ABSTRACT
Anaplastic thyroid carcinoma is arguably the most lethal human malignancy. It often co-occurs with differentiated thyroid cancers, yet the molecular origins of its aggressivity are unknown. We sequenced tumor DNA from 329 regions of thyroid cancer, including 213 from patients with primary anaplastic thyroid carcinomas. We also whole genome sequenced 9 patients using multi-region sequencing of both differentiated and anaplastic thyroid cancer components. Using these data, we demonstrate thatanaplastic thyroid carcinomas have a higher burden of mutations than other thyroid cancers, with distinct mutational signatures and molecular subtypes. Further, different cancer driver genes are mutated in anaplastic and differentiated thyroid carcinomas, even those arising in a single patient. Finally, we unambiguously demonstrate that anaplastic thyroid carcinomas share a genomic origin with co-occurring differentiated carcinomas and emerge from a common malignant field through acquisition of characteristic clonal driver mutations.
Subject(s)
Adenocarcinoma , Thyroid Carcinoma, Anaplastic , Thyroid Neoplasms , Humans , Thyroid Carcinoma, Anaplastic/genetics , Thyroid Carcinoma, Anaplastic/pathology , Thyroid Neoplasms/genetics , Thyroid Neoplasms/pathology , Mutation/genetics , GenomicsABSTRACT
Oral squamous cell carcinoma (OSCC) remains an understudied and significant global cancer killer and dismal survival rates have not changed in decades. A better understanding of the molecular basis of OSCC progression and metastasis is needed to develop new approaches for treating this disease. The supportive network surrounding cancer tumor cells known as the tumor microenvironment (TME) has gained increasing interest lately since it performs essential protumorigenic functions. Cancer-associated fibroblasts (CAFs) are one of the main cell types in the TME and are known to play a key role in influencing the biological behavior of tumors. CAFs present a heterogeneity both in phenotype as well as functions, leading to the suggestion of different CAF subtypes in several cancer forms. The task to subtype CAFs in OSCC has, however, just begun, and there is today no united way of subtyping CAFs in this disease. This review aims to define the features of CAFs and to summarize CAF subtype research in malignancy with focus on OSCC including aspects as disease prognosis and therapeutic opportunities.
Subject(s)
Cancer-Associated Fibroblasts , Carcinoma, Squamous Cell , Head and Neck Neoplasms , Mouth Neoplasms , Humans , Carcinoma, Squamous Cell/pathology , Squamous Cell Carcinoma of Head and Neck/metabolism , Mouth Neoplasms/pathology , Cancer-Associated Fibroblasts/metabolism , Head and Neck Neoplasms/metabolism , Tumor Microenvironment , Fibroblasts/metabolismABSTRACT
BACKGROUND: Survival rates for oral squamous cell carcinoma (OSCC) have remained poor for decades, a fact largely attributable to late-stage diagnoses and high recurrence rates. We report analysis of serum miRNA expression in samples from patients with high-risk oral lesions (HRL, including OSCC/carcinoma in situ lesions) and healthy non-cancer controls, with the aim of non-invasively detecting primary or recurrent disease before it is clinically evident. METHODS: Discovery, test, and validation sets were defined from a total of 468 serum samples (305 HRL and 163 control samples). Samples were analysed using multiple qRT-PCR platforms. RESULTS: A two-miRNA classifier comprised of miR-125b-5p and miR-342-3p was defined following discovery and test analyses. Analysis in an independent validation cohort reported sensitivity and specificity of ~74% for this classifier. Significantly, when this classifier was applied to serial serum samples taken from patients both before treatment and during post-treatment surveillance, it identified recurrence an average of 15 months prior to clinical presentation. CONCLUSIONS: These results indicate this serum miRNA classifier is effective as a simple, non-invasive monitoring tool for earlier detection of recurrent disease when lesions are typically smaller and amenable to a wider array of treatment options to improve survival.
