Differential Expression Pattern of THBS1 and THBS2 in Lung Cancer: Clinical Outcome and a Systematic-Analysis of Microarray Databases

Morphological basis of the lung adenocarcinoma subtypes

Lung adenocarcinoma (LUAD), which accounts for a large proportion of lung cancers, is divided into five major subtypes based on histologic characteristics. The clinical characteristics, prognosis, and responses to treatments vary among subtypes. Here, we demonstrate that the variations of cell-cell contact energy result in the LUAD subtype-specific morphogenesis. We reproduced the morphologies of the papillary LUAD subtypes with the cellular Potts Model (CPM). Simulations and experimental validations revealed modifications of cell-cell contact energy changed the morphology from a papillary-like structure to micropapillary or solid subtype-like structures. Remarkably, differential gene expression analysis revealed subtype-specific expressions of genes relating to cell adhesion. Knockdown experiments of the micropapillary upregulated ITGA11 gene resulted in the morphological changes of the spheroids produced from an LUAD cell line PC9. This work shows the consequences of gene mutations and gene expressions on patient prognosis through differences in tissue composing physical forces among LUAD subtypes.

Prediction of novel biomarkers for gastric intestinal metaplasia and gastric adenocarcinoma using bioinformatics analysis

Background & aim

The histologic and molecular changes from intestinal metaplasia (IM) to gastric cancer (GC) have not been fully characterized. The present study sought to identify potential alterations in signaling pathways in IM and GC to predict disease progression; these alterations can be considered therapeutic targets.

Materials & methods

Seven gene expression profiles were selected from the GEO database. Discriminate differentially expressed genes (DEGs) were analyzed by EnrichR. The STRING database, Cytoscape, Gene Expression Profiling Interactive Analysis (GEPIA), cBioPortal, NetworkAnalyst, MirWalk database, OncomiR, and bipartite miRNA‒mRNA correlation network was used for downstream analyses of selected module genes.

Results

Analyses revealed that extracellular matrix-receptor interactions (ITGB1, COL1A1, COL1A2, COL4A1, FN1, COL6A3, and THBS2) in GC and PPAR signaling pathway interactions (FABP1, APOC3, APOA1, HMGCS2, and PPARA and PCK1) in IM may play key roles in both the carcinogenesis and progression of underlying GC from intestinal metaplasia. IM enrichment indicated that this is closely related to digestion and absorption. The TF-hub gene regulatory network revealed that AR, TCF4, SALL4, and ESR1 were more important for hub gene expression. It was revealed that the development and prediction of GC may be affected by hsa-miR-29. It was found that PTGR1, C1orf115, CRYL1, ALDOB, and SULT1B1 were downregulated in GC and upregulated in IM. Therefore, they might have tumor suppressor activity in GC progression.

Conclusion

New potential biomarkers and pathways involved in GC and IM were identified that are important for the transformation of GC from IM to adenocarcinoma and can be therapeutic targets for GC.

THBS1 and THBS2 Enhance the In Vitro Proliferation, Adhesion, Migration and Invasion of Intrahepatic Cholangiocarcinoma Cells

In intrahepatic cholangiocarcinoma (iCCA), thrombospondin 1 (THBS1) and 2 (THBS2) are soluble mediators released in the tumor microenvironment (TME) that contribute to the metastatic spreading of iCCA cells via a lymphatic network by the trans-differentiation of vascular endothelial cells to a lymphatic-like phenotype. To study the direct role of THBS1 and THBS2 on the iCCA cells, well-established epithelial (HuCCT-1) and mesenchymal (CCLP1) iCCA cell lines were subjected to recombinant human THBS1 and THBS2 (rhTHBS1, rhTHBS2) for cellular function assays. Cell growth, cell adhesion, migration, and invasion were all enhanced in both CCLP1 and HuCCT-1 cells by the treatment with either rhTHBS1 or rhTHBS2, although they showed some variability in their intensity of speeding up cellular processes. rhTHBS2 was more intense in inducing invasiveness and in committing the HuCCT-1 cells to a mesenchymal-like phenotype and was therefore a stronger enhancer of the malignant behavior of iCCA cells compared to rhTHBS1. Our data extend the role of THBS1 and THBS2, which are not only able to hinder the vascular network and promote tumor-associated lymphangiogenesis but also exacerbate the malignant behavior of the iCCA cells.

Serum THBS2 is a potential biomarker for the diagnosis of non-small cell lung cancer

OBJECTIVE

This study primarily aimed to analyze the levels of THBS2 in the serum of patients diagnosed with non-small cell lung cancer (NSCLC), and subsequently evaluate its potential as a diagnostic biomarker for NSCLC.

METHODS

Serum samples were collected from 150 diagnosed NSCLC patients and 150 healthy individuals. The THBS2 concentration in these samples was determined using an enzyme-linked immunosorbent assay (ELISA). The study also investigated the correlation between THBS2 levels and various clinicopathological characteristics in NSCLC patients. The diagnostic sensitivity and specificity of serum THBS2 for NSCLC were assessed using receiver operating characteristic (ROC) curves and their corresponding area under the curve (AUC).

RESULTS

Serum THBS2 levels in NSCLC patients were significantly elevated compared to those in healthy individuals. THBS2 levels showed a significant correlation with tumor differentiation grade, tumor size, TNM stage, lymph node metastasis, and distant metastasis. No significant correlation was identified between serum THBS2 levels and other parameters such as gender, age, height, weight, BMI, smoking history, and tumor histological type. At a cutoff value of 7.62 ng/mL, THBS2 could effectively differentiate NSCLC patients from healthy individuals, with a sensitivity of 85.31% and a specificity of 88.92%. The AUC for NSCLC diagnosis using THBS2 was 0.812, significantly surpassing the performance of traditional tumor markers tested, including CEA (0.728), and CYFRA 21‑1 (0.685).

CONCLUSIONS

Elevated serum THBS2 levels in NSCLC patients suggest its potential as a novel and reliable diagnostic biomarker for NSCLC. Its superior diagnostic performance could potentially outperform traditional tumor markers, leading to improved patient outcomes.

Single-cell RNA sequencing reveals enhanced antitumor immunity after combined application of PD-1 inhibitor and Shenmai injection in non-small cell lung cancer

BACKGROUND

Immune checkpoint inhibitors (ICIs) have altered the clinical management of non-small cell lung cancer (NSCLC). However, the low response rate, severe immune-related adverse events (irAEs), and hyperprogressive disease following ICIs monotherapy require attention. Combination therapy may overcome these limitations and traditional Chinese medicine with immunomodulatory effects provides a promising approach. Shenmai injection (SMI) is a clinically effective adjuvant treatment for cancer with chemotherapy and radiotherapy. Therefore, the combined effects and mechanisms of SMI and programmed death-1 (PD-1) inhibitor against NSCLC was focused on this study.

METHODS

A Lewis lung carcinoma mouse model and a lung squamous cell carcinoma humanized mouse model were used to investigate the combined efficacy and safety of SMI and PD-1 inhibitor. The synergistic mechanisms of the combination therapy against NSCLC were explored using single-cell RNA sequencing. Validation experiments were performed using immunofluorescence analysis, in vitro experiment, and bulk transcriptomic datasets.

RESULTS

In both models, combination therapy alleviated tumor growth and prolonged survival without increasing irAEs. The GZMA^high and XCL1^high natural killer (NK) cell subclusters with cytotoxic and chemokine signatures increased in the combination therapy, while malignant cells from combination therapy were mainly in the apoptotic state, suggesting that mediating tumor cell apoptosis through NK cells is the main synergistic mechanisms of combination therapy. In vitro experiment confirmed that combination therapy increased secretion of Granzyme A by NK cells. Moreover, we discovered that PD-1 inhibitor and SMI combination blocked inhibitory receptors on NK and T cells and restores their antitumoral activity in NSCLC better than PD-1 inhibitor monotherapy, and immune and stromal cells exhibited a decrease of angiogenic features and attenuated cancer metabolism reprogramming in microenvironment of combination therapy.

CONCLUSIONS

This study demonstrated that SMI reprograms tumor immune microenvironment mainly by inducing NK cells infiltration and synergizes with PD-1 inhibitor against NSCLC, suggested that targeting NK cells may be an important strategy for combining with ICIs. Video Abstract.

