Comprehensive RNA-seq reveals molecular changes in kidney malignancy among people living with HIV.

To heighten the awareness of kidney malignancy in patients with HIV infection to facilitate the early diagnosis of kidney cancer, the differentially expressed mRNAs were analyzed in this malignant tumor using RNA sequencing. We identified 2,962 protein-coding transcripts in HIV-associated kidney cancer. KISS1R, CAIX, and NPTX2 mRNA expression levels were specifically increased in HIV-associated kidney cancer while UMOD and TMEM213 mRNA were decreased in most cases based on real-time PCR analyses. These findings were similar to those noted for the general population with renal cell carcinoma. Immunohistochemical staining analysis also showed that a total of 18 malignant kidney cases among the people living with HIV (PLWH) exhibited positive staining for KISS1R and CAIX. Pathway analysis of the differentially expressed mRNAs in HIV-associated kidney cancer revealed that several key pathways were involved, including vascular endothelial growth factor-activated receptor activity, IgG binding, and lipopolysaccharide receptor activity. Altogether, our findings reveal the identified molecular changes in kidney malignancy, which may offer a helpful explanation for cancer progression and open up new therapeutic avenues that may decrease mortality after a cancer diagnosis among PLWH.

Profiling of specific long non-coding RNA signatures identifies ST8SIA6-AS1 AS a novel target for breast cancer.

BACKGROUND: Breast cancer is the most commonly diagnosed cancer among women and is also the leading cause of cancer death for which the treatment and methods of diagnosis remain unsatisfied. Long non-coding RNA (lncRNA) plays an important role in the occurrence and development of tumors, including breast cancer. We aimed to seek new and efficient treatment targets by analyzing the lncRNA expression profiles of breast cancer. METHODS: A competitive endogenous RNA microarray was used to investigate the profiles of differentially expressed lncRNAs. Quantitative real-time polymerase chain reaction analysis (qRT-PCR) validated the top differentially expressed lncRNAs in 107 pairs of breast cancer tissues and adjacent normal tissues. cis- and trans-regulation mRNAs of lncRNAs were used to perform enrichment analysis. Cell function assays were used to explore the functions of ST8SIA6-AS1. RESULTS: Seven lncRNAs, comprising ST8SIA6-AS1, lnc-HIST1H2BJ-5:1, lnc-PRICKLE2-3:2, RP1-86C11.7, RP11-15F12.1, ZNF670-ZNF695 and lnc-STRN3-12:1, were shown to be significantly up-regulated in breast cancer. lncRNA ST8SIA6-AS1 was associated with TNM staging and Ki-67 index. The cell function assays showed that ST8SIA6-AS1 can promote the proliferation, migration and invasion of breast cancer cells. The functions of ST8SIA6-AS1 were explored and the competing endogenous RNA mode showed that miR-4252 was a potential candidate. Its target genes were further predicted. The lncRNA-protein mode showed three potential candidate RNA binding proteins: NONO, QKI and RBMX. CONCLUSIONS: lncRNA ST8SIA6-AS1 can promote the proliferation, migration and invasion of breast cancer cells. By hypothesizing two different functional modes of ST8SIA6-AS1, we found lncRNA ST8SIA6-AS1 may contribute to breast cancer progression through miR-4252 or interacting with RNA binding proteins: NONO, QKI and RBMX.

Screening and bioinformatics analysis of a ceRNA network based on the circular RNAs, miRNAs, and mRNAs in pan-cancer.

BACKGROUND: The pan-cancer analysis has recently brought us into a novel level of cancer research. Nowadays, the Circular RNAs (circRNAs) is becoming increasingly important in the occurrence and progression of tumors. Nevertheless, the specific expression patterns and functions of circRNAs in the pan-cancer remains unclear. Here we aimed to explore the expression patterns and functions of circRNAs in pan-cancer. METHODS: We combined our microarray with seven circRNA arrays from the Gene Expression Omnibus (GEO) database and transcriptome profiles were acquired from The Cancer Genome Atlas (TCGA) database. A circRNA-miRNA-mRNA network was created and analyzed using multiple bioinformatic approaches including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, Search Tool for the Retrieval of Interacting Genes (STRING) database, cytoHubba and MCODE app. Cell function assays including CCK-8 analysis, colony formation, and transwell assay were used to explore pan-circRNAs' functions. RESULTS: A panel of 6 circRNAs, 11 miRNAs, and 318 mRNAs was found to be differentially expressed (DE) in pan-cancer. A circRNA-miRNA-mRNA network was also constructed. Then, a circRNA-miRNA-hub gene network was created according to 5 pan-circRNAs, 8 pan-miRNAs, and 16 pan-mRNAs. Enrichment analysis pointed out the possible association of DEmRNAs with pan-cancer is transcriptional misregulation in cancer. Overexpression of hsa_circ_0004639 and silence of hsa_circ_0008310 can inhibit the malignant biological properties of cancer cells. CONCLUSIONS: Six pan-circRNAs were discovered and their regulating mechanisms were predicted. Those findings together will give a new insight into pan-cancer research and present potential therapy targeting as well as promising biomarkers.

