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Blázquez-Encinas R, Moreno-Montilla MT, García-Vioque V, Gracia-Navarro F, Alors-Pérez E, Pedraza-Arevalo S, Ibáñez-Costa A, Castaño JP. The uprise of RNA biology in neuroendocrine neoplasms: altered splicing and RNA species unveil translational opportunities. Rev Endocr Metab Disord 2023; 24:267-282. [PMID: 36418657 PMCID: PMC9685014 DOI: 10.1007/s11154-022-09771-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/15/2022] [Indexed: 11/25/2022]
Abstract
Neuroendocrine neoplasms (NENs) comprise a highly heterogeneous group of tumors arising from the diffuse neuroendocrine system. NENs mainly originate in gastrointestinal, pancreatic, and pulmonary tissues, and despite being rare, show rising incidence. The molecular mechanisms underlying NEN development are still poorly understood, although recent studies are unveiling their genomic, epigenomic and transcriptomic landscapes. RNA was originally considered as an intermediary between DNA and protein. Today, compelling evidence underscores the regulatory relevance of RNA processing, while new RNA molecules emerge with key functional roles in core cell processes. Indeed, correct functioning of the interrelated complementary processes comprising RNA biology, its processing, transport, and surveillance, is essential to ensure adequate cell homeostasis, and its misfunction is related to cancer at multiple levels. This review is focused on the dysregulation of RNA biology in NENs. In particular, we survey alterations in the splicing process and available information implicating the main RNA species and processes in NENs pathology, including their role as biomarkers, and their functionality and targetability. Understanding how NENs precisely (mis)behave requires a profound knowledge at every layer of their heterogeneity, to help improve NEN management. RNA biology provides a wide spectrum of previously unexplored processes and molecules that open new avenues for NEN detection, classification and treatment. The current molecular biology era is rapidly evolving to facilitate a detailed comprehension of cancer biology and is enabling the arrival of personalized, predictive and precision medicine to rare tumors like NENs.
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Affiliation(s)
- Ricardo Blázquez-Encinas
- Maimonides Biomedical Research Institute of Córdoba, Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Córdoba, Spain
| | - María Trinidad Moreno-Montilla
- Maimonides Biomedical Research Institute of Córdoba, Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Córdoba, Spain
| | - Víctor García-Vioque
- Maimonides Biomedical Research Institute of Córdoba, Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Córdoba, Spain
| | - Francisco Gracia-Navarro
- Maimonides Biomedical Research Institute of Córdoba, Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Córdoba, Spain
| | - Emilia Alors-Pérez
- Maimonides Biomedical Research Institute of Córdoba, Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Córdoba, Spain
| | - Sergio Pedraza-Arevalo
- Maimonides Biomedical Research Institute of Córdoba, Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofía, Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Córdoba, Spain
| | - Alejandro Ibáñez-Costa
- Maimonides Biomedical Research Institute of Córdoba, Córdoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain.
- Hospital Universitario Reina Sofía, Córdoba, Spain.
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Córdoba, Spain.
| | - Justo P Castaño
- Maimonides Biomedical Research Institute of Córdoba, Córdoba, Spain.
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain.
- Hospital Universitario Reina Sofía, Córdoba, Spain.
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), Córdoba, Spain.
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Latini A, Vancheri C, Amati F, Morini E, Grelli S, Claudia M, Vita P, Colona VL, Murdocca M, Andreoni M, Malagnino V, Raponi M, Cocciadiferro D, Novelli A, Borgiani P, Novelli G. Expression analysis of miRNA hsa-let7b-5p in naso-oropharyngeal swabs of COVID-19 patients supports its role in regulating ACE2 and DPP4 receptors. J Cell Mol Med 2022; 26:4940-4948. [PMID: 36073344 PMCID: PMC9538662 DOI: 10.1111/jcmm.17492] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/13/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the novel coronavirus responsible for worldwide coronavirus disease (COVID-19). We previously observed that Angiotensin-converting enzyme 2 (ACE2) and Dipeptidyl peptidase-4 (DPP4) are significantly overexpressed in naso-oropharyngeal swabs (NPS) of COVID-19 patients, suggesting their putative functional role in the disease progression. ACE2 and DPP4 overexpression in COVID-19 patients may be associated to epigenetic mechanism, such as miRNA differential expression. We investigated if hsa-let7b-5p, reported to target both ACE2 and DPP4 transcripts, could be involved in the regulation of these genes. We verified that the inhibition and overexpression of hsa-let7b-5p matched to a modulation of both ACE2 and DPP4 levels. Then, we observed a statistically significant downregulation (FC = -1.5; p < 0.05) of hsa-let7b-5p in the same COVID-19 and control samples of our previous study. This is the first study that shows hsa-let7b-5p low expression in naso-oropharyngeal swabs of COVID-19 patients and demonstrates a functional role of this miR in regulating ACE2 and DPP4 levels. These data suggest the involvement of hsa-let7b-5p in the regulation of genes necessary for SARS-CoV-2 infections and its putative role as a therapeutic target for COVID-19.
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Affiliation(s)
- Andrea Latini
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Chiara Vancheri
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Francesca Amati
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Elena Morini
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Sandro Grelli
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Matteucci Claudia
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Petrone Vita
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | - Michela Murdocca
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Massimo Andreoni
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Vincenzo Malagnino
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | | | | | - Paola Borgiani
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Genetics Unit, University of Rome "Tor Vergata", Rome, Italy.,Bambino Gesù Pediatric Hospital, IRCCS, Rome, Italy.,Neuromed IRCCS Institute, Pozzilli, Italy.,School of Medicine, Reno University of Nevada, Reno, Nevada, USA
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3
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Buglyó G, Magyar Z, Romicsné Görbe É, Bánusz R, Csóka M, Micsik T, Mezei M, Yani JAS, Varga P, Sápi Z, Nagy B. miRNA Profiling of Hungarian Regressive Wilms' Tumor Formalin-Fixed Paraffin-Embedded (FFPE) Samples by Quantitative Real-Time Polymerase Chain Reaction (RT-PCR). Med Sci Monit 2021; 27:e932731. [PMID: 34608109 PMCID: PMC8501895 DOI: 10.12659/msm.932731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Wilms' tumor is a common renal malignancy of early childhood with a generally favorable prognosis depending upon histological subtype. It is becoming increasingly clear that differences in miRNA (microRNA) expression signature represent important clues helping us predict a tumor's response to chemotherapy. In our study, we aimed to reveal miRNAs deregulated in regressive Wilms' tumors from FFPE (formalin-fixed, paraffin-embedded) samples, also showing whether such samples are reliable miRNA sources in Wilms' tumor. MATERIAL AND METHODS Samples from 8 Hungarian patients (3 males, 5 females, aged 1 to 7 years) were analyzed by qRT-PCR (quantitative real-time PCR). A PCR array was used in a pilot experiment, and selected miRNAs (miR-128-3p, miR-184, miR-194-5p, miR-203a) were studied in the rest of the samples using individual primers. RESULTS miR-194-5p was underexpressed in all tumor samples. miR-184 and miR-203a were underexpressed in 7 cases, the exception being a case with a high ratio of necrotic blastemal tissue. Results obtained with miR-128-3p are difficult to interpret due to varying directions of expression changes. CONCLUSIONS We conclude that a downregulation of miR-184, miR-194-5p, and miR-203a expression is observed in both regressive and blastemal tumors, but larger-scale studies are needed to confirm whether the degree of their underexpression correlates with the number of blastemal elements in a sample. In most of our FFPE samples aged up to 9 years, RNA extraction provided miRNA with quantity and quality sufficient for qRT-PCR-based analysis, emphasizing the relevance of pathological archives as miRNA sources in future studies.
