression profile of RNA-binding proteins (RBPs).

METHODS

COAD samples retrieved from the TCGA and GEO datasets were utilized for a training dataset and a validation dataset. Totally, 14 shared RBP genes with prognostic significance were identified. Non-negative matrix factorization clusters defined by these RBPs could stratify COAD patients into two molecular subtypes. Cox regression analysis and identification of 8-gene signature categorized COAD patients into high- and low-risk populations with significantly different prognosis and immunotherapy responses.

RESULTS

Our prediction signature was superior to another five well-established prediction models. A nomogram was generated to quantificationally predict the overall survival (OS) rate, validated by calibration curves. Our findings also indicated that high-risk populations possessed an enhanced immune evasion capacity and low-risk populations might benefit immunotherapy, especially for the joint combination of PD-1 and CTLA4 immunosuppressants. DHX15 and LARS2 were detected with significantly different expressions in both datasets, which were further confirmed by qRTPCR and immunohistochemical staining.

CONCLUSION

Our observations supported an eight-RBP-related signature that could be applied for survival prediction and immunotherapy response of patients with COAD.

Identification and characterization of a novel molecular classification incorporating oxidative stress and metabolism-related genes for stomach adenocarcinoma in the framework of predictive, preventive, and personalized medicine

BACKGROUND

Stomach adenocarcinoma (STAD) is one of the primary contributors to deaths that are due to cancer globally. At the moment, STAD does not have any universally acknowledged biological markers, and its predictive, preventive, and personalized medicine (PPPM) remains sufficient. Oxidative stress can promote cancer by increasing mutagenicity, genomic instability, cell survival, proliferation, and stress resistance pathways. As a direct and indirect result of oncogenic mutations, cancer depends on cellular metabolic reprogramming. However, their roles in STAD remain unclear.

METHOD

743 STAD samples from GEO and TCGA platforms were selected. Oxidative stress and metabolism-related genes (OMRGs) were acquired from the GeneCard Database. A pan-cancer analysis of 22 OMRGs was first performed. We categorized STAD samples by OMRG mRNA levels. Additionally, we explored the link between oxidative metabolism scores and prognosis, immune checkpoints, immune cell infiltration, and sensitivity to targeted drugs. A series of bioinformatics technologies were employed to further construct the OMRG-based prognostic model and clinical-associated nomogram.

RESULTS

We identified 22 OMRGs that could evaluate the prognoses of patients with STAD. Pan-cancer analysis concluded and highlighted the crucial part of OMRGs in the appearance and development of STAD. Subsequently, 743 STAD samples were categorized into three clusters with the enrichment scores being C2 (upregulated) > C3 (normal) > C1 (downregulated). Patients in C2 had the lowest OS rate, while C1 had the opposite. Oxidative metabolic score significantly correlates with immune cells and immune checkpoints. Drug sensitivity results reveal that a more tailored treatment can be designed based on OMRG. The OMRG-based molecular signature and clinical nomogram have good accuracy for predicting the adverse events of patients with STAD. Both transcriptional and translational levels of ANXA5, APOD, and SLC25A15 exhibited significantly higher in STAD samples.

CONCLUSION

The OMRG clusters and risk model accurately predicted prognosis and personalized medicine. Based on this model, high-risk patients might be identified in the early stage so that they can receive specialized care and preventative measures, and choose targeted drug beneficiaries to deliver individualized medical services. Our results showed oxidative metabolism in STAD and led to a new route for improving PPPM for STAD.

Constraints on Heavy Decaying Dark Matter from 570 Days of LHAASO Observations

The kilometer square array (KM2A) of the large high altitude air shower observatory (LHAASO) aims at surveying the northern γ-ray sky at energies above 10 TeV with unprecedented sensitivity. γ-ray observations have long been one of the most powerful tools for dark matter searches, as, e.g., high-energy γ rays could be produced by the decays of heavy dark matter particles. In this Letter, we present the first dark matter analysis with LHAASO-KM2A, using the first 340 days of data from 1/2-KM2A and 230 days of data from 3/4-KM2A. Several regions of interest are used to search for a signal and account for the residual cosmic-ray background after γ/hadron separation. We find no excess of dark matter signals, and thus place some of the strongest γ-ray constraints on the lifetime of heavy dark matter particles with mass between 10^{5} and 10^{9}  GeV. Our results with LHAASO are robust, and have important implications for dark matter interpretations of the diffuse astrophysical high-energy neutrino emission.

