Identification of microRNA differentially expressed in three subtypes of non-small cell lung cancer and in silico functional analysis

MiRNA expression profiling in adenocarcinoma and squamous cell lung carcinoma reveals both common and specific deregulated microRNAs

The current study investigated the expression signatures of miRNAs in lung adenocarcinoma (LUAD) and squamous cell lung carcinoma (LUSC). miRNA profiling was performed using microarray in 12 LUAD and 12 LUSC samples and adjacent normal tissues. In LUAD, 107 miRNAs were significantly deregulated, whereas 235 miRNAs were deregulated in LUSC. Twenty-six miRNAs were common between the 2 cancer subtypes and 8 were prioritized for validation, in addition to 6 subtype-specific miRNAs. The RT-qPCR validation samples included 50 LUAD, 50 LUSC, and adjacent normal tissues. Eight miRNAs were validated in LUAD: 3 upregulated - miR-7-5p, miR-375-5p, miR-6785-3p, and 5 downregulated - miR-101-3p, miR-139-5p, miR-140-3p, miR-144-3p, miR-195-5p. Ten miRNAs were validated in the LUSC group: 3 upregulated - miR-7-5p, miR-21-3p, miR-650, and 7 downregulated - miR-95-5p, miR-140-3p, miR-144-3p, miR-195-5p, miR-375, miR-744-3p, and miR-4689-3p. Reactome pathway analysis revealed that the target genes of the deregulated miRNAs in LUAD were significantly enriched in cell cycle, membrane trafficking, gene expression processes, and EGFR signaling, while in LUSC, they were enriched in the immune system, transcriptional regulation by TP53, and FGFR signaling. This study identified distinct miRNA profiles in LUSC and LUAD, which are common and specific miRNAs that could be further investigated as biomarkers for diagnosis and prognosis.

APE1 controls DICER1 expression in NSCLC through miR-33a and miR-130b

Increasing evidence suggests different, not completely understood roles of microRNA biogenesis in the development and progression of lung cancer. The overexpression of the DNA repair protein apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) is an important cause of poor chemotherapeutic response in lung cancer and its involvement in onco-miRNAs biogenesis has been recently described. Whether APE1 regulates miRNAs acting as prognostic biomarkers of lung cancer has not been investigated, yet. In this study, we analyzed miRNAs differential expression upon APE1 depletion in the A549 lung cancer cell line using high-throughput methods. We defined a signature of 13 miRNAs that strongly correlate with APE1 expression in human lung cancer: miR-1246, miR-4488, miR-24, miR-183, miR-660, miR-130b, miR-543, miR-200c, miR-376c, miR-218, miR-146a, miR-92b and miR-33a. Functional enrichment analysis of this signature revealed its biological relevance in cancer cell proliferation and survival. We validated DICER1 as a direct functional target of the APE1-regulated miRNA-33a-5p and miR-130b-3p. Importantly, IHC analyses of different human tumors confirmed a negative correlation existing between APE1 and Dicer1 protein levels. DICER1 downregulation represents a prognostic marker of cancer development but the mechanisms at the basis of this phenomenon are still completely unknown. Our findings, suggesting that APE1 modulates DICER1 expression via miR-33a and miR-130b, reveal new mechanistic insights on DICER1 regulation, which are of relevance in lung cancer chemoresistance and cancer invasiveness.

Exosomal microRNA expression profiles derived from A549 human lung cells in response to influenza A/H1N1pdm09 infection

Exosomes participate in intercellular communication by shuttling various small molecules from donor to recipient cells. We aimed to examine the role of exosomes and exosomal miRNAs in influenza virus infection. The results showed that influenza A/H1N1pdm09 infection could promote A549 cells to secrete exosomes, while blocking the generation of exosomes reduced viral RNA production. A total of 97 exosomal miRNAs with significantly altered expression were identified during influenza infection. Of 12 candidate miRNAs chosen for further validation, ten were confirmed by qRT-PCR. Among 5978 predicted target genes，we found 37 interferon pathway-related genes to be the potential targets of 29 differentially expressed miRNAs. Many target genes were annotated to various KEGG signaling pathways, some of which played important roles in influenza infection. These data will help to further understand the mechanism of influenza virus-host interactions, which is important for the development of preventative and therapeutic strategies against influenza virus.

