101
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Extracellular RNA: Emerging roles in cancer cell communication and biomarkers. Cancer Lett 2020; 495:33-40. [PMID: 32916182 DOI: 10.1016/j.canlet.2020.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/15/2020] [Accepted: 09/02/2020] [Indexed: 01/05/2023]
Abstract
Extracellular RNAs (exRNAs) are a type of RNA molecules that present in various biological fluids. exRNAs are heterogenous populations including small (e.g., miRNA) and long non-coding RNAs and coding RNAs (e.g., mRNA). They can exist in a free form or associate with carriers range from lipo- and ribo-proteins to extracellular vesicles such as exosomes in the extracellular fluids. exRNAs participate in cell-to-cell communication to regulate a broad array of physiological and pathological processes. exRNAs have been widely studied as a biomarker for cancer and other diseases. In this review, we will discuss the sorts of exRNAs with potential carriers as well as their roles in cancer.
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102
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Green ES, Arck PC. Pathogenesis of preterm birth: bidirectional inflammation in mother and fetus. Semin Immunopathol 2020; 42:413-429. [PMID: 32894326 PMCID: PMC7508962 DOI: 10.1007/s00281-020-00807-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/14/2020] [Indexed: 12/18/2022]
Abstract
Preterm birth (PTB) complicates 5–18% of pregnancies globally and is a leading cause of maternal and fetal morbidity and mortality. Most PTB is spontaneous and idiopathic, with largely undefined causes. To increase understanding of PTB, much research in recent years has focused on using animal models to recapitulate the pathophysiology of PTB. Dysfunctions of maternal immune adaptations have been implicated in a range of pregnancy pathologies, including PTB. A wealth of evidence arising from mouse models as well as human studies is now available to support that PTB results from a breakdown in fetal-maternal tolerance, along with excessive, premature inflammation. In this review, we examine the current knowledge of the bidirectional communication between fetal and maternal systems and its role in the immunopathogenesis of PTB. These recent insights significantly advance our understanding of the pathogenesis of PTB, which is essential to ultimately designing more effective strategies for early prediction and subsequent prevention of PTB.
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Affiliation(s)
- Ella Shana Green
- Department of Obstetrics and Fetal Medicine, Laboratory for Experimental Feto-Maternal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251, Hamburg, Germany
| | - Petra Clara Arck
- Department of Obstetrics and Fetal Medicine, Laboratory for Experimental Feto-Maternal Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251, Hamburg, Germany.
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103
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Yao J, Wu DC, Nottingham RM, Lambowitz AM. Identification of protein-protected mRNA fragments and structured excised intron RNAs in human plasma by TGIRT-seq peak calling. eLife 2020; 9:e60743. [PMID: 32876046 PMCID: PMC7518892 DOI: 10.7554/elife.60743] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Human plasma contains > 40,000 different coding and non-coding RNAs that are potential biomarkers for human diseases. Here, we used thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) combined with peak calling to simultaneously profile all RNA biotypes in apheresis-prepared human plasma pooled from healthy individuals. Extending previous TGIRT-seq analysis, we found that human plasma contains largely fragmented mRNAs from > 19,000 protein-coding genes, abundant full-length, mature tRNAs and other structured small non-coding RNAs, and less abundant tRNA fragments and mature and pre-miRNAs. Many of the mRNA fragments identified by peak calling correspond to annotated protein-binding sites and/or have stable predicted secondary structures that could afford protection from plasma nucleases. Peak calling also identified novel repeat RNAs, miRNA-sized RNAs, and putatively structured intron RNAs of potential biological, evolutionary, and biomarker significance, including a family of full-length excised intron RNAs, subsets of which correspond to mirtron pre-miRNAs or agotrons.
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Affiliation(s)
- Jun Yao
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
| | - Douglas C Wu
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
| | - Ryan M Nottingham
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
| | - Alan M Lambowitz
- Institute for Cellular and Molecular Biology and Departments of Molecular Biosciences and Oncology, University of TexasAustinUnited States
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104
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Peterson LS, Stelzer IA, Tsai AS, Ghaemi MS, Han X, Ando K, Winn VD, Martinez NR, Contrepois K, Moufarrej MN, Quake S, Relman DA, Snyder MP, Shaw GM, Stevenson DK, Wong RJ, Arck P, Angst MS, Aghaeepour N, Gaudilliere B. Multiomic immune clockworks of pregnancy. Semin Immunopathol 2020; 42:397-412. [PMID: 32020337 PMCID: PMC7508753 DOI: 10.1007/s00281-019-00772-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/31/2019] [Indexed: 12/15/2022]
Abstract
Preterm birth is the leading cause of mortality in children under the age of five worldwide. Despite major efforts, we still lack the ability to accurately predict and effectively prevent preterm birth. While multiple factors contribute to preterm labor, dysregulations of immunological adaptations required for the maintenance of a healthy pregnancy is at its pathophysiological core. Consequently, a precise understanding of these chronologically paced immune adaptations and of the biological pacemakers that synchronize the pregnancy "immune clock" is a critical first step towards identifying deviations that are hallmarks of peterm birth. Here, we will review key elements of the fetal, placental, and maternal pacemakers that program the immune clock of pregnancy. We will then emphasize multiomic studies that enable a more integrated view of pregnancy-related immune adaptations. Such multiomic assessments can strengthen the biological plausibility of immunological findings and increase the power of biological signatures predictive of preterm birth.
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Affiliation(s)
- Laura S Peterson
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ina A Stelzer
- Department of Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Amy S Tsai
- Department of Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Mohammad S Ghaemi
- Department of Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiaoyuan Han
- Department of Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Kazuo Ando
- Department of Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Virginia D Winn
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Nadine R Martinez
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kevin Contrepois
- Stanford Metabolic Health Center, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Center for Genomics and Personalized Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Mira N Moufarrej
- Department of Bioengineering, Stanford University School of Engineering, Stanford, CA, USA
| | - Stephen Quake
- Department of Bioengineering, Stanford University School of Engineering, Stanford, CA, USA
| | - David A Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
| | - Michael P Snyder
- Stanford Center for Genomics and Personalized Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Gary M Shaw
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - David K Stevenson
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ronald J Wong
- Division of Neonatal and Developmental Medicine, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Petra Arck
- Department of Obstetrics and Fetal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin S Angst
- Department of Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nima Aghaeepour
- Department of Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Brice Gaudilliere
- Department of Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA.
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105
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Xie Y, Li J, Li P, Li N, Zhang Y, Binang H, Zhao Y, Duan W, Chen Y, Wang Y, Du L, Wang C. RNA-Seq Profiling of Serum Exosomal Circular RNAs Reveals Circ-PNN as a Potential Biomarker for Human Colorectal Cancer. Front Oncol 2020; 10:982. [PMID: 32626660 PMCID: PMC7314951 DOI: 10.3389/fonc.2020.00982] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/18/2020] [Indexed: 12/24/2022] Open
Abstract
Circular RNAs (circRNAs) are emerging as cardinal areas of focus in the non-coding RNA field. Growing evidences have revealed exosomal circRNAs as potential biomarkers for detection of various cancers. However, the clinical importance of most serum exosomal circRNAs in colorectal cancer (CRC) have rarely been investigated. In this study, we examined the possible clinical application of serum exosomal circRNAs in the diagnosis of CRC. Firstly, we conducted RNA sequencing (RNA-seq) analysis using fifty CRC and fifty healthy control serum samples to identify CRC-related circRNAs. The sequencing data showed 122 differentially expressed circRNAs including 100 up-regulated and 22 down-regulated circRNA transcripts in CRC patients. Then, eight most dysregulated circRNAs were selected for validation by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assay. Validation analysis revealed that the serum exosomal circ-PNN (hsa_circ_0101802) levels were significantly up-regulated in CRC cases compared with those in the healthy control groups. Receiver operating characteristic curve (ROC) analysis suggested that circ-PNN had significant value in CRC diagnosis with areas under the ROC curve (AUC) of 0.855 and 0.826 in the training and validation sets, respectively. We also found that the AUC of serum exosomal circ-PNN for early-stage CRC was 0.854. Finally, a network map based on circ-PNN was constructed to determine its potential miRNA-mRNAs binding. We also demonstrated that the expression of hsa-miR-6833-3P, hsa-let-7i-3p and hsa-miR-1301-3P were negatively correlated with circ-PNN in CRC patients. Collectively, our findings indicated that serum exosomal circ-PNN might be a potential non-invasive biomarker for the detection of CRC and may play a crucial role in the pathogenesis of CRC.
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Affiliation(s)
- Yan Xie
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Juan Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Peilong Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Ning Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Ying Zhang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Helen Binang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Yinghui Zhao
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Weili Duan
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Yingjie Chen
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Yunshan Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China.,Tumor Marker Detection Engineering Laboratory of Shandong Province, Jinan, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China.,Tumor Marker Detection Engineering Laboratory of Shandong Province, Jinan, China
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106
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Yang Q, Chen L, Yang L, Huang Y. Diagnostic and prognostic values of circular RNAs for lung cancer: a meta-analysis. Postgrad Med J 2020; 97:286-293. [PMID: 32518074 DOI: 10.1136/postgradmedj-2019-137178] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 05/06/2020] [Accepted: 05/10/2020] [Indexed: 12/09/2022]
Abstract
Circular RNAs (circRNAs) may serve as potential biomarkers for patients with lung cancer. The aim of this meta-analysis was to analyse the diagnostic, prognostic and clinicopathological values of circRNAs in lung cancer patients. A systematic search of PubMed, Embase, Web of Science, Scopus and the Cochrane Library databases was performed for relevant articles from inception to 29 January 2020. Pooled parameters including sensitivity, specificity and area under the curve (AUC) were used to assess the diagnostic performance, HRs and 95% CIs were used to evaluate overall survival (OS) and ORs were used to estimate clinicopathological parameters. 52 studies from 45 articles were enrolled in this study, including 17 on diagnosis and 35 on prognosis. For diagnostic values, circRNAs could discriminate lung cancer patients from the controls, with AUC of 0.83 (95% CI: 0.79 to 0.86), a relatively high sensitivity of 0.77 (95% CI: 0.73 to 0.81) and specificity of 0.75 (95% CI: 0.71 to 0.79). For prognostic significances, overexpression of 23 upregulated circRNAs was relevant to a poor prognosis (OS: HR=2.21, 95% CI: 1.96 to 2.49, p<0.001), and overexpression of 9 downregulated circRNAs was correlated with a favourable prognosis (OS: HR=0.62, 95% CI: 0.53 to 0.73, p<0.001). As for clinicopathological parameters, high expression of 23 upregulated circRNAs was associated with unfavourable clinicopathological features while 9 downregulated circRNAs proved the contrary. In conclusion, this study confirmed that circRNAs might serve as important biomarkers for diagnostic and prognostic values of lung cancer.
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Affiliation(s)
- Qian Yang
- Department of Transfusion, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Lizhen Chen
- Prenatal Diagnosis Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Li Yang
- Department of Transfusion, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yuanshuai Huang
- Department of Transfusion, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
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107
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Ratti M, Lampis A, Ghidini M, Salati M, Mirchev MB, Valeri N, Hahne JC. MicroRNAs (miRNAs) and Long Non-Coding RNAs (lncRNAs) as New Tools for Cancer Therapy: First Steps from Bench to Bedside. Target Oncol 2020; 15:261-278. [PMID: 32451752 PMCID: PMC7283209 DOI: 10.1007/s11523-020-00717-x] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Non-coding RNAs represent a significant proportion of the human genome. After having been considered as 'junk' for a long time, non-coding RNAs are now well established as playing important roles in maintaining cellular homeostasis and functions. Some non-coding RNAs show cell- and tissue-specific expression patterns and are specifically deregulated under pathological conditions (e.g. cancer). Therefore, non-coding RNAs have been extensively studied as potential biomarkers in the context of different diseases with a focus on microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) for several years. Since their discovery, miRNAs have attracted more attention than lncRNAs in research studies; however, both families of non-coding RNAs have been established to play an important role in gene expression control, either as transcriptional or post-transcriptional regulators. Both miRNAs and lncRNAs can regulate key genes involved in the development of cancer, thus influencing tumour growth, invasion, and metastasis by increasing the activation of oncogenic pathways and limiting the expression of tumour suppressors. Furthermore, miRNAs and lncRNAs are also emerging as important mediators in drug-sensitivity and drug-resistance mechanisms. In the light of these premises, a number of pre-clinical and early clinical studies are exploring the potential of non-coding RNAs as new therapeutics. The aim of this review is to summarise the latest knowledge of the use of miRNAs and lncRNAs as therapeutic tools for cancer treatment.
