Identification and Characterization of Senescence Phenotype in Lung Adenocarcinoma with High Drug Sensitivity.

Lung adenocarcinoma (LUAD) is a major health problem and has poor prognosis. Heterogeneity is a central determinant of the treatment outcome, requiring identification of new subclasses of LUAD. Senescence has emerged as a crucial regulator of metastasis and drug response. Ionizing radiation- and doxorubicin-induced senescence-associated genes in lung fibroblasts were used in K-means clustering to identify high- and low-senescence (HS and LS) classes among The Cancer Genome Atlas- LUAD (TCGA-LUAD) patients. The LS group showed significantly poorer survival (P = 0.01) and greater activation of proliferative signaling pathways, proliferation, wound healing, and genetic aberrations (P < 0.05). The TP53 mutation rate was significantly greater in the HS group (P < 0.0001), explaining the phenotype. Also, genome-wide hypomethylation was significantly greater in the LS group than in the HS group. Interestingly, pathway analysis identified silencing of Wnt signaling in the HS group. The machine learning-based recursive feature elimination technique was used to identify a 20-gene senescence signature in TCGA-LUAD samples. The presence of a senescence phenotype with poor survival was validated in an independent patient cohort and a cell-line cohort using unsupervised clustering of samples based on a 20-gene signature. On further analysis, HS cells were more resistant to drugs, particularly histone deacetylase inhibitors. Taken together, this study identified a novel subtype of LUAD with reduced Wnt signaling and high drug resistance.

Transforming growth factor beta orchestrates PD-L1 enrichment in tumor-derived exosomes and mediates CD8 T-cell dysfunction regulating early phosphorylation of TCR signalome in breast cancer.

Tumor cells promote immune evasion through upregulation of programmed death-ligand 1 (PD-L1) that binds with programmed cell death protein 1 (PD1) on cytotoxic T cells and promote dysfunction. Though therapeutic efficacy of anti-PD1 antibody has remarkable effects on different type of cancers it is less effective in breast cancer (BC). Hence, more details understanding of PD-L1-mediated immune evasion is necessary. Here, we report BC cells secrete extracellular vesicles in form of exosomes carry PD-L1 and are highly immunosuppressive. Transforming growth factor beta (TGF-ß) present in tumor microenvironment orchestrates BC cell secreted exosomal PD-L1 load. Circulating exosomal PD-L1 content is highly correlated with tumor TGF-ß level. The later also found to be significantly associated with CD8+CD39+, CD8+PD1+ T-cell phenotype. Recombinant TGF-ß1 dose dependently induces PD-L1 expression in Texos in vitro and blocking of TGF-ß dimmed exosomal PD-L1 level. PD-L1 knocked down exosomes failed to suppress effector activity of activated CD8 T cells like tumor exosomes. While understanding its effect on T-cell receptor signaling, we found siPD-L1 exosomes failed to block phosphorylation of src family proteins, linker for activation of T cells and phosphoinositide phospholipase Cγ of CD8 T cells more than PD-L1 exosomes. In vivo inhibition of exosome release and TGF-ß synergistically attenuates tumor burden by promoting Granzyme and interferon gamma release in tumor tissue depicting rejuvenation of exhausted T cells. Thus, we establish TGF-ß as a promoter of exosomal PD-L1 and unveil a mechanism that tumor cells follow to promote CD8 T-cell dysfunction.

MicroRNA-222 reprogrammed cancer-associated fibroblasts enhance growth and metastasis of breast cancer.