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Affiliation(s)
- Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsófia Magyar
- Department of Obstetrics and Gynaecology, Baross Street Division, Semmelweis University, Budapest, Hungary
| | - Éva Romicsné Görbe
- Department of Obstetrics and Gynaecology, Baross Street Division, Semmelweis University, Budapest, Hungary
| | - Rita Bánusz
- 2nd Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Monika Csóka
- 2nd Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Tamás Micsik
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Márta Mezei
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Jaxi Ayman Shawky Yani
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Péter Varga
- Department of Obstetrics and Gynaecology, Baross Street Division, Semmelweis University, Budapest, Hungary
| | - Zoltán Sápi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Bálint Nagy
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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Verel-Yilmaz Y, Fernández JP, Schäfer A, Nevermann S, Cook L, Gercke N, Helmprobst F, Jaworek C, Pogge von Strandmann E, Pagenstecher A, Bartsch DK, Bartsch JW, Slater EP. Extracellular Vesicle-Based Detection of Pancreatic Cancer. Front Cell Dev Biol 2021; 9:697939. [PMID: 34368146 PMCID: PMC8343017 DOI: 10.3389/fcell.2021.697939] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
Due to a grim prognosis, there is an urgent need to detect pancreatic ductal adenocarcinoma (PDAC) prior to metastasis. However, reliable diagnostic imaging methods or biomarkers for PDAC or its precursor lesions are still scarce. ADAM8, a metalloprotease-disintegrin, is highly expressed in PDAC tissue and negatively correlates with patient survival. The aim of our study was to determine the ability of ADAM8-positive extracellular vesicles (EVs) and cargo microRNAs (miRNAs) to discriminate precursor lesions or PDAC from healthy controls. In order to investigate enrichment of ADAM8 on EVs, these were isolated from serum of patients with PDAC (n = 52), precursor lesions (n = 7) and healthy individuals (n = 20). Nanoparticle Tracking Analysis and electron microscopy indicated successful preparation of EVs that were analyzed for ADAM8 by FACS. Additionally, EV cargo analyses of miRNAs from the same serum samples revealed the presence of miR-720 and miR-451 by qPCR and was validated in 20 additional PDAC samples. Statistical analyses included Wilcoxon rank test and ROC curves. FACS analysis detected significant enrichment of ADAM8 in EVs from patients with PDAC or precursor lesions compared to healthy individuals (p = 0.0005). ADAM8-dependent co-variates, miR-451 and miR-720 were also diagnostic, as patients with PDAC had significantly higher serum levels of miR-451 and lower serum levels of miR-720 than healthy controls and reached high sensitivity and specificity (AUC = 0.93 and 1.00, respectively) to discriminate PDAC from healthy control. Thus, detection of ADAM8-positive EVs and related cargo miR-720 and miR-451 may constitute a specific biomarker set for screening individuals at risk for PDAC.
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Affiliation(s)
- Yesim Verel-Yilmaz
- Department of Visceral, Thoracic and Vascular Surgery, Philipps University Marburg, Marburg, Germany
| | - Juan Pablo Fernández
- Department of Visceral, Thoracic and Vascular Surgery, Philipps University Marburg, Marburg, Germany
| | - Agnes Schäfer
- Department of Neurosurgery, Philipps University Marburg, Marburg, Germany
| | - Sheila Nevermann
- Department of Visceral, Thoracic and Vascular Surgery, Philipps University Marburg, Marburg, Germany
| | - Lena Cook
- Department of Neurosurgery, Philipps University Marburg, Marburg, Germany
| | - Norman Gercke
- Department of Visceral, Thoracic and Vascular Surgery, Philipps University Marburg, Marburg, Germany
| | - Frederik Helmprobst
- Department of Neuropathology, Philipps University Marburg, Marburg, Germany.,Core Facility-Mouse Pathology and Electron Microscopy (MPEM), Philipps University Marburg, Marburg, Germany
| | - Christian Jaworek
- Department of Neurosurgery, Philipps University Marburg, Marburg, Germany
| | | | - Axel Pagenstecher
- Department of Neuropathology, Philipps University Marburg, Marburg, Germany
| | - Detlef K Bartsch
- Department of Visceral, Thoracic and Vascular Surgery, Philipps University Marburg, Marburg, Germany
| | - Jörg W Bartsch
- Department of Neurosurgery, Philipps University Marburg, Marburg, Germany
| | - Emily P Slater
- Department of Visceral, Thoracic and Vascular Surgery, Philipps University Marburg, Marburg, Germany
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Bojanowski K, Ma S, Applebaum R, Zhao H. Transbuccal platform for delivery of lipogenic actives to facial skin: Because fat matters. J Tissue Eng Regen Med 2020; 14:1169-1174. [PMID: 32592290 DOI: 10.1002/term.3087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/11/2020] [Accepted: 06/15/2020] [Indexed: 11/07/2022]
Abstract
The ability to control facial skin physiology and appearance through the oral mucosa (transbuccally) is largely unexplored. Here, a hypothesis was tested that transbuccal delivery of fat tissue-supportive actives may trigger beneficial cosmetic responses at the level of the skin. First, the importance of the fat tissue for skin structure and function was established by comparative analysis of human biopsies cultured defatted or in the presence of hypodermis, using macroscopic observation, quantitative polymerase chain reaction, and histochemistry. Then, the ability to improve epidermal function and structure through the application of a lipoactive patch to oral mucosa was demonstrated in a clinical case study by the quantification of several epidermal microRNAs (miRNAs). It was found that removal of the hypodermal fat layer accelerated skin biopsy aging as demonstrated by the deterioration of the physical appearance at the macroscopic and microscopic (hematoxylin and eosin stain) levels and the decrease of expression of genes implicated in the structure and function of the skin, such as AQP3 and LOR. Furthermore, when adipogenic actives were applied to the oral mucosa under a form of bioadhesive film in a clinical case study, an improvement in the expression of miRNA biomarkers of senescence and inflammation was observed in the epidermis. Taken together, these results indicate that the transbuccal delivery of lipogenic compounds to face is a novel method for the improvement of facial skin structure and function.
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Affiliation(s)
- Krzysztof Bojanowski
- Department of Cosmetic Dermatology, Sunny BioDiscovery Inc., Santa Paula, CA, USA
| | - Stephanie Ma
- Department of Cosmetic Dermatology, Sunny BioDiscovery Inc., Santa Paula, CA, USA.,College of Nursing, California Baptist University, Riverside, CA, USA
| | | | - Hui Zhao
- Department of Cosmetic Dermatology, Sunny BioDiscovery Inc., Santa Paula, CA, USA
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Senousy MA, Shaker OG, Sayed NH, Fathy N, Kortam MA. LncRNA GAS5 and miR-137 Polymorphisms and Expression are Associated with Multiple Sclerosis Risk: Mechanistic Insights and Potential Clinical Impact. ACS Chem Neurosci 2020; 11:1651-1660. [PMID: 32348112 DOI: 10.1021/acschemneuro.0c00150] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The pathogenesis of multiple sclerosis (MS) is influenced by the interaction of genetic and epigenetic mechanisms. The long noncoding RNA GAS5 acts as a competing endogenous RNA for microRNA-137 and is involved in demyelination. We investigated the association of GAS5 and miR-137 expression and their polymorphisms with MS susceptibility. One hundred and eight MS patients and 104 healthy controls were included. Expression analysis and genotyping of GAS5-rs2067079 and miR-137-rs1625579 single nucleotide polymorphisms were performed by qPCR. Serum GAS5 was upregulated, while serum miR-137 was downregulated in MS compared with the controls. Serum miR-137 was an excellent discriminator of MS patients from the controls (AUC = 0.97) and a negative independent predictor of MS in multivariate logistic analysis. Serum GAS5 expression was positively correlated with the expanded disability status scale scores in the relapsing-remitting MS patients. The rs2067079TT minor homozygote genotype was associated with an increased MS risk, while the rs1625579G minor allele was protective. rs1625579 showed an age-specific effect, while the rs2067079 affected the MS risk in gender- and age-specific manners. In MS patients, rs2067079TT was associated with a higher serum GAS5 than other genotypes, while serum miR-137 did not differ between rs1625579 genotypes. Our results suggest serum GAS5 and miR-137 as MS biomarkers, with miR-137 as a negative predictor of MS risk and GAS5 as a marker of MS severity. We propose rs2067079 and rs1625579 as novel genetic markers of MS susceptibility, and at least, rs2067079 possibly impacts the crosstalk between GAS5 and miR-137.