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Affiliation(s)
- Margherita Ratti
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Medical Department, Division of Oncology, ASST di Cremona, Ospedale di Cremona, Cremona, Italy
| | - Andrea Lampis
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Michele Ghidini
- Division of Medical Oncology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Massimiliano Salati
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Milko B Mirchev
- Clinic of Gastroenterology, Medical University, Varna, Bulgaria
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, UK
| | - Jens C Hahne
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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108
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Hannan NJ, Stock O, Spencer R, Whitehead C, David AL, Groom K, Petersen S, Henry A, Said JM, Seeho S, Kane SC, Gordon L, Beard S, Chindera K, Karegodar S, Hiscock R, Pritchard N, Kaitu'u-Lino TJ, Walker SP, Tong S. Circulating mRNAs are differentially expressed in pregnancies with severe placental insufficiency and at high risk of stillbirth. BMC Med 2020; 18:145. [PMID: 32438913 PMCID: PMC7243334 DOI: 10.1186/s12916-020-01605-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/24/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Fetuses affected by placental insufficiency do not receive adequate nutrients and oxygenation, become growth restricted and acidemic, and can demise. Preterm fetal growth restriction is a severe form of placental insufficiency with a high risk of stillbirth. We set out to identify maternal circulating mRNA transcripts that are differentially expressed in preterm pregnancies complicated by very severe placental insufficiency, in utero fetal acidemia, and are at very high risk of stillbirth. METHODS We performed a cohort study across six hospitals in Australia and New Zealand, prospectively collecting blood from 128 pregnancies complicated by preterm fetal growth restriction (delivery < 34 weeks' gestation) and 42 controls. RNA-sequencing was done on all samples to discover circulating mRNAs associated with preterm fetal growth restriction and fetal acidemia in utero. We used RT-PCR to validate the associations between five lead candidate biomarkers of placental insufficiency in an independent cohort from Europe (46 with preterm fetal growth restriction) and in a third cohort of pregnancies ending in stillbirth. RESULTS In the Australia and New Zealand cohort, we identified five mRNAs that were highly differentially expressed among pregnancies with preterm fetal growth restriction: NR4A2, EMP1, PGM5, SKIL, and UGT2B1. Combining three yielded an area under the receiver operative curve (AUC) of 0.95. Circulating NR4A2 and RCBTB2 in the maternal blood were dysregulated in the presence of fetal acidemia in utero. We validated the association between preterm fetal growth restriction and circulating EMP1, NR4A2, and PGM5 mRNA in a cohort from Europe. Combining EMP1 and PGM5 identified fetal growth restriction with an AUC of 0.92. Several of these genes were differentially expressed in the presence of ultrasound parameters that reflect placental insufficiency. Circulating NR4A2, EMP1, and RCBTB2 mRNA were differentially regulated in another cohort destined for stillbirth, compared to ongoing pregnancies. EMP1 mRNA appeared to have the most consistent association with placental insufficiency in all cohorts. CONCLUSIONS Measuring circulating mRNA offers potential as a test to identify pregnancies with severe placental insufficiency and at very high risk of stillbirth. Circulating mRNA EMP1 may be promising as a biomarker of severe placental insufficiency.
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Affiliation(s)
- Natalie J Hannan
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Level 4, Studley Rd, Heidelberg, Victoria, 3084, Australia.,Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria, 3084, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Owen Stock
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Level 4, Studley Rd, Heidelberg, Victoria, 3084, Australia.,Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria, 3084, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Rebecca Spencer
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, WC1E 6BT, UK.,University of Leeds, Leeds, LS2 9JT, UK
| | - Clare Whitehead
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Level 4, Studley Rd, Heidelberg, Victoria, 3084, Australia.,Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria, 3084, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, 3010, Australia.,The University of Sydney Northern Clinical School, Women and Babies Research, St Leonards, New South Wales, 2065, Australia
| | - Anna L David
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, WC1E 6BT, UK
| | - Katie Groom
- Department of Maternal Fetal Medicine, Royal Women's Hospital, Parkville, Victoria, 3052, Australia
| | - Scott Petersen
- Liggins Institute, University of Auckland, Auckland, 1023, New Zealand
| | - Amanda Henry
- Centre for Maternal Fetal Medicine, Mater Mothers' Hospital, South Brisbane, Queensland, 4101, Australia
| | - Joanne M Said
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, 3010, Australia.,School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Sydney, Australia
| | - Sean Seeho
- Maternal Fetal Medicine, Joan Kirner Women's & Children's Sunshine Hospital, St Albans, Victoria, 3021, Australia
| | - Stefan C Kane
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, 3010, Australia.,The University of Sydney Northern Clinical School, Women and Babies Research, St Leonards, New South Wales, 2065, Australia
| | - Lavinia Gordon
- University of Melbourne Centre for Cancer Research, Parkville, Victoria, 3010, Australia
| | - Sally Beard
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Level 4, Studley Rd, Heidelberg, Victoria, 3084, Australia.,Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria, 3084, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Kantaraja Chindera
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, WC1E 6BT, UK
| | - Smita Karegodar
- Elizabeth Garrett Anderson Institute for Women's Health, University College London, London, WC1E 6BT, UK
| | - Richard Hiscock
- Department of anesthesia, Mercy Hospital for Women, Heidelberg, Victoria, 3084, Australia
| | - Natasha Pritchard
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Level 4, Studley Rd, Heidelberg, Victoria, 3084, Australia.,Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria, 3084, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Tu'uhevaha J Kaitu'u-Lino
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Level 4, Studley Rd, Heidelberg, Victoria, 3084, Australia.,Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria, 3084, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Susan P Walker
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Level 4, Studley Rd, Heidelberg, Victoria, 3084, Australia.,Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria, 3084, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Stephen Tong
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, University of Melbourne, Mercy Hospital for Women, Level 4, Studley Rd, Heidelberg, Victoria, 3084, Australia. .,Mercy Perinatal, Mercy Hospital for Women, Heidelberg, Victoria, 3084, Australia. .,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, 3010, Australia.
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109
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Li B, Li Y, Hu L, Liu Y, Zhou Q, Wang M, An Y, Li P. Role of Circular RNAs in the Pathogenesis of Cardiovascular Disease. J Cardiovasc Transl Res 2020; 13:572-583. [PMID: 32399680 DOI: 10.1007/s12265-019-09912-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/02/2019] [Indexed: 02/06/2023]
Abstract
Circular RNAs (circRNAs) are single-strand covalently closed circular noncoding RNAs that are endogenous transcripts generated from linear precursor mRNA through a backsplicing mechanism. With the development of high-throughput sequencing technology, a number of circRNAs have been identified and proved to play key roles in various pathophysiological processes, such as metabolic diseases, cancers, and cardiovascular diseases. An increasing number of studies have shown that circRNAs are widely expressed in cardiac tissues and play important roles in the development of multiple cardiovascular diseases. Here, we review the current understanding of circRNA biogenesis and functions and the roles of circRNAs in cardiovascular diseases. We also highlight the molecular mechanisms underlying the role of circRNAs in the pathogenesis of cardiovascular diseases. A better understanding of the biological function of circRNAs in cardiovascular diseases will be helpful for the development of effective biomarkers for the diagnosis and treatment of these diseases.
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Affiliation(s)
- Baowei Li
- Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China
| | - Yuzhen Li
- Department of Pathophysiology, Institute of Basic Medical Science, PLA General Hospital, Beijing, 100853, China
| | - Longgang Hu
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, 266021, China
| | - Ying Liu
- Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China
| | - Qihui Zhou
- Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China
| | - Man Wang
- Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China
| | - Yi An
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, 266021, China.
| | - Peifeng Li
- Institute for Translational Medicine, Qingdao University, Qingdao, 266021, China.
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110
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LncRNAs Act as a Link between Chronic Liver Disease and Hepatocellular Carcinoma. Int J Mol Sci 2020; 21:ijms21082883. [PMID: 32326098 PMCID: PMC7216144 DOI: 10.3390/ijms21082883] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are emerging as important contributors to the biological processes underlying the pathophysiology of various human diseases, including hepatocellular carcinoma (HCC). However, the involvement of these molecules in chronic liver diseases, such as nonalcoholic fatty liver disease (NAFLD) and viral hepatitis, has only recently been considered in scientific research. While extensive studies on the pathogenesis of the development of HCC from hepatic fibrosis have been conducted, their regulatory molecular mechanisms are still only partially understood. The underlying mechanisms related to lncRNAs leading to HCC from chronic liver diseases and cirrhosis have not yet been entirely elucidated. Therefore, elucidating the functional roles of lncRNAs in chronic liver disease and HCC can contribute to a better understanding of the molecular mechanisms, and may help in developing novel diagnostic biomarkers and therapeutic targets for HCC, as well as in preventing the progression of chronic liver disease to HCC. Here, we comprehensively review and briefly summarize some lncRNAs that participate in both hepatic fibrosis and HCC.
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111
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Hirata AHDL, Rocha LADJ, da Silva VA, de Almeida RJ, Bacigalupo LDS, Varela P, Martins L, Pesquero JB, Dellê H, Camacho CP. Circulating RNA Transcriptome of Pregnant Women with TSH Just Above the Trimester-Specific Reference and its Correlation with the Hypertensive Phenotype. Sci Rep 2020; 10:6439. [PMID: 32296081 PMCID: PMC7160149 DOI: 10.1038/s41598-020-63040-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/19/2020] [Indexed: 11/09/2022] Open
Abstract
During gestation, a woman’s body undergoes physiological changes that alter thyroid function. Pregnant women with hypothyroidism may exhibit gestational complications, including hypertension and preeclampsia. We investigated differentially expressed genes (DEGs) in circulating RNAs from pregnant women with TSH levels just above the normal range to determine the impact of a mild elevation of TSH in pregnancy. We selected three women with healthy thyroid pregnancy (HTP), three pregnant women with gestational hypothyroidism (GHT), and three nonpregnant women (NPG) to construct transcriptome libraries. We also compared our results with data from the GEO dataset and DisGeNET. We identified 1500 DEG in GHT and 1656 DEG in HTP. From GEO dataset, we recognized 453 DEGs in trimester-specific plasma RNA, 1263 DEGs in placental tissues from healthy women, 1031 DEGs from preeclamptic uteroplacental tissues and 1657 DEGs from placental tissues from severely preeclamptic women. In this scenario, 12.26% and 12.86% genes were shared between these datasets in GHT and HTP, respectively. We stablished 62 genes in GHT DEGs related to hypertensive phenotype hallmarks. In conclusion, even in women with a mild TSH increment, we were able to detect some DEGs that could be associated with a hypertensive phenotype.
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Affiliation(s)
- Andréa Harumy de Lima Hirata
- Molecular Innovation and Biotechnology Laboratory, Postgraduate Program in Medicine, Universidade Nove de Julho (Uninove), São Paulo, SP, Brazil
| | - Luiz Antônio de Jesus Rocha
- Molecular Innovation and Biotechnology Laboratory, Postgraduate Program in Medicine, Universidade Nove de Julho (Uninove), São Paulo, SP, Brazil
| | - Valdelena Alessandra da Silva
- Molecular Innovation and Biotechnology Laboratory, Postgraduate Program in Medicine, Universidade Nove de Julho (Uninove), São Paulo, SP, Brazil
| | - Robson José de Almeida
- Molecular Innovation and Biotechnology Laboratory, Postgraduate Program in Medicine, Universidade Nove de Julho (Uninove), São Paulo, SP, Brazil
| | - Lucas Dos Santos Bacigalupo
- Molecular Innovation and Biotechnology Laboratory, Postgraduate Program in Medicine, Universidade Nove de Julho (Uninove), São Paulo, SP, Brazil.,Department of Obstetrics and Gynecology, Conjunto Hospitalar do Mandaqui, São Paulo, SP, Brazil
| | - Patrícia Varela
- Center for Research and Molecular Diagnostic of Genetic Diseases, Department of Biophysics, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Leonardo Martins
- Center for Research and Molecular Diagnostic of Genetic Diseases, Department of Biophysics, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - João Bosco Pesquero
- Center for Research and Molecular Diagnostic of Genetic Diseases, Department of Biophysics, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, Brazil
| | - Humberto Dellê
- Molecular Innovation and Biotechnology Laboratory, Postgraduate Program in Medicine, Universidade Nove de Julho (Uninove), São Paulo, SP, Brazil
| | - Cleber Pinto Camacho
- Molecular Innovation and Biotechnology Laboratory, Postgraduate Program in Medicine, Universidade Nove de Julho (Uninove), São Paulo, SP, Brazil.
