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Bivona G, Sammataro S, Ghersi G. Nucleic Acids-Based Biomarkers for Alzheimer's Disease Diagnosis and Novel Molecules to Treat the Disease. Int J Mol Sci 2024; 25:7893. [PMID: 39063135 PMCID: PMC11277093 DOI: 10.3390/ijms25147893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Alzheimer's disease (AD) represents the most common form of dementia and affects million people worldwide, with a high social burden and considerable economic costs. AD diagnosis benefits from a well-established panel of laboratory tests that allow ruling-in patients, along with FDG and amyloid PET imaging tools. The main laboratory tests used to identify AD patients are Aβ40, Aβ42, the Aβ42/Aβ40 ratio, phosphorylated Tau 181 (pTau181) and total Tau (tTau). Although they are measured preferentially in the cerebrospinal fluid (CSF), some evidence about the possibility for blood-based determination to enter clinical practice is growing up. Unfortunately, CSF biomarkers for AD and, even more, the blood-based ones, present a few flaws, and twenty years of research in this field did not overcome these pitfalls. The tale even worsens when the issue of treating AD is addressed due to the lack of effective strategies despite the many decades of attempts by pharmaceutic industries and scientists. Amyloid-based drugs failed to stop the disease, and no neuroinflammation-based drugs have been demonstrated to work so far. Hence, only symptomatic therapy is available, with no disease-modifying treatment on hand. Such a desolate situation fully justifies the active search for novel biomarkers to be used as reliable tests for AD diagnosis and molecular targets for treating patients. Recently, a novel group of molecules has been identified to be used for AD diagnosis and follow-up, the nuclei acid-based biomarkers. Nucleic acid-based biomarkers are a composite group of extracellular molecules consisting of DNA and RNA alone or in combination with other molecules, including proteins. This review article reports the main findings from the studies carried out on these biomarkers during AD, and highlights their advantages and limitations.
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Affiliation(s)
- Giulia Bivona
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, 90127 Palermo, Italy
| | - Selene Sammataro
- Department of Precision Medicine in Medical, Surgical and Critical Care (Me.Pre.C.C.), University of Palermo, 90127 Palermo, Italy;
| | - Giulio Ghersi
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy;
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2
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Shigematsu M, Kawamura T, Deshpande DA, Kirino Y. Immunoactive signatures of circulating tRNA- and rRNA-derived RNAs in chronic obstructive pulmonary disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599707. [PMID: 38948719 PMCID: PMC11212963 DOI: 10.1101/2024.06.19.599707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Chronic obstructive pulmonary disease (COPD) is the most prevalent lung disease, and macrophages play a central role in the inflammatory response in COPD. We here report a comprehensive characterization of circulating short non-coding RNAs (sncRNAs) in plasma from patients with COPD. While circulating sncRNAs are increasingly recognized for their regulatory roles and biomarker potential in various diseases, the conventional RNA-seq method cannot fully capture these circulating sncRNAs due to their heterogeneous terminal structures. By pre-treating the plasma RNAs with T4 polynucleotide kinase, which converts all RNAs to those with RNA-seq susceptible ends (5'-phosphate and 3'-hydroxyl), we comprehensively sequenced a wide variety of non-microRNA sncRNAs, such as 5'-tRNA halves containing a 2',3'-cyclic phosphate. We discovered a remarkable accumulation of the 5'-half derived from tRNA ValCAC in plasma from COPD patients, whereas the 5'-tRNA GlyGCC half is predominant in healthy donors. Further, the 5'-tRNA ValCAC half activates human macrophages via Toll-like receptor 7 and induces cytokine production. Additionally, we identified circulating rRNA-derived fragments that were upregulated in COPD patients and demonstrated their ability to induce cytokine production in macrophages. Our findings provide evidence of circulating, immune-active sncRNAs in patients with COPD, suggesting that they serve as inflammatory mediators in the pathogenesis of COPD.
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3
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Wen Q, Wittens MMJ, Engelborghs S, van Herwijnen MHM, Tsamou M, Roggen E, Smeets B, Krauskopf J, Briedé JJ. Beyond CSF and Neuroimaging Assessment: Evaluating Plasma miR-145-5p as a Potential Biomarker for Mild Cognitive Impairment and Alzheimer's Disease. ACS Chem Neurosci 2024; 15:1042-1054. [PMID: 38407050 PMCID: PMC10921410 DOI: 10.1021/acschemneuro.3c00740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024] Open
Abstract
Alzheimer's disease (AD) is the most common cause of dementia. New strategies for the early detection of MCI and sporadic AD are crucial for developing effective treatment options. Current techniques used for diagnosis of AD are invasive and/or expensive, so they are not suitable for population screening. Cerebrospinal fluid (CSF) biomarkers such as amyloid β1-42 (Aβ1-42), total tau (T-tau), and phosphorylated tau181 (P-tau181) levels are core biomarkers for early diagnosis of AD. Several studies have proposed the use of blood-circulating microRNAs (miRNAs) as potential novel early biomarkers for AD. We therefore applied a novel approach to identify blood-circulating miRNAs associated with CSF biomarkers and explored the potential of these miRNAs as biomarkers of AD. In total, 112 subjects consisting of 28 dementia due to AD cases, 63 MCI due to AD cases, and 21 cognitively healthy controls were included. We identified seven Aβ1-42-associated plasma miRNAs, six P-tau181-associated plasma miRNAs, and nine Aβ1-42-associated serum miRNAs. These miRNAs were involved in AD-relevant biological processes, such as PI3K/AKT signaling. Based on this signaling pathway, we constructed an miRNA-gene target network, wherein miR-145-5p has been identified as a hub. Furthermore, we showed that miR-145-5p performs best in the prediction of both AD and MCI. Moreover, miR-145-5p also improved the prediction performance of the mini-mental state examination (MMSE) score. The performance of this miRNA was validated using different datasets including an RT-qPCR dataset from plasma samples of 23 MCI cases and 30 age-matched controls. These findings indicate that blood-circulating miRNAs that are associated with CSF biomarkers levels and specifically plasma miR-145-5p alone or combined with the MMSE score can potentially be used as noninvasive biomarkers for AD or MCI screening in the general population, although studies in other AD cohorts are necessary for further validation.
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Affiliation(s)
- Qingfeng Wen
- Department
of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
- MHeNS,
School for Mental Health and Neuroscience, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Mandy Melissa Jane Wittens
- Department
of Biomedical Sciences, Institute Born-Bunge, University of Antwerp, Universiteitsplein 1, BE-2610 Antwerpen, Belgium
- Neuroprotection
and Neuromodulation (NEUR), Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussel, Belgium
- Department
of Neurology, Universitair Ziekenhuis Brussel
(UZ Brussel), Laarbeeklaan
101, 1090 Brussel, Belgium
| | - Sebastiaan Engelborghs
- Department
of Biomedical Sciences, Institute Born-Bunge, University of Antwerp, Universiteitsplein 1, BE-2610 Antwerpen, Belgium
- Neuroprotection
and Neuromodulation (NEUR), Center for Neurosciences (C4N), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussel, Belgium
- Department
of Neurology, Universitair Ziekenhuis Brussel
(UZ Brussel), Laarbeeklaan
101, 1090 Brussel, Belgium
| | - Marcel H. M. van Herwijnen
- Department
of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Maria Tsamou
- ToxGenSolutions
(TGS), 6229EV Maastricht, The Netherlands
| | - Erwin Roggen
- ToxGenSolutions
(TGS), 6229EV Maastricht, The Netherlands
| | - Bert Smeets
- Department
of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
- MHeNS,
School for Mental Health and Neuroscience, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Julian Krauskopf
- Department
of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Jacco Jan Briedé
- Department
of Toxicogenomics, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
- MHeNS,
School for Mental Health and Neuroscience, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
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4
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Kunze R, Fischer S, Marti HH, Preissner KT. Brain alarm by self-extracellular nucleic acids: from neuroinflammation to neurodegeneration. J Biomed Sci 2023; 30:64. [PMID: 37550658 PMCID: PMC10405513 DOI: 10.1186/s12929-023-00954-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/22/2023] [Indexed: 08/09/2023] Open
Abstract
Neurological disorders such as stroke, multiple sclerosis, as well as the neurodegenerative diseases Parkinson's or Alzheimer's disease are accompanied or even powered by danger associated molecular patterns (DAMPs), defined as endogenous molecules released from stressed or damaged tissue. Besides protein-related DAMPs or "alarmins", numerous nucleic acid DAMPs exist in body fluids, such as cell-free nuclear and mitochondrial DNA as well as different species of extracellular RNA, collectively termed as self-extracellular nucleic acids (SENAs). Among these, microRNA, long non-coding RNAs, circular RNAs and extracellular ribosomal RNA constitute the majority of RNA-based DAMPs. Upon tissue injury, necrosis or apoptosis, such SENAs are released from neuronal, immune and other cells predominantly in association with extracellular vesicles and may be translocated to target cells where they can induce intracellular regulatory pathways in gene transcription and translation. The majority of SENA-induced signaling reactions in the brain appear to be related to neuroinflammatory processes, often causally associated with the onset or progression of the respective disease. In this review, the impact of the diverse types of SENAs on neuroinflammatory and neurodegenerative diseases will be discussed. Based on the accumulating knowledge in this field, several specific antagonistic approaches are presented that could serve as therapeutic interventions to lower the pathological outcome of the indicated brain disorders.
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Affiliation(s)
- Reiner Kunze
- Institute of Physiology and Pathophysiology, Department of Cardiovascular Physiology, Ruprecht-Karls-University, Im Neuenheimer Feld 326, 69120 Heidelberg, Germany
| | - Silvia Fischer
- Department of Biochemistry, Medical School, Justus-Liebig-University, Giessen, Germany
| | - Hugo H. Marti
- Institute of Physiology and Pathophysiology, Department of Cardiovascular Physiology, Ruprecht-Karls-University, Im Neuenheimer Feld 326, 69120 Heidelberg, Germany
| | - Klaus T. Preissner
- Department of Biochemistry, Medical School, Justus-Liebig-University, Giessen, Germany
- Kerckhoff-Heart-Research-Institute, Department of Cardiology, Medical School, Justus-Liebig-University, Giessen, Germany
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5
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Xiao P, Shi Z, Liu C, Hagen DE. Characteristics of circulating small noncoding RNAs in plasma and serum during human aging. Aging Med (Milton) 2023; 6:35-48. [PMID: 36911092 PMCID: PMC10000275 DOI: 10.1002/agm2.12241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 02/24/2023] Open
Abstract
Objective Aging is a complicated process that triggers age-related disease susceptibility through intercellular communication in the microenvironment. While the classic secretome of senescence-associated secretory phenotype (SASP) including soluble factors, growth factors, and extracellular matrix remodeling enzymes are known to impact tissue homeostasis during the aging process, the effects of novel SASP components, extracellular small noncoding RNAs (sncRNAs), on human aging are not well established. Methods Here, by utilizing 446 small RNA-seq samples from plasma and serum of healthy donors found in the Extracellular RNA (exRNA) Atlas data repository, we correlated linear and nonlinear features between circulating sncRNAs expression and age by the maximal information coefficient (MIC) relationship determination. Age predictors were generated by ensemble machine learning methods (Adaptive Boosting, Gradient Boosting, and Random Forest) and core age-related sncRNAs were determined through weighted coefficients in machine learning models. Functional investigation was performed via target prediction of age-related miRNAs. Results We observed the number of highly expressed transfer RNAs (tRNAs) and microRNAs (miRNAs) showed positive and negative associations with age respectively. Two-variable (sncRNA expression and individual age) relationships were detected by MIC and sncRNAs-based age predictors were established, resulting in a forecast performance where all R 2 values were greater than 0.96 and root-mean-square errors (RMSE) were less than 3.7 years in three ensemble machine learning methods. Furthermore, important age-related sncRNAs were identified based on modeling and the biological pathways of age-related miRNAs were characterized by their predicted targets, including multiple pathways in intercellular communication, cancer and immune regulation. Conclusion In summary, this study provides valuable insights into circulating sncRNAs expression dynamics during human aging and may lead to advanced understanding of age-related sncRNAs functions with further elucidation.
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Affiliation(s)
- Ping Xiao
- Department of Animal and Food Sciences Oklahoma State University Stillwater Oklahoma USA
| | - Zhangyue Shi
- School of Industrial Engineering and Management Oklahoma State University Stillwater Oklahoma USA
| | - Chenang Liu
- School of Industrial Engineering and Management Oklahoma State University Stillwater Oklahoma USA
| | - Darren E Hagen
- Department of Animal and Food Sciences Oklahoma State University Stillwater Oklahoma USA
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Functions and cellular signaling by ribosomal extracellular RNA (rexRNA): Facts and hypotheses on a non-typical DAMP. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119408. [PMID: 36503009 DOI: 10.1016/j.bbamcr.2022.119408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/07/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022]
Abstract
Upon microbial infections with the subsequent host response of innate immunity, a variety of fragmented RNA- and DNA-based "Pathogen-associated molecular patterns" (PAMPs) are recognized mainly by endosomal or cytoplasmic host cell "Pattern recognition receptors" (PRRs), particularly "Toll-like receptors" (TLRs). Concomitantly, various self-extracellular RNA species (exRNAs) are present in extracellular body fluids where they contribute to diverse physiological and homeostatic processes. In principle, such exRNAs, including the most abundant one, ribosomal exRNA (rexRNA), are designated as "Danger-associated molecular patterns" (DAMPs) and are prevented by e.g. natural modifications from uncontrolled signaling via TLRs to avoid hyper-inflammatory responses or autoimmunity. Upon cellular stress or tissue damage/necrosis, the levels and composition of released self-exRNA species, either in free form, in complex with proteins or in association with extracellular vesicles (EVs), can change considerably. Among the self-exRNAs, rexRNA is considered as a non-typical DAMP, since it may induce inflammatory responses by cell membrane receptors, both in the absence or presence of PAMPs. Yet, its mode of receptor activation to mount inflammatory responses remains obscure. RexRNA also serves as a universal damaging factor in cardiovascular and other diseases independent of PRRs. In general, RNase1 provides a profound antagonist in these pathologies and in rexRNA-mediated inflammatory cell responses. Based on the extrapolation of the here described aspects of rexRNA-biology, further activities of this molecular entity are hypothesized that may stimulate additional research in this area.