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Affiliation(s)
- Mahmoud A. Senousy
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Olfat G. Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Cairo 11562, Egypt
| | - Noha H. Sayed
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Nevine Fathy
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
| | - Mona A. Kortam
- Biochemistry Department, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt
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7
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Clemente E, Efthymakis K, Carletti E, Capone V, Sperduti S, Bologna G, Marchisio M, Di Nicola M, Neri M, Sallese M. An explorative study identifies miRNA signatures for the diagnosis of non-celiac wheat sensitivity. PLoS One 2019; 14:e0226478. [PMID: 31834915 PMCID: PMC6910677 DOI: 10.1371/journal.pone.0226478] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/26/2019] [Indexed: 02/06/2023] Open
Abstract
Non-celiac wheat sensitivity (NCWS), also referred to as non-celiac gluten sensitivity, is a recently described disorder triggered by wheat/gluten ingestion. NCWS elicits a wide range of symptoms including diarrhoea, intestinal discomfort, and fatigue in analogy with other wheat/gluten-related disorders and celiac disease in particular. From the pathological standpoint, NCWS patients only have a slight increase of intraepithelial lymphocytes, while antibodies to tissue transglutaminase (tTG) and villous atrophy, otherwise diagnostic features of celiac disease, are absent. To date, the diagnosis of NCWS relies on symptoms and exclusion of confounding diseases, since biomarkers are not yet available. Here, the expression levels of selected miRNAs were examined in duodenal biopsies and peripheral blood leukocytes collected from newly diagnosed patients with NCWS and, as controls, from patients with celiac disease and gluten-independent gastrointestinal problems. We identified a few miRNAs whose expression is higher in the intestinal mucosa of patients affected by NCWS in comparison to control patients affect by gluten-independent dyspeptic symptoms (Helicobacter pylori-negative) and celiac disease. The present study provided the first evidence that NCWS patients have a characteristic miRNA expression patterns, such peculiarity could be exploited as a biomarker to the diagnosis of this disease.
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Affiliation(s)
- Emanuela Clemente
- Department of Medical, Oral and Biotechnological Sciences, “G. d'Annunzio” University of Chieti–Pescara, Chieti, Italy
- Centre for Advanced Studies and Technology (CAST), “G. d'Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Konstantinos Efthymakis
- Centre for Advanced Studies and Technology (CAST), “G. d'Annunzio” University of Chieti-Pescara, Chieti, Italy
- Department of Medicine and Ageing Sciences, “G. d'Annunzio” University of Chieti–Pescara, Chieti, Italy
| | - Erminia Carletti
- Department of Medical, Oral and Biotechnological Sciences, “G. d'Annunzio” University of Chieti–Pescara, Chieti, Italy
- Centre for Advanced Studies and Technology (CAST), “G. d'Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Vanessa Capone
- Department of Medical, Oral and Biotechnological Sciences, “G. d'Annunzio” University of Chieti–Pescara, Chieti, Italy
- Centre for Advanced Studies and Technology (CAST), “G. d'Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Samantha Sperduti
- Department of Medical, Oral and Biotechnological Sciences, “G. d'Annunzio” University of Chieti–Pescara, Chieti, Italy
- Centre for Advanced Studies and Technology (CAST), “G. d'Annunzio” University of Chieti-Pescara, Chieti, Italy
| | - Giuseppina Bologna
- Centre for Advanced Studies and Technology (CAST), “G. d'Annunzio” University of Chieti-Pescara, Chieti, Italy
- Department of Medicine and Ageing Sciences, “G. d'Annunzio” University of Chieti–Pescara, Chieti, Italy
| | - Marco Marchisio
- Centre for Advanced Studies and Technology (CAST), “G. d'Annunzio” University of Chieti-Pescara, Chieti, Italy
- Department of Medicine and Ageing Sciences, “G. d'Annunzio” University of Chieti–Pescara, Chieti, Italy
| | - Marta Di Nicola
- Department of Medical, Oral and Biotechnological Sciences, “G. d'Annunzio” University of Chieti–Pescara, Chieti, Italy
| | - Matteo Neri
- Centre for Advanced Studies and Technology (CAST), “G. d'Annunzio” University of Chieti-Pescara, Chieti, Italy
- Department of Medicine and Ageing Sciences, “G. d'Annunzio” University of Chieti–Pescara, Chieti, Italy
- * E-mail: (MS); (MN)
| | - Michele Sallese
- Department of Medical, Oral and Biotechnological Sciences, “G. d'Annunzio” University of Chieti–Pescara, Chieti, Italy
- Centre for Advanced Studies and Technology (CAST), “G. d'Annunzio” University of Chieti-Pescara, Chieti, Italy
- * E-mail: (MS); (MN)
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8
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Madadi S, Schwarzenbach H, Lorenzen J, Soleimani M. MicroRNA expression studies: challenge of selecting reliable reference controls for data normalization. Cell Mol Life Sci 2019; 76:3497-3514. [PMID: 31089747 PMCID: PMC11105490 DOI: 10.1007/s00018-019-03136-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/13/2019] [Accepted: 05/06/2019] [Indexed: 02/06/2023]
Abstract
Accurate determination of microRNA expression levels is a prerequisite in using these small non-coding RNA molecules as novel biomarkers in disease diagnosis and prognosis. Quantitative PCR is the method of choice for measuring the expression levels of microRNAs. However, a major obstacle that affects the reliability of results is the lack of validated reference controls for data normalization. Various non-coding RNAs have previously been used as reference controls, but their use may lead to variations and lack of comparability of microRNA data among the studies. Despite the growing number of studies investigating microRNA profiles to discriminate between healthy and disease stages, robust reference controls for data normalization have so far not been established. In the present article, we provide an overview of different reference controls used in various diseases, and highlight the urgent need for the identification of suitable reference controls to produce reliable data. Our analysis shows, among others, that RNU6 is not an ideal normalizer in studies using patient material from different diseases. Finally, our article tries to disclose the challenges to find a reference control which is uniformly and stably expressed across all body tissues, fluids, and diseases.
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Affiliation(s)
- Soheil Madadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Heidi Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Johan Lorenzen
- Department of Nephrology, University Hospital Zürich, Zurich, Switzerland
| | - Meysam Soleimani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran.