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112
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Li S, Teng S, Xu J, Su G, Zhang Y, Zhao J, Zhang S, Wang H, Qin W, Lu ZJ, Guo Y, Zhu Q, Wang D. Microarray is an efficient tool for circRNA profiling. Brief Bioinform 2020; 20:1420-1433. [PMID: 29415187 DOI: 10.1093/bib/bby006] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/29/2017] [Indexed: 12/17/2022] Open
Abstract
Circular RNAs (circRNAs) are emerging as a new class of endogenous and regulatory noncoding RNAs in latest years. With the widespread application of RNA sequencing (RNA-seq) technology and bioinformatics prediction, large numbers of circRNAs have been identified. However, at present, we lack a comprehensive characterization of all these circRNAs in interested samples. In this study, we integrated 87 935 circRNAs sequences that cover most of circRNAs identified till now represented in circBase to design microarray probes targeting back-splice site of each circRNA to profile expression of those circRNAs. By comparing the circRNA detection efficiency of RNA-seq with this circRNA microarray, we revealed that microarray is more efficient than RNA-seq for circRNA profiling. Then, we found ∼80 000 circRNAs were expressed in cervical tumors and matched normal tissues, and ∼25 000 of them were differently expressed. Notably, many of these circRNAs detected by this microarray can be validated by quantitative reverse transcription polymerase chain reaction (RT-qPCR) or RNA-seq. Strikingly, as many as ∼18 000 circRNAs could be robustly detected in cell-free plasma samples, and the expression of ∼2700 of them differed after surgery for tumor removal. Our findings provided a comprehensive and genome-wide characterization of circRNAs in paired normal tissues and tumors and plasma samples from multiple individuals. In addition, we also provide a rich resource with 41 microarray data sets and 10 RNA-seq data sets and strong evidences for circRNA expression in cervical cancer. In conclusion, circRNAs could be efficiently profiled by circRNA microarray to target their reported back-splice sites in interested samples.
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113
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Guo Z, Yang F, Zhang J, Zhang Z, Li K, Tian Q, Hou H, Xu C, Lu Q, Ren Z, Yang X, Lv Z, Wang K, Yang X, Wu Y, Yang X. Whole-Genome Promoter Profiling of Plasma DNA Exhibits Diagnostic Value for Placenta-Origin Pregnancy Complications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1901819. [PMID: 32274292 PMCID: PMC7141029 DOI: 10.1002/advs.201901819] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 02/03/2020] [Indexed: 06/06/2023]
Abstract
Placenta-origin pregnancy complications, including preeclampsia (PE), gestational diabetes mellitus (GDM), fetal growth restriction (FGR), and macrosomia (MA) are common occurrences in pregnancy, resulting in significant morbidity and mortality for both mother and fetus. However, despite their frequency, there are no reliable methods for the early diagnosis of these complications. Since cfDNA is mainly derived from placental trophoblasts and maternal hematopoietic cells, it might have information for gene expression which can be used for disease prediction. Here, low coverage whole-genome sequencing on plasma DNA from 2,199 pregnancies is performed based on retrospective cohorts of 3,200 pregnant women. Read depth in the promoter regions is examined to define read-depth distribution patterns of promoters for pregnancy complications and controls. Using machine learning methods, classifiers for predicting pregnancy complications are developed. Using these classifiers, complications are successfully predicted with an accuracy of 80.3%, 78.9%, 72.1%, and 83.0% for MA, FGR, GDM, and PE, respectively. The findings suggest that promoter profiling of cfDNA may be used as a biological biomarker for predicting pregnancy complications at early gestational age.
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Affiliation(s)
- Zhiwei Guo
- Institute of Antibody EngineeringSchool of Laboratory Medicine and BiotechnologySouthern Medical UniversityGuangzhou510515China
| | - Fang Yang
- Department of Obstetrics and GynecologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Jun Zhang
- Department of ObstetricsThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510630China
| | - Zhigang Zhang
- Department of PathologyCangzhou People's HospitalCangzhou061000China
| | - Kun Li
- Institute of Antibody EngineeringSchool of Laboratory Medicine and BiotechnologySouthern Medical UniversityGuangzhou510515China
| | - Qi Tian
- Department of ObstetricsThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510630China
| | - Hongying Hou
- Department of ObstetricsThe Third Affiliated Hospital of Sun Yat‐sen UniversityGuangzhou510630China
| | - Cailing Xu
- Department of Obstetrics and GynecologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Qianwen Lu
- Department of Obstetrics and GynecologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Zhonglu Ren
- Department of Obstetrics and GynecologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Xiaoxue Yang
- Department of Obstetrics and GynecologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Zenglu Lv
- Department of PathologyCangzhou People's HospitalCangzhou061000China
| | - Ke Wang
- Department of Obstetrics and GynecologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Xinping Yang
- Department of Obstetrics and GynecologyNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Yingsong Wu
- Institute of Antibody EngineeringSchool of Laboratory Medicine and BiotechnologySouthern Medical UniversityGuangzhou510515China
| | - Xuexi Yang
- Institute of Antibody EngineeringSchool of Laboratory Medicine and BiotechnologySouthern Medical UniversityGuangzhou510515China
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114
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Luo HL, Peng Y, Luo H, Zhang JA, Liu GB, Xu H, Huang GX, Sun YF, Huang J, Zheng BY, Zhong JX, Xu JF. Circular RNA hsa_circ_0001380 in peripheral blood as a potential diagnostic biomarker for active pulmonary tuberculosis. Mol Med Rep 2020; 21:1890-1896. [PMID: 32319627 PMCID: PMC7057807 DOI: 10.3892/mmr.2020.10992] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/22/2019] [Indexed: 11/08/2022] Open
Abstract
Numerous studies have suggested that circular RNAs (circRNAs), a type of non-coding RNA lacking 5′-caps and 3′-poly(A) tails, are involved in the biological processes of various human diseases. However, little is known about their functions and diagnostic value in active pulmonary tuberculosis (APTB). The aim of the present study was to examine whether hsa_circ_0001380 is able to serve as a diagnostic biomarker for patients with APTB. The expression level of hsa_circ_0001380 was detected in the peripheral blood of 32 patients with APTB and 31 healthy volunteers by reverse transcription-quantitative PCR. The functional prediction of hsa_circ_0001380 was performed in silico. RNase R was used to detect the stability of hsa_circ_0001380. Finally, the diagnostic value of hsa_circ_0001380 was evaluated by receiver operating characteristic (ROC) curve analysis. The results showed that hsa_circ_0001380 was significantly downregulated in the peripheral blood of patients with APTB. In addition, hsa_circ_0001380 was found to be resistant to RNase R treatment. Moreover, four N6-adenosine methylation modification sites and two potential microRNA binding sites were predicted in silico. Importantly, the area under the ROC curve was 0.9502, which suggested that hsa_circ_0001380 may act as a diagnostic biomarker for APTB. Taken together, the results indicated that circRNA hsa_circ_0001380 was downregulated in the peripheral blood of patients with APTB, and could serve as a diagnostic biomarker.
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Affiliation(s)
- Hou-Long Luo
- Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Ying Peng
- Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Hong Luo
- Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Jun-Ai Zhang
- Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Gan-Bin Liu
- Department of Respiration, Dongguan Sixth Hospital, Dongguan, Guangdong 523008, P.R. China
| | - Huan Xu
- Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Gui-Xian Huang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan, Guangdong 523808, P.R. China
| | - Yin-Fu Sun
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan, Guangdong 523808, P.R. China
| | - Ji Huang
- Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Bi-Ying Zheng
- Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
| | - Ji-Xin Zhong
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jun-Fa Xu
- Institute of Laboratory Medicine, Guangdong Medical University, Dongguan, Guangdong 523808, P.R. China
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115
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Huang E, Fu J, Yu Q, Xie P, Yang Z, Ji H, Wang L, Luo G, Zhang Y, Li K. CircRNA hsa_circ_0004771 promotes esophageal squamous cell cancer progression via miR-339-5p/CDC25A axis. Epigenomics 2020; 12:587-603. [PMID: 32050790 DOI: 10.2217/epi-2019-0404] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Aim: The role of circRNAs in esophageal squamous cell cancer (ESCC) remains unclear. Materials & methods: Here we profiled six pair plasma circRNA in ESCC based on RNA sequencing, and then verified the elevation of hsa_circ_0004771 in 20 cancer tissues and 105 pair case-control plasma samples by quantitative reverse transcriptase PCR. Results: The upregulation of hsa_circ_0004771 was correlated with heavier tumor burden and poor prognosis, knockdown of it inhibited the ESCC cells proliferation both in vitro and in vivo. Mechanistically, hsa_circ_0004771 positively regulated CDC25A by acting as a molecular sponge of miR-339-5p and rescue assay confirmed this regulatory relationship. Conclusion: These results suggested that hsa_circ_0004771 can serve as a general less-invasive biomarker and may provide diagnostic and prognostic value in carcinoma.
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Affiliation(s)
- Enmin Huang
- Department of General Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, PR China
| | - Junhui Fu
- Department of Surgical Oncology, Shantou Central Hospital, Shantou, Guangdong, PR China
| | - Qiuyan Yu
- Department of Public Health, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Peixin Xie
- Department of Surgical Oncology, Shantou Central Hospital, Shantou, Guangdong, PR China
| | - Zhongxian Yang
- Department of Medical Imaging, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, PR China
| | - Huanlin Ji
- Department of Public Health, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Li Wang
- Department of Public Health, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Ganfeng Luo
- Department of Public Health, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Yanting Zhang
- Department of Public Health, Shantou University Medical College, Shantou, Guangdong, PR China
| | - Ke Li
- Department of Public Health, Shantou University Medical College, Shantou, Guangdong, PR China
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116
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Han J, Zhang L, Hu L, Yu H, Xu F, Yang B, Zhang R, Zhang Y, An Y. Circular RNA-Expression Profiling Reveals a Potential Role of Hsa_circ_0097435 in Heart Failure via Sponging Multiple MicroRNAs. Front Genet 2020; 11:212. [PMID: 32211036 PMCID: PMC7076158 DOI: 10.3389/fgene.2020.00212] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/24/2020] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs represent a new type of non-coding RNA molecules that influence the occurrence and development of various human diseases by sponging microRNAs, although their roles in heart failure have not been clarified. In this study, peripheral blood samples from 5 patients with heart failure and 4 healthy volunteers were analyzed by next-generation sequencing (NGS) to screen for differentially expressed Circular RNAs. Fifty-six differentially expressed Circular RNAs were identified, of which 29 were up-regulated and 27 were down-regulated. Dysregulated expression of 6 Circular RNAs was verified by quantitative polymerase chain reaction (PCR) analysis, and hsa_circ_0097435 expression was confirmed to be significantly up-regulated in 40 patients with heart failure. Further study with extracted exosomes showed that hsa_circ_0097435 expression was significantly higher in patients with heart failure. In cardiomyocytes, hsa_circ_0097435 was up-regulated after doxorubicin treatment, promoting cardiomyocyte apoptosis. Hsa_circ_0097435 overexpression promoted cardiomyocyte apoptosis, and silencing hsa_circ_0097435 inhibited apoptosis. Moreover, RNA-pulldown experiments and AGO2-immunoprecipitation experiments revealed that hsa_circ_0097435 potentially served a role in heart failure by sponging multiple microRNAs. Collectively, these results suggest that hsa_circ_0097435 can be used as a biological blood marker and revealed a new pathway involved in regulating myocardial cell injury. Our findings may provide a rational basis for developing new treatments for heart failure.
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Affiliation(s)
- Jiaqi Han
- Department of Medicine, Qingdao University, Qingdao, China
| | - Liwei Zhang
- Department of Medicine, Qingdao University, Qingdao, China
| | - Longgang Hu
- Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Hua Yu
- Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Fengqiang Xu
- Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Bin Yang
- Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Rui Zhang
- Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yongtao Zhang
- Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yi An
- Department of Medicine, Qingdao University, Qingdao, China.,Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
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117
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Shridhar V, Chu T, Simhan H, Shaw PA, Peters DG. High‐resolution analysis of the human placental DNA methylome in early gestation. Prenat Diagn 2020; 40:481-491. [DOI: 10.1002/pd.5618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 09/27/2019] [Accepted: 10/09/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Varsha Shridhar
- Department of Obstetrics, Gynecology and Reproductive SciencesUniversity of Pittsburgh Pittsburgh Pennsylvania
- Magee‐Womens Research Institute Pittsburgh Pennsylvania
| | - Tianjiao Chu
- Department of Obstetrics, Gynecology and Reproductive SciencesUniversity of Pittsburgh Pittsburgh Pennsylvania
- Magee‐Womens Research Institute Pittsburgh Pennsylvania
| | - Hyagriv Simhan
- Department of Obstetrics, Gynecology and Reproductive SciencesUniversity of Pittsburgh Pittsburgh Pennsylvania
- Magee‐Womens Research Institute Pittsburgh Pennsylvania
| | | | - David G. Peters
- Department of Obstetrics, Gynecology and Reproductive SciencesUniversity of Pittsburgh Pittsburgh Pennsylvania
- Magee‐Womens Research Institute Pittsburgh Pennsylvania
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118
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Han L, Zhang X, Wang A, Ji Y, Cao X, Qin Q, Yu T, Huang H, Yin L. A Dual-Circular RNA Signature as a Non-invasive Diagnostic Biomarker for Gastric Cancer. Front Oncol 2020; 10:184. [PMID: 32154178 PMCID: PMC7047344 DOI: 10.3389/fonc.2020.00184] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/03/2020] [Indexed: 12/16/2022] Open
Abstract
Gastric cancer (GC) is the TOP3 leading cause of human mortality in malignant tumors. Notwithstanding, the association between GC and circRNAs is not clear. The purpose of this research was to determine the association between GC progression and circRNAs. The data of circRNAs was obtained from the Gene Expression Omnibus (GEO) database to identify gene, which differentially expressed circRNAs in GC tissues and paired normal tissues. The expression of circRNAs in cancer tissues and normal tissues were tested, and the target circRNA was verified before and after surgery in the plasma. A circRNA-micro(mi)RNA-mRNA competing endogenous RNAs (ceRNAs) network was established, and GO and KEGG analysis are performed. Five candidate circRNAs were identified through bioinformatics analysis. Hsa_circ_0021087 and hsa_circ_0005051 were both downregulated in GC tissues, cells and plasma by RTq-PCR. Additionally, there was a significant difference in the expression of plasma hsa_circ_0021087 in patients with GC at the preoperative and postoperative stages (P < 0.001). Hsa_circ_0021087 also promoted the proliferation of GC cells in vitro. Next, the circRNA-miRNA-mRNA network of hsa_circ_0021087 was predicted, which may be associated with the development of GC by bioinformatics analysis. In summary, the aforementioned dual-circular RNAs may have important implications on the potential, novel and non-invasive diagnostic method for patients with GC.