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7
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Albrecht LJ, Höwner A, Griewank K, Lueong SS, von Neuhoff N, Horn PA, Sucker A, Paschen A, Livingstone E, Ugurel S, Zimmer L, Horn S, Siveke JT, Schadendorf D, Váraljai R, Roesch A. Circulating cell-free messenger RNA enables non-invasive pan-tumour monitoring of melanoma therapy independent of the mutational genotype. Clin Transl Med 2022; 12:e1090. [PMID: 36320118 PMCID: PMC9626658 DOI: 10.1002/ctm2.1090] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/09/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Plasma-derived tumour-specific cell-free nucleic acids are increasingly utilized as a minimally invasive, real-time biomarker approach in many solid tumours. Circulating tumour DNA of melanoma-specific mutations is currently the best studied liquid biopsy biomarker for melanoma. However, the combination of hotspot genetic alterations covers only around 80% of all melanoma patients. Therefore, alternative approaches are needed to enable the follow-up of all genotypes, including wild-type. METHODS We identified KPNA2, DTL, BACE2 and DTYMK messenger RNA (mRNA) upregulated in melanoma versus nevi tissues by unsupervised data mining (N = 175 melanoma, N = 20 normal skin, N = 6 benign nevi) and experimentally confirmed differential mRNA expression in vitro (N = 18 melanoma, N = 8 benign nevi). Circulating cell-free RNA (cfRNA) was analysed in 361 plasma samples (collected before and during therapy) from 100 melanoma patients and 18 healthy donors. Absolute cfRNA copies were quantified on droplet digital PCR. RESULTS KPNA2, DTL, BACE2 and DTYMK cfRNA demonstrated high diagnostic accuracy between melanoma patients' and healthy donors' plasma (AUC > 86%, p < .0001). cfRNA copies increased proportionally with increasing tumour burden independently of demographic variables and even remained elevated in individuals with radiological absence of disease. Re-analysis of single-cell transcriptomes revealed a pan-tumour origin of cfRNA, including endothelial, cancer-associated fibroblasts, macrophages and B cells beyond melanoma cells as cellular sources. Low baseline cfRNA levels were associated with significantly longer progression-free survival (PFS) (KPNA2 HR = .54, p = .0362; DTL HR = .60, p = .0349) and overall survival (KPNA2 HR = .52, p = .0237; BACE2 HR = .55, p = .0419; DTYMK HR = .43, p = .0393). Lastly, we found that cfRNA copies significantly increased during therapy in non-responders compared to responders regardless of therapy and mutational subtypes and that the increase of KPNA2 (HR = 1.73, p = .0441) and DTYMK (HR = 1.82, p = .018) cfRNA during therapy was predictive of shorter PFS. CONCLUSIONS In sum, we identified a new panel of cfRNAs for a pan-tumour liquid biopsy approach and demonstrated its utility as a prognostic, therapy-monitoring tool independent of the melanoma mutational genotype.
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Affiliation(s)
- Lea Jessica Albrecht
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Anna Höwner
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Klaus Griewank
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Smiths S. Lueong
- Bridge Institute of Experimental Tumor TherapyWest German Cancer CenterUniversity Hospital of EssenUniversity of Duisburg‐EssenEssenGermany
- Division of Solid Tumor Translational OncologyGerman Cancer Consortium (DKTK Partner Site Essen) and German Cancer Research CenterDKFZHeidelbergGermany
| | - Nils von Neuhoff
- Department of Pediatric Hematology and OncologyDepartment for Pediatrics IIIUniversity Hospital of EssenEssenGermany
| | - Peter A. Horn
- Institute for Transfusion MedicineUniversity Hospital of EssenEssenGermany
| | - Antje Sucker
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Annette Paschen
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Elisabeth Livingstone
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Selma Ugurel
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Lisa Zimmer
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Susanne Horn
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
- Faculty Rudolf‐Schönheimer‐Institute for BiochemistryUniversity of LeipzigLeipzigGermany
| | - Jens T. Siveke
- Bridge Institute of Experimental Tumor TherapyWest German Cancer CenterUniversity Hospital of EssenUniversity of Duisburg‐EssenEssenGermany
- Division of Solid Tumor Translational OncologyGerman Cancer Consortium (DKTK Partner Site Essen) and German Cancer Research CenterDKFZHeidelbergGermany
| | - Dirk Schadendorf
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Renáta Váraljai
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
| | - Alexander Roesch
- Department of DermatologyUniversity Hospital of EssenWest German Cancer CenterUniversity Duisburg‐Essen and the German Cancer Consortium (DKTK)EssenGermany
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Ward Z, Schmeier S, Pearson J, Cameron VA, Frampton CM, Troughton RW, Doughty RN, Richards AM, Pilbrow AP. Identifying Candidate Circulating RNA Markers for Coronary Artery Disease by Deep RNA-Sequencing in Human Plasma. Cells 2022; 11:3191. [PMID: 36291058 PMCID: PMC9599983 DOI: 10.3390/cells11203191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2023] Open
Abstract
Advances in RNA sequencing (RNA-Seq) have facilitated transcriptomic analysis of plasma for the discovery of new diagnostic and prognostic markers for disease. We aimed to develop a short-read RNA-Seq protocol to detect mRNAs, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in plasma for the discovery of novel markers for coronary artery disease (CAD) and heart failure (HF). Circulating cell-free RNA from 59 patients with stable CAD (half of whom developed HF within 3 years) and 30 controls was sequenced to a median depth of 108 paired reads per sample. We identified fragments from 3986 messenger RNAs (mRNAs), 164 long non-coding RNAs (lncRNAs), 405 putative novel lncRNAs and 227 circular RNAs in plasma. Circulating levels of 160 mRNAs, 10 lncRNAs and 2 putative novel lncRNAs were altered in patients compared with controls (absolute fold change >1.2, p < 0.01 adjusted for multiple comparisons). The most differentially abundant transcripts were enriched in mRNAs encoded by the mitochondrial genome. We did not detect any differences in the plasma RNA profile between patients who developed HF compared with those who did not. In summary, we show that mRNAs, lncRNAs and circular RNAs can be reliably detected in plasma by deep RNA-Seq. Multiple coding and non-coding transcripts were altered in association with CAD, including several mitochondrial mRNAs, which may indicate underlying myocardial ischaemia and oxidative stress. If validated, circulating levels of these transcripts could potentially be used to help identify asymptomatic individuals with established CAD prior to an acute coronary event.
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Affiliation(s)
- Zoe Ward
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Sebastian Schmeier
- School of Natural and Computational Sciences, Massey University, Auckland 0632, New Zealand
- Evotec SE, Essener Bogen 7, 22419 Hamburg, Germany
| | - John Pearson
- Biostatistics and Computational Biology Unit, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Vicky A Cameron
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Chris M Frampton
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Richard W Troughton
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
| | - Rob N Doughty
- Heart Health Research Group, University of Auckland, Auckland 1023, New Zealand
| | - A. Mark Richards
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
- Cardiovascular Research Institute, National University of Singapore, Singapore 119228, Singapore
| | - Anna P Pilbrow
- Christchurch Heart Institute, Department of Medicine, University of Otago—Christchurch, Christchurch 8140, New Zealand
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Choi EJ, Kim YJ. Liquid biopsy for early detection and therapeutic monitoring of hepatocellular carcinoma. JOURNAL OF LIVER CANCER 2022; 22:103-114. [PMID: 37383403 PMCID: PMC10035729 DOI: 10.17998/jlc.2022.09.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 06/30/2023]
Abstract
Advances in our knowledge of the molecular characteristics of hepatocellular carcinoma (HCC) have enabled significant progress in the detection and therapeutic prediction of HCC. As a non-invasive alternative to tissue biopsy, liquid biopsy examines circulating cellular components such as exosomes, nucleic acids, and cell-free DNA found in body fluids (e.g., urine, saliva, ascites, and pleural effusions) and provides information about tumor characteristics. Technical advances in liquid biopsy have led to the increasing adoption of diagnostic and monitoring applications for HCC. This review summarizes the various analytes, ongoing clinical trials, and case studies of United States Food and Drug Administrationapproved in vitro diagnostic applications for liquid biopsy, and provides insight into its implementation in managing HCC.
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Affiliation(s)
| | - Young-Joon Kim
- LepiDyne Co., Ltd., Seoul, Korea
- Department of Biochemistry, Yonsei University, Seoul, Korea
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10
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Nofi CP, Wang P, Aziz M. Chromatin-Associated Molecular Patterns (CAMPs) in sepsis. Cell Death Dis 2022; 13:700. [PMID: 35961978 PMCID: PMC9372964 DOI: 10.1038/s41419-022-05155-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 01/21/2023]
Abstract
Several molecular patterns have been identified that recognize pattern recognition receptors. Pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs) are commonly used terminologies to classify molecules originating from pathogen and endogenous molecules, respectively, to heighten the immune response in sepsis. Herein, we focus on a subgroup of endogenous molecules that may be detected as foreign and similarly trigger immune signaling pathways. These chromatin-associated molecules, i.e., chromatin containing nuclear DNA and histones, extracellular RNA, mitochondrial DNA, telomeric repeat-containing RNA, DNA- or RNA-binding proteins, and extracellular traps, may be newly classified as chromatin-associated molecular patterns (CAMPs). Herein, we review the release of CAMPs from cells, their mechanism of action and downstream immune signaling pathways, and targeted therapeutic approaches to mitigate inflammation and tissue injury in inflammation and sepsis.
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Affiliation(s)
- Colleen P. Nofi
- grid.250903.d0000 0000 9566 0634Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY USA ,Elmezi Graduate School of Molecular Medicine, Manhasset, NY USA ,grid.512756.20000 0004 0370 4759Department of Surgery, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY USA
| | - Ping Wang
- grid.250903.d0000 0000 9566 0634Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY USA ,Elmezi Graduate School of Molecular Medicine, Manhasset, NY USA ,grid.512756.20000 0004 0370 4759Department of Surgery, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY USA ,grid.512756.20000 0004 0370 4759Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY USA
| | - Monowar Aziz
- grid.250903.d0000 0000 9566 0634Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY USA ,Elmezi Graduate School of Molecular Medicine, Manhasset, NY USA ,grid.512756.20000 0004 0370 4759Department of Surgery, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY USA ,grid.512756.20000 0004 0370 4759Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY USA
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Salim H, Pero-Gascon R, Pont L, Giménez E, Benavente F. A review of sample preparation for purification of microRNAs and analysis by mass spectrometry methods. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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12
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Liu Z, Wang T, Yang X, Zhou Q, Zhu S, Zeng J, Chen H, Sun J, Li L, Xu J, Geng C, Xu X, Wang J, Yang H, Zhu S, Chen F, Wang WJ. Polyadenylation ligation-mediated sequencing (PALM-Seq) characterizes cell-free coding and non-coding RNAs in human biofluids. Clin Transl Med 2022; 12:e987. [PMID: 35858042 PMCID: PMC9299576 DOI: 10.1002/ctm2.987] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/16/2022] [Accepted: 07/03/2022] [Indexed: 11/16/2022] Open
Abstract
Background Cell‐free messenger RNA (cf‐mRNA) and long non‐coding RNA (cf‐lncRNA) are becoming increasingly important in liquid biopsy by providing biomarkers for disease prediction, diagnosis and prognosis, but the simultaneous characterization of coding and non‐coding RNAs in human biofluids remains challenging. Methods Here, we developed polyadenylation ligation‐mediated sequencing (PALM‐Seq), an RNA sequencing strategy employing treatment of RNA with T4 polynucleotide kinase to generate cell‐free RNA (cfRNA) fragments with 5′ phosphate and 3′ hydroxyl and RNase H to deplete abundant RNAs, achieving simultaneous quantification and characterization of cfRNAs. Results Using PALM‐Seq, we successfully identified well‐known differentially abundant mRNA, lncRNA and microRNA in the blood plasma of pregnant women. We further characterized cfRNAs in blood plasma, saliva, urine, seminal plasma and amniotic fluid and found that the detected numbers of different RNA biotypes varied with body fluids. The profiles of cf‐mRNA reflected the function of originated tissues, and immune cells significantly contributed RNA to blood plasma and saliva. Short fragments (<50 nt) of mRNA and lncRNA were major in biofluids, whereas seminal plasma and amniotic fluid tended to retain long RNA. Body fluids showed distinct preferences of pyrimidine at the 3′ end and adenine at the 5′ end of cf‐mRNA and cf‐lncRNA, which were correlated with the proportions of short fragments. Conclusion Together, PALM‐Seq enables a simultaneous characterization of cf‐mRNA and cf‐lncRNA, contributing to elucidating the biology and promoting the application of cfRNAs.