Transcriptome analysis of adipocytokines and their-related LncRNAs in lung adenocarcinoma revealing the association with prognosis, immune infiltration, and metabolic characteristics

Lung adenocarcinoma (LUAD) is amongst the major contributors to cancer-related deaths on a global scale. Adipocytokines and long non-coding RNAs (lncRNAs) are indispensable participants in cancer. We performed a pan-cancer analysis of the mRNA expression, single nucleotide variation, copy number variation, and prognostic value of adipocytokines. LUAD samples were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Simultaneously, train, internal and external cohorts were grouped. After a stepwise screening of optimized genes through least absolute shrinkage and selection operator regression analysis, random forest algorithm,, and Cox regression analysis, an adipocytokine-related prognostic signature (ARPS) with superior performance compared with four additional well-established signatures for survival prediction was constructed. After determination of risk levels, the discrepancy of immune microenvironment, immune checkpoint gene expression, immune subtypes, and immune response in low- and high-risk cohorts were explored through multiple bioinformatics methods. Abnormal pathways underlying high- and low-risk subgroups were identified through gene set enrichment analysis (GSEA). Immune-and metabolism-related pathways that were correlated with risk score were selected through single sample GSEA. Finally, a nomogram with satisfied predictive survival probability was plotted. In summary, this study offers meaningful information for clinical treatment and scientific investigation.

[A multicenter study on childhood Hodgkin lymphoma treated with HL-2013 regimen in China]

Objective: To evaluate the efficacy of the Hodgkin lymphoma (HL)-2013 regimen in the treatment of children with HL, and to investigate the prognostic factors of childhood HL. Methods: Clinical data of 145 children (aged ≤18 years) with newly diagnosed HL, treated with HL-2013 regimen in 8 tertiary referral centers for childhood cancer from August 2011 to April 2021 were analyzed retrospectively. All the diagnosis were confirmed by histopathological morphology and immunohistochemical examination. The clinical characteristics and treatment outcomes were summarized, and the patients were divided into different groups according to clinical characteristics. Kaplan-Meier method was used for survival analysis, and the comparison of survival rates between groups was performed with Log-rank test. Results: Of the 145 cases, there were 115 males and 30 females, the age at diagnosis was 7.9 (5.8, 10.6) years. Cervical lymph node enlargement (114 cases, 78.6%) was the common symptom of the disease, and 57 patients (39.3%) were accompanied by large masses. The most common pathological classification was mixed cell type (93 cases, 64.1%). According to the Ann Arbor staging system, there were 9 cases of stage Ⅰ, 62 cases of stage Ⅱ, 45 cases of stage Ⅲ, 29 cases of stage Ⅳ. According to the risk stratification: there were 14 cases of low-risk group, 76 cases of medium-risk group and 55 cases of high-risk group. Of all patients, 68 cases (46.9%) achieved an early complete remission (CR) after 2 courses of chemotherapy, and the CR rate was 93.8% (136/145) after first-line treatment. Disease recurrence or progression occurred in 22 cases (15.2%). Of all patients, 125 cases survived, 6 cases died and 14 cases were lost to follow-up. Among the survived cases, 123 cases were continuously at CR state,and the follow-up time was 55 (40, 76) months. The 5-year overall survival (OS) and event free survival (EFS) rates were (95.3±1.9)% and (84.2±3.0)% for the entire group, respectively. 5-year OS and EFS rates for patients with stage Ⅲ-Ⅳ were both lower than those for patients with stage Ⅰ-Ⅱ (χ²=6.28 and 7.58, both P<0.05), the 5-year OS and EFS rates for patients in high-risk group were both lower than those for patients in low-risk and medium-risk group (χ²=10.93, 7.79, both P<0.05). The 5-year OS rates for the patient with early CR and without early CR were 100.0% and (90.9±3.6)% (χ²=5.77, P=0.016). EFS rates for the patient with early CR (68 cases) and without early CR (77 cases) were (93.8±3.0)% and (75.8±5.0)% (χ²=8.78, P=0.003). Conclusions: HL-2013 regimen is significantly effective in the treatment of pediatric HL. However, the patients in high-risk group and those without early CR are prone to disease recurrence or progression. Stage Ⅲ-Ⅳ and without early CR were associated with worse prognosis.

