PCAO2: an ontology for integration of prostate cancer associated genotypic, phenotypic and lifestyle data.

Disease ontologies facilitate the semantic organization and representation of domain-specific knowledge. In the case of prostate cancer (PCa), large volumes of research results and clinical data have been accumulated and needed to be standardized for sharing and translational researches. A formal representation of PCa-associated knowledge will be essential to the diverse data standardization, data sharing and the future knowledge graph extraction, deep phenotyping and explainable artificial intelligence developing. In this study, we constructed an updated PCa ontology (PCAO2) based on the ontology development life cycle. An online information retrieval system was designed to ensure the usability of the ontology. The PCAO2 with a subclass-based taxonomic hierarchy covers the major biomedical concepts for PCa-associated genotypic, phenotypic and lifestyle data. The current version of the PCAO2 contains 633 concepts organized under three biomedical viewpoints, namely, epidemiology, diagnosis and treatment. These concepts are enriched by the addition of definition, synonym, relationship and reference. For the precision diagnosis and treatment, the PCa-associated genes and lifestyles are integrated in the viewpoint of epidemiological aspects of PCa. PCAO2 provides a standardized and systematized semantic framework for studying large amounts of heterogeneous PCa data and knowledge, which can be further, edited and enriched by the scientific community. The PCAO2 is freely available at https://bioportal.bioontology.org/ontologies/PCAO, http://pcaontology.net/ and http://pcaontology.net/mobile/.

Stabilization of heavy metals in municipal solid waste incineration fly ash using organic chelating agents: Insight into risk assessment and function mechanism.

Landfill treatment of municipal solid waste incineration fly ash (MSWI FA) after stabilization is the primary disposal technology. However, only few studies have assessed the stability of MSWI-FA-chelated products in different landfill scenarios. In this study, three commonly used dithiocarbamate (DTC)-based organic chelating agents (CAs) (TS-300, SDD, and PD) were selected to stabilize heavy metals (HMs) in MSWI FA. In addition, the leaching toxicity and environmental risks of the chelated products were assessed in different disposal environments. The results demonstrate that the HM leaching concentrations of the chelated products met the concentration limits of the sanitary landfill standard (GB16889-2008; mixed Landfill Scenario) for the three CAs at a low additive level (0.3 %). However, in the compartmentalized landfill scenario (the leaching agent was acid rain), the leaching of HMs from the chelated products met the standard when TS-300, SDD, and PD were added at 1.5 %, 6.0 %, and 8.0 %, respectively. Additionally, Pb, Zn, and Cd in the chelated products from the 1.5 %-TS-300 and 6.0 %-SDD groups met the leaching limits within the pH ranges 6-12 and 7-12, 6-12 and 7-12, and 8-12 and 8-12, respectively. This was primarily due of TS-300's multiple DTC groups forming stable chain-like macromolecular chelates with Pb. However, although the environmental risks associated with Pb, Zn, and Cd in the initial (0-d) chelated products of the 1.5 %-TS-300 and 6.0 %-SDD groups were minimized to low and negligible levels, there was a significant increase in the leaching of the three HMs after 28 d of storage. Therefore, with appropriate CA addition, although the leaching concentration of HMs in the chelated product may comply with the GB16889-2008 standards, it remains essential to consider its environmental risk, particularly in highly acidic or alkaline environments and during prolonged storage of the product.

Development of a novel forensic age estimation strategy for aged blood samples by combining piRNA and miRNA markers.

In forensic investigations, age estimation is vital for determining whether a suspect is under or over the legally defined adult age. With breakthroughs in RNA sequencing technology, small noncoding RNAs have provided new ways to solve problems related to the age estimation of trace or aged samples, owing to their small molecular weight and better stability. In our previous study, we had applied miRNAs for the age estimation of bloodstains; however, further improvement of the existing model is needed. PIWI-interacting RNAs (PiRNAs), which are 24-32 nt noncoding small RNA molecules involved in the PIWI-piRNA pathway, play an important role in the aging process. In this study, we explored the possibility of simultaneously analyzing piRNAs and miRNAs for better age estimation purpose. Through massively parallel sequencing, five age-related piRNAs were identified in blood samples that had been stored for eight years. Further real-time PCR analysis revealed that two piRNAs (piR-000753 and piR-020548) showed relatively higher efficiency in age estimation. Additionally, two age-related miRNAs (miR-324-3p and miR-330-5p) were used to build the estimation model. Among all algorithms tested, gradient boosting showed the lowest mean absolute error (MAE) and root mean square error (RMSE) values (3.171 and 4.403 years, respectively) for the validation dataset (n = 110). The errors of the model were less than 5 years and 10 years for 81.82% and 96.36% of the samples, respectively. The results suggest that the combined use of piRNA and miRNA markers may increase the accuracy of age estimation, and our new model has great potential for application in forensic casework.

Comprehensive analysis and molecular map of Hippo signaling pathway in lower grade glioma: the perspective toward immune microenvironment and prognosis.

Background: The activation of YAP/TAZ transcriptional co-activators, downstream effectors of the Hippo/YAP pathway, is commonly observed in human cancers, promoting tumor growth and invasion. The aim of this study was to use machine learning models and molecular map based on the Hippo/YAP pathway to explore the prognosis, immune microenvironment and therapeutic regimen of patients with lower grade glioma (LGG). Methods: SW1783 and SW1088 cell lines were used as in vitro models for LGG, and the cell viability of the XMU-MP-1 (a small molecule inhibitor of the Hippo signaling pathway) treated group was evaluated using a Cell Counting Kit-8 (CCK-8). Univariate Cox analysis on 19 Hippo/YAP pathway related genes (HPRGs) was performed to identify 16 HPRGs that exhibited significant prognostic value in meta cohort. Consensus clustering algorithm was used to classify the meta cohort into three molecular subtypes associated with Hippo/YAP Pathway activation profiles. The Hippo/YAP pathway's potential for guiding therapeutic interventions was also investigated by evaluating the efficacy of small molecule inhibitors. Finally, a composite machine learning models was used to predict individual patients' survival risk profiles and the Hippo/YAP pathway status. Results: The findings showed that XMU-MP-1 significantly enhanced the proliferation of LGG cells. Different Hippo/YAP Pathway activation profiles were associated with different prognostic and clinical features. The immune scores of subtype B were dominated by MDSC and Treg cells, which are known to have immunosuppressive effects. Gene Set Variation Analysis (GSVA) indicated that subtypes B with a poor prognosis exhibited decreased propanoate metabolic activity and suppressed Hippo pathway signaling. Subtype B had the lowest IC50 value, indicating sensitivity to drugs that target the Hippo/YAP pathway. Finally, the random forest tree model predicted the Hippo/YAP pathway status in patients with different survival risk profiles. Conclusions: This study demonstrates the significance of the Hippo/YAP pathway in predicting the prognosis of patients with LGG. The different Hippo/YAP Pathway activation profiles associated with different prognostic and clinical features suggest the potential for personalized treatments.

Solidification/stabilization and risk assessment of heavy metals in municipal solid waste incineration fly ash: A review.

Incineration is currently the most common method of treating municipal solid waste. Municipal solid waste incineration fly ash (MSWI FA) contains a high concentration of toxic heavy metals (HMs), making it a hazardous waste. A series of detoxification treatments are required to reduce the toxicity of fly ash. Furthermore, the environmental risk of MSWI FA after treatment is becoming a cause of concern. This paper reviews the primary ash properties, pH, liquid-solid ratio, and other factors (microorganism, type of leaching agents, etc.) that affect the leaching of HMs from MSWI FA, compares and summarizes the most widely applied solidification/stabilization (S/S) techniques. In particular, models and methods for the environmental risk assessment and prediction of HMs are classified and described in detail. Finally, the inadequacy of current S/S techniques for MSWI FA is pointed out, which may be useful for upcoming studies on this topic.

Surgical Implications and Radiologic Classification for the Upward Bulging of the Planum Sphenoidale in Patients With Anterior Skull Base Meningiomas Involving the Tuberculum Sellae Area.

OBJECTIVE: To investigate the surgical implications and morphologic type of upward bulging of the planum sphenoidale (PS) in anterior skull base meningiomas involving the tuberculum sellae area. METHODS: Between January 2014 and June 2021, 96 patients with anterior skull base meningiomas underwent surgery at the Sanbo Brain Hospital of Capital Medical University. A total of 96 patients with nonintracranial space-occupying lesions were selected as the control group. The height of upward bulging of the PS was measured and classified. The authors performed univariate and multivariate analyses to evaluate the rate and effects of upward bulging of the PS. RESULTS: The PS upward bulging rate was 23.00% versus 66.70% (P<0.001) between the control and meningioma groups. Multiple linear regression showed that it was correlated with the tumor midsagittal anteroposterior length (P=0.025) and the midsagittal height diameter (P=0.012). According to the height of PS upward bulging, it was divided into types 1, 2, and 3. The tumor gross-total resection rates were 96.9%, 92.3%, and 76.0%, respectively (P=0.042). CONCLUSIONS: Anterior skull base meningiomas involving the tuberculum sellae area can cause PS upward bulging, which lowers the tumor resection rate and should be considered while determining the treatment approach.

Epithelial-mesenchymal transition is the main way in which glioma-associated microglia/macrophages promote glioma progression.

Microglia/macrophages make up the largest population of tumor-infiltrating cells. Numerous studies have demonstrated that glioma-associated microglia/macrophages (GAMs) could promote the malignant progression of gliomas in various pathways. However, the primary function of GAMs in glioma remains inconclusive. First, by the CIBERSORT algorithm, we evaluated the content of microglia/macrophages in glioma tissues by bioinformatic analysis of omic data from thousands of glioma samples. Subsequently, we analyzed and confirmed the significant relationship between GAMs and the malignant phenotype of glioma, including survival time, IDH mutation status, and time of symptom onset. Afterward, Epithelial-Mesenchymal Transition (EMT) was identified by Gene Set Enrichment Analysis (GSEA) from numerous biological processes as the most relevant mechanism of malignant progression to GAMs. Moreover, a series of clinical samples were detected, including normal brain and various-grade glioma tissues. The results not only showed that GAMs were significantly associated with gliomas and their malignancy but also that GAMs were highly correlated with the degree of EMT in gliomas. In addition, we isolated GAMs from glioma samples and constructed co-culture models (in vitro) to demonstrate the promotion of the EMT process in glioma cells by GAMs. In conclusion, our study clarified that GAMs exert oncogenic effects with EMT in gliomas, suggesting the possibility of GAMs as immunotherapeutic targets.

Distinguishing between monozygotic twins' blood samples through immune repertoire sequencing.

Monozygotic (MZ) twins with highly similar genomic DNA sequences can not be distinguished by conventional forensic DNA testing. The immune repertoire (IR) reflects an individual's immune history, which is unique between individuals, has been applied to individualized treatment in precision medicine. However, the application of IR in forensic genetics has not been reported to date. In this study, the diversity in the complementary determining region 3 (CDR3) of both the T-cell receptor ß chain (TCRß) and B-cell receptor heavy chain (also known as immunoglobulin heavy chain, IGH) in four pairs of MZ twins were analyzed. The results showed that the amino acid sequences length distribution frequency of TCRß CDR3 had 4-10 differences, and the nucleic acid sequences length distribution frequency of TCRß CDR3 had 2-7 differences between MZ twins. The shared difference of four pairs of MZ twins focused on the length distribution frequency of 34 bp nucleotide sequences in TCRß. By analyzing the usage frequency of V and J genes in TCRß and IGH CDR3 DNA sequence rearrangements, we also found that there were biases between each pair of MZ twins, and the usage frequency of TRBJ2-3 showed common differences between each pair of MZ twins. Furthermore, each pair of MZ twins had its own unique V-J genes combination mode in TCRß and IGH CDR3 DNA sequences. This study, for the first time, suggested that IR can be used as a potential biological marker to distinguish MZ twins.

Next-Generation Sequencing Markup Language (NGSML): A Medium for the Representation and Exchange of NGS Data.

With the increasing demand for low-cost high-throughput sequencing of large genomes, next-generation sequencing (NGS) technology has developed rapidly. NGS can not only be used in basic scientific research but also in clinical diagnostics and healthcare. Numerous software systems and tools have been developed to analyze NGS data, and various data formats have been produced to accommodate different sequencing equipment providers or analytical software. However, the data interoperability between these tools brings great challenges to researchers. A generic format that could be shared by most of the software and tools in the NGS field would make data interoperability and sharing easier. In this paper, we defined a general XML-based NGS markup language (NGSML) format for the representation and exchange of NGS data. We also developed a user-friendly GUI tool, NGSMLEditor, for presenting, creating, editing, and converting NGSML files. By using NGSML, various types of NGS data can be saved in one unified format. Compared with the unstructured plain text file, a structured data format based on XML technology solves the incompatibility of various NGS data formats. The NGSML specifications are freely available from http://www.sysbio.org.cn/NGSML. NGSMLEditor is open source under GNU GPL and can be downloaded from the website.

Transcriptome analysis reveals potential marker genes for diagnosis of Alzheimer's disease and vascular dementia.

Alzheimer's disease (AD) and vascular dementia (VD) are the two most common forms of dementia, share similar symptoms, and are sometimes difficult to distinguish. To investigate the potential mechanisms by which they differ, we identified differentially expressed genes in blood and brain samples from patients with these diseases, and performed weighted gene co-expression network analysis and other bioinformatics analyses. Weighted gene co-expression network analysis resulted in mining of different modules based on differences in gene expression between these two diseases. Enrichment analysis and generation of a protein-protein interaction network were used to identify core pathways for each disease. Modules were significantly involved in cAMP and AMPK signaling pathway, which may be regulated cell death in AD and VD. Genes of cAMP and neurotrophin signaling pathways, including ATP1A3, PP2A, NCEH1, ITPR1, CAMKK2, and HDAC1, were identified as key markers. Using the least absolute shrinkage and selection operator method, a diagnostic model for AD and VD was generated and verified through analysis of gene expression in blood of patients. Furthermore, single sample gene set enrichment analysis was used to characterize immune cell infiltration into brain tissue. That results showed that infiltration of DCs and pDCs cells was increased, and infiltration of B cells and TFH cells was decreased in the brain tissues of patients with AD and VD. In summary, classification based on target genes showed good diagnostic efficiency, and filled the gap in the diagnostic field or optimizes the existing diagnostic model, which could be used to distinguish between AD and VD.

Postoperative hydrocephalus is a high-risk lethal factor for patients with low-grade optic pathway glioma.

OBJECTIVES: To explore the prognostic factors of patients with low-grade optic pathway glioma (OPG) and the optimal treatment to reduce the incidence of postoperative hydrocephalus. PATIENTS AND METHODS: This single-center study retrospectively analyzed data from 66 patients with OPGs who underwent surgery. The patients were followed, and overall survival (OS) and progression-free survival (PFS) were determined. The effects of different treatments on the hydrocephalus of patients were compared. RESULTS: Postoperative hydrocephalus was identified as a factor to increase the risk of mortality by 1.99-fold (p = .028). And, 5-year survival rate was significantly lower among patients with postoperative hydrocephalus (p = .027). The main factors leading to preoperative hydrocephalus in patients are large tumor volume and invasion into the third ventricle. Gross total resections (GTR) could reduce the risk of long-term hydrocephalus (p = .046). Age younger than 4 years (p = .046) and tumor invasion range/classification (p = .029) are the main factors to reduce the five-year survival rate. Postoperative radiotherapy (RT) and chemotherapy (CT) had no significant effects on OS. Extraventricular drainage (EVD) was not associated with perioperative infection (p = .798 > .05) and bleeding (p = .09 > .05). Compared with 2 stage surgery (external ventricular drainage or ventriculoperitoneal shunt (VPS) was first placed, followed by tumor resection), 1 stage surgery (direct resection of tumor) had no complication increase. CONCLUSIONS: Postoperative hydrocephalus is mostly obstructive hydrocephalus, and it is an important factor that reduces the OS of patients with low-grade OPGs. Surgery to remove the tumor to the greatest extent improves cerebrospinal fluid circulation is effective at reducing the incidence postoperative hydrocephalus. For patients whose ventricles are still dilated after surgery, in addition to considering poor ventricular compliance, they need to be aware of the persistence and progression of hydrocephalus.

Evaluation on nitrogen conversion during biomass torrefaction and its blend co-combustion with coal.

In this work, biomass torrefaction was combined with coal co-combustion to illustrate the differences in biomass performance and the mechanisms of migration and transformation of nitrogen over the entire course of thermal treatments. XPS analysis illustrated that torrefaction in CO2 suppressed the conversion of pyrrole-N (N-5) to quaternary-N (N-Q), whereas the trend for an O2 atmosphere moved in the opposite direction. During co-combustion, the impact on NO emission reduction shifted from positive to negative as the pretreatment temperature was raised, which is closely related to the six elementary reactions involving the intermediacy of NCO and NH, as well as to heterogeneous reduction of NO with char. In addition, torrefaction in a N2/O2 atmosphere at a lower temperature of 250 °C improved the properties of biomass and achieved the lowest NO emission during co-combustion, which provides the supporting theory needed for using effluent in power plants as a torrefaction medium.

Alterations in the RTK/Ras/PI3K/AKT pathway serve as potential biomarkers for immunotherapy outcome of diffuse gliomas.

BACKGROUND: Diffuse gliomas are the most common malignant brain tumors, and immune checkpoint inhibitors have limited therapeutic effects against this cancer. Three oncogenic pathways are altered in diffuse gliomas: the RTK/Ras/PI3K/AKT signaling, TP53, and RB pathways. Although these pathways may affect the tumor immune microenvironment, their association with immunotherapy biomarkers remains unclear. METHODS: We used copy number variation and mutation data to stratify patients with specific oncogenic signaling alterations, and evaluated their correlation with predictive immunotherapy biomarkers, including tumor mutation burden (TMB), immune cytolytic activity (CYT), tumor purity, and tumor-infiltrating CD8+ T cells. Immune checkpoint expression and interferon-γ signaling activity were also compared in these samples. RESULTS: We identified differentially expressed genes in three distinct oncogenic pathways. Gene ontology analysis of these genes revealed the involvement of RTK/Ras/PI3K/AKT-associated genes in immune and inflammatory responses. Moreover, significantly elevated TMB, CYT, and numbers of CD8+ T cells and decreased tumor purity were correlated with altered RTK/Ras/PI3K/AKT signaling. Single cell sequencing also confirmed that this tumor subgroup had increased immune checkpoint expression and interferon-γ signaling activity. Immune phenotyping based on the presence of CD274 and TMB or CD274 and CD8 T+ cells indicated that tumors with altered RTK/Ras/PI3K/AKT pathways represent a beneficial subtype and are associated with improved survival. CONCLUSION: Altered RTK/Ras/PI3K/AKT signaling and immunotherapy biomarkers are strongly correlated in gliomas. Gliomas with altered expression of RTK/Ras/PI3K/AKT pathway components may be sensitive to immunotherapy. A combination of small-molecule kinase inhibitors and immunotherapy is proposed for this subgroup of tumors.

Sensitive Detection and Conjoint Analysis of Promoter Methylation by Conjugated Polymers for Differential Diagnosis and Prognosis of Glioma.

Glioma is the most common primary tumor in the central nervous system (CNS) with the worst prognosis. Accurate pathological diagnosis has always been a challenge for optimal management of glioma. Promoter methylation is an important mechanism of epigenetic silencing tumor-suppressor genes and a potential biomarker for differential diagnosis and prognosis. Herein, using the cationic conjugated polymer (CCP)-based fluorescence resonance energy transfer (FRET) technique, we realized a highly sensitive detection of promoter methylation in clinical samples of minimal methylation degree (1.25%) and trace DNA quantity (10 ng/µL). Results for three glioma-related genes (MGMT, CDKN2A, and TERT) were combined in a diagnostic classifier to analyze the glioma-CpG island methylator phenotype (G-CIMP), which achieved a sensitivity of 80% at a maximum specificity of 100% for a glioma diagnosis. Kaplan-Meier survival curves and Pearson correlation analysis revealed that the prognosis of glioma patients with high G-CIMP scores (>5) was significantly better than those with low G-CIMP scores, especially in diffuse midline glioma and astrocytoma. This CCP-based FRET technique for determining G-CIMP status could provide patients with rapid and reasonably accurate diagnosis of glioma, as well as a valuable prognostic prediction that can guide individual treatment.

Development of a prognostic model based on an immunogenomic landscape analysis of medulloblastoma.

Medulloblastoma (MB) is one of the most common central nervous system tumors in children. At present, the vital role of immune abnormalities has been proved in tumorigenesis and progression. However, the immune mechanism in MB is still poorly understood. In the present study, 51 differentially expressed immune-related genes (DE-IRGs) and 226 survival associated immune-related genes (Sur-IRGs) were screened by an integrated analysis of multi-array. Moreover, the potential pathways were enriched by functional analysis, such as 'cytokine-cytokine receptor interaction', 'Ras signaling pathway', 'PI3K-Akt signaling pathway' and 'pathways in cancer'. Furthermore, 10 core IRGs were identified from DE-IRGs and Sur-IRGs. And the potential regulatory mechanisms of core IRGs were also explored. Additionally, a new prognostic model, including 7 genes (HDGF, CSK, PNOC, S100A13, RORB, FPR1, and ICAM2) based on IRGs, was established by multivariable COX analysis. In summary, our study revealed the underlying immune mechanism of MB. Moreover, we developed a prognostic model associated with clinical characteristics and could reflect the infiltration of immune cells.

PCLiON: An Ontology for Data Standardization and Sharing of Prostate Cancer Associated Lifestyles.

BACKGROUND: Researches on Lifestyle medicine (LM) have emerged in recent years to garner wide attention. Prostate cancer (PCa) could be prevented and treated by positive lifestyles, but the association between lifestyles and PCa is always personalized. OBJECTIVES: In order to solve the heterogeneity and diversity of different data types related to PCa, establish a standardized lifestyle ontology, promote the exchange and sharing of disease lifestyle knowledge, and support text mining and knowledge discovery. METHODS: The overall construction of PCLiON was created in accordance with the principles and methodology of ontology construction. Following the principles of evidence-based medicine, we screened and integrated the lifestyles and their related attributes. Protégé was used to construct and validate the semantic framework. All annotations in PCLiON were based on SNOMED CT, NCI Thesaurus, the Cochrane Library and FooDB, etc. HTML5 and ASP.NET was used to develop the independent Web page platform and corresponding intelligent terminal application. The PCLiON also uploaded to the National Center for Biomedical Ontology BioPortal. RESULTS: PCLiON integrates 397 lifestyles and lifestyle-related factors associated with PCa, and is the first of its kind for a specific disease. It contains 320 attribute annotations and 11 object attributes. The logical relationship and completeness meet the ontology requirements. Qualitative analysis was carried out for 329 terms in PCLiON, including factors which are protective, risk or associated but functional unclear, etc. PCLiON is publicly available both at http://pcaontology.net/PCaLifeStyleDefault.aspx and https://bioportal.bioontology.org/ontologies/PCALION. CONCLUSIONS: Through the bilingual online platforms, complex lifestyle research data can be transformed into standardized, reliable and responsive knowledge, which can promote the shared-decision making (SDM) on lifestyle intervention and assist patients in lifestyle self-management toward the goal of PCa targeted prevention.

ANCA: A Web Server for Amino Acid Networks Construction and Analysis.

Amino acid network (AAN) models empower us to gain insights into protein structures and functions by describing a protein 3D structure as a graph, where nodes represent residues and edges as amino acid interactions. Here, we present the ANCA, an interactive Web server for Amino Acids Network Construction and Analysis based on a single structure or a set of structures from the Protein Data Bank. The main purpose of ANCA is to provide a portal for three types of an environment-dependent residue contact energy (ERCE)-based network model, including amino acid contact energy network (AACEN), node-weighted amino acid contact energy network (NACEN), and edge-weighted amino acid contact energy network (EACEN). For comparison, the C-alpha distance-based network model is also included, which can be extended to protein-DNA/RNA complexes. Then, the analyses of different types of AANs were performed and compared from node, edge, and network levels. The network and corresponding structure can be visualized directly in the browser. The ANCA enables researchers to investigate diverse concerns in the framework of AAN, such as the interpretation of allosteric regulation and functional residues. The ANCA portal, together with an extensive help, is available at http://sysbio.suda.edu.cn/anca/.

Tumor-associated macrophages based signaling pathway analysis and hub genes identification in glioma.

ABSTRACT: Tumor-associated macrophages (TAMs) play a crucial role in the immune response to many malignancies, but the signaling pathways by which the glioma microenvironment cross-talk with TAMs are poorly understood. The aim of this study was to uncover the potential signaling pathways of the regulation of TAMs and identify candidate targets for therapeutic intervention of glioma through bioinformatics analysis.Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) datasets were used to download RNA-Seq data and microarray data of human glioma specimen. Differentially expressed genes (DEGs) between CD68-high samples and CD68-low samples were sorted. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the DEGs was conducted. Protein-protein interaction (PPI) network were formed to identify the hub genes.The prognostic value of TAMs in glioma patients was confirmed. A total of 477 specific DEGs were sorted. The signaling pathway was identified in pathway enrichment and the DEGs showed prominent representations of immune response networks in glioma. The hub genes including C3, IL6, ITGB2, PTAFR, TIMP1 and VAMP8 were identified form the PPI network and they were all correlated positively with the expression of CD68 and showed the excellent prognostic value in glioma patients.TAMs can be used as a good prognostic indicator in glioma patients. By analyzing comprehensive bioinformatics data, we uncovered the underlying signaling pathway of the DEGs between glioma patients with high and low expression level of CD68. Furthermore, the 6 hub genes identified were closely associated with TAMs in glioma microenvironment and need further investigation.

Immune cell infiltration and cytokine secretion analysis reveal a non-inflammatory microenvironment of medulloblastoma.

Medulloblastoma (MB) is the most common lethal malignant pediatric brain tumor. Adjuvant immunotherapy for medulloblastoma has been proposed in both pre-clinical and clinical practice. To provide a precision strategy of designing immunotherapy for MB, the present study performed a descriptive analysis of immune microenvironment in a cohort and compared the differences between four subgroups of MB. Subtypes (WNT, SHH Group 3 and Group 4) of medulloblastoma were identified using K-means clustering according to the expression of signature genes. Tumor infiltrating immune cell population was assessed by both bio-informative algorithm based on gene expression and immunohistochemistry staining. Cytokines in tumor microenvironment were detected using Luminex. Gene Set Enrichment Analysis demonstrated a raised immune response in the SHH subgroup. Lymphocyte infiltration was low in all four subgroups, while more CD4+ T cells were observed in the Group 4 subtype. Programmed cell death protein 1 (PD1)/ ligand 1 (PD-L1) expression was absent in the cohort. The SHH subtype recruited more activated tumor associated macrophage/microglia compared with the other subgroups. Cytokines within the MB microenvironment were low compared with the glioblastoma samples. In contrast to glioblastoma, the immune microenvironment of pediatric MB is non-inflammatory and does not recruit many immune cells. These observations provide important considerations for the design of immunotherapeutic approaches for MB, such as inducing more lymphocytes into the tumor microenvironment.

iODA: An integrated tool for analysis of cancer pathway consistency from heterogeneous multi-omics data.

The latest advances in the next generation sequencing technology have greatly facilitated the extensive research of genomics and transcriptomics, thereby promoting the decoding of carcinogenesis with unprecedented resolution. Considering the contribution of analyzing high-throughput multi-omics data to the exploration of cancer molecular mechanisms, an integrated tool for heterogeneous multi-omics data analysis (iODA) is proposed for the systems-level interpretation of multi-omics data, i.e., transcriptomic profiles (mRNA or miRNA expression data) and protein-DNA interactions (ChIP-Seq data). Considering the data heterogeneity, iODA can compare six statistical algorithms in differential analysis for the selected sample data and assist users in choosing the globally optimal one for dysfunctional mRNA or miRNA identification. Since molecular signatures are more consistent at the pathway level than at the gene level, the tool is able to enrich the identified dysfunctional molecules onto the KEGG pathways and extracted the consistent items as key components for further pathogenesis investigation. Compared with other tools, iODA is multi-functional for the systematic analysis of different level of omics data, and its analytical power was demonstrated through case studies of single and cross-level prostate cancer omics data. iODA is open source under GNU GPL and can be downloaded from http://www.sysbio.org.cn/iODA.