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Diamantopoulos MA, Adamopoulos PG, Scorilas A. Small non-coding RNAs as diagnostic, prognostic and predictive biomarkers of gynecological cancers: an update. Expert Rev Mol Diagn 2024:1-17. [PMID: 39390687 DOI: 10.1080/14737159.2024.2408740] [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: 05/07/2024] [Accepted: 09/22/2024] [Indexed: 10/12/2024]
Abstract
INTRODUCTION Non-coding RNAs (ncRNAs) comprise a heterogeneous cluster of RNA molecules. Emerging evidence suggests their involvement in various aspects of tumorigenesis, particularly in gynecological malignancies. Notably, ncRNAs have been implicated as mediators within tumor signaling pathways, exerting their influence through interactions with RNA or proteins. These findings further highlight the hypothesis that ncRNAs constitute therapeutic targets and point out their clinical potential as stratification biomarkers. AREAS COVERED The review outlines the use of small ncRNAs, including miRNAs, tRNA-derived small RNAs, PIWI-interacting RNAs and circular RNAs, for diagnostic, prognostic, and predictive purposes in gynecological cancers. It aims to increase our knowledge of their functions in tumor biology and their translation into clinical practice. EXPERT OPINION By leveraging interdisciplinary collaborations, scientists can decipher the riddle of small ncRNA biomarkers as diagnostic, prognostic and predictive biomarkers of gynecological tumors. Integrating small ncRNA-based assays into clinical practice will allow clinicians to provide cure plans for each patient, reducing the likelihood of adverse responses. Nevertheless, addressing challenges such as standardizing experimental methodologies and refining diagnostic assays is imperative for advancing small ncRNA research in gynecological cancer.
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Affiliation(s)
- Marios A Diamantopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
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Li S, Kouznetsova VL, Kesari S, Tsigelny IF. piRNA in Machine-Learning-Based Diagnostics of Colorectal Cancer. Molecules 2024; 29:4311. [PMID: 39339306 PMCID: PMC11434383 DOI: 10.3390/molecules29184311] [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: 08/29/2024] [Accepted: 09/06/2024] [Indexed: 09/30/2024] Open
Abstract
Objective biomarkers are crucial for early diagnosis to promote treatment and raise survival rates for diseases. With the smallest non-coding RNAs-piwi-RNAs (piRNAs)-and their transcripts, we sought to identify if these piRNAs could be used as biomarkers for colorectal cancer (CRC). Using previously published data from serum samples of patients with CRC, 13 differently expressed piRNAs were selected as potential biomarkers. With this data, we developed a machine learning (ML) algorithm and created 1020 different piRNA sequence descriptors. With the Naïve Bayes Multinomial classifier, we were able to isolate the 27 most influential sequence descriptors and achieve an accuracy of 96.4%. To test the validity of our model, we used data from piRBase with known associations with CRC that we did not use to train the ML model. We were able to achieve an accuracy of 85.7% with these new independent data. To further validate our model, we also tested data from unrelated diseases, including piRNAs with a correlation to breast cancer and no proven correlation to CRC. The model scored 44.4% on these piRNAs, showing that it can identify a difference between biomarkers of CRC and biomarkers of other diseases. The final results show that our model is an effective tool for diagnosing colorectal cancer. We believe that in the future, this model will prove useful for colorectal cancer and other diseases diagnostics.
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Affiliation(s)
- Sienna Li
- CureScience Institute, San Diego, CA 92121, USA; (S.L.); (V.L.K.)
| | - Valentina L. Kouznetsova
- CureScience Institute, San Diego, CA 92121, USA; (S.L.); (V.L.K.)
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Santosh Kesari
- Pacific Neuroscience Institute, Santa Monica, CA 90404, USA;
| | - Igor F. Tsigelny
- CureScience Institute, San Diego, CA 92121, USA; (S.L.); (V.L.K.)
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
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Li B, Wang K, Cheng W, Fang B, Li YH, Yang SM, Zhang MH, Wang YH, Wang K. Recent advances of PIWI-interacting RNA in cardiovascular diseases. Clin Transl Med 2024; 14:e1770. [PMID: 39083321 PMCID: PMC11290350 DOI: 10.1002/ctm2.1770] [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: 02/04/2024] [Revised: 06/25/2024] [Accepted: 07/08/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND The relationship between noncoding RNAs (ncRNAs) and human diseases has been a hot topic of research, but the study of ncRNAs in cardiovascular diseases (CVDs) is still in its infancy. PIWI-interacting RNA (piRNA), a small ncRNA that binds to the PIWI protein to maintain genome stability by silencing transposons, was widely studied in germ lines and stem cells. In recent years, piRNA has been shown to be involved in key events of multiple CVDs through various epigenetic modifications, revealing the potential value of piRNA as a new biomarker or therapeutic target. CONCLUSION This review explores origin, degradation, function, mechanism and important role of piRNA in CVDs, and the promising therapeutic targets of piRNA were summarized. This review provide a new strategy for the treatment of CVDs and lay a theoretical foundation for future research. KEY POINTS piRNA can be used as a potential therapeutic target and biomaker in CVDs. piRNA influences apoptosis, inflammation and angiogenesis by regulating epigenetic modificaions. Critical knowledge gaps remain in the unifying piRNA nomenclature and PIWI-independent function.
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Affiliation(s)
- Bo Li
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of ChinaShandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao UniversityJinanShandongChina
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Kai Wang
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Wei Cheng
- Department of Cardiovascular SurgeryBeijing Children's Hospital, Capital Medical UniversityNational Center for Children's HealthBeijingChina
| | - Bo Fang
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Ying Hui Li
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
| | - Su Min Yang
- Department of Cardiovascular SurgeryThe Affiliated Hospital of Qingdao UniversityQingdaoShandongChina
| | - Mei Hua Zhang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of ChinaShandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao UniversityJinanShandongChina
| | - Yun Hong Wang
- Hypertension CenterBeijing Anzhen HospitalCapital Medical UniversityBeijingChina
| | - Kun Wang
- Key Laboratory of Maternal & Fetal Medicine of National Health Commission of ChinaShandong Provincial Maternal and Child Health Care Hospital affiliated to Qingdao UniversityJinanShandongChina
- Institute for Translational MedicineThe Affiliated Hospital of Qingdao University, College of Medicine, Qingdao UniversityQingdaoShandongChina
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Ahmadi Asouri S, Aghadavood E, Mirzaei H, Abaspour A, Esmaeil Shahaboddin M. PIWI-interacting RNAs (PiRNAs) as emerging biomarkers and therapeutic targets in biliary tract cancers: A comprehensive review. Heliyon 2024; 10:e33767. [PMID: 39040379 PMCID: PMC11261894 DOI: 10.1016/j.heliyon.2024.e33767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 06/09/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024] Open
Abstract
Cancers affecting the biliary tract, such as gallbladder cancer and cholangiocarcinoma, make up a small percentage of adult gastrointestinal malignancies, but their incidence is on the rise. Due to the lack of dependable molecular biomarkers for diagnosis and prognosis, these cancers are often not detected until later stages and have limited treatment options. Piwi-interacting RNAs (piRNAs) are a type of small noncoding RNA that interacts with Piwi proteins and has been linked to various diseases, especially cancer. Manipulation of piRNA expression has the potential to serve as an important biomarker and target for therapy. This review uncovers the relationship between PIWI-interacting RNA (piRNA) and a variety of gastrointestinal cancers, including biliary tract cancer (BTC). It is evident that piRNAs have the ability to impact gene expression and regulate key genes and pathways related to the advancement of digestive cancers. Abnormal expression of piRNAs plays a significant role in the development and progression of digestive-related malignancies. The potential of piRNAs as potential biomarkers for diagnosis and prognosis, as well as therapeutic targets in BTC, is noteworthy. Nevertheless, there are obstacles and limitations that require further exploration to fully comprehend piRNAs' role in BTC and to devise effective diagnostic and therapeutic approaches using piRNAs. In summary, this review underscores the value of piRNAs as valuable biomarkers and promising targets for treating BTC, as we delve into the association between piRNAs and various gastrointestinal cancers, including BTC, and how piRNAs can impact gene expression and control essential pathways for digestive cancer advancement. The present research consists of a thorough evaluation presented in a storytelling style. The databases utilized to locate original sources were PubMed, MEDLINE, and Google Scholar, and the search was conducted using the designated keywords.
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Affiliation(s)
- Sahar Ahmadi Asouri
- Department of Clinical Biochemistry, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Esmat Aghadavood
- Department of Clinical Biochemistry, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamed Mirzaei
- Institute for Basic Sciences, Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Alireza Abaspour
- Department of Pathobiology and Laboratory Sciences, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mohammad Esmaeil Shahaboddin
- Department of Clinical Biochemistry, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Institute for Basic Sciences, Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
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Ma Y, Hou B, Zong J, Liu S. Potential molecular mechanisms and clinical implications of piRNAs in preeclampsia: a review. Reprod Biol Endocrinol 2024; 22:73. [PMID: 38915084 PMCID: PMC11194991 DOI: 10.1186/s12958-024-01247-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
Preeclampsia is a multisystem progressive condition and is one of the most serious complications of pregnancy. Owing to its unclear pathogenesis, there are no precise and effective therapeutic targets for preeclampsia, and the only available treatment strategy is to terminate the pregnancy and eliminate the clinical symptoms. In recent years, non-coding RNAs have become a hotspot in preeclampsia research and have shown promise as effective biomarkers for the early diagnosis of preeclampsia over conventional biochemical markers. PIWI-interacting RNAs, novel small non-coding RNA that interact with PIWI proteins, are involved in the pathogenesis of various diseases at the transcriptional or post-transcriptional level. However, the mechanisms underlying the role of PIWI-interacting RNAs in the pathogenesis of preeclampsia remain unclear. In this review, we discuss the findings of existing studies on PIWI-interacting RNA biogenesis, functions, and their possible roles in preeclampsia, providing novel insights into the potential application of PIWI-interacting RNAs in the early diagnosis and clinical treatment of preeclampsia.
