Salivary microRNAs identified by small RNA sequencing as potential predictors of response to intensity-modulated radiotherapy in head and neck cancer patients

PURPOSE

Progress in radiation therapy of head and neck squamous cell carcinomas (HNSCCs) is logically linked to the development of molecular predictors that would help to enhance individually tailored treatment. MicroRNA (miRNA) expression profiles in tumors have repeatedly been tested to optimize the molecular diagnostics of HNSCC. In addition to tumor tissues, miRNAs are stably present in body fluids, including saliva, and can thus be collected non-invasively. The aim of our current study was to evaluate whether salivary miRNAs have potential as response predictors in HNSCC patients treated with intensity modulated radiation therapy (IMRT).

METHODS

In total 48 HNSCC patients treated by definitive IMRT were enrolled in our prospective study. To identify predictive salivary miRNAs, we used small RNA sequencing in 14 saliva samples of HNSCC patients and qRT-PCR validation of selected miRNA candidates in an independent set of 34 patients.

RESULTS

We found that salivary miR-15a-5p and miR-15b-5p exhibited differential levels between patients with and without complete remission (p = 0.025 and p = 0.028, respectively). Subsequent Kaplan-Meier analysis confirmed that patients with higher levels of miR-15a-5p reached a significantly longer locoregional progression-free survival (LPFS) than those with low levels (p = 0.024). Finally, multivariate Cox regression analysis revealed that miR-15a-5p may serve as an independent predictive biomarker of LPFS in HNSCC patients treated with IMRT (HR 0.104; 95% CI 0.004-0.911; p = 0.04).

CONCLUSIONS

We conclude that salivary miR-15a-5p may represent a potential biomarker for individualized treatment decision-making in HNSCC patients.

Critical function of circular RNAs in lung cancer

Lung cancer is one of the main causes of cancer-related death in the world, especially due to its frequency and ineffective therapeutically approaches in the late stages of the disease. Despite the recent advent of promising new targeted therapies, lung cancer diagnostic strategies still have difficulty in identifying the disease at an early stage. Therefore, the characterizations of more sensible and specific cancer biomarkers have become an important goal for clinicians. Circular RNAs (circRNAs), a type of RNA with covalently closed continuous loop structures that display high structural resistance and tissue specificity pointed toward a potential biomarker role. Current investigations have identified that circRNAs have a prominent function in the regulation of oncogenic pathways, by regulating gene expression both at transcriptional and post-transcriptional level. The aim of this review is to provide novel information regarding the implications of circRNAs in lung cancer, with an emphasis on the role in disease development and progression. Initially, we explored the potential utility of circRNAs as biomarkers, focusing on function, mechanisms, and correlation with disease progression in lung cancer. Further, we will describe the interaction between circRNAs and other non-coding species of RNA (particularly microRNA) and their biological significance in lung cancer. Describing the nature of these interactions and their therapeutic potential will provide additional insight regarding the altered molecular landscape of lung cancer and consolidate the potential clinical value of these circular transcripts. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.

Hepatocellular carcinoma: Gene expression profiling and regulation of xenobiotic-metabolizing cytochromes P450

Hepatocellular carcinoma (HCC) remains a highly prevalent and deadly disease, being among the top causes of cancer-related deaths worldwide. Despite the fact that the liver is the major site of biotransformation, studies on drug metabolizing enzymes in HCC are scarce. It is known that malignant transformation of hepatocytes leads to a significant alteration of their metabolic functions and overall deregulation of gene expression. Advanced stages of the disease are thus frequently associated with liver failure, and severe alteration of drug metabolism. However, the impact of dysregulation of metabolic enzymes on therapeutic efficacy and toxicity in HCC patients is largely unknown. Here we demonstrate a significant down-regulation in European Caucasian patients of cytochromes P450 (CYPs), the major xenobiotic-metabolizing enzymes, in HCC tumour samples as compared to their surrounding non-cancerous (reference) tissue. Moreover, we report for the first time the association of the unique CYP profiles with specific transcriptome changes, and interesting correlations with expression levels of nuclear receptors and with the histological grade of the tumours. Integrated analysis has suggested certain co-expression profiles of CYPs with lncRNAs that need to be further characterized. Patients with large tumours with down-regulated CYPs could be more vulnerable to drug toxicity; on the other hand, such tumours would eliminate drugs more slowly and should be more sensitive to pharmacotherapy (except in the case of pro-drugs where activation is necessary).

