X-box binding protein 1 (XBP1): a potential role in chemotherapy response,clinical pathologic features,non-inflamed tumour microenvironment for breast cancer

X-box binding protein 1 (XBP1) is mainly expressed in breast cancer (BC) in human cancers. Its tumorigenesis and favourable prognosis are contradictory, and its essential role in chemotherapeutic response and immunosuppression is unknown in BC. The study firstly identified XBP1 who received neoadjuvant chemotherapy (NAC) from {"type":"entrez-geo","attrs":{"text":"GSE25055","term_id":"25055"}}GSE25055 and {"type":"entrez-geo","attrs":{"text":"GSE24460","term_id":"24460"}}GSE24460. Associations between XBP1 expression and clinicopathological characteristics was investigated using Oncomine, TCGA, UALCAN and bc-GenExMiner. The prognostic value of XBP1 was assessed using the Kaplan–Meier Plotter, bc-GenExMiner, {"type":"entrez-geo","attrs":{"text":"GSE25055","term_id":"25055"}}GSE25055, and {"type":"entrez-geo","attrs":{"text":"GSE25056","term_id":"25056"}}GSE25056. Furthermore, we systematically correlated XBP1 and immunological characteristics in the BC tumour microenvironment (TME) using TISIDB, TIMER, {"type":"entrez-geo","attrs":{"text":"GSE25055","term_id":"25055"}}GSE25055, {"type":"entrez-geo","attrs":{"text":"GSE25056","term_id":"25056"}}GSE25056 and TCGA dataset. Finally, an essential role of XBP1 in chemotherapy response was evaluated based on {"type":"entrez-geo","attrs":{"text":"GSE25055","term_id":"25055"}}GSE25055, {"type":"entrez-geo","attrs":{"text":"GSE25065","term_id":"25065"}}GSE25065, {"type":"entrez-geo","attrs":{"text":"GSE24460","term_id":"24460"}}GSE24460, {"type":"entrez-geo","attrs":{"text":"GSE5846","term_id":"5846"}}GSE5846, ROC Plotter and CELL databases. Furthermore, XBP1 mRNA expression levels were obviously highest in BC among human cancers and were significantly related to a good prognosis. In addition, XBP1 mRNA and protein levels were higher in the luminal subtype than in normal tissues and basal-like subtype, which might be attributed to membrane transport-related processes. Apart from BC, negative immunological correlations of XBP1 were not observed in other malignancies. XBP1 might shape the non-inflamed TME in BC. Finally, XBP1 expression was higher in chemo-resistive than chemo-sensitive cases, it had a predictive value and could independently predict chemotherapy response in BC patients receiving NAC. Our study suggests that the essential role of XBP1 in clinical pathologic features, non-inflamed TME, chemotherapy response in BC.     

A miRNA-HERC4 pathway promotes breast tumorigenesis by inactivating tumor suppressor LATS1

The E3 ligase HERC4 is overexpressed in human breast cancer and its expression levels correlated with the prognosis of breast cancer patients. However, the roles of HERC4 in mammary tumorigenesis remain unclear. Here we demonstrate that the knockdown of HERC4 in human breast cancer cells dramatically suppressed their proliferation, survival, migration, and tumor growth in vivo, while the overexpression of HERC4 promoted their aggressive tumorigenic activities. HERC4 is a new E3 ligase for the tumor suppressor LATS1 and destabilizes LATS1 by promoting the ubiquitination of LATS1. miRNA-136-5p and miRNA-1285-5p, expression of which is decreased in human breast cancers and is inversely correlated with the prognosis of breast cancer patients, are directly involved in suppressing the expression of HERC4. In summary, we discover a miRNA-HERC4-LATS1 pathway that plays important roles in the pathogenesis of breast cancer and represents new therapeutic targets for human breast cancer.     