A five-collagen-based risk model in lung adenocarcinoma: prognostic significance and immune landscape

As part of the tumor microenvironment (TME), collagen plays a significant role in cancer fibrosis formation. However, the collagen family expression profile and clinical features in lung adenocarcinoma (LUAD) are poorly understood. The objective of the present work was to investigate the expression pattern of genes from the collagen family in LUAD and to develop a predictive signature based on collagen family. The Cancer Genome Atlas (TCGA) samples were used as the training set, and five additional cohort samples obtained from the Gene Expression Omnibus (GEO) database were used as the validation set. A predictive model based on five collagen genes, including COL1A1, COL4A3, COL5A1, COL11A1, and COL22A1, was created by analyzing samples from the TCGA cohort using LASSO Cox analysis and univariate/multivariable Cox regression. Using Collagen-Risk scores, LUAD patients were then divided into high- and low-risk groups. KM survival analysis showed that collagen signature presented a robust prognostic power. GO and KEGG analyses confirmed that collagen signature was associated with extracellular matrix organization, ECM-receptor interaction, PI3K-Akts and AGE-RAGE signaling activation. High-risk patients exhibited a considerable activation of the p53 pathway and cell cycle, according to GSEA analysis. The Collage-Risk model showed unique features in immune cell infiltration and tumor-associated macrophage (TAM) polarization of the TME. Additionally, we deeply revealed the association of collagen signature with immune checkpoints (ICPs), tumor mutation burden (TMB), and tumor purity. We first constructed a reliable prognostic model based on TME principal component-collagen, which would enable clinicians to treat patients with LUAD more individually.

Circ_0079530 stimulates THBS2 to promote the malignant progression of non-small cell lung cancer by sponging miR-584-5p

BACKGROUND

Circ_0079530 has been confirmed to be a novel potential oncogene in non-small cell lung cancer (NSCLC). This study aims to explore the role and mechanism of circ_0079530 in NSCLC progression.

METHODS

Levels of circ_0079530, microRNA (miR)-584-5p, thrombospondin-2 (THBS2), PCNA, Bax, E-cadherin, and ki67 were detected by quantitative real-time PCR (qRT-PCR), western blotting and immunohistochemistry. The proliferation of NSCLC cells was measured using cell counting kit 8 (CCK8) assay, colony formation assay, and EdU staining. Cell apoptosis and motility were respectively detected by flow cytometry and transwell assays. Interaction between miR-584-5p and circ_0079530 or THBS2 was predicted by bioinformatics analysis and confirmed via luciferase reporter assay and RNA immunoprecipitation (RIP) assay. A xenograft tumor model was used to analyze the role of circ_0079530 in tumor growth in vivo.

RESULTS

Circ_0079530 was highly expressed in NSCLC tissues and cell lines. Circ_0079530 overexpression facilitated proliferation, migration, and invasion whereas it restrained the apoptosis of NSCLC cells. Circ_0079530 silence showed the opposite effects on the above malignant biological behaviors. Mechanistic analysis showed that circ_0079530 functioned as a sponge of miR-584-5p to relieve the suppressive action of miR-584-5p on its target THBS2. Additionally, circ_0079530 knockdown impeded the growth of xenografts in vivo.

CONCLUSION

Circ_0079530 promoted NSCLC progression by regulating the miR-584-5p/THBS2 axis, providing a possible circRNA-targeted therapy for NSCLC.

Transcriptomic responses in the blood and sputum of cigarette smokers compared to e-cigarette vapers

RATIONALE

Electronic (e)-cigarettes are popular among youth and cigarette smokers attempting to quit. Studies to date have focused on the utility of e-cigarettes as a smoking cessation tool, but the biological effects are largely unknown.

OBJECTIVES

To identify transcriptomic differences in the blood and sputum of e-cigarette users compared to conventional cigarettes smokers and healthy controls and describe biological pathways affected by these tobacco products.

METHODS

Cross-sectional analysis of whole blood and sputum RNA-sequencing data from 8 smokers, 9 e-cigarette users (e-cigs) and 4 controls. Weighted gene co-network analysis (WGCNA) identified gene module associations. Ingenuity Pathway Analysis (IPA) identified canonical pathways associated with tobacco products.

MAIN RESULTS

In blood, a three-group comparison showed 16 differentially expressed genes (DEGs); pair-wise comparison showed 7 DEGs between e-cigs and controls, 35 DEGs between smokers and controls, and 13 DEGs between smokers and e-cigs. In sputum, 438 DEGs were in the three-group comparison. In pair-wise comparisons, there were 2 DEGs between e-cigs and controls, 270 DEGs between smokers and controls, and 468 DEGs between smokers and e-cigs. Only 2 genes in the smokers vs. control comparison overlapped between blood and sputum. Most gene modules identified through WGCNA associated with tobacco product exposures also were associated with cotinine and exhaled CO levels. IPA showed more canonical pathways altered by conventional cigarette smoking than by e-cigarette use.

CONCLUSION

Cigarette smoking and e-cigarette use led to transcriptomic changes in both blood and sputum. However, conventional cigarettes induced much stronger transcriptomic responses in both compartments.

Controlled extracellular proteolysis of thrombospondins

Limited proteolysis of thrombospondins is a powerful mechanism to ensure dynamic tuning of their activities in the extracellular space. Thrombospondins are multifunctional matricellular proteins composed of multiple domains, each with a specific pattern of interactions with cell receptors, matrix components and soluble factors (growth factors, cytokines and proteases), thus with different effects on cell behavior and responses to changes in the microenvironment. Therefore, the proteolytic degradation of thrombospondins has multiple functional consequences, reflecting the local release of active fragments and isolated domains, exposure or disruption of active sequences, altered protein location, and changes in the composition and function of TSP-based pericellular interaction networks. In this review current data from the literature and databases is employed to provide an overview of cleavage of mammalian thrombospondins by different proteases. The roles of the fragments generated in specific pathological settings, with particular focus on cancer and the tumor microenvironment, are discussed.

Mesenchymal stem cell-derived extracellular vesicles transfer miR-598 to inhibit the growth and metastasis of non-small-cell lung cancer by targeting THBS2

Non-small-cell lung cancer (NSCLC) is the subtype of lung cancer, which accounts for about 85% of diagnosed lung cancer cases, and is without any effective therapy. Emerging evidence has revealed microRNA-598 (miR-598) as potential therapeutic target and diagnostic marker of NSCLC. In the present study, we sought to define the role of mesenchymal stem cells (MSCs)-derived extracellular vesicles (EVs) containing miR-598 in NSCLC. Co-culture experiments were conducted to examine the secretion of miR-598 by MSCs and the uptake of EVs by NSCLC cells. The expression of miR-598 in NSCLC cell lines, tissues, and MSC-derived EVs was detected by the RT-qPCR. After treatment with MSCs-EVs, CCK-8 and Transwell assays were adopted to evaluate the effects of miR-598 on proliferation, migration, and invasion capacities of NSCLC cells. Finally, the effects of miR-598 on tumor growth and metastasis were further validated in vivo through subcutaneous tumorigenesis and experimental pulmonary metastasis in nude mice. We found that MSCs-derived EVs could deliver miR-598 into NSCLC cells, where miR-598 specifically targeted and bound with mRNA of THBS2 to inhibit its translational process. By suppressing the promoting effects of THBS2 on the proliferation, migration, and invasion of NSCLC cells, the EV treatment reduced the progression of NSCLC. Notably, these inhibitory effects were reversed by concomitantly overexpressing THBS2. Overall, we find that MSCs-derived EVs containing miR-598 targets THBS2 to inhibit the proliferation and migration of NSCLC cells in vivo and in vitro.

Role of Moonlighting Proteins in Disease: Analyzing the Contribution of Canonical and Moonlighting Functions in Disease Progression

The term moonlighting proteins refers to those proteins that present alternative functions performed by a single polypeptide chain acquired throughout evolution (called canonical and moonlighting, respectively). Over 78% of moonlighting proteins are involved in human diseases, 48% are targeted by current drugs, and over 25% of them are involved in the virulence of pathogenic microorganisms. These facts encouraged us to study the link between the functions of moonlighting proteins and disease. We found a large number of moonlighting functions activated by pathological conditions that are highly involved in disease development and progression. The factors that activate some moonlighting functions take place only in pathological conditions, such as specific cellular translocations or changes in protein structure. Some moonlighting functions are involved in disease promotion while others are involved in curbing it. The disease-impairing moonlighting functions attempt to restore the homeostasis, or to reduce the damage linked to the imbalance caused by the disease. The disease-promoting moonlighting functions primarily involve the immune system, mesenchyme cross-talk, or excessive tissue proliferation. We often find moonlighting functions linked to the canonical function in a pathological context. Moonlighting functions are especially coordinated in inflammation and cancer. Wound healing and epithelial to mesenchymal transition are very representative. They involve multiple moonlighting proteins with a different role in each phase of the process, contributing to the current-phase phenotype or promoting a phase switch, mitigating the damage or intensifying the remodeling. All of this implies a new level of complexity in the study of pathology genesis, progression, and treatment. The specific protein function involved in a patient's progress or that is affected by a drug must be elucidated for the correct treatment of diseases.