Comprehensive characterization of extracellular matrix-related genes in PAAD identified a novel prognostic panel related to clinical outcomes and immune microenvironment: A silico analysis with in vivo and vitro validation

The extracellular matrix (ECM) is a vital component of the tumor microenvironment, which interplays with stromal and tumor cells to stimulate the capacity of cancer cells to proliferate, migrate, invade, and undergo angiogenesis. Nevertheless, the crucial functions of ECM-related genes (ECMGs) in pancreatic adenocarcinoma (PAAD) have not been systematically evaluated. Hence, a comprehensive evaluation of the ECMGs is required in pan-cancer, especially in PAAD. First, a pan-cancer overview of ECMGs was explored through the integration of expression profiles, prognostic values, mutation information, methylation levels, and pathway-regulation relationships. Seven ECMGs (i.e. LAMB3, LAMA3, ITGB6, ITGB4, ITGA2, LAMC2, and COL11A1) were identified to be hub genes of PAAD, which were obviously up-regulated in PAAD and considerably linked to tumor stage as well as prognosis. Subsequently, patients with PAAD were divided into 3 clusters premised on ECMG expression and ECM scores. Cluster 2 was the subtype with the best prognosis accompanied by the lowest ECM scores, further verifying ECM’s significant contribution to the pathophysiological processes of PAAD. Significant differences were observed for oncogene and tumor suppressor gene expression, immune microenvironment, and chemotherapy sensitivity across three ECM subtypes. After applying a variety of bioinformatics methods, a novel and robust ECM-associated mRNA-lncRNA-based prognostic panel (ECM-APP) was developed and validated for accurately predicting clinical outcomes of patients with PAAD. Patients with PAAD were randomly categorized into the train, internal validation, and external validation cohorts; meanwhile, each patient was allocated into high-risk (unfavorable prognosis) and low-risk (favorable prognosis) populations premised on the expression traits of ECM-related mRNAs and lncRNAs. The discrepancy in the tumor mutation burden and immune microenvironment might be responsible for the difference in prognoses across the high-risk and low-risk populations. Overall, our findings identified and validated seven ECMGs remarkably linked to the onset and progression of PAAD. ECM-based molecular classification and prognostic panel aid in the prognostic assessment and personalized intervention of patients with PAAD.

Metabolic reprogramming enables the auxiliary diagnosis of breast cancer by automated breast volume scanner

Breast cancer is the leading cause of female cancer-related deaths worldwide. New technologies with enhanced sensitivity and specificity for early diagnosis and monitoring of postoperative recurrence are in critical demand. Automatic breast full volume scanning system (ABVS) is an emerging technology used as an alternative imaging method for breast cancer screening. Despite its improved detection rate of malignant tumors, ABVS cannot accurately stage breast cancer preoperatively in 30–40% of cases. As a major hallmark of breast cancer, the characteristic metabolic reprogramming may provide potential biomarkers as an auxiliary method for ABVS.

Objective

The objective of this study was to identify differential metabolomic signatures between benign and malignant breast tumors and among different subtypes of breast cancer patients based on untargeted metabolomics and improve breast cancer detection rate by combining key metabolites and ABVS.

Methods

Untargeted metabolomics approach was used to profile serum samples from 70 patients with different subtypes of breast cancer and benign breast tumor to determine specific metabolomic profiles through univariate and multivariate statistical data analysis.

Results

Metabolic profiles correctly distinguished benign and malignant breast tumors patients, and a total of 791 metabolites were identified. There were 54 different metabolites between benign and malignant breast tumors and 17 different metabolites between invasive and non-invasive breast cancer. Notably, the missed diagnosis rate of ABVS could be reduced by differential metabolite analysis. Moreover, the diagnostic performance analyses of combined metabolites (pelargonic acid, N-acetylasparagine, and cysteine-S-sulfate) with ABVS performance gave a ROC area under the curve of 0.967 (95% CI: 0.926, 0.993).