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9
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Buglyó G, Magyar Z, Romicsné Görbe É, Bánusz R, Csóka M, Micsik T, Berki Z, Varga P, Sápi Z, Nagy B. Quantitative RT-PCR-based miRNA profiling of blastemal Wilms' tumors from formalin-fixed paraffin-embedded samples. J Biotechnol 2019; 298:11-15. [PMID: 30959135 DOI: 10.1016/j.jbiotec.2019.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 02/08/2023]
Abstract
Blastemal Wilms' tumors are associated with poor chemo-responsiveness and an adverse prognosis. Our aim was to contribute to the miRNA profiling of the disease, while demonstrating the value of archived formalin-fixed, paraffin-embedded (FFPE) samples as miRNA sources. MiRNA was extracted from tumor and normal tissues of 8 patients diagnosed with blastemal Wilms' tumor in Hungary. A quantitative real-time PCR-based protocol was used to identify miRNAs of interest and study the expression of selected miRNAs in all samples. Profiling of miRNA expression from FFPE samples turned out to be cost-effective in Wilms' tumor, as most miRNAs (including miRNA-194-5p, which was studied in all patients) showed expression alterations similar to the ones reported in the literature. MiR-184 expression was found to be lower than in previous studies, while the downregulation of miR-203a is a novel finding. MiR-184 may be downregulated in a subset of blastemal and other Wilms' tumors. A loss of miR-203a may or may not be specific to blastemal cells, but available evidence hints at its importance in the pathogenesis of Wilms' tumor. It should be considered for inclusion in future studies of miRNA expression.
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Affiliation(s)
- Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 1 Egyetem tér, 4032, Debrecen, Hungary.
| | - Zsófia Magyar
- Department of Obstetrics and Gynaecology, Baross Street Division, Semmelweis University, 27 Baross utca, 1088, Budapest, Hungary.
| | - Éva Romicsné Görbe
- Department of Obstetrics and Gynaecology, Baross Street Division, Semmelweis University, 27 Baross utca, 1088, Budapest, Hungary.
| | - Rita Bánusz
- 2(nd) Department of Paediatrics, Semmelweis University, 7-9 Tűzoltó utca, 1094, Budapest, Hungary.
| | - Monika Csóka
- 2(nd) Department of Paediatrics, Semmelweis University, 7-9 Tűzoltó utca, 1094, Budapest, Hungary.
| | - Tamás Micsik
- 1(st) Department of Pathology and Experimental Cancer Research, Semmelweis University, 26 Üllői út, 1085, Budapest, Hungary.
| | - Zsanett Berki
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 1 Egyetem tér, 4032, Debrecen, Hungary.
| | - Péter Varga
- Department of Obstetrics and Gynaecology, Baross Street Division, Semmelweis University, 27 Baross utca, 1088, Budapest, Hungary.
| | - Zoltán Sápi
- 1(st) Department of Pathology and Experimental Cancer Research, Semmelweis University, 26 Üllői út, 1085, Budapest, Hungary.
| | - Bálint Nagy
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 1 Egyetem tér, 4032, Debrecen, Hungary.
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10
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Kolora SRR, Weigert A, Saffari A, Kehr S, Walter Costa MB, Spröer C, Indrischek H, Chintalapati M, Lohse K, Doose G, Overmann J, Bunk B, Bleidorn C, Grimm-Seyfarth A, Henle K, Nowick K, Faria R, Stadler PF, Schlegel M. Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation. Gigascience 2019; 8:giy160. [PMID: 30535196 PMCID: PMC6381762 DOI: 10.1093/gigascience/giy160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/19/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Lacerta viridis and Lacerta bilineata are sister species of European green lizards (eastern and western clades, respectively) that, until recently, were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed the first high-quality de novo genome assemblies for both L. viridis and L. bilineata through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signatures of selection on non-coding RNA, and on protein-coding genes. FINDINGS Here we show that gene flow was primarily unidirectional from L. bilineata to L. viridis after their split at least 1.15 million years ago. We detected positive selection of the non-coding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction, and behavior, as well as in ultraviolet-response, possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species needs to be further evaluated. CONCLUSION The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation-related issues in lacertids.
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Affiliation(s)
- Sree Rohit Raj Kolora
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
| | - Anne Weigert
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - Amin Saffari
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Human Biology Group, Institute for Zoology, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 1–3, Berlin, D-14195, Germany
| | - Stephanie Kehr
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
| | - Maria Beatriz Walter Costa
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Embrapa Agroenergia, Parque Estacaeo Biologica (PqEB), Asa Norte, Brasilia/DF, 70770-901, Brazil
| | - Cathrin Spröer
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, 38124, Germany
| | - Henrike Indrischek
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden, 01307, Germany
- Max Planck Institute for Physics of Complex Systems, Noethnitzerstrasse 38, 01187 Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01397 Dresden, Germany
| | - Manjusha Chintalapati
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom
| | - Gero Doose
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
| | - Jörg Overmann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, 38124, Germany
| | - Boyke Bunk
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, 38124, Germany
| | - Christoph Bleidorn
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Department of Animal Evolution and Biodiversity, University of Göttingen, Untere Karspüle 2, Göttingen, 37073, Germany
- Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), Madrid, 28006, Spain
| | - Annegret Grimm-Seyfarth
- Department of Conservation Biology, UFZ - Helmholtz Center for Environmental Research, Permoserstrasse 15, Leipzig, 04318, Germany
- Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, Potsdam, 14476, Germany
| | - Klaus Henle
- Department of Conservation Biology, UFZ - Helmholtz Center for Environmental Research, Permoserstrasse 15, Leipzig, 04318, Germany
| | - Katja Nowick
- Human Biology Group, Institute for Zoology, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 1–3, Berlin, D-14195, Germany
| | - Rui Faria
- Department of Animal and Plant Sciences, Alfred Building, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Peter F Stadler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Universität Leipzig, Augustusplatz 12, Leipzig, 04107, Germany
- Max-Planck-Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany
- Fraunhofer Institut Für Zelltherapie Und Immunologie, Perlickstrasse 1, Leipzig, 04103, Germany
- Department of Theoretical Chemistry, University of Vienna, Währinger strasse 17, Wien, 1090, Austria
- Center for non-Coding RNA in Technology and Health, University of Copenhagen, Gronnegardsvej 3, Frederiksberg C, 1870, Denmark
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico, 87501, USA
| | - Martin Schlegel
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
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11
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Gundara JS, Jamal K, Kurzawinski T. Dictating genomic destiny: Epigenetic regulation of pancreatic neuroendocrine tumours. Mol Cell Endocrinol 2018; 469:85-91. [PMID: 28385665 DOI: 10.1016/j.mce.2017.03.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/30/2017] [Accepted: 03/30/2017] [Indexed: 12/21/2022]
Abstract
Pancreatic neuroendocrine tumours are a diverse group of neoplasms with an increasingly well-defined genomic basis. Despite this, much of what drives this disease is still unknown and epigenetic influences represent the next tier of gene, and hence disease modifiers that are of unquestionable importance. Moreover, they are of arguably more significance than the genes themselves given their malleable nature and potential to be exploited for not only diagnosis and prognosis, but also therapy. This review summarises what is known regarding the key epigenetic modifiers of disease through the domains of diagnosis, prognosis and treatment.