miR-1306 Promotes Lung Squamous Cell Carcinoma Progression and Predicts Clinical Prognosis of Patients

Purpose

Lung squamous cell carcinoma (LUSC) is one of the major subtypes of non-small cell lung cancer (NSCLC) with high mortality. Identification of novel biomarkers of the development of LUSC could provide basis for clinical treatment and improve patients’ prognosis. The function of miR-1306 in the development of LUSC was investigated.

Patients and Methods

A total of 103 paired LUSC and normal tissues were collected from LUSC patients. The expression of miR-1306 in collected tissues and cultured cells was evaluated by PCR. The clinical significance of miR-1306 was assessed by a series of statistical analyses, and the biological effect of miR-1306 was also estimated with the CCK8 and Transwell assay.

Results

The significant upregulation of miR-1306 was observed in LUSC, which was associated with positive lymph node metastasis and advanced TNM stage of patients. miR-1306 was also identified as an independent prognostic factor negatively associated with the prognosis of patients. Additionally, the upregulation of miR-1306 was found to promote the proliferation, migration, and invasion of LUSC cells, indicating its tumor enhancer role in the development of LUSC. While miR-1306 was also found to regulate RBM3, which was speculated to be the mechanism underlying the function of miR-1306.

Conclusion

miR-1306 functions as a prognostic indicator and tumor promoter of LUSC through targeting RBM3, which provides a potential therapeutic target of LUSC.

Prognostic value of miR-1181 in non-small cell lung cancer and its regulatory effect on tumor progression

Non-small cell lung cancer (NSCLC) is one of the most important causes of cancer-related death. miR-1181 has been reported to have roles in various cancer types and its function in the progression of NSCLC was investigated in the present study. A total of 118 patients with NSCLC were recruited and their tumor tissues were collected. The expression of miR-1181 in NSCLC tissues and cells was detected by reverse transcription-quantitative PCR. The prognostic value of miR-1181 was evaluated by Kaplan-Meier and Cox regression analysis and the roles of miR-1181 in cell proliferation, migration and invasion of NSCLC were analyzed by Cell Counting Kit-8 and Transwell assays. miR-1181 was indicated to be upregulated in NSCLC tissues and cell lines, and to be associated with lymph node metastasis and the TNM stage of patients. Patients with high miR-1181 expression had a poorer prognosis than those with low miR-1181 expression. miR-1181 levels and TNM stage were determined to be two independent prognostic factors for NSCLC. In addition, overexpression of miR-1181 exerted enhancing effects on cell proliferation, migration and invasion of NSCLC, while its knockdown inhibited these cellular processes. In conclusion, upregulation of miR-1181 in NSCLC was associated with lymph node metastasis and TNM stage of patients and was indicative of poor prognosis. miR-1181 was indicated to exert promoting effects on cell proliferation, migration and invasion of NSCLC cells and to be involved in tumor progression, providing novel insight for the development of biomarkers and therapies for NSCLC.

Soluble Biomarkers with Prognostic and Predictive Value in Advanced Non-Small Cell Lung Cancer Treated with Immunotherapy

Simple Summary

Immunotherapy, most notably immune checkpoint inhibitors (ICIs), has revolutionized the treatment of advanced non-small cell lung cancer (NSCLC). Although some patients respond well to ICIs, many patients do not benefit from ICIs, leading to disease progression and/or immune-related adverse events. Biological markers can help to improve patient selection. However, currently available markers such as PD-1 and its ligand (PD-L1) have important limitations. For this reason, new biomarkers obtained by non-invasive methods are urgently needed. In the present review, we describe recent advances in the development of novel soluble biological markers (e.g., circulating immune cells, TMB, circulating tumor cells, circulating tumor DNA, soluble factor PD-L1, tumor necrosis factor, etc.) for patients with NSCLC treated with immunotherapy.