CircMMP11 acts as a ce-circRNA in breast cancer progression by regulating miR-1204.

BACKGROUND: Numerous studies have found that circular RNAs (circRNA) can serve as competing endogenous RNA (ceRNA) in cancer progression while the expression profiles and functions of competitive endogenous circRNAs (ce-circRNAs) in breast cancer (BC) have not been determined. METHODS: Six pairs of tissue samples were selected to perform ceRNA microarray, and The Cancer Genome Atlas (TCGA) data was also included to explore the ce-circRNA profiling of BC. The expression of one of the top upregulated circRNAs, circMMP11, was confirmed by qRT-PCR in both breast cancer cell lines and tissues. We also analyzed the clinical impact of circMMP11 on BC. To explore the functions of circMMP11 in BC, experiments referring to cell proliferation and migration were performed. The regulatory effect of circMMP11 on miRNA and its target genes was explored to confirm its ce-circRNA mechanisms in BC. RESULTS: qRT-PCR analyses verified that circMMP11 was successfully transfected and positively associated with a poorer clinicopathology of BC. The inhibition of circMMP11 suppressed cell proliferation and migration of BC. The luciferase reporter assay revealed that circMMP11 and MMP11 could bind to miR-1204 and that circMMP11 acted as a ce-circRNA by regulating the expression of MMP11 via sponging miR-1204. CONCLUSIONS: The circMMP11/miR-1204/MMP11 axis regulates breast cancer progression via a competitive endogenous RNA (ceRNA) mechanism. CircMMP11 may serve as a potential therapeutic target in BC.

Identification of Specific Long Non-Coding Ribonucleic Acid Signatures and Regulatory Networks in Prostate Cancer in Fine-Needle Aspiration Biopsies.

Prostate cancer (PCa) is one of the most common tumors in men and can be lethal, especially if left untreated. A substantial majority of PCa patients not only are diagnosed based on fine needle aspiration (FNA) biopsies, but their treatment choices are also largely driven by the pathological findings obtained with these FNA specimens. It is widely believed that lncRNAs have strong biological significance, but their specific functions and regulatory networks have not been elucidated. LncRNAs may serve as key players and regulators of PCa carcinogenesis and could be novel biomarkers of this cancer. To identify potential markers for early detection of PCa, in this study, we employed a competing endogenous RNA (ceRNA) microarray to identify differentially expressed lncRNAs (DelncRNAs) in PCa tissue and quantitative real-time PCR (qRT-PCR) analysis to validate these DelncRNAs in FNA biopsies. We demonstrated that a total of 451 lncRNAs were differentially expressed in four pairs of PCa/adjacent tissues, and upregulation of the lncRNAs RP11-33A14.1, RP11-423H2.3, and LAMTOR5-AS1 was confirmed in FNA biopsies of PCa by qRT-PCR and was consistent with the ceRNA array data. The association between the expression of the lncRNA LAMTOR5-AS1 and aggressive cancer was also investigated. Regulatory network analysis of DelncRNAs showed that the lncRNAs RP11-33A14.1 and RP11-423H2.3 targeted miR-7, miR-24-3p, and miR-30 and interacted with the RNA binding protein FUS. Knockdown of these DelncRNAs in PCa cells also demonstrated the effects of RP11-423H2.3 on miR-7/miR-24/miR-30 or LAMTOR5-AS1 on miR-942-5p/miR-542-3p via direct interaction. The results of these studies indicate that these three specific lncRNA signatures and regulatory networks might serve as risk prediction and diagnostic biomarkers for prostate cancer, even in biopsies obtained by FNA.

Profiling and integrated analysis of differentially expressed circRNAs as novel biomarkers for breast cancer.