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Affiliation(s)
- Justin S Gundara
- Centre for Endocrine Surgery, University College London Hospital, London, United Kingdom.
| | - Karim Jamal
- Centre for Endocrine Surgery, University College London Hospital, London, United Kingdom
| | - Tom Kurzawinski
- Centre for Endocrine Surgery, University College London Hospital, London, United Kingdom
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12
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Malczewska A, Kidd M, Matar S, Kos-Kudla B, Modlin IM. A Comprehensive Assessment of the Role of miRNAs as Biomarkers in Gastroenteropancreatic Neuroendocrine Tumors. Neuroendocrinology 2018; 107:73-90. [PMID: 29566385 DOI: 10.1159/000487326] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/25/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND/AIMS A key issue in neuroendocrine neoplasia management is the identification of blood signatures that specifically define the activity of a cancer or local tumor microenvironment. MicroRNAs (miRNAs) may represent such a candidate. To evaluate their clinical utility as biomarkers in gastroenteropancreatic neuroendocrine tumors (GEP-NETs), we assessed their expression in tissue and blood. METHODS A systematic review of PubMed was undertaken to identify studies investigating miRNAs in GEP-NETs and their utility as blood or tissue biomarkers. RESULTS Twenty-two studies using a range of methodologies with different normalization protocols were identified: tumor - gastric NET type 1 (n = 1 study: MiR-222, regulates p27KIP1), pancreatic (n = 6: MiR-21 [inflammatory marker, oncogene] and MiR-144 [PI3K/AKT signaling], both up- and downregulated depending on the method), small intestinal (n = 7: no consistent signature), and colorectal (n = 3: no consistent signature); blood - gastric NET type 1 (n = 1: MiR-222), pancreatic (n = 3: MiR-21), and small intestinal (n = 3: no consistent signature). The studies all included heterogeneous cohorts, were insufficiently powered, and utilized different methodologies, and age- and gender-matched controls were not used. Different miRNA isolation methods and detection protocols resulted in inconsistent expression comparing tumor and blood. A scientific discrepancy was the downregulated expression of some circulating candidates compared to tissue levels, suggesting methodological issues or physiological responses to the tumor. Both are of concern in defining the biometrics of a marker. CONCLUSIONS A potential biomarker for GEP-NETs included MiR-21 (small bowel and pancreas), but this epithelial tumor marker requires prospective validation. Overall, significant scientific investigation remains to identify and demonstrate neuroendocrine specificity and to validate candidate miRNA biomarkers.
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Affiliation(s)
- Anna Malczewska
- Department of Endocrinology and Neuroendocrine Tumors, Medical University of Silesia, Katowice, Poland
| | - Mark Kidd
- Wren Laboratories, Branford, Connecticut, USA
| | - Somer Matar
- Wren Laboratories, Branford, Connecticut, USA
| | - Beata Kos-Kudla
- Department of Endocrinology and Neuroendocrine Tumors, Medical University of Silesia, Katowice, Poland
| | - Irvin M Modlin
- Yale University School of Medicine, New Haven, Connecticut, USA
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13
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Suárez-Arriaga MC, Torres J, Camorlinga-Ponce M, Gómez-Delgado A, Piña-Sánchez P, Valdez-Salazar HA, Ribas-Aparicio RM, Fuentes-Pananá EM, Ruiz-Tachiquín ME. A proposed method for the relative quantification of levels of circulating microRNAs in the plasma of gastric cancer patients. Oncol Lett 2017; 13:3109-3117. [PMID: 28521416 PMCID: PMC5431292 DOI: 10.3892/ol.2017.5816] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/26/2017] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer (GC) is the fifth most common type of malignancy and the third leading cause of cancer-associated mortality worldwide. It is necessary to identify novel methods aimed at improving the early diagnosis and treatment of GC. MicroRNA expression profiles in the plasma of patients with GC have demonstrated a potential use in the opportune diagnosis of this neoplasm. However, there are currently no standardized targets for use in the normalization of microRNA Cq values for different neoplasms. The present study tested two normalization approaches while analyzing plasma derived from patients with GC and non-atrophic gastritis. The first method utilized a panel of small nucleolar RNAs (snoRNAs) and a small nuclear RNA (snRNA) provided by a commercial array. The second normalization approach involved the use of hsa-miR-18a-5p and hsa-miR-29a-3p, which were identified by a stability analysis of the samples being tested. The results revealed that the snoRNAs and snRNA were not expressed in all samples tested. Only the stable microRNAs allowed a narrow distribution of the data and enabled the identification of specific downregulation of hsa-miR-200c-3p and hsa-miR-26b-5p in patients with GC. hsa-miR-200c-3p and hsa-miR-26b-5p have been previously linked to cancer, and a Kyoto Encyclopedia of Genes and Genomes analysis demonstrated that these microRNAs were associated with cell adhesion, cell cycle and cancer pathways.
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Affiliation(s)
- Mayra-Cecilia Suárez-Arriaga
- Medical Research Unit in Human Genetics, Pediatrics Hospital 'Dr Silvestre Frenk Freud', XXI Century National Medical Center, Mexican Institute of Social Security, 06720 Mexico City, Mexico.,Department of Microbiology, National School of Biological Sciences, National Polytechnic Institute, 11340 Mexico City, Mexico
| | - Javier Torres
- Medical Research Unit in Infectious and Parasitic Diseases, Pediatrics Hospital 'Dr Silvestre Frenk Freud', XXI Century National Medical Center, Mexican Institute of Social Security, 06720 Mexico City, Mexico
| | - Margarita Camorlinga-Ponce
- Medical Research Unit in Infectious and Parasitic Diseases, Pediatrics Hospital 'Dr Silvestre Frenk Freud', XXI Century National Medical Center, Mexican Institute of Social Security, 06720 Mexico City, Mexico
| | - Alejandro Gómez-Delgado
- Medical Research Unit in Infectious and Parasitic Diseases, Pediatrics Hospital 'Dr Silvestre Frenk Freud', XXI Century National Medical Center, Mexican Institute of Social Security, 06720 Mexico City, Mexico
| | - Patricia Piña-Sánchez
- Medical Research Unit in Oncological Diseases, Oncology Hospital, XXI Century National Medical Center, Mexican Institute of Social Security, 06720 Mexico City, Mexico
| | - Hilda-Alicia Valdez-Salazar
- Medical Research Unit in Infectious and Parasitic Diseases, Pediatrics Hospital 'Dr Silvestre Frenk Freud', XXI Century National Medical Center, Mexican Institute of Social Security, 06720 Mexico City, Mexico
| | - Rosa-María Ribas-Aparicio
- Department of Microbiology, National School of Biological Sciences, National Polytechnic Institute, 11340 Mexico City, Mexico
| | - Ezequiel M Fuentes-Pananá
- Virology and Cancer Research Unit, Children's Hospital of Mexico 'Federico Gómez', 06720 Mexico City, Mexico
| | - Martha-Eugenia Ruiz-Tachiquín
- Medical Research Unit in Human Genetics, Pediatrics Hospital 'Dr Silvestre Frenk Freud', XXI Century National Medical Center, Mexican Institute of Social Security, 06720 Mexico City, Mexico
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14
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Liu Y, Lu Q. Extracellular vesicle microRNAs: biomarker discovery in various diseases based on RT-qPCR. Biomark Med 2016; 9:791-805. [PMID: 26287938 DOI: 10.2217/bmm.15.45] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In recent years, biomarker discovery based on extracellular microRNAs (miRNAs), especially exosome miRNAs, has drawn wide attention. While exosome isolation and identification technologies are increasingly sophisticated, the preanalytical process of exosome miRNAs seems to be no longer a crucial problem. Though next-generation sequencing, microarray and digital PCR have been recommended as good downstream analytical platforms for exosome miRNA quantification, they are still more constrained in clinical utility compared with RT-qPCR method at present. In this review, we will trace back to the origin and summarize current studies of biomarker discovery based on extracellular vesicle miRNAs, and provide an overview and latest developments of RT-qPCR-based data normalization, in order to further assist the development of translational medicine.