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Affiliation(s)
| | | | - Xi Yang
- BGI-Shenzhen, Shenzhen, China
| | | | - Sujun Zhu
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Juan Zeng
- Obstetrics Department, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | | | - Jinghua Sun
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | | | | | - Xun Xu
- BGI-Shenzhen, Shenzhen, China
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13
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Salomon C, Das S, Erdbrügger U, Kalluri R, Kiang Lim S, Olefsky JM, Rice GE, Sahoo S, Andy Tao W, Vader P, Wang Q, Weaver AM. Extracellular Vesicles and Their Emerging Roles as Cellular Messengers in Endocrinology: An Endocrine Society Scientific Statement. Endocr Rev 2022; 43:441-468. [PMID: 35552682 PMCID: PMC10686249 DOI: 10.1210/endrev/bnac009] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Indexed: 12/15/2022]
Abstract
During the last decade, there has been great interest in elucidating the biological role of extracellular vesicles (EVs), particularly, their hormone-like role in cell-to-cell communication. The field of endocrinology is uniquely placed to provide insight into the functions of EVs, which are secreted from all cells into biological fluids and carry endocrine signals to engage in paracellular and distal interactions. EVs are a heterogeneous population of membrane-bound vesicles of varying size, content, and bioactivity. EVs are specifically packaged with signaling molecules, including lipids, proteins, and nucleic acids, and are released via exocytosis into biofluid compartments. EVs regulate the activity of both proximal and distal target cells, including translational activity, metabolism, growth, and development. As such, EVs signaling represents an integral pathway mediating intercellular communication. Moreover, as the content of EVs is cell-type specific, it is a "fingerprint" of the releasing cell and its metabolic status. Recently, changes in the profile of EV and bioactivity have been described in several endocrine-related conditions including diabetes, obesity, cardiovascular diseases, and cancer. The goal of this statement is to highlight relevant aspects of EV research and their potential role in the field of endocrinology.
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Affiliation(s)
- Carlos Salomon
- Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women’s Hospital, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Saumya Das
- Cardiovascular Research Center of Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Uta Erdbrügger
- Department of Medicine, Nephrology Division, University of Virginia, Charlottesville, VA, USA
| | - Raghu Kalluri
- Department of Cancer Biology, Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sai Kiang Lim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Jerrold M Olefsky
- Department of Medicine, University of California-San Diego, La Jolla, CA, USA
| | | | - Susmita Sahoo
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - W Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Pieter Vader
- CDL Research, Division LAB, UMC Utrecht, Utrecht, the Netherlands Faculty of Medicine, Utrecht University, Utrecht, the Netherlands; Laboratory of Experimental Cardiology, UMC Utrecht, Utrecht, The Netherlands
| | - Qun Wang
- Key Laboratory of Infection and Immunity of Shandong Province, Department of Immunology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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14
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Noncoding RNA as Diagnostic and Prognostic Biomarkers in Cerebrovascular Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8149701. [PMID: 35498129 PMCID: PMC9042605 DOI: 10.1155/2022/8149701] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/22/2022] [Indexed: 02/06/2023]
Abstract
Noncoding RNAs (ncRNAs), such as microRNAs, long noncoding RNAs, and circular RNAs, play an important role in the pathophysiology of cerebrovascular diseases (CVDs). They are effectively detectable in body fluids, potentially suggesting new biomarkers for the early detection and prognosis of CVDs. In this review, the physiological functions of circulating ncRNAs and their potential role as diagnostic and prognostic markers in patients with cerebrovascular diseases are discussed, especially in acute ischemic stroke, subarachnoid hemorrhage, and moyamoya disease.
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15
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Myklebust MP, Søviknes AM, Halvorsen OJ, Thor A, Dahl O, Ræder H. MicroRNAs in Differentiation of Embryoid Bodies and the Teratoma Subtype of Testicular Cancer. Cancer Genomics Proteomics 2022; 19:178-193. [PMID: 35181587 DOI: 10.21873/cgp.20313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Testicular germ cell tumours (TGCTs) are the most frequent tumour type among young, adult men. TGCTs can be efficiently treated, but metastases of the teratoma subtype, for which there are no circulating biomarkers, represent a challenge. MATERIALS AND METHODS Global microRNA expression in teratoma tissue and embryoid bodies was assessed using next-generation sequencing. Levels of microRNAs identified as potential biomarkers were obtained from serum of patients with teratoma and matched healthy men. RESULTS We identified miR-222-5p, miR-200a-5p, miR-196b-3p and miR-454-5p as biomarker candidates from the tumour tissue and embryoid body screening but the expression of these microRNAs was very low in serum and not statistically different between patients and controls. miR-375-3p was highly expressed, being highest in patients with teratoma (p=0.012) but the levels of expression in serum from these patients and healthy controls overlapped. miR-371a-3p was not expressed in serum from patients with pure teratoma, only in patients with mixed tumours. CONCLUSION The microRNA profiles of the teratoma subtype of TGCT and embryoid bodies were obtained and assessed for candidate circulating biomarkers, but none with high sensitivity and specificity for teratoma were identified in our study. We conclude that neither the proposed teratoma marker miR-375-3p nor miR-371a-3p are suitable as circulating teratoma markers.
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Affiliation(s)
| | - Anne Mette Søviknes
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ole Johan Halvorsen
- Gade Laboratory for Pathology, Department of Clinical Medicine, Centre for Cancer Biomarkers CCBIO, University of Bergen, Bergen, Norway
| | - Anna Thor
- Department of Urology and CLINTEC Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Olav Dahl
- Department of Oncology and Medical Physics, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Helge Ræder
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
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16
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Hime GR, Stonehouse SLA, Pang TY. Alternative models for transgenerational epigenetic inheritance: Molecular psychiatry beyond mice and man. World J Psychiatry 2021; 11:711-735. [PMID: 34733638 PMCID: PMC8546770 DOI: 10.5498/wjp.v11.i10.711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/19/2021] [Accepted: 08/25/2021] [Indexed: 02/06/2023] Open
Abstract
Mental illness remains the greatest chronic health burden globally with few in-roads having been made despite significant advances in genomic knowledge in recent decades. The field of psychiatry is constantly challenged to bring new approaches and tools to address and treat the needs of vulnerable individuals and subpopulations, and that has to be supported by a continuous growth in knowledge. The majority of neuropsychiatric symptoms reflect complex gene-environment interactions, with epigenetics bridging the gap between genetic susceptibility and environmental stressors that trigger disease onset and drive the advancement of symptoms. It has more recently been demonstrated in preclinical models that epigenetics underpins the transgenerational inheritance of stress-related behavioural phenotypes in both paternal and maternal lineages, providing further supporting evidence for heritability in humans. However, unbiased prospective studies of this nature are practically impossible to conduct in humans so preclinical models remain our best option for researching the molecular pathophysiologies underlying many neuropsychiatric conditions. While rodents will remain the dominant model system for preclinical studies (especially for addressing complex behavioural phenotypes), there is scope to expand current research of the molecular and epigenetic pathologies by using invertebrate models. Here, we will discuss the utility and advantages of two alternative model organisms–Caenorhabditis elegans and Drosophila melanogaster–and summarise the compelling insights of the epigenetic regulation of transgenerational inheritance that are potentially relevant to human psychiatry.
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Affiliation(s)
- Gary R Hime
- Department of Anatomy and Physiology, The University of Melbourne, Parkville 3010, VIC, Australia
| | - Sophie LA Stonehouse
- Mental Health Theme, The Florey Institute of Neuroscience and Mental Health, Parkville 3052, VIC, Australia
| | - Terence Y Pang
- Department of Anatomy and Physiology, The University of Melbourne, Parkville 3010, VIC, Australia
- Mental Health Theme, The Florey Institute of Neuroscience and Mental Health, Parkville 3052, VIC, Australia
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17
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Nagasaka M, Uddin MH, Al-Hallak MN, Rahman S, Balasubramanian S, Sukari A, Azmi AS. Liquid biopsy for therapy monitoring in early-stage non-small cell lung cancer. Mol Cancer 2021; 20:82. [PMID: 34074295 PMCID: PMC8170728 DOI: 10.1186/s12943-021-01371-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 05/13/2021] [Indexed: 12/19/2022] Open
Abstract
Liquid biopsy is now considered a valuable diagnostic tool for advanced metastatic non-small cell lung cancer (NSCLC). In NSCLC, circulating tumor DNA (ctDNA) analysis has been shown to increase the chances of identifying the presence of targetable mutations and has been adopted by many clinicians owing to its low risk. Serial monitoring of ctDNA may also help assess the treatment response or for monitoring relapse. As the presence of detectable plasma ctDNA post-surgery likely indicates residual tumor burden, studies have been performed to quantify plasma ctDNA to assess minimal residual disease (MRD) in early-stage resected NSCLC. Most data on utilizing liquid biopsy for monitoring MRD in early-stage NSCLC are from small-scale studies using ctDNA. Here, we review the recent research on liquid biopsy in NSCLC, not limited to ctDNA, and focus on novel methods such as micro RNAs (miRNA) and long non-coding (lncRNA).
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Affiliation(s)
- Misako Nagasaka
- Department of Oncology, Wayne State University School of Medicine, Karmanos Cancer Institute, 4100 John R, Detroit, MI, 48201, USA.
- Division of Neurology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan.
| | - Mohammed Hafiz Uddin
- Department of Oncology, Wayne State University School of Medicine, Karmanos Cancer Institute, 4100 John R, Detroit, MI, 48201, USA
| | - Mohammed Najeeb Al-Hallak
- Department of Oncology, Wayne State University School of Medicine, Karmanos Cancer Institute, 4100 John R, Detroit, MI, 48201, USA
| | - Sarah Rahman
- Department of Cell and Molecular Biology, Grand Valley State University, Allendale, MI, 49401, USA
| | - Suresh Balasubramanian
- Department of Oncology, Wayne State University School of Medicine, Karmanos Cancer Institute, 4100 John R, Detroit, MI, 48201, USA
| | - Ammar Sukari
- Department of Oncology, Wayne State University School of Medicine, Karmanos Cancer Institute, 4100 John R, Detroit, MI, 48201, USA
| | - Asfar S Azmi
- Department of Oncology, Wayne State University School of Medicine, Karmanos Cancer Institute, 4100 John R, Detroit, MI, 48201, USA
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18
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Zhang Z, Zhang L, Wang Y, Yao J, Wang T, Weng Z, Yang L, Xie G. Ultrasensitive electrochemical biosensor for attomolar level detection of let 7a based on toehold mediated strand displacement reaction circuits and molecular beacon mediated circular strand displacement polymerization. Anal Chim Acta 2021; 1147:108-115. [PMID: 33485569 DOI: 10.1016/j.aca.2020.12.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/26/2020] [Accepted: 12/27/2020] [Indexed: 12/12/2022]
Abstract
In this study, an ultrasensitive electrochemical miRNA biosensor based on toehold mediated strand displacement reaction circuits (SDRCs) and molecular beacon mediated isothermal circular strand displacement polymerization reaction (ICSDPR) has been proposed. During the SDRCs module, the cascade strand displacement reaction induces the recycling of the target let 7a and generation of a large amount of strand A (SA). The SA recognition opens the hairpin capture probe immobilized on the gold electrode, thus, varying the distance between the redox molecules and electrode surface. The primer mediated ICSDPR is observed to further generate a large amount of SA, thus, leading to a reduction in the signal. Considering these merits, the proposed method is observed to exhibit a log-linear linearity from 10 aM to 100 pM and ultrahigh sensitivity towards let 7a down to 6.2 aM, with a capability of distinguishing the let 7a family members, thereby, providing a new electrochemical route for early cancer screening.
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Affiliation(s)
- Zhang Zhang
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China; Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, PR China
| | - Li Zhang
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China
| | - Youqiang Wang
- Department of Laboratory Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, PR China
| | - Juan Yao
- Department of Laboratory Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, PR China
| | - Ting Wang
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China; Department of Laboratory Medicine, Chongqing Fuling People's Hospital, Chongqing, PR China
| | - Zhi Weng
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China
| | - Liu Yang
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China
| | - Guoming Xie
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, PR China.
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19
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Parker VL, Cushen BF, Gavriil E, Marshall B, Waite S, Pacey A, Heath PR. Comparison and optimisation of microRNA extraction from the plasma of healthy pregnant women. Mol Med Rep 2021; 23:1. [PMID: 33576446 PMCID: PMC7893782 DOI: 10.3892/mmr.2021.11897] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 12/15/2020] [Indexed: 01/01/2023] Open
Abstract
Circulating microRNA (miRNA) biomarkers are implicated in the diagnosis, monitoring and prediction of various disease processes. Before embarking upon biomarker discovery, miRNA extraction techniques must first be optimised in the biofluid and population under study. Using plasma from a healthy pregnant woman, it was attempted to optimise and compare the performance of two commercially available miRNA extraction kits; Qiagen (miRNeasy Serum/Plasma) and Promega (Maxwell® RSC miRNA from Tissue or Plasma or Serum). Sample miRNA content (concentration and percentage) was assessed using Agilent Bioanalyzer Small RNA chips and reverse transcription-quantitative PCR (RT-qPCR) using four constitutively expressed miRNAs (hsa-miR-222-3p, hsa-let-7i-3p, hsa-miR-148-3p and hsa-miR-30e-5p). Quality control spike-ins monitored RNA extraction (UniSp2, 4 and 5) and cDNA synthesis (UniSp6, cel-miR-39-3p) efficiency. Optimisation approaches included: i) Starting volume of plasma; the addition of ii) Proteinase K; iii) a RNA bacteriophage carrier (MS2); and iv) a glycogen carrier. The two kits exhibited equivalence in terms of miRNA recovery based on Bioanalyzer and RT-qPCR ΔΔCq results. Optimisation attempts for both kits failed to improve upon miRNA content compared with standard methodology. Comparing the standard methodology, the Qiagen kit was more consistent (smaller variance of ΔCq values) compared with the Promega kit. The standard methodology of either kit would be suitable for the investigation of miRNA biomarkers in a healthy pregnant population.