Analysis of scRNA-seq and bulk RNA-seq demonstrates the effects of EVI2B or CD361 on CD8+ T cells in osteosarcoma

Osteosarcoma (OS) is a common primary malignant tumor of the bone in children and adolescents. The five-year survival rate is estimated to be ~70% based on the currently available treatment modalities. It is well known that tumor-infiltrating immune cells (TIICs) that are the most important components in the tumor microenvironment can exert a killing effect on tumor cells. Therefore, in the present study, 85 RNA-sequencing OS samples were categorized into high- and low-immune score groups with ESTIAMATE. Based on the immune score groups, 474 differentially expressed genes (DEGs) were acquired using the LIMMA package of R language. Subsequently, 86 DEGs were taken through univariate COX regression analysis, of which 14 were screened out by least absolute shrinkage and selection operator regression analysis. Furthermore, multivariate COX regression analysis was performed to obtain 4 DEGs. Finally, ecotropic virus integration site 2B (EVI2B) or CD361 gene was screened out via Kaplan-Meier analysis. In addition, CIBERSORT algorithm was used to evaluate the proportion of 22 kinds of TIICs in OS. Correlation analysis revealed that the high expression level of EVI2B can elevate the infiltrated proportion of CD8⁺ T cells. Moreover, analysis of single cell RNA-sequencing transcriptome datasets and immunohistochemical staining uncovered that EVI2B was mainly expressed on CD8⁺ T cells and that EVI2B could promote the expression of granzyme A and K of CD8⁺ T cells to exhibit a potent killing effect on tumor cells. Therefore, EVI2B was identified as a protective immune-related gene and contributed to good prognosis in OS patients.

MiR-3612 targeting THBS1 suppresses nasopharyngeal carcinoma progression by PI3K/AKT signaling pathway

BACKGROUND

MicroRNA-3612 (miR-3612) is considered a tumor suppressor in different cancers. Nonetheless, its function in nasopharyngeal carcinoma (NPC) has yet to be uncovered.

METHODS

NPC cells and tissues were tested by means of reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis and western blotting to quantify the expressions of miR-3612 and Thrombospondin 1 (THBS1). Cell Counting Kit-8 (CCK-8) and scratch experiments were carried out to evaluate the migration and proliferation of NPC cells. NPC cell adhesion was also assessed. The predicted interaction of miR-3612 with THBS1 was verified by means of a luciferase reporter assay. In vivo experiments were also conducted to examine how miR-3612 overexpression affects in vivo tumorigenicity. Lastly, phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway status was assessed via western blotting.

RESULTS

MiR-3612 was downregulated in NPC cells and tissues, whereas THBS1 expression showed an opposite trend. The MiR-3612 mimic inhibited the NPC cell proliferation, adhesion, and migration and also inactivated the PI3K/AKT signaling pathway. Furthermore, miR-3612 mimic also hampered NPC tumorigenesis in vivo. MiR-3612 targeted THBS1 and downregulated THBS1 expression. THBS1 offset the miR-3612-overexpression-induced repression of the migration, adhesion, and proliferation of NPC cells via the activation of the PI3K/AKT pathway.

CONCLUSION

MiR-3612 retarded NPC cell migration, adhesion, and proliferation by targeting THBS1 and inactivating the PI3K/AKT signaling pathway. This provides a novel therapeutic approach for NPC intervention.

A Pilot Analysis of Circulating cfRNA Transcripts for the Detection of Lung Cancer

Lung cancers are the leading cause of cancer-related deaths worldwide. Studies have shown that non-small cell lung cancer (NSCLC), which constitutes the majority of lung cancers, is significantly more responsive to early-stage interventions. However, the early stages are often asymptomatic, and current diagnostic methods are limited in their precision and safety. The cell-free RNAs (cfRNAs) circulating in plasma (liquid biopsies) offer a non-invasive detection of spatial and temporal changes occurring in primary tumors since the early stages. To address gaps in the current cfRNA knowledge base, we conducted a pilot study for the comprehensive analysis of transcriptome-wide changes in plasma cfRNA in NSCLC patients. Total cfRNA was extracted from archived plasma collected from NSCLC patients (N = 12), cancer-free former smokers (N = 12), and non-smoking healthy volunteers (N = 12). Plasma cfRNA expression levels were quantified by using a tagmentation-based library preparation and sequencing. The comparisons of cfRNA expression levels between patients and the two control groups revealed a total of 2357 differentially expressed cfRNAs enriched in 123 pathways. Of these, 251 transcripts were previously reported in primary NSCLCs. A small subset of genes (N = 5) was validated in an independent sample (N = 50) using qRT-PCR. Our study provides a framework for developing blood-based assays for the early detection of NSCLC and warrants further validation.

Extracellular matrix profiles determine risk and prognosis of the squamous cell carcinoma subtype of non-small cell lung carcinoma

BACKGROUND

Squamous cell carcinoma (SqCC) is a subtype of non-small cell lung cancer for which patient prognosis remains poor. The extracellular matrix (ECM) is critical in regulating cell behavior; however, its importance in tumor aggressiveness remains to be comprehensively characterized.

METHODS

Multi-omics data of SqCC human tumor specimens was combined to characterize ECM features associated with initiation and recurrence. Penalized logistic regression was used to define a matrix risk signature for SqCC tumors and its performance across a panel of tumor types and in SqCC premalignant lesions was evaluated. Consensus clustering was used to define prognostic matreotypes for SqCC tumors. Matreotype-specific tumor biology was defined by integration of bulk RNAseq with scRNAseq data, cell type deconvolution, analysis of ligand-receptor interactions and enriched biological pathways, and through cross comparison of matreotype expression profiles with aging and idiopathic pulmonary fibrosis lung profiles.

RESULTS

This analysis revealed subtype-specific ECM signatures associated with tumor initiation that were predictive of premalignant progression. We identified an ECM-enriched tumor subtype associated with the poorest prognosis. In silico analysis indicates that matrix remodeling programs differentially activate intracellular signaling in tumor and stromal cells to reinforce matrix remodeling associated with resistance and progression. The matrix subtype with the poorest prognosis resembles ECM remodeling in idiopathic pulmonary fibrosis and may represent a field of cancerization associated with elevated cancer risk.

CONCLUSIONS

Collectively, this analysis defines matrix-driven features of poor prognosis to inform precision medicine prevention and treatment strategies towards improving SqCC patient outcome.

Expression profiling of inflammation-related genes including IFI-16, NOTCH2, CXCL8, THBS1 in COVID-19 patients

The present study aimed to scrutinize the expression profile of inflammatory-related genes (IFI-16, NOTCH2, CXCL8, and THBS1) from acute to post-acute stage of this infectious epidemic. The current cross-sectional study consisted of 53 acute-phase COVID-19 patients and 53 healthy individuals between February and March 2021. The extraction of total RNA was performed from PBMC specimens and also expression level of selected genes (IFI-16, NOTCH2, CXCL8, and THBS1) was evaluated by real-time PCR. Subsequently, levels of these factors were re-measured six weeks after the acute phase to determine if the levels of chosen genes returned to normal after the acute phase of COVID-19. Receiver operating characteristic (ROC) curve was plotted to test potential of genes as a diagnostic biomarker. The expression levels of inflammatory-related genes were significantly different between healthy and COVID-19 subjects. Besides, a significant higher CXCL8 level was found in the acute-phase COVID-19 compared to post-acute-phase infection which may be able to be considered as a potential biomarker for distinguishing between the acute phases from the post-acute-phase status. Deregulation of the inflammatory-related genes in COVID-19 patients, especially CXCL-8, can be serving as potent biomarkers to manage the COVID-19 infection.

Tsp2 Facilitates Tumor-associated Fibroblasts Formation and Promotes Tumor Progression in Retroperitoneal Liposarcoma

Retroperitoneal liposarcoma (RLPS) is the most common subtype of retroperitoneal soft tissue sarcoma, characterized by a high recurrence rate and insensitivity to radiotherapy and chemotherapy. The function of tumor microenvironmental components, especially tumor-associated fibroblasts (TAFs), remains unclear in RLPS. The crosstalk between tumor cells and stromal cells should be clarified for therapy target discovery in RLPS. In this study, we demonstrated that TAFs from dedifferentiated liposarcoma (DDLPS) could attract LPS cells and promote their proliferation and migration. However, although α-SMA is positively expressed in RLPS, its expression does not indicate prognosis. By screening differentially expressed genes, performing Oncomine visualization, TCGA gene expression correlation analysis and qPCR verification, we determined that thrombospondin-2 (THBS2) gene expression was related to TAFs. The expression of Tsp2 protein, which was encoded by THBS2, was correlated with α-SMA expression, and it was an independent predictive factor for disease-free survival and recurrence-free survival in patients with RLPS. In vitro, Tsp2 facilitated the transformation of bone marrow-derived fibroblasts (BMFs) to TAFs and promoted the malignant biological behaviors of LPS cells by activating the MAPK/MEK/ERK pathway. Therefore, suppression of Tsp2 is expected to be a promising treatment method for RLPS patients.