Breast cancer (BC) is a globally common cancer with the highest and increasing morbidity and mortality among females. Novel biomarkers are warranted to be discovered for the early detection, treatment, and prognosis of BC. In this study, we investigated the profiles of differentially expressed (DE) circular RNAs (circRNAs) by competing endogenous RNAs (ceRNA) microarray to construct a genome-wide circRNA profile. Then, we performed Gene Ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis of the host genes (HGs) of circRNAs. A total of 4,370 DE circRNAs were detected and GO and KEGG analysis showed that they were significantly associated with cell cycle, DNA replication, BC, and familial BC. We validated the differential circRNAs and relevant HGs through quantitative real-time polymerase chain reaction and constructed a putative circRNA-microRNA-messenger RNA regulatory network. Eight circRNAs, including hsa_circ_0069094, hsa_circ_0062558, hsa_circ_0074026, hsa_circ_0079876, hsa_circ_0017536, hsa_circ_0023302, hsa_circ_0017650, and hsa_circ_0017545, were validated significantly DE in BC tissue and associated with TNM staging, lymph node infiltration, and Ki67. Hsa_circ_0069094, hsa_circ_0079876, hsa_circ_0017650, and hsa_circ_0017526 were upregulated in plasma. This study revealed the general expression characteristics of specific DE circRNAs in BC and hsa_circ_0069094, hsa_circ_0079876, hsa_circ_0017650, and hsa_circ_0017526 might be promising candidate targets.

Metabolomics: a promising diagnostic and therapeutic implement for breast cancer.

Breast cancer (BC) is the most commonly diagnosed cancer among women and the leading cause of cancer death. Despite the advent of numerous diagnosis and treatment methods in recent years, this heterogeneous disease still presents great challenges in early diagnosis, curative treatments and prognosis monitoring. Thus, finding promising early diagnostic biomarkers and therapeutic targets and approaches is meaningful. Metabolomics, which focuses on the analysis of metabolites that change during metabolism, can reveal even a subtle abnormal change in an individual. In recent decades, the exploration of cancer-related metabolomics has increased. Metabolites can be promising biomarkers for the screening, response evaluation and prognosis of BC. In this review, we summarized the workflow of metabolomics, described metabolite signatures based on molecular subtype as well as reclassification and then discussed the application of metabolomics in the early diagnosis, monitoring and prognosis of BC to offer new insights for clinicians in breast cancer diagnosis and treatment.

Hepatomas are exquisitely sensitive to pharmacologic ascorbate (P-AscH-).

Rationale: Ascorbate is an essential micronutrient known for redox functions at normal physiologic concentrations. In recent decades, pharmacological ascorbate has been found to selectively kill tumour cells. However, the dosing frequency of pharmacologic ascorbate in humans has not yet been defined. Methods: We determined that among five hepatic cell lines, Huh-7 cells were the most sensitive to ascorbate. The effects of high-dose ascorbate on hepatoma were therefore assessed using Huh-7 cells and xenograft tumour mouse model. Results: In Huh-7 cells, ascorbate induced a significant increase in the percentage of cells in the G0/G1 phase, apoptosis and intracellular levels of ROS. High doses of ascorbate (4.0 pmol cell-1), but not low doses of ascorbate (1.0 pmol cell-1), also served as a pro-drug that killed hepatoma cells by altering mitochondrial respiration. Furthermore, in a Huh-7 cell xenograft tumour mouse model, intraperitoneal injection of ascorbate (4.0 g/kg/3 days) but not a lower dose of ascorbate (2.0 g/kg/3 days) significantly inhibited tumour growth. Gene array analysis of HCC tumour tissue from xenograft mice given IP ascorbate (4.0 g/kg/3 days) identified changes in the transcript levels of 192 genes/ncRNAs involved in insulin receptor signalling, metabolism and mitochondrial respiration. Consistent with the array data, gene expression levels of AGER, DGKK, ASB2, TCP10L2, Lnc-ALCAM-3, and Lnc-TGFBR2-1 were increased 2.05-11.35 fold in HCC tumour tissue samples from mice treated with high-dose ascorbate, and IHC staining analysis also verified that AGER/RAGE and DGKK proteins were up-regulated, which implied that AGER/RAGE and DGKK activation might be related to oxidative stress, leading to hepatoma cell death. Conclusions: Our studies identified multiple mechanisms are responsible for the anti-tumour activity of ascorbate and suggest high doses of ascorbate with less frequency will act as a novel therapeutic agent for liver cancer in vivo.