Identification of hub genes associated with neutrophils infiltration in colorectal cancer

Colorectal cancer (CRC) is the leading cause of cancer-related mortality in the world. Accumulating evidence indicate that tumour infiltrating immune cells participated in cancer progression. Among them, tumour infiltrating neutrophils (TINs) are reported to play crucial role in various cancers. In this study, we used CIBERSORTx, a digital cytometry tool to evaluate the neutrophils infiltration in CRC based on gene expression data of CRC tissues from GSE39582 data set and The Cancer Genome Atlas data set (TCGA-COAD and TCGA-READ). Weighted gene co-expression network analysis (WGCNA) was conducted in GSE39582 data set to identify hub genes associated with neutrophil infiltration. The association of hub gene and neutrophils was then validated in TCGA cohorts and an independent RJ cohort. Functional analysis was performed to investigate the molecular mechanisms of the interested hub gene. We found that neutrophil infiltration is elevated in CRC tissues, and it is related to a poorer prognosis. A total of 18 gene modules are identified by WGCNA in GSE39582 data set, among which lightcyan module is significantly correlated with neutrophils infiltration. Furthermore, Superoxide Dismutase 2 (SOD2) in lightcyan module was proved to correlated with neutrophils infiltration in various cancer types. In addition, SOD2 expression is highly associated with several chemokines, including CXCL8, a neutrophils-related attractant, and functional analysis revealed that SOD2 is involved in neutrophils recruitment biological process. These results indicate that an ‘SOD2-CXCL8-neutrophil recruitment’ axis plays a potential role in colorectal cancer progression.     

Revisiting CCL-type chemokines in breast cancer and its milieu: prominent targetable chemokines,CCL8 and CCL21

The patterns of chemokine expression play a decisive role in both breast cancer prognosis and metastasis. In a recent article published in Bioscience Reports, ‘Bioinformatics identification of CCL8/21 as potential prognostic biomarkers in breast cancer microenvironment’, Chen et al. presented that expression of both CCL8 and CCL21 among CCL-type chemokines is prominent for prognosis of the breast cancer, metastasis and chemoresistance (Biosci Rep (2020) 40(11); DOI: 10.1042/BSR20202042). Identifying the sources of the CCL8 and CCL21 in the tumor microenvironment and developing targeting strategies for these chemokines to prevent tumor growth will improve both prognosis and therapeutic outcomes.     

Tumor Secretion of CCL22 Activates Intratumoral Treg Infiltration and Is Independent Prognostic Predictor of Breast Cancer

It has been reported that dense intratumoral infiltration of Foxp3 ⁺Tregs (Tregs) was an independent factor for poor prognosis of breast cancer (BC) patients. However, the cytokines activating the Treg infiltration are not known. This study was undertaken to evaluate the role of CCL22 and TGF-β1 in this cascade and their prognostic significance for BC patients. 417 cases of invasive breast cancer were selected from the prior study cohort and the expressions of CCL22 and TGF-β1 were assessed by immunohistochemistry. It was identified that tumor secretion of CCL22 was positively correlated with the intratumoral Treg infiltration (P<0.0001), but its association with lymphoid aggregates surrounding the tumor was not proven to be significant (P=0.056). Moreover, CCL22 expression was found to be associated with the tumor histological features known to be related with unfavorable prognosis of patients, including high histological grade (P<0.0001), negative ER (P<0.0001), negative PR (P=0.001), and HER2 amplification (P=0.028). Similar to intratumoral Treg infiltrates, CCL22 tumor secretion correlated with the prognosis of the molecular subtypes of breast carcinoma (P<0.0001). Univariate analysis revealed CCL22 to be an independent prognostic factor for overall survival (OS, P<0.0001) and progression-free survival (PFS, P<0.0001) of BC patients that were confirmed by multivariate analysis (P=0.011 and P=0.010 respectively). In contrast, although TGF-β1 expression was positively correlated with both Tregs infiltrates into the tumor bed and lymphoid aggregates surrounding the tumor (P=0.023; P=0.046, respectively), its expression was not significantly associated with the molecular subtypes of breast carcinoma and the prognosis of the patients. Our study indicates that both CCL22 and TGF-β1 are candidate chemoattractants for intratumoral Foxp3 ⁺Tregs infiltration; however, unlike the later, CCL22 is an independent prognostic predictor of BC patients, and it therefore may have the potential to serve as a target for immunotherapeutic strategy of BC.     