Combination of levofloxacin and cisplatin enhances anticancer efficacy via co-regulation of eight cancer-associated genes

Chemosensitizer or combined chemotherapy can sensitize cancer cells to therapy and minimize drug resistance. We reveal that levofloxacin has broad-spectrum anticancer activity. Here we report that combination of levofloxacin and cisplatin further enhanced cytotoxicity in cancer cells by further promotion of apoptosis. Levofloxacin concentration-dependently promoted the inhibition of clone formation in cancer cells treated by cisplatin, and their combination further suppressed the tumor growth in mice. Levofloxacin and cisplatin co-regulated genes in directions supporting the enhancement of anticancer efficacy, of which, THBS1, TNFAIP3, LAPTM5, PI3 and IL24 were further upregulated, NCOA5, SRSF6 and SFPQ were further downregulated. Out of the 24 apoptotic pathways significantly enriched in the combination group, TNFAIP3, THBS1, SRSF6 and SFPQ overlapped in 14, 13, 3 and 1 pathway respectively. Jak-STAT/Cytokine-cytokine receptor interaction pathway network and extrinsic apoptotic signaling pathway were significantly enriched in levofloxacin group, cisplatin group and combination group. Jak-STAT/Cytokine-cytokine receptor interaction/Focal adhesion/EMC-receptor interaction pathway network was significantly enriched in the combination group, and IL24 and THBS1 were the overlapped genes. In conclusion, enhancement of anticancer efficacy in combination group was associated with the further regulation of THBS1, TNFAIP3, LAPTM5, PI3, IL24 and NCOA5, SFPQ, SRSF6. Targeting of Jak-STAT/Cytokine-cytokine receptor interaction/Focal adhesion/EMC-receptor interaction pathway network was correlated to the enhancement. With additional benefit to cancer patients for treatment or prophylaxis of an infectious syndrome, levofloxacin can benefit cancer chemotherapy no matter it is used independently or used with other chemotherapeutic drugs.

Integrative, In Silico and Comparative Analysis of Breast Cancer Secretome Highlights Invasive-Ductal-Carcinoma-Grade Progression Biomarkers

Globally, BC is the most frequently diagnosed cancer in women. The aim of this study was to identify novel secreted biomarkers that may indicate progression to high-grade BC malignancies and therefore predict metastatic potential. A total of 33 studies of breast cancer and 78 of other malignancies were screened via a systematic review for eligibility, yielding 26 datasets, 8 breast cancer secretome datasets, and 18 of other cancers that were included in the comparative secretome analysis. Sequential bioinformatic analysis using online resources enabled the identification of enriched GO_terms, overlapping clusters, and pathway reconstruction. This study identified putative predictors of IDC grade progression and their association with breast cancer patient mortality outcomes, namely, HSPG2, ACTG1, and LAMA5 as biomarkers of in silico pathway prediction, offering a putative approach by which the abovementioned proteins may mediate their effects, enabling disease progression. This study also identified ITGB1, FBN1, and THBS1 as putative pan-cancer detection biomarkers. The present study highlights novel, putative secretome biomarkers that may provide insight into the tumor biology and could inform clinical decision making in the context of IDC management in a non-invasive manner.

Predicting the Lung Adenocarcinoma and Its Biomarkers by Integrating Gene Expression and DNA Methylation Data

The early symptoms of lung adenocarcinoma patients are inapparent, and the clinical diagnosis of lung adenocarcinoma is primarily through X-ray examination and pathological section examination, whereas the discovery of biomarkers points out another direction for the diagnosis of lung adenocarcinoma with the development of bioinformatics technology. However, it is not accurate and trustworthy to diagnose lung adenocarcinoma due to omics data with high-dimension and low-sample size (HDLSS) features or biomarkers produced by utilizing only single omics data. To address the above problems, the feature selection methods of biological analysis are used to reduce the dimension of gene expression data (GSE19188) and DNA methylation data (GSE139032, GSE49996). In addition, the Cartesian product method is used to expand the sample set and integrate gene expression data and DNA methylation data. The classification is built by using a deep neural network and is evaluated on K-fold cross validation. Moreover, gene ontology analysis and literature retrieving are used to analyze the biological relevance of selected genes, TCGA database is used for survival analysis of these potential genes through Kaplan-Meier estimates to discover the detailed molecular mechanism of lung adenocarcinoma. Survival analysis shows that COL5A2 and SERPINB5 are significant for identifying lung adenocarcinoma and are considered biomarkers of lung adenocarcinoma.

Analyzing and validating the prognostic value and immune microenvironment of clear cell renal cell carcinoma

Tumor immune microenvironment (TIME) plays an important role in tumor diagnosis, prevention, treatment and prognosis. However, the correlation and potential mechanism between clear cell renal cell carcinoma (ccRCC) and its TIME are not clear. Therefore, we aimed to identify potential prognostic biomarkers related to TIME of ccRCC. Unsupervised consensus clustering analysis was performed to divide patients into different immune subgroups according to their single-sample gene set enrichment analysis (ssGSEA) scores. Then, we validated the differences in immune cell infiltration, prognosis, clinical characteristics and expression levels of HLA and immune checkpoint genes between different immune subgroups. Weighted gene coexpression network analysis (WGCNA) was used to identify the significant modules and hub genes that were related to the immune subgroups. A nomogram was established to predict the overall survival (OS) outcomes after independent prognostic factors were identified by least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression analyses. Five clusters (immune subgroups) were identified. There was no significant difference in age, sex or N stage. And there were significant differences in race, T stage, M stage, grade, prognosis and tumor microenvironment. WGCNA revealed that the red module has an important relationship with TIME, and obtained 14 hub genes. In addition, the nomogram containing LAG3 and GZMK accurately predicted OS outcomes of ccRCC patients. LAG3 and GZMK have a certain correlation with the prognosis of ccRCC patients, and play an important role in the TIME. These two hub genes deserve further study as biomarkers of the TIME.

THBS2 is Closely Related to the Poor Prognosis and Immune Cell Infiltration of Gastric Cancer

Background: The potential functions of Thrombospondin 2 (THBS2) in the progression and immune infiltration of gastric cancer (GC) remain unclear. The purpose of this study was to clarify the role of THBS2 in GC prognosis and the relationship between THBS2 and GC immune cell infiltration.

Material and Methods: The differential expression levels of THBS2 in the GC and cancer-adjacent tissues were identified using the TCGA databases and verified using real-time polymerase chain reaction (PCR), immunohistochemical staining and two datasets from Gene Expression Omnibus (GEO). THBS2 related differential expressed genes (DEGs) were identified and used for further functional enrichment analysis and Gene Set Enrichment Analysis (GSEA). Furthermore, a THBS2-related immune infiltration analysis was also performed. Kaplan-Meier and Cox regression analyses were utilized to illustrate the effects of THBS2 on the prognosis and clinical variables of GC. Finally, a nomogram was constructed to predict the survival probability of patients with GC.

Results: The THBS2 expression in GC was significantly higher than that in cancer-adjacent tissues (p < 0.001), which was verified using real-time PCR, immunohistochemical staining and datasets from GEO. The 599 identified DEGs were primarily enriched in pathways related to tumorigenesis and tumor progression, including the focal adhesion pathway, signaling by vascular endothelial growth factor, and Wnt signaling. THBS2 expression was positively correlated with the enrichment of the macrophages (r = 0.590, p < 0.001), which was also confirmed by immunohistochemistry; however, negatively correlated with the enrichment of Th17 cells (r = 0.260, p < 0.001). The high expression of THBS2 was significantly correlated with the pathological grade (p < 0.01), histological grade (p < 0.05), histological type (p < 0.05), T stage (p < 0.001), and poor overall survival (OS) (P = 0.003) of GC. The constructed nomogram can well predict the 1-, 3-, and 5-years OS probability of patients with GC (C-index [95% confidence interval] = 0.725 [0.701–0.750]).

Conclusion: THBS2 is closely related to the poor prognosis and immune infiltration of gastric cancer.

Levofloxacin exerts broad-spectrum anticancer activity via regulation of THBS1, LAPTM5, SRD5A3, MFAP5 and P4HA1

One cost-effective way for identifying novel cancer therapeutics is in the repositioning of available drugs for which current therapies are inadequate. Levofloxacin prevents DNA duplication in bacteria by inhibiting the activity of DNA helicase. As eukaryotic cells have similar intracellular biologic characteristics as prokaryotic cells, we speculate that antibiotics inhibiting DNA duplication in bacteria may also affect the survival of cancer cells. Here we report that levofloxacin significantly inhibited the proliferation and clone formation of cancer cells and xenograft tumor growth through cell cycle arrest at G2/M and by enhancing apoptosis. Levofloxacin significantly altered gene expression in a direction favoring anticancer activity. THBS1 and LAPTM5 were dose-dependently upregulated whereas SRD5A3, MFAP5 and P4HA1 were downregulated. Pathway analysis revealed that levofloxacin significantly regulated canonical oncogenic pathways. Specific network enrichment included a MAPK/apoptosis/cytokine-cytokine receptor interaction pathway network that associates with cell growth, differentiation, cell death, angiogenesis and development and repair processes and a bladder cancer/P53 signaling pathway network mediating the inhibition of angiogenesis and metastasis. THBS1 overlapped in 16 of the 22 enriched apoptotic pathways and the 2 pathways in the bladder cancer/P53 signaling pathway network. P4HA1 enriched in 7 of the top 10 molecular functions regulated by differential downregulated genes. Our results indicate that levofloxacin has broad-spectrum anticancer activity with the potential to benefit cancer patients already treated or requiring prophylaxis for an infectious syndrome. The efficacy we find with levofloxacin may provide insight into the discovery and the design of novel less toxic anticancer drugs.