Conclusions

Our study identified metabolic features both in benign and malignant breast tumors and in invasive and non-invasive breast cancer. Combined ultrasound ABVS and a panel of differential serum metabolites could further improve the accuracy of preoperative diagnosis of breast cancer and guide surgical therapy.

Characterizing the prognostic and therapeutic value of necroptosis in sarcoma based on necroptosis subtypes

Necroptosis, a type of necrotic cell death independent of caspase regulation, is mainly mediated by receptor interacting serine/threonine kinase 1 (RIPK1), receptor interacting serine/threonine kinase 3 (RIPK3) and mixed lineage kinase domain-like (MLKL). Necroptosis plays an essential role in many tumors. However, the potential roles of necroptosis in tumor microenvironment (TME) of sarcoma (SARC) remain unknown. This study analyzed the expression, prognosis, genetic alterations of necroptosis genes in SARC. We identified two subtypes (cluster A and B) by performing unsupervised consensus clustering. Cluster A and B greatly differed in prognosis and immune infiltration, with cluster A showing more favorable prognosis, higher immune infiltration and higher expression levels of necroptosis genes than cluster B. Based on the differentially expressed genes (DEGs) between two clusters, a necroptosis scoring system was developed for predicting overall survival of SARC patients. Patients with high necroptosis score had worse survival status, with a decreased infiltration level of most immune cells. Our findings demonstrated the potential role of necroptosis in regulating tumor microenvironment and the prognostic value of necroptosis-related genes for SARC patients.

Machine learning identification of cuproptosis and necroptosis-associated molecular subtypes to aid in prognosis assessment and immunotherapy response prediction in low-grade glioma

Both cuproptosis and necroptosis are typical cell death processes that serve essential regulatory roles in the onset and progression of malignancies, including low-grade glioma (LGG). Nonetheless, there remains a paucity of research on cuproptosis and necroptosis-related gene (CNRG) prognostic signature in patients with LGG. We acquired patient data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) and captured CNRGs from the well-recognized literature. Firstly, we comprehensively summarized the pan-cancer landscape of CNRGs from the perspective of expression traits, prognostic values, mutation profiles, and pathway regulation. Then, we devised a technique for predicting the clinical efficacy of immunotherapy for LGG patients. Non-negative matrix factorization (NMF) defined by CNRGs with prognostic values was performed to generate molecular subtypes (i.e., C1 and C2). C1 subtype is characterized by poor prognosis in terms of disease-specific survival (DSS), progression-free survival (PFS), and overall survival (OS), more patients with G3 and tumour recurrence, high abundance of immunocyte infiltration, high expression of immune checkpoints, and poor response to immunotherapy. LASSO-SVM-random Forest analysis was performed to aid in developing a novel and robust CNRG-based prognostic signature. LGG patients in the TCGA and GEO databases were categorized into the training and test cohorts, respectively. A five-gene signature, including SQSTM1, ZBP1, PLK1, CFLAR, and FADD, for predicting OS of LGG patients was constructed and its predictive reliability was confirmed in both training and test cohorts. In both the training and the test datasets (cohorts), higher risk scores were linked to a lower OS rate. The time-dependent ROC curve proved that the risk score had outstanding prediction efficiency for LGG patients in the training and test cohorts. Univariate and multivariate Cox regression analyses showed the CNRG-based prognostic signature independently functioned as a risk factor for OS in LGG patients. Furthermore, we developed a highly reliable nomogram to facilitate the clinical practice of the CNRG-based prognostic signature (AUC > 0.9). Collectively, our results gave a promising understanding of cuproptosis and necroptosis in LGG, as well as a tailored prediction tool for prognosis and immunotherapeutic responses in patients.