Comprehensive Molecular Profiling for Relapsed/Refractory Pediatric Burkitt Lymphomas-Retrospective Analysis of Three Real-Life Clinical Cases-Addressing Issues on Randomization and Customization at the Bedside

In order to identify reasons for treatment failures when using targeted therapies, we have analyzed the comprehensive molecular profiles of three relapsed, poor-prognosis Burkitt lymphoma cases. All three cases had resembling clinical presentation and histology and all three patients relapsed, but their outcomes differed significantly. The samples of their tumor tissue were analyzed using whole-exome sequencing, gene expression profiling, phosphoproteomic assays, and single-cell phosphoflow cytometry. These results explain different treatment responses of the three histologically identical but molecularly different tumors. Our findings support a personalized approach for patient with high risk, refractory, and rare diseases and may contribute to personalized and customized treatment efforts for patients with limited treatment options like relapsed/refractory Burkitt lymphoma.

MiR-376b-3p Is Associated With Long-term Response to Sunitinib in Metastatic Renal Cell Carcinoma Patients

BACKGROUND/AIM

Sunitinib is a tyrosine kinase inhibitor routinely used as first-line therapy in metastatic renal cell carcinoma (mRCC). Emerging evidence suggests that microRNAs (miRNAs) could be suitable biomarkers with predictive potential in mRCC. The aim of this study was to identify miRNA-based predictive biomarkers of therapy response to avoid unnecessary therapy to non-responding patients.

PATIENTS AND METHODS

High-throughput miRNA microarray profiling was performed on a cohort of 47 patients treated with sunitinib. Validation of candidate miRNAs was carried out on an independent cohort of 132 mRCC patients using qRT-PCR.

RESULTS

Out of 158 miRNAs (65 down-regulated, 93 up-regulated), six miRNAs were chosen for independent validation and miR-376b-3p was confirmed to be differentially expressed in tumors of patients with primary resistance versus long-term response (p<0.0002).

CONCLUSION

A predictive miRNA associated with progression-free survival in metastatic renal cell carcinoma patients treated with sunitinib was identified.

Assessment of Tumor Mutational Burden in Pediatric Tumors by Real-Life Whole-Exome Sequencing and In Silico Simulation of Targeted Gene Panels: How the Choice of Method Could Affect the Clinical Decision?

Background: Tumor mutational burden (TMB) is an emerging genomic biomarker in cancer that has been associated with improved response to immune checkpoint inhibitors (ICIs) in adult cancers. It was described that variability in TMB assessment is introduced by different laboratory techniques and various settings of bioinformatic pipelines. In pediatric oncology, no study has been published describing this variability so far. Methods: In our study, we performed whole exome sequencing (WES, both germline and somatic) and calculated TMB in 106 patients with high-risk/recurrent pediatric solid tumors of 28 distinct cancer types. Subsequently, we used WES data for TMB calculation using an in silico approach simulating two The Food and Drug Administration (FDA)-approved/authorized comprehensive genomic panels for cancer. Results: We describe a strong correlation between WES-based and panel-based TMBs; however, we show that this high correlation is significantly affected by inclusion of only a few hypermutated cases. In the series of nine cases, we determined TMB in two sequentially collected tumor tissue specimens and observed an increase in TMB along with tumor progression. Furthermore, we evaluated the extent to which potential ICI indication could be affected by variability in techniques and bioinformatic pipelines used for TMB assessment. We confirmed that this technological variability could significantly affect ICI indication in pediatric cancer patients; however, this significance decreases with the increasing cut-off values. Conclusions: For the first time in pediatric oncology, we assessed the reliability of TMB estimation across multiple pediatric cancer types using real-life WES and in silico analysis of two major targeted gene panels and confirmed a significant technological variability to be introduced by different laboratory techniques and various settings of bioinformatic pipelines.

Personalized Treatment of H3K27M-Mutant Pediatric Diffuse Gliomas Provides Improved Therapeutic Opportunities