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Affiliation(s)
- Ying Liu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, #139 Renmin Middle Rd, Changsha, Hunan 410011, PR China
| | - Qianjin Lu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, #139 Renmin Middle Rd, Changsha, Hunan 410011, PR China
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15
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Zehentmayr F, Hauser-Kronberger C, Zellinger B, Hlubek F, Schuster C, Bodenhofer U, Fastner G, Deutschmann H, Steininger P, Reitsamer R, Fischer T, Sedlmayer F. Hsa-miR-375 is a predictor of local control in early stage breast cancer. Clin Epigenetics 2016; 8:28. [PMID: 26962366 PMCID: PMC4784328 DOI: 10.1186/s13148-016-0198-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 03/02/2016] [Indexed: 12/17/2022] Open
Abstract
Background A long-term analysis by the Early Breast Cancer Trialist Group (EBCTG) revealed a strong correlation between local control and cancer-specific mortality. MicroRNAs (miRs), short (20–25 nucleotides) non-coding RNAs, have been described as prognosticators and predictors for breast cancer in recent years. The aim of the current study was to identify miRs that can predict local control after breast conserving therapy (BCT) in early stage breast cancer. Results Clinical data of 46 early stage breast cancer patients with local relapse after BCT were selected from the institutional database. These patients were matched to 101 control patients showing identical clinical features but without local relapse. The study was conducted in two steps. (1) In the pilot study, 32 patients (16 relapses versus 16 controls) were screened for the most de-regulated microRNAs (= candidate microRNAs) in a panel of 1250 miRs by microarray technology. Eight miRs were found to be significantly de-regulated. (2) In the validation study, the candidate microRNAs were analyzed in an independent cohort of 115 patients (30 relapses versus 85 controls) with reverse transcription quantitative polymerase chain reaction (RT-qPCR). From these eight candidates, hsa-miR-375 could be validated. Its median fold change was 2.28 (Mann-Whitney U test, corrected p value = 0.008). In the log-rank analysis, high expression levels of hsa-miR-375 correlated with a significantly higher risk of local relapse (p = 0.003). In a multivariate analysis (forward stepwise regression) including established predictors and prognosticators, hsa-miR-375 was the only variable that was able to distinguish the statistical significance between relapse and control groups (raw p value = 0.000195 HR = 0.76, 95 % CI 0.66–0.88; corrected p value = 0.005). Conclusions Hsa-miR-375 predicts local control in patient with early stage breast cancer, especially in estrogen receptor α (ER-α)-positive patients. It can therefore serve as an additional molecular marker for treatment choice independently from known predictors and prognosticators. Validation in larger prospective studies is warranted. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0198-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Franz Zehentmayr
- Department of Radiation Oncology, Paracelsus Medical University, SALK, Müllner Hauptstraße 48, A-5020 Salzburg, Austria ; radART - Institute for Research and Development on Advanced Radiation Technologies, Paracelsus Medical University, Salzburg, Austria
| | | | - Barbara Zellinger
- radART - Institute for Research and Development on Advanced Radiation Technologies, Paracelsus Medical University, Salzburg, Austria ; Department of Pathology, Paracelsus Medical University, SALK, Salzburg, Austria
| | - Falk Hlubek
- Department of Pathology, Ludwig Maximilian University, Munich, Germany
| | - Claudia Schuster
- Department of Pathology, Ludwig Maximilian University, Munich, Germany
| | - Ulrich Bodenhofer
- Institute of Bioinformatics, Johannes Kepler University, Linz, Austria
| | - Gerd Fastner
- Department of Radiation Oncology, Paracelsus Medical University, SALK, Müllner Hauptstraße 48, A-5020 Salzburg, Austria
| | - Heinz Deutschmann
- Department of Radiation Oncology, Paracelsus Medical University, SALK, Müllner Hauptstraße 48, A-5020 Salzburg, Austria ; radART - Institute for Research and Development on Advanced Radiation Technologies, Paracelsus Medical University, Salzburg, Austria
| | - Philipp Steininger
- radART - Institute for Research and Development on Advanced Radiation Technologies, Paracelsus Medical University, Salzburg, Austria
| | - Roland Reitsamer
- Department of Gynecology and Obstetrics, Paracelsus Medical University, SALK, Salzburg, Austria
| | - Thorsten Fischer
- Department of Gynecology and Obstetrics, Paracelsus Medical University, SALK, Salzburg, Austria
| | - Felix Sedlmayer
- Department of Radiation Oncology, Paracelsus Medical University, SALK, Müllner Hauptstraße 48, A-5020 Salzburg, Austria ; radART - Institute for Research and Development on Advanced Radiation Technologies, Paracelsus Medical University, Salzburg, Austria
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16
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Wang G, Zhu S, Gu Y, Chen Q, Liu X, Fu H. MicroRNA-145 and MicroRNA-133a Inhibited Proliferation, Migration, and Invasion, While Promoted Apoptosis in Hepatocellular Carcinoma Cells Via Targeting FSCN1. Dig Dis Sci 2015; 60:3044-52. [PMID: 26173501 DOI: 10.1007/s10620-015-3706-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 05/06/2015] [Indexed: 01/29/2023]
Abstract
BACKGROUND Deregulation of FSCN1 has been observed in human cancers. However, the regulatory mechanism of FSCN1 in hepatocellular carcinoma (HCC) remains largely unknown. AIMS Our study aimed to reveal the roles of microRNA (miR)-133a, miR-145, and FSCN1 in HCC cells. METHODS Real-time RT-PCR and western blot were performed to determine the expression of miR-133a, miR-145, and FSCN1. Luciferase reporter assay was used to determine whether FSCN1 was a target of miR-133a and miR-145. Effects of miR-133a, miR-145, and FSCN1 on HCC cell proliferation, apoptosis, migration, and invasion were then investigated. RESULTS We showed that the expression of FSCN1 was increased in HCC tissues compared to the normal adjacent tissues. Moreover, upregulation of FSCN1 and downregulation of miR-145 and miR-133a co-existed in HCC. Functional studies revealed that miR-145 and miR-133a negatively regulated the expression of FSCN1 in HCC cells, via directly binding to the 3'-untranslational region of FSCN1 mRNA. Overexpression of miR-145 and miR-133a led to decreased FSCN1 expression, and downregulation of miR-145 and miR-133a resulted in increased FSCN1 expression in HCC cells. Furthermore, overexpression of miR-145 and miR-133a inhibited cellular proliferation, migration, and invasion, while promoted apoptosis in HCC cells. On the contrary, inhibition of miR-145 and miR-133a promoted cellular proliferation, migration, and invasion, while suppressed apoptosis in HCC cells. CONCLUSION Our study suggests that the abnormal upregulation of FSCN1 in HCC is associated with downregulation of miR-145 and miR-133a, and miR-145 and miR-133a inhibit malignant progression of HCC in vitro, possibly via directly targeting FSCN1.
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Affiliation(s)
- Guohui Wang
- Centre of Experimental Medicine, Third Xiangya Hospital of Central South University, Changsha, 410013, Hunan, China
| | - Shaihong Zhu
- Centre of Experimental Medicine, Third Xiangya Hospital of Central South University, Changsha, 410013, Hunan, China
| | - Yonghong Gu
- Department of Pathology, Third Xiangya Hospital of Central South University, No. 138 Tongzipo Road, Changsha, 410013, Hunan, China
| | - Qian Chen
- Department of Pathology, Third Xiangya Hospital of Central South University, No. 138 Tongzipo Road, Changsha, 410013, Hunan, China
| | - Xinrong Liu
- Department of Pathology, Third Xiangya Hospital of Central South University, No. 138 Tongzipo Road, Changsha, 410013, Hunan, China
| | - Hua Fu
- Department of Pathology, Third Xiangya Hospital of Central South University, No. 138 Tongzipo Road, Changsha, 410013, Hunan, China.