[Accuracy and retention of denture bases fabricated by injection molding, milling, and three-dimensional printing]

Objective: To compare the accuracy and retention of denture bases fabricated by injection molding, milling, and three-dimensional (3D) printing fabricating, in order to provide some references for clinical practice. Methods: A maxillary edentulous jaw model made was used to duplicated 10 working casts. The casts were numbered and scanned. The wax pattern was designed by digital ways and conventional methods and then the denture bases were fabricated by injection molding, milling, and 3D printing. The tissue surface of experimental denture base was obtained using a dental laboratory scanner. The deviation between the tissue surface of the fabricated denture bases and the working model was evaluated. A digital force gauge was used to measure the traction force. Results: The milling group [(0.076±0.026) mm] was more accurate than the 3D printing group [(0.117±0.041) mm] (P<0.05) and the injection group [(0.120± 0.025) mm] (P<0.05). The accuracy of 3D printing group and that of injection group were not statistically significant (P>0.05). The milling group [(9.55±2.44) N] demonstrated greater retentive force than 3D printing group [(5.19±0.06) N] and injection molding group [(1.52±0.52) N] (P<0.05). Conclusions: The denture base fabricated by milling was more accurate and showed the greatest retentive force than the other groups. And 3D printing group showed better retentive force than the injection molding group. Both digital manufacturing methods can meet the requirements of clinical application.

Angiorganoid: vitalizing the organoid with blood vessels

The emergence of the organoid simulates the native organs and this mini organ offers an excellent platform for probing multicellular interaction, disease modeling and drug discovery. Blood vessels constitute the instructive vascular niche which is indispensable for organ development, function and regeneration. Therefore, it is expected that the introduction of infiltrated blood vessels into the organoid might further pump vitality and credibility into the system. While the field is emerging and growing with new concepts and methodologies, this review aims at presenting various sources of vascular ingredients for constructing vascularized organoids and the paired methodology including de- and recellularization, bioprinting and microfluidics. Representative vascular organoids corresponding to specific tissues are also summarized and discussed to elaborate on the next generation of organoid development.

Integration of transcriptomics, proteomics, and metabolomics data to reveal HER2-associated metabolic heterogeneity in gastric cancer with response to immunotherapy and neoadjuvant chemotherapy

Background

Currently available prognostic tools and focused therapeutic methods result in unsatisfactory treatment of gastric cancer (GC). A deeper understanding of human epidermal growth factor receptor 2 (HER2)-coexpressed metabolic pathways may offer novel insights into tumour-intrinsic precision medicine.

Methods

The integrated multi-omics strategies (including transcriptomics, proteomics and metabolomics) were applied to develop a novel metabolic classifier for gastric cancer. We integrated TCGA-STAD cohort (375 GC samples and 56753 genes) and TCPA-STAD cohort (392 GC samples and 218 proteins), and rated them as transcriptomics and proteomics data, resepectively. 224 matched blood samples of GC patients and healthy individuals were collected to carry out untargeted metabolomics analysis.

Results

In this study, pan-cancer analysis highlighted the crucial role of ERBB2 in the immune microenvironment and metabolic remodelling. In addition, the metabolic landscape of GC indicated that alanine, aspartate and glutamate (AAG) metabolism was significantly associated with the prevalence and progression of GC. Weighted metabolite correlation network analysis revealed that glycolysis/gluconeogenesis (GG) and AAG metabolism served as HER2-coexpressed metabolic pathways. Consensus clustering was used to stratify patients with GC into four subtypes with different metabolic characteristics (i.e. quiescent, GG, AAG and mixed subtypes). The GG subtype was characterised by a lower level of ERBB2 expression, a higher proportion of the inflammatory phenotype and the worst prognosis. However, contradictory features were found in the mixed subtype with the best prognosis. The GG and mixed subtypes were found to be highly sensitive to chemotherapy, whereas the quiescent and AAG subtypes were more likely to benefit from immunotherapy.

Conclusions

Transcriptomic and proteomic analyses highlighted the close association of HER-2 level with the immune status and metabolic features of patients with GC. Metabolomics analysis highlighted the co-expressed relationship between alanine, aspartate and glutamate and glycolysis/gluconeogenesis metabolisms and HER2 level in GC. The novel integrated multi-omics strategy used in this study may facilitate the development of a more tailored approach to GC therapy.