Diffuse gliomas with K27M histone mutations (H3K27M glioma) are generally characterized by a fatal prognosis, particularly affecting the pediatric population. Based on the molecular heterogeneity observed in this tumor type, personalized treatment is considered to substantially improve therapeutic options. Therefore, clinical evidence for therapy, guided by comprehensive molecular profiling, is urgently required. In this study, we analyzed feasibility and clinical outcomes in a cohort of 12 H3K27M glioma cases treated at two centers. Patients were subjected to personalized treatment either at primary diagnosis or disease progression and received backbone therapy including focal irradiation. Molecular analyses included whole-exome sequencing of tumor and germline DNA, RNA-sequencing, and transcriptomic profiling. Patients were monitored with regular clinical as well as radiological follow-up. In one case, liquid biopsy of cerebrospinal fluid (CSF) was used. Analyses could be completed in 83% (10/12) and subsequent personalized treatment for one or more additional pharmacological therapies could be recommended in 90% (9/10). Personalized treatment included inhibition of the PI3K/AKT/mTOR pathway (3/9), MAPK signaling (2/9), immunotherapy (2/9), receptor tyrosine kinase inhibition (2/9), and retinoic receptor agonist (1/9). The overall response rate within the cohort was 78% (7/9) including one complete remission, three partial responses, and three stable diseases. Sustained responses lasting for 28 to 150 weeks were observed for cases with PIK3CA mutations treated with either miltefosine or everolimus and additional treatment with trametinib/dabrafenib in a case with BRAFV600E mutation. Immune checkpoint inhibitor treatment of a case with increased tumor mutational burden (TMB) resulted in complete remission lasting 40 weeks. Median time to progression was 29 weeks. Median overall survival (OS) in the personalized treatment cohort was 16.5 months. Last, we compared OS to a control cohort (n = 9) showing a median OS of 17.5 months. No significant difference between the cohorts could be detected, but long-term survivors (>2 years) were only present in the personalized treatment cohort. Taken together, we present the first evidence of clinical efficacy and an improved patient outcome through a personalized approach at least in selected cases of H3K27M glioma.

Urinary MicroRNAs as Emerging Class of Noninvasive Biomarkers

MicroRNAs (miRNAs) are endogenous noncoding RNAs, which regulate gene expression on the post-transcriptional level. Since miRNAs are involved in the regulation of apoptosis, cellular proliferation, differentiation, and other important cellular processes, their deregulation is important for the development of a wide range of diseases including cancer. Apart from tissue, specific disease-related miRNA signatures can be found in body fluids as well. Especially for urologic diseases or injuries, urine miRNAs represent a promising group of biomarkers. Despite a large number of studies describing the importance of urinary miRNAs, there is a lack of recommendations for urine management and subsequent miRNA analysis. Thus, in this chapter, we aim to describe the origin and functions of urinary miRNAs and discuss the technical aspects of their detection including the pre-analytical phase principles and new directions in quantification, which could forward urine miRNA into clinical practice.

GENE-03. SPECIFIC SIGNATURES OF microRNA IN CEREBROSPINAL FLUID OF PATIENTS WITH PRIMARY BRAIN TUMORS AND METASTASES

Cerebrospinal fluid (CSF) baths extracellular environment of the central nervous system, and thus, it is ideal source of tumor diagnostic biomarkers like microRNAs (miRNAs), short non-coding RNAs involved in the pathogenesis of many cancers. As dysregulated levels of brain tumor specific miRNAs have been already observed in CSF, analysis of CSF miRNAs in brain tumor patients might help to develop new diagnostic platform. Next-Generation sequencing (NGS) was performed for analysis of small RNAs in 89 CSF samples taken from 32 glioblastomas (GBM), 14 low-grade gliomas (LGG), 11 meningiomas, 13 brain metastases and 19 non-tumor donors. Subsequently, according to NGS results levels of 10 miRNAs were measured in independent set of CSF samples (41 GBM, 44 meningiomas, 12 brain metastases and 20 non-tumor donors) using TaqMan Advanced miRNA Assays. NGS analysis revealed 22, 12 and 35 CSF miRNAs with significantly different levels in GBM, meningiomas, and brain metastases (adj.p < 0.0005, adj.p < 0.01, and adj.p < 0.005) respectively, in comparison with non-tumor CSF samples. Subsequent validation of selected CSF miRNAs has confirmed different levels of 7 miRNAs in GBM, 2 in meningiomas, and 2 in brain metastases compared to non-tumors. Panel of miR-30e-5p and miR-140-5p was able to distinguish brain metastases with 65% sensitivity and 100% specificity compared to non-tumor samples (AUC = 0.8167); panel of miR-21-3p and miR-196-5p classified metastatic patients with 78% sensitivity and 92 % specificity in comparison to GBM (AUC = 0.90854) and with 75% sensitivity and 83% specificity compared to meningiomas (AUC = 0.84848). We have observed that CSFs from patients with various primary brain tumors and metastases are characterized by specific miRNA signatures. This work was supported by the Ministry of Health, Czech Republic grant nr. NV18-03-00398 and the Ministry of Education, Youth and Sports, Czech Republic under the project CEITEC 2020 (LQ1601).