Abstract

Numerous targeted therapies have been evaluated for the treatment of non-small cell lung cancer (NSCLC). To date, however, only a few agents have shown promising results. Recent advances in cancer immunotherapy, most notably immune checkpoint inhibitors (ICI), have transformed the treatment scenario for these patients. Although some patients respond well to ICIs, many patients do not benefit from ICIs, leading to disease progression and/or immune-related adverse events. New biomarkers capable of reliably predicting response to ICIs are urgently needed to improve patient selection. Currently available biomarkers—including programmed death protein 1 (PD-1) and its ligand (PD-L1), and tumor mutational burden (TMB)—have major limitations. At present, no well-validated, reliable biomarkers are available. Ideally, these biomarkers would be obtained through less invasive methods such as plasma determination or liquid biopsy. In the present review, we describe recent advances in the development of novel soluble biomarkers (e.g., circulating immune cells, TMB, circulating tumor cells, circulating tumor DNA, soluble factor PD-L1, tumor necrosis factor, etc.) for patients with NSCLC treated with ICIs. We also describe the potential use of these biomarkers as prognostic indicators of treatment response and toxicity.

The Role of MicroRNAs in Lung Cancer: Implications for Diagnosis and Therapy

Lung cancer is the first cause of cancer death in the world due to its high prevalence, aggressiveness, late diagnosis, lack of effective treatment and poor prognosis. It also shows high rate of recurrence, metastasis and drug resistance. All these problems highlight the urgent needs for developing new strategies using noninvasive biomarkers for early detection, metastasis and recurrence of disease. MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression post-transcriptionally. These molecules found to be abnormally expressed in increasing number of human disease conditions including cancer. miRNAs could be detected in body fluids such as blood, serum, urine and sputum, which leads us towards the idea of using them as non-invasive biomarker for cancer detection and monitoring cancer treatment and recurrence. miRNAs are found to be deregulated in lung cancer initiation and progression and could regulate lung cancer cell proliferation and invasion. In this review, we summarized recent progress and discoveries in microRNAs regulatory role in lung cancer initiation and progression. In addition, the role of microRNAs in EGFR signaling pathway regulation is discussed briefly.

Silencing lung cancer genes using miRNAs identified by 7mer-seed matching

Lung cancer (LC) is the main cause of cancer-associated deaths in both men and women globally with a very high mortality rate. The microRNAs (miRNAs) are a class of noncoding RNAs consisting of 18-25 nucleotides. They inhibit translation of protein through binding to complementary target mRNAs. The non-coding miRNAs are recognized as potent biomarkers for detection, development and treatment of malignancy. In this study, we screened a set of 12 genes over expressed in small cell lung cancer, non small cell lung cancer and the genes involved in both categories and their binding sites for human miRNAs as no work was reported yet. Screening of human miRNAs revealed that a few genes showed numerous miRNA binding sites. Free energy values of mRNA sequences revealed that they might acquire compact folded structure causing complexity for miRNAs to interact. GC content in the target site was relatively higher than that of their flanks. It was observed through analysis of cosine similarity metric and compAI parameters that the genes related to lung cancer were encoded with non optimal codons and thus might be translationally less efficient for producing polypeptides. Gene ontology analysis was carried out to understand the diverse functions of these 12 genes.