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Affiliation(s)
- Yuanxuan Ma
- Prenatal Diagnosis Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266003, Shandong, China
- Department of Medical Genetics, the Affiliated Hospital of Qingdao University, Qingdao , Shandong, 266003, China
| | - Bo Hou
- Department of Cardiology, the Affiliated Hospital of Qingdao University, Qingdao , Shandong, 266003, China
| | - Jinbao Zong
- Department of Laboratory, Qingdao Hiser Hospital Affliated of Qingdao University (Oingdao Traditional Chinese Medicine Hospital), 4 Renmin Road, Qingdao, 266033, China.
| | - Shiguo Liu
- Prenatal Diagnosis Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266003, Shandong, China.
- Department of Medical Genetics, the Affiliated Hospital of Qingdao University, Qingdao , Shandong, 266003, China.
- Medical Genetic Department, the Affiliated Hospital of Qingdao University, 16 Jiangsu Road, Qingdao, 266003, China.
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Magowan D, Abdulshafea M, Thompson D, Rajamoorthy SI, Owen R, Harris D, Prosser S. Blood-based biomarkers and novel technologies for the diagnosis of colorectal cancer and adenomas: a narrative review. Biomark Med 2024; 18:493-506. [PMID: 38900496 DOI: 10.1080/17520363.2024.2345583] [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: 01/01/2024] [Accepted: 03/12/2024] [Indexed: 06/21/2024] Open
Abstract
Aim: Blood-based biomarkers have shown promise for diagnosing colorectal cancer (CRC) and adenomas (CRA). This review summarizes recent studies in this area. Methods: A literature search was undertaken for 01/01/2017-01/03/2023. Criteria included CRC, CRA, liquid-biopsy, blood-based tests and diagnosis. Results: 12,378 studies were reduced to 178 for data extraction. Sixty focused on proteomics, 53 on RNA species, 30 on cfDNA methylation, seven on antigens and autoantibodies and 28 on novel techniques. 169 case control and nine cohort studies. Number of participants ranged 100-54,297, mean age 58.26. CRC sensitivity and specificity ranged 9.10-100% and 20.40-100%, respectively. CRA sensitivity and specificity ranged 8.00-95.70% and 4.00-97.00%, respectively. Conclusion: Sensitive and specific blood-based tests exist for CRC and CRA. However, studies demonstrate heterogenous techniques and reporting quality. Further work should concentrate on validation and meta-analyzes.
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Affiliation(s)
- Drew Magowan
- Swansea University, Singleton Park, SA2 8PP, Swansea, UK
- Swansea Bay University Health Board, Department of General Surgery, Morriston Hospital, SA6 6NL, Swansea, UK
| | - Mansour Abdulshafea
- Swansea Bay University Health Board, Department of General Surgery, Morriston Hospital, SA6 6NL, Swansea, UK
| | - Dominic Thompson
- Swansea Bay University Health Board, Department of General Surgery, Morriston Hospital, SA6 6NL, Swansea, UK
| | - Shri-Ishvarya Rajamoorthy
- Swansea Bay University Health Board, Department of General Surgery, Morriston Hospital, SA6 6NL, Swansea, UK
| | - Rhiannon Owen
- Swansea University, Singleton Park, SA2 8PP, Swansea, UK
| | - Dean Harris
- Swansea University, Singleton Park, SA2 8PP, Swansea, UK
- Swansea Bay University Health Board, Department of General Surgery, Morriston Hospital, SA6 6NL, Swansea, UK
| | - Susan Prosser
- Swansea Bay University Health Board, Department of General Surgery, Morriston Hospital, SA6 6NL, Swansea, UK
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Lei Q, Du C, Ma Y, Shou Y, Chen L, Feng C, Zheng Y, Yu D, Jin Y. Identifying piRNAs that regulate BaP-induced lung injuries: A bottom-up approach from toxicity pathway investigation to animal validation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 277:116330. [PMID: 38636406 DOI: 10.1016/j.ecoenv.2024.116330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/18/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024]
Abstract
PIWI-interacting RNAs (piRNAs) is an emerging class of small non-coding RNAs that has been recently reported to have functions in infertility, tumorigenesis, and multiple diseases in humans. Previously, 5 toxicity pathways were proposed from hundreds of toxicological studies that underlie BaP-induced lung injuries, and a "Bottom-up" approach was established to identify small non-coding RNAs that drive BaP-induced pulmonary effects by investigating the activation of these pathways in vitro, and the expression of the candidate microRNAs were validated in tissues of patients with lung diseases from publications. Here in this study, we employed the "Bottom-up" approach to identifying the roles of piRNAs and further validated the mechanisms in vivo using mouse acute lung injury model. Specifically, by non-coding RNA profiling in in vitro BaP exposure, a total of 3 suppressed piRNAs that regulate 5 toxicity pathways were proposed, including piR-004153 targeting CYP1A1, FGFR1, ITGA5, IL6R, NGRF, and SDHA, piR-020326 targeting CDK6, and piR-020388 targeting RASD1. Animal experiments demonstrated that tail vein injection of respective formulated agomir-piRNAs prior to BaP exposure could all alleviate acute lung injury that was shown by histopathological and biochemical evidences. Immunohistochemical evaluation focusing on NF-kB and Bcl-2 levels showed that exogenous piRNAs protect against BaP-induced inflammation and apoptosis, which further support that the inhibition of the 3 piRNAs had an important impact on BaP-induced lung injuries. This mechanism-driven, endpoint-supported result once again confirmed the plausibility and efficiency of the approach integrating in silico, in vitro, and in vivo evidences for the purpose of identifying key molecules.
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Affiliation(s)
- Qinkai Lei
- School of Public Health, Qingdao University, Qingdao, China
| | - Chenlong Du
- School of Public Health, Qingdao University, Qingdao, China
| | - Yumei Ma
- School of Public Health, Qingdao University, Qingdao, China
| | - Yingqing Shou
- School of Public Health, Qingdao University, Qingdao, China
| | - Li Chen
- School of Public Health, Qingdao University, Qingdao, China
| | - Chiyuan Feng
- School of Public Health, Qingdao University, Qingdao, China
| | - Yuxin Zheng
- School of Public Health, Qingdao University, Qingdao, China
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, China
| | - Yuan Jin
- School of Public Health, Qingdao University, Qingdao, China.
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Taghizadeh M, Jafari-Koshki T, Jafarlou V, Raeisi M, Alizadeh L, Roosta Y, Matin S, Jabari R, Sur D, Karimi A. The role of piRNAs in predicting and prognosing in cancer: a focus on piRNA-823 (a systematic review and meta-analysis). BMC Cancer 2024; 24:484. [PMID: 38627675 PMCID: PMC11022431 DOI: 10.1186/s12885-024-12180-2] [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: 11/09/2023] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
INTRODUCTION This article examines the potential of using liquid biopsy with piRNAs to study cancer survival outcomes. While previous studies have explored the relationship between piRNA expression and cancer patient outcomes, a comprehensive investigation is still lacking. To address this gap, we conducted a systematic review and meta-analysis of existing literature. METHODS We searched major online databases up to February 2024 to identify articles reporting on the role of piRNA in cancer patient survival outcomes. Our meta-analysis used a random-effects model to pool hazard ratios with 95% confidence intervals (CI) and assess the prognostic value of deregulated piRNA-823. For survival analysis, the Kaplan-Meier method and COX analysis were used. RESULTS Out of 6104 articles screened, 20 met our inclusion criteria. Our analysis revealed that dysregulated piRNA expression is associated with cancer patient survival outcomes. Specifically, our meta-analysis found that overexpression of piR-823 is significantly linked with poorer overall survival in patients with colorectal cancer and renal cell cancer (HR: 3.82, 95% CI = [1.81, 8.04], I2 = 70%). CONCLUSION Our findings suggest that various piRNAs may play a role in cancer survival outcomes and that piRNA-823 in particular holds promise as a prognostic biomarker for multiple human cancers. IMPLICATIONS FOR CANCER SURVIVORS Our systematic review and meta-analysis of piRNA-823 has important implications for cancer survivors. Our findings suggest that piRNA-823 can be used as a prognostic biomarker for predicting cancer recurrence and survival rates. This information can help clinicians develop personalized treatment plans for cancer survivors, which can improve their quality of life and reduce the risk of recurrence.