Safety and tolerance of Lacticaseibacillus paracasei N1115 in caesarean-born young children: a randomised, placebo-controlled trial

The administration of probiotics may help to improve dysbiosis and related health problems in children delivered by caesarean section. However, the effects are strain specific, and safety combined tolerance are considered a priority. The aim of this study was to evaluate the safety and tolerance of Lacticaseibacillus paracasei N1115 in caesarean-born children aged 6-24 months via a randomised, placebo-controlled intervention study. In total, 101 children were included and randomised to receive either a sachet of L. paracasei N1115 (2×1010 cfu/g, 2 g/day) or placebo (maltodextrin, 2 g/day) per day for 12 weeks. Anthropometric parameters were measured by trained nurses, and defecation characteristics, gastrointestinal symptoms, (serious) adverse events ((s)AEs), crying patterns and lifestyle behaviours were recorded by parents or guardians. Neurocognitive development was assessed by the Ages and Stages Questionnaires-3 (ASQ-3) before and after the intervention. The only difference between groups regarding defecation characteristics was a significant treatment × time effect on stool frequency (P=0.007), as the number of defecations was significantly higher in the probiotic group (around 1.2-1.3 times/day) than in the placebo group (around 1.0 times/day) in the later intervention period (P=0.035 at week 9; P=0.048 at week 10; P=0.026 at week 12). The use of L. paracasei N1115 also reduced the incidence rate of constipation (Incidence rate ratio (IRR): 0.120; 95% confidence interval (CI): 0.015, 0.967; P=0.046) and abdominal pain (IRR: 0.562; 95% CI: 0.358, 0.882; P=0.012). Changes in anthropometric parameters, including weight, height and head circumference, did not differ significantly between groups, nor did measures of crying, sleep, outdoor activity, temper, appetite or the ASQ-3 scores. No adverse events associated with consumption of the probiotic were reported. Thus, the administration of L. paracasei N1115 is safe and well-tolerated in caesarean-born children aged 6-24 months. Furthermore, it may ameliorate gastrointestinal function to some extent.

Retraction Note: The carcinogenic complex lncRNA FOXP4-AS1/EZH2/LSD1 accelerates proliferation, migration and invasion of gastric cancer

The article "The carcinogenic complex lncRNA FOXP4-AS1/EZH2/LSD1 accelerates proliferation, migration and invasion of gastric cancer, by R.-Y. Chen, Q. Ju, L.-M. Feng, Q. Yuan, L. Zhang, published in Eur Rev Med Pharmacol Sci 2019; 23 (19): 8371-8376-DOI: 10.26355/eurrev_201910_19148-PMID: 31646567" has been retracted by the authors. After publication, the authors raised concerns about the reliability of the data used to conduct the study by stating that some data cannot be repeated by further research. The Publisher apologizes for any inconvenience this may cause. https://www.europeanreview.org/article/19148.

Identifying the role of transient receptor potential channels (TRPs) in kidney renal clear cell carcinoma and their potential therapeutic significances using genomic and transcriptome analyses

Kidney renal clear cell carcinoma (KIRC) is among the major causes of cancer-caused mortality around the world. Transient receptor potential channels (TRPs), due to their role in various human diseases, might become potential drug targets in cancer. The mRNA expression, copy number variation, single-nucleotide variation, prognostic values, drug sensitivity, and pathway regulation of TRPs were studied across cancer types. The ArrayExpress and The Cancer Genome Atlas (TCGA) databases were used to retrieve KIRC samples. Simultaneously, training, internal, and external cohorts were grouped. In KIRC, a prognostic signature with superior survival prediction in contrast with other well-established signatures was created after a stepwise screening of optimized genes linked to TRPs using univariate Cox, weighted gene co-expression network analysis, multivariate Cox, and least absolute shrinkage and selection operator regression analyses. Subsequent to the determination of risk levels, the variations in the expression of immune checkpoint genes, tumor mutation burden, and immune subtypes and response between low-risk and high-risk subgroups were studied using a variety of bioinformatics algorithms, including ESTIMATE, XCELL, EPIC, CIBERSORT-ABS, CIBERSORT, MCPCOUNTER, TIMER, and QUANTISEQ. Gene set enrichment analysis helped in the identification of abnormal pathways across the low- and high-risk subgroups. Besides, high-risk KIRC patients might benefit from ABT888, AZD6244, AZD7762, Bosutinib, Camptothecin, CI1040, JNK inhibitor VIII, KU55933, Lenalidomide, Nilotinib, PLX4720, RO3306, Vinblastine, and ZM.447439; however, low-risk populations might benefit from Bicalutamide, FH535, and OSI906. Finally, calibration curves were used to validate the nomogram with a satisfactory predictive survival probability. In conclusion, this research provides useful insight that can aid and guide clinical practice and scientific research.