Role of Thrombospondin‑1 in sepsis‑induced myocardial injury

Sepsis often causes myocardial injury with a high mortality. The aim of the present study was to investigate the effects of thrombospondin‑1 (THBS1) on myocardial cell injury, oxi‑dative stress and apoptosis in sepsis. The expression of THBS1 mRNA in lipopolysaccharide (LPS)‑induced mouse primary cardiomyocytes was detected by reverse transcription‑quantitative PCR (RT‑qPCR). A eukaryotic small interfering (si)RNA expression vector was constructed and transfected into myocardial cells to knockdown THBS1 mRNA expression, which was confirmed by RT‑qPCR. Four in vitro experimental groups were used: i) Control, ii) LPS, iii) THBS1 siRNA (siTHBS1) and iv) siTHBS + LPS. ELISA was used to detect cardiac troponin I (cTnI), pro‑brain natriuretic peptide (proBNP), reactive oxygen species (ROS), caspase‑3, IL‑6 and TNF‑α. In vivo mouse sepsis models were also established, and H&E, TUNEL and caspase‑3 staining were used to evaluate myocardial cell injury and apoptosis. Clinical samples were collected to analyze the serum THBS1 levels and to associate this with the prognosis of patients with sepsis‑induced myocardial injury. The expression level of THBS1 mRNA in myocardial cells induced by LPS was increased, and the serum THBS1 level in patients with myocardial injury in sepsis was also significantly increased compared with patients without sepsis‑induced myocardial injury. In the siTHBS1‑treated mice with myocardial injury, the levels of cTnI and proBNP were significantly decreased, the levels of the inflammatory cytokines IL‑6 and TNF‑α were significantly decreased, ROS were significantly decreased, caspase‑3 was significantly decreased, and myocardial cell apoptosis was also reduced, compared with the LPS group. Data from the present study suggested that THBS1 may be closely related to the biological behavior of myocardial cells and may be a therapeutic target for myocardial injury in sepsis.

Molecular-Genetic Portrait of Breast Cancer with Triple Negative Phenotype

Simple Summary

Breast cancer is a genetically heterogeneous disease with different molecular biological and clinical characteristics. The available knowledge about the genetic heterogeneity of the most aggressive molecular subtype of breast cancer—triple-negative—has led to discoveries in drug treatment. Identification of the molecular-genetic phenotype of breast cancer is an important prognostic factor of the disease and allows personalization of the patient’s treatment.

Abstract

Understanding of the genetic mechanisms and identification of the biological markers of tumor progression that form the individual molecular phenotype of transformed cells can characterize the degree of tumor malignancy, the ability to metastasize, the hormonal sensitivity, and the effectiveness of chemotherapy, etc. Breast cancer (BC) is a genetically heterogeneous disease with different molecular biological and clinical characteristics. The available knowledge about the genetic heterogeneity of the most aggressive molecular subtype of breast cancer—triple-negative (TN)—has led to discoveries in drug treatment, including the use of DNA damaging agents (platinum and PARP inhibitors) for these tumors, as well as the use of immunotherapy. Most importantly, the ability to prescribe optimal drug treatment regimens for patients with TNBC based on knowledge of the molecular-genetic characteristics of this subtype of BC will allow the achievement of high rates of overall and disease-free survival. Thus, identification of the molecular-genetic phenotype of breast cancer is an important prognostic factor of the disease and allows personalization of the patient’s treatment.

Clinical Value of Serum Thrombospondin-2 Combined with CA19-9 in Early Diagnosis of Gastric Cancer

Gastric cancer (GC) is a kind of common cancer worldwide. Too late in diagnosis results in poor prognosis of patients with GC. Thrombospondin-2 (THBS2) is a type of secreted protein that has been found to be a diagnostic biomarker in a variety of cancers. Our study aimed to uncover the clinical value of THBS2 in early detection for patients with gastric cancer. THBS2 was upregulated in gastric cancer tissue compared with normal tissue via analyzing data obtained from The Cancer Genome Atlas (TCGA) database. Additionally, the enzyme-linked immunosorbent assay revealed that the level of serum THBS2 and carcinoembryonic antigen, CA19-9, was higher dramatically in patients with early gastric cancer (EGC) than that in healthy control (HC) in addition to patients with benign gastric tumor (BGT), which suggested that THBS2 indeed associated with GC. Receiver operator characteristic (ROC) curve assay was conducted to demonstrate that serum THBS2 was similar to CA19-9 to distinguish patients with early gastric cancer from healthy control and patients with benign gastric tumor and that THBS2 combined with CA19-9 improved the detective performance of THBS2 for early gastric cancer. Furthermore, we applied the gene set enrichment analysis assay to analyze signaling pathways related to THBS2. We found that THBS2 positively controlled MAPK and WNT signaling pathways, which indicated that THBS2 might exert its functions via the pathway mentioned above. Thus, our study expounded that serum THBS2 could serve as a vital early diagnostic marker for patients with gastric cancer.

Prognostic and Immunological Role of THBS2 in Colorectal cancer

Objective

Thrombospondin 2 (THBS2) acts as oncogenic or tumor suppressive gene in diverse cancers. Here we studied the prognostic and immunological role of THBS2 in colorectal cancer (CRC) using bioinformatic analysis.

Methods

The genetic and protein expression of THBS2 in CRC were explored across several databases, including ONCOMINE, GEPIA2, TIMER 2.0, UALCAN and HPA databases. Correlation between THBS2 expression and clinical features in CRC was assessed using UALCAN tool. Prognostic analysis was performed using GEPIA2 and PrognoScan. Immune infiltration correlation with THBS2 in CRC was investigated with TIMER 2.0 and TISIDB. THBS2 binding and correlated genes were analyzed using String, GEPIA2, and TIMER 2.0.

Results

THBS2 was significantly higher in CRC across multiple databases. Age and histological subtype were correlated with THBS2 level. High THBS2 expression correlated with short overall and disease-free survival. THBS2 expression was positively correlated with immune infiltrates in CRC. Moreover, extracellular matrix structural constituent and organization, PI3K-Akt pathway, were involved in the functional mechanisms of THBS2.

Conclusions

THBS2 correlates with poor prognosis and immune infiltration in CRC. THBS2 may act as a prognostic and immunological biomarker for CRC.

The Fibrosis-Targeted Collagen/Integrins Gene Profile Predicts Risk of Metastasis in Pulmonary Neuroendocrine Neoplasms

Recently, collagen/integrin genes have shown promise as predictors of metastasis mainly in non-small cell lung cancer and breast cancer. However, it is unknown if these gene expression profiling differ in metastatic potential of pulmonary neuroendocrine neoplasms (PNENs). In this study, we sought to identify differentially expressed collagen/integrin genes in PNENs in order to understand the molecular mechanisms underlying the development of stroma-associated fibrosis for invasion and metastasis. We compared collagen/integrin gene expression profiling between PNE tumors (PNETs) and PNE carcinomas (PNECs) using a two-stage design. First, we used PCR Array System for 84 ECM-related genes, and among them, we found COL1A2, COL3A1, COL5A2, ITGA5, ITGAV, and ITGB1 functionally involved in the formation of the stroma-associated fibrosis among PNENs histological subtypes. Second, we examined the clinical association between the six collagen/integrin genes in tumor tissues from 24 patients with surgically excised PNENs. However, the pathological exam of their resected tissues demonstrated that 10 developed lymph node metastasis and 7 distant metastasis. We demonstrated and validated up regulation of the six fibrogenic genes in PNECs and down regulation in PNETs that were significantly associated with metastasis-free and overall survival (P<0.05). Our study implicates up regulation of fibrogenic genes as a critical molecular event leading to lymph node and distant metastasis in PNENs.