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Affiliation(s)
- Mohammad Taghizadeh
- Department of Molecular Medicine, Faculty of Advanced Medical School, Tabriz University of Medical Sciences, Tabriz, 5166614756, Iran
| | - Tohid Jafari-Koshki
- Department of Statistics and Epidemiology, Faculty of Health, Tabriz University of Medical Sciences, Tabriz, 5166616471, Iran
| | - Vahid Jafarlou
- Cancer Institute of Imam Khomeini Hospital, Tehran University of Medical Science, Tehran, 1419733141, Iran
| | - Mortaza Raeisi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, 5166616471, Iran
| | - Leila Alizadeh
- Gastroenterology and Liver Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 5166616471, Iran
| | - Yousef Roosta
- Department of Internal Medicine, School of Medicine, Urmia University of Medical Sciences, Urmia, 5714783734, Iran
- Solid Tumor Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, 5714783734, Iran
- Hematology, Immune Cell Therapy, and Stem Cells Transplantation Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, 5714783734, Iran
| | - Somaieh Matin
- Department of Internal Medicine, School of Medicine, Ardabil University of Medical Sciences, Ardabil, 8599156189, Iran
| | - Rahele Jabari
- Department of Nutrition Science, Faculty of Medical Science, Urmia University of Medical Science, Urmia, 5714783734, Iran
| | - Daniel Sur
- Department of Oncology, The Oncology Institute "Prof. Dr. Ion Chiricu¸tă", Cluj-Napoca, 400015, Romania.
- Department of Medical Oncology, The Oncology Institute "Prof. Dr. Ion Chiricu ̧t ̆a", 400015 Str. Republicii 34-36, Cluj-Napoca, 400006, Romania.
| | - Abbas Karimi
- Department of Molecular Medicine, Faculty of Advanced Medical School, Tabriz University of Medical Sciences, Tabriz, 5166614756, Iran.
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Golgasht St., Tabriz, East Azerbaijan, 5166614756, Iran.
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Garcia-Borja E, Siegl F, Mateu R, Slaby O, Sedo A, Busek P, Sana J. Critical appraisal of the piRNA-PIWI axis in cancer and cancer stem cells. Biomark Res 2024; 12:15. [PMID: 38303021 PMCID: PMC10836005 DOI: 10.1186/s40364-024-00563-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Small noncoding RNAs play an important role in various disease states, including cancer. PIWI proteins, a subfamily of Argonaute proteins, and PIWI-interacting RNAs (piRNAs) were originally described as germline-specific molecules that inhibit the deleterious activity of transposable elements. However, several studies have suggested a role for the piRNA-PIWI axis in somatic cells, including somatic stem cells. Dysregulated expression of piRNAs and PIWI proteins in human tumors implies that, analogously to their roles in undifferentiated cells under physiological conditions, these molecules may be important for cancer stem cells and thus contribute to cancer progression. We provide an overview of piRNA biogenesis and critically review the evidence for the role of piRNA-PIWI axis in cancer stem cells. In addition, we examine the potential of piRNAs and PIWI proteins to become biomarkers in cancer.
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Affiliation(s)
- Elena Garcia-Borja
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, U Nemocnice 478/5, Prague 2, 128 53, Czech Republic
| | - Frantisek Siegl
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
- Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Rosana Mateu
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, U Nemocnice 478/5, Prague 2, 128 53, Czech Republic
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Aleksi Sedo
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, U Nemocnice 478/5, Prague 2, 128 53, Czech Republic
| | - Petr Busek
- Laboratory of Cancer Cell Biology, Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, U Nemocnice 478/5, Prague 2, 128 53, Czech Republic.
| | - Jiri Sana
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic.
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic.
- Department of Pathology, University Hospital Brno, Brno, Czech Republic.
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Hammad G, Mamdouh S, Seoudi DM, Seleem MI, Safwat G, Mohamed RH. Elevated expression patterns of P-element Induced Wimpy Testis (PIWI) transcripts are potential candidate markers for Hepatocellular Carcinoma. Cancer Biomark 2024; 39:95-111. [PMID: 38043006 PMCID: PMC11002723 DOI: 10.3233/cbm-230134] [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: 05/02/2023] [Accepted: 09/25/2023] [Indexed: 12/04/2023]
Abstract
BACKGROUND P-Element-induced wimpy testis (PIWI) proteins, when in combination with PIWI-interacting RNA (piRNA), are engaged in the epigenetic regulation of gene expression in germline cells. Different types of tumour cells have been found to exhibit abnormal expression of piRNA, PIWIL-mRNAs, and proteins. We aimed to determine the mRNA expression profiles of PIWIL1, PIWIL2, PIWIL3, & PIWIL4, in hepatocellular carcinoma patients, and to associate their expression patterns with clinicopathological features. METHODS The expression patterns of PIWIL1, PIWIL2, PIWIL3, PIWIL4 mRNA, was assessed via real-time quantitative polymerase chain reaction (RT-QPCR), on tissue and serum samples from HCC patients, their impact for diagnosis was evaluated by ROC curves, prognostic utility was determined, and In Silico analysis was conducted for predicted variant detection, association with HCC microRNAs and Network Analysis. RESULTS Expression levels were significantly higher in both HCC tissue and serum samples than in their respective controls (p< 0.001). Additionally, the diagnostic performance was assessed, Risk determination was found to be statistically significant. CONCLUSION PIWIL mRNAs are overexpressed in HCC tissue and serum samples, the expression patterns could be valuable molecular markers for HCC, due to their association with age, tumour grade and pattern. To the best of our knowledge, our study is the first to report the expression levels of all PIWIL mRNA and to suggest their remarkable values as diagnostic and prognostic biomarkers, in addition to their correlation to HCC development. Additionally, a therapeutic opportunity might be also suggested through in silico miRNA prediction for HCC and PIWIL genes through DDX4 and miR-124-3p.
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Affiliation(s)
- Gehan Hammad
- Faculty of Biotechnology, October University for Modern Sciences & Arts (MSA), Giza, Egypt
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Samah Mamdouh
- Department of Biochemistry and Molecular Biology, Theodor Bilharz Research Institute, Cairo, Egypt
| | - Dina Mohamed Seoudi
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Mohamed Ismail Seleem
- Department of Surgery, National Hepatology and Tropical Medicine Research Institute, Cairo, Egypt
| | - Gehan Safwat
- Faculty of Biotechnology, October University for Modern Sciences & Arts (MSA), Giza, Egypt
| | - Rania Hassan Mohamed
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
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Andrabi MQ, Kesavan Y, Ramalingam S. Non-coding RNAs as Biomarkers for Survival in Colorectal Cancer Patients. Curr Aging Sci 2024; 17:5-15. [PMID: 36733201 DOI: 10.2174/1874609816666230202101054] [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: 06/16/2022] [Revised: 11/25/2022] [Accepted: 12/19/2022] [Indexed: 02/04/2023]
Abstract
Colorectal cancer (CRC) has a high incidence and fatality rate worldwide. It ranks second concerning death worldwide. Cancer patients are diagnosed with the disease at a later stage due to the absence of early diagnostic methods, which leads to increased death. With the help of recent advancements in the fields of diagnosis and therapy, the development of novel methods using new targets could be helpful for the long-term survival of CRC patients when CRC is detected early. However, the prognosis for the advanced stage of CRC is abysmal. New biomarkers are emerging as promising alternatives since they can be utilized for early detection of CRC, are simple to use, and non-invasive. Non-coding RNAs (ncRNAs) have been seen to have an aberrant expression in the development of many malignancies, including CRC. In the past two decades, much research has been done on non-coding RNAs, which may be valuable as biomarkers and targets for antitumor therapy. Non-coding RNAs can be employed in detecting and treating CRC. Non-coding RNAs play an essential role in regulating gene expression. This article reviews ncRNAs and their expression levels in CRC patients that could be used as potential biomarkers. Various ncRNAs have been associated with CRC, such as microRNAs, long non-coding RNAs, circular RNAs, etc. The expression of these non-coding RNAs may provide insights into the stages of cancer and the prognosis of cancer patients and therefore proper precautionary measures can be taken to decrease cancer-related deaths.
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Affiliation(s)
- Mohammad Qasim Andrabi
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Yasodha Kesavan
- Department of Biotechnology, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
| | - Satish Ramalingam
- Department of Genetic Engineering, School of Bio-Engineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu, 603203, India
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Mohammadpour S, Noukabadi FN, Esfahani AT, Kazemi F, Esmaeili S, Zafarjafarzadeh N, Sarpash S, Nazemalhosseini-Mojarad E. Non-coding RNAs in Precursor Lesions of Colorectal Cancer: Their Role in Cancer Initiation and Formation. Curr Mol Med 2024; 24:565-575. [PMID: 37226783 DOI: 10.2174/1566524023666230523155719] [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: 09/08/2022] [Revised: 04/01/2023] [Accepted: 04/04/2023] [Indexed: 05/26/2023]
Abstract
Colorectal cancer (CRC) is one of the world's most common types of malignancy. The proliferation of precancerous lesions causes this type of cancer. Two distinct pathways for CRC carcinogenesis have been identified: the conventional adenoma-carcinoma pathway and the serrated neoplasia pathway. Recently, evidence has demonstrated the regulatory roles of noncoding RNAs (ncRNAs) in the initiation and progression of precancerous lesions, especially in the adenoma-carcinoma pathway and serrated neoplasia pathway. By expanding the science of molecular genetics and bioinformatics, several studies have identified dysregulated ncRNAs that function as oncogenes or tumor suppressors in cancer initiation and formation by diverse mechanisms via intracellular signaling pathways known to act on tumor cells. However, many of their roles are still unclear. This review summarizes the functions and mechanisms of ncRNAs (such as long non-coding RNAs, microRNAs, long intergenic non-coding RNAs, small interfering RNAs, and circRNAs) in the initiation and formation of precancerous lesions.