BACKGROUND: Cancer-associated fibroblasts (CAFs) are known to impact on tumour behaviour, but the mechanisms controlling this are poorly understood. METHODS: Breast normal fibroblasts (NFs) or CAFs were isolated from cancers by laser microdissection or were cultured. Fibroblasts were transfected to manipulate miR-222 or Lamin B receptor (LBR). The fibroblast-conditioned medium was collected and used to treat epithelial BC lines MDA-MB-231 and MDA-MB-157. Migration, invasion, proliferation or senescence was assessed using transwell, MTT or X-gal assays, respectively. RESULTS: MiR-222 was upregulated in CAFs as compared with NFs. Ectopic miR-222 expression in NFs induced CAF-like expression profiles, while miR-222 knockdown in CAFs inhibited CAF phenotypes. LBR was identified as a direct miR-222 target, and was functionally relevant since LBR knockdown phenocopied miR-222 overexpression and LBR overexpression phenocopied miR-222 knockdown. MiR-222 overexpression, or LBR knockdown, was sufficient to induce NFs to show the CAF characteristics of enhanced migration, invasion and senescence, and furthermore, the conditioned medium from these fibroblasts induced increased BC cell migration and invasion. The reverse manipulations in CAFs inhibited these behaviours in fibroblasts, and inhibited paracrine influences on BC cells. CONCLUSION: MiR-222/LBR have key roles in controlling pro-progression influences of CAFs in BC. This pathway may present therapeutic opportunities to inhibit CAF-induced cancer progression.

Heterodimer formation by Oct4 and Smad3 differentially regulates epithelial-to-mesenchymal transition-associated factors in breast cancer progression.

The multifunctional cytokine TGF-ß crucially participates in breast cancer (BCa) metastasis and works differently in the disease stages, thus contributing in BCa progression. We address connections between TGF-ß and the stem cell-related transcription factor (TF) Oct4 in BCa. In 147 BCa patients with infiltrating duct carcinoma, we identified a significantly higher number of cases with both moderate/high Oct4 expression and high TGF-ß in late stages compared to early stages of the disease. In vitro studies showed that TGF-ß elevated Oct4 expression, which in turn, regulated Epithelial-to-Mesenchymal transition (EMT)-regulatory gene (Snail and Slug) expression, migratory ability, chemotactic invasiveness and extracellular matrix (ECM) degradation potential of BCa cells. Putative binding sites for Oct4 on the snail, slug and cxcl13 promoters and for Smad3 on the snail and slug promoters were identified. Promoter activities of snail and slug were greater in dual-treated cells than only TGF-ß-treated or Oct4-overexpressing cells. CXCL13 mRNA fold changes, however, were low in cells induced with TGF-ß, compared to dual-treated or Oct4-overexpressing cells. Our co-IP studies confirmed that Oct4 and Smad3 form heterodimers that recognize specific promoter sequences to promote Snail and Slug expression, but which in turn, indirectly inhibits Smad3-mediated repression of CXCL13 expression, allowing Oct4 to act as a positive TF for CXCL13. Taken together, these data suggest that TGF-ß signaling and Oct4 cooperate to induce expression of EMT-related genes Snail, Slug and CXCL13, which accelerates disease progression, particularly in the late stages, and may indicate a poor prognosis for BCa patients.

miR-216b suppresses breast cancer growth and metastasis by targeting SDCBP.

Breast cancer is the most deadly cancer among women and the second leading cause of cancer death worldwide. Treatment effectiveness is complicated with tumor invasiveness/drug resistance. To tailor treatments more effectively to individual patients, it is important to define tumor growth and metastasis at molecular levels. SDCBP is highly overexpressed and associated with a strikingly poor prognosis in breast cancer. However the post transcriptional regulation of SDCBP overexpression remains to be an unexplored area. Our study reveals that miR-216b directly regulates SDCBP expression by binding to its 3'UTR region. miR-216b is a tumor suppressive miRNA and it is underexpressed during metastatic breast cancer. Consequently, overexpression of miR-216b resulted in decreased proliferation, migration and invasion in BC cell lines by modulating the expression of SDCBP. Inhibition of miR-216b divergent the tumor suppressive role by inducing the growth proliferation, migration and invasion in vitro. There is therefore a negative correlation between the expression of miR-216b and its target gene SDCBP in the BC tissue samples as well as cell lines. Simultaneous expression of miR-216b and SDCBP rescued the growth, migration and invasion effect suggesting that tumor suppressive action of miR-216b may be directly mediated by SDCBP. In summary, the study identifies miR-216b as a regulator of SDCBP expression in breast cancer which can potentially be targeted for developing newer therapies for the effective treatment of this killer disease.