Risk Factors and Outcomes of Early Relapse After Curative Resection of Intrahepatic Cholangiocarcinoma.

Early relapse after hepatectomy for intrahepatic cholangiocarcinoma (ICC) has a tremendous influence on the long-term survival outcomes of ICC patients. The purpose of our study was to investigate risk factors for early tumor relapse and confirm whether early relapse was correlated with ICC patients' long-term survival outcomes. Three hundred and twenty-two consecutive ICC patients undergoing partial hepatectomy at Liver Surgery Department of Zhongshan Hospital (Fudan University, Shanghai, China) between January 2005 and December 2011 were included in this retrospectively study. The definition of early relapse had been described as tumor relapse within 24 months after hepatectomy in ICC patients. We identified a total of 168 ICC patients with early relapse and 23 ICC patients with late relapse after hepatectomy. From the time of relapse, the long-term survival outcomes were worse among patients who had early vs. late relapse (median OS 16.5 vs. 44.7 months, respectively; P < 0.0001). The overall survival of the early relapse group was lower than that of the late relapse group (P < 0.0001). Multivariate Cox regression analysis indicated that multiple tumors (hazard ratio [HR], 1.951; 95% CI, 1.382-2.755; P < 0.001), lymphonodus metastasis (HR, 1.517; 95% CI, 1.061-2.168; P = 0.022), and higher serum CA19-9 levels (HR, 1.495; 95% CI, 1.095-2.039; P = 0.011) were independent risk factors of early relapse. Moreover, multiple tumors (HR, 1.641; 95% CI, 1.120-2.406; P = 0.011), lymphonodus metastasis (HR, 2.008; 95% CI, 1.367-2.949; P < 0.001), elevated NLR (HR, 1.921; 95% CI, 1.331-2.774; P < 0.001) and higher serum CA19-9 levels (HR, 1.990; 95% CI, 1.409-2.812; P < 0.001) were independent predictors of overall survival for ICC patients with early relapse. Collectively, our findings demonstrated that multiple tumors, lymphonodus metastasis, and higher serum CA19-9 levels were associated with the increased risks of early relapse and worse prognoses of ICC after curative-intent resection.

Roles of circular RNA in breast cancer: present and future.

Breast cancer is one of the most common cancers with the highest morbidity and mortality among women despite the treatment approaches have advanced including surgery, endocrine therapy and targeted therapy. Novel biomarkers are warranted to be discovered for the early detection, treatment and prognosis for breast cancer. CircRNA is a class of covalently closed single-stranded circular RNA molecules without free 5' or 3' end which makes them well expressed and more stable than their linear counterparts. In this review, we mainly discuss the oncogenic or anti-oncogenic roles of circRNAs can be utilized in the treatment and prognosis of breast cancer. A large number of circRNAs have shown great potential to function in carcinogenesis, metastasis or chemoresistance of breast cancer through transcriptional regulation of RNAs including miRNA and mRNA, in addition to their promise as stable biomarkers that can be used for monitoring breast cancer progression. However, the translation phenomenon of circRNAs in breast cancer and the diagnostic value of circRNAs in breast cancer requires further investigation for which the detection of circRNAs in plasma exosomes could be worthy of a try. Above all, engineered exosomes preloaded with engineered anti-oncogenic circRNAs are likely to provide a novel direction in the personal medicine of breast cancer.

Identification of novel biomarkers for hepatocellular carcinoma using transcriptome analysis.

Hepatocellular carcinoma (HCC) is the third leading cause of death from cancer in the world. To comprehensively investigate the utility of microRNAs (miRNAs) and protein-encoding transcripts (messenger RNAs [mRNAs]) in HCC as potential biomarkers for early detection and diagnosis, we exhaustively mined genomic data from three available omics datasets (GEO, Oncomine, and TCGA), analyzed the overlaps among gene expression studies from 920 hepatocellular carcinoma samples and 508 healthy (or adjacent normal) liver tissue samples available from six laboratories, and identified 178 differentially expressed genes (DEGs) associated with HCC. Paired with miRNA and lncRNA data, we identified 23 core genes that were targeted by nine differentially expressed miRNAs and 21 HCC-specific lncRNAs. We further demonstrated that alterations in these 23 genes were quite frequent, with five genes altered in over 5% of the population. Patients with high levels of YWHAZ, ENAH, and HMGN4 tended to have high-grade tumors and shorter overall survival, suggesting that these genes could be promising candidate biomarkers for disease and poor prognosis in patients with HCC. Our comprehensive mRNA, miRNA, and lncRNA omics analyses from multiple independent datasets identified robust molecules that may be used as biomarkers for early HCC detection and diagnosis.