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Affiliation(s)
- Victoria L Parker
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield S10 2SF, UK
| | - Bryony F Cushen
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield S10 2SF, UK
| | - Eleftherios Gavriil
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield S10 2SF, UK
| | - Benjamin Marshall
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield S10 2SF, UK
| | - Sarah Waite
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield S10 2SF, UK
| | - Allan Pacey
- Department of Oncology and Metabolism, The University of Sheffield, Sheffield S10 2SF, UK
| | - Paul R Heath
- Sheffield Institute of Translational Neuroscience, The University of Sheffield, Sheffield S10 2HQ, UK
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20
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Jiang Y, Sun-Waterhouse D, Chen Y, Li F, Li D. Epigenetic mechanisms underlying the benefits of flavonoids in cardiovascular health and diseases: are long non-coding RNAs rising stars? Crit Rev Food Sci Nutr 2021; 62:3855-3872. [PMID: 33427492 DOI: 10.1080/10408398.2020.1870926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cardiovascular diseases (CVDs) rank as the first leading cause of death globally. High dietary polyphenol (especially flavonoids) intake has strongly been associated with low incidence of the primary outcome, overall mortality, blood pressure, inflammatory biomarkers, onset of new-onset type 2 diabetes mellitus (T2DM), and obesity. Phytogenic flavonoids affect the physiological and pathological processes of CVDs by modulating various biochemical signaling pathways. Non-coding RNAs (ncRNAs) have attracted increasing attention as fundamental regulator of gene expression involved in CVDs. Among the different ncRNA subgroups, long ncRNAs (lncRNAs) have recently emerged as regulatory eukaryotic transcripts and therapeutic targets with important and diverse functions in health and diseases. lncRNAs may be associated with the initiation, development and progression of CVDs by modulating acute and chronic inflammation, adipogenesis and lipid metabolism, and cellular physiology. This review summarizes this research on the modulatory effects of lncRNAs and their roles in mediating cellular processes. The mechanisms of action of flavonoids underlying their therapeutic effects on CVDs are also discussed. Based on our review, flavonoids might facilitate a significant epigenetic modification as part (if not full) of their tissue-/cell-related biological effects. This finding may be attributed to their interaction with cellular signaling pathways involved in chronic diseases. Certain lncRNAs might be the target of specific flavonoids, and some critical signaling processes involved in the intervention of CVDs might mediate the therapeutic roles of flavonoids.
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Affiliation(s)
- Yang Jiang
- College of Food Science and Engineering, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Shandong Agricultural University, Taian, PR China
| | | | - Yilun Chen
- College of Food Science and Engineering, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Shandong Agricultural University, Taian, PR China
| | - Feng Li
- College of Food Science and Engineering, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Shandong Agricultural University, Taian, PR China
| | - Dapeng Li
- College of Food Science and Engineering, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Shandong Agricultural University, Taian, PR China
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21
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Drag MH, Kilpeläinen TO. Cell-free DNA and RNA-measurement and applications in clinical diagnostics with focus on metabolic disorders. Physiol Genomics 2020; 53:33-46. [PMID: 33346689 DOI: 10.1152/physiolgenomics.00086.2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) and RNA (cfRNA) hold enormous potential as a new class of biomarkers for the development of noninvasive liquid biopsies in many diseases and conditions. In recent years, cfDNA and cfRNA have been studied intensely as tools for noninvasive prenatal testing, solid organ transplantation, cancer screening, and monitoring of tumors. In obesity, higher cfDNA concentration indicates accelerated cellular turnover of adipocytes during expansion of adipose mass and may be directly involved in the development of adipose tissue insulin resistance by inducing inflammation. Furthermore, cfDNA and cfRNA have promising diagnostic value in a range of obesity-related metabolic disorders, such as nonalcoholic fatty liver disease, type 2 diabetes, and diabetic complications. Here, we review the current and future applications of cfDNA and cfRNA within clinical diagnostics, discuss technical and analytical challenges in the field, and summarize the opportunities of using cfDNA and cfRNA in the diagnostics and prognostics of obesity-related metabolic disorders.
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Affiliation(s)
- Markus H Drag
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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22
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Preissner KT, Fischer S, Deindl E. Extracellular RNA as a Versatile DAMP and Alarm Signal That Influences Leukocyte Recruitment in Inflammation and Infection. Front Cell Dev Biol 2020; 8:619221. [PMID: 33392206 PMCID: PMC7775424 DOI: 10.3389/fcell.2020.619221] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022] Open
Abstract
Upon vascular injury, tissue damage, ischemia, or microbial infection, intracellular material such as nucleic acids and histones is liberated and comes into contact with the vessel wall and circulating blood cells. Such "Danger-associated molecular patterns" (DAMPs) may thus have an enduring influence on the inflammatory defense process that involves leukocyte recruitment and wound healing reactions. While different species of extracellular RNA (exRNA), including microRNAs and long non-coding RNAs, have been implicated to influence inflammatory processes at different levels, recent in vitro and in vivo work has demonstrated a major impact of ribosomal exRNA as a prominent DAMP on various steps of leukocyte recruitment within the innate immune response. This includes the induction of vascular hyper-permeability and vasogenic edema by exRNA via the activation of the "vascular endothelial growth factor" (VEGF) receptor-2 system, as well as the recruitment of leukocytes to the inflamed endothelium, the M1-type polarization of inflammatory macrophages, or the role of exRNA as a pro-thrombotic cofactor to promote thrombosis. Beyond sterile inflammation, exRNA also augments the docking of bacteria to host cells and the subsequent microbial invasion. Moreover, upon vessel occlusion and ischemia, the shear stress-induced release of exRNA initiates arteriogenesis (i.e., formation of natural vessel bypasses) in a multistep process that resembles leukocyte recruitment. Although exRNA can be counteracted for by natural circulating RNase1, under the conditions mentioned, only the administration of exogenous, thermostable, non-toxic RNase1 provides an effective and safe therapeutic regimen for treating the damaging activities of exRNA. It remains to be investigated whether exRNA may also influence viral infections (including COVID-19), e.g., by supporting the interaction of host cells with viral particles and their subsequent invasion. In fact, as a consequence of the viral infection cycle, massive amounts of exRNA are liberated, which can provoke further tissue damage and enhance virus dissemination. Whether the application of RNase1 in this scenario may help to limit the extent of viral infections like COVID-19 and impact on leukocyte recruitment and emigration steps in immune defense in order to limit the extent of associated cardiovascular diseases remains to be studied.
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Affiliation(s)
- Klaus T. Preissner
- Department of Biochemistry, Medical School, Justus Liebig University Giessen, Giessen, Germany
- Kerckhoff-Heart-Research-Institute, Department of Cardiology, Medical School, Justus Liebig University Giessen, Giessen, Germany
| | - Silvia Fischer
- Department of Biochemistry, Medical School, Justus Liebig University Giessen, Giessen, Germany
| | - Elisabeth Deindl
- Walter-Brendel-Centre of Experimental Medicine, University Hospital, LMU Munich, Munich, Germany
- Biomedical Center, Institute of Cardiovascular Physiology and Pathophysiology, LMU Munich, Munich, Germany
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23
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Chettimada S, Lorenz DR, Misra V, Wolinsky SM, Gabuzda D. Small RNA sequencing of extracellular vesicles identifies circulating miRNAs related to inflammation and oxidative stress in HIV patients. BMC Immunol 2020; 21:57. [PMID: 33176710 PMCID: PMC7656686 DOI: 10.1186/s12865-020-00386-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 10/26/2020] [Indexed: 12/27/2022] Open
Abstract
Background Extracellular vesicles (EVs) are nano-sized particles secreted by most cells. EVs carry nucleic acids that hold promise as potential biomarkers in various diseases. Human immunodeficiency virus type 1 (HIV) infects CD4+ T cells and induces immune dysfunction, inflammation, and EV secretion, but little is known about EV small RNA cargo in relation to immune dysregulation in HIV-infected individuals. Here, we characterize small RNA carried by circulating EVs in HIV-positive subjects on antiretroviral therapy (ART) relative to uninfected controls by next-generation RNA sequencing. Results Plasma EVs isolated from HIV-positive and HIV-negative subjects in test (n = 24) and validation (n = 16) cohorts were characterized by electron microscopy, nanoparticle tracking analysis, and immunoblotting for exosome markers. EVs were more abundant in plasma from HIV-positive compared to HIV-negative subjects. Small RNA sequencing of plasma EVs in the test cohort identified diverse small RNA species including miRNA, piRNA, snRNA, snoRNA, tRNA, and rRNA, with miRNA being the most abundant. A total of 351 different miRNAs were detected in plasma EVs, with the top 50 miRNAs accounting for 90% of all miRNA reads. miR-26a-5p was the most abundant miRNA, followed by miR-21-5p and miR-148-3p. qRT-PCR analysis showed that six miRNAs (miR-10a-5p, − 21-5p, −27b-3p, − 122-5p, −146a-5p, − 423-5p) were significantly increased in plasma EVs from HIV-positive compared to HIV-negative subjects in the validation cohort. Furthermore, miR-21-5p, −27b-3p, −146a-5p, and − 423-5p correlated positively with metabolite markers of oxidative stress and negatively with anti-inflammatory polyunsaturated fatty acids. Over-representation and pathway enrichment analyses of miRNAs and their target genes predicted functional association with oxidative stress responses, interferon gamma signaling, Toll-like receptor signaling, TGF beta signaling, and Notch signaling. Conclusions HIV-positive individuals on ART have increased abundance of circulating EVs carrying diverse small RNAs, with miRNAs being the most abundant. Several miRNAs associated with inflammation and oxidative stress are increased in circulating EVs of HIV-positive individuals, representing potential biomarkers of targetable pathways that contribute to disease pathogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s12865-020-00386-5.
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Affiliation(s)
- Sukrutha Chettimada
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David R Lorenz
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vikas Misra
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Dana Gabuzda
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Department of Neurology, Harvard Medical School, Boston, MA, USA.
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24
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Gad A, Sánchez JM, Browne JA, Nemcova L, Laurincik J, Prochazka R, Lonergan P. Plasma extracellular vesicle miRNAs as potential biomarkers of superstimulatory response in cattle. Sci Rep 2020; 10:19130. [PMID: 33154526 PMCID: PMC7645755 DOI: 10.1038/s41598-020-76152-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
The ability to predict superstimulatory response would be a beneficial tool in assisted reproduction. Using small RNAseq technology, we profiled extracellular vesicle microRNA (EV-miRNA) abundance in the blood plasma of heifers exhibiting variable responses to superstimulation. Estrous synchronized crossbred beef heifers (n = 25) were superstimulated and blood samples were collected from each heifer on Day 7 of consecutive unstimulated (U) and superstimulated (S) cycles. A subset of high (H) and low (L) responders was selected depending on their response to superstimulation and EV-miRNA profiles were analysed at both time-points in each heifer. Approximately 200 known miRNAs were detected in each sample with 144 commonly detected in all samples. A total of 12 and 14 miRNAs were dysregulated in UH vs. UL and in SH vs. SL heifers, respectively. Interestingly, miR-206 and miR-6517 exhibited the same differential expression pattern in H compared to L heifers both before and after superstimulation. Pathway analysis indicated that circadian rhythm and signaling pathways were among the top pathways enriched with genes targeted by dysregulated miRNAs in H vs. L responding heifers. In conclusion, heifers with divergent ovarian responses exhibited differential expression of plasma EV-miRNAs which may be used as a potential biomarker to predict superstimulation response.
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Affiliation(s)
- Ahmed Gad
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.,Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - José María Sánchez
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - John A Browne
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Lucie Nemcova
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Jozef Laurincik
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.,Constantine the Philosopher University in Nitra, Nitra, Slovakia
| | - Radek Prochazka
- Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Pat Lonergan
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland.
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25
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Lin Y, Zheng J, Lin D. PIWI-interacting RNAs in human cancer. Semin Cancer Biol 2020; 75:15-28. [PMID: 32877760 DOI: 10.1016/j.semcancer.2020.08.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/16/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022]
Abstract
P-element-induced wimpy testis (PIWI) interacting RNAs (piRNAs) are a class of small regulatory RNAs mechanistically similar to but much less studied than microRNAs and small interfering RNAs. Today the best understood function of piRNAs is transposon control in animal germ cells, which has earned them the name 'guardians of the germline'. Several molecular/cellular characteristics of piRNAs, including high sequence diversity, lack of secondary structures, and target-oriented generation seem to serve this purpose. Recently, aberrant expressions of piRNAs and PIWI proteins have been implicated in a variety of malignant tumors and associated with cancer hallmarks such as cell proliferation, inhibited apoptosis, invasion, metastasis and increased stemness. Researchers have also demonstrated multiple mechanisms of piRNA-mediated target deregulation associated with cancer initiation, progression or dissemination. We review current research findings on the biogenesis, normal functions and cancer associations of piRNAs, highlighting their potentials as cancer diagnostic/prognostic biomarkers and therapeutic tools. Whenever applicable, we draw connections with other research fields to encourage intercommunity conversations. We also offer recommendations and cautions regarding the general process of cancer-related piRNA studies and the methods/tools used at each step. Finally, we call attention to some issues that, if left unsolved, might impede the future development of this field.