Concomitant expression of the chemokines RANTES and MCP-1 in human breast cancer: a basis for tumor-promoting interactions

The chemokines RANTES (CCL5) and MCP-1 (CCL2) were suggested to contribute, independently, to breast malignancy. In the present study, we asked if the two chemokines are jointly expressed in clinical samples of breast cancer patients, and do they interact in breast tumor cells. We found that RANTES and MCP-1 were expressed by breast tumor cells in primary tumors of Ductal Carcinoma In Situ and of Invasive Ductal Carcinoma, but minimally in normal breast epithelial duct cells. The chemokines were also detected in metastases and pleural effusions. Novel findings showed that co-expression of RANTES and MCP-1 in the same tumor was associated with more advanced stages of disease, suggesting that breast tumors "benefit" from interactions between the two chemokines. Accordingly, MCP-1 significantly promoted the release of RANTES from endogenous pre-made vesicles, in an active process that depended on calcium from intracellular and extracellular sources, and on intracellular transport of RANTES towards exocytosis. Our findings show a chemokine-triggered release of stored pro-malignancy chemokine from breast tumor cells. These observations support a major tumor-promoting role for co-expression of the chemokines in breast malignancy, and agree with the significant association of joint RANTES and MCP-1 expression with advanced stages of breast cancer.     

应用GSEA和WGCNA方法分析细菌性败血症宿主关键差异基因及意义

【目的】采用生物信息学方法分析公共数据库来源的细菌性败血症患者全血转录组学表达谱,探讨细菌败血症相关的宿主关键差异基因及意义。【方法】基于GEO数据库中GSE80496和GSE72829全血转录组基因数据集,采用GEO2R、基因集富集分析(GSEA)联用加权基因共表达网络分析(WGCNA)筛选细菌性败血症患者相比健康人群显著改变的差异基因,通过R软件对交集基因进行GO功能分析和KEGG富集分析。同时,通过String 11.0和Cytoscape分析枢纽基因,验证枢纽基因在数据集GSE72809(Health组52例,Definedsepsis组52例)全血标本中的表达情况,并探讨婴儿性别、月(胎)龄、出生体重、是否接触抗生素等因素与靶基因表达谱间的关系。【结果】分析GSE80496和GSE72829数据集分别筛选得到932个基因和319个基因,联合WGCNA枢纽模块交集得到与细菌性败血症发病相关的10个枢纽基因(MMP9、ITGAM、CSTD、GAPDH、PGLYRP1、FOLR3、OSCAR、TLR5、IL1RN和TIMP1);GSEA分析获得关键通路(氨基酸糖类-核糖代谢、PPAR信号通路、聚糖生物合成通路、自噬调控通路、补体、凝血因子级联反应、尼古丁和烟酰胺代谢、不饱和脂肪酸生物合成和阿尔兹海默症通路)及生物学过程(类固醇激素分泌、腺苷酸环化酶的激活、细胞外基质降解和金属离子运输)。【结论】本项研究通过GEO2R、GSEA联用WGCNA分析,筛选出与细菌性败血症发病相关的2个枢纽模块、10个枢纽基因以及一些关键信号通路和生物学过程,可为后续深入研究细菌性败血症致病机制奠定理论依据。     

乳腺癌中Abi1和c-Abl及WAVE 2的表达及其相互关系

目的研究乳腺癌组织中Abi1、c-Abl和WAVE2蛋白的表达及其相互关系。方法应用免疫组化SP法检测66例乳腺癌组织和24例正常乳腺组织中Abi1、c-Abl和WAVE2蛋白的表达情况。结果 1.正常乳腺组织与乳腺癌组织相比,Abi1和WAVE2蛋白表达有显著性差异(P0.05),而c-Abl蛋白表达无显著性差异(P0.05),但有定位的改变。2.Abi1强阳性率与乳腺癌的肿瘤大小、组织学分级、淋巴结转移及临床分期呈负相关性(P0.05);与患者年龄无关(P0.05)。c-Abl阳性率及WAVE2强阳性率均与乳腺癌的组织学分级、淋巴结转移及临床分期呈负相关性(P0.05);与患者年龄及肿瘤大小无关(P0.05)。3.Abi1蛋白表达与c-Abl和WAVE2蛋白表达呈正相关(P0.05)。结论乳腺癌中Abi1低表达与预后不良有关。乳腺癌中Abi1蛋白表达的变化可影响c-Abl蛋白的定位和WAVE2蛋白的表达。推测Abi1在Abl/Abi1/WAVE2通路中具有至关重要的地位。     