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Affiliation(s)
- Li Han
- School of Nursing, Qingdao University, Qingdao, China.,Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaoying Zhang
- Department of Emergency Internal Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Aimin Wang
- School of Nursing, Qingdao University, Qingdao, China
| | - Yang Ji
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xuelei Cao
- Department of Emergency Internal Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qiaoji Qin
- Department of Emergency Internal Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Tao Yu
- Department of Emergency Internal Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Huan Huang
- Department of Emergency Internal Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lei Yin
- Department of Emergency Internal Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
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119
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Lenaerts L, Tuveri S, Jatsenko T, Amant F, Vermeesch JR. Detection of incipient tumours by screening of circulating plasma DNA: hype or hope? Acta Clin Belg 2020; 75:9-18. [PMID: 31578135 DOI: 10.1080/17843286.2019.1671653] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Background: The last half-decade has been marked by a rapid expansion of research efforts in the field of so-called liquid biopsies, thereby investigating the potential of blood-derived cell-free tumour DNA (ctDNA) markers for application in clinical oncological management. The analysis of cfDNA appears to be particularly attractive for therapy monitoring purposes, while in terms of early cancer diagnosis and screening the potentials are just starting to be explored. Challenges, both of biological and technical nature, need to be addressed. One such challenge is to overcome the low levels of ctDNA in the circulation, intrinsic to many early-stage cancers. Methods: Here, we give an overview of the features of ctDNA and the approaches that are currently being applied with the ultimate aim to detect tumours in a presymptomatic stage. Conclusion: Although many studies report encouraging results, further technical development and larger studies are warranted before application of ctDNA analysis may find its place in clinic.
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Affiliation(s)
| | | | | | - Frédéric Amant
- Department of Oncology, KU Leuven, Leuven, Belgium
- Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
- Center for Gynecological Oncology Amsterdam, Academic Medical Centre Amsterdam-University of Amsterdam and The Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Joris Robert Vermeesch
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium
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120
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Vilades D, Martínez‐Camblor P, Ferrero‐Gregori A, Bär C, Lu D, Xiao K, Vea À, Nasarre L, Sanchez Vega J, Leta R, Carreras F, Thum T, Llorente‐Cortés V, de Gonzalo‐Calvo D. Plasma circular RNA hsa_circ_0001445 and coronary artery disease: Performance as a biomarker. FASEB J 2020; 34:4403-4414. [DOI: 10.1096/fj.201902507r] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 12/20/2019] [Accepted: 01/13/2020] [Indexed: 12/19/2022]
Affiliation(s)
- David Vilades
- Cardiac Imaging Unit, Cardiology Service Hospital de la Santa Creu i Sant Pau Universitat Autònoma de Barcelona (UAB) Barcelona Spain
| | | | - Andreu Ferrero‐Gregori
- Cardiology Service Hospital de la Santa Creu i Sant Pau Universitat Autònoma de Barcelona (UAB) Barcelona Spain
- CIBER Cardiovascular (CIBERCV) Institute of Health Carlos III Madrid Spain
| | - Christian Bär
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS) Hannover Medical School Hannover Germany
- REBIRTH Center for Translational Regenerative Medicine Hannover Medical School Hannover Germany
| | - Dongchao Lu
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS) Hannover Medical School Hannover Germany
| | - Ke Xiao
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS) Hannover Medical School Hannover Germany
| | - Àngela Vea
- Biomedical Research Institute Sant Pau (IIB Sant Pau) Barcelona Spain
| | - Laura Nasarre
- Biomedical Research Institute Sant Pau (IIB Sant Pau) Barcelona Spain
| | - Jesus Sanchez Vega
- Cardiac Imaging Unit, Cardiology Service Hospital de la Santa Creu i Sant Pau Universitat Autònoma de Barcelona (UAB) Barcelona Spain
| | - Rubén Leta
- Cardiac Imaging Unit, Cardiology Service Hospital de la Santa Creu i Sant Pau Universitat Autònoma de Barcelona (UAB) Barcelona Spain
| | - Francesc Carreras
- Cardiac Imaging Unit, Cardiology Service Hospital de la Santa Creu i Sant Pau Universitat Autònoma de Barcelona (UAB) Barcelona Spain
- CIBER Cardiovascular (CIBERCV) Institute of Health Carlos III Madrid Spain
- Biomedical Research Institute Sant Pau (IIB Sant Pau) Barcelona Spain
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS) Hannover Medical School Hannover Germany
- REBIRTH Center for Translational Regenerative Medicine Hannover Medical School Hannover Germany
| | - Vicenta Llorente‐Cortés
- CIBER Cardiovascular (CIBERCV) Institute of Health Carlos III Madrid Spain
- Biomedical Research Institute Sant Pau (IIB Sant Pau) Barcelona Spain
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC) Barcelona Spain
| | - David de Gonzalo‐Calvo
- CIBER Cardiovascular (CIBERCV) Institute of Health Carlos III Madrid Spain
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS) Hannover Medical School Hannover Germany
- Biomedical Research Institute Sant Pau (IIB Sant Pau) Barcelona Spain
- Institute of Biomedical Research of Barcelona (IIBB), Spanish National Research Council (CSIC) Barcelona Spain
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Ibarra A, Zhuang J, Zhao Y, Salathia NS, Huang V, Acosta AD, Aballi J, Toden S, Karns AP, Purnajo I, Parks JR, Guo L, Mason J, Sigal D, Nova TS, Quake SR, Nerenberg M. Non-invasive characterization of human bone marrow stimulation and reconstitution by cell-free messenger RNA sequencing. Nat Commun 2020; 11:400. [PMID: 31964864 PMCID: PMC6972916 DOI: 10.1038/s41467-019-14253-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 12/17/2019] [Indexed: 01/13/2023] Open
Abstract
Circulating cell-free mRNA (cf-mRNA) holds great promise as a non-invasive diagnostic biomarker. However, cf-mRNA composition and its potential clinical applications remain largely unexplored. Here we show, using Next Generation Sequencing-based profiling, that cf-mRNA is enriched in transcripts derived from the bone marrow compared to circulating cells. Further, longitudinal studies involving bone marrow ablation followed by hematopoietic stem cell transplantation in multiple myeloma and acute myeloid leukemia patients indicate that cf-mRNA levels reflect the transcriptional activity of bone marrow-resident hematopoietic lineages during bone marrow reconstitution. Mechanistically, stimulation of specific bone marrow cell populations in vivo using growth factor pharmacotherapy show that cf-mRNA reflects dynamic functional changes over time associated with cellular activity. Our results shed light on the biology of the circulating transcriptome and highlight the potential utility of cf-mRNA to non-invasively monitor bone marrow involved pathologies. Circulating cell-free mRNA holds great promise as a non-invasive diagnostic biomarker. Here the authors show that cell-free mRNA captures transcripts from the bone marrow and can be used to non-invasively monitor dynamic changes in bone marrow physiology.
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Affiliation(s)
- Arkaitz Ibarra
- Molecular Stethoscope, Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA.
| | - Jiali Zhuang
- Molecular Stethoscope, Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Yue Zhao
- Molecular Stethoscope, Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Neeraj S Salathia
- Molecular Stethoscope, Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Vera Huang
- Molecular Stethoscope, Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Alexander D Acosta
- Molecular Stethoscope, Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Jonathan Aballi
- Molecular Stethoscope, Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Shusuke Toden
- Molecular Stethoscope, Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Amy P Karns
- Molecular Stethoscope, Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Intan Purnajo
- Molecular Stethoscope, Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Julianna R Parks
- Molecular Stethoscope, Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Lucy Guo
- Molecular Stethoscope, Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - James Mason
- Scripps Clinic Medical Group, Scripps Green Hospital, 10666 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Darren Sigal
- Scripps Clinic Medical Group, Scripps Green Hospital, 10666 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Tina S Nova
- Molecular Stethoscope, Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Stephen R Quake
- Department of Bioengineering and Department of Applied Physics, Stanford University and Chan Zuckerberg Biohub, 318 Campus Drive, Stanford, CA, 94305, USA
| | - Michael Nerenberg
- Molecular Stethoscope, Inc., 3210 Merryfield Row, San Diego, CA, 92121, USA.
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Abstract
Circular RNAs (circRNAs) are a type of single-stranded RNA molecules that normally do not encode proteins. circRNAs are involved in many physiological processes as well as the pathogenesis of diseases. Cardiac fibrosis is increasingly recognized as a pathological force in advanced heart diseases. A growing number of studies have reported that the occurrence and development of cardiac fibrosis is closely associated with the regulation of circRNAs. This review summarizes the current understanding of circRNA biogenesis and function and will highlight the recent updates regarding the involvement of circRNAs in cardiac fibrosis, and their potential as emerging biomarkers and therapeutic targets.
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Affiliation(s)
- Fatemeh Yousefi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-154, Tehran, Iran
| | - Bahram M Soltani
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box 14115-154, Tehran, Iran.
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123
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Moufarrej MN, Wong RJ, Shaw GM, Stevenson DK, Quake SR. Investigating Pregnancy and Its Complications Using Circulating Cell-Free RNA in Women's Blood During Gestation. Front Pediatr 2020; 8:605219. [PMID: 33381480 PMCID: PMC7767905 DOI: 10.3389/fped.2020.605219] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
In recent years, there have been major advances in the application of non-invasive techniques to predict pregnancy-related complications, for example by measuring cell-free RNA (cfRNA) in maternal blood. In contrast to cell-free DNA (cfDNA), which is already in clinical use to diagnose fetal aneuploidy, circulating RNA levels can correspond with tissue-specific gene expression and provide a snapshot of prenatal health across gestation. Here, we review the physiologic origins of cfRNA and its novel applications and corresponding challenges to monitor fetal and maternal health and predict pregnancy-related complications.
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Affiliation(s)
- Mira N Moufarrej
- Departments of Bioengineering and Applied Physics, Stanford University, and Chan Zuckerberg Biohub, Stanford, CA, United States
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Stephen R Quake
- Departments of Bioengineering and Applied Physics, Stanford University, and Chan Zuckerberg Biohub, Stanford, CA, United States
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124
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Kirby E, Tse WH, Patel D, Keijzer R. First steps in the development of a liquid biopsy in situ hybridization protocol to determine circular RNA biomarkers in rat biofluids. Pediatr Surg Int 2019; 35:1329-1338. [PMID: 31570973 DOI: 10.1007/s00383-019-04558-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/12/2019] [Indexed: 12/24/2022]
Abstract
PURPOSE Epigenetic factors are involved in the pathogenesis of congenital diaphragmatic hernia (CDH). Circular RNAs (circRNAs) are epigenetic regulators amenable to biomarker profiling. Here, we aimed to develop a liquid biopsy protocol to detect pathognomonic circRNA changes in biofluids. METHODS Our protocol is adapted from the existing BaseScope™ in situ hybridization technique. Rat biofluids were fixed in a gelatin-coated 96-well plate with formalin. Probes were designed to target circRNAs with significant fold change in nitrofen-induced CDH. FastRED fluorescence was assessed using a plate reader and confirmed with confocal microscopy. We tested maternal serum and amniotic fluid samples from control and nitrofen-treated rats. RESULTS We detected circRNAs in rat serum and amniotic fluid from control and CDH (nitrofen-treated) rats using fluorescent readout. CircRNA signal was observed in fixed biofluids as fluorescent punctate foci under confocal laser scanning microscopy. This was confirmed by comparison to BaseScope™ lung tissue sections. Signal was concentration dependent and DNase resistant. CONCLUSION We successfully adapted BaseScope™ to detect circRNAs in rat biofluids: serum and amniotic fluid. We detected signal from probes targeted to circRNAs that are dysregulated in rat CDH. This work establishes the preliminary feasibility of circRNA detection in prenatal diagnostics.