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Moreno JM, Núñez MJ, Quiñonero A, Martínez S, de la Orden M, Simón C, Pellicer A, Díaz-García C, Domínguez F. Follicular fluid and mural granulosa cells microRNA profiles vary in in vitro fertilization patients depending on their age and oocyte maturation stage. Fertil Steril 2015. [PMID: 26209829 DOI: 10.1016/j.fertnstert.2015.07.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
OBJECTIVE To determine whether there is any difference in the follicular fluid (FF) microRNA (miRNA) profiles from in vitro fertilization (IVF) patients according to their age and oocyte maturation stage. DESIGN Observational prospective study. SETTING IVF clinic/hospital facilities. PATIENTS(S) We included 30 women with primary infertility undergoing intracytoplasmic sperm injection treatment and excluded patients with polycystic ovarian syndrome, endometriosis, severe male factor, and low ovarian reserve. INTERVENTION(S) After the collection of FF and granulosa cells from each patient, the samples were processed for total RNA extraction. RNA was pooled into different groups (three samples per pool) for microarray analysis to evaluate the expression of a total of 866 human miRNAs. Individual samples were analyzed to validate the pooled microarray results using real-time polymerase chain reaction. MAIN OUTCOME MEASURE(S) Evaluation of the expression of a total of 866 human miRNAs in FF and granulosa cells. RESULT(S) We identified only one differentially expressed miRNA, hsa-miR-424, which is present in higher proportions in FF from patients with advanced age. When we compared the FF from metaphase II (MII) versus GV (germinal vesicle) oocytes, we found 13 differentially expressed miRNAs (two up- and 11 downregulated). When we compared FF from MII versus MI, we found seven differentially expressed miRNAs in MII (three up- and four downregulated). CONCLUSION(S) We have described the FF miRNA profiles according to IVF patients' age and the maturation stage of their oocytes. This descriptive study may aid our understanding of the physiology and regulation of oocyte maturation and could identify some potential miRNA biomarkers for this process. CLINICAL TRIAL REGISTRATION NUMBER Not applicable.
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Affiliation(s)
- Juan Manuel Moreno
- Fundación Instituto Valenciano de Infertilidad, Instituto Universitario IVI, Valencia, Spain
| | - María José Núñez
- Reproductive Medicine Research Group, Instituto de Investigación Sanitaria La Fe, La Fe University Hospital, Valencia, Spain
| | - Alicia Quiñonero
- Fundación Instituto Valenciano de Infertilidad, Instituto Universitario IVI, Valencia, Spain
| | - Sebastian Martínez
- Fundación Instituto Valenciano de Infertilidad, Instituto Universitario IVI, Valencia, Spain
| | - Marina de la Orden
- Reproductive Medicine Research Group, Instituto de Investigación Sanitaria La Fe, La Fe University Hospital, Valencia, Spain
| | - Carlos Simón
- Fundación Instituto Valenciano de Infertilidad, Instituto Universitario IVI, Valencia, Spain; INCLIVA Biomedical Research Institute, Valencia, Spain; Department of Obstetrics and Gynecology, Stanford University, Stanford, California
| | - Antonio Pellicer
- Fundación Instituto Valenciano de Infertilidad, Instituto Universitario IVI, Valencia, Spain; Reproductive Medicine Research Group, Instituto de Investigación Sanitaria La Fe, La Fe University Hospital, Valencia, Spain
| | - César Díaz-García
- Reproductive Medicine Research Group, Instituto de Investigación Sanitaria La Fe, La Fe University Hospital, Valencia, Spain
| | - Francisco Domínguez
- Fundación Instituto Valenciano de Infertilidad, Instituto Universitario IVI, Valencia, Spain; INCLIVA Biomedical Research Institute, Valencia, Spain.
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Stability Assessment of Candidate Reference Genes in Urine Sediment of Prostate Cancer Patients for miRNA Applications. DISEASE MARKERS 2015; 2015:973597. [PMID: 26078486 PMCID: PMC4452852 DOI: 10.1155/2015/973597] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/30/2015] [Indexed: 12/19/2022]
Abstract
We aimed at assessing the stability of candidate reference genes in urine sediments of men subjected to digital rectal examination for suspected prostate cancer (PCa). Two microRNAs (miR-191 and miR-25) and 1 small nucleolar RNA (SNORD48) were assayed in 35 post-DRE urine sediments of men with PCa and in 26 subjects with histologically confirmed benign prostatic hyperplasia (BPH). The stability of candidate reference genes was assessed through BestKeeper algorithm and equivalence test. miR-200b and miR-452 were used to test for the effect of normalization on target genes. Our results proved miR-191 to be the most stable gene, showing the lowest degree of variation and the highest stability value. miR-25 and SNORD48 values fell beyond the cutoff of acceptability. In conclusion, we recommend the use of miR-191 for normalization purposes in post-DRE urine sediments.
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Miller HC, Kidd M, Castellano L, Frilling A. Molecular genetic findings in small bowel neuroendocrine neoplasms: a review of the literature. INTERNATIONAL JOURNAL OF ENDOCRINE ONCOLOGY 2015. [DOI: 10.2217/ije.14.41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Small bowel neuroendocrine neoplasms (SBNEN) are the most common small bowel tumor and have an increasing incidence. Despite many treatment options, therapeutic strategy remains a key clinical challenge due to the paucity of large-scale, randomized controlled trials. The heterogeneity of SBNEN coupled with a lack of detailed information about the tumor biology, impedes patient stratification into groups based on tumor phenotypes or treatment response. More detailed analysis of the genetic and epigenetic characteristics of SBNEN, will allow treatment to move toward a more personalized medicine approach through the identification of novel biomarkers and therapeutic targets, with the aim to increase survival.
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Affiliation(s)
- Helen C Miller
- Department of Surgery & Cancer, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0HS, UK
| | - Mark Kidd
- Department of Surgery, Yale University, School of Medicine, 333 Cedar Street, New Haven, CT 06520–8062, USA
| | - Leandro Castellano
- Department of Surgery & Cancer, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0HS, UK
| | - Andrea Frilling
- Department of Surgery & Cancer, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0HS, UK
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Wang H, Wang J, Sun S, Wang Y, Guo J, Ning C, Yang K, Liu JF. Identification of reference microRNAs for quantitative expression analysis in porcine peripheral blood mononuclear cells treated with polyinosinic-polycytidylic acid. Int J Immunogenet 2015; 42:217-25. [PMID: 25817599 DOI: 10.1111/iji.12198] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 03/02/2015] [Accepted: 03/08/2015] [Indexed: 11/29/2022]
Abstract
Peripheral blood mononuclear cells (PBMCs) are clinically important cells. Detection of microRNAs (miRNAs) expression in PBMCs can be useful for miRNA biomarker discovery for various diseases. Quantitative real-time PCR (qRT-PCR) has become an important method used for measuring miRNAs expression. However, the reliability of qRT-PCR data critically depends on proper selection of reference genes. Here, we performed qRT-PCR to quantify the expression levels of nine miRNAs (Ssc-miR-16, Hsa-miR-25, Ssc-miR-34a, Hsa-miR-93, Bta-miR-92b, Ssc-miR-103, Ssc-miR-106a, Ssc-miR-128 and Ssc-miR-107) and one small nuclear RNA (U6) in PBMCs treated with polyinosinic-polycytidylic acid [poly (I:C)] that widely used for simulating viral infection. We used the four statistical algorithms (GeNorm 3.5, NormFinder, BestKeeper and comparative ∆ Ct method) to evaluate gene expression stability and observed that Ssc-miR-34a was the best single reference gene and the pair of Ssc-miR-107 and Ssc-miR-103 was the best combination of reference miRNAs for porcine PBMCs treated with poly (I:C). Our study shows the first evidence of careful selection of reference miRNAs in porcine PBMCs and maybe helpful for discovering miRNA biomarkers for double-stranded RNA-induced disease.