Continuous Delivery of Neutralizing Antibodies Elevate CCL2 Levels in Mice Bearing MCF10CA1d Breast Tumor Xenografts

Chemokines are small soluble molecules that play critical roles in wound healing, infection, and cancer progression. In particular, overexpression of the C-C motif chemokine ligand 2 (CCL2) in multiple cancer types correlates with poor patient prognosis. Animal studies have shown that CCL2 signals to macrophages and breast cancer cells to promote tumor growth, invasion, and metastasis, indicating that CCL2 is a promising therapeutic target. However, the effectiveness of human-specific neutralizing antibodies has not been fully evaluated. Furthermore, controversies remain on the use of neutralizing antibodies to target CCL2 and could be due to mode of drug delivery. Here, we investigated the effects of continuous delivery of human CCL2-neutralizing antibodies on breast cancer progression. Nude mice bearing MCF10CA1d breast tumor xenografts were implanted with osmotic pumps containing control IgG or anti-CCL2 and analyzed for CCL2 levels and tumor progression over 4 weeks. Despite inhibiting CCL2-induced migration in vitro, CCL2-neutralizing antibodies did not significantly affect tumor growth, invasion, macrophage recruitment, or tumor angiogenesis. CCL2 antibodies did not affect murine CCL2 levels but significantly increased human CCL2 levels in circulating blood and tumor interstitial fluid. CCL2-neutralizing antibodies reduced CCL2 levels in cultured cells short term at high concentrations. Enzyme-linked immunosorbent assay analysis of CCL2 in cultured fibroblasts and breast cancer cells revealed that the neutralizing antibodies sequestered CCL2 in the media. CCL2 levels were restored once the antibodies were removed. These studies reveal limitations in CCL2-neutralizing antibodies as a therapeutic agent, with important implications for translating CCL2 targeting to the clinic.     

Hypermethylated and downregulated MEIS2 are involved in stemness properties and oxaliplatin-based chemotherapy resistance of colorectal cancer

The resistance against oxaliplatin (L-OHP) based regimens remains a major obstacle for its efficient usage in treating metastatic colorectal cancer (mCRC). In this study, we performed weighted gene coexpression network analysis (WGCNA) to systematically screen the relevant hub genes for L-OHP resistance using the raw microarray data of 30 consecutive mCRC samples from our earlier study (GSE69657). The results were further confirmed through datasets from Gene Expression Omnibus (GEO). From L-OHP resistance module, nine genes in both the coexpression and protein–protein interaction networks were chosen as hub genes. Among these genes, Meis Homeobox 2 (MEIS2) had the highest correlation with L-OHP resistance (r = −0.443) and was deregulated in L-OHP resistant tissues compared with L-OHP sensitive tissues in both our own dataset and GSE104645 testing dataset. The receiver operating characteristic curve validated that MEIS2 had a good ability in predicting L-OHP response in both our own dataset (area under the curve [AUC] = 0.802) and GSE104645 dataset (AUC = 0.746). Then, the down expression of MEIS2 was observed in CRC tissue compared with normal tissue in 12 GEO-sourced datasets and The Cancer Genome Atlas (TCGA) and was correlated with poor event-free survival. Furthermore, analyzing methylation data from TCGA showed that MEIS2 had increased promoter hypermethylation. In addition, MEIS2 expression was significantly decreased in CRC stem cells compared with nonstem cells in two GEO datasets (GSE14773 and GSE24747). Further methylation analysis from GSE104271 demonstrated that CRC stem cells had higher MEIS2 promoter methylation levels in cg00366722 and cg00610348 sites. Gene set enrichment analysis showed that MEIS2 might be involved in the Wnt/β-catenin pathway. In the overall view, MEIS2 had increased promoter hypermethylation and was downregulated in poor L-OHP response mCRC tissues. MEIS2 might be involved in the Wnt/β-catenin pathway to maintain CRC stemness, which leads to L-OHP resistance.     