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Affiliation(s)
- Eimear Kirby
- Trinity Biomedical Sciences Institute, Trinity College Dublin School of Medicine, Dublin, Ireland
- Division of Pediatric Surgery, Departments of Surgery, Pediatrics & Child Health and Physiology & Pathophysiology, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Wai Hei Tse
- Division of Pediatric Surgery, Departments of Surgery, Pediatrics & Child Health and Physiology & Pathophysiology, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Daywin Patel
- Division of Pediatric Surgery, Departments of Surgery, Pediatrics & Child Health and Physiology & Pathophysiology, University of Manitoba, Winnipeg, MB, Canada
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Richard Keijzer
- Division of Pediatric Surgery, Departments of Surgery, Pediatrics & Child Health and Physiology & Pathophysiology, University of Manitoba, Winnipeg, MB, Canada.
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.
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125
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Ye DX, Wang SS, Huang Y, Chi P. A 3-circular RNA signature as a noninvasive biomarker for diagnosis of colorectal cancer. Cancer Cell Int 2019; 19:276. [PMID: 31700498 PMCID: PMC6829842 DOI: 10.1186/s12935-019-0995-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023] Open
Abstract
Background Circular RNAs (circRNAs), a novel type of noncoding RNAs, play critical roles in the initiation and progression of cancer. Emerging studies also shows that circRNAs may function as potential markers for cancer diagnosis and treatment. However, the diagnostic value of circRNAs in colorectal cancer (CRC) remains need to be unearthed. Methods CircRNA microarray was performed to detect the differentially expressed circRNAs in eight plasma samples, including four colorectal cancer (CRC) and four normal samples. Besides, the results of microarray were validated by quantitative real-time polymerase chain reaction (qRT-PCR). Moreover, ROC curve evaluation was performed to calculate the diagnostic value of significantly dysregulated circRNAs. In order to predict the potential mechanism of the significant circRNAs, circRNA-miRNA-mRNA network was constructed based on the TargetScan, miRTarBase and MIRDB database, as well as CircInteractome online software. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed to further predict the function of meaningful circRNAs. Results Totally three differentially expressed circRNAs were identified in CRC plasma compared to normal plasma by circRNA microarray analysis, and the results was validated by qRT-PCR. Hsa_circ_0082182, hsa_circ_0000370 and hsa_circ_0035445 were identified and ROC curves analysis was used to calculate the single and joint diagnostic value. Furthermore, GO and KEGG analyses revealed that functions were mainly cancer-related, which indicated that the circRNAs were meaningfully associated with CRC cell proliferation and metastasis. Conclusion In conclusion, we have identified three circRNAs that are dysregulated in CRC plasma, including hsa_circ_0082182, hsa_circ_0000370 and hsa_circ_0035445. ROC curves showed that these circRNAs might have diagnostic value for colorectal cancer. Furthermore, bioinformatics analysis indicated that the above-mentioned circRNAs might be involved in the development of CRC.
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Affiliation(s)
- Dao-Xiong Ye
- Department of General Surgery, Fujian Medical University Union Hospital, No.29 Xinquan Road, Fuzhou, 350001 China
| | - Si-Si Wang
- Department of General Surgery, Fujian Medical University Union Hospital, No.29 Xinquan Road, Fuzhou, 350001 China
| | - Ying Huang
- Department of General Surgery, Fujian Medical University Union Hospital, No.29 Xinquan Road, Fuzhou, 350001 China
| | - Pan Chi
- Department of General Surgery, Fujian Medical University Union Hospital, No.29 Xinquan Road, Fuzhou, 350001 China
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126
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Kalmbach A, Schröder C, Klein-Hitpass L, Nordström K, Ulz P, Heitzer E, Speicher MR, Rahmann S, Wieczorek D, Horsthemke B, Bramswig NC. Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome. Cytogenet Genome Res 2019; 159:1-11. [PMID: 31658463 DOI: 10.1159/000503266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 01/15/2023] Open
Abstract
The switch/sucrose non-fermenting (SWI/SNF) complex is an ATP-dependent chromatin remodeller that regulates the spacing of nucleosomes and thereby controls gene expression. Heterozygous mutations in genes encoding subunits of the SWI/SNF complex have been reported in individuals with Coffin-Siris syndrome (CSS), with the majority of the mutations in ARID1B. CSS is a rare congenital disorder characterized by facial dysmorphisms, digital anomalies, and variable intellectual disability. We hypothesized that mutations in genes encoding subunits of the ubiquitously expressed SWI/SNF complex may lead to alterations of the nucleosome profiles in different cell types. We performed the first study on CSS-patient samples and investigated the nucleosome landscapes of cell-free DNA (cfDNA) isolated from blood plasma by whole-genome sequencing. In addition, we studied the nucleosome landscapes of CD14+ monocytes from CSS-affected individuals by nucleosome occupancy and methylome-sequencing (NOMe-seq) as well as their expression profiles. In cfDNA of CSS-affected individuals with heterozygous ARID1B mutations, we did not observe major changes in the nucleosome profile around transcription start sites. In CD14+ monocytes, we found few genomic regions with different nucleosome occupancy when compared to controls. RNA-seq analysis of CD14+ monocytes of these individuals detected only few differentially expressed genes, which were not in proximity to any of the identified differential nucleosome-depleted regions. In conclusion, we show that heterozygous mutations in the human SWI/SNF subunit ARID1B do not have a major impact on the nucleosome landscape or gene expression in blood cells. This might be due to functional redundancy, cell-type specificity, or alternative functions of ARID1B.
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127
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Lin J, Cai D, Li W, Yu T, Mao H, Jiang S, Xiao B. Plasma circular RNA panel acts as a novel diagnostic biomarker for colorectal cancer. Clin Biochem 2019; 74:60-68. [PMID: 31669510 DOI: 10.1016/j.clinbiochem.2019.10.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common cancers worldwide, and emerging lines of evidence have implicated circular RNAs (circRNAs), a novel class of endogenous noncoding RNAs, in CRC development. However, whether plasma circRNAs might be novel diagnostic biomarkers for CRC remains unclear. METHODS We investigated the plasma levels of selected circRNAs by quantitative real-time PCR (qRT-PCR). The presence of the candidate circRNAs was confirmed through RNase R assays, qRT-PCR and DNA sequencing, and their diagnostic value was evaluated using a receiver operating characteristic (ROC) curve. RESULTS The plasma levels of three circRNAs (circ-CCDC66, circ-ABCC1 and circ-STIL) were significantly decreased in CRC patients (n = 45) compared with healthy controls (n = 61). The ROC curve analysis showed that the area under the ROC curve (AUC) of the three-circRNA panel was 0.780, which is higher than that of traditional protein biomarkers, such as carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9 (CA19-9). Combining the circRNA panel with CEA and CA19-9 might improve the ability to diagnose CRC (AUC = 0.855). In addition, the plasma circ-ABCC1 level was related to tumor growth and progression, and the plasma circ-CCDC66 and circ-ABCC1 levels were decreased in precursor lesions of CRC, including colon adenomas and adenomatous polyps. More importantly, circ-CCDC66 and circ-STIL were found to be useful for diagnosing early-stage CRC, and the three-circRNA panel improved the ability to diagnose CEA-negative and CA19-9-negative CRC. CONCLUSION Our study provides the first identification of a panel of three plasma circRNAs that could serve as a novel and independent diagnostic biomarker for CRC.
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Affiliation(s)
- Jie Lin
- Department of Clinical Laboratory, The 904th Hospital of The People's Liberation Army, Wuxi 214044, PR China.
| | - Dongping Cai
- Department of Clinical Laboratory, The 904th Hospital of The People's Liberation Army, Wuxi 214044, PR China
| | - Wei Li
- Department of Pharmacy, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Ting Yu
- Department of Clinical Laboratory, The 89th Hospital of The People's Liberation Army, Weifang 261000, PR China
| | - Hui Mao
- Department of Clinical Laboratory, The 904th Hospital of The People's Liberation Army, Wuxi 214044, PR China
| | - Shan Jiang
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, PR China.
| | - Bin Xiao
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China.
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128
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Ulz P, Perakis S, Zhou Q, Moser T, Belic J, Lazzeri I, Wölfler A, Zebisch A, Gerger A, Pristauz G, Petru E, White B, Roberts CES, John JS, Schimek MG, Geigl JB, Bauernhofer T, Sill H, Bock C, Heitzer E, Speicher MR. Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection. Nat Commun 2019; 10:4666. [PMID: 31604930 PMCID: PMC6789008 DOI: 10.1038/s41467-019-12714-4] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 09/24/2019] [Indexed: 12/19/2022] Open
Abstract
Deregulation of transcription factors (TFs) is an important driver of tumorigenesis, but non-invasive assays for assessing transcription factor activity are lacking. Here we develop and validate a minimally invasive method for assessing TF activity based on cell-free DNA sequencing and nucleosome footprint analysis. We analyze whole genome sequencing data for >1,000 cell-free DNA samples from cancer patients and healthy controls using a bioinformatics pipeline developed by us that infers accessibility of TF binding sites from cell-free DNA fragmentation patterns. We observe patient-specific as well as tumor-specific patterns, including accurate prediction of tumor subtypes in prostate cancer, with important clinical implications for the management of patients. Furthermore, we show that cell-free DNA TF profiling is capable of detection of early-stage colorectal carcinomas. Our approach for mapping tumor-specific transcription factor binding in vivo based on blood samples makes a key part of the noncoding genome amenable to clinical analysis.
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Affiliation(s)
- Peter Ulz
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Samantha Perakis
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Qing Zhou
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Tina Moser
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Isaac Lazzeri
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Albert Wölfler
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - Armin Zebisch
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - Armin Gerger
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, Graz, Austria
| | - Gunda Pristauz
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | - Edgar Petru
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | | | | | | | - Michael G Schimek
- Institute of Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Jochen B Geigl
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Thomas Bauernhofer
- Department of Internal Medicine, Division of Oncology, Medical University of Graz, Graz, Austria
| | - Heinz Sill
- Department of Internal Medicine, Division of Hematology, Medical University of Graz, Graz, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
- Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken, Germany
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria.
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
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129
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Kumar VS. Cell-free RNA as a Fetal Timekeeper. Clin Chem 2019; 64:1800-1801. [PMID: 30487194 DOI: 10.1373/clinchem.2018.295527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 10/02/2018] [Indexed: 11/06/2022]
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130
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Liu X, Helenius D, Skotte L, Beaumont RN, Wielscher M, Geller F, Juodakis J, Mahajan A, Bradfield JP, Lin FTJ, Vogelezang S, Bustamante M, Ahluwalia TS, Pitkänen N, Wang CA, Bacelis J, Borges MC, Zhang G, Bedell BA, Rossi RM, Skogstrand K, Peng S, Thompson WK, Appadurai V, Lawlor DA, Kalliala I, Power C, McCarthy MI, Boyd HA, Marazita ML, Hakonarson H, Hayes MG, Scholtens DM, Rivadeneira F, Jaddoe VWV, Vinding RK, Bisgaard H, Knight BA, Pahkala K, Raitakari O, Helgeland Ø, Johansson S, Njølstad PR, Fadista J, Schork AJ, Nudel R, Miller DE, Chen X, Weirauch MT, Mortensen PB, Børglum AD, Nordentoft M, Mors O, Hao K, Ryckman KK, Hougaard DM, Kottyan LC, Pennell CE, Lyytikainen LP, Bønnelykke K, Vrijheid M, Felix JF, Lowe WL, Grant SFA, Hyppönen E, Jacobsson B, Jarvelin MR, Muglia LJ, Murray JC, Freathy RM, Werge TM, Melbye M, Buil A, Feenstra B. Variants in the fetal genome near pro-inflammatory cytokine genes on 2q13 associate with gestational duration. Nat Commun 2019; 10:3927. [PMID: 31477735 PMCID: PMC6718389 DOI: 10.1038/s41467-019-11881-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 08/05/2019] [Indexed: 12/17/2022] Open
Abstract
The duration of pregnancy is influenced by fetal and maternal genetic and non-genetic factors. Here we report a fetal genome-wide association meta-analysis of gestational duration, and early preterm, preterm, and postterm birth in 84,689 infants. One locus on chromosome 2q13 is associated with gestational duration; the association is replicated in 9,291 additional infants (combined P = 3.96 × 10-14). Analysis of 15,588 mother-child pairs shows that the association is driven by fetal rather than maternal genotype. Functional experiments show that the lead SNP, rs7594852, alters the binding of the HIC1 transcriptional repressor. Genes at the locus include several interleukin 1 family members with roles in pro-inflammatory pathways that are central to the process of parturition. Further understanding of the underlying mechanisms will be of great public health importance, since giving birth either before or after the window of term gestation is associated with increased morbidity and mortality.