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Affiliation(s)
- H Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - J Wang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - S Sun
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Y Wang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - J Guo
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - C Ning
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - K Yang
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu, China
| | - J-F Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Serum interferon-related microRNAs as biomarkers to predict the response to interferon therapy in chronic hepatitis C genotype 4. PLoS One 2015; 10:e0121524. [PMID: 25811198 PMCID: PMC4374907 DOI: 10.1371/journal.pone.0121524] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 02/03/2015] [Indexed: 12/31/2022] Open
Abstract
Background Hepatitis C virus genotype 4 (HCV-4) infection is common in the Middle East and Africa, with an extraordinarily high prevalence in Egypt. MicroRNAs (miRNAs) play an important role in various diseases, including HCV infection. The aim of the present study was to assess serum miR-122, miR-221 and miR-21 expression profiles in HCV-4 patients prior to treatment with HCV-4 combination therapy (pegylated alpha interferon and ribavirin) and to determine whether the miRNAs were associated with the drug response. Methods RNA was extracted from pretreatment serum samples, and miR-122, miR-221 and miR-21 levels were measured by quantitative PCR. The results were compared among patients with sustained virological responses (SVR) and non-responders (NR). Results The expression levels of miR-21 and miR-122 were significantly different between the SVR and NR groups. Receiver operator characteristic (ROC) analysis revealed that the sensitivity, specificity and positive predictive values of miR-21 were 82.2%, 77.3% and 88.1%, respectively, with a cut-off value of 1.7. The sensitivity, specificity and positive predictive values of miR-122 were 68.9%, 59.1% and 77.5%, respectively, with a cut-off value of 3.5. Conclusion and Significance miR-21 and miR-122 might be useful predictors for SVR in HCV-4 patients prior to the administration of combination therapy. A higher predictive response power was obtained for miR-21 than for miR-122. These results should reduce ineffective treatments.
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Serum interferon-related microRNAs as biomarkers to predict the response to interferon therapy in chronic hepatitis C genotype 4. PLoS One 2015; 10:e0120794. [PMID: 25790297 PMCID: PMC4366211 DOI: 10.1371/journal.pone.0120794] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 01/26/2015] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs are messengers during interferon-virus interplay and are involved in antiviral immunity, however, little is known about interferon-related microRNAs regarding their detection in serum and their potential use as non-invasive diagnostic and prognostic biomarkers in chronic hepatitis C (CHC). To elucidate some of the molecular aspects underlying failure of pegylated interferon-α/ribavirin therapy, we investigated pretreatment expression profiles of seven selected interferon-related microRNAs (miR-146a, miR-34a, miR-130a, miR-19a, miR-192, miR-195, and miR-296) by quantitative RT-PCR custom array technology in serum of Egyptian CHC genotype 4 patients and whether their pretreatment levels would predict patient response to the combination therapy. One hundred and six CHC patients and forty matched healthy controls were included. Patients were divided into sustained virological response (SVR) and non-responder (NR) groups. Serum miR-34a, miR-130a, miR-19a, miR-192, miR-195, and miR-296 were upregulated, whereas serum miR-146a was downregulated in CHC compared to controls. Significant correlations were found between expression levels of studied microRNAs and also with clinical data. Pretreatment levels of miR-34a, miR-130a, and miR-195 were significantly higher, whereas miR-192 and miR-296 levels were significantly lower in SVR than NR patients. miR-19a and miR-146a levels were not significantly different between the two groups. miR-34a was superior to differentiate CHC from controls, whereas miR-296 was superior to discriminate SVR from NR patients by receiver operating characteristic analysis. Multivariate logistic analysis revealed miR-34a and miR-195 as independent predictors for SVR and miR-192 as an independent variable for non-response. In conclusion, pretreatment expression profiles of five interferon-related microRNAs are associated with treatment outcome in CHC. Of these, miR-34a, miR-195, and miR-192 could predict treatment response. The profiling results could be used as novel non-invasive diagnostic and prognostic pharmacogenetic biomarkers for treatment personalization in CHC and could help to identify new microRNA-based antivirals.
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Moore-Olufemi SD, Olsen AB, Hook-Dufresne DM, Bandla V, Cox CS. Transforming growth factor-beta 3 alters intestinal smooth muscle function: implications for gastroschisis-related intestinal dysfunction. Dig Dis Sci 2015; 60:1206-14. [PMID: 25431043 PMCID: PMC4427617 DOI: 10.1007/s10620-014-3439-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 11/11/2014] [Indexed: 12/31/2022]
Abstract
BACKGROUND Gastroschisis (GS) is a congenital abdominal wall defect that results in the development of GS-related intestinal dysfunction (GRID). Transforming growth factor-β, a pro-inflammatory cytokine, has been shown to cause organ dysfunction through alterations in vascular and airway smooth muscle. The purpose of this study was to evaluate the effects of TGF-β3 on intestinal smooth muscle function and contractile gene expression. METHODS Archived human intestinal tissue was analyzed using immunohistochemistry and RT-PCR for TGF-β isoforms and markers of smooth muscle gene and micro-RNA contractile phenotype. Intestinal motility was measured in neonatal rats ± TGF-β3 (0.2 and 1 mg/kg). Human intestinal smooth muscle cells (hiSMCs) were incubated with fetal bovine serum ± 100 ng/ml of TGF-β 3 isoforms for 6, 24 and 72 h. The effects of TGF-β3 on motility, hiSMC contractility and hiSMC contractile phenotype gene and micro-RNA expression were measured using transit, collagen gel contraction assay and RT-PCR analysis. Data are expressed as mean ± SEM, ANOVA (n = 6-7/group). RESULTS GS infants had increased immunostaining of TGF-β3 and elevated levels of micro-RNA 143 & 145 in the intestinal smooth muscle. Rats had significantly decreased intestinal transit when exposed to TGF-β3 in a dose-dependent manner compared with Sham animals. TGF-β3 significantly increased hiSMC gel contraction and contractile protein gene and micro-RNA expression. CONCLUSION TGF-β3 contributed to intestinal dysfunction at the organ level, increased contraction at the cellular level and elevated contractile gene expression at the molecular level. A hyper-contractile response may play a role in the persistent intestinal dysfunction seen in GRID.
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Affiliation(s)
- S. D. Moore-Olufemi
- Department of Pediatric Surgery, The University of Texas Medical School at Houston, 6431 Fannin Street, MSB 5.222, Houston, TX 77030 USA
| | - A. B. Olsen
- Department of Pediatric Surgery, The University of Texas Medical School at Houston, 6431 Fannin Street, MSB 5.222, Houston, TX 77030 USA
| | - D. M. Hook-Dufresne
- Department of Surgery, The University of Texas Medical School at Houston, Houston, TX USA
| | - V. Bandla
- Department of Pediatrics, The University of Texas Medical School at Houston, Houston, TX USA
| | - C. S. Cox
- Department of Pediatric Surgery, The University of Texas Medical School at Houston, 6431 Fannin Street, MSB 5.222, Houston, TX 77030 USA
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