A novel tailored immune gene pairs signature for overall survival prediction in lower-grade gliomas

Lower-grade gliomas (LGGs) have a good prognosis with a wide range of overall survival (OS) outcomes. An accurate prognostic system can better predict survival time. An RNA-Sequencing (RNA-seq) prognostic signature showed a better predictive power than clinical predictor models. A signature constructed using gene pairs can transcend changes from biological heterogeneity, technical biases, and different measurement platforms. RNA-seq coupled with corresponding clinical information were extracted from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA). Immune-related gene pairs (IRGPs) were used to establish a prognostic signature through univariate and multivariate Cox proportional hazards regression. Weighted gene co-expression network analysis (WGCNA) was used to evaluate module eigengenes correlating with immune cell infiltration and to construct gene co-expression networks. Samples in the training and testing cohorts were dichotomized into high- and low-risk groups. Risk score was identified as an independent predictor, and exhibited a closed relationship with prognosis. WGCNA presented a gene set that was positively correlated with age, WHO grade, isocitrate dehydrogenase (IDH) mutation status, 1p/19 codeletion, risk score, and immune cell infiltrations (CD4 T cells, B cells, dendritic cells, and macrophages). A nomogram comprising of age, WHO grade, 1p/19q codeletion, and three gene pairs (BIRC5|SSTR2, BMP2|TNFRSF12A, and NRG3|TGFB2) was established as a tool for predicting OS. The IPGPs signature, which is associated with immune cell infiltration, is a novel tailored tool for individual-level prediction.     

Identification of glioblastoma gene prognosis modules based on weighted gene co-expression network analysis

Background

Glioblastoma multiforme, the most prevalent and aggressive brain tumour, has a poor prognosis. The molecular mechanisms underlying gliomagenesis remain poorly understood. Therefore, molecular research, including various markers, is necessary to understand the occurrence and development of glioma.

Method

Weighted gene co-expression network analysis (WGCNA) was performed to construct a gene co-expression network in TCGA glioblastoma samples. Gene ontology (GO) and pathway-enrichment analysis were used to identify significance of gene modules. Cox proportional hazards regression model was used to predict outcome of glioblastoma patients.

Results

We performed weighted gene co-expression network analysis (WGCNA) and identified a gene module (yellow module) related to the survival time of TCGA glioblastoma samples. Then, 228 hub genes were calculated based on gene significance (GS) and module significance (MS). Four genes (OSMR + SOX21?+?MED10?+?PTPRN) were selected to construct a Cox proportional hazards regression model with high accuracy (AUC?=?0.905). The prognostic value of the Cox proportional hazards regression model was also confirmed in GSE16011 dataset (GBM: n?=?156).

Conclusion

We developed a promising mRNA signature for estimating overall survival in glioblastoma patients.

     

Long Intergenic Non-Coding RNAs (LincRNAs) Identified by RNA-Seq in Breast Cancer

In an attempt to find the correlation of aberrant expression of long intergenic noncoding RNAs (lincRNAs) with cancer, twenty-five samples of breast cancer tissue and respective adjacent normal tissue were studied for the expression of lincRNAs by RNA-seq. Among the 538 lincRNAs studied, 124 lincRNAs were exclusively expressed in cancer adjacent tissues and 62 lincRNAs were exclusively expressed in the cancer tissues. Furthermore, the expression of 134 lincRNAs was higher while 272 lower in breast cancer tissue compared with adjacent tissue. The expression of four selected lincRNAs (BC2, BC4, BC5, and BC8) was validated by semi-quantitative and real-time PCR. It was revealed that expression of lincRNA-BC5 was positively correlated with patients'' age, pathological stage, and progesterone receptor concentration, while lincRNA-BC8 was negatively correlated with progesterone receptor expression. Higher expression of lincRNA-BC4 was seen in advanced breast cancer grade. LincRNA-BC2 showed no specific changes in the pathological features studied. Interactions between selected lincRNAs and breast cancer associated proteins were highly suggested by RPIseq based on the specific secondary structure. The results demonstrated that this group of lincRNAs was aberrantly expressed in breast cancer. They might play important roles in the function of oncogenes or tumor suppressors affecting the development and progression of breast cancer.     