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Affiliation(s)
- Yuan Lin
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.
| | - Jian Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China
| | - Dongxin Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060, China; Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
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26
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Tosar JP, Cayota A. Extracellular tRNAs and tRNA-derived fragments. RNA Biol 2020; 17:1149-1167. [PMID: 32070197 PMCID: PMC7549618 DOI: 10.1080/15476286.2020.1729584] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 01/08/2023] Open
Abstract
Fragmentation of tRNAs generates a family of small RNAs collectively known as tRNA-derived fragments. These fragments vary in sequence and size but have been shown to regulate many processes involved in cell homoeostasis and adaptations to stress. Additionally, the field of extracellular RNAs (exRNAs) is rapidly growing because exRNAs are a promising source of biomarkers in liquid biopsies, and because exRNAs seem to play key roles in intercellular and interspecies communication. Herein, we review recent descriptions of tRNA-derived fragments in the extracellular space in all domains of life, both in biofluids and in cell culture. The purpose of this review is to find consensus on which tRNA-derived fragments are more prominent in each extracellular fraction (including extracellular vesicles, lipoproteins and ribonucleoprotein complexes). We highlight what is becoming clear and what is still controversial in this field, in order to stimulate future hypothesis-driven studies which could clarify the role of full-length tRNAs and tRNA-derived fragments in the extracellular space.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit, Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Department of Medicine, University Hospital, Universidad de la República, Montevideo, Uruguay
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27
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Wang L, Wang J, Jia E, Liu Z, Ge Q, Zhao X. Plasma RNA sequencing of extracellular RNAs reveals potential biomarkers for non-small cell lung cancer. Clin Biochem 2020; 83:65-73. [PMID: 32526228 DOI: 10.1016/j.clinbiochem.2020.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 01/31/2023]
Abstract
BACKGROUND Lung cancer is one of the most common malignancies, and it has extremely high incidence and mortality rates. Although there have been many studies focused on lung cancer biomarkers, few have reported the extracellular RNA profiles of lung cancer. In this study, we used RNA-seq technology to analyze extracellular RNAs in low volume peripheral blood plasma; we compared the differentially expressed genes from the plasma of non-small cell lung cancer (NSCLC) patients with that of healthy controls. METHODS We used RNA-seq technology and bioinformatics to analyze the extracellular RNA (exRNA) sequences of 12 human plasma samples (500 μl per sample), 6 from NSCLC patients and 6 from healthy controls. Subsequently, we used gene ontology (GO) enrichment, KEGG analysis and coexpression experiments to compare the differentially expressed genes (DEGs) and identify tumor biomarkers that were highly correlated with NSCLC. These DEGs were further verified by quantitative PCR. RESULTS Approximately 20 million clean reads were produced for each plasma sample; 50-80% of the reads aligned to the human references, and hundreds of thousands of reads were counted in each plasma sample. In addition, a total of 640 genes (368 upregulated and 272 downregulated) were differentially expressed between NSCLC plasma and normal plasma. Further, we identified 7 key DEGs that are highly correlated with lung tumorigenesis: COX1, COX2, COX3, ND1, ND2, ND4L, and ATP6. CONCLUSION exRNA-seq from a small amount (400-500 μl) of plasma opens new possibilities for exploring lung cancer biomarkers in the plasma.
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Affiliation(s)
- Liujing Wang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Jun Wang
- Nanjing Med Univ, Jiangsu Prov Peoples Hosp, Dept Thorac Surg, Nanjing, Jiangsu, China.
| | - Erteng Jia
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Zhiyu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Xiangwei Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China.
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28
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Profiling the circulating mRNA transcriptome in human liver disease. Oncotarget 2020; 11:2216-2232. [PMID: 32577166 PMCID: PMC7289528 DOI: 10.18632/oncotarget.27617] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/16/2020] [Indexed: 01/05/2023] Open
Abstract
The human circulation contains cell-free DNA and non-coding microRNA (miRNA). Less is known about the presence of messenger RNA (mRNA). This report profiles the human circulating mRNA transcriptome in people with liver cirrhosis (LC) and hepatocellular carcinoma (HCC) to determine whether mRNA analytes can be used as biomarkers of liver disease. Using RNAseq and RT-qPCR, we investigate circulating mRNA in plasma from HCC and LC patients and demonstrate detection of transcripts representing more than 19,000 different protein coding genes. Remarkably, the circulating mRNA expression levels were similar from person to person over the 21 individuals whose samples were analyzed by RNAseq. Liver derived circulating transcripts such as albumin (ALB), apolipoprotein (APO) A1, A2 & H, serpin A1 & E1, ferritin light chain (FTL) and fibrinogen like 1 (FGL1) were significantly upregulated in HCC patient samples. Higher levels of some of these liver-specific transcripts in the plasma of HCC patients were confirmed by RT-qPCR in another cohort of 20 individuals. Several less abundant circulating transcripts associated with cancer were detected in most HCC samples, but not in healthy subjects. Liver specificity of circulating transcripts was confirmed by investigating their expression in HCC tumor and liver cancer cell lines. Liver specific mRNA sequences in the plasma were predominantly present outside circulating extracellular vesicles. Conclusions: The circulating “mRNA” transcriptome is remarkably consistent in diversity and expression from person to person. Detection of transcripts corresponding to disease selective polypeptides suggests the possibility that circulating mRNA can work as a biomarker analyte for cancer detection.
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29
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Grabuschnig S, Soh J, Heidinger P, Bachler T, Hirschböck E, Rosales Rodriguez I, Schwendenwein D, Sensen CW. Circulating cell-free DNA is predominantly composed of retrotransposable elements and non-telomeric satellite DNA. J Biotechnol 2020; 313:48-56. [DOI: 10.1016/j.jbiotec.2020.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/26/2020] [Accepted: 03/04/2020] [Indexed: 12/19/2022]
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30
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The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research. Cell 2020; 177:231-242. [PMID: 30951667 DOI: 10.1016/j.cell.2019.03.023] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Extracellular RNA Communication Consortium (ERCC) was launched to accelerate progress in the new field of extracellular RNA (exRNA) biology and to establish whether exRNAs and their carriers, including extracellular vesicles (EVs), can mediate intercellular communication and be utilized for clinical applications. Phase 1 of the ERCC focused on exRNA/EV biogenesis and function, discovery of exRNA biomarkers, development of exRNA/EV-based therapeutics, and construction of a robust set of reference exRNA profiles for a variety of biofluids. Here, we present progress by ERCC investigators in these areas, and we discuss collaborative projects directed at development of robust methods for EV/exRNA isolation and analysis and tools for sharing and computational analysis of exRNA profiling data.
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31
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Tielking K, Fischer S, Preissner KT, Vajkoczy P, Xu R. Extracellular RNA in Central Nervous System Pathologies. Front Mol Neurosci 2019; 12:254. [PMID: 31680858 PMCID: PMC6811659 DOI: 10.3389/fnmol.2019.00254] [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: 07/01/2019] [Accepted: 09/30/2019] [Indexed: 12/14/2022] Open
Abstract
The discovery of extracellular RNA (exRNA) has shifted our understanding of the role of RNA in complex cellular functions such as cell-to-cell communication and a variety of pathologies. ExRNAs constitute a heterogenous group of RNAs ranging from small (such as microRNAs) and long non-coding to coding RNAs or ribosomal RNAs. ExRNAs can be liberated from cells in a free form or bound to proteins as well as in association with microvesicles (MVs), exosomes, or apoptotic bodies. Their composition and quantity depend heavily on the cellular or non-cellular component, the origin, and the RNA species being investigated; ribosomal RNA provides the majority of exRNA and miRNAs are predominantly associated with exosomes or MVs. Several studies showed that ribosomal exRNA (rexRNA) constitutes a proinflammatory and prothrombotic alarmin. It is released by various cell types upon inflammatory stimulation and by damaged cells undergoing necrosis or apoptosis and contributes to innate immunity responses. This exRNA has the potential to directly promote the release of cytokines such as tumor necrosis factor factor-α (TNF-α) or interleukin-6 from immune cells, thereby leading to a proinflammatory environment and promoting cardiovascular pathologies. The potential role of exRNA in different pathologies of the central nervous system (CNS) has become of increasing interest in recent years. Although various exRNA species including both ribosomal exRNA as well as miRNAs have been associated with CNS pathologies, their precise roles remain to be further elucidated. In this review, the different entities of exRNA and their postulated roles in CNS pathologies including tumors, vascular pathologies and neuroinflammatory diseases will be discussed. Furthermore, the potential role of exRNAs as diagnostic markers for specific CNS diseases will be outlined, as well as possible treatment strategies addressing exRNA inhibition or interference.
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Affiliation(s)
- Katharina Tielking
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Silvia Fischer
- Department of Biochemistry, Medical School, Justus Liebig University Giessen, Giessen, Germany
| | - Klaus T Preissner
- Department of Biochemistry, Medical School, Justus Liebig University Giessen, Giessen, Germany
| | - Peter Vajkoczy
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Ran Xu
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
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32
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Zhang Z, Ruan H, Liu CJ, Ye Y, Gong J, Diao L, Guo AY, Han L. tRic: a user-friendly data portal to explore the expression landscape of tRNAs in human cancers. RNA Biol 2019; 17:1674-1679. [PMID: 31432762 DOI: 10.1080/15476286.2019.1657744] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Transfer RNAs (tRNAs) play critical roles in human cancer. Currently, no database provides the expression landscape and clinical relevance of tRNAs across a variety of human cancers. Utilizing miRNA-seq data from The Cancer Genome Atlas, we quantified the relative expression of tRNA genes and merged them into the codon level and amino level across 31 cancer types. The expression of tRNAs is associated with clinical features of patient smoking history and overall survival, and disease stage, subtype, and grade. We further analysed codon frequency and amino acid frequency for each protein coding gene and linked alterations of tRNA expression with protein translational efficiency. We include these data resources in a user-friendly data portal, tRic (tRNA in cancer, https://hanlab.uth.edu/tRic/ or http://bioinfo.life.hust.edu.cn/tRic/), which can be of significant interest to the research community.
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Affiliation(s)
- Zhao Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston , Houston, TX, USA
| | - Hang Ruan
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston , Houston, TX, USA
| | - Chun-Jie Liu
- Department of Bioinformatics and Systems Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan, Hubei, PR China
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston , Houston, TX, USA
| | - Jing Gong
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston , Houston, TX, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center , Houston, TX, USA
| | - An-Yuan Guo
- Department of Bioinformatics and Systems Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology , Wuhan, Hubei, PR China
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston , Houston, TX, USA.,Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , Houston, TX, USA
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33
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Pardini B, Sabo AA, Birolo G, Calin GA. Noncoding RNAs in Extracellular Fluids as Cancer Biomarkers: The New Frontier of Liquid Biopsies. Cancers (Basel) 2019; 11:E1170. [PMID: 31416190 PMCID: PMC6721601 DOI: 10.3390/cancers11081170] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/04/2019] [Accepted: 08/10/2019] [Indexed: 02/06/2023] Open
Abstract
The last two decades of cancer research have been devoted in two directions: (1) understanding the mechanism of carcinogenesis for an effective treatment, and (2) improving cancer prevention and screening for early detection of the disease. This last aspect has been developed, especially for certain types of cancers, thanks also to the introduction of new concepts such as liquid biopsies and precision medicine. In this context, there is a growing interest in the application of alternative and noninvasive methodologies to search for cancer biomarkers. The new frontiers of the research lead to a search for RNA molecules circulating in body fluids. Searching for biomarkers in extracellular body fluids represents a better option for patients because they are easier to access, less painful, and potentially more economical. Moreover, the possibility for these types of samples to be taken repeatedly, allows a better monitoring of the disease progression or treatment efficacy for a better intervention and dynamic treatment of the patient, which is the fundamental basis of personalized medicine. RNA molecules, freely circulating in body fluids or packed in microvesicles, have all the characteristics of the ideal biomarkers owing to their high stability under storage and handling conditions and being able to be sampled several times for monitoring. Moreover, as demonstrated for many cancers, their plasma/serum levels mirror those in the primary tumor. There are a large variety of RNA species noncoding for proteins that could be used as cancer biomarkers in liquid biopsies. Among them, the most studied are microRNAs, but recently the attention of the researcher has been also directed towards Piwi-interacting RNAs, circular RNAs, and other small noncoding RNAs. Another class of RNA species, the long noncoding RNAs, is larger than microRNAs and represents a very versatile and promising group of molecules which, apart from their use as biomarkers, have also a possible therapeutic role. In this review, we will give an overview of the most common noncoding RNA species detectable in extracellular fluids and will provide an update concerning the situation of the research on these molecules as cancer biomarkers.
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Affiliation(s)
- Barbara Pardini
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy.
- Unit of Molecular Epidemiology and Exposome, Italian Institute for Genomic Medicine (IIGM), 10126 Turin, Italy.
| | - Alexandru Anton Sabo
- Department of Pediatrics, Marie Curie Emergency Clinical Hospital for Children, 077120 Bucharest, Romania
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy
- Unit of Molecular Epidemiology and Exposome, Italian Institute for Genomic Medicine (IIGM), 10126 Turin, Italy
| | - George Adrian Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Berg MD, Giguere DJ, Dron JS, Lant JT, Genereaux J, Liao C, Wang J, Robinson JF, Gloor GB, Hegele RA, O'Donoghue P, Brandl CJ. Targeted sequencing reveals expanded genetic diversity of human transfer RNAs. RNA Biol 2019; 16:1574-1585. [PMID: 31407949 PMCID: PMC6779403 DOI: 10.1080/15476286.2019.1646079] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Transfer RNAs are required to translate genetic information into proteins as well as regulate other cellular processes. Nucleotide changes in tRNAs can result in loss or gain of function that impact the composition and fidelity of the proteome. Despite links between tRNA variation and disease, the importance of cytoplasmic tRNA variation has been overlooked. Using a custom capture panel, we sequenced 605 human tRNA-encoding genes from 84 individuals. We developed a bioinformatic pipeline that allows more accurate tRNA read mapping and identifies multiple polymorphisms occurring within the same variant. Our analysis identified 522 unique tRNA-encoding sequences that differed from the reference genome from 84 individuals. Each individual had ~66 tRNA variants including nine variants found in less than 5% of our sample group. Variants were identified throughout the tRNA structure with 17% predicted to enhance function. Eighteen anticodon mutants were identified including potentially mistranslating tRNAs; e.g., a tRNASer that decodes Phe codons. Similar engineered tRNA variants were previously shown to inhibit cell growth, increase apoptosis and induce the unfolded protein response in mammalian cell cultures and chick embryos. Our analysis shows that human tRNA variation has been underestimated. We conclude that the large number of tRNA genes provides a buffer enabling the emergence of variants, some of which could contribute to disease.