SARS-CoV-2 encoded microRNAs are involved in the process of virus infection and host immune response

The outbreak of COVID-19 caused by SARS-CoV-2 is spreading worldwide, with the pathogenesis mostly unclear. Both virus and host-derived microRNA (miRNA) play essential roles in the pathology of virus infection. This study aims to uncover the mechanism for SARS-CoV-2 pathogenicity from the perspective of miRNA. We scanned the SARS-CoV-2 genome for putative miRNA genes and miRNA targets and conducted in vivo experiments to validate the virus-encoded miRNAs and their regulatory role on the putative targets. One of such virus-encoded miRNAs, MR147-3p, was overexpressed that resulted in significantly decreased transcript levels of all of the predicted targets in human,i.e., EXOC7, RAD9A, and TFE3 in the virus-infected cells. The analysis showed that the immune response and cytoskeleton organization are two of the most notable biological processes regulated by the infection-modulated miRNAs. Additionally, the genomic mutation of SARS-CoV-2 contributed to the changed miRNA repository and targets, suggesting a possible role of miRNAs in the attenuated phenotype of SARS-CoV-2 during its evolution. This study provided a comprehensive view of the miRNA-involved regulatory system during SARS-CoV-2 infection, indicating possible antiviral therapeutics against SARS-CoV-2 through intervening miRNA regulation.

Diagnostic and Therapeutic Implications of microRNAs in Non-Small Cell Lung Cancer

microRNAs (miRNAs), endogenous suppressors of target mRNAs, are deeply involved in every step of non-small cell lung cancer (NSCLC) development, from tumor initiation to progression and metastasis. They play roles in cell proliferation, apoptosis, angiogenesis, epithelial-to-mesenchymal transition, migration, invasion, and metastatic colonization, as well as immunosuppression. Due to their versatility, numerous attempts have been made to use miRNAs for clinical applications. miRNAs can be used as cancer subtype classifiers, diagnostic markers, drug-response predictors, prognostic markers, and therapeutic targets in NSCLC. Many challenges remain ahead of their actual clinical application; however, when achieved, the use of miRNAs in the clinic is expected to enable great progress in the diagnosis and treatment of patients with NSCLC.

Regulatory role of microRNAs in cancer through Hippo signaling pathway

Cancer is the major cause of death worldwide in countries of all income levels. The Hippo signaling pathway is a Drosophila kinase gene that was identified to regulate organ size, cell regeneration, and contribute to tumorigenesis. A huge variety of extrinsic and intrinsic signals regulate the Hippo signaling pathway. The Hippo signaling pathway consists of a wide array of components that merge numerous signals such as mechanical signals to address apoptosis resistance, cell proliferation, cellular outputs of growth, cell death and survival at cellular and tissue level. Recent studies have shed new light on the regulatory role of microRNAs in Hippo signaling and how they contribute to cancer progression. MicroRNAs influence various cancer-related processes such as, apoptosis, proliferation, migration, cell cycle and metabolism. Inhibition and overexpression of miRNAs via miRNA mimics and miRNA inhibitors, respectively, can uncover a hopeful and reliable insight for treatment and early diagnosis of cancer patients. In this review we will discuss our current understanding of regulatory role of miRNAs in Hippo signaling pathway.

Overexpression of microRNA-203 can downregulate survivin and function as a potential therapeutic target in papillary thyroid cancer

Papillary thyroid cancer (PTC) is the most common type of thyroid carcinoma. PTC has a considerably high five-year survival rate; however, the possibility of recurrence is also high. Therefore, there is a requirement to clarify the molecular mechanism of PTC to promote understanding regarding the development of the disease and further improve prognosis. A number of studies have demonstrated that microRNAs (miRNAs or miRs) contribute to the progression of PTC. The present study revealed that the expression level of miR-203 was significantly lower in PTC tissues and cell lines compared with in the normal controls. In addition, inhibition of miR-203 was identified to be associated with an overexpression of survivin, which was observed in PTC samples. miR-203 regulates the expression of Bcl-2 via its downstream regulator survivin. Furthermore, the present study identified that inhibition of miR-203 histone acetylation was associated with high expression levels of miR-203 in PTC tissue samples. In summary, the results indicate that miR-203 functions as a biomarker and may serve as a candidate target for the development of novel therapeutic strategies to treat PTC.

miR-944 inhibits lung adenocarcinoma tumorigenesis by targeting STAT1 interaction

Lung adenocarcinoma (LAC) is a leading cause of cancer-associated mortalities, particularly in developed countries. The aberrant expression of microRNAs (miRNAs) has been proven to regulate numerous diseases in the past two decades. miRNAs have been identified in almost all human cancer types. In the present study, the role of miR-944 in LAC proliferation was examined. It was identified that miR-944 was downregulated in LAC tissues and cells, and miR-944 overexpression inhibited A549 and H1299 cell proliferation, as determined by the Cell Counting Kit-8 and colony formation assay. Signal transducer and activator of transcription 1 (STAT1) was upregulated in LAC tissues and cells. Kaplan-Meier analysis demonstrated that the 5-year overall survival in patients with high STAT1 levels was significantly reduced, compared with patients with negative and low STAT1 expression. STAT1 was the direct target of miR-944. Additionally, a miR-944 mimic inhibited A549 cell growth in vitro. Collectively, these data demonstrate that miR-944 serves a pivotal role in LAC tumor growth by targeting STAT1. The data obtained indicated that miR-944 may be a novel biomarker and could result in potential therapies for LAC.

Predictive role of plasmatic biomarkers in advanced non-small cell lung cancer treated by nivolumab

Immune checkpoint inhibitors, as nivolumab, are used in advanced non-small cell lung cancer (NSCLC). However, no associated biomarker is validated in clinical practice with this drug. We investigated herein immune-related blood markers in patients with advanced NSCLC treated with nivolumab. Plasma of 43 consecutive patients were prospectively collected at time of the diagnosis of cancer, at the initiation of nivolumab and at the first tumour evaluation (2 months). Concentrations of PD-L1 (sPD-L1), soluble PD-L2 (sPD-L2), Interleukine-2 (sIl-2), Interferon-gamma (sIFN-γ), and Granzyme B (sGranB) were quantified by ELISA. Cell free RNA was quantified by Reverse Transcriptase -PCR), and plasmatic microRNAs (miRNAs) were evaluated by targeted sequencing. Expression of PD-L1 on tumour biopsies was performed by immunohistochemistry using E13LN. High sPD-L1 at 2 months and increase of sPD-L1 concentrations were associated with poor response and absence of clinical benefit (nivolumab treatment less than 6 months). The variation of sPD-L1 concentrations were confirmed by RNA quantification. sPD-L1 concentrations were not correlated with PD-L1 expression on corresponding tumour samples. Low sGranB at nivolumab initiation was also associated with poor response. High sPD-L1 and low sGranB were associated with poor progression-free survival (PFS) and overall survival (OS). Low sPD-L2, low sIl-2 and high sIFN-γ were associated with grade 3-4 toxicities. Finally, miRNA screening showed that patients with clinical benefit (n = 9) had down-expression of miRNA-320b and -375 compared to patients with early progression at 2 months (n = 9). In conclusion, our results highlight the interest of circulating biomarkers in patients treated with nivolumab.

Antitumor activity of kinetochore-associated protein 2 siRNA against lung cancer patient-derived tumor xenografts

It has been widely reported that patient-derived tumor xenografts (PDXs) are more similar to tumor tissues than conventional cancer cell lines. Kinetochore-associated protein 2 (KNTC2) is known to be upregulated specifically in tumor tissues of cancer patients and is recognized as a potential target for cancer therapy. Previously, in vivo antitumor activities of KNTC2 short interfering RNA encapsulated into a lipid nanoparticle (KNTC2-LNP) were reported in orthotopic hepatocellular carcinoma mouse models. However, it remains unclear whether KNTC2-LNP exhibits antitumor activities against lung cancer PDXs. In the present study, the antitumor activities of KNTC2-LNP were clarified in a three-dimensional culture system and a subcutaneous tumor model of lung cancer PDX, LC-60, which was resistant to erlotinib. Growth inhibitory activities of KNTC2-LNP were associated with knockdown activities. Furthermore, KNTC2-LNP also exhibited in vivo antitumor activity against another lung cancer PDX, LC-45, which was sensitive to erlotinib. These results suggest that KNTC2 is a promising target for patients with lung cancer.