Subject(s)
Carcinoma, Squamous Cell , Head and Neck Neoplasms , MicroRNAs , Mouth Neoplasms , Humans , MicroRNAs/metabolism , Carcinoma, Squamous Cell/diagnosis , Carcinoma, Squamous Cell/genetics , Carcinoma, Squamous Cell/metabolism , Squamous Cell Carcinoma of Head and Neck/genetics , Mouth Neoplasms/diagnosis , Mouth Neoplasms/genetics , Mouth Neoplasms/metabolism , Biomarkers, Tumor/metabolism , Neoplasm Recurrence, Local/diagnosis , Neoplasm Recurrence, Local/genetics , Chronic Disease , Head and Neck Neoplasms/genetics , Gene Expression Profiling/methods , Gene Expression Regulation, NeoplasticABSTRACT
Introduction: Oral squamous cell carcinoma (OSCC) is the most common form of head and neck cancer and has a survival rate of â¼50% over 5 years. New treatment strategies are sorely needed to improve survival rates-and a better understanding of the mechanisms underlying tumorigenesis is needed to develop these strategies. The role of the tumor microenvironment (TME) has increasingly been identified as crucial in tumor progression and metastasis. One of the main constituents of the TME, cancer-associated fibroblasts (CAFs), plays a key role in influencing the biological behavior of tumors. Multiple mechanisms contribute to CAF activation, such as TGFß signaling, but the role of extracellular vesicles (EVs) in CAF activation in OSCC is poorly understood. Assessing the impact of oral cancer-derived EVs on CAF activation will help to better illuminate OSCC pathophysiology and may drive development of novel treatments options. Methods: EVs were isolated from OSCC cell lines (Cal 27, SCC-9, SCC-25) using differential centrifugation. Nanoparticle tracking analysis was used for EV characterization, and Western blot to confirm the presence of EV protein markers. Oral fibroblasts were co-cultured with enriched EVs, TGFß, or PBS over 72 h to assess activation. Flow cytometry was used to evaluate CAF markers. RNA collected from fibroblasts was extracted and the transcriptome was sequenced. Conditioned media from the co-cultures was evaluated with cytokine array profiling. Results: OSCC-derived EVs can activate oral fibroblasts into CAFs that are different from those activated by TGFß, suggesting different mechanisms of activation and different functional properties. Gene set enrichment analysis showed several upregulated inflammatory pathways in those CAFs exposed to OSCC-derived EVs. Marker genes for inflammatory CAF subtypes were also upregulated, but not in CAFs activated by TGFß. Finally, cytokine array analysis on secreted proteins revealed elevated levels of several pro-inflammatory cytokines from EV-activated CAFs, for instance IL-8 and CXCL5. Discussion: Our results reveal the ability of OSCC-derived EVs to activate fibroblasts into CAFs. These CAFs seem to have unique properties, differing from TGFß-activated CAFs. Gaining an understanding of the interplay between EVs and stromal cells such as CAFs could lead to further insights into OSCC tumorigenesis and potential novel therapeutics.
ABSTRACT
Liquid biopsies have emerged as a promising tool for the detection of metastases as well as local and regional recurrence in lung cancer. Liquid biopsy tests involve analyzing a patient's blood, urine, or other body fluids for the detection of biomarkers, including circulating tumor cells or tumor-derived DNA/RNA that have been shed into the bloodstream. Studies have shown that liquid biopsies can detect lung cancer metastases with high accuracy and sensitivity, even before they are visible on imaging scans. Such tests are valuable for early intervention and personalized treatment, aiming to improve patient outcomes. Liquid biopsies are also minimally invasive compared to traditional tissue biopsies, which require the removal of a sample of the tumor for further analysis. This makes liquid biopsies a more convenient and less risky option for patients, particularly those who are not good candidates for invasive procedures due to other medical conditions. While liquid biopsies for lung cancer metastases and relapse are still being developed and validated, they hold great promise for improving the detection and treatment of this deadly disease. Herein, we summarize available and novel approaches to liquid biopsy tests for lung cancer metastases and recurrence detection and describe their applications in clinical practice.