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Affiliation(s)
- Matthew D Berg
- Department of Biochemistry, The University of Western Ontario , London , ON , Canada
| | - Daniel J Giguere
- Department of Biochemistry, The University of Western Ontario , London , ON , Canada
| | - Jacqueline S Dron
- Department of Biochemistry, The University of Western Ontario , London , ON , Canada.,Robarts Research Institute, The University of Western Ontario , London , ON , Canada
| | - Jeremy T Lant
- Department of Biochemistry, The University of Western Ontario , London , ON , Canada
| | - Julie Genereaux
- Department of Biochemistry, The University of Western Ontario , London , ON , Canada
| | - Calwing Liao
- Department of Biochemistry, The University of Western Ontario , London , ON , Canada.,Robarts Research Institute, The University of Western Ontario , London , ON , Canada
| | - Jian Wang
- Robarts Research Institute, The University of Western Ontario , London , ON , Canada
| | - John F Robinson
- Robarts Research Institute, The University of Western Ontario , London , ON , Canada
| | - Gregory B Gloor
- Department of Biochemistry, The University of Western Ontario , London , ON , Canada
| | - Robert A Hegele
- Department of Biochemistry, The University of Western Ontario , London , ON , Canada.,Robarts Research Institute, The University of Western Ontario , London , ON , Canada.,Department of Medicine, The University of Western Ontario , London , ON , Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, The University of Western Ontario , London , ON , Canada.,Department of Chemistry, The University of Western Ontario , London , ON , Canada
| | - Christopher J Brandl
- Department of Biochemistry, The University of Western Ontario , London , ON , Canada
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35
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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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36
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Diversity and heterogeneity of extracellular RNA in human plasma. Biochimie 2019; 164:22-36. [PMID: 31108123 DOI: 10.1016/j.biochi.2019.05.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/14/2019] [Indexed: 12/15/2022]
Abstract
Extracellular RNAs (exRNAs) are secreted by nearly all cell types and are now known to play multiple physiological roles. In humans, exRNA populations are found in nearly any physiological liquid and are attracting growing interest as a potential source for biomarker discovery. Human plasma, a readily available sample for biomedical analysis, reported to contain various subpopulations of exRNA, some of which are most likely components of plasma ribonucleoproteins (RNPs), while others are encapsulated into extracellular vesicles (EVs) of different size, origin and composition. This variation explains the extreme complexity of the human exRNA fraction in plasma. In this work, we aimed to characterize exRNA species from blood samples of healthy human donors to achieve the most comprehensive overview of the species, sizes and origins of the exRNA present in plasma fractions. Unbiased analysis of exRNA composition was performed with prefractionation of plasma exRNA followed by library preparation, sequencing and bioinformatics analysis. Our results demonstrate that, in addition to "mature", adaptor ligation-competent RNA species (5'-P/3'-OH), human plasma contains a substantial proportion of degraded RNA fragments (5'-OH/3'-P or cycloP), which can be made competent for ligation using appropriate treatments. These degraded RNAs represent the major fraction in the overall population and mostly correspond to rRNA, in contrast to mature products, which mostly contain miRNAs and hY4 RNA fragments. Precipitation polyethylene glycol (PEG)-based kits for EV isolation yield a fraction that is highly contaminated by large RNPs and by RNA loosely bound to EVs. Purer EV preparations are obtained by using proteinase K and RNase A treatment, as well as by size-exclusion chromatography (SEC). These samples have rather distinct RNA compositions compared to PEG-precipitated EV preparations and contain a substantial proportion of exRNA of non-human origin, arising from human skin and gut microbiota, including viral microbiota. These exogenous exRNAs represent up to 75-80% of total RNA reads in highly purified extracellular vesicles, paving the way for biomedical exploitation of these non-human biomarkers.
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37
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Akat KM, Lee YA, Hurley A, Morozov P, Max KE, Brown M, Bogardus K, Sopeyin A, Hildner K, Diacovo TG, Neurath MF, Borggrefe M, Tuschl T. Detection of circulating extracellular mRNAs by modified small-RNA-sequencing analysis. JCI Insight 2019; 5:127317. [PMID: 30973829 DOI: 10.1172/jci.insight.127317] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Extracellular mRNAs (ex-mRNAs) potentially supersede extracellular miRNAs (ex-miRNAs) and other RNA classes as biomarkers. We performed conventional small-RNA-sequencing (sRNA-seq) and sRNA-seq with T4 polynucleotide kinase (PNK) end-treatment of total exRNA isolated from serum and platelet-poor EDTA, ACD, and heparin plasma to study the effect on ex-mRNA capture. Compared to conventional sRNA-seq PNK-treatment increased the detection of informative ex-mRNAs reads up to 50-fold. The exRNA pool was dominated by hematopoietic cells and platelets, with additional contribution from the liver. About 60% of the 15- to 42-nt reads originated from the coding sequences, in a pattern reminiscent of ribosome-profiling. Blood sample type had a considerable influence on the exRNA profile. On average approximately 350 to 1,100 distinct ex-mRNA transcripts were detected depending on plasma type. In serum, additional transcripts from neutrophils and hematopoietic cells increased this number to near 2,300. EDTA and ACD plasma showed a destabilizing effect on ex mRNA and non-coding RNA ribonucleoprotein complexes compared to other plasma types. In a proof-of-concept study, we investigated differences between the exRNA profiles of patients with acute coronary syndrome (ACS) and healthy controls. The improved tissue resolution of ex mRNAs after PNK-treatment enabled us to detect a neutrophil-signature in ACS that escaped detection by ex miRNA analysis.
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Affiliation(s)
| | | | - Arlene Hurley
- Center for Translational Science, The Rockefeller University, New York, New York, USA
| | | | | | | | | | | | - Kai Hildner
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Kussmaul Campus for Medical Research, Erlangen, Bavaria, Germany
| | - Thomas G Diacovo
- Departments of Pediatrics and Cell Biology and Pathology, Columbia University Medical Center, New York, New York, USA
| | - Markus F Neurath
- Department of Medicine 1, University Hospital Erlangen, University of Erlangen-Nuremberg, Kussmaul Campus for Medical Research, Erlangen, Bavaria, Germany
| | - Martin Borggrefe
- First Department of Medicine, University Medical Center Mannheim, Faculty of Medicine Mannheim, University of Heidelberg, European Center for AngioScience, and DZHK (German Center for Cardiovascular Research), partner site Heidelberg/Mannheim, Mannheim, Baden-Wuerttemberg, Germany
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38
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Rozowsky J, Kitchen RR, Park JJ, Galeev TR, Diao J, Warrell J, Thistlethwaite W, Subramanian SL, Milosavljevic A, Gerstein M. exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling. Cell Syst 2019; 8:352-357.e3. [PMID: 30956140 DOI: 10.1016/j.cels.2019.03.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/31/2019] [Accepted: 03/06/2019] [Indexed: 01/09/2023]
Abstract
Small RNA sequencing has been widely adopted to study the diversity of extracellular RNAs (exRNAs) in biofluids; however, the analysis of exRNA samples can be challenging: they are vulnerable to contamination and artifacts from different isolation techniques, present in lower concentrations than cellular RNA, and occasionally of exogenous origin. To address these challenges, we present exceRpt, the exRNA-processing toolkit of the NIH Extracellular RNA Communication Consortium (ERCC). exceRpt is structured as a cascade of filters and quantifications prioritized based on one's confidence in a given set of annotated RNAs. It generates quality control reports and abundance estimates for RNA biotypes. It is also capable of characterizing mappings to exogenous genomes, which, in turn, can be used to generate phylogenetic trees. exceRpt has been used to uniformly process all ∼3,500 exRNA-seq datasets in the public exRNA Atlas and is available from genboree.org and github.gersteinlab.org/exceRpt.
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Affiliation(s)
- Joel Rozowsky
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Robert R Kitchen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jonathan J Park
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Timur R Galeev
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - James Diao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jonathan Warrell
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - William Thistlethwaite
- Bioinformatics Research Laboratory, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
| | - Sai L Subramanian
- Bioinformatics Research Laboratory, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
| | - Aleksandar Milosavljevic
- Bioinformatics Research Laboratory, Molecular and Human Genetics Department, Baylor College of Medicine, Houston, TX, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Department of Computer Science, Yale University, New Haven, CT, USA.
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39
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Ramzan F, Mitchell CJ, Milan AM, Schierding W, Zeng N, Sharma P, Mitchell SM, D'Souza RF, Knowles SO, Roy NC, Sjödin A, Wagner KH, Cameron-Smith D. Comprehensive Profiling of the Circulatory miRNAome Response to a High Protein Diet in Elderly Men: A Potential Role in Inflammatory Response Modulation. Mol Nutr Food Res 2019; 63:e1800811. [PMID: 30892810 DOI: 10.1002/mnfr.201800811] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/21/2019] [Indexed: 12/11/2022]
Abstract
SCOPE MicroRNA are critical to the coordinated post-transcriptional regulation of gene expression, yet few studies have addressed the influence of habitual diet on microRNA expression. High protein diets impact cardiometabolic health and body composition in the elderly suggesting the possibility of a complex systems response. Therefore, high-throughput small RNA sequencing technology is applied in response to doubling the protein recommended dietary allowance (RDA) over 10 weeks in older men to examine alterations in circulating miRNAome. METHODS AND RESULTS Older men (n = 31; 74.1 ± 0.6 y) are randomized to consume either RDA (0.8 g kg-1 day-1 ) or 2RDA (1.6 g kg-1 day-1 ) of protein for 10 weeks. Downregulation of five microRNAs (miR-125b-5p, -100-5p, -99a-5p, -23b-3p, and -203a) is observed following 2RDA with no changes in the RDA. In silico functional analysis highlights target gene enrichment in inflammation-related pathways. qPCR quantification of predicted inflammatory genes (TNFα, IL-8, IL-6, pTEN, PPP1CB, and HOXA1) in peripheral blood mononuclear cells shows increased expression following 2RDA diet (p ≤ 0.05). CONCLUSION The study findings suggest a possible selective alteration in the post-transcriptional regulation of the immune system following a high protein diet. However, very few microRNAs are altered despite a large change in the dietary protein.
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Affiliation(s)
- Farha Ramzan
- Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand.,Riddet Institute, Massey University, Palmerston North, 4442, New Zealand
| | - Cameron J Mitchell
- Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand
| | - Amber M Milan
- Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand
| | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand
| | - Nina Zeng
- Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand
| | - Pankaja Sharma
- Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand.,Riddet Institute, Massey University, Palmerston North, 4442, New Zealand
| | - Sarah M Mitchell
- Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand.,Riddet Institute, Massey University, Palmerston North, 4442, New Zealand
| | - Randall F D'Souza
- Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand
| | - Scott O Knowles
- Food Nutrition and Health Team, AgResearch Ltd., Grasslands Research Centre, Palmerston North, 4442, New Zealand
| | - Nicole C Roy
- Food Nutrition and Health Team, AgResearch Ltd., Grasslands Research Centre, Palmerston North, 4442, New Zealand.,Riddet Institute, Massey University, Palmerston North, 4442, New Zealand.,The High-Value Nutrition National Science Challenge, Auckland, 1023, New Zealand
| | - Anders Sjödin
- Department of Nutrition, Exercise and Sport, Copenhagen University, 1165, Denmark
| | - Karl-Heinz Wagner
- Department of Nutritional Sciences and Research Platform Active Ageing, University of Vienna, 1010, Vienna, Austria
| | - David Cameron-Smith
- Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand.,Riddet Institute, Massey University, Palmerston North, 4442, New Zealand.,Food & Bio-Based Products Group, AgResearch Ltd., Hamilton, 3214, New Zealand
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40
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Sole C, Arnaiz E, Manterola L, Otaegui D, Lawrie CH. The circulating transcriptome as a source of cancer liquid biopsy biomarkers. Semin Cancer Biol 2019; 58:100-108. [PMID: 30684535 DOI: 10.1016/j.semcancer.2019.01.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 01/16/2019] [Accepted: 01/22/2019] [Indexed: 02/07/2023]
Abstract
Non-invasive biomarkers or liquid biopsies have the potential to revolutionise cancer patient management as repeated sampling allows real-time monitoring of disease progression and response to treatment. This allows for earlier intervention and dynamic treatment management; both cornerstones of personalised medicine. The circulating transcriptome represents a rich source of potential cancer biomarkers that includes many classes of RNA, both coding and non-coding, that are only now beginning to be explored. In particular the increasing power and availability of RNAseq techniques have pushed studies beyond circulating miRNAs, to other classes of RNA including mRNA, snRNA, snoRNA, piRNA, YRNA, lncRNA and circRNA. In this review we focus on the emerging potential for these different classes of RNA as cancer biomarkers, and in particular the barriers and limitations that remain to be overcome if these molecules are to become part of routine clinical practice.