Risk factors of clinically relevant postoperative pancreatic fistula after pancreaticoduodenectomy: A systematic review and meta-analysis

BACKGROUND

Clinically relevant postoperative pancreatic fistula (CR-POPF) is a common and troublesome complication after pancreatoduodenectomy (PD). We conducted a systematic review and meta-analysis to identify the risk factors of CR-POPF after PD.

METHODS

We searched PubMed, EMBASE, and Cochrane Library databases for studies related to risk factors of CR-POPF after PD. Odds ratios (ORs) with corresponding 95% confidence intervals (CIs) were extracted from the included studies, then a meta-analysis was conducted. If necessary, sensitivity analysis would be performed by changing the effect model or excluding 1 study at a time. Publication bias was assessed by funnel plot and Begg test and Egger test.

RESULTS

A total of 27 studies with 24,740 patients were included, and CR-POPF occurred in 3843 patients (incidence = 17%, 95% CI: 16%-19%). Male (OR = 1.56, 95% CI: 1.42-1.70), body mass index >25 kg/m2 (OR = 1.98, 95% CI: 1.23-3.18), pancreatic duct diameter <3 mm (OR = 1.87, 95% CI: 1.66-2.12), soft pancreatic texture (OR = 3.49, 95% CI: 2.61-4.67), and blood transfusion (OR = 3.10, 95% CI: 2.01-4.77) can significantly increase the risk of CR-POPF. Pancreatic adenocarcinoma (OR = 0.54, 95% CI: 0.47-0.61), vascular resection (OR = 0.57, 95% CI: 0.39-0.83), and preoperative chemoradiotherapy (OR = 0.68, 95% CI: 0.57-0.81) can significantly decrease the factor of CR-POPF. Diabetes mellitus was not statistically associated with CR-POPF (OR = 0.66, 95% CI: 0.40-1.08). However, the analysis of body mass index, pancreatic texture, and diabetes mellitus had a high heterogeneity, then sensitivity analysis was performed, and the result after sensitivity analysis showed diabetes mellitus can significantly decrease the risk of CR-POPF. There was no significant publication bias in this meta-analysis.

CONCLUSIONS

The current review assessed the effects of different factors on CR-POPF. This can provide a basis for the prevention and management of CR-POPF. Effective interventions targeting the above risk factors should be investigated in future studies for decreasing the occurrence of CR-POPF.

Single-Cell Transcriptomic Atlas of Gingival Mucosa in Type 2 Diabetes

The oral gingival barrier is a constantly stimulated and dynamic environment where homeostasis is often disrupted, resulting in inflammatory periodontal diseases. Type 2 diabetes (T2D) has been reported to be associated with gingival barrier dysfunction, but the effect and underlying mechanism are inconclusive. Herein, we performed single-cell RNA sequencing (scRNA-seq) of gingiva from leptin receptor-deficient mice (db/db) to examine the gingival heterogeneity in the context of T2D. Periodontal health of control mice is characterized by populations of Krt14⁺-expressing epithelial cells and Col1a1⁺-fibroblasts mediating immune homeostasis primarily through the enrichment of innate lymphoid cells. The db/db gingiva exhibited decreased epithelial/stromal ratio and dysfunctional barrier. We further observed stromal, particularly fibroblast immune hyperresponsiveness, linked to the recruitment of myeloid-derived cells at the db/db gingiva. Both scRNA-seq and histological analysis suggested the inflammatory signaling between fibroblasts and neutrophils as a potential driver of diabetes-induced periodontal damage. Notably, the "immune-like" stromal cells were wired toward the induction of gingival γδ T hyperresponsiveness in db/db mice. Our work reveals that the "immune-like" fibroblasts with transcriptional diversity are involved in the innate immune homeostasis at the diabetic gingiva. It highlights a potentially significant role of these cell types in its pathogenesis.