Subject(s)
Lung Neoplasms , Neoplastic Cells, Circulating , Humans , Biomarkers, Tumor/genetics , Neoplasm Recurrence, Local , Liquid Biopsy/methods , Lung Neoplasms/diagnosis , Biopsy/methods , Neoplastic Cells, Circulating/pathologyABSTRACT
Sudden sensorineural hearing loss (SSNHL) is an acquired idiopathic hearing loss. Serum levels of small, non-coding RNAs and microRNAs (miRNAs) miR-195-5p/-132-3p/-30a-3p/-128-3p/-140-3p/-186-5p/-375-3p/-590-5p are differentially expressed in SSNHL patients within 28 days of hearing loss onset. This study determines if these changes persist by comparing the serum miRNA expression profile of SSNHL patients within 1 month of hearing loss onset with that of patients 3-12 months after hearing loss onset. We collected serum from consenting adult SSNHL patients at presentation or during clinic follow-up. We matched patient samples drawn 3-12 months after hearing loss onset (delayed group, n = 9 patients) by age and sex to samples drawn from patients within 28 days of hearing loss onset (immediate group, n = 14 patients). We compared the real-time PCR-determined expression levels of the target miRNAs between the two groups. We calculated the air conduction pure-tone-averaged (PTA) audiometric thresholds in affected ears at the initial and final follow-up visits. We undertook inter-group comparisons of hearing outcome status and initial and final PTA audiometric thresholds. There was no significant inter-group difference in miRNA expression level, hearing recovery status and initial and final affected ear PTA audiometric thresholds.
Subject(s)
Deafness , Hearing Loss, Sensorineural , Hearing Loss, Sudden , MicroRNAs , Adult , Humans , MicroRNAs/genetics , Hearing Loss, Sensorineural/genetics , Hearing Loss, Sudden/genetics , Hearing/genetics , Retrospective StudiesABSTRACT
Capturing rare disease-associated biomarkers from body fluids can offer an early-stage diagnosis of different cancers. Circulating tumor cells (CTCs) are one of the major cancer biomarkers that provide insightful information about the cancer metastasis prognosis and disease progression. The most common clinical solutions for quantifying CTCs rely on the immunomagnetic separation of cells in whole blood. Microfluidic systems that perform magnetic particle separation have reported promising outcomes in this context, however, most of them suffer from limited efficiency due to the low magnetic force generated which is insufficient to trap cells in a defined position within microchannels. In this work, a novel method for making soft micromagnet patterns with optimized geometry and magnetic material is introduced. This technology is integrated into a bilayer microfluidic chip to localize an external magnetic field, consequently enhancing the capture efficiency (CE) of cancer cells labeled with the magnetic nano/hybrid microgels that are developed in the previous work. A combined numerical-experimental strategy is implemented to design the microfluidic device and optimize the capturing efficiency and to maximize the throughput. The proposed design enables high CE and purity of target cells and real-time time on-chip monitoring of their behavior. The strategy introduced in this paper offers a simple and low-cost yet robust opportunity for early-stage diagnosis and monitoring of cancer-associated biomarkers.
Subject(s)
Microfluidic Analytical Techniques , Microgels , Neoplastic Cells, Circulating , Humans , Cell Separation/methods , Microfluidics , Immunomagnetic Separation/methods , Neoplastic Cells, Circulating/pathology , Cell Line, Tumor , Magnetic Phenomena , Microfluidic Analytical Techniques/methodsABSTRACT
Nasopharyngeal carcinoma (NPC) is unique among head and neck cancers for its strong causative association with Epstein Barr-Virus and high levels of immune infiltration that play a role in pathogenesis. As such, immunotherapy for the treatment of NPC is a promising area of research in the pursuit of improving patient outcomes. Understanding the tumour immune microenvironment (TIME) of NPC is the key to developing targeted immunotherapies and stratifying patients to determine optimal treatment regimens. Recent research has uncovered distinct characteristics of the TIME in NPC as well as important differences between the different disease subtypes; however, reviewing the state of the field reveals a further need for the application of novel techniques like multiplexed hyperspectral imaging and mass cytometry. These techniques can be used to identify spatial, compositional, and functional aspects of the TIME in NPC such as immune cell sociology, novel immune populations, and differences in immune-related signalling pathways in NPC in order to identify clinically relevant characteristics for targeted immunotherapy development and biomarker discovery.