An Organoruthenium Anticancer Agent Shows Unexpected Target Selectivity For Plectin.

Organometallic metal(arene) anticancer agents require ligand exchange for their anticancer activity and this is generally believed to confer low selectivity for potential cellular targets. However, using an integrated proteomics-based target-response profiling approach as a potent hypothesis-generating procedure, we found an unexpected target selectivity of a ruthenium(arene) pyridinecarbothioamide (plecstatin) for plectin, a scaffold protein and cytolinker, which was validated in a plectin knock-out model in vitro. Plectin targeting shows potential as a strategy to inhibit tumor invasiveness as shown in cultured tumor spheroids while oral administration of plecstatin-1 to mice reduces tumor growth more efficiently in the invasive B16 melanoma than in the CT26 colon tumor model.

Interleukin-33 as a Potential Therapeutic Target in Gastric Cancer Patients: Current Insights.

Gastric cancer is a significant global health problem as it is the fifth most prevalent cancer worldwide and the fourth leading cause of cancer-related mortality. While cytotoxic chemotherapy remains the primary treatment for advanced GC, response rates are limited. Recent progresses, focused on molecular signalling within gastric cancer, have ignited new hope for potential therapeutic targets that may improve survival and/or reduce the toxic effects of traditional therapies. Carcinomas are generally initiated when critical regulatory genes get mutated, but the progression to malignancy is usually supported by the non-neoplastic cells that create a conducive environment for transformation and progression to occur. Interleukin 33 (IL-33) functions as a dual activity cytokine as it is also a nuclear factor. IL-33 is usually present in the nuclei of the cells. Upon tissue damage, it is released into the extracellular space and binds to its receptor, suppression of tumorigenicity 2 (ST2) L, which is expressed on the membranes of the target cells. IL-33 signalling activates the T Helper 2 (Th2) immune response among other responses. Although the studies on the role of IL-33 in gastric cancer are still in the early stages, they have revealed potentially important (though sometimes conflicting) functions or roles in cancer development and progression. The pro-tumorigenic roles include induction and the recruitment of tumor-associated immune cells, promoting metaplasia progression, and inducing stem cell like and EMT properties in gastric cancer cells. Therapeutic interventions to disrupt these functions may provide a unique strategy for gastric cancer prevention and treatment. This review aims to provide a summary of the role of IL-33 in GC, state its multiple functions in relation to GC, and show potential avenues for promising therapeutic investigation.

Pan-cancer integrated bioinformatic analysis of RNA polymerase subunits reveal RNA Pol I member CD3EAP regulates cell growth by modulating autophagy.

Transcription is a crucial stage in gene expression. An integrated study of 34 RNA polymerase subunits (RNAPS) in the six most frequent cancer types identified several genetic and epigenetic modification. We discovered nine mutant RNAPS with a mutation frequency of more than 1% in at least one tumor type. POLR2K and POLR2H were found to be amplified and overexpressed, whereas POLR3D was deleted and downregulated. Multiple RNAPS were also observed to be regulated by variations in promoter methylation. 5-Aza-2-deoxycytidine mediated re-expression in cell lines verified methylation-driven inhibition of POLR2F and POLR2L expression in BRCA and NSCLC, respectively. Next, we showed that CD3EAP, a Pol I subunit, was overexpressed in all cancer types and was associated with worst survival in breast, liver, lung, and prostate cancers. The knockdown studies showed that CD3EAP is required for cell proliferation and induces autophagy but not apoptosis. Furthermore, autophagy inhibition rescued the cell proliferation in CD3EAP knockdown cells. CD3EAP expression correlated with S and G2 phase cell cycle regulators, and CD3EAP knockdown inhibited the expression of S and G2 CDK/cyclins. We also identified POLR2D, an RNA pol II subunit, as a commonly overexpressed and prognostic gene in multiple cancers. POLR2D knockdown also decreased cell proliferation. POLR2D is related to the transcription of just a subset of RNA POL II transcribe genes, indicating a distinct role. Taken together, we have shown the genetic and epigenetic regulation of RNAPS genes in most common tumors. We have also demonstrated the cancer-specific function of CD3EAP and POLR2D genes.