Identification and Verification of the Ferroptosis- and Pyroptosis-Associated Prognostic Signature for low-grade Glioma

Accumulating evidence reveals that ferroptosis and pyroptosis play pivotal roles in tumorigenesis of low-grade glioma (LGG). In this research, we aimed to classify molecular subtypes and further identify and verify a novel multigene signature in LGG on the basis of ferroptosis- and pyroptosis-related genes (FPRGs). Raw sequencing data and corresponding clinical data of LGG samples retrieved from The Cancer Genome Atlas and Chinese Glioma Genome Atlas databases were obtained for the training and validation datasets. Non-negative matrix factorization (NMF) clustering defined by FPRGs associated with prognosis was performed to classify molecular subtypes of LGG patients. Least absolute shrinkage and selection operator-support vector machine-random forest analysis was carried out to develop a FPRG signature to predict the survival and benefit of immunotherapy of LGG patients. NMF clustering defined by FPRGs with prognostic values acted to categorize LGG patients into two molecular subtypes with different prognosis, clinical traits, and immune microenvironments. A six-FPRG prognostic signature was constructed, accompanied by the optimal p-value. The AUC values of our signature exhibited great prognostic performances. Our signature was superior to other four well-recognized signatures in predicting the survival probability of LGG patients. Immune characteristics, tumor mutation profile, tumor stemness indices, MGMT methylation, and immunotherapy response biomarkers showed significant differences between high- and low-risk populations. Finally, a nomogram was created for quantitative prediction of the survival probability of LGG patients, with the AUC values of the nomogram being 0.916, 0.888, and 0.836 for 1-, 3-, and 5-year survival, sequentially. Overall, the FPRG signature may function as an effective indicator for the prognosis prediction and immunotherapy response of LGG patients.

Percutaneous CT-Guided Microwave Ablation Combined with Vertebral Augmentation for Treatment of Painful Spinal Metastases

BACKGROUND AND PURPOSE

Percutaneous thermal ablation followed by vertebral augmentation is an emerging minimally invasive therapeutic alternative for the management of spinal metastases. This study aimed to retrospectively evaluate the effectiveness and safety of microwave ablation combined with vertebral augmentation for the treatment of painful vertebral metastases.

MATERIALS AND METHODS

Overall, 91 patients with 140 metastatic vertebrae who experienced refractory moderate-to-severe pain were treated with CT-guided microwave ablation and vertebral augmentation. Procedural effectiveness was determined using the visual analog scale, daily morphine consumption, and the Oswestry Disability Index preprocedurally and during follow-up. Local tumor control was assessed at follow-up imaging.

RESULTS

The procedure was technically successful in all patients. The median visual analog scale score and mean morphine dose were 6 (range, 4-10) and 77.8 (SD, 31.5) mg (range, 15-143 mg), preprocedurally; 5 (range 3-8) and 34.5 (SD, 23.8) mg (range, 0-88 mg) at 3 days; 4 (range, 2-7) and 28.7 (SD, 16.4) mg (range, 0-73 mg) at 1 week; 3 (range, 1-6) and 24.6 (SD, 13.2) mg (range, 0-70 mg) at 1 month; 3 (range, 1-6) and 21.70 (SD, 10.0) mg (range, 0-42 mg) at 3 months; and 3 (range, 1-8) and 21.0 (SD, 9.9) mg (range, 0-46 mg) at 6 months postprocedurally (all P < .05). A decrease in the Oswestry Disability Index score was also observed (P < .01). Local control was achieved in 94.8% of the treated metastatic vertebrae during the 6-month follow-up period. Asymptomatic cement leakage occurred in 42 (30%) treated vertebrae. A grade 3 neural injury was observed in 1 patient (1.1%). The patient's neurologic function returned to normal following treatment with mannitol, glucocorticoids, and radiation therapy.

CONCLUSIONS

This study demonstrates that percutaneous CT-guided microwave ablation combined with vertebral augmentation is a safe and effective minimally invasive intervention for the treatment of painful spinal metastases.