Circular RNA Expression Profiling Identifies Prostate Cancer- Specific circRNAs in Prostate Cancer.

BACKGROUND/AIMS: Prostate cancer (PCa) is one of the main cancers that damage males' health severely with high morbidity and mortality, but there is still no ideal molecular marker for the diagnosis and prognosis of prostate cancer. METHODS: To determine whether the differentially expressed circRNAs in prostate cancer can serve as novel biomarkers for prostate cancer diagnosis, we screened differentially expressed circRNAs using SBC-ceRNA array in 4 pairs of prostate tumor and paracancerous tissues. A circRNA-miRNA-mRNA regulatory network for the differential circRNAs and their host genes was constructed by Cytoscape3.5.1 software. Quantitative real-time polymerase chain reaction analysis (qRT-PCR) was performed to confirm the microarray data. RESULTS: We found 1021 differentially expressed circRNAs in PCa tumor using SBC-ceRNA array and confirmed the expression of circ_0057558, circ_0062019 and SLC19A1 in PCa cell lines and tumor tissues through qRT-PCR analysis. We demonstrated that combination of PSA level and two differentially expressed circRNAs showed significantly increased AUC, sensitivity and specificity (0.938, 84.5% and 90.9%, respectively) than PSA alone (AUC of serum PSA was 0.854). Moreover, circ_0057558 was correlated positively with total cholesterol. The functional network of circRNA-miRNA-mRNA analysis showed that circ_0057558 and circ_0034467 regulated miR-6884, and circ_0062019 and circ_0060325 regulated miR-5008. CONCLUSION: Our results demonstrated that differentially expressed circRNAs (circ_0062019 and circ_0057558) and host gene SLC19A1 of circ_0062019 could be used as potential novel biomarkers for prostate cancer.

Molecular Changes of Lung Malignancy in HIV Infection.

Malignancy of the lung is a major source of morbidity and mortality in persons with human immunodeficiency virus infection; as the most prevalent non-acquired immunodeficiency syndrome-defining malignancy, it represents an important and growing problem confronting HIV-infected patients. To evaluate the molecular changes of lung malignancy in HIV infection, we analyzed differential gene expression profiles and screened for early detection biomarkers of HIV-associated lung cancer using Affymetrix arrays and IPA analysis. A total of 59 patients were diagnosed with HIV-associated lung cancer from Jan 2010 to May 2018. The primary outcome was a significant difference in survival outcome between stages III-IV (10.46 ± 1.87 months) and I-II (17.66 ± 2.88 months). We identified 758 differentially expressed genes in HIV-associated lung cancer. The expression levels of SIX1 and TFAP2A are specifically increased in HIV-associated lung cancer and are associated with poorly differentiated tumor tissue. We also found decreased ADH1B, INMT and SYNPO2 mRNA levels in HIV lung cancer. A comprehensive network and pathway analysis of the dysregulated genes revealed that these genes were associated with four network functions and six canonical pathways relevant to the development of HIV-associated lung cancer. The molecular changes in lung malignancy may help screen the growing population of HIV patients who have or will develop this malignancy.

Immunotherapeutic interventions of Triple Negative Breast Cancer.

Triple Negative Breast Cancer (TNBC) is a highly heterogeneous subtype of breast cancer that lacks the expression of oestrogen receptors, progesterone receptors and human epidermal growth factor receptor 2. Although TNBC is sensitive to chemotherapy, the overall outcomes of TNBC are worse than for other breast cancers, and TNBC is still one of the most fatal diseases for women. With the discovery of antigens specifically expressed in TNBC cells and the developing technology of monoclonal antibodies, chimeric antigen receptors and cancer vaccines, immunotherapy is emerging as a novel promising option for TNBC. This review is mainly focused on the tumour microenvironment and host immunity, Triple Negative Breast Cancer and the clinical treatment of TNBC, novel therapies for cancer and immunotherapy for TNBC, and the future outlook for the treatment for TNBC and the interplay between the therapies, including immune checkpoint inhibitors, combination of immune checkpoint inhibitors with targeted treatments in TNBC, adoptive cell therapy, cancer vaccines. The review also highlights recent reports on the synergistic effects of immunotherapy and chemotherapy, antibody-drug conjugates, and exosomes, as potential multifunctional therapeutic agents in TNBC.