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Abeysinghe P, Turner N, Morean Garcia I, Mosaad E, Peiris HN, Mitchell MD. The Role of Exosomal Epigenetic Modifiers in Cell Communication and Fertility of Dairy Cows. Int J Mol Sci 2020; 21:ijms21239106. [PMID: 33266010 PMCID: PMC7731370 DOI: 10.3390/ijms21239106] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 11/27/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023] Open
Abstract
Abnormal uterine function affects conception rate and embryo development, thereby leading to poor fertility and reproduction failure. Exosomes are a nanosized subclass of extracellular vesicles (EV) that have important functions as intercellular communicators. They contain and carry transferable bioactive substances including micro RNA (miRNA) for target cells. Elements of the cargo can provide epigenetic modifications of the recipient cells and may have crucial roles in mechanisms of reproduction. The dairy industry accounts for a substantial portion of the economy of many agricultural countries. Exosomes can enhance the expression of inflammatory mediators in the endometrium, which contribute to various inflammatory diseases in transition dairy cows. This results in reduced fertility which leads to reduced milk production and increased cow maintenance costs. Thus, gaining a clear knowledge of exosomal epigenetic modifiers is critical to improving the breeding success and profitability of dairy farms. This review provides a brief overview of how exosomal miRNA contributes to inflammatory diseases and hence to poor fertility, particularly in dairy cows.
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Rohan TE, Wang T, Weinmann S, Wang Y, Lin J, Ginsberg M, Loudig O. A miRNA Expression Signature in Breast Tumor Tissue Is Associated with Risk of Distant Metastasis. Cancer Res 2019; 79:1705-1713. [PMID: 30760517 DOI: 10.1158/0008-5472.can-18-2779] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/17/2018] [Accepted: 02/06/2019] [Indexed: 11/16/2022]
Abstract
Dysregulation of miRNA expression may influence breast cancer progression, and experimental evidence suggests that miRNA silencing might suppress breast cancer metastasis. However, the relationship between miRNA and metastasis must be confirmed before this approach can be applied in the clinic. To this end, we conducted a two-stage study in a cohort of 3,760 patients with breast cancer to first identify and then validate the association between miRNA expression and risk of distant metastasis. The first stage (discovery) entailed miRNA sequencing of 126 case-control pairs; qPCR was used to validate the findings in a separate set of 80 case-control pairs. The 13 miRNAs most differentially expressed between cases and controls were combined into an miRNA score that was significantly associated with risk of distant metastasis in a logistic regression model that also included clinical variables (tumor size and number of positive lymph nodes) (ORper unit increase in score = 1.30; 95% confidence interval, 1.03-1.66). The results of this study suggest that in women with invasive breast cancer, a miRNA score that incorporates both clinical variables and miRNA expression levels in breast tumor tissue is moderately predictive of risk of subsequent distant metastasis. SIGNIFICANCE: A novel predictive scoring system for patients with breast cancer includes clinical variables and the expression levels of 13 miRNAs and may help to identify those at increased risk of distant metastasis.
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Affiliation(s)
- Thomas E Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York.
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Sheila Weinmann
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon
| | - Yihong Wang
- Department of Pathology and Laboratory of Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Juan Lin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Mindy Ginsberg
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York
| | - Olivier Loudig
- Hackensack University Medical Center, Hackensack, New Jersey
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Melnik BC, Schmitz G. Milk's Role as an Epigenetic Regulator in Health and Disease. Diseases 2017; 5:diseases5010012. [PMID: 28933365 PMCID: PMC5456335 DOI: 10.3390/diseases5010012] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/02/2017] [Accepted: 03/07/2017] [Indexed: 12/16/2022] Open
Abstract
It is the intention of this review to characterize milk's role as an epigenetic regulator in health and disease. Based on translational research, we identify milk as a major epigenetic modulator of gene expression of the milk recipient. Milk is presented as an epigenetic "doping system" of mammalian development. Milk exosome-derived micro-ribonucleic acids (miRNAs) that target DNA methyltransferases are implicated to play the key role in the upregulation of developmental genes such as FTO, INS, and IGF1. In contrast to miRNA-deficient infant formula, breastfeeding via physiological miRNA transfer provides the appropriate signals for adequate epigenetic programming of the newborn infant. Whereas breastfeeding is restricted to the lactation period, continued consumption of cow's milk results in persistent epigenetic upregulation of genes critically involved in the development of diseases of civilization such as diabesity, neurodegeneration, and cancer. We hypothesize that the same miRNAs that epigenetically increase lactation, upregulate gene expression of the milk recipient via milk-derived miRNAs. It is of critical concern that persistent consumption of pasteurized cow's milk contaminates the human food chain with bovine miRNAs, that are identical to their human analogs. Commercial interest to enhance dairy lactation performance may further increase the epigenetic miRNA burden for the milk consumer.
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Affiliation(s)
- Bodo C Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, Faculty of Human Sciences, University of Osnabrück, Am Finkenhügel 7a, D-49076 Osnabrück, Germany.
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, University of Regensburg, Franz-Josef-Strauß-Allee 11, D-93053 Regensburg, Germany.
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Loudig O, Wang T, Ye K, Lin J, Wang Y, Ramnauth A, Liu C, Stark A, Chitale D, Greenlee R, Multerer D, Honda S, Daida Y, Spencer Feigelson H, Glass A, Couch FJ, Rohan T, Ben-Dov IZ. Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens. Int J Mol Sci 2017; 18:ijms18030627. [PMID: 28335433 PMCID: PMC5372640 DOI: 10.3390/ijms18030627] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/02/2017] [Accepted: 03/08/2017] [Indexed: 01/30/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years. We then evaluated this cDNA library preparation protocol by performing a miRNA expression analysis of archived breast ductal carcinoma in situ (DCIS) specimens, selected for their relation to the risk of subsequent breast cancer development and obtained from six different institutions. Our analyses identified six miRNAs (miR-29a, miR-221, miR-375, miR-184, miR-363, miR-455-5p) differentially expressed between DCIS lesions from women who subsequently developed an invasive breast cancer (cases) and women who did not develop invasive breast cancer within the same time interval (control). Our thorough evaluation and application of this laboratory-based miRNA sequencing analysis indicates that the preparation of small RNA cDNA libraries can reliably be performed on older, archived, clinically-classified specimens.
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Affiliation(s)
- Olivier Loudig
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Kenny Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Juan Lin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Yihong Wang
- Department of Pathology, Rhode Island Hospital, Providence, RI 02903, USA.
| | - Andrew Ramnauth
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Christina Liu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Azadeh Stark
- Department of Pathology and Breast Oncology Program, Henry Ford Health System, Detroit, MI 48202, USA.
| | - Dhananjay Chitale
- Department of Pathology and Breast Oncology Program, Henry Ford Health System, Detroit, MI 48202, USA.
| | - Robert Greenlee
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA.
| | - Deborah Multerer
- Center for Clinical Epidemiology and Population Health, Marshfield Clinic Research Foundation, Marshfield, WI 54449, USA.
| | - Stacey Honda
- Department of Pathology, Center for Health Research, Kaiser Permanente, 3288 Moanalua Road, Honolulu, HI 96819, USA.
| | - Yihe Daida
- Department of Pathology, Center for Health Research, Kaiser Permanente, 3288 Moanalua Road, Honolulu, HI 96819, USA.
| | | | - Andrew Glass
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR 97227, USA.
| | - Fergus J Couch
- Health Sciences Research, Mayo Clinic, Rochester, NY 55902, USA.
| | - Thomas Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
- Montefiore Medical Center, Bronx, NY 10467, USA.
| | - Iddo Z Ben-Dov
- Laboratory of Medical Transcriptomics, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel.
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Kavitha N, Vijayarathna S, Jothy SL, Oon CE, Chen Y, Kanwar JR, Sasidharan S. MicroRNAs: biogenesis, roles for carcinogenesis and as potential biomarkers for cancer diagnosis and prognosis. Asian Pac J Cancer Prev 2015; 15:7489-97. [PMID: 25292018 DOI: 10.7314/apjcp.2014.15.18.7489] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs of 20-24 nucleotides that play important roles in carcinogenesis. Accordingly, miRNAs control numerous cancer-relevant biological events such as cell proliferation, cell cycle control, metabolism and apoptosis. In this review, we summarize the current knowledge and concepts concerning the biogenesis of miRNAs, miRNA roles in cancer and their potential as biomarkers for cancer diagnosis and prognosis including the regulation of key cancer-related pathways, such as cell cycle control and miRNA dysregulation. Moreover, microRNA molecules are already receiving the attention of world researchers as therapeutic targets and agents. Therefore, in-depth knowledge of microRNAs has the potential not only to identify their roles in cancer, but also to exploit them as potential biomarkers for cancer diagnosis and identify therapeutic targets for new drug discovery.