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Affiliation(s)
- Carla Sole
- Molecular Oncology Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n, San Sebastián, 20014, Spain
| | - Esther Arnaiz
- Molecular Oncology Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n, San Sebastián, 20014, Spain
| | - Lorea Manterola
- Molecular Oncology Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n, San Sebastián, 20014, Spain
| | - David Otaegui
- Multiple Sclerosis Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n, San Sebastián, 20014, Spain
| | - Charles H Lawrie
- Molecular Oncology Group, Biodonostia Research Institute, Paseo Doctor Begiristain, s/n, San Sebastián, 20014, Spain; Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom; IKERBASQUE, Basque Foundation for Science, María Díaz Haroko Kalea, 3, 48013, Bilbao, Spain.
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41
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Solé C, Tramonti D, Schramm M, Goicoechea I, Armesto M, Hernandez LI, Manterola L, Fernandez-Mercado M, Mujika K, Tuneu A, Jaka A, Tellaetxe M, Friedländer MR, Estivill X, Piazza P, Ortiz-Romero PL, Middleton MR, Lawrie CH. The Circulating Transcriptome as a Source of Biomarkers for Melanoma. Cancers (Basel) 2019; 11:cancers11010070. [PMID: 30634628 PMCID: PMC6356785 DOI: 10.3390/cancers11010070] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/02/2019] [Accepted: 01/04/2019] [Indexed: 12/18/2022] Open
Abstract
The circulating transcriptome is a valuable source of cancer biomarkers, which, with the exception of microRNAs (miRNAs), remains relatively unexplored. To elucidate which RNAs are present in plasma from melanoma patients and which could be used to distinguish cancer patients from healthy individuals, we used next generation sequencing (NGS), and validation was carried out by qPCR and/or ddPCR. We identified 442 different microRNAs in samples, eleven of which were differentially expressed (p < 0.05). Levels of miR-134-5p and miR-320a-3p were significantly down-regulated (p < 0.001) in melanoma samples (n = 96) compared to healthy controls (n = 28). Differentially expressed protein-encoding mRNA 5'-fragments were enriched for the angiopoietin, p21-activated kinase (PAK), and EIF2 pathways. Levels of ATM1, AMFR, SOS1, and CD109 gene fragments were up-regulated (p < 0.001) in melanoma samples (n = 144) compared to healthy controls (n = 41) (AUC = 0.825). Over 40% of mapped reads were YRNAs, a class of non-coding RNAs that to date has been little explored. Expression levels of RNY3P1, RNY4P1, and RNY4P25 were significantly higher in patients with stage 0 disease than either healthy controls or more advanced stage disease (p < 0.001). In conclusion, we have identified a number of novel RNA biomarkers, which, most importantly, we validated in multi-center retrospective and prospective cohorts, suggesting potential diagnostic use of these RNA species.
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Affiliation(s)
- Carla Solé
- Molecular Oncology group, Biodonostia Research Institute, San Sebastián 20012, Spain.
| | - Daniela Tramonti
- Department of Oncology, University of Oxford, Oxford OX3 9DU, UK.
| | - Maike Schramm
- Molecular Oncology group, Biodonostia Research Institute, San Sebastián 20012, Spain.
- Faculty of Biosciences, University of Heidelberg, Heidelberg 69120, Germany.
| | - Ibai Goicoechea
- Molecular Oncology group, Biodonostia Research Institute, San Sebastián 20012, Spain.
| | - María Armesto
- Molecular Oncology group, Biodonostia Research Institute, San Sebastián 20012, Spain.
| | - Luiza I Hernandez
- Molecular Oncology group, Biodonostia Research Institute, San Sebastián 20012, Spain.
| | - Lorea Manterola
- Molecular Oncology group, Biodonostia Research Institute, San Sebastián 20012, Spain.
| | | | - Karmele Mujika
- Onkologikoa-Oncology Institute Gipuzkoa, Gipuzkoa 20012, Spain.
| | - Anna Tuneu
- Department of Dermatology, Hospital Universitario de Donostia, San Sebastian 20012, Spain.
| | - Ane Jaka
- Department of Dermatology, Hospital Universitario de Donostia, San Sebastian 20012, Spain.
| | - Maitena Tellaetxe
- Molecular Oncology group, Biodonostia Research Institute, San Sebastián 20012, Spain.
| | - Marc R Friedländer
- Genomics and Disease group, Centre for Genomic Regulation (CRG), Barcelona 08003, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain.
- Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Barcelona 08002, Spain.
- Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain.
- Science for Life Laboratory, The Wenner-Gren Institute, Stockholm University, Stockholm SE-106 9, Sweden.
| | - Xavier Estivill
- Genomics and Disease group, Centre for Genomic Regulation (CRG), Barcelona 08003, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain.
- Centro de Investigación Biomédica en Red Epidemiología y Salud Pública (CIBERESP), Barcelona 08002, Spain.
- Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain.
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
- Imperial BRC Genomics Facility, Imperial College London, London SW7 2AZ, UK.
| | - Pablo L Ortiz-Romero
- Department of Dermatology, 12 de Octubre Hospital, Madrid 28041, Spain.
- Medical School, Universidad Complutense, Institute i+12, Centro de Investigación Biomédica en Red en Oncologia (CIBERONC), Madrid 28040, Spain.
| | - Mark R Middleton
- Department of Oncology, University of Oxford, Oxford OX3 9DU, UK.
| | - Charles H Lawrie
- Molecular Oncology group, Biodonostia Research Institute, San Sebastián 20012, Spain.
- Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK.
- IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain.
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Zhang Z, Ye Y, Gong J, Ruan H, Liu CJ, Xiang Y, Cai C, Guo AY, Ling J, Diao L, Weinstein JN, Han L. Global analysis of tRNA and translation factor expression reveals a dynamic landscape of translational regulation in human cancers. Commun Biol 2018; 1:234. [PMID: 30588513 PMCID: PMC6303286 DOI: 10.1038/s42003-018-0239-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/27/2018] [Indexed: 12/14/2022] Open
Abstract
The protein translational system, including transfer RNAs (tRNAs) and several categories of enzymes, plays a key role in regulating cell proliferation. Translation dysregulation also contributes to cancer development, though relatively little is known about the changes that occur to the translational system in cancer. Here, we present global analyses of tRNAs and three categories of enzymes involved in translational regulation in ~10,000 cancer patients across 31 cancer types from The Cancer Genome Atlas. By analyzing the expression levels of tRNAs at the gene, codon, and amino acid levels, we identified unequal alterations in tRNA expression, likely due to the uneven distribution of tRNAs decoding different codons. We find that overexpression of tRNAs recognizing codons with a low observed-over-expected ratio may overcome the translational bottleneck in tumorigenesis. We further observed overall overexpression and amplification of tRNA modification enzymes, aminoacyl-tRNA synthetases, and translation factors, which may play synergistic roles with overexpression of tRNAs to activate the translational systems across multiple cancer types.
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Affiliation(s)
- Zhao Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Jing Gong
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Hang Ruan
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Chun-Jie Liu
- Department of Bioinformatics and Systems Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology Wuhan, 430074 Hubei, People’s Republic of China
| | - Yu Xiang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - Chunyan Cai
- Department of Internal Medicine, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
| | - An-Yuan Guo
- Department of Bioinformatics and Systems Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology Wuhan, 430074 Hubei, People’s Republic of China
| | - Jiqiang Ling
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742 USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - John N. Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030 USA
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
- Center for Precision Health, The University of Texas Health Science Center at Houston, Houston, TX 77030 USA
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43
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Abstract
SIGNIFICANCE To maintain homeostasis, gene expression has to be tightly regulated by complex and multiple mechanisms occurring at the epigenetic, transcriptional, and post-transcriptional levels. One crucial regulatory component is represented by long noncoding RNAs (lncRNAs), nonprotein-coding RNA species implicated in all of these levels. Thus, lncRNAs have been associated with any given process or pathway of interest in a variety of systems, including the heart. Recent Advances: Mounting evidence implicates lncRNAs in cardiovascular diseases (CVD) and progression and their presence in the blood of heart disease patients indicates that they are attractive potential biomarkers. CRITICAL ISSUES Our understanding of the regulation and molecular mechanisms of action of most lncRNAs remains rudimentary. A challenge is represented by their often low evolutionary sequence conservation that limits the use of animal models for preclinical studies. Nevertheless, a growing number of lncRNAs with an impact on heart function is rapidly accumulating. In this study, we will discuss (i) lncRNAs that control heart homeostasis and disease; (ii) concepts, approaches, and methodologies necessary to study lncRNAs in the heart; and (iii) challenges posed and opportunities presented by lncRNAs as potential therapeutic targets and biomarkers. FUTURE DIRECTIONS A deeper knowledge of the molecular mechanisms underpinning CVDs is necessary to develop more effective treatments. Further studies are needed to clarify the regulation and function of lncRNAs in the heart before they can be considered as therapeutic targets and disease biomarkers. Antioxid. Redox Signal. 29, 880-901.
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Affiliation(s)
- Simona Greco
- 1 Molecular Cardiology Laboratory, IRCCS Policlinico San Donato , Milan, Italy
| | - Antonio Salgado Somoza
- 2 Cardiovascular Research Unit, Luxembourg Institute of Health (LIH) , Luxembourg, Luxembourg
| | - Yvan Devaux
- 2 Cardiovascular Research Unit, Luxembourg Institute of Health (LIH) , Luxembourg, Luxembourg
| | - Fabio Martelli
- 1 Molecular Cardiology Laboratory, IRCCS Policlinico San Donato , Milan, Italy
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44
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Poller W, Dimmeler S, Heymans S, Zeller T, Haas J, Karakas M, Leistner DM, Jakob P, Nakagawa S, Blankenberg S, Engelhardt S, Thum T, Weber C, Meder B, Hajjar R, Landmesser U. Non-coding RNAs in cardiovascular diseases: diagnostic and therapeutic perspectives. Eur Heart J 2018; 39:2704-2716. [PMID: 28430919 PMCID: PMC6454570 DOI: 10.1093/eurheartj/ehx165] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/14/2017] [Accepted: 03/15/2017] [Indexed: 02/06/2023] Open
Abstract
Recent research has demonstrated that the non-coding genome plays a key role in genetic programming and gene regulation during development as well as in health and cardiovascular disease. About 99% of the human genome do not encode proteins, but are transcriptionally active representing a broad spectrum of non-coding RNAs (ncRNAs) with important regulatory and structural functions. Non-coding RNAs have been identified as critical novel regulators of cardiovascular risk factors and cell functions and are thus important candidates to improve diagnostics and prognosis assessment. Beyond this, ncRNAs are rapidly emgerging as fundamentally novel therapeutics. On a first level, ncRNAs provide novel therapeutic targets some of which are entering assessment in clinical trials. On a second level, new therapeutic tools were developed from endogenous ncRNAs serving as blueprints. Particularly advanced is the development of RNA interference (RNAi) drugs which use recently discovered pathways of endogenous short interfering RNAs and are becoming versatile tools for efficient silencing of protein expression. Pioneering clinical studies include RNAi drugs targeting liver synthesis of PCSK9 resulting in highly significant lowering of LDL cholesterol or targeting liver transthyretin (TTR) synthesis for treatment of cardiac TTR amyloidosis. Further novel drugs mimicking actions of endogenous ncRNAs may arise from exploitation of molecular interactions not accessible to conventional pharmacology. We provide an update on recent developments and perspectives for diagnostic and therapeutic use of ncRNAs in cardiovascular diseases, including atherosclerosis/coronary disease, post-myocardial infarction remodelling, and heart failure.
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Affiliation(s)
- Wolfgang Poller
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Stefanie Dimmeler
- Institute for Cardiovascular Regeneration, Center of Molecular Medicine, Johann Wolfgang Goethe Universität, Theodor-Stern-Kai 7, Frankfurt am Main, Germany
- DZHK, Site Rhein-Main, Frankfurt, Germany
| | - Stephane Heymans
- Center for Heart Failure Research, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands
| | - Tanja Zeller
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Jan Haas
- Institute for Cardiomyopathies Heidelberg (ICH), Universitätsklinikum Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
- DZHK, Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Mahir Karakas
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - David-Manuel Leistner
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Philipp Jakob
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
| | - Shinichi Nakagawa
- RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama, Japan
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita 12-jo Nishi 6-chome, Kita-ku, Sapporo, Japan
| | - Stefan Blankenberg
- Clinic for General and Interventional Cardiology, University Heart Center Hamburg, Martinistrasse 52, Hamburg, Germany
- DZHK, Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Stefan Engelhardt
- Institute for Pharmacology and Toxikology, Technische Universität München, Biedersteiner Strasse 29, München, Germany
- DZHK, Site Munich, Munich, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Hannover, Germany
| | - Christian Weber
- DZHK, Site Munich, Munich, Germany
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität, Pettenkoferstrasse 8a/9, Munich, Germany
| | - Benjamin Meder
- Institute for Cardiomyopathies Heidelberg (ICH), Universitätsklinikum Heidelberg, Im Neuenheimer Feld 669, Heidelberg, Germany
- DZHK, Site Heidelberg/Mannheim, Heidelberg, Germany
| | - Roger Hajjar
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ulf Landmesser
- Department of Cardiology, CBF, CC11, Charite Universitätsmedizin Berlin, Campus Benjamin Franklin, Charite Centrum 11 (Cardiovascular Medicine), Hindenburgdamm 20, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, Berlin, Germany
- Berlin Institute of Health, Kapelle-Ufer 2, Berlin, Germany
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45
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Wang C, Jing Q. Non-coding RNAs as biomarkers for acute myocardial infarction. Acta Pharmacol Sin 2018; 39:1110-1119. [PMID: 29698386 DOI: 10.1038/aps.2017.205] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 12/25/2017] [Indexed: 12/13/2022] Open
Abstract
Acute myocardial infarction (AMI) is a main threat to human lives worldwide. Early and accurate diagnoses warrant immediate medical care, which would reduce mortality and improve prognoses. Circulating non-coding RNAs have been demonstrated to serve as competent biomarkers for various diseases. Following the identification of cardiac-specific microRNA miR-208a in circulation, more non-coding RNAs (miR-1, miR-499 and miR-133) have been identified as biomarkers not only for the diagnosis of AMI but also for prognosis post infarction. Here, we summarized recent findings on non-coding RNAs as biomarkers for early diagnosis of ST-segment elevation myocardial infarction and for disease monitoring of myocardial infarction. In addition, the prognostic potential of non-coding RNAs in patients treated with percutaneous coronary intervention was also described. We also include studies based on biobanks, and build a miRNA release spectrum after AMI, which provides quantitative and time-lapse monitoring of AMI progress. With this spectrum, we are able to customize personal medical care, which prevents further damage. By constructing a network of circulating non-coding RNAs with high specificity and sensitivity, detailed diagnostic information was provided for personalized medicine. Unveiling the roles and kinetics of circulating non-coding RNAs may lead to a revolution in clinical diagnosis.