Growth, metastasis, and expression of CCL2 and CCL5 by murine mammary carcinomas are dependent upon Myd88

Previously we reported that lipopolysaccharide (LPS) treatment of murine mammary carcinomas resulted in decreased growth of the tumors. Here we show the decreased growth following LPS treatment was mediated through effects downstream of TLR4 and Myd88. Perhaps more notably, simply reducing TLR4 or Myd88 levels was sufficient to slow tumor growth rates. Moreover, reduced levels of Myd88 correlated with a significant reduction in lung metastasis as well as decreased CCL2 and CCL5 expression. To determine whether inhibiting Myd88 function could also alter tumor growth and chemokine expression we used a Myd88 homodimerization inhibitory peptide. Indeed, inhibiting Myd88 function in four different murine mammary carcinomas as well as the human breast cancer cell line MDA-MB-231 led to decreased growth as well as CCL2 and CCL5 expression. These data imply that Myd88 is important for growth and metastasis of breast cancer, and expression of at least two proinflammatory chemokines.     

A four-gene signature predicts the efficacy of paclitaxel-based neoadjuvant therapy in human epidermal growth factor receptor 2–negative breast cancer

Neoadjuvant chemotherapy (NAC) is the major preoperative treatment of breast cancer (BC) with negative human epidermal growth factor receptor 2 (HER2), and the efficacy of NAC and the optimization of regimen are under intensive research. The current study aimed to define the predictive biomarkers for paclitaxel (PTX) response in NAC of HER2-negative BC. Data from GSE25065, GSE26065, GSE41998, as well as drug sensitivity data of breast and ovarian cancer cell line from NCI60, were used. Through logistic regression, COX regression, and correlation analysis with bootstrapping, we found that four genes (CDK8, FAM64A, MARC2, and OCEL1) were associated with drug sensitivity of PTX. The four gene “≥3” model had the best classification accuracy. Subgroup analysis found that the model performed well in the hormone receptor positive, HER2-negative subgroup and did not perform well in the triple-negative subgroup. Decision curve analysis showed that the model could enhance the predictive effect of clinical features. Subsequent gene set enrichment analysis, network analysis showed that these genes may be related to the cell cycle, mitosis and other pathways. The current study demonstrated the promising potential of the novel four-gene signature as a predictive biomarker for pathological complete response of HER2-negative BC patients and indicated the drug sensitivity of PTX.     

SARS-CoV-2病毒感染潜在关键分子生物标志物及免疫浸润特征分析

应用生物信息学方法筛选新型冠状病毒肺炎（corona virus disease 2019,COVID-19）感染的潜在关键分子生物标志物并分析其免疫浸润特征。从GEO数据库下载GSE152418数据集,其中COVID-19患者17例,健康对照17例。用加权基因共表达网络分析（weighted gene co-expression network analysis,WGCNA）方法筛选出COVID-19最相关的模块基因。与差异基因取交集得到共同基因,进行功能及信号通路富集分析,构建蛋白互作网络筛选关键基因,构建关键基因的miRNATF-mRNA调控网络,用CIBERSORT算法预测样本免疫细胞浸润特征。差异分析得到2 049个差异基因。WGCNA分析7个模块中“土耳其蓝色”模块与COVID-19相关性最高（r=0.91,P<0.001）。模块中基因显著性和模块隶属度呈显著正相关（r=0.96,P<0.001）。得到共同基因766个,主要参与有丝分裂、微管结合、阳离子通道活性及卵母细胞减数分裂、细胞衰老等。蛋白互作网络筛选到前10位关键基因分别为CDK1、BUB1、CCNA2...