Development and validation of stemness associated LncRNA based prognostic model for lung adenocarcinoma patients.

BACKGROUND: An increasing number of studies are indicating that the stemness phenotype is a critical determinant of the Lung adenocarcinoma (LUAD) patient's response. Thus, it is crucial to identify novel biomarkers for stemness determination. OBJECTIVE: Here, we aim to develop a robust LncRNAs based prognostic signature with a stemness association for the LUAD patients. METHODS: RNA-seq and clinical data were downloaded from the existing database. The data were analysed using Cox regression, KM-plot, GSEA, and T-test. RESULTS: Initially, we used the TCGA dataset to characterize the stemness phenotype in LUAD. The commonly expressed LncRNAs in TCGA and MCTP cohort were then used as input for the Cox-regression analysis. The top three LncRNAs were selected to build a prognostic model, which was the best prognosticator in multivariate analysis with stage and previously published prognosticators. The characterization of poor surviving patients using various analysis showed high stemness properties and low expression of differentiation markers. Furthermore, we validated the prognostic score in an independent MCTP cohort of patients. In the MCTP cohort, prognostic score significantly predicted survival independent of stage and previous prognosticators. CONCLUSION: Taken together, in this study, we have developed and validated a new prognostic score associated with the stemness phenotype.

An epithelial-mesenchymal plasticity signature identifies two novel LncRNAs with the opposite regulation.

The epithelial to mesenchymal transition (EMT) is crucial for cancer progression and chemoresistance. EMT is a dynamic process with multiple phases that change cell migration and invasion activity. We used pan-cancer expression data to find 14-LncRNAs that had a high correlation with the EMT markers VIM, CDH1, FN1, SNAI1, and SNAI2. The expression of 14 EMT-associated LncRNA, which also showed high cancer specificity, was used to calculate the pan-cancer EMT score. The EMT score was then applied to the 32 cancer types to classify them as epithelial, epithelial-mesenchymal, mesenchymal-epithelial, or mesenchymal tumors. We discovered that the EMT score is a poor prognostic predictor and that as tumor mesenchymal nature increased, patient survival decreased. We also showed that the cell of origin did not influence the EMT nature of tumors. Pathway analysis employing protein expression data revealed that the PI3K pathway is the most crucial in determining the EMTness of tumors. Further, we divided CCLE-cell lines into EMT classes and discovered that mesenchymal cells, which exhibited higher PI3K pathway activation, were more sensitive to PI3K inhibitors than epithelial cells. We identified Linc01615 as a mesenchymal LncRNA whose expression significantly correlated with survival in several cancer types. We showed that Linc01615 is regulated by the TGFß-STAT3 pathway in a feedback loop. Knockdown of Linc01615 inhibited cell proliferation and migration by regulating the PI3K pathway and mesenchymal markers. We also identified RP4-568C11.4 as an epithelial cancer marker. We showed that knocking down RP4-568C11.4 decreased cell growth but not migration. In addition, we discovered that ESR1 regulates RP4-5681C11.4 in breast cancer. Taken together, we have developed a pan-cancer EMT signature. Also, we found two new LncRNAs that have different effects on cancer development and EMT.

Genetic and epigenetic landscape of leukocyte infiltration identifies an immune prognosticator in lung adenocarcinoma.