ColPortal, an integrative multiomic platform for analysing epigenetic interactions in colorectal cancer

Colorectal cancer (CRC) is the third leading cause of cancer mortality worldwide. Different pathological pathways and molecular drivers have been described and some of the associated markers are used to select effective anti-neoplastic therapy. More recent evidence points to a causal role of microbiota and altered microRNA expression in CRC carcinogenesis, but their relationship with pathological drivers or molecular phenotypes is not clearly established. Joint analysis of clinical and omics data can help clarify such relations. We present ColPortal, a platform that integrates transcriptomic, microtranscriptomic, methylomic and microbiota data of patients with colorectal cancer. ColPortal also includes detailed information of histological features and digital histological slides from the study cases, since histology is a morphological manifestation of a complex molecular change. The current cohort consists of Caucasian patients from Europe. For each patient, demographic information, location, histology, tumor staging, tissue prognostic factors, molecular biomarker status and clinical outcomes are integrated with omics data. ColPortal allows one to perform multiomics analyses for groups of patients selected by their clinical data.

Measurement(s)	miRNA • methylation • clinical history • histology • transcription profiling assay • microbiome
Technology Type(s)	DNA sequencing • clinical monitoring • RNA sequencing • amplicon sequencing • ex vivo photography with digital image analysis • methylation profiling by array
Factor Type(s)	tumor status
Sample Characteristic - Organism	Homo sapiens

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9785795

Molecular Links between Central Obesity and Breast Cancer

Worldwide, breast cancer (BC) is the most common malignancy in women, in regard to incidence and mortality. In recent years, the negative role of obesity during BC development and progression has been made abundantly clear in several studies. However, the distribution of body fat may be more important to analyze than the overall body weight. In our review of literature, we reported some key findings regarding the role of obesity in BC development, but focused more on central adiposity. Firstly, the adipose microenvironment in obese people bears many similarities with the tumor microenvironment, in respect to associated cellular composition, chronic low-grade inflammation, and high ratio of reactive oxygen species to antioxidants. Secondly, the adipose tissue functions as an endocrine organ, which in obese people produces a high level of tumor-promoting hormones, such as leptin and estrogen, and a low level of the tumor suppressor hormone, adiponectin. As follows, in BC this leads to the activation of oncogenic signaling pathways: NFκB, JAK, STAT3, AKT. Moreover, overall obesity, but especially central obesity, promotes a systemic and local low grade chronic inflammation that further stimulates the increase of tumor-promoting oxidative stress. Lastly, there is a constant exchange of information between BC cells and adipocytes, mediated especially by extracellular vesicles, and which changes the transcription profile of both cell types to an oncogenic one with the help of regulatory non-coding RNAs.

A Comprehensive Review on MAPK: A Promising Therapeutic Target in Cancer

The mitogen-activated protein kinase (MAPK) pathway is an important bridge in the switch from extracellular signals to intracellular responses. Alterations of signaling cascades are found in various diseases, including cancer, as a result of genetic and epigenetic changes. Numerous studies focused on both the homeostatic and the pathologic conduct of MAPK signaling; however, there is still much to be deciphered in terms of regulation and action models in both preclinical and clinical research. MAPK has implications in the response to cancer therapy, particularly the activation of the compensatory pathways in response to experimental MAPK inhibition. The present paper discusses new insights into MAPK as a complex cell signaling pathway with roles in the sustenance of cellular normal conduit, response to cancer therapy, and activation of compensatory pathways. Unfortunately, most MAPK inhibitors trigger resistance due to the activation of compensatory feed-back loops in tumor cells and tumor microenvironment components. Therefore, novel combinatorial therapies have to be implemented for cancer management in order to restrict the possibility of alternative pathway activation, as a perspective for developing novel therapies based on integration in translational studies.

Current Concepts of Non-Coding RNAs in the Pathogenesis of Non-Clear Cell Renal Cell Carcinoma

Renal cell carcinoma (RCC) is a relatively rare malignancy of the urinary tract system. RCC is a heterogenous disease in terms of underlying histology and its associated underlying pathobiology, prognosis and treatment schedule. The most prevalent histological RCC subtype is clear-cell renal cell carcinoma (ccRCC), accounting for about 70-80% of all RCCs. Though the pathobiology and treatment schedule for ccRCC are well-established, non-ccRCC subtypes account for 20%-30% of RCC altogether, and their underlying molecular biology and treatment options are poorly defined. The class of non-coding RNAs-molecules that are generally not translated into proteins-are new cancer drivers and suppressors in all types of cancer. Of these, small non-coding microRNAs (miRNAs) contribute to carcinogenesis by regulating posttranscriptional gene silencing. Additionally, a growing body of evidence supports the role of long non-coding RNAs (lncRNAs) in cancer development and progression. Most studies on non-coding RNAs in RCC focus on clear-cell histology, and there is a relatively limited number of studies on non-ccRCC subtypes. The aim of this review is to give an overview of the current knowledge regarding the role of non-coding RNAs (including short and long non-coding RNAs) in non-ccRCC and to highlight possible implications as diagnostic, prognostic and predictive biomarkers.