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46
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Buschmann D, Kirchner B, Hermann S, Märte M, Wurmser C, Brandes F, Kotschote S, Bonin M, Steinlein OK, Pfaffl MW, Schelling G, Reithmair M. Evaluation of serum extracellular vesicle isolation methods for profiling miRNAs by next-generation sequencing. J Extracell Vesicles 2018; 7:1481321. [PMID: 29887978 PMCID: PMC5990937 DOI: 10.1080/20013078.2018.1481321] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/18/2018] [Indexed: 01/08/2023] Open
Abstract
Extracellular vesicles (EVs) are intercellular communicators with key functions in physiological and pathological processes and have recently garnered interest because of their diagnostic and therapeutic potential. The past decade has brought about the development and commercialization of a wide array of methods to isolate EVs from serum. Which subpopulations of EVs are captured strongly depends on the isolation method, which in turn determines how suitable resulting samples are for various downstream applications. To help clinicians and scientists choose the most appropriate approach for their experiments, isolation methods need to be comparatively characterized. Few attempts have been made to comprehensively analyse vesicular microRNAs (miRNAs) in patient biofluids for biomarker studies. To address this discrepancy, we set out to benchmark the performance of several isolation principles for serum EVs in healthy individuals and critically ill patients. Here, we compared five different methods of EV isolation in combination with two RNA extraction methods regarding their suitability for biomarker discovery-focused miRNA sequencing as well as biological characteristics of captured vesicles. Our findings reveal striking method-specific differences in both the properties of isolated vesicles and the ability of associated miRNAs to serve in biomarker research. While isolation by precipitation and membrane affinity was highly suitable for miRNA-based biomarker discovery, methods based on size-exclusion chromatography failed to separate patients from healthy volunteers. Isolated vesicles differed in size, quantity, purity and composition, indicating that each method captured distinctive populations of EVs as well as additional contaminants. Even though the focus of this work was on transcriptomic profiling of EV-miRNAs, our insights also apply to additional areas of research. We provide guidance for navigating the multitude of EV isolation methods available today and help researchers and clinicians make an informed choice about which strategy to use for experiments involving critically ill patients.
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Affiliation(s)
- Dominik Buschmann
- Institute of Human Genetics, University Hospital, LMU Munich, Munich, Germany.,Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Benedikt Kirchner
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.,Dr. von Hauner Children's Hospital, LMU Munich, Munich, Germany
| | - Stefanie Hermann
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Melanie Märte
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany
| | - Christine Wurmser
- Chair of Animal Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany
| | | | | | - Ortrud K Steinlein
- Institute of Human Genetics, University Hospital, LMU Munich, Munich, Germany
| | - Michael W Pfaffl
- Division of Animal Physiology and Immunology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, LMU Munich, Munich, Germany
| | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, LMU Munich, Munich, Germany
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47
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Danielson KM, Shah R, Yeri A, Liu X, Camacho Garcia F, Silverman M, Tanriverdi K, Das A, Xiao C, Jerosch-Herold M, Heydari B, Abbasi S, Van Keuren-Jensen K, Freedman JE, Wang YE, Rosenzweig A, Kwong RY, Das S. Plasma Circulating Extracellular RNAs in Left Ventricular Remodeling Post-Myocardial Infarction. EBioMedicine 2018; 32:172-181. [PMID: 29779700 PMCID: PMC6020713 DOI: 10.1016/j.ebiom.2018.05.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 05/07/2018] [Accepted: 05/08/2018] [Indexed: 01/08/2023] Open
Abstract
Despite substantial declines in mortality following myocardial infarction (MI), subsequent left ventricular remodeling (LVRm) remains a significant long-term complication. Extracellular small non-coding RNAs (exRNAs) have been associated with cardiac inflammation and fibrosis and we hypothesized that they are associated with post-MI LVRm phenotypes. RNA sequencing of exRNAs was performed on plasma samples from patients with "beneficial" (decrease LVESVI ≥ 20%, n = 11) and "adverse" (increase LVESVI ≥ 15%, n = 11) LVRm. Selected differentially expressed exRNAs were validated by RT-qPCR (n = 331) and analyzed for their association with LVRm determined by cardiac MRI. Principal components of exRNAs were associated with LVRm phenotypes post-MI; specifically, LV mass, LV ejection fraction, LV end systolic volume index, and fibrosis. We then investigated the temporal regulation and cellular origin of exRNAs in murine and cell models and found that: 1) plasma and tissue miRNA expression was temporally regulated; 2) the majority of the miRNAs were increased acutely in tissue and at sub-acute or chronic time-points in plasma; 3) miRNA expression was cell-specific; and 4) cardiomyocytes release a subset of the identified miRNAs packaged in exosomes into culture media in response to hypoxia/reoxygenation. In conclusion, we find that plasma exRNAs are temporally regulated and are associated with measures of post-MI LVRm.
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Affiliation(s)
- Kirsty M Danielson
- Cardiology Division and Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Department of Surgery & Anaesthesia, University of Otago, Wellington 6242, New Zealand
| | - Ravi Shah
- Cardiology Division and Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ashish Yeri
- Cardiology Division and Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Xiaojun Liu
- Cardiology Division and Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Fernando Camacho Garcia
- Cardiology Division and Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Michael Silverman
- Cardiology Division and Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Kahraman Tanriverdi
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Avash Das
- Cardiology Division and Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Chunyang Xiao
- Cardiology Division and Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Michael Jerosch-Herold
- Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bobak Heydari
- Division of Cardiology, Department of Cardiac Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Siddique Abbasi
- Noninvasive Cardiovascular Imaging Section, Cardiovascular Division, Department of Medicine and Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Jane E Freedman
- Division of Cardiovascular Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Yaoyu E Wang
- Dana Farber Cancer Institute Center for Computational Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony Rosenzweig
- Cardiology Division and Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Raymond Y Kwong
- Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Saumya Das
- Cardiology Division and Corrigan Minehan Heart Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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48
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Xue VW, Ng SSM, Leung WW, Ma BBY, Cho WCS, Au TCC, Yu ACS, Tsang HFA, Wong SCC. The Effect of Centrifugal Force in Quantification of Colorectal Cancer-Related mRNA in Plasma Using Targeted Sequencing. Front Genet 2018; 9:165. [PMID: 29868115 PMCID: PMC5963087 DOI: 10.3389/fgene.2018.00165] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 04/26/2018] [Indexed: 12/24/2022] Open
Abstract
In our previous study, we detected the effects of centrifugal forces on plasma RNA quantification by quantitative reverse transcription PCR. The aims of this study were to perform targeted mRNA sequencing and data analysis in healthy donors' plasma prepared by two centrifugation protocols and to investigate the effects of centrifugal forces on plasma mRNA quality and quantity. Targeted mRNA sequencing was performed using a custom panel with 108 colorectal cancer-related genes in 18 healthy donors' plasma that prepared by (1) 3,500 g for 10 min at 4°C and (2) 1,600 g for 10 min at 4°C followed by 16,000 g for 10 min at 4°C. Results showed that plasma ribosomal RNA was detected in 16/18 (88.9%) 3,500 g and 6/18 (33.3%) 1,600 g followed by 16,000 g centrifuged plasma. For targeted sequencing, 75/108 (69.4%) and 86/108 (79.6%) genes were detected in 3,500 and 1,600 g followed by 16,000 g, respectively, while 16/108 (14.8%) genes were not detected in both centrifugations. Detailed analysis showed that 2 of 108 (1.85%) genes showed lower expressions in 3,500 g than in 1,600 g followed by 16,000 g. The median expressions of genes in 3,500 g were positively correlated with the expressions in 1,600 g followed by 16,000 g (R2 = 0.9471, P < 0.0001, Spearman rank correlation). Meanwhile, plasma samples were not distinctively clustered based on centrifugal forces according to hierarchical clustering. Targeted mRNA sequencing and subsequent data analysis were performed in this study to investigate the effects of two different centrifugal forces that are commonly used in plasma collection. Our targeted sequencing results help to understand the centrifugal force effects on plasma mRNA, and these findings show that the centrifugation protocol for plasma mRNA research using targeted sequencing can be standardized which facilitates multicenter studies for comparison and quality assurance in the future.
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Affiliation(s)
- Vivian Weiwen Xue
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Simon Siu Man Ng
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Wing Wa Leung
- Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Brigette Buig Yue Ma
- State Key Laboratory in Oncology in South China, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | | | - Thomas Chi Chuen Au
- State Key Laboratory in Oncology in South China, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Allen Chi Shing Yu
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Hin Fung Andy Tsang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Sze Chuen Cesar Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Kowloon, Hong Kong
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49
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Zaporozhchenko IA, Ponomaryova AA, Rykova EY, Laktionov PP. The potential of circulating cell-free RNA as a cancer biomarker: challenges and opportunities. Expert Rev Mol Diagn 2018; 18:133-145. [DOI: 10.1080/14737159.2018.1425143] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Ivan A. Zaporozhchenko
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia
- Laboratory of Biomedical Technologies, Centre of New Surgical Technologies, E.N. Meshalkin Siberian Federal Biomedical Research Center, Novosibirsk, Russia
| | - Anastasia A. Ponomaryova
- Laboratory of Immunology, Tomsk Cancer Research Institute of SB RAMS, Tomsk, Russia
- Department of Applied Physics, National Research Tomsk Polytechnic University, Tomsk, Russia
| | - Elena Yu Rykova
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia
- Laboratory of Biomedical Technologies, Centre of New Surgical Technologies, E.N. Meshalkin Siberian Federal Biomedical Research Center, Novosibirsk, Russia
| | - Pavel P. Laktionov
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia
- Laboratory of Biomedical Technologies, Centre of New Surgical Technologies, E.N. Meshalkin Siberian Federal Biomedical Research Center, Novosibirsk, Russia
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50
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Umu SU, Langseth H, Bucher-Johannessen C, Fromm B, Keller A, Meese E, Lauritzen M, Leithaug M, Lyle R, Rounge TB. A comprehensive profile of circulating RNAs in human serum. RNA Biol 2017; 15:242-250. [PMID: 29219730 PMCID: PMC5798962 DOI: 10.1080/15476286.2017.1403003] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Non-coding RNA (ncRNA) molecules have fundamental roles in cells and many are also stable in body fluids as extracellular RNAs. In this study, we used RNA sequencing (RNA-seq) to investigate the profile of small non-coding RNA (sncRNA) in human serum. We analyzed 10 billion Illumina reads from 477 serum samples, included in the Norwegian population-based Janus Serum Bank (JSB). We found that the core serum RNA repertoire includes 258 micro RNAs (miRNA), 441 piwi-interacting RNAs (piRNA), 411 transfer RNAs (tRNA), 24 small nucleolar RNAs (snoRNA), 125 small nuclear RNAs (snRNA) and 123 miscellaneous RNAs (misc-RNA). We also investigated biological and technical variation in expression, and the results suggest that many RNA molecules identified in serum contain signs of biological variation. They are therefore unlikely to be random degradation by-products. In addition, the presence of specific fragments of tRNA, snoRNA, Vault RNA and Y_RNA indicates protection from degradation. Our results suggest that many circulating RNAs in serum can be potential biomarkers.
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Affiliation(s)
- Sinan Uğur Umu
- a Department of Research , Cancer Registry of Norway , Oslo , Norway
| | - Hilde Langseth
- a Department of Research , Cancer Registry of Norway , Oslo , Norway
| | | | - Bastian Fromm
- b Department of Tumor Biology , Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital , Nydalen, Oslo , Norway
| | - Andreas Keller
- c Department of Clinical Bioinformatics , Saarland University , Saarbruecken , Germany
| | - Eckart Meese
- d Department of Human Genetics , Saarland University , Homburg/Saar , Germany
| | | | - Magnus Leithaug
- e Department of Medical Genetics , Oslo University Hospital and University of Oslo , Oslo , Norway
| | - Robert Lyle
- e Department of Medical Genetics , Oslo University Hospital and University of Oslo , Oslo , Norway.,f PharmaTox Strategic Research Initiative, School of Pharmacy, Faculty of Mathematics and Natural Sciences , University of Oslo , Oslo , Norway
| | - Trine B Rounge
- a Department of Research , Cancer Registry of Norway , Oslo , Norway
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