BACKGROUND: Leukocyte infiltration plays an critical role in outcome of various diseases including Lung adenocarcinoma (LUAD). OBJECTIVES: To understand the genetic and epigenetic factors affecting leukocyte infiltration and identification and validation of immune based biomarkers. METHOD: Correlation analysis was done to get the associations of the factors. CIBERSORT analysis was done for immune cell infiltration. Genetic and epigenetic analysis were performed. Cox regression was carried out for survival. RESULTS: We categorized the TCGA-LUAD patients based on Leukocyte fraction (LF) and performed extensive immunogenomic analysis. Interestingly, we showed that LF has a negative correlation with copy number variation (CNV) but not with mutational load. However, several individual genetic mutations, including KRAS and KEAP1, were significantly linked with LF. Also, as expected, patients with high LF showed significantly increased expression of genes involved in leukocyte migration and activation. DNA methylation changes also showed a strong association with LF and regulated a significant proportion of genes associated with LF. We also developed and validated an independent prognostic immune signature using the top six prognostic genes associated with LF. CONCLUSION: Together, we have identified clinical, genetic, and epigenetic variations associated with LUAD LF and developed an immune gene-based signature for disease prognostication.

A Greedy Algorithm-Based Stem Cell LncRNA Signature Identifies a Novel Subgroup of Lung Adenocarcinoma Patients With Poor Prognosis.

Cancer stem cells play an essential role in therapy response and aggressiveness of various cancers, including lung adenocarcinoma (LUAD). Interestingly it also shares many features of embryonic stem cells (ESCs). Recently, long non-coding RNAs (lncRNAs) have emerged as a critical regulator of cell physiology. Here, we used expression data of ESCs, LUAD, and normal lung to identify 198 long non-coding hESC-associated lncRNAs (hESC-lncRNAs). Intriguingly, K-means clustering of hESC-associated lncRNAs identified a subgroup of LUAD patients [undifferentiated LUAD (uLUAD)] with high stem cell-like characteristic, decreased differentiation genes expression, and poor survival. We also observed that the uLUAD patients had overexpression of proteins associated with cell proliferation. Interestingly, uLUAD patients were highly enriched with the stemness-related gene sets, and had higher mutation load. A notable result observed was high infiltration of T cells and a higher level of neopeptides in uLUAD patients, making these patients an optimal candidate for immunotherapy. Further, feature selection using greedy algorithm identified 17-hESC-lncRNAs signature, which showed significant consistency with 198 hESC-lncRNAs-based classification, and identified a group of patients with high stem cell-like characteristic in the 10 most common cancer types and CCLE cell lines. These results suggest the conventional role of hESC-lncRNAs in stem cell biology. In summary, we identified a novel subgroup of LUAD patients (uLUAD) using a set of hESC-lncRNAs. The uLUAD patients had high stem cell-like characteristic and reduced survival rate and may be referred for immunotherapy. Furthermore, our analysis also showed the importance of lncRNAs in cancer and cancer stem cells.

The first examples of multiply bonded dirhenium(iii,ii) paramagnetic complexes containing nitrobenzoate ligands: spectroscopic, structural, cytotoxicity and computational studies.

4-Nitrobenzoic acid, 3-nitrobenzoic acid and 4'-nitro[1,1'-biphenyl]-4-carboxylic acid react with the multiply bonded paramagnetic dirhenium(iii,ii) complex Re2(µ-O2CCH3)Cl4(µ-Ph2PCH2PPh2)2 (1) in refluxing ethanol to afford the paramagnetic substitution products of the type Re2(µ-L)Cl4(µ-Ph2PCH2PPh2)2, where L represents the nitrobenzoate ligands [L = 4-nitrobenzoate, 2; 3-nitrobenzoate, 3; 4'-nitro[1,1'-biphenyl]-4-carboxylate, 4]. These are the first examples of paramagnetic dirhenium complexes containing nitrobenzoate ligands. The spectral (UV-vis, IR, and EPR) and electrochemical properties of the complexes are described. The identity of 4 has been established by single-crystal X-ray structure determination (Re-Re distance of 2.2967(4) Å). The electronic structures of the complexes were scrutinized by density functional theory (DFT) calculations. X-band EPR spectral measurements along with the DFT analysis show that the unpaired electron resides in the metal-metal δ* antibonding orbital. The complexes were also screened in vitro for their antiproliferative properties against the human breast cancer cell line MCF-7 by the MTT assay. Flow cytometry analysis showed that the complexes arrested the sub-G0/G1 phase.