Decreased Thrombospondin-1 and Bone Morphogenetic Protein-4 Serum Levels as Potential Indices of Advanced Stage Lung Cancer

Introduction: Lung cancer belongs to the most common carcinoma worldwide and is the leading cause of cancer-related death. Bone morphogenetic protein-4 (BMP-4) is extracellular signaling molecule involved in many important processes, including cell proliferation and mobility, apoptosis and angiogenesis. Thrombospondin-1 (TSP-1) belongs to the extracellular matrix proteins. It participates in the cell-to-cell and cell-to-matrix interactions and thus plays important role in tumor microenvironment for cancer development and metastasis formation. Aim: To investigate serum levels of TSP-1 and BMP-4 together with BMP-4 polymorphism in lung cancer patients. Material and Methods: A total of 111 patients (76 men) with newly diagnosed lung cancer, including 102 patients with non-small cell lung cancer and 9 patients with small-cell lung cancer. Advanced stage of lung cancer was diagnosed in 99 (89%) of patients: stage IV—in 48, stage IIIB—in 33, stage IIIA—in 18 patients; there were six patients with stage II and six patients with stage I. The control group consisted of 61 healthy persons. In all the subjects, serum levels of BMP-4 and TSP-1 were measured by ELISA. With a Real-Time PCR system genotyping of BMP-4 was performed. Results: BMP-4 and TSP-1 serum levels were significantly lower in the patients with lung cancer than in the controls (TSP-1:10,109.2 ± 9581 ng/mL vs. 11,415.09 ± 9781 ng/mL, p < 0.05; BMP-4: 138.35 ± 62.59 pg/mL vs. 226.68 ± 135.86 pg/mL p < 0.001). In lung cancer patients TSP-1 levels were lower in advanced stages (9282.07 ± 4900.78 ng/mL in the stages III-IV vs. 16,933.60 ± 6299.02 ng/mL in the stages I-II, p < 0.05) and in the patients with than without lymph nodes involvement (10,000.13 ± 9021.41 ng/mL vs. 18,497.75 ± 12,548.25 ng/mL, p = 0.01). There was no correlation between TSP-1 and BMP-4 serum levels. BMP-4 gene polymorphism did not influence the results of the study. Conclusion: Decreased levels of TSP-1 and BMP-4 may serve as potential indices of lung cancer, with additional importance of low TSP-1 level as a marker of advanced stage of the disease.

Collagen XI alpha 1 chain, a potential therapeutic target for cancer

Extracellular matrix (ECM) plays an important role in the progression of cancer. Collagen is the most abundant component in ECM, and it is involved in the biological formation of cancer. Although type XI collagen is a minor fibrillar collagen, collagen XI alpha 1 chain (COL11A1) has been found to be upregulated in a variety of cancers including ovarian cancer, breast cancer, thyroid cancer, pancreatic cancer, non-small-cell lung cancer, and transitional cell carcinoma of the bladder. High levels of COL11A1 usually predict poor prognosis, while COL11A1 is related to angiogenesis, invasion, and drug resistance of cancer. However, little is known about the specific mechanism by which COL11A1 regulates tumor progression. Here, we have organized and summarized the recent developments regarding elucidation of the relationship between COL11A1 and various cancers, as well as the interaction between COL11A1 and intracellular signaling pathways. In addition, we have selected therapeutic agents targeting COL11A1. All these indicate the possibility of using COL11A1 as a target for cancer treatment.

Circ_0091702 serves as a sponge of miR-545-3p to attenuate sepsis-related acute kidney injury by upregulating THBS2

Circular RNA (circRNA) has been shown to play an important function in the progression of human diseases, including sepsis with acute kidney injury (AKI). However, the role and mechanism of circ_0091702 in sepsis-induced AKI have yet to be confirmed. Lipopolysaccharide (LPS) was used to induce HK2 cells to construct AKI cell models in vitro. Quantitative real-time PCR was used to measure the expression of circ_0091702, inflammatory cytokines, microRNA (miR)-545-3p and thrombospondin 2 (THBS2). Cell counting kit 8 assay and flow cytometry were used to assess cell viability and apoptosis. Besides, the protein levels of apoptosis markers and THBS2 were evaluated by western blot analysis. In addition, the concentrations of inflammatory cytokines were detected by enzyme-linked immunosorbent assay (ELISA). Cell oxidative stress was determined by detecting the contents of oxidative stress markers. Dual-luciferase reporter assay and RIP assay were used to confirm the relationship between miR-545-3p and circ_0091702 or miR-545-3p and THBS2. Circ_0091702 was downregulated in septic AKI patients and LPS-induced HK2 cells. Circ_0091702 could attenuate LPS-induced HK2 cell injury, while its silencing had an opposite effect. In the terms of mechanism, circ_0091702 could act as a sponge of miR-545-3p, and miR-545-3p could directly target THBS2. Functional experiments revealed that miR-545-3p could reverse the alleviating effect of circ_0091702 on LPS-induced HK2 cell injury, and THBS2 knockdown also could overturn the suppressing effect of miR-545-3p inhibitor on LPS-induced HK2 cell injury. Additionally, we also suggested that circ_0091702 could sponge miR-545-3p to regulate THBS2 expression. In conclusion, our results showed that circ_0091702 could suppress LPS-induced HK2 cell injury via the miR-545-3p/THBS2 axis, indicating that circ_0091702 might be an important biomarker for relieving sepsis-related AKI.

Construction of a prognostic model for non-small-cell lung cancer based on ferroptosis-related genes

We wished to construct a prognostic model based on ferroptosis-related genes and to simultaneously evaluate the performance of the prognostic model and analyze differences between high-risk and low-risk groups at all levels. The gene-expression profiles and relevant clinical data of patients with non-small-cell lung cancer (NSCLC) were downloaded from public databases. Differentially expressed genes (DEGs) were obtained by analyzing differences between cancer tissues and paracancerous tissues, and common genes between DEGs and ferroptosis-related genes were identified as candidate ferroptosis-related genes. Next, a risk-score model was constructed using univariate Cox analysis and least absolute shrinkage and selection operator (Lasso) analysis. According to the median risk score, samples were divided into high-risk and low-risk groups, and a series of bioinformatics analyses were conducted to verify the predictive ability of the model. Single-sample gene set enrichment analysis (ssGSEA) was used to investigate differences in immune status between high-risk and low-risk groups, and differences in gene mutations between the two groups were investigated. A risk-score model was constructed based on 21 ferroptosis-related genes. A Kaplan-Meier curve and receiver operating characteristic curve showed that the model had good prediction ability. Univariate and multivariate Cox analyses revealed that ferroptosis-related genes associated with the prognosis may be used as independent prognostic factors for the overall survival time of NSCLC patients. The pathways enriched with DEGs in low-risk and high-risk groups were analyzed, and the enriched pathways were correlated significantly with immunosuppressive status.

Of mice and men - and guinea pigs?

This year marks the twentieth anniversary of the publication of the first draft of the human genome and its broad availability to the scientific community. In parallel, the annotation of the mouse genome led to the identification and analysis of countless genes by means of genetic manipulation. Today, when comparing both genomes, it might surprise that some genes are still seeking their respective homologs in either species. In this review, we aim at raising awareness for the remarkable differences between the researcher's favorite rodents, i.e., mice and rats, when it comes to the generation of rodent research models regarding genes with a particular delicate localization, namely the pseudoautosomal region on both sex chromosomes. Many of these genes are of utmost clinical relevance in humans and still miss a rodent disease model giving their absence in mice and rats or low sequence similarity compared to humans. The abundance of rodents within mammals prompted us to investigate different branches of rodents leading us to the re-discovery of the guinea pig as a mammalian research model for a distinct group of genes.

Pathological Significance and Prognostic Roles of Thrombospondin-3, 4 and 5 in Bladder Cancer

BACKGROUND/AIM

The pathological significance of thrombospondin (TSP)-1 and -2 in bladder cancer (BC) is well-known whereas that of TSP-3, 4 and 5 remains unclear. Our aim is to clarify the pathological significance and prognostic roles of TSP-3 to 5 expression in BC patients.

PATIENTS AND METHODS

TSP-3 to 5 expression, proliferation index (PI), apoptotic index (AI) and microvessel density (MVD) were evaluated in 206 BC patients by immunohistochemical techniques.

RESULTS

TSP-5 expression was positively associated with grade, T stage, metastasis, and worse prognosis. PI in TSP-5-positive tissues was significantly higher compared to negative tissues. In contrast, AI in TSP-5-positive tissues was significantly lower compared to negative tissues. Expressions of TSP-3 and 4 were not associated with any clinicopathological features, survival, PI, or AI.

CONCLUSION

TSP-5 plays important roles in malignant behavior via cell survival regulation whereas the pathological significance of TSP-3 and TSP-4 in BC might be minimal.

Cancer-Associated Fibroblasts Promote Aggressive Gastric Cancer Phenotypes via Heat Shock Factor 1-Mediated Secretion of Extracellular Vesicles

Gastric cancer is the third most lethal cancer worldwide, and evaluation of the genomic status of gastric cancer cells has not translated into effective prognostic or therapeutic strategies. We therefore hypothesize that outcomes may depend on the tumor microenvironment (TME), in particular, cancer-associated fibroblasts (CAF). However, very little is known about the role of CAFs in gastric cancer. To address this, we mapped the transcriptional landscape of human gastric cancer stroma by microdissection and RNA sequencing of CAFs from patients with gastric cancer. A stromal gene signature was associated with poor disease outcome, and the transcription factor heat shock factor 1 (HSF1) regulated the signature. HSF1 upregulated inhibin subunit beta A and thrombospondin 2, which were secreted in CAF-derived extracellular vesicles to the TME to promote cancer. Together, our work provides the first transcriptional map of human gastric cancer stroma and highlights HSF1 and its transcriptional targets as potential diagnostic and therapeutic targets in the genomically stable tumor microenvironment. SIGNIFICANCE: This study shows how HSF1 regulates a stromal transcriptional program associated with aggressive gastric cancer and identifies multiple proteins within this program as candidates for therapeutic intervention. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/7/1639/F1.large.jpg.

Identification of Potential Biomarkers Associated with Prognosis in Gastric Cancer via Bioinformatics Analysis

Background

Gastric cancer (GC) is one of the leading causes of cancer-related mortality worldwide. We aimed to identify differentially expressed genes (DEGs) and their potential mechanisms associated with the prognosis of GC patients.

Material/Methods

This study was based on gene profiling information for 37 paired samples of GC and adjacent normal tissues from the GSE118916, GSE79973, and GSE19826 datasets in the Gene Expression Omnibus database. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to investigate the biological role of the DEGs. The protein–protein interaction (PPI) network was constructed by Cytoscape, and the Kaplan-Meier plotter was used for prognostic analysis.

Results

We identified 119 DEGs, including 21 upregulated and 98 downregulated genes, in GC. The 21 upregulated genes were mainly enriched in extracellular matrix-receptor interaction, focal adhesion, and transforming growth factor-β signaling, while the 98 downregulated genes were significantly associated with gastric acid secretion, retinol metabolism, and metabolism of xenobiotics by cytochrome P450. Thirty hub DEGs were obtained for further analysis. Twenty-five of the 30 hub DEGs were significantly associated with the prognosis of GC, and 21 of the 25 hub DEGs showed consistent expression trends within the 3 profile datasets. KEGG reanalysis of these 21 hub DEGs showed that COL1A1, COL1A2, COL2A1, COL11A1, THBS2, and SPP1 were mainly enriched in the extracellular matrix-receptor interaction pathways.

Conclusions

We identified 6 genes that were significantly related to the prognosis of GC patients. These genes and pathways could serve as potential prognostic markers and be used to develop treatments for GC patients.

Feature selection and classification approaches in gene expression of breast cancer

<abstract> <p>DNA microarray technology with biological data-set can monitor the expression levels of thousands of genes simultaneously. Microarray data analysis is important in phenotype classification of diseases. In this work, the computational part basically predicts the tendency towards mortality using different classification techniques by identifying features from the high dimensional dataset. We have analyzed the breast cancer transcriptional genomic data of 1554 transcripts captured over from 272 samples. This work presents effective methods for gene classification using Logistic Regression (LR), Random Forest (RF), Decision Tree (DT) and constructs a classifier with an upgraded rate of accuracy than all features together. The performance of these underlying methods are also compared with dimension reduction method, namely, Principal Component Analysis (PCA). The methods of feature reduction with RF, LR and decision tree (DT) provide better performance than PCA. It is observed that both techniques LR and RF identify TYMP, ERS1, C-MYB and TUBA1a genes. But some features corresponding to the genes such as ARID4B, DNMT3A, TOX3, RGS17 and PNLIP are uniquely pointed out by LR method which are leading to a significant role in breast cancer. The simulation is based on <italic>R</italic>-software.</p> </abstract>

Identification of MYCN-Related Gene as a Potential Biomarker for Neuroblastoma Prognostic Model by Integrated Analysis and Quantitative Real-Time PCR

Neuroblastoma (NB) has the highest incidence of all extracranial solid tumors in children and is highly lethal. This study aims to establish a prognostic model of NB with MYCN-related genes. We determined the gene expression profiles of 900 NB samples from the UCSC database and four Gene Expression Omnibus (GEO) data sets, and performed a comprehensive bioinformatics analysis and clinical sample verification. After univariate Cox regression, least absolute shrinkage and selection operator (Lasso), and multivariate Cox regression analyses, four (AKR1C1, CHD5, PDE4DIP, and PRKACB) genes were finally selected and used to construct a risk score prognostic model. In the UCSC data set, the high-risk group exhibited a significantly worse prognosis than the low-risk group. In addition, the nomogram, which includes prognostic markers and clinical factors, demonstrates high prognostic value. Finally, the differential expression of the four genes in the model was verified by quantitative real-time PCR in clinical tissues. These findings of MYCN-related genes provide a new and reliable prognostic model for NB related to MYCN.

Differences in key genes in human alveolar macrophages between phenotypically normal smokers and nonsmokers: diagnostic and prognostic value in lung cancer

OBJECTIVE

To explore the effect of smoking on gene expression in human alveolar macrophages and the value of identified key genes in the early diagnosis and prognosis of lung cancers.

METHODS

We downloaded three data sets (GSE8823, GSE2125, and GSE3212) from the Gene Expression Omnibus (GEO) database, including 31 non-smoking and 33 smoking human alveolar macrophage samples. We identified common differentially expressed genes (DEGs), from which we obtained module genes and hub genes by using STRING and Cytoscape. Then we analyzed the protein-protein interaction (PPI) network of DEGs, hub genes, and module genes and used David online analysis tool to carry out functional enrichment analysis of DEGs and module genes.

RESULTS

A total of 85 differentially expressed genes was obtained, including 42 up-regulated genes and 43 down-regulated genes. The Human Protein Atlas and Survival analysis showed that GBP1, ITGAM, CSF1, SPP1, COL1A1, LAMB1 and THBS1 may be closely associated with the carcinogenesis and prognosis of lung cancer.

CONCLUSION

DEGs, module, and hub genes identified in the present study help explain the effects of smoking on human alveolar macrophages and provide candidate targets for diagnosis and treatment of smoking-related lung cancer.

The Role of the ECM in Lung Cancer Dormancy and Outgrowth

The dissemination of tumor cells to local and distant sites presents a significant challenge in the clinical management of many solid tumors. These cells may remain dormant for months or years before overt metastases are re-awakened. The components of the extracellular matrix, their posttranslational modifications and their associated factors provide mechanical, physical and chemical cues to these disseminated tumor cells. These cues regulate the proliferative and survival capacity of these cells and lay the foundation for their engraftment and colonization. Crosstalk between tumor cells, stromal and immune cells within primary and secondary sites is fundamental to extracellular matrix remodeling that feeds back to regulate tumor cell dormancy and outgrowth. This review will examine the role of the extracellular matrix and its associated factors in establishing a fertile soil from which individual tumor cells and micrometastases establish primary and secondary tumors. We will focus on the role of the lung extracellular matrix in providing the architectural support for local metastases in lung cancer, and distant metastases in many solid tumors. This review will define how the matrix and matrix associated components are collectively regulated by lung epithelial cells, fibroblasts and resident immune cells to orchestrate tumor dormancy and outgrowth in the lung. Recent advances in targeting these lung-resident tumor cell subpopulations to prevent metastatic disease will be discussed. The development of novel matrix-targeted strategies have the potential to significantly reduce the burden of metastatic disease in lung and other solid tumors and significantly improve patient outcome in these diseases.

Mass spectrometry-based analysis of formalin-fixed, paraffin-embedded distal cholangiocarcinoma identifies stromal thrombospondin-2 as a potential prognostic marker

Background

Distal cholangiocarcinoma is an aggressive malignancy with a dismal prognosis. Diagnostic and prognostic biomarkers for distal cholangiocarcinoma are lacking. The aim of the present study was to identify differentially expressed proteins between distal cholangiocarcinoma and normal bile duct samples.

Methods

A workflow utilizing discovery mass spectrometry and verification by parallel reaction monitoring was used to analyze surgically resected formalin-fixed, paraffin-embedded samples from distal cholangiocarcinoma patients and normal bile duct samples. Bioinformatic analysis was used for functional annotation and pathway analysis. Immunohistochemistry was performed to validate the expression of thrombospondin-2 and investigate its association with survival.

Results

In the discovery study, a total of 3057 proteins were identified. Eighty-seven proteins were found to be differentially expressed (q < 0.05 and fold change ≥ 2 or ≤ 0.5); 31 proteins were upregulated and 56 were downregulated in the distal cholangiocarcinoma samples compared to controls. Bioinformatic analysis revealed an abundance of differentially expressed proteins associated with the tumor reactive stroma. Parallel reaction monitoring verified 28 proteins as upregulated and 18 as downregulated in distal cholangiocarcinoma samples compared to controls. Immunohistochemical validation revealed thrombospondin-2 to be upregulated in distal cholangiocarcinoma epithelial and stromal compartments. In paired lymph node metastases samples, thrombospondin-2 expression was significantly lower; however, stromal thrombospondin-2 expression was still frequent (72%). Stromal thrombospondin-2 was an independent predictor of poor disease-free survival (HR 3.95, 95% CI 1.09–14.3; P = 0.037).

Conclusion

Several proteins without prior association with distal cholangiocarcinoma biology were identified and verified as differentially expressed between distal cholangiocarcinoma and normal bile duct samples. These proteins can be further evaluated to elucidate their biomarker potential and role in distal cholangiocarcinoma carcinogenesis. Stromal thrombospondin-2 is a potential prognostic marker in distal cholangiocarcinoma.

Genome-wide identification and characterization of long non-coding RNAs involved in acquired resistance to gefitinib in non-small-cell lung cancer

Acquired resistance is a major obstacle to the therapeutic efficacy of gefitinib in non-small-cell lung cancer (NSCLC). Current knowledge about the role of long non-coding RNAs (lncRNAs) in this phenomenon is insufficient. In this study, we searched RNA sequencing data for lncRNAs associated with acquired resistance to gefitinib in NSCLC, and constructed a functional lncRNA-mRNA co-expression network and protein-protein interaction (PPI) network to analyze their putative target genes and biological functions. The expression levels of 14 outstanding dysregulated lncRNAs and mRNA were verified using real-time PCR. Changes in the expression levels of 39 lncRNAs and 121 mRNAs showed common patterns in our two pairs of gefitinib-sensitive and gefitinib-resistant NSCLC cell lines. The co-expression network included 1235 connections among these common differentially expressed lncRNAs and mRNAs. The significantly enriched signaling pathways based on dysregulated mRNAs were mainly involved in the Hippo signaling pathway; proteoglycans in cancer; and valine, leucine, and isoleucine biosynthesis. The results show that LncRNAs play an important part in acquired gefitinib resistance in NSCLC by regulating mRNA expression and function, and may represent potential new molecular biomarkers and therapeutic targets for gefitinib-resistant NSCLC.

Identification of gene modules associated with survival of diffuse large B-cell lymphoma treated with CHOP-based chemotherapy

Diffuse Large B-cell Lymphoma (DLBCL), a heterogeneous disease, is influenced by complex network of gene interactions. Most previous studies focused on individual genes, but ignored the importance of intergenic correlations. In current study, we aimed to explore the association between gene networks and overall survival (OS) of DLBCL patients treated with CHOP-based chemotherapy (cyclophosphamide combination with doxorubicin, vincristine and prednisone). Weighted gene co-expression network analysis was conducted to obtain insights into the molecular characteristics of DLBCL. Ten co-expression gene networks (modules) were identified in training dataset (n = 470), and their associations with patients' OS after chemotherapy were tested. The results were validated in four independent datasets (n = 802). Gene ontology (GO) biological function enrichment analysis was conducted with Metascape. Three modules (purple, brown and red), which were enriched in T-cell immune, cell-cell adhesion and extracellular matrix (ECM), respectively, were found to be related to longer OS. Higher expression of several hub genes within these three co-expression modules, for example, LCP2 (HR = 0.77, p = 5.40 × 10^-2), CD2 (HR = 0.87, p = 6.31 × 10^-2), CD3D (HR = 0.83, p = 6.94 × 10^-3), FYB (HR = 0.82, p = 1.40 × 10^-2), GZMK (HR = 0.92, p = 1.19 × 10^-1), FN1 (HR = 0.88, p = 7.06 × 10^-2), SPARC (HR = 0.82, p = 2.06 × 10^-2), were found to be associated with favourable survival. Moreover, the associations of the modules and hub genes with OS in different molecular subtypes and different chemotherapy groups were also revealed. In general, our research revealed the key gene modules and several hub genes were upregulated correlated with good survival of DLBCL patients, which might provide potential therapeutic targets for future clinical research.

Combined Expression of Plasma Thrombospondin-2 and CA19-9 for Diagnosis of Pancreatic Cancer and Distal Cholangiocarcinoma: A Proteome Approach

Background

Minimally invasive diagnostic biomarkers for patients with pancreatic ductal adenocarcinoma (PDAC) and distal cholangiocarcinoma (dCCA) are warranted to facilitate accurate diagnosis. This study identified diagnostic plasma proteins based on proteomics of tumor secretome.

Materials and Methods

Secretome of tumor and normal tissue was collected after resection of PDAC and dCCA. Differentially expressed proteins were measured by mass spectrometry. Selected candidate biomarkers and carbohydrate antigen 19‐9 (CA19‐9) were validated by enzyme‐linked immunosorbent assay in plasma from patients with PDAC (n = 82), dCCA (n = 29), benign disease (BD; n = 30), and healthy donors (HDs; n = 50). Areas under the curve (AUCs) of receiver operator characteristic curves were calculated to determine the discriminative power.

Results

In tumor secretome, 696 discriminatory proteins were identified, including 21 candidate biomarkers. Thrombospondin‐2 (THBS2) emerged as promising biomarker. Abundance of THBS2 in plasma from patients with cancer was significantly higher compared to HDs (p < .001, AUC = 0.844). Combined expression of THBS2 and CA19‐9 yielded the optimal discriminatory capacity (AUC = 0.952), similarly for early‐ and late‐stage disease (AUC = 0.971 and AUC = 0.911). Remarkably, this combination demonstrated a power similar to CA19‐9 to discriminate cancer from BD (AUC = 0.764), and THBS2 provided an additive value in patients with high expression levels of bilirubin.

Conclusion

Our proteome approach identified a promising set of candidate biomarkers. The combined plasma expression of THBS2/CA19‐9 is able to accurately distinguish patients with PDAC or dCCA from HD and BD.

Implications for Practice

The combined plasma expression of thrombospondin‐2 and carbohydrate antigen 19‐9 is able to accurately diagnose patients with pancreatic cancer and distal cholangiocarcinoma. This will facilitate minimally invasive diagnosis for these patients by distinguishing them from healthy individuals and benign diseases.

This article identifies diagnostic plasma proteins to distinguish patients with pancreatic ductal adenocarcinoma and distal cholangiocarcinoma from benign disease and health donors and evaluates these new markers for additive value with CA19‐9 at different disease stages.

Detection of key gene InDels in TGF-β pathway and its relationship with growth traits in four sheep breeds

TGF-β signaling pathway plays an important role in regulating cell proliferation and differentiation, embryonic development, bone formation, etc. LTBP1, THBS1, SMAD4 and other genes are important members of TGF-β signaling pathway. LTBP1 binds to TGF-β, while THBS1 binds to LTBP1, which is an important signal transduction molecule in the TGF-β pathway. In order to explore the effects of the insertion/deletion variation of three genes (LTBP1, THBS1, SMAD4) in the TGF-β signaling pathway on the growth traits such as body length and body weight of sheep, a total of 625 healthy individuals from 4 breeds of the Tong sheep, Hu sheep, small-tail Han sheep and Lanzhou fat-tail sheep were identified and analyzed. In this study, we identified 4 InDel loci: one loci of LTBP1, two loci of THBS1, and one loci of SMAD4, respectively named as: InDel-1 (deletion 13 bp), InDel-2 (deletion 16 bp), InDel-3 (deletion 22 bp), InDel-4 (deletion 7 bp). Among the 4 analyzed breeds, association analysis showed that all new InDel polymorphisms were significantly associated with 10 different growth traits (p < 0.05), which may provide a theoretical basis for sheep breeding to accelerate the progression of marker-assisted selection in sheep breeding.

Transcriptomic characterisation of the optimised rat model of Walker 256 breast cancer cell-induced bone pain

In patients with breast cancer, metastases of cancer cells to the axial skeleton may cause excruciating pain, particularly in the advanced stages. The current drug treatments available to alleviate this debilitating pain condition often lack efficacy and/or produce undesirable side effects. Preclinical animal models of cancer-induced bone pain are key to studying the mechanisms that cause this pain and for the success of drug discovery programs. In a previous study conducted in our laboratory, we validated and characterised the rat model of Walker 256 cell-induced bone pain, which displayed several key resemblances to the human pain condition. However, gene level changes that occur in the pathophysiology of cancer-induced bone pain in this preclinical model are unknown. Hence, in this study, we performed the transcriptomic characterisation of the Walker 256 cell line cultured in vitro to predict the molecular genetic profile of this cell line. We also performed transcriptomic characterisation of the Walker 256 cell-induced bone pain model in rats using the lumbar spinal cord and lumbar dorsal root ganglia tissues. Here we show that the Walker 256 cell line resembles the basal-B molecular subtype of human breast cancer cell lines. We also identify several genes that may underpin the progression of pain hypersensitivities in this condition, however, this needs further confirmatory studies. These transcriptomic insights have the potential to direct future studies aimed at identifying various mechanisms underpinning pain hypersensitivities in this model that may also assist in discovery of novel pain therapeutics for breast cancer-induced bone pain.