ABSTRACT
Objective: Nasopharyngeal carcinomas (NPC) are tumors arising from epithelium of the nasopharynx. The 5-year survival rate of primary NPC is 80% with significant risks of recurrence. The objective here is to provide an evidence-based systemic review of the diagnostic value of different modalities in detecting local, regional, and distal recurrent NPC, as well as the associated costs with these modalities. Methods: MEDLINE, EMBASE, and the Cochrane review database were queried. Two hundred and twenty-three abstracts were generated using the inclusion criteria: patients >18 years of age; histopathological reference standard; and modalities pertaining to imaging or microbiology. Results: Twenty-four manuscripts fulfilled the inclusion criteria and 5 surveillance tools identified: endoscopy, MR, FDG-PET, Tc-99m MIBI and 201TI SPECT, and EBV DNA. Conclusions: For local surveillance, endoscopy is the gold standard recommendation, with increased efficacy if Narrow Band Imaging or contact endoscopy are utilized. MRI and FDG-PET is also recommended to help with local to distal spread; however, Tc-99m MIBI and 201TI SPECT are options as well. EBV DNA is recommended as a cheap and accessible adjunct surveillance tool if an available as an option.
ABSTRACT
MicroRNAs (miRNAs) regulate gene expressions and control a wide variety of cellular functions. House Ear Institute-Organ of Corti 1 (HEI-OC1) cells are widely used to screen ototoxic drugs and to investigate cellular and genetic alterations in response to various conditions. HEI-OC1 cells are almost exclusively studied under permissive conditions that promote cell replication at the expense of differentiation. Many researchers suggest that permissive culture condition findings are relevant to understanding human hearing disorders. The mature human cochlea however consists of differentiated cells and lacks proliferative capacity. This study therefore aimed to compare the miRNA profiles and cellular characteristics of HEI-OC1 cells cultured under permissive (P-HEI-OC1) and non-permissive (NP-HEI-OC1) conditions. A significant increase in the level of expression of tubulin ß1 class VI (Tubb1), e-cadherin (Cdh1), espin (Espn), and SRY (sex determining region Y)-box2 (Sox2) mRNAs was identified in non-permissive cells compared with permissive cells (P < 0.05, Kruskal-Wallis H test, 2-sided). miR-200 family, miR-34b/c, and miR-449a/b functionally related cluster miRNAs, rodent-specific maternally imprinted gene Sfmbt2 intron 10th cluster miRNAs (-466a/ -467a), and miR-17 family were significantly (P < 0.05, Welch's t-test, 2-tailed) differentially expressed in non-permissive cells when compared with permissive cells. Putative target genes were significantly predominantly enriched in mitogen-activated protein kinase (MAPK), epidermal growth factor family of receptor tyrosine kinases (ErbB), and Ras signaling pathways in non-permissive cells compared with permissive cells. This distinct miRNA signature of differentiated HEI-OC1 cells could help in understanding miRNA-mediated cellular responses in the adult cochlea.
Subject(s)
MicroRNAs , Apoptosis , Cell Differentiation , Cell Line , Humans , MicroRNAs/genetics , MicroRNAs/metabolism , Organ of Corti , Signal TransductionABSTRACT
Communication between cancer cells and the surrounding stromal cells of the tumor microenvironment (TME) plays a key role in promoting metastasis, which is the major cause of cancer death. Small membrane-bound particles called extracellular vesicles (EVs) are released from both cancer and stromal cells and have a key role in mediating this communication through transport of cargo such as various RNA species (mRNA, miRNA, lncRNA), proteins, and lipids. Tumor-secreted EVs have been observed to induce a pro-tumorigenic phenotype in non-malignant cells of the stroma, including fibroblasts, endothelial cells, and local immune cells. These cancer-associated cells then drive metastasis by mechanisms such as increasing the invasiveness of cancer cells, facilitating angiogenesis, and promoting the formation of the pre-metastatic niche. This review will cover the role of EV-mediated signaling in the TME during metastasis and highlight the therapeutic potential of targeting these pathways to develop biomarkers and novel treatment strategies.
Subject(s)
Cell Communication/genetics , Extracellular Vesicles/genetics , Neoplasms/genetics , Tumor Microenvironment/genetics , Endothelial Cells/metabolism , Endothelial Cells/pathology , Extracellular Vesicles/metabolism , Fibroblasts/metabolism , Fibroblasts/pathology , Humans , Neoplasm Metastasis , Neoplasms/metabolism , Neoplasms/pathology , Stromal Cells/metabolism , Stromal Cells/pathologyABSTRACT
Although advances in targeted therapies have driven great progress in cancer treatment and outcomes, drug resistance remains a major obstacle to improving patient survival. Several mechanisms are involved in developing resistance to both conventional chemotherapy and molecularly targeted therapies, including drug efflux, secondary mutations, compensatory genetic alterations occurring upstream or downstream of a drug target, oncogenic bypass, drug activation and inactivation, and DNA damage repair. Extracellular vesicles (EVs) are membrane-bound lipid bilayer vesicles that are involved in cell-cell communication and regulating biological processes. EVs derived from cancer cells play critical roles in tumor progression, metastasis, and drug resistance by delivering protein and genetic material to cells of the tumor microenvironment. Understanding the biochemical and genetic mechanisms underlying drug resistance will aid in the development of new therapeutic strategies. Herein, we review the role of EVs as mediators of drug resistance in the context of cancer.
Subject(s)
Drug Resistance, Neoplasm , Extracellular Vesicles/metabolism , Animals , Extracellular Vesicles/genetics , Humans , Tumor MicroenvironmentABSTRACT
Extracellular vesicles (EVs) play a key role in the communication between cancer cells and stromal components of the tumor microenvironment (TME). In this context, cancer cell-derived EVs can regulate the activation of a CAF phenotype in TME cells, which can be mediated by several EV cargos (e.g., miRNA, proteins, mRNA and lncRNAs). On the other hand, CAF-derived EVs can mediate several processes during tumorigenesis, including tumor growth, invasion, metastasis, and therapy resistance. This review aimed to discuss the molecular aspects of EV-based cross-talk between CAFs and cancer cells during tumorigenesis, in addition to assessing the roles of EV cargo in therapy resistance and pre-metastatic niche formation.
Subject(s)
Cancer-Associated Fibroblasts/metabolism , Cell Transformation, Neoplastic/metabolism , Extracellular Vesicles/metabolism , Neoplasms/metabolism , Tumor Microenvironment , Cancer-Associated Fibroblasts/pathology , Cell Communication/genetics , Cell Communication/physiology , Cell Transformation, Neoplastic/genetics , Cell Transformation, Neoplastic/pathology , Drug Resistance, Neoplasm/genetics , Extracellular Vesicles/genetics , Humans , MicroRNAs/genetics , MicroRNAs/metabolism , Neoplasms/genetics , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , Signal Transduction/geneticsABSTRACT
OBJECTIVE: This scoping review aims to identify and systematically map the available evidence concerning the prognostic biomarkers for malignant transformation of oral potentially malignant disorders (OPMDs), and to identify and analyze possible knowledge gaps in this field of literature. INTRODUCTION: It is hypothesized that diagnosis and treatment of oral cancer in its early stages may be the key to improving the prognosis and reducing treatment-related consequences. Oral potentially malignant disorders represent tissue alterations with a higher risk of malignant transformation compared to the normal mucosa. Therefore, the study of prognostic biomarkers for OPMD could represent new diagnosis and therapeutic targets and, consequently, contribute to the reduction of oral cancer burden worldwide. INCLUSION CRITERIA: Longitudinal studies investigating prognostic biomarkers regarding the malignant transformation of OPMD will be included. The initial OPMD diagnosis and the malignant transformation must have been confirmed by histopathological analysis. To achieve minimal heterogeneity, studies that assess biomarkers in other locations (blood, plasma or others) will be excluded. METHODS: Five electronic databases and three grey literature databases will be consulted. No restrictions regarding publication date will be applied. Only studies published in the Latin (Roman) alphabet, which comprises most of the European languages, will be included. Study selection will be performed by two authors in a two-phase process; if any disagreement arises, a third author will be consulted to make a final decision. Data extraction will be performed by two authors using a standardized extraction tool. The results will be described in details accordantly with the aims of this scoping review.
Subject(s)
Mouth Neoplasms , Biomarkers , Cell Transformation, Neoplastic , Humans , Mouth Neoplasms/diagnosis , Prognosis , Review Literature as TopicABSTRACT
This scoping review aimed to map evidence regarding biomarkers for malignant transformation of oral potentially malignant disorders (OPMD). Seventy-three longitudinal studies investigating prognostic biomarkers for OPMD malignant transformation were included, encompassing 5612 disorders and 108 biomarkers, of which 72 were investigated by immunohistochemistry. Most biomarkers were assessed in one or two studies, while five (p53, Ki-67, podoplanin, p16, and DNA ploidy) were analyzed in five or more studies. All studies investigating podoplanin (n = 8) reported a significant association between positive/high immunoexpression and malignant transformation. Similarly, all studies assessing DNA ploidy (n = 5) found that aneuploidy or gross genomic aberrations were significantly associated with malignant transformation. Included studies often presented mixed data from different OPMD subtypes, inadequate description of population characteristics, and lack of adjusted analysis for confounding factors. One hundred and eight biomarkers were identified and, from these, podoplanin immunoexpression and DNA ploidy were considered promising candidates for future long-term clinical research.
Subject(s)
Mouth Neoplasms , Precancerous Conditions , Biomarkers , Biomarkers, Tumor/genetics , Cell Transformation, Neoplastic , Humans , Immunohistochemistry , PrognosisABSTRACT
Neutral sphingomyelinase 2 (nSMase2), the product of the sphingomyelin phosphodiesterase 3 (SMPD3) gene, catalyzes the hydrolysis of sphingomyelin to ceramide. Ceramide acts on various signaling pathways to influence cell proliferation, survival, and stress response. Altered levels of sphingolipids and ceramides have been reported in various cancer types, including oral squamous cell carcinoma (OSCC). OSCC patients exhibit a poor 5-year survival rate of 50%, a figure that has remained stagnant for decades. To overcome this requires a better understanding of the molecular events driving this disease. The molecular analysis of the oral cavity reported here has identified the SMPD3 promoter region as a site of frequent hypermethylation and downregulation in pre-malignant and malignant tissues as compared with healthy control tissues. While lentivirus-induced overexpression of SMPD3 in cell models of oral dysplasia and OSCC did not significantly alter proliferation, it did decrease migration and invasion and increased resistance to the epidermal growth factor receptor (EGFR) inhibitor erlotinib. These results suggest that SMPD3 downregulation is a common event in OSCC progression and may promote the spread of tumor cells.
ABSTRACT
OBJECTIVES: To compare the circulating microRNA (miRNA) expression profiles between sudden sensory neural hearing loss (SSNHL) patients and age-matched normal hearing controls. STUDY DESIGN: Prospective cohort multi-center study. METHODS: Patients presenting within 28 days of onset of SSNHL were prospectively recruited along with contemporaneous age-matched controls. Pooled sera of four patient (n = 09, mean age = 53.0 years; 07, 55.0; 10, 52.9; 10, 51.6) and two control (09, 51.2 and 03, 50.0) groups were assessed using a TaqMan Low Density Array. The patients' sera were also divided into two pools, untreated (04, 57.7) and treated (32, 52.6) for additional analysis. miRNA expression level was derived from cycle threshold (Ct) values normalized to a global mean. Inter-group mean Ct differences with fold changes ≥2.0 and ≤0.5 at P < .05 were considered significant. Bioinformatic databases were used to identify putative target mRNAs or validated genes and their functional annotations. RESULTS: Thirty-six SSNHL patients (mean age 53.0 ± standard deviation (SD) 15.2 years) and 12 controls (50.9 ± 11.9) were studied. Eight miRNAs hsa-miR-590-5p/ -186-5p/ -195-5p/ -140-3p/ -128-3p/ -132-3p/ -375-3p, and -30a-3p were identified as significantly differentially expressed in SSNHL patients. Most of these miRNAs were abundantly identified in the nervous system and the putative target messenger RNAs (mRNAs) were enriched in signaling pathways such as phosphatidyl inositol 3 kinase/protein Kinase B (PI3K/Akt), Ras and mitogen-activated protein kinase (MAPK). CONCLUSION: These findings suggest the possible cellular signaling pathways that underlie the disruption of auditory signal transmission in SSNHL. LEVEL OF EVIDENCE: 2 Laryngoscope, 130:E416-E422, 2020.
Subject(s)
Genetic Predisposition to Disease/genetics , Hearing Loss, Sudden/genetics , MicroRNAs/blood , Adult , Aged , Auditory Perception/genetics , Case-Control Studies , Female , Genetic Markers , Humans , Male , Middle Aged , Prospective Studies , Signal Transduction/geneticsABSTRACT
Head and neck squamous cell carcinoma (HNSCC) has a poor survival rate mainly due to late stage diagnosis and recurrence. Despite genomic efforts to identify driver mutations and changes in protein-coding gene expression, developing effective diagnostic and prognostic biomarkers remains a priority to guide disease management and improve patient outcome. Recent reports of previously-unannotated microRNAs (miRNAs) from multiple somatic tissues have raised the possibility of HNSCC-specific miRNAs. In this study, we applied a customized in-silico analysis pipeline to identify novel miRNAs from raw small-RNA sequencing datasets from public repositories. We discovered 146 previously-unannotated sequences expressed in head and neck samples that share structural properties highly characteristic of miRNAs. The combined expression of the novel miRNAs revealed tissue and context-specific patterns. Furthermore, comparison of tumor with non-malignant tissue samples (n = 43 pairs) revealed 135 of these miRNAs as differentially expressed, most of which were overexpressed or exclusively found in tumor samples. Additionally, a subset of novel miRNAs was significantly associated with HPV infection status and patient outcome. A prognostic-model combining novel and known miRNA was developed (multivariate Cox regression analysis) leading to an improved death and relapse risk stratification (log rank p < 1e-7). The presence of these miRNAs was corroborated both in an independent dataset and by RT-qPCR analysis, supporting their potential involvement in HNSCC. In this study, we report the discovery of 146 novel miRNAs in head and neck tissues and demonstrate their potential biological significance and clinical relevance to head and neck cancer, providing a new resource for the study of HNSCC.
ABSTRACT
Recent studies have uncovered microRNAs (miRNAs) that have been overlooked in early genomic explorations, which show remarkable tissue- and context-specific expression. Here, we aim to identify and characterize previously unannotated miRNAs expressed in gastric adenocarcinoma (GA). Raw small RNA-sequencing data were analyzed using the miRMaster platform to predict and quantify previously unannotated miRNAs. A discovery cohort of 475 gastric samples (434 GA and 41 adjacent nonmalignant samples), collected by The Cancer Genome Atlas (TCGA), were evaluated. Candidate miRNAs were similarly assessed in an independent cohort of 25 gastric samples. We discovered 170 previously unannotated miRNA candidates expressed in gastric tissues. The expression of these novel miRNAs was highly specific to the gastric samples, 143 of which were significantly deregulated between tumor and nonmalignant contexts (p-adjusted < 0.05; fold change > 1.5). Multivariate survival analyses showed that the combined expression of one previously annotated miRNA and two novel miRNA candidates was significantly predictive of patient outcome. Further, the expression of these three miRNAs was able to stratify patients into three distinct prognostic groups (p = 0.00003). These novel miRNAs were also present in the independent cohort (43 sequences detected in both cohorts). Our findings uncover novel miRNA transcripts in gastric tissues that may have implications in the biology and management of gastric adenocarcinoma.
Subject(s)
Adenocarcinoma/genetics , Biomarkers, Tumor , MicroRNAs/genetics , Stomach Neoplasms/genetics , Adenocarcinoma/pathology , Adult , Aged , Computational Biology , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Male , Middle Aged , Neoplasm Grading , Neoplasm Staging , Prognosis , Stomach Neoplasms/pathology , TranscriptomeABSTRACT
Exosomes are small (â¼30-140 nm) lipid bilayer-enclosed particles of endosomal origin. They are a subset of extracellular vesicles (EVs) that are secreted by most cell types. There has been growing interest in exosome research in the last decade due to their emerging role as intercellular messengers and their potential in disease diagnosis. Indeed, exosomes contain proteins, lipids, and RNAs that are specific to their cell origin and could deliver cargo to both nearby and distant cells. As a result, investigation of exosome cargo contents could offer opportunities for disease detection and treatment. Moreover, exosomes have been explored as natural drug delivery vehicles since they can travel safely in extracellular fluids and deliver cargo to destined cells with high specificity and efficiency. Despite significant efforts made in this relatively new field of research, progress has been held back by challenges such as inefficient separation methods, difficulties in characterization, and lack of specific biomarkers. In this review, we summarize the current knowledge in exosome biogenesis, their roles in disease progression, and therapeutic applications and opportunities in bioengineering. Furthermore, we highlight the established and emerging technological developments in exosome isolation and characterization. We aim to consider critical challenges in exosome research and provide directions for future studies.