Translational Potential of MicroRNAs for Preoperative Staging and Prediction of Chemoradiotherapy Response in Rectal Cancer

Colorectal cancer is the third most common cancer and the second cause of cancer-related deaths. Rectal cancer presents roughly one-third of all colorectal cancer cases and differs from it on both anatomical and molecular levels. While standard treatment of colon cancer patients is radical surgery, rectal cancer is usually treated with pre-operative chemoradiotherapy followed by total mesorectal excision, which requires precise estimation of TNM staging. Unfortunately, stage evaluation is based solely on imaging modalities, and they often do not correlate with postoperative pathological findings. Moreover, approximately half of rectal cancer patients do not respond to such pre-operative therapy, so they are exposed to its toxic effects without any clinical benefit. Thus, biomarkers that could precisely predict pre-operative TNM staging, and especially response to therapy, would significantly advance rectal cancer treatment—but till now, no such biomarker has been identified. In cancer research, microRNAs are emerging biomarkers due to their connection with carcinogenesis and exceptional stability. Circulating miRNAs are promising non-invasive biomarkers that could allow monitoring of a patient throughout the whole therapeutic process. This mini-review aims to summarize the current knowledge on miRNAs and circulating miRNAs involved in the prediction of response to treatment and pre-operative staging in rectal cancer patients.

In silico study of pseudoprogression in glioblastoma: collaboration of radiologists and radiation oncologists in the estimation of extent of high dose RT region

BACKGROUND AND AIM

Oncologists play a vital role in the interpretation of radiographic results in glioblastoma patients. Molecular pathology and information on radiation treatment protocols among others are all important for accurate interpretation of radiology images. One important issue that may arise in interpreting such images is the phenomenon of tumor "pseudoprogression"; oncologists need to be able to distinguish this effect from true disease progression.Exact knowledge about the location of high-dose radiotherapy region is needed for valid determination of pseudoprogression according to RANO (Response Assessment in Neuro-Oncology) criteria in neurooncology. The aim of the present study was to evaluate the radiologists' understanding of a radiotherapy high-dose region in routine clinical practice since radiation oncologists do not always report 3-dimensional isodoses when ordering follow up imaging.

METHODS

Eight glioblastoma patients who underwent postresection radiotherapy were included in this study. Four radiologists worked with their pre-radiotherapy planning MR, however, they were blinded to RT target volumes which were defined by radiation oncologists according to current guidelines. The aim was to draw target volume for high dose RT fields (that is the region, where they would consider that there may be a pseudoprogression in future MRI scans). Many different indices describing structure differences were analyzed in comparison with original per-protocol RT target volumes.

RESULTS

The median volume for RT high dose field was 277 ccm (range 218 to 401 ccm) as defined per protocol by radiation oncologist and 87 ccm (range 32-338) as defined by radiologists (median difference of paired difference 31%, range 15-112%). The Median Dice index of similarity was 0.46 (range 0.14 - 0.78), the median Hausdorff distance 25 mm.

CONCLUSION

Continuing effort to improve education on specific procedures in RT and in radiology as well as automatic tools for exporting RT targets is needed in order to increase specificity and sensitivity in response evaluation.

Abstract 3575: Dysregulated expression of lncRNAs in glioblastoma multiforme and their association with overall survival

Introduction: Glioblastoma multiforme (GBM) is the most frequent primary brain malignancy of astrocytic origin. The prognosis remains very poor with the median overall survival (OS) being between 12 and 16 months from diagnosis despite early use of conventional medical therapy. Identifying new therapeutic targets, as well as prognostic and predictive biomarkers for accurate stratification of patients is therefore of utmost importance. Long non-coding RNAs (lncRNAs) are regulators of gene expression having critical impact on both physiological processes and the molecular pathology of GBM, indicating their potential as biomarkers and therapeutic targets.

Material and Methods: Our study included 219 GBM patients and 29 patients with non-dominant anterior temporal cortexes resected during surgery for intractable epilepsy. Informed consent approved by the local Ethical Commission was obtained from each patient. RNA (RIN &gt; 8) from 77 specimens was used for next-generation RNA sequencing (RNAseq). rRNA depletion and cDNA library preparation were done with RiboCop rRNA Depletion Kit V1.2 (Lexogen) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB), respectively. RNAseq was performed using NextSeq 500 High Output Kit and NextSeq 500 instrument (both Illumina). 8,414 lncRNAs and their sequential variants with non-zero RPKM at least in one sample were statistically evaluated. The alignment and target counts were performed with CLC genomic workbench. Selected significantly dysregulated lncRNAs between GBM and non-tumor controls were analyzed in a larger cohort of 188 specimens by qRT-PCR and the expression data normalized to PPIA was then evaluated by Mann-Whitney U test.

Results: Statistical analysis revealed 538 (P &lt; 0.001) dysregulated lncRNAs in GBMs compared to non-tumor brain tissue samples. The expression of top 10 downregulated lncRNAs (SNAI3-AS1, LINC00882, RFPL1S, MIR137HG, TTLL7-IT1, PWAR6, LINC00634, LINC00632, DGCR5, LINC00982; logFC ≤ -2; P &lt; 0.001) and 1 upregulated lncRNA (BTN2A3P; logFC ≥ 2; P &lt; 0.001) in GBM and non-tumor controls was successfully validated by qRT-PCR (P &lt; 0.0001). Moreover, the statistical analysis revealed 22 lncRNAs significantly dysregulated between patients with OS less than 12 months and those with OS equal or more than 12 months (P &lt; 0.01).

Conclusion: We observed significant dysregulation of lncRNAs in GBM tissues compared to non-tumor controls based on the results of both RNASeq and qRT-PCR. We also found 22 lncRNAs to be dysregulated in relation to overall survival. Our study indicates that lncRNAs could serve as promising diagnostic and prognostic biomarkers in GBM. This work was supported by Ministry of Health of the Czech Republic grant nr. NV18-03-00398, grant of Czech Grant Agency nr. 17-17636S, and by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601).

Citation Format: Marek Vecera, Jan Oppelt, Lenka Radova, Radim Lipina, Stefan Reguli, Martin Smrcka, Radim Jancalek, Michal Filip, Marketa Hermanova, Leos Kren, Jiri Sana, Alena Kopkova, Julia Kovacova, Ondrej Slaby. Dysregulated expression of lncRNAs in glioblastoma multiforme and their association with overall survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3575.

Abstract 1806: Global analysis and validation of miRNA levels in cerebrospinal fluid of brain tumor patients

Introduction. Incidence rate of primary brain tumors and brain metastases counts yearly around 40 patients per 100 000 persons in the world and is still growing. Prognosis and therapy differs between brain tumor types and, therefore, accurate and early diagnosis might improve survival and life quality of patients. However, current diagnostic approaches are limited by localization and tissue heterogeneity of brain tumors. Cerebrospinal fluid (CSF) bathes central nervous system (CNS) and thus is supposed to reflect all pathological conditions. From this perspective, CSF looks as ideal source of diagnostic biomarkers of brain tumors. MicroRNAs, short non-coding RNAs involved in the pathogenesis of many cancers including brain tumors, might represent group of new biomarkers. In addition, dysregulated levels of brain tumor specific miRNAs have been already observed also in CSF. Following these facts, analysis of CSF miRNAs in brain tumor patients promises a new diagnostic approach enabling more accurate diagnosis.

Material and methods. Next-generation sequencing was performed for analysis of small RNAs in 89 CSF samples taken from 32 GBM, 14 low-grade glioma (LGG), 11 meningioma, 13 brain metastasis patients and 19 non-tumor donors. CleanTag Small RNA Library Prep Kit (TriLink BioTechnologies) was used for cDNA library preparation. NextSeq 500 instrument together with Next 500/550 High Output v2 Kit - 75 cycles (both Illumina) were used for final sequencing analysis. Subsequently, according to NGS results we measured levels of 13 miRNAs in independent set of CSF samples (35 GBM, 42 meningiomas, 8 metastasis patients and 19 control) using TaqMan Advanced miRNA Assays (ThermoFisher Scientific).

Results. NGS analysis revealed 25, 3, 2 and 14 CSF miRNAs significantly differently expressed in GBM, meningiomas, LGG and metastasis patients (p &lt; 0.001, for LGG p &lt; 0.05), respectively, in comparison with control CSF samples. In addition, 6 miRNAs showed different levels between GBM and LGG (p &lt; 0.05). Subsequent validation of selected CSF miRNAs has confirmed different levels of 7 miRNAs in GBM (miR-10a, miR-196a, miR-196b, miR-30e, miR-30c, miR-7b, miR-7c), 3 in meningioma (miR-140, miR-21, miR-30e) and 2 in brain metastasis (miR-30e and miR-7c) compared to control CSF samples (p &lt; 0.05). Validation of miRNA levels in LGG CSF samples is in progress and will be part of the poster presentation.

Conclusion. We have observed that CSF from patients with various brain tumors (GBM, LGG, meningioma, and brain metastasis) is characterized by specific miRNA signature. Our results suggest potential of CSF miRNAs to be useful biomarkers in brain tumors. This work was supported by Ministry of Health of the Czech Republic grant nr. NV18-03-00398, grant of Czech Grant Agency nr. 17-17636S and by the Ministry of Education, Youth and Sports of the Czech Republic under the project CEITEC 2020 (LQ1601).

Citation Format: Alena Kopkova, Jiri Sana, Marek Vecera, Tana Machackova, Pavel Fadrus, Julia Kovacova, Ondrej Slaby. Global analysis and validation of miRNA levels in cerebrospinal fluid of brain tumor patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1806.

Abstract 1800: miR-376b and miR-4668 predict therapeutic response to sunitinib in metastatic renal cell carcinoma

Introduction: Metastatic renal cell carcinoma (mRCC) is routinely treated with sunitinib, a tyrosine kinase inhibitor (TKI) of VEGF signalisation. Although disease eventually progresses in most mRCC patients, length of progression-free survival (PFS) is ranging from few weeks up to more than 24 months. Patients with initial resistance to sunitinib could be redirected to other therapeutical options, as there are several other TKIs available for use in second and third line. However, without a reliable biomarker no result can be predicted. MicroRNAs (miRNAs) belong to class of short non-coding RNAs and could serve as biomarkers of therapy response due to their unique character and presence in tissues and body fluids. Their biomarker potential has been discussed concerning many diseases including mRCC, but current knowledge is very weak, has several discrepancies and is acquired on relatively small cohorts.

Material and method: Candidate microRNAs have been chosen based on global expression profiling using Affymetrix GeneChip 4.0 in 47 samples of FFPE mRCC tissue of patients treated with sunitinib (good response n=25, PFS longer than 17 months; poor response n=22, PFS shorter than 9 months). Validation was performed using qRT-PCR TaqMan assays on an independent cohort of 136 FFPE samples from mRCC patients treated with sunitinib with variable length of PFS. Local ethical committees at all involved centres approved the study protocol. The study was performed according to the World Medical Association Declaration of Helsinki and all patients signed an informed consent.

Results and discussion: Of all tested miRNAs, expression of miR-4668-5p and miR-376b was the most significantly deregulated in non-responding patients with high statistical significance (p&gt;0,005) and combined AUC higher than 0,8. Although other independent validations are necessary, microRNAs presented here seem to be very promising as tools for therapy personalization.

Conclusion: We have successfully validated miR-4668-5p and miR-376b to have predictive potential in estimation of therapeutical response to sunitinib. Further functional analyses could shed more light on their involvement in development of therapy resistance. This work was supported by Ministry of Health of the Czech Republic, grant nr. NV18-03-00554. All rights reserved.

Citation Format: Julia Kovacova, Jaroslav Juracek, Alexandr Poprach, Tomas Buchler, Ondrej Fiala, Lenka Radova, Marek Svoboda, Alena Kopkova, Marek Vecera, Ondrej Slaby. miR-376b and miR-4668 predict therapeutic response to sunitinib in metastatic renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1800.

MicroRNA-15b-5p Predicts Locoregional Relapse in Head and Neck Carcinoma Patients Treated With Intensity-modulated Radiotherapy

BACKGROUND/AIM

Head and neck cancers are a heterogenous group of epithelial tumors represented mainly by squamous cell carcinomas (HNSCC), which are the sixth most common type of cancer worldwide. Surgery together with radiotherapy (RT) is among the basic treatment modalities for most HNSCC patients. Various biomarkers aiming to predict patients' response to RT are currently investigated. The reason behind this effort is, on one hand, to distinguish radioresistant patients that show weak benefit from RT and, on the other hand, reduce the ionizing radiation dose in less aggressive radiosensitive HNSCC with possibly less acute or late toxicity.

MATERIALS AND METHODS

A total of 94 HNSCC patients treated by definitive intensity-modulated radiotherapy were included in our retrospective study. We used a global expression analysis of microRNAs (miRNAs) in 43 tumor samples and validated a series of selected miRNAs in an independent set of 51 tumors.

RESULTS

We identified miR-15b-5p to be differentially expressed between patients with short and long time of locoregional control (LRC). Kaplan-Meier analysis confirmed that HNSCC patients with higher expression of miR-15b-5p reach a significantly longer locoregional relapse-free survival compared to patients expressing low levels. Finally, multivariable Cox regression analysis revealed that miR-15b-5p is an independent predictive biomarker of LRC in HNSCC patients (HR=0.25; 95% CI=0.05-0.78; p<0.016).

CONCLUSION

miR-15b-5p represents a potentially helpful biomarker for individualized treatment decisions concerning the management of HNSCC patients.

Identification of microRNA signatures in umbilical cord blood associated with maternal characteristics

Background

Umbilical cord blood could serve as useful source of blood markers enabling more efficient and reliable prenatal and neonatal diagnostics. MicroRNAs (miRNAs) are ubiquitous in body fluids where they were used for detecting and monitoring various physiological and pathological conditions. In this descriptive study, we aimed to identify changes in miRNA expression profiles associated with basic maternal somatic and epidemiological characteristics.

Methods

Study is based on 24 mothers from the Pilot phase of CELSPAC: TNG (Central European Longitudinal Studies of Parents and Children: The Next Generation) study. Cord blood was collected at time of delivery and global miRNA profiling was performed using microRNA Ready-to-use PCR Human Panel I+II TaqMan microarrays. Expression profiles were statistically evaluated in relation to maternal age, BMI, pregnancy weight gain, blood type, Rh factor status, allergies during pregnancy, addictive substance abuse and smoking status.

Results

We analyzed expression of 752 human mature miRNAs in 24 samples of umbilical cord blood. For all maternal characteristics tested we described a specific signature of significantly deregulated miRNAs (P < 0.05). Analysis revealed seven miRNA associated with maternal age (three increased and four decreased in women younger than 35 years), 14 miRNAs associated with BMI status (five miRNAs increased and nine miRNAs decreased in women with BMI > 25) and nine miRNAs associated with maternal weight gain during pregnancy (eight miRNAs increased, and one miRNA decreased in women with weight gain < 12 kg). Additionally, 17 miRNAs correlated to blood type (two miRNAs decreased in blood type A, 11 increased in blood type B, two miRNAs increased in blood type AB and two miRNAs increased in blood type 0) and 17 miRNAs to Rh status of mother. We also detected seven miRNAs deregulated in umbilical cord blood of women with allergy (four increased and three decreased in women with allergy), four miRNAs associated to addictive substance abuse status (two up- and two downregulated in women with addictive substance abuse) and eight miRNAs associated with maternal cigarette smoking during pregnancy.

Conclusions

We successfully described differences in miRNA profiles in umbilical cord blood associated with basic characteristics connected with mother. Our data suggest that miRNAs in umbilical cord blood are detectable and associated with a wide range of maternal characteristics. These results indicate that miRNAs could potentially serve, and should be studied, as biomarkers for screening and diagnosis of pregnancy-associated complications and pathologies.

Correction to: Intervertebral disc penetration by antibiotics used prophylactically in spinal surgery: implications for the current standards and treatment of disc infections

Unfortunately, the complete conflict of interest statement was missed out in the original publication. The same is given below.

Evaluation of miRNA detection methods for the analytical characteristic necessary for clinical utilization

miRNAs are promising biomarkers but methods for their measurement are not clear. We therefore examined three miRNA detection technologies and considered the analytical characteristics essential for clinical utilization. TaqMan assays, SplintR-qPCR and miREIA were compared for their absolute quantification bias, conformity and robustness. Absolute concentrations of miR-142-5p, miR-23a-3p and miR-93-5p were measured with all three methods using 30 samples. Robustness was evaluated by measurement of miR-21-5p in five uniform experiments. Correlations were miRNA-specific, but we observed a different absolute concentration range in RT-qPCR (fmol/μl) and methods evading the RT process (amol/μl). Consistently, RT-less methods reported better robustness (CV 8-19%) than RT-qPCR (CV 39-50%). The calibration curve in TaqMan Advanced assay was influenced by dilution media. Methods avoiding RT seem to be a promising future alternative for miRNA measurement.