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Affiliation(s)
- Somayeh Mohammadpour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences. Tehran, Iran
| | - Fatemeh Naderi Noukabadi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences. Tehran, Iran
| | - Amir Torshizi Esfahani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences. Tehran, Iran
| | - Fatemeh Kazemi
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Medical Sciences, Islamic Azad University Tehran, Tehran, Iran
| | - Sahar Esmaeili
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Medical Sciences, Islamic Azad University Tehran, Tehran, Iran
| | - Nikta Zafarjafarzadeh
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Medical Sciences, Islamic Azad University Tehran, Tehran, Iran
| | - SeyedKasra Sarpash
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Medical Sciences, Islamic Azad University Tehran, Tehran, Iran
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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13
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Sohn EJ, Han ME, Park YM, Kim YH, Oh SO. The potential of piR-823 as a diagnostic biomarker in oncology: A systematic review. PLoS One 2023; 18:e0294685. [PMID: 38060527 PMCID: PMC10703285 DOI: 10.1371/journal.pone.0294685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Emerging evidence has demonstrated that PIWI-interacting RNAs (piRNAs) play important roles in various physiological processes and contribute to cancer progression. Moreover, piRNAs and PIWI protein levels are associated with the prognosis and chemoresistance of various cancers. The limitations of biomarkers challenge early detection and monitoring of chemoresistance and cancer relapse. METHODS To evaluate the potential of piRNA as a diagnostic biomarker in oncology, we systematically reviewed previous studies on the subject. PubMed, Embase, and Cochrane databases were searched to evaluate the diagnostic relevance of piRNAs in cancer. Eighteen studies (2,352 patients) were included. The quality of each study was evaluated with AMSTAR and QUADAS-2 tool. RESULTS & CONCLUSIONS The area under the curve (AUC) values of 26 piRNAs in patients with cancer ranged from 0.624 to 0.978, with piR-9491 showing the highest value (0.978). The sensitivity of the total of 21 piRNAs in cancer patients was between 42.86 and 100, with piR-9491 showing the highest sensitivity (100). The specificity of these 21 piRNAs ranged from 60.10 to 96.67 (with piR-018569 showing the highest specificity (96.67)). Their odds ratios were between 1.61 and 44.67, and piR-12488 showed the highest odds ratio (44.67). Generally, the piRNAs in this review showed better sensitivity and AUC values than current clinical diagnostic biomarkers, although current biomarkers appear to be more specific. Reviewed piRNAs showed better diagnostic performance than currently used clinical biomarkers. Notably, piR-823 showed a significant diagnostic performance in four types of cancer (colorectal, esophageal, gastric, and renal cell cancer). However, all 18 studies included in this review were a case-control study. So, further prospective studies are required for their validation.
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Affiliation(s)
- Eun Jung Sohn
- Research Center for Molecular Control of Cancer Cell Diversity, Pusan National University, Yangsan, Republic of Korea
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Myoung-Eun Han
- Research Center for Molecular Control of Cancer Cell Diversity, Pusan National University, Yangsan, Republic of Korea
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Young Mok Park
- Department of Surgery, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Yun Hak Kim
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
- Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Sae-Ock Oh
- Research Center for Molecular Control of Cancer Cell Diversity, Pusan National University, Yangsan, Republic of Korea
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea
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Dabi Y, Suisse S, Marie Y, Delbos L, Poilblanc M, Descamps P, Golfier F, Jornea L, Forlani S, Bouteiller D, Touboul C, Puchar A, Bendifallah S, Daraï E. New class of RNA biomarker for endometriosis diagnosis: The potential of salivary piRNA expression. Eur J Obstet Gynecol Reprod Biol 2023; 291:88-95. [PMID: 37857147 DOI: 10.1016/j.ejogrb.2023.10.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023]
Abstract
OBJECTIVES In contrast to miRNA expression, little attention has been given to piwiRNA (piRNA) expression among endometriosis patients. The aim of the present study was to explore the human piRNAome and to investigate a potential piRNA saliva-based diagnostic signature for endometriosis. METHODS Data from the prospective "ENDOmiRNA" study (ClinicalTrials.gov Identifier: NCT04728152) were used. Saliva samples from 200 patients were analyzed in order to evaluate human piRNA expression using the piRNA bank. Next Generation Sequencing (NGS), barcoding of unique molecular identifiers and both Artificial Intelligence (AI) and machine learning (ML) were used. For each piRNA, sensitivity, specificity, and ROC AUC values were calculated for the diagnosis of endometriosis. RESULTS 201 piRNAs were identified, none had an AUC ≥ 0.70, and only three piRNAs (piR-004153, piR001918, piR-020401) had an AUC between ≥ 0.6 and < 0.70. Seven were differentially expressed: piR-004153, piR-001918, piR-020401, piR-012864, piR-017716, piR-020326 and piR-016904. The respective correlation and accuracy to diagnose endometriosis according to the F1-score, sensitivity, specificity, and AUC ranged from 0 to 0.862 %, 0-0.961 %, 0.085-1, and 0.425-0.618. A correlation was observed between the patients' age (≥35 years) and piR-004153 (p = 0.002) and piR-017716 (p = 0.030). Among the 201 piRNAs, four were differentially expressed in patients with and without hormonal treatment: piR-004153 (p = 0.015), piR-020401 (p = 0.001), piR-012864 (p = 0.036) and piR-017716 (p = 0.009). CONCLUSION Our results support the link between piRNAs and endometriosis physiopathology and establish its utility as a potential diagnostic biomarker using saliva samples. Per se, piRNA expression should be analyzed along with the clinical status of a patient.
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Affiliation(s)
- Yohann Dabi
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris, France; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), France.
| | | | - Yannick Marie
- Department of Obstetrics and Reproductive Medicine - CHU d'Angers, France
| | - Léa Delbos
- Department of Obstetrics and Reproductive Medicine - CHU d'Angers, France; Endometriosis Expert Center - Pays de la Loire, France
| | - Mathieu Poilblanc
- Department of Obstetrics and Reproductive Medicine, Lyon South University Hospital, Lyon Civil Hospices, France; Endometriosis Expert Center - Steering Center of the EndAURA Network, France
| | - Philippe Descamps
- Department of Obstetrics and Reproductive Medicine - CHU d'Angers, France; Endometriosis Expert Center - Pays de la Loire, France
| | - Francois Golfier
- Department of Obstetrics and Reproductive Medicine, Lyon South University Hospital, Lyon Civil Hospices, France; Endometriosis Expert Center - Steering Center of the EndAURA Network, France
| | - Ludmila Jornea
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Inserm U1127, CNRS UMR 7225, AP-HP - Hôpital Pitié-Salpêtrière, Paris, France
| | - Sylvie Forlani
- Sorbonne Université, Paris Brain Institute - Institut du Cerveau - ICM, Inserm U1127, CNRS UMR 7225, AP-HP - Hôpital Pitié-Salpêtrière, Paris, France
| | - Delphine Bouteiller
- Gentoyping and Sequencing Core Facility, iGenSeq, Institut du Cerveau et de la Moelle épinière, ICM, Hôpital Pitié-Salpêtrière, 47-83 Boulevard de l'Hôpital, 75013 Paris, France
| | - Cyril Touboul
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris, France; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), France
| | - Anne Puchar
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris, France; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), France
| | - Sofiane Bendifallah
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris, France; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), France
| | - Emile Daraï
- Department of Obstetrics and Reproductive Medicine, Hôpital Tenon, 4 rue de la Chine, 75020 Paris, France; Clinical Research Group (GRC) Paris 6: Centre Expert Endométriose (C3E), Sorbonne University (GRC6 C3E SU), France
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15
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Liu Q, Chen Q, Zhou Z, Tian Z, Zheng X, Wang K. piRNA-18 Inhibition Cell Proliferation, Migration and Invasion in Colorectal Cancer. Biochem Genet 2023; 61:1881-1897. [PMID: 36879083 DOI: 10.1007/s10528-023-10348-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023]
Abstract
Colorectal cancer is one of the most prevalent malignancies worldwide. Evidences indicate that piRNA-18 are closely involved and contributed to tumorigenesis and cancer progression. Therefore, it is very necessary to investigate the effects of piRNA-18 on the proliferation, migration, and invasiveness of colorectal cancer cells, so as to provide theoretical basis for finding new biomarkers and accurate diagnosis and treatment of colorectal cancer. Here, Five pairs of colorectal cancer tissue samples and their corresponding adjacent samples were analyzed by real-time immunofluorescence quantitative PCR and the difference in piRNA-18 expression among colorectal cancer cell lines was further verified. MTT assay were used to study the changes in the proliferation of colorectal cancer cell lines after piRNA-18 overexpression. Wound-healing assay and Transwell assay were used to study the changes in migration and invasion. Flow cytometry were used to study the changes in apoptosis and cycle. SC inoculation of colorectal cancer cell lines into nude mice were used to observe the effect in the proliferation. piRNA-18 was lowlier expressed than adjacent tissues and normal intestinal mucosal epithelial cells in colorectal cancer and colorectal cancer cell line. After overexpression of piRNA-18, cell proliferation and migration as well as invasiveness in SW480 and LOVO cells decreased. The cell lines with piRNA-18 overexpression had obvious G1/S phase arrest in cell cycle, and the weight and volume of subcutaneously transplanted tumors are decreased. Our findings highlighted that piRNA-18 may play an inhibitory role in colorectal cancer.
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Affiliation(s)
- Qi Liu
- Department of Comprehensive Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan Province, People's Republic of China.