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Affiliation(s)
- Nowroji Kavitha
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia E-mail :
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Buitrago DH, Patnaik SK, Kadota K, Kannisto E, Jones DR, Adusumilli PS. Small RNA sequencing for profiling microRNAs in long-term preserved formalin-fixed and paraffin-embedded non-small cell lung cancer tumor specimens. PLoS One 2015; 10:e0121521. [PMID: 25812157 PMCID: PMC4374839 DOI: 10.1371/journal.pone.0121521] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 02/03/2015] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The preservation of microRNAs in formalin-fixed and paraffin-embedded (FFPE) tissue makes them particularly useful for biomarker studies. The utility of small RNA sequencing for microRNA expression profiling of FFPE samples has yet to be determined. METHODS Total RNA was extracted from de-paraffinized and proteinase K-treated FFPE specimens (15-20 years old) of 8 human lung adenocarcinoma tumors by affinity chromatography on silica columns. MicroRNAs in the RNA preparations were quantified by the Illumina HiSeq 2000 sequencing platform with sequencing libraries prepared with the TruSeq Small RNA Sample Preparation Kit (version 2.0) to obtain unpaired reads of 50 b for small RNA fragments. MicroRNAs were also quantified using Agilent Human miRNA (release 16.0) microarrays that can detect 1,205 mature microRNAs and by quantitative reverse transcription (RT)-PCR assays. RESULTS Between 9.1-16.9 million reads were obtained by small RNA sequencing of extracted RNA samples. Of these, only 0.6-2.3% (mean = 1.5%) represented microRNAs. The sequencing method detected 454-625 microRNAs/sample (mean = 550) compared with 200-349 (mean = 286) microRNAs detected by microarray. In Spearman correlation analyses, the average correlation coefficient for the 126 microRNAs detected in all samples by both methods was 0.37, and >0.5 for 63 microRNAs. In correlation analyses of the sequencing- and RT-PCR-based measurements, the coefficients were 0.19-0.95 (mean = 0.73) and >0.7, respectively, for 7 of 9 examined microRNAs. The average inter-replicate Spearman correlation coefficient for the sequencing method was 0.81. CONCLUSIONS Small RNA sequencing can be used to obtain microRNA profiles of FFPE tissue specimens with performance characteristics similar to those of microarrays, in spite of the fragmentation of ribosomal and messenger RNAs that reduces the method's informative capacity. The accuracy of the method can conceivably be improved by increasing sequencing depth and/or depleting FFPE tissue RNAs of ribosomal RNA fragments.
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Affiliation(s)
- Daniel H. Buitrago
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Santosh K. Patnaik
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Kyuichi Kadota
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Eric Kannisto
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - David R. Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Prasad S. Adusumilli
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Center of Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- * E-mail:
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Fassan M, Volinia S, Palatini J, Pizzi M, Fernandez-Cymering C, Balistreri M, Realdon S, Battaglia G, Souza R, Odze RD, Zaninotto G, Croce CM, Rugge Md Facg M. MicroRNA Expression Profiling in the Histological Subtypes of Barrett's Metaplasia. Clin Transl Gastroenterol 2013; 4:e34. [PMID: 23677165 PMCID: PMC3671360 DOI: 10.1038/ctg.2013.5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVES: The histological definition of Barrett's esophagus (BE) is debated, particularly regarding the phenotype of its metaplastic columnar epithelium. Histologically proven intestinal metaplasia (IM) was the sine qua non condition for a diagnosis of BE but, more recently, non-intestinalized (i.e., cardiac gastric-type; GM) columnar metaplasia has been re-included in the spectrum of Barrett's histology. MicroRNAs modulate cell commitment, and are also reportedly dysregulated in Barrett's carcinogenesis. This study investigates miRNA expression in the histological spectrum of esophageal columnar metaplastic changes, specifically addressing the biological profile of GM vs. IM. METHODS: A study was performed to discover microRNA microarray in 30 matching mucosa samples obtained from 10 consecutive BE patients; for each patient, biopsy tissue samples were obtained from squamous, GM and intestinalized epithelium. Microarray findings were further validated by qRT-PCR analysis in another bioptic series of 75 mucosa samples. RESULTS: MicroRNA profiling consistently disclosed metaplasia-specific microRNA signatures. Six microRNAs were significantly dysregulated across the histological phenotypes considered; five of them (two overexpressed (hsa-miR-192; -miR-215) and three under-expressed (hsa-miR-18a* -miR-203, and -miR-205)) were progressively dysregulated in the phenotypic sequence from squamous to gastric-type, to intestinal-type mucosa samples. CONCLUSIONS: A consistent microRNA expression signature underlies both gastric- and intestinal-type esophageal metaplasia. The pattern of microRNA dysregulation suggests that GM may further progress to IM. The clinico-pathological implications of these molecular profiles prompt further study on the “personalized” cancer risk associated with each of these metaplastic transformations.
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Affiliation(s)
- Matteo Fassan
- 1] Department of Medicine (DIMED), Surgical Pathology and Cytopathology Unit, University of Padua, Padua, Italy [2] Department of Surgical, Oncological and Gastroenterological Sciences (DiSCOG), General Oncology Unit, University of Padua, Padua, Italy
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Kotorashvili A, Ramnauth A, Liu C, Lin J, Ye K, Kim R, Hazan R, Rohan T, Fineberg S, Loudig O. Effective DNA/RNA co-extraction for analysis of microRNAs, mRNAs, and genomic DNA from formalin-fixed paraffin-embedded specimens. PLoS One 2012; 7:e34683. [PMID: 22514653 PMCID: PMC3326040 DOI: 10.1371/journal.pone.0034683] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 03/08/2012] [Indexed: 01/03/2023] Open
Abstract
Background Retrospective studies of archived human specimens, with known clinical follow-up, are used to identify predictive and prognostic molecular markers of disease. Due to biochemical differences, however, formalin-fixed paraffin-embedded (FFPE) DNA and RNA have generally been extracted separately from either different tissue sections or from the same section by dividing the digested tissue. The former limits accurate correlation whilst the latter is impractical when utilizing rare or limited archived specimens. Principal Findings For effective recovery of genomic DNA and total RNA from a single FFPE specimen, without splitting the proteinase-K digested tissue solution, we optimized a co-extraction method by using TRIzol and purifying DNA from the lower aqueous and RNA from the upper organic phases. Using a series of seven different archived specimens, we evaluated the total amounts of genomic DNA and total RNA recovered by our TRIzol-based co-extraction method and compared our results with those from two commercial kits, the Qiagen AllPrep DNA/RNA FFPE kit, for co-extraction, and the Ambion RecoverAll™ Total Nucleic Acid Isolation kit, for separate extraction of FFPE-DNA and -RNA. Then, to accurately assess the quality of DNA and RNA co-extracted from a single FFPE specimen, we used qRT-PCR, gene expression profiling and methylation assays to analyze microRNAs, mRNAs, and genomic DNA recovered from matched fresh and FFPE MCF10A cells. These experiments show that the TRIzol-based co-extraction method provides larger amounts of FFPE-DNA and –RNA than the two other methods, and particularly provides higher quality microRNAs and genomic DNA for subsequent molecular analyses. Significance We determined that co-extraction of genomic DNA and total RNA from a single FFPE specimen is an effective recovery approach to obtain high-quality material for parallel molecular and high-throughput analyses. Our optimized approach provides the option of collecting DNA, which would otherwise be discarded or degraded, for additional or subsequent studies.
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Affiliation(s)
- Adam Kotorashvili
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Andrew Ramnauth
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Christina Liu
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Juan Lin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Kenny Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Ryung Kim
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Rachel Hazan
- Department of Pathology, Albert Einstein College of Medicine of Yeshiva University, Bronx , New York, United States of America
| | - Thomas Rohan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
| | - Susan Fineberg
- Department of Pathology, Albert Einstein College of Medicine of Yeshiva University, Bronx , New York, United States of America
| | - Olivier Loudig
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York, United States of America
- Department of Pathology, Albert Einstein College of Medicine of Yeshiva University, Bronx , New York, United States of America
- * E-mail:
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Hébert SS, Nelson PT. Studying microRNAs in the brain: technical lessons learned from the first ten years. Exp Neurol 2011; 235:397-401. [PMID: 22178329 DOI: 10.1016/j.expneurol.2011.12.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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