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Affiliation(s)
- Xueping Liu
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Dorte Helenius
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Julius Juodakis
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Jonathan P Bradfield
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Quantinuum Research, LLC, San Diego, CA, USA
| | - Frederick T J Lin
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Suzanne Vogelezang
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Niina Pitkänen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520, Turku, Finland
| | - Carol A Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, NSW, Australia
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maria C Borges
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ge Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
| | - Bruce A Bedell
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Robert M Rossi
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kristin Skogstrand
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Statens Serum Institut, Center for Neonatal Screening, Department for Congenital Disorders, Copenhagen, Denmark
| | - Shouneng Peng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Wesley K Thompson
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Vivek Appadurai
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Ilkka Kalliala
- Department of Surgery and Cancer, IRDB, Faculty of Medicine, Imperial College, London, W12 0NN, UK
- Department of Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu, 200029 HUS, Finland
| | - Christine Power
- Population, Policy and Practice, Great Ormond Street Institute for Child Health, University College London, London, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LJ, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Heather A Boyd
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Anthropology, Northwestern University, Evanston, IL, USA
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Denise M Scholtens
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Fernando Rivadeneira
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rebecca K Vinding
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Bridget A Knight
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - Katja Pahkala
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520, Turku, Finland
- Paavo Nurmi Centre, Sports & Exercise Medicine Unit, Department of Health and Physical Activity, University of Turku, 20520, Turku, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20521, Turku, Finland
| | - Øyvind Helgeland
- K. G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
- Norwegian Institute of Public Health, Division of Health data and Digitalization, Department of Genetic Research and Bioinformatics, Oslo, Norway
| | - Stefan Johansson
- K. G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Pål R Njølstad
- K. G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - João Fadista
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Andrew J Schork
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Ron Nudel
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Daniel E Miller
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Preben Bo Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Mental Health Center Copenhagen, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Kelli K Ryckman
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
- Department of Epidemiology, University of Iowa, Iowa City, IA, USA
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Statens Serum Institut, Center for Neonatal Screening, Department for Congenital Disorders, Copenhagen, Denmark
| | - Leah C Kottyan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Craig E Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, NSW, Australia
| | - Leo-Pekka Lyytikainen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, 33520, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, 33014, Tampere, Finland
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Martine Vrijheid
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - William L Lowe
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Struan F A Grant
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elina Hyppönen
- Population, Policy and Practice, Great Ormond Street Institute for Child Health, University College London, London, UK
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
| | - Marjo-Riitta Jarvelin
- Institute of Health Sciences, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Medical Research Council-Health Protection Agency Centre for Environment and Health, Faculty of Medicine, Imperial College London, London, UK
| | - Louis J Muglia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Rachel M Freathy
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Thomas M Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alfonso Buil
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.
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131
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Chen M, Yao YL, Yang Y, Zhu M, Tang Y, Liu S, Li K, Tang Z. Comprehensive Profiles of mRNAs and miRNAs Reveal Molecular Characteristics of Multiple Organ Physiologies and Development in Pigs. Front Genet 2019; 10:756. [PMID: 31552085 PMCID: PMC6737989 DOI: 10.3389/fgene.2019.00756] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/17/2019] [Indexed: 12/13/2022] Open
Abstract
The pig (Sus scrofa) is not only an important livestock animal but also widely used as a biomedical model. However, the understanding of the molecular characteristics of organs and of the developmental skeletal muscle of the pig is severely limited. Here, we performed a comprehensive transcriptome profiling of mRNAs and miRNAs across nine tissues and three skeletal muscle developmental stages in the Guizhou miniature pig. The reproductive organs (ovary and testis) had greater transcriptome complexity and activity than other tissues, and the highest transcriptome similarity was between skeletal muscle and heart (R = 0.79). We identified 1,819 mRNAs and 96 miRNAs to be tissue-specific in nine organs. Testis had the largest number of tissue-specific mRNAs (992) and miRNAs (40). Only 15 genes and two miRNAs were specifically expressed in skeletal muscle and fat, respectively. During postnatal skeletal muscle development, the mRNAs associated with focal adhesion, Notch signaling, protein digestion, and absorption pathways were up-regulated from D0 to D30 and then down-regulated from D30 and D240, while genes with opposing expression patterns were significantly enriched in the oxidative phosphorylation and proteasome pathways. The miRNAs mainly regulated genes associated with insulin, Wnt, fatty acid biosynthesis, Notch, MAPK, TGF-beta, insulin secretion, ECM-receptor interaction, focal adhesion, and calcium signaling pathways. We also identified 37 new miRNA-mRNA interaction pairs involved in skeletal muscle development. Overall, our data not only provide a rich resource for understanding pig organ physiology and development but also aid the study of the molecular functions of mRNA and miRNA in mammals.
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Affiliation(s)
- Muya Chen
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yi Long Yao
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yalan Yang
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Min Zhu
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yijie Tang
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Siyuan Liu
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kui Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonglin Tang
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.,Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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132
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A cell-free DNA metagenomic sequencing assay that integrates the host injury response to infection. Proc Natl Acad Sci U S A 2019; 116:18738-18744. [PMID: 31451660 DOI: 10.1073/pnas.1906320116] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
High-throughput metagenomic sequencing offers an unbiased approach to identify pathogens in clinical samples. Conventional metagenomic sequencing, however, does not integrate information about the host, which is often critical to distinguish infection from infectious disease, and to assess the severity of disease. Here, we explore the utility of high-throughput sequencing of cell-free DNA (cfDNA) after bisulfite conversion to map the tissue and cell types of origin of host-derived cfDNA, and to profile the bacterial and viral metagenome. We applied this assay to 51 urinary cfDNA isolates collected from a cohort of kidney transplant recipients with and without bacterial and viral infection of the urinary tract. We find that the cell and tissue types of origin of urinary cfDNA can be derived from its genome-wide profile of methylation marks, and strongly depend on infection status. We find evidence of kidney and bladder tissue damage due to viral and bacterial infection, respectively, and of the recruitment of neutrophils to the urinary tract during infection. Through direct comparison to conventional metagenomic sequencing as well as clinical tests of infection, we find this assay accurately captures the bacterial and viral composition of the sample. The assay presented here is straightforward to implement, offers a systems view into bacterial and viral infections of the urinary tract, and can find future use as a tool for the differential diagnosis of infection.
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133
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Zhong PS, Li R, Santo S. Homogeneity tests of covariance matrices with high-dimensional longitudinal data. Biometrika 2019; 106:619-634. [PMID: 31427823 DOI: 10.1093/biomet/asz011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 12/22/2022] Open
Abstract
This paper deals with the detection and identification of changepoints among covariances of high-dimensional longitudinal data, where the number of features is greater than both the sample size and the number of repeated measurements. The proposed methods are applicable under general temporal-spatial dependence. A new test statistic is introduced for changepoint detection, and its asymptotic distribution is established. If a changepoint is detected, an estimate of the location is provided. The rate of convergence of the estimator is shown to depend on the data dimension, sample size, and signal-to-noise ratio. Binary segmentation is used to estimate the locations of possibly multiple changepoints, and the corresponding estimator is shown to be consistent under mild conditions. Simulation studies provide the empirical size and power of the proposed test and the accuracy of the changepoint estimator. An application to a time-course microarray dataset identifies gene sets with significant gene interaction changes over time.
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Affiliation(s)
- Ping-Shou Zhong
- Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, 851 S. Morgan Street, Chicago, Illinois 60607, USA
| | - Runze Li
- Department of Statistics and The Methodology Center, Pennsylvania State University, University Park, Pennsylvania 16801, USA
| | - Shawn Santo
- Department of Statistics and Probability, Michigan State University, 619 Red Cedar Road, East Lansing, Michigan 48824, USA
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134
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Jiang P, Chan KCA, Lo YMD. Liver-derived cell-free nucleic acids in plasma: Biology and applications in liquid biopsies. J Hepatol 2019; 71:409-421. [PMID: 31004682 DOI: 10.1016/j.jhep.2019.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/01/2019] [Accepted: 04/05/2019] [Indexed: 02/09/2023]
Abstract
There is much global research interest surrounding the use of cell-free DNA (cfDNA) for liquid biopsies. cfDNA-based non-invasive prenatal testing for foetal chromosomal aneuploidies was the first successful application of cfDNA technology that transformed clinical practice - it has since been rapidly adopted in dozens of countries and is used by millions of pregnant women every year. Prompted by such developments, efforts to use cfDNA in other fields, especially for cancer detection and monitoring have been actively pursued in recent years. Cancer-associated aberrations including single nucleotide mutations, copy number aberrations, aberrations in methylation and alterations in DNA fragmentation patterns have been detected in the cfDNA of patients suffering from a wide variety of cancers. In addition, the analysis of methylation and fragmentomic patterns has enabled the tissue origin of cfDNA to be determined. In this review, different approaches for detecting circulating liver-derived nucleic acids and cancer-associated aberrations, as well as their potential clinical applications for the detection, monitoring and management of hepatocellular carcinoma, will be discussed.
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Affiliation(s)
- Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region; State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region
| | - K C Allen Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region; State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region
| | - Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region; Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region; State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong Special Administrative Region.
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135
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Heitzer E, Haque IS, Roberts CES, Speicher MR. Current and future perspectives of liquid biopsies in genomics-driven oncology. Nat Rev Genet 2019; 20:71-88. [PMID: 30410101 DOI: 10.1038/s41576-018-0071-5] [Citation(s) in RCA: 803] [Impact Index Per Article: 160.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Precision oncology seeks to leverage molecular information about cancer to improve patient outcomes. Tissue biopsy samples are widely used to characterize tumours but are limited by constraints on sampling frequency and their incomplete representation of the entire tumour bulk. Now, attention is turning to minimally invasive liquid biopsies, which enable analysis of tumour components (including circulating tumour cells and circulating tumour DNA) in bodily fluids such as blood. The potential of liquid biopsies is highlighted by studies that show they can track the evolutionary dynamics and heterogeneity of tumours and can detect very early emergence of therapy resistance, residual disease and recurrence. However, the analytical validity and clinical utility of liquid biopsies must be rigorously demonstrated before this potential can be realized.
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Affiliation(s)
- Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria. .,BioTechMed-Graz, Graz, Austria. .,Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Graz, Austria.
| | | | | | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
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136
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Petty LE, Highland HM, Gamazon ER, Hu H, Karhade M, Chen HH, de Vries PS, Grove ML, Aguilar D, Bell GI, Huff CD, Hanis CL, Doddapaneni H, Munzy DM, Gibbs RA, Ma J, Parra EJ, Cruz M, Valladares-Salgado A, Arking DE, Barbeira A, Im HK, Morrison AC, Boerwinkle E, Below JE. Functionally oriented analysis of cardiometabolic traits in a trans-ethnic sample. Hum Mol Genet 2019; 28:1212-1224. [PMID: 30624610 PMCID: PMC6423424 DOI: 10.1093/hmg/ddy435] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 11/13/2018] [Accepted: 11/20/2018] [Indexed: 01/02/2023] Open
Abstract
Interpretation of genetic association results is difficult because signals often lack biological context. To generate hypotheses of the functional genetic etiology of complex cardiometabolic traits, we estimated the genetically determined component of gene expression from common variants using PrediXcan (1) and determined genes with differential predicted expression by trait. PrediXcan imputes tissue-specific expression levels from genetic variation using variant-level effect on gene expression in transcriptome data. To explore the value of imputed genetically regulated gene expression (GReX) models across different ancestral populations, we evaluated imputed expression levels for predictive accuracy genome-wide in RNA sequence data in samples drawn from European-ancestry and African-ancestry populations and identified substantial predictive power using European-derived models in a non-European target population. We then tested the association of GReX on 15 cardiometabolic traits including blood lipid levels, body mass index, height, blood pressure, fasting glucose and insulin, RR interval, fibrinogen level, factor VII level and white blood cell and platelet counts in 15 755 individuals across three ancestry groups, resulting in 20 novel gene-phenotype associations reaching experiment-wide significance across ancestries. In addition, we identified 18 significant novel gene-phenotype associations in our ancestry-specific analyses. Top associations were assessed for additional support via query of S-PrediXcan (2) results derived from publicly available genome-wide association studies summary data. Collectively, these findings illustrate the utility of transcriptome-based imputation models for discovery of cardiometabolic effect genes in a diverse dataset.
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Affiliation(s)
- Lauren E Petty
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Heather M Highland
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Eric R Gamazon
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Clare Hall, University of Cambridge, Cambridge, UK
| | - Hao Hu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - Mandar Karhade
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hung-Hsin Chen
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Paul S de Vries
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Megan L Grove
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - David Aguilar
- Department of Cardiology, Baylor College of Medicine Houston, TX, USA
| | - Graeme I Bell
- Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Chad D Huff
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - Craig L Hanis
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Donna M Munzy
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jianzhong Ma
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Esteban J Parra
- Department of Anthropology, University of Toronto at Mississauga, Mississauga, Ontario, Canada
| | - Miguel Cruz
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - Adan Valladares-Salgado
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, IMSS, Mexico City, Mexico
| | - Dan E Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alvaro Barbeira
- Section of Genetic Medicine, Department of Medicine, University of Chicago, IL, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, IL, USA
| | - Alanna C Morrison
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
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137
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Eskandari M, Manoochehrabadi S, Pashaiefar H, Zaimy MA, Ahmadvand M. Clinical significance of cell-free DNA as a prognostic biomarker in patients with diffuse large B-cell lymphoma. Blood Res 2019; 54:114-119. [PMID: 31309089 PMCID: PMC6614089 DOI: 10.5045/br.2019.54.2.114] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/03/2019] [Accepted: 01/07/2019] [Indexed: 12/22/2022] Open
Abstract
Background Cell-free DNA (cfDNA) has the potential to serve as a non-invasive prognostic biomarker in some types of neoplasia. The investigation of plasma concentration of cfDNA may reveal its use as a valuable biomarker for risk stratification of diffuse large B-cell lymphoma (DLBCL). The present prognostic value of plasma cfDNA has not been widely confirmed in DLBCL subjects. Here, we evaluated cfDNA plasma concentration and assessed its potential prognostic value as an early DLBCL diagnostic tool. Methods cfDNA concentrations in plasma samples from 40 patients with DLBCL during diagnosis and of 38 normal controls were determined with quantitative polymerase chain reaction (qPCR) for the multi-locus L1PA2 gene. Results Statistically significant elevation in plasma cfDNA concentrations was observed in patients with DLBCL as compared to that in normal controls (P<0.05). A cutoff point of 2.071 ng/mL provided 82.5% sensitivity and 62.8% specificity and allowed successful discrimination of patients with DLBCL from normal controls (area under the curve=0.777; P=0.00003). Furthermore, patients with DLBCL showing higher concentrations of cfDNA had shorter overall survival (median, 9 mo; P=0.022) than those with lower cfDNA levels. In addition, elevated cfDNA concentration was significantly associated with age, B-symptoms, International Prognostic Index (IPI) score, and different stages of disease (all P<0.05). Conclusion Quantification of cfDNA with qPCR at the time of diagnosis may allow identification of patients with high cfDNA concentration, which correlates with aggressive clinical outcomes and adverse prognosis.
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Affiliation(s)
- Mahsa Eskandari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Saba Manoochehrabadi
- Medical Genetics, Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Pashaiefar
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Cell Therapy and Hematopoietic Stem Cell Transplantation Research Center, Hematologic Malignancies Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Zaimy
- Department of Medical Genetics, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Mohammad Ahmadvand
- Hematology-Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Cell Therapy and Hematopoietic Stem Cell Transplantation Research Center, Hematologic Malignancies Research Center, Tehran University of Medical Sciences, Tehran, Iran
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138
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Chen M, Mithraprabhu S, Ramachandran M, Choi K, Khong T, Spencer A. Utility of Circulating Cell-Free RNA Analysis for the Characterization of Global Transcriptome Profiles of Multiple Myeloma Patients. Cancers (Basel) 2019; 11:cancers11060887. [PMID: 31242667 PMCID: PMC6628062 DOI: 10.3390/cancers11060887] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/12/2019] [Accepted: 06/21/2019] [Indexed: 12/13/2022] Open
Abstract
In this study, we evaluated the utility of extracellular RNA (exRNA) derived from the plasma of multiple myeloma (MM) patients for whole transcriptome characterization. exRNA from 10 healthy controls (HC), five newly diagnosed (NDMM), and 12 relapsed and refractory (RRMM) MM patients were analyzed and compared. We showed that ~45% of the exRNA genes were protein-coding genes and ~85% of the identified genes were covered >70%. Compared to HC, we identified 632 differentially expressed genes (DEGs) in MM patients, of which 26 were common to NDMM and RRMM. We further identified 54 and 191 genes specific to NDMM and RRMM, respectively, and these included potential biomarkers such as LINC00863, MIR6754, CHRNE, ITPKA, and RGS18 in NDMM, and LINC00462, PPBP, RPL5, IER3, and MIR425 in RRMM, that were subsequently validated using droplet digital PCR. Moreover, single nucleotide polymorphisms and small indels were identified in the exRNA, including mucin family genes that demonstrated different rates of mutations between NDMM and RRMM. This is the first whole transcriptome study of exRNA in hematological malignancy and has provided the basis for the utilization of exRNA to enhance our understanding of the MM biology and to identify potential biomarkers relevant to the diagnosis and prognosis of MM patients.
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Affiliation(s)
- Maoshan Chen
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
| | - Sridurga Mithraprabhu
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
- Malignant Haematology and Stem Cell Transplantation, Alfred Hospital, Melbourne 3004, Australia.
| | - Malarmathy Ramachandran
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
- Malignant Haematology and Stem Cell Transplantation, Alfred Hospital, Melbourne 3004, Australia.
| | - Kawa Choi
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
- Malignant Haematology and Stem Cell Transplantation, Alfred Hospital, Melbourne 3004, Australia.
| | - Tiffany Khong
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
- Malignant Haematology and Stem Cell Transplantation, Alfred Hospital, Melbourne 3004, Australia.
| | - Andrew Spencer
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
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139
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Huang CC, Du M, Wang L. Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer. Cancers (Basel) 2019; 11:cancers11060805. [PMID: 31212602 PMCID: PMC6627444 DOI: 10.3390/cancers11060805] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/03/2019] [Accepted: 06/06/2019] [Indexed: 12/28/2022] Open
Abstract
Molecular analysis of cell-free DNA (cfDNA) that circulates in plasma and other body fluids represents a "liquid biopsy" approach for non-invasive cancer screening or monitoring. The rapid development of sequencing technologies has made cfDNA a promising source to study cancer development and progression. Specific genetic and epigenetic alterations have been found in plasma, serum, and urine cfDNA and could potentially be used as diagnostic or prognostic biomarkers in various cancer types. In this review, we will discuss the molecular characteristics of cancer cfDNA and major bioinformatics approaches involved in the analysis of cfDNA sequencing data for detecting genetic mutation, copy number alteration, methylation change, and nucleosome positioning variation. We highlight specific challenges in sensitivity to detect genetic aberrations and robustness of statistical analysis. Finally, we provide perspectives regarding the standard and continuing development of bioinformatics analysis to move this promising screening tool into clinical practice.
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Affiliation(s)
- Chiang-Ching Huang
- Zilber School of Public Health, University of Wisconsin, Milwaukee, WI 53205, USA.
| | - Meijun Du
- Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Liang Wang
- Department of Pathology and MCW Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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Giraldez MD, Spengler RM, Etheridge A, Goicochea AJ, Tuck M, Choi SW, Galas DJ, Tewari M. Phospho-RNA-seq: a modified small RNA-seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma. EMBO J 2019; 38:e101695. [PMID: 31053596 PMCID: PMC6545557 DOI: 10.15252/embj.2019101695] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/14/2019] [Accepted: 04/15/2019] [Indexed: 12/25/2022] Open
Abstract
Extracellular RNAs (exRNAs) in biofluids have attracted great interest as potential biomarkers. Although extracellular microRNAs in blood plasma are extensively characterized, extracellular messenger RNA (mRNA) and long non-coding RNA (lncRNA) studies are limited. We report that plasma contains fragmented mRNAs and lncRNAs that are missed by standard small RNA-seq protocols due to lack of 5' phosphate or presence of 3' phosphate. These fragments were revealed using a modified protocol ("phospho-RNA-seq") incorporating RNA treatment with T4-polynucleotide kinase, which we compared with standard small RNA-seq for sequencing synthetic RNAs with varied 5' and 3' ends, as well as human plasma exRNA Analyzing phospho-RNA-seq data using a custom, high-stringency bioinformatic pipeline, we identified mRNA/lncRNA transcriptome fingerprints in plasma, including tissue-specific gene sets. In a longitudinal study of hematopoietic stem cell transplant patients, bone marrow- and liver-enriched exRNA genes were tracked with bone marrow recovery and liver injury, respectively, providing proof-of-concept validation as a biomarker approach. By enabling access to an unexplored realm of mRNA and lncRNA fragments, phospho-RNA-seq opens up new possibilities for plasma transcriptomic biomarker development.
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Affiliation(s)
- Maria D Giraldez
- Department of Internal Medicine, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI, USA
- Institute of Biomedicine of Seville (IBiS), Seville, Spain
- Unit of Digestive Diseases, Virgen del Rocio University Hospital, Seville, Spain
| | - Ryan M Spengler
- Department of Internal Medicine, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI, USA
| | | | - Annika J Goicochea
- Department of Internal Medicine, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI, USA
| | - Missy Tuck
- Department of Internal Medicine, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI, USA
| | - Sung Won Choi
- Department of Pediatrics, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI, USA
| | - David J Galas
- Pacific Northwest Research Institute, Seattle, WA, USA
| | - Muneesh Tewari
- Department of Internal Medicine, Hematology/Oncology Division, University of Michigan, Ann Arbor, MI, USA
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
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141
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George AK, Master K, Majumder A, Homme RP, Laha A, Sandhu HS, Tyagi SC, Singh M. Circular RNAs constitute an inherent gene regulatory axis in the mammalian eye and brain. Can J Physiol Pharmacol 2019; 97:463-472. [DOI: 10.1139/cjpp-2018-0505] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Circular RNAs (circRNAs) are being hailed as a newly rediscovered class of covalently closed transcripts that are produced via alternative, noncanonical pre-mRNA back-splicing events. These single-stranded RNA molecules have been identified in organisms ranging from the worm (Cortés-López et al. 2018. BMC Genomics, 19: 8; Ivanov et al. 2015. Cell Rep. 10: 170–177) to higher eukaryotes (Yang et al. 2017. Cell Res. 27: 626–641) to plants (Li et al. 2017. Biochem. Biophys. Res. Commun. 488: 382–386). At present, research on circRNAs is an active area because of their diverse roles in development, health, and diseases. Partly because their circularity makes them resistant to degradation, they hold great promise as unique biomarkers for ocular and central nervous system (CNS) disorders. We believe that further work on their applications could help in developing them as “first-in-class” diagnostics, therapeutics, and prognostic targets for numerous eye conditions. Interestingly, many circRNAs play key roles in transcriptional regulation by acting as miRNAs sponges, meaning that they serve as master regulators of RNA and protein expression. Since the retina is an extension of the brain and is part of the CNS, we highlight the current state of circRNA biogenesis, properties, and function and we review the crucial roles that they play in the eye and the brain. We also discuss their regulatory roles as miRNA sponges, regulation of their parental genes or linear mRNAs, translation into micropeptides or proteins, and responses to cellular stress. We posit that future advances will provide newer insights into the fields of RNA metabolism in general and diseases of the aging eye and brain in particular. Furthermore, in keeping pace with the rapidly evolving discipline of RNA“omics”-centered metabolism and to achieve uniformity among researchers, we recently introduced the term “cromics” (circular ribonucleic acids based omics) (Singh et al. 2018. Exp. Eye Res. 174: 80–92).
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Affiliation(s)
- Akash K. George
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Kruyanshi Master
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Avisek Majumder
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Rubens Petit Homme
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Anwesha Laha
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Harpal S. Sandhu
- Department of Ophthalmology and Visual Sciences, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Kentucky Lions Eye Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Suresh C. Tyagi
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Mahavir Singh
- Eye and Vision Science Laboratory, Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Physiology, University of Louisville School of Medicine, Louisville, KY 40202, USA
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Östling H, Kruse R, Helenius G, Lodefalk M. Placental expression of microRNAs in infants born small for gestational age. Placenta 2019; 81:46-53. [PMID: 31138431 DOI: 10.1016/j.placenta.2019.05.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 03/22/2019] [Accepted: 05/01/2019] [Indexed: 12/22/2022]
Abstract
INTRODUCTION The molecular mechanisms behind poor foetal growth are not fully known. The aim of this study was to explore global microRNA expression in placentas of infants born small for gestational age (SGA) compared to infants with a normal birth weight (NBW). METHODS Placental biopsies from term infants were identified in a biobank and divided into four groups: infants born SGA with (n = 13) or without (n = 9) exposure to low maternal gestational weight gain (GWG) and infants born with NBWs with (n = 20) or without (n = 26) exposure to low GWG. All women and infants were healthy, and no woman smoked during pregnancy. Only vaginal deliveries were included. Next-generation sequencing was performed with single read sequencing of >9 million reads per sample. Differential microRNA expression was analysed using ANOVA for unequal variances (Welch) with multiple testing corrections through the Benjamini-Hochberg method. A fold change >2 and a corrected p value < 0.05 were considered significant. Adjustments for possible confounding factors were made using a linear regression model. RESULTS A total of 1870 known, mature human microRNAs were detected in the sample. MiR-3679-5p and miR-193b-3p were significantly upregulated, and miR-379-3p, miR-335-3p, miR-4532, miR-519e-3p, miR-3065-5p, and miR-105-5p were significantly downregulated after adjustment for potential confounding factors in SGA infants with normal GWG compared to infants with NBWs and normal GWG. DISCUSSION Infants born unexplained SGA show differential microRNA expression in their placenta. Important pathways for the differentially expressed microRNAs include inflammation and the insulin-IGF system.
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Affiliation(s)
- H Östling
- Department of Obstetrics and Gynecology, School of Medical Sciences, Örebro University, SE-701 82, Örebro, Sweden
| | - R Kruse
- Department of Clinical Research Laboratory, Faculty of Medicine and Health, Örebro University, SE-701 82, Örebro, Sweden
| | - G Helenius
- Department of Laboratory Medicine, Faculty of Medicine and Health, SE-701 82, Örebro University, Örebro, Sweden
| | - M Lodefalk
- Department of Pediatrics, School of Medical Sciences, Örebro University, SE-701 82, Örebro, Sweden; University Health Care Research Center, Faculty of Medicine and Health, Örebro University, SE-701 82, Örebro, Sweden.
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143
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Emerging Epigenetic Regulation of Circular RNAs in Human Cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 16:589-596. [PMID: 31082792 PMCID: PMC6517616 DOI: 10.1016/j.omtn.2019.04.011] [Citation(s) in RCA: 174] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 03/30/2019] [Accepted: 04/12/2019] [Indexed: 01/16/2023]
Abstract
Circular RNAs (circRNAs) are novel members of the noncoding RNA family. Their characteristic covalent closed-loop structure endows circRNAs that are much more stable than the corresponding linear transcript. circRNAs are ubiquitous in eukaryotic cells, and their functions are diverse and include adsorbing microRNAs (miRNAs; acting as miRNA sponges), regulating transcription, interacting with RNA-binding proteins, and translating and deriving pseudogenes. Moreover, circRNAs are associated with the occurrence and progression of a variety of cancers, acting as new biomarkers for early diagnosis to evaluate curative effects and patient prognosis. Here, this paper briefly describes the characteristics and functions of circRNAs, and it further concludes the relationship between circRNAs and human cancer.
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145
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Wang Z, Zhu Z, Wang H, Qin B, Liu J, Yao X, Li W, Chen K. Downregulation of circDYNC1H1 exhibits inhibitor effect on cell proliferation and migration in hepatocellular carcinoma through miR‐140‐5p. J Cell Physiol 2019; 234:17775-17785. [PMID: 30864145 DOI: 10.1002/jcp.28403] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/15/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Zheng‐Yang Wang
- Department of Pathology The First Affiliated Hospital of Zhengzhou University Zhengzhou China
- Department of Pathology School of Basic Medicine, Zhengzhou University Zhengzhou China
- Henan Key Laboratory for Tumor Pathology Zhengzhou China
| | - Zhu Zhu
- Department of Biological Sample Bank The First Affiliated Hospital of Zhengzhou University Zhengzhou China
| | - Hua‐Fei Wang
- Department of Biological Sample Bank The First Affiliated Hospital of Zhengzhou University Zhengzhou China
| | - Bo Qin
- Department of Translational Medicine Center The First Affiliated Hospital of Zhengzhou University Zhengzhou China
| | - Jing Liu
- Department of Pathology The First Affiliated Hospital of Zhengzhou University Zhengzhou China
- Department of Pathology School of Basic Medicine, Zhengzhou University Zhengzhou China
- Henan Key Laboratory for Tumor Pathology Zhengzhou China
| | - Xiao‐Han Yao
- Department of Medical Research Center The First Affiliated Hospital of Zhengzhou University Zhengzhou China
| | - Wen‐Cai Li
- Department of Pathology The First Affiliated Hospital of Zhengzhou University Zhengzhou China
- Department of Pathology School of Basic Medicine, Zhengzhou University Zhengzhou China
- Henan Key Laboratory for Tumor Pathology Zhengzhou China
| | - Kui‐Sheng Chen
- Department of Pathology The First Affiliated Hospital of Zhengzhou University Zhengzhou China
- Department of Pathology School of Basic Medicine, Zhengzhou University Zhengzhou China
- Henan Key Laboratory for Tumor Pathology Zhengzhou China
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146
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Long non-coding RNAs in vascular biology and disease. Vascul Pharmacol 2019; 114:13-22. [DOI: 10.1016/j.vph.2018.03.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 03/28/2018] [Accepted: 03/28/2018] [Indexed: 12/17/2022]
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147
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Liu XX, Yang YE, Liu X, Zhang MY, Li R, Yin YH, Qu YQ. A two-circular RNA signature as a noninvasive diagnostic biomarker for lung adenocarcinoma. J Transl Med 2019; 17:50. [PMID: 30777071 PMCID: PMC6380039 DOI: 10.1186/s12967-019-1800-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 02/14/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Recently, circular RNAs (circRNAs) have been reported to be microRNA sponges and play essential roles in cancer development. This study aimed to evaluate whether circulating circRNAs could be used as diagnostic biomarkers for lung adenocarcinoma (LUAD). METHODS The Gene Expression Omnibus (GEO) dataset was used to investigate differentially expressed circRNAs (DEcircRNAs) in paired LUAD tissues and adjacent nontumor tissues. The expression levels of the host genes were analyzed in The Cancer Genome Atlas (TCGA)-LUAD dataset, and the prognostic value was assessed using the Kaplan-Meier plotter. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression of candidate circRNAs in the LUAD plasma and cells. The CCK8 assay was used to measure the function of circRNAs in cell proliferation. Competing endogenous RNA (ceRNA) network, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to predict the possible mechanisms and functions of circRNAs in LUAD. RESULTS Two upregulated and two downregulated circRNAs were identified as candidate circRNAs using bioinformatics analysis. qRT-PCR demonstrated that hsa_circ_0005962 was upregulated in LUAD plasma and cells, whereas hsa_circ_0086414 was downregulated. Receiver operating characteristic (ROC) curve analysis confirmed that a signature comprising the two circRNAs had good diagnostic potential, with an area under the ROC curve (AUC) of 0.81 (P < 0.0001). In addition, we observed that overexpression of plasma hsa_circ_0086414 was related to EGFR mutations (P = 0.001). Plasma hsa_circ_0005962 displayed significantly different expression before and after surgery in patients with LUAD (P < 0.0001). In vitro experiments suggested that hsa_circ_0005962 promoted LUAD cell proliferation. For future studies, we predicted the circRNA-miRNA-mRNA network for hsa_circ_0005962. Bioinformatics analysis revealed that hsa_circ_0005962 might be involved in LUAD development. CONCLUSION A circRNA signature was identified as a potential noninvasive biomarker for LUAD diagnosis.
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Affiliation(s)
- Xiao-Xia Liu
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yi-E Yang
- Department of Clinical Laboratory, Qianfoshan Hospital of Shandong Province, Jinan, 250014, China
| | - Xiao Liu
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Meng-Yu Zhang
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Rui Li
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yun-Hong Yin
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yi-Qing Qu
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China.
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Epigenetic Biomarkers in Cell-Free DNA and Applications in Liquid Biopsy. Genes (Basel) 2019; 10:genes10010032. [PMID: 30634483 PMCID: PMC6356936 DOI: 10.3390/genes10010032] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 12/20/2018] [Accepted: 01/02/2019] [Indexed: 12/21/2022] Open
Abstract
Cell-free circulating DNA (cfDNA) in plasma has gained global interest as a diagnostic material for noninvasive prenatal testing and cancer diagnosis, or the so-called “liquid biopsy”. Recent studies have discovered a great number of valuable genetic and epigenetic biomarkers for cfDNA-based liquid biopsy. Considering that the genetic biomarkers, e.g., somatic mutations, usually vary from case to case in most cancer patients, epigenetic biomarkers that are generalizable across various samples thus possess certain advantages. In this study, we reviewed the most recent studies and advances on utilizing epigenetic biomarkers for liquid biopsies. We first reviewed more traditional methods of using tissue/cancer-specific DNA methylation biomarkers and digital PCR or sequencing technologies for cancer diagnosis, as well as tumor origin determination. In the second part, we discussed the emerging novel approaches for exploring the biological basis and clinical applications of cfDNA fragmentation patterns. We further provided our comments and points of view on the future directions on epigenetic biomarker development for cfDNA-based liquid biopsies.
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Peng H, Wan LY, Liang JJ, Zhang YQ, Ai WB, Wu JF. The roles of lncRNA in hepatic fibrosis. Cell Biosci 2018; 8:63. [PMID: 30534359 PMCID: PMC6282372 DOI: 10.1186/s13578-018-0259-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/22/2018] [Indexed: 01/01/2023] Open
Abstract
Increasing evidence indicates that long non-coding RNAs (lncRNAs) regulate gene or protein expression; however, their function in the progression of hepatic fibrosis remains unclear. Hepatic fibrosis is a continuous wound-healing process caused by numerous chronic hepatic diseases, and the activation of hepatic stellate cells (HSCs) is generally considered to be a pivotal step in hepatic fibrosis. In the process of hepatic fibrosis, some lncRNAs regulates diverse cellular processes. Here are several examples: the lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and liver fibrosis-associated lncRNA1 (lnc-LFAR1) promote HSC activation in the progression of hepatic fibrosis via the transforming growth factor-β signaling pathway; the lncRNA HIF 1 alpha-antisense RNA 1 (HIF1A-AS1) and Maternally expressed gene 3 reduce HSC activation which are associated with DNA methylation; the lncRNA plasmacytoma variant translocation 1, Homeobox (HOX) transcript antisense RNA and MALAT1 promote HSC activation as competing endogenous RNAs (ceRNAs); the long intergenic non-coding RNA-p21 (lncRNA-p21) and Growth arrest-specific transcript 5 reduce HSC activation as ceRNAs. As we get to know more about the function of lncRNAs in hepatic fibrosis, more and more ideas for the molecular targeted therapy in hepatic fibrosis will be put forward.
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Affiliation(s)
- Hu Peng
- 1Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002 China.,3Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002 China.,4Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002 China
| | - Lin-Yan Wan
- 1Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002 China.,2Digestive Medicine, The People's Hospital of China Three Gorges University, 31 Huti Subdistrict, Xi Ling District, Yichang, 443000 Hubei China.,3Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002 China
| | - Jia-Jie Liang
- 1Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002 China.,3Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002 China.,4Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002 China
| | - Yan-Qiong Zhang
- 1Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002 China.,3Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002 China.,4Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002 China
| | - Wen-Bing Ai
- The Yiling Hospital of Yichang, 31 Donghu Road, Yi Ling District, Yichang, 443100 Hubei China
| | - Jiang-Feng Wu
- 1Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002 China.,2Digestive Medicine, The People's Hospital of China Three Gorges University, 31 Huti Subdistrict, Xi Ling District, Yichang, 443000 Hubei China.,3Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002 China.,4Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002 China.,The Yiling Hospital of Yichang, 31 Donghu Road, Yi Ling District, Yichang, 443100 Hubei China
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Abstract
Dementia is a complex clinical syndrome characterised by progressive decline in cognitive function. It usually presents itself as impairment in memory, loss of judgement, abstract thinking and other disturbances that are severe enough to interfere with activities of daily living. It has long been considered as one of the major challenges at present posing an ever-increasing demand on global health and social care systems. Of all the different forms of dementia, Alzheimer's disease (AD) is the most common. The term non-coding RNA (ncRNA) refers to RNA sequences which do not have the ability to be translated into proteins and therefore mainly fall within the realm of the recently acknowledged ‘dark matter’ of the genome. This genomic dark matter encompasses a whole spectrum of differing ncRNA families such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), PIWI-interacting RNAs (piRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snoRNAs) and circular RNAs (circRNAs), to name but a few. Consequently, due to the widespread influences of miRNAs and lncRNAs across all disease pathways, it is of critical importance for researchers in the field of dementia to focus their attention on possible ncRNA-induced pathogeneses, with the ultimate goal of identifying novel diagnostic procedures and drug targets, together with the development of novel therapies to control such a devastating mental condition in the patient population.
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