- Hunan Emergency Center, No. 90 Pingchuan Road, Changsha, 410000, Hunan, China.
| | - Qian Chen
- Department of Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan Province, People's Republic of China
| | - Zheng Zhou
- Department of Comprehensive Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan Province, People's Republic of China
| | - Zeyu Tian
- Department of Comprehensive Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan Province, People's Republic of China
| | - Ximin Zheng
- Department of Comprehensive Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan Province, People's Republic of China
| | - Kaixuan Wang
- Department of Comprehensive Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410005, Hunan Province, People's Republic of China
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16
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Labbé M, Menoret E, Letourneur F, Saint‐Pierre B, de Beaurepaire L, Veziers J, Dreno B, Denis MG, Blanquart C, Boisgerault N, Fonteneau J, Fradin D. TP53 mutations correlate with the non-coding RNA content of small extracellular vesicles in melanoma. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e105. [PMID: 38939511 PMCID: PMC11080853 DOI: 10.1002/jex2.105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/04/2023] [Accepted: 07/16/2023] [Indexed: 06/29/2024]
Abstract
Non-coding RNAs (ncRNAs) are important regulators of gene expression. They are expressed not only in cells, but also in cell-derived extracellular vesicles (EVs). The mechanisms controlling their loading and sorting remain poorly understood. Here, we investigated the impact of TP53 mutations on the non-coding RNA content of small melanoma EVs. After purification of small EVs from six different patient-derived melanoma cell lines, we characterized them by small RNA sequencing and lncRNA microarray analysis. We found that TP53 mutations are associated with a specific micro and long non-coding RNA content in small EVs. Then, we showed that long and small non-coding RNAs enriched in TP53 mutant small EVs share a common sequence motif, highly similar to the RNA-binding motif of Sam68, a protein interacting with hnRNP proteins. This protein thus may be an interesting partner of p53, involved in the expression and loading of the ncRNAs. To conclude, our data support the existence of cellular mechanisms associate with TP53 mutations which control the ncRNA content of small EVs in melanoma.
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Affiliation(s)
- Maureen Labbé
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, Université d'AngersCRCI2NANantesFrance
| | - Estelle Menoret
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, Université d'AngersCRCI2NANantesFrance
- LabEx IGO “Immunotherapy, Graft, Oncology,”NantesFrance
| | | | | | | | - Joëlle Veziers
- INSERM Unit 1229, Regenerative Medicine and SkeletonNantesFrance
- CHU Nantes, PHU4 OTONNNantesFrance
- SC3M, SFR Santé F. Bonamy, FED 4203, UMS Inserm 016NantesFrance
| | - Brigitte Dreno
- Dermatology DepartmentDirector of the Unit of Cell and Gene Therapy CHU Nantes, CIC 1413, CRCINA, University NantesFrance
| | - Marc G. Denis
- Department of BiochemistryNantes University HospitalNantesFrance
| | - Christophe Blanquart
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, Université d'AngersCRCI2NANantesFrance
| | - Nicolas Boisgerault
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, Université d'AngersCRCI2NANantesFrance
| | | | - Delphine Fradin
- Nantes Université, Inserm UMR 1307, CNRS UMR 6075, Université d'AngersCRCI2NANantesFrance
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Kabzinski J, Kucharska-Lusina A, Majsterek I. RNA-Based Liquid Biopsy in Head and Neck Cancer. Cells 2023; 12:1916. [PMID: 37508579 PMCID: PMC10377854 DOI: 10.3390/cells12141916] [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: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Head and neck cancer (HNC) is a prevalent and diverse group of malignancies with substantial morbidity and mortality rates. Early detection and monitoring of HNC are crucial for improving patient outcomes. Liquid biopsy, a non-invasive diagnostic approach, has emerged as a promising tool for cancer detection and monitoring. In this article, we review the application of RNA-based liquid biopsy in HNC. Various types of RNA, including messenger RNA (mRNA), microRNA (miRNA), long non-coding RNA (lncRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), circular RNA (circRNA) and PIWI-interacting RNA (piRNA), are explored as potential biomarkers in HNC liquid-based diagnostics. The roles of RNAs in HNC diagnosis, metastasis, tumor resistance to radio and chemotherapy, and overall prognosis are discussed. RNA-based liquid biopsy holds great promise for the early detection, prognosis, and personalized treatment of HNC. Further research and validation are necessary to translate these findings into clinical practice and improve patient outcomes.
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Affiliation(s)
- Jacek Kabzinski
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Aleksandra Kucharska-Lusina
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
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18
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Aguilar MA, Ebanks S, Markus H, Lewis MM, Midya V, Vrana K, Huang X, Hall MA, Kawasawa YI. Neuronally enriched microvesicle RNAs are differentially expressed in the serums of Parkinson's patients. Front Neurosci 2023; 17:1145923. [PMID: 37483339 PMCID: PMC10357515 DOI: 10.3389/fnins.2023.1145923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
Background Circulating small RNAs (smRNAs) originate from diverse tissues and organs. Previous studies investigating smRNAs as potential biomarkers for Parkinson's disease (PD) have yielded inconsistent results. We investigated whether smRNA profiles from neuronally-enriched serum exosomes and microvesicles are altered in PD patients and discriminate PD subjects from controls. Methods Demographic, clinical, and serum samples were obtained from 60 PD subjects and 40 age- and sex-matched controls. Exosomes and microvesicles were extracted and isolated using a validated neuronal membrane marker (CD171). Sequencing and bioinformatics analyses were used to identify differentially expressed smRNAs in PD and control samples. SmRNAs also were tested for association with clinical metrics. Logistic regression and random forest classification models evaluated the discriminative value of the smRNAs. Results In serum CD171 enriched exosomes and microvesicles, a panel of 29 smRNAs was expressed differentially between PD and controls (false discovery rate (FDR) < 0.05). Among the smRNAs, 23 were upregulated and 6 were downregulated in PD patients. Pathway analysis revealed links to cellular proliferation regulation and signaling. Least absolute shrinkage and selection operator adjusted for the multicollinearity of these smRNAs and association tests to clinical parameters via linear regression did not yield significant results. Univariate logistic regression models showed that four smRNAs achieved an AUC ≥ 0.74 to discriminate PD subjects from controls. The random forest model had an AUC of 0.942 for the 29 smRNA panel. Conclusion CD171-enriched exosomes and microvesicles contain the differential expression of smRNAs between PD and controls. Future studies are warranted to follow up on the findings and understand the scientific and clinical relevance.
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Affiliation(s)
- Morris A. Aguilar
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Shauna Ebanks
- Department of Neurology, College of Medicine, The Pennsylvania State University, Hershey, PA, United States
| | - Havell Markus
- Department of Neurology, College of Medicine, The Pennsylvania State University, Hershey, PA, United States
| | - Mechelle M. Lewis
- Department of Neurology, College of Medicine, The Pennsylvania State University, Hershey, PA, United States
- Department of Pharmacology, College of Medicine, The Pennsylvania State University, Hershey, PA, United States
| | - Vishal Midya
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Kent Vrana
- Department of Pharmacology, College of Medicine, The Pennsylvania State University, Hershey, PA, United States
| | - Xuemei Huang
- Department of Neurology, College of Medicine, The Pennsylvania State University, Hershey, PA, United States
- Department of Pharmacology, College of Medicine, The Pennsylvania State University, Hershey, PA, United States
| | - Molly A. Hall
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, United States
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Yuka Imamura Kawasawa
- Department of Pharmacology, College of Medicine, The Pennsylvania State University, Hershey, PA, United States
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
- Institute for Personalized Medicine, College of Medicine, The Pennsylvania State University, Hershey, PA, United States
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19
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Limanówka P, Ochman B, Świętochowska E. PiRNA Obtained through Liquid Biopsy as a Possible Cancer Biomarker. Diagnostics (Basel) 2023; 13:diagnostics13111895. [PMID: 37296747 DOI: 10.3390/diagnostics13111895] [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: 04/20/2023] [Revised: 05/21/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023] Open
Abstract
In recent years PIWI-interacting RNAs (piRNAs) have gained the interest of scientists, mainly because of their possible implications in cancer. Many kinds of research showed how their expression can be linked to malignant diseases. However, most of them evaluated the expression of piRNAs in tumor tissues. It was shown how these non-coding RNAs can interfere with many signaling pathways involved in the regulation of proliferation or apoptosis. A comparison of piRNA expression in tumor tissue and adjacent healthy tissues has demonstrated they can be used as biomarkers. However, this way of obtaining samples has a significant drawback, which is the invasiveness of such a procedure. Liquid biopsy is an alternative for acquiring biological material with little to no harm to a patient. Several different piRNAs in various types of cancer were shown to be expressed in bodily fluids such as blood or urine. Furthermore, their expression significantly differed between cancer patients and healthy individuals. Hence, this review aimed to assess the possible use of liquid biopsy for cancer diagnosis with piRNAs as biomarkers.
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Affiliation(s)
- Piotr Limanówka
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Błażej Ochman
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Elżbieta Świętochowska
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
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Zhou J, Xie H, Liu J, Huang R, Xiang Y, Tian D, Bian E. PIWI-interacting RNAs: Critical roles and therapeutic targets in cancer. Cancer Lett 2023; 562:216189. [PMID: 37076042 DOI: 10.1016/j.canlet.2023.216189] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are a novel class of small regulatory RNAs (approximately 24-31 nucleotides in length) that often bind to members of the PIWI protein family. piRNAs regulate transposons in animal germ cells; piRNAs are also specifically expressed in many human tissues and regulate pivotal signaling pathways. Additionally, the abnormal expression of piRNAs and PIWI proteins has been associated with various malignant tumours, and multiple mechanisms of piRNA-mediated target gene dysregulation are involved in tumourigenesis and progression, suggesting that they have the potential to serve as new biomarkers and therapeutic targets for tumours. However, the functions and potential mechanisms of action of piRNAs in cancer have not yet been elucidated. This review summarises the current findings on the biogenesis, function, and mechanisms of piRNAs and PIWI proteins in cancer. We also discuss the clinical significance of piRNAs as diagnostic or prognostic biomarkers and therapeutic tools for cancer. Finally, we present some critical questions regarding piRNA research that need to be addressed to provide insight into the future development of the field.
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Affiliation(s)
- Jialin Zhou
- Department of Clinical Medicine, The Second School of Clinical Medical, Anhui Medical University, Hefei, China
| | - Han Xie
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China; Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - Jun Liu
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China; Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - Ruixiang Huang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China; Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - Yufei Xiang
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China; Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China
| | - Dasheng Tian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China; Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China.
| | - Erbao Bian
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, 678 Fu Rong Road, Hefei, Anhui Province, 230601, China; Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230601, China.
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21
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Haque E, Esmail A, Muhsen I, Salah H, Abdelrahim M. Recent Trends and Advancements in the Diagnosis and Management of Gastric Cancer. Cancers (Basel) 2022; 14:5615. [PMID: 36428707 PMCID: PMC9688354 DOI: 10.3390/cancers14225615] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/10/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022] Open
Abstract
Gastric cancer is an enigmatic malignancy that has recently been shown to be increasing in incidence globally. There has been recent progress in emerging technologies for the diagnosis and treatment of the disease. Improvements in non-invasive diagnostic techniques with serological tests and biomarkers have led to decreased use of invasive procedures such as endoscopy. A multidisciplinary approach is used to treat gastric cancer, with recent significant advancements in systemic therapies used in combination with cytotoxic chemotherapies. New therapeutic targets have been identified and clinical trials are taking place to assess their efficacy and safety. In this review, we provide an overview of the current and emerging treatment strategies and diagnostic techniques for gastric cancer.
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Affiliation(s)
- Emaan Haque
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Abdullah Esmail
- Section of GI Oncology, Houston Methodist Neal Cancer Center, Houston, TX 77030, USA
| | - Ibrahim Muhsen
- Section of Hematology and Oncology, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haneen Salah
- Department of Pathology, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Maen Abdelrahim
- Section of GI Oncology, Houston Methodist Neal Cancer Center, Houston, TX 77030, USA
- Cockrell Center for Advanced Therapeutic Phase I Program, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA
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22
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Yao J, Xie M, Ma X, Song J, Wang Y, Xue X. PIWI-interacting RNAs in cancer: Biogenesis, function, and clinical significance. Front Oncol 2022; 12:965684. [PMID: 36212439 PMCID: PMC9539321 DOI: 10.3389/fonc.2022.965684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/01/2022] [Indexed: 12/02/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a less-studied class of small non-coding RNAs approximately 24–31 nucleotides in length. They express in germline and somatic cells and form complexes with PIWI proteins to exert regulatory effects. New studies show that piRNAs are aberrantly expressed in various cancers. In this review, we focus on those piRNAs that are associated with cancer hallmarks such as proliferation, invasion, and chemoresistance and discuss their potential as biomarkers for cancer diagnosis and prognosis.
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Affiliation(s)
- Jie Yao
- Department of Respiratory and Critical Care, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Mei Xie
- Department of Respiratory and Critical Care, The Chinese People's Liberation Army of China (PLA) General Hospital, Beijing, China
| | - Xidong Ma
- Department of Respiratory and Critical Care, The Chinese People's Liberation Army of China (PLA) General Hospital, Beijing, China
| | - Jialin Song
- Department of Respiratory and Critical Care, Weifang Medical College, Weifang, China
| | - Yuanyong Wang
- Department of Thoracic Surgery, Tangdu Hospital of Air Force Military Medical University, Xi’an, China
| | - Xinying Xue
- Department of Respiratory and Critical Care, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
- Department of Respiratory and Critical Care, Weifang Medical College, Weifang, China
- *Correspondence: Xinying Xue,
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23
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Non-coding RNAs as emerging regulators and biomarkers in colorectal cancer. Mol Cell Biochem 2022; 477:1817-1828. [PMID: 35332394 DOI: 10.1007/s11010-022-04412-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/10/2022] [Indexed: 11/09/2022]
Abstract
CRC is the third most common cancer occurring worldwide and the second leading cause of cancer deaths. In the year 2020, 1,931,590 new cases of CRC and 935,173 deaths were reported. The last two decades have witnessed an intensive study of noncoding RNAs and their implications in various pathological conditions including cancer. Noncoding RNAs such as miRNAs, tsRNAs, piRNAs, lncRNAs, pseudogenes, and circRNAs have emerged as promising prognostic and diagnostic biomarkers in preclinical studies of cancer. Some of these noncoding RNAs have also been shown as promising therapeutic targets for cancer treatment. In this review, we have discussed the emerging roles of various types of noncoding RNAs in CRC and their future implications in colorectal cancer management and research.
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24
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Raza A, Khan AQ, Inchakalody VP, Mestiri S, Yoosuf ZSKM, Bedhiafi T, El-Ella DMA, Taib N, Hydrose S, Akbar S, Fernandes Q, Al-Zaidan L, Krishnankutty R, Merhi M, Uddin S, Dermime S. Dynamic liquid biopsy components as predictive and prognostic biomarkers in colorectal cancer. J Exp Clin Cancer Res 2022; 41:99. [PMID: 35292091 PMCID: PMC8922757 DOI: 10.1186/s13046-022-02318-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/07/2022] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide. The diagnosis, prognosis and therapeutic monitoring of CRC depends largely on tissue biopsy. However, due to tumor heterogeneity and limitations such as invasiveness, high cost and limited applicability in longitudinal monitoring, liquid biopsy has gathered immense attention in CRC. Liquid biopsy has several advantages over tissue biopsy including ease of sampling, effective monitoring, and longitudinal assessment of treatment dynamics. Furthermore, the importance of liquid biopsy is signified by approval of several liquid biopsy assays by regulatory bodies indicating the powerful approach of liquid biopsy for comprehensive CRC screening, diagnostic and prognostics. Several liquid biopsy biomarkers such as novel components of the microbiome, non-coding RNAs, extracellular vesicles and circulating tumor DNA are extensively being researched for their role in CRC management. Majority of these components have shown promising results on their clinical application in CRC including early detection, observe tumor heterogeneity for treatment and response, prediction of metastases and relapse and detection of minimal residual disease. Therefore, in this review, we aim to provide updated information on various novel liquid biopsy markers such as a) oral microbiota related bacterial network b) gut microbiome-associated serum metabolites c) PIWI-interacting RNAs (piRNAs), microRNA(miRNAs), Long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and d) circulating tumor DNAs (ctDNA) and circulating tumor cells (CTC) for their role in disease diagnosis, prognosis, treatment monitoring and their applicability for personalized management of CRC.
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Affiliation(s)
- Afsheen Raza
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Varghese Philipose Inchakalody
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Sarra Mestiri
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | | | - Takwa Bedhiafi
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Dina Moustafa Abo El-Ella
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Nassiba Taib
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Shereena Hydrose
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Shayista Akbar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Queenie Fernandes
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.,College of Medicine, Qatar University, Doha, Qatar
| | - Lobna Al-Zaidan
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Roopesh Krishnankutty
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Maysaloun Merhi
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Said Dermime
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar.
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25
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Alsop E, Meechoovet B, Kitchen R, Sweeney T, Beach TG, Serrano GE, Hutchins E, Ghiran I, Reiman R, Syring M, Hsieh M, Courtright-Lim A, Valkov N, Whitsett TG, Rakela J, Pockros P, Rozowsky J, Gallego J, Huentelman MJ, Shah R, Nakaji P, Kalani MYS, Laurent L, Das S, Van Keuren-Jensen K. A Novel Tissue Atlas and Online Tool for the Interrogation of Small RNA Expression in Human Tissues and Biofluids. Front Cell Dev Biol 2022; 10:804164. [PMID: 35317387 PMCID: PMC8934391 DOI: 10.3389/fcell.2022.804164] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/28/2022] [Indexed: 12/20/2022] Open
Abstract
One promising goal for utilizing the molecular information circulating in biofluids is the discovery of clinically useful biomarkers. Extracellular RNAs (exRNAs) are one of the most diverse classes of molecular cargo, easily assayed by sequencing and with expressions that rapidly change in response to subject status. Despite diverse exRNA cargo, most evaluations from biofluids have focused on small RNA sequencing and analysis, specifically on microRNAs (miRNAs). Another goal of characterizing circulating molecular information, is to correlate expression to injuries associated with specific tissues of origin. Biomarker candidates are often described as being specific, enriched in a particular tissue or associated with a disease process. Likewise, miRNA data is often reported to be specific, enriched for a tissue, without rigorous testing to support the claim. Here we provide a tissue atlas of small RNAs from 30 different tissues and three different blood cell types. We analyzed the tissues for enrichment of small RNA sequences and assessed their expression in biofluids: plasma, cerebrospinal fluid, urine, and saliva. We employed published data sets representing physiological (resting vs. acute exercise) and pathologic states (early- vs. late-stage liver fibrosis, and differential subtypes of stroke) to determine differential tissue-enriched small RNAs. We also developed an online tool that provides information about exRNA sequences found in different biofluids and tissues. The data can be used to better understand the various types of small RNA sequences in different tissues as well as their potential release into biofluids, which should help in the validation or design of biomarker studies.
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Affiliation(s)
- Eric Alsop
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Bessie Meechoovet
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Robert Kitchen
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Thadryan Sweeney
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Thomas G. Beach
- Banner Sun Health Research Institute, Sun City, AZ, United States
| | - Geidy E. Serrano
- Banner Sun Health Research Institute, Sun City, AZ, United States
| | - Elizabeth Hutchins
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Ionita Ghiran
- Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, United States
| | - Rebecca Reiman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Michael Syring
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Michael Hsieh
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Amanda Courtright-Lim
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Nedyalka Valkov
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Timothy G. Whitsett
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | | | - Paul Pockros
- Division of Gastroenterology/Hepatology, Scripps Clinic, La Jolla, CA, United States
| | - Joel Rozowsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Juan Gallego
- Institute for Behavioral Science, The Feinstein Institute for Medical Research, Manhasset, NY, United States
- Division of Psychiatry Research, The Zucker Hillside Hospital, Glen Oaks, NY, United States
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States
| | - Matthew J. Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ, United States
| | - Ravi Shah
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Peter Nakaji
- Department of Neurosurgery, Banner Health, Phoenix, AZ, United States
| | - M. Yashar S. Kalani
- Department of Neurosurgery, St. John Medical Center, Tulsa, OK, United States
| | - Louise Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, San Diego, CA, United States
| | - Saumya Das
- Cardiovascular Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
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26
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Ghaseminezhad Z, Sharifi M, Bahreini A, Mehrzad V. Investigation of the expression of P-element-induced wimpy testis-interacting RNAs in human acute myeloid leukemia. Meta Gene 2022. [DOI: 10.1016/j.mgene.2021.100998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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27
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A universal catalytic hairpin assembly system for direct plasma biopsy of exosomal PIWI-interacting RNAs and microRNAs. Anal Chim Acta 2022; 1192:339382. [DOI: 10.1016/j.aca.2021.339382] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 12/22/2022]
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28
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Toden S, Goel A. Non-coding RNAs as liquid biopsy biomarkers in cancer. Br J Cancer 2022; 126:351-360. [PMID: 35013579 PMCID: PMC8810986 DOI: 10.1038/s41416-021-01672-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/17/2021] [Accepted: 12/07/2021] [Indexed: 01/12/2023] Open
Abstract
Although non-coding RNAs have long been considered as non-functional "junk" RNAs, accumulating evidence in the past decade indicates that they play a critical role in pathogenesis of various cancers. In addition to their biological significance, the recognition that their expression levels are frequently dysregulated in multiple cancers have fueled the interest for exploiting their clinical potential as cancer biomarkers. In particular, microRNAs (miRNAs), a subclass of small non-coding RNAs that epigenetically modulate gene-transcription, have become one of the most well-studied substrates for the development of liquid biopsy biomarkers for cancer patients. The emergence of high-throughput sequencing technologies has enabled comprehensive molecular characterisation of various non-coding RNA expression profiles in multiple cancers. Furthermore, technological advances for quantifying lowly expressed RNAs in the circulation have facilitated robust identification of previously unrecognised and undetectable biomarkers in cancer patients. Here we summarise the latest progress on the utilisation of non-coding RNAs as non-invasive cancer biomarkers. We evaluated the suitability of multiple non-coding RNA types as blood-based cancer biomarkers and examined the impact of recent technological breakthroughs on the development of non-invasive molecular biomarkers in cancer.
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Affiliation(s)
- Shusuke Toden
- Molecular Stethoscope Inc., South San Francisco, CA 94080 USA
| | - Ajay Goel
- grid.410425.60000 0004 0421 8357Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA 91016 USA ,grid.410425.60000 0004 0421 8357City of Hope Comprehensive Cancer Center, Duarte, CA 91010 USA
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29
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Cai A, Hu Y, Zhou Z, Qi Q, Wu Y, Dong P, Chen L, Wang F. PIWI-Interacting RNAs (piRNAs): Promising Applications as Emerging Biomarkers for Digestive System Cancer. Front Mol Biosci 2022; 9:848105. [PMID: 35155584 PMCID: PMC8829394 DOI: 10.3389/fmolb.2022.848105] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 12/24/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a novel type of small non-coding RNAs (sncRNAs), which are 26–31 nucleotides in length and bind to PIWI proteins. Although piRNAs were originally discovered in germline cells and are thought to be essential regulators for germline preservation, they can also influence gene expression in somatic cells. An increasing amount of data has shown that the dysregulation of piRNAs can both promote and repress the emergence and progression of human cancers through DNA methylation, transcriptional silencing, mRNA turnover, and translational control. Digestive cancers are currently a major cause of cancer deaths worldwide. piRNAs control the expression of essential genes and pathways associated with digestive cancer progression and have been reported as possible biomarkers for the diagnosis and treatment of digestive cancer. Here, we highlight recent advances in understanding the involvement of piRNAs, as well as potential diagnostic and therapeutic applications of piRNAs in various digestive cancers.
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Affiliation(s)
- Aiting Cai
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yuhao Hu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Zhou Zhou
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Qianyi Qi
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yixuan Wu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Peixin Dong
- Department of Obstetrics and Gynecology, Hokkaido University School of Medicine, Hokkaido University, Sapporo, Japan
- *Correspondence: Peixin Dong, ; Lin Chen, ; Feng Wang,
| | - Lin Chen
- Department of Gastroenterology and Laboratory Medicine, Nantong Third Hospital Affiliated to Nantong University, Nantong, China
- *Correspondence: Peixin Dong, ; Lin Chen, ; Feng Wang,
| | - Feng Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
- *Correspondence: Peixin Dong, ; Lin Chen, ; Feng Wang,
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30
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Hanusek K, Poletajew S, Kryst P, Piekiełko-Witkowska A, Bogusławska J. piRNAs and PIWI Proteins as Diagnostic and Prognostic Markers of Genitourinary Cancers. Biomolecules 2022; 12:biom12020186. [PMID: 35204687 PMCID: PMC8869487 DOI: 10.3390/biom12020186] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 12/30/2022] Open
Abstract
piRNAs (PIWI-interacting RNAs) are small non-coding RNAs capable of regulation of transposon and gene expression. piRNAs utilise multiple mechanisms to affect gene expression, which makes them potentially more powerful regulators than microRNAs. The mechanisms by which piRNAs regulate transposon and gene expression include DNA methylation, histone modifications, and mRNA degradation. Genitourinary cancers (GC) are a large group of neoplasms that differ by their incidence, clinical course, biology, and prognosis for patients. Regardless of the GC type, metastatic disease remains a key therapeutic challenge, largely affecting patients’ survival rates. Recent studies indicate that piRNAs could serve as potentially useful biomarkers allowing for early cancer detection and therapeutic interventions at the stage of non-advanced tumour, improving patient’s outcomes. Furthermore, studies in prostate cancer show that piRNAs contribute to cancer progression by affecting key oncogenic pathways such as PI3K/AKT. Here, we discuss recent findings on biogenesis, mechanisms of action and the role of piRNAs and the associated PIWI proteins in GC. We also present tools that may be useful for studies on the functioning of piRNAs in cancers.
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Affiliation(s)
- Karolina Hanusek
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, 01-813 Warsaw, Poland;
| | - Sławomir Poletajew
- Centre of Postgraduate Medical Education, II Department of Urology, 01-813 Warsaw, Poland; (S.P.); (P.K.)
| | - Piotr Kryst
- Centre of Postgraduate Medical Education, II Department of Urology, 01-813 Warsaw, Poland; (S.P.); (P.K.)
| | - Agnieszka Piekiełko-Witkowska
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, 01-813 Warsaw, Poland;
- Correspondence: (A.P.-W.); (J.B.)
| | - Joanna Bogusławska
- Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, 01-813 Warsaw, Poland;
- Correspondence: (A.P.-W.); (J.B.)
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31
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Circulating MicroRNAs as Cancer Biomarkers in Liquid Biopsies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1385:23-73. [DOI: 10.1007/978-3-031-08356-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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32
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Riquelme I, Pérez-Moreno P, Letelier P, Brebi P, Roa JC. The Emerging Role of PIWI-Interacting RNAs (piRNAs) in Gastrointestinal Cancers: An Updated Perspective. Cancers (Basel) 2021; 14:202. [PMID: 35008366 PMCID: PMC8750603 DOI: 10.3390/cancers14010202] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 02/07/2023] Open
Abstract
Gastrointestinal (GI) cancers produce ~3.4 million related deaths worldwide, comprising 35% of all cancer-related deaths. The high mortality among GI cancers is due to late diagnosis, the presence of metastasis and drug resistance development. Additionally, current clinical markers do not adequately guide patient management, thereby new and more reliable biomarkers and therapeutic targets are still needed for these diseases. RNA-seq technology has allowed the discovery of new types of RNA transcripts including PIWI-interacting RNAs (piRNAs), which have particular characteristics that enable these molecules to act via diverse molecular mechanisms for regulating gene expression. Cumulative evidence has described the potential role of piRNAs in the development of several tumor types as a likely explanation for certain genomic abnormalities and signaling pathways' deregulations observed in cancer. In addition, these piRNAs might be also proposed as promising diagnostic or prognostic biomarkers or as potential therapeutic targets in malignancies. This review describes important topics about piRNAs including their molecular characteristics, biosynthesis processes, gene expression silencing mechanisms, and the manner in which these transcripts have been studied in samples and cell lines of GI cancers to elucidate their implications in these diseases. Moreover, this article discusses the potential clinical usefulness of piRNAs as biomarkers and therapeutic targets in GI cancers.
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Affiliation(s)
- Ismael Riquelme
- Institute of Biomedical Sciences, Faculty of Health Sciences, Universidad Autónoma de Chile, Temuco 4810101, Chile;
| | - Pablo Pérez-Moreno
- Millennium Institute on Immunology and Immunotherapy, Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8380000, Chile;
| | - Pablo Letelier
- Precision Health Research Laboratory, Departamento de Procesos Diagnósticos y Evaluación, Facultad de Ciencias de la Salud, Universidad Católica de Temuco, Manuel Montt 56, Temuco 4813302, Chile;
| | - Priscilla Brebi
- Millennium Institute on Immunology and Immunotherapy, Laboratory of Integrative Biology (LIBi), Center for Excellence in Translational Medicine—Scientific and Technological Bioresource Nucleus (CEMT-BIOREN), Universidad de La Frontera, Temuco 4810296, Chile;
| | - Juan Carlos Roa
- Millennium Institute on Immunology and Immunotherapy, Department of Pathology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago 8380000, Chile;
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Merkerova MD, Krejcik Z. Transposable elements and Piwi‑interacting RNAs in hemato‑oncology with a focus on myelodysplastic syndrome (Review). Int J Oncol 2021; 59:105. [PMID: 34779490 DOI: 10.3892/ijo.2021.5285] [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: 06/21/2021] [Accepted: 10/12/2021] [Indexed: 11/06/2022] Open
Abstract
Our current understanding of hematopoietic stem cell differentiation and the abnormalities that lead to leukemogenesis originates from the accumulation of knowledge regarding protein‑coding genes. However, the possible impact of transposable element (TE) mobilization and the expression of P‑element‑induced WImpy testis‑interacting RNAs (piRNAs) on leukemogenesis has been beyond the scope of scientific interest to date. The expression profiles of these molecules and their importance for human health have only been characterized recently due to the rapid progress of high‑throughput sequencing technology development. In the present review, current knowledge on the expression profile and function of TEs and piRNAs was summarized, with specific focus on their reported involvement in leukemogenesis and pathogenesis of myelodysplastic syndrome.
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Affiliation(s)
| | - Zdenek Krejcik
- Institute of Hematology and Blood Transfusion, 128 20 Prague, Czech Republic
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Li J, Wang N, Zhang F, Jin S, Dong Y, Dong X, Chen Y, Kong X, Tong Y, Mi Q, Zhao Y, Zhang Y. PIWI-interacting RNAs are aberrantly expressed and may serve as novel biomarkers for diagnosis of lung adenocarcinoma. Thorac Cancer 2021; 12:2468-2477. [PMID: 34346164 PMCID: PMC8447905 DOI: 10.1111/1759-7714.14094] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/16/2021] [Accepted: 07/16/2021] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is the main subtype of primary lung cancer and is a leading cause of cancer-related death worldwide. PIWI-interacting RNAs (piRNAs) are a type of small non-coding RNAs that may play crucial roles in cancer progression and serve as biomarkers for tumor detection. This study aimed to explore the expression profiles and diagnostic values of piRNAs in LUAD. METHODS Small RNA sequencing was performed to investigate tissue piRNA profiles of LUAD. The expression of selected upregulated piRNAs were detected in tissues and serum exosome samples by quantitative real-time polymerase chain reaction (qRT-PCR). Serum exosomes were identified by transmission electron microscope, nanoparticle tracking analysis, and western blot analysis. Receiver operating characteristic (ROC) curve was adopted to quantify the diagnostic potentials of piRNAs in LUAD. Finally, a piRNA panel was developed by multivariate logistic regression model. RESULTS We identified that 76 piRNAs were overexpressed and 9 piRNAs were underexpressed in LUAD tissues compared with adjacent non-tumor tissues. Among the top 10 overexpressed piRNAs, 4 piRNAs (piR-hsa-26925, piR-hsa-5444, piR-hsa-30636, and piR-hsa-8757) were verified by qRT-PCR to be significantly upregulated in LUAD tissues. Moreover, piR-hsa-26925 and piR-hsa-5444 had a significantly higher level in serum exosome samples of LUAD patients than those of healthy controls. We finally established a 2-piRNA panel composed of piR-hsa-26925 and piR-hsa-5444, which showed higher diagnostic performance for LUAD with an AUC of 0.833. CONCLUSIONS Our finding revealed the abnormally expressed piRNAs in LUAD, and serum exosomal piR-hsa-26925 and piR-hsa-5444 could serve as potential biomarkers for LUAD diagnosis.
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Affiliation(s)
- Juan Li
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Nan Wang
- School of Public HealthShandong First Medical University & Shandong Academy of Medical SciencesTaianChina
| | - Fang Zhang
- Department of PharmacyCentral Hospitlal Affiliated to Shandong First Medical UniversityJinanChina
| | - Shan Jin
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Yaqi Dong
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Xiangjun Dong
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Yuqing Chen
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Xue Kong
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Yao Tong
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Qi Mi
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Yinghui Zhao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of MedicineShandong UniversityJinanChina
| | - Yi Zhang
- Department of Respiratory and Critical Care MedicineQilu Hospital of Shandong UniversityJinanChina
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Yuan C, Qin H, Ponnusamy M, Chen Y, Lin Z. PIWI‑interacting RNA in cancer: Molecular mechanisms and possible clinical implications (Review). Oncol Rep 2021; 46:209. [PMID: 34328192 DOI: 10.3892/or.2021.8160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/05/2021] [Indexed: 11/06/2022] Open
Abstract
PIWI‑interacting RNA is a class of non‑coding small RNA that is ~30 nt long and is primarily found in mammalian germ cells from mice and humans. In cooperation with the members of PIWI protein family, this macromolecule participates in germ cell development, inhibits DNA self‑-replication and maintains genomic stability. Increasing evidence has demonstrated that PIWI‑interacting RNA (piRNAs) are abnormally expressed in various human cancers, such as liver cancer, stomach cancer, colorectal cancer, osteosarcoma, breast cancer, lung cancer, prostate cancer, etc. piRNAs abnormal expression is also associated with the occurrence and development of human cancers, such as liver cancer, stomach cancer, colorectal cancer, etc. Despite their unclear molecular mechanisms, piRNAs may act as oncogenes or tumor suppressors by interacting with multiple cancer‑related signal pathways including STAT3/Bcl‑xl or coding genes, such as heat shock transcription factor‑1. Hence, piRNAs may be potential markers and targets and provide new opportunities for cancer diagnosis, treatment or prognosis monitoring. The current review mainly aims to highlight the latest research progress made in the biological functions and regulation of piRNAs in mammals, their involvement in various cancer forms and their potential clinical applications.
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Affiliation(s)
- Chao Yuan
- Department of Basic Medicine, Key Lab for Immunology in Universities of Shandong Province, Immunology Lab, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Hao Qin
- Department of Public Health, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Murugavel Ponnusamy
- Department of Basic Medicine, Institute for Translational Medicine, Qingdao University, Qingdao, Shandong 266021, P.R. China
| | - Yong Chen
- Department of Basic Medicine, Key Lab for Immunology in Universities of Shandong Province, Immunology Lab, Weifang Medical University, Weifang, Shandong 261053, P.R. China
| | - Zhijuan Lin
- Department of Basic Medicine, Key Lab for Immunology in Universities of Shandong Province, Immunology Lab, Weifang Medical University, Weifang, Shandong 261053, P.R. China
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Circulating non-coding RNAs as new biomarkers and novel therapeutic targets in colorectal cancer. Clin Transl Oncol 2021; 23:2220-2236. [PMID: 34275108 DOI: 10.1007/s12094-021-02639-0] [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: 10/14/2020] [Accepted: 05/06/2021] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors, and a large number of patients are diagnosed and die every year. Due to the lack of appropriate diagnosis, prediction and treatment, early diagnosis rate of CRC is low and the prognosis is poor. Studies have found that abnormally expressed non-coding RNAs (ncRNAs) (including microRNAs (miRNAs), circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs),etc.) play an important regulatory role in the occurrence and development of CRC. Some studies have shown that they are stable in the blood and can be detected repeatedly. They are expected to be non-invasive biomarkers for early diagnosis, prognosis evaluation, and prediction of drug sensitivity of CRC, as well as potential applications in the treatment of CRC.
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Chen S, Ben S, Xin J, Li S, Zheng R, Wang H, Fan L, Du M, Zhang Z, Wang M. The biogenesis and biological function of PIWI-interacting RNA in cancer. J Hematol Oncol 2021; 14:93. [PMID: 34118972 PMCID: PMC8199808 DOI: 10.1186/s13045-021-01104-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
Small non-coding RNAs (ncRNAs) are vital regulators of biological activities, and aberrant levels of small ncRNAs are commonly found in precancerous lesions and cancer. PIWI-interacting RNAs (piRNAs) are a novel type of small ncRNA initially discovered in germ cells that have a specific length (24-31 nucleotides), bind to PIWI proteins, and show 2'-O-methyl modification at the 3'-end. Numerous studies have revealed that piRNAs can play important roles in tumorigenesis via multiple biological regulatory mechanisms, including silencing transcriptional and posttranscriptional gene processes and accelerating multiprotein interactions. piRNAs are emerging players in the malignant transformation of normal cells and participate in the regulation of cancer hallmarks. Most of the specific cancer hallmarks regulated by piRNAs are involved in sustaining proliferative signaling, resistance to cell death or apoptosis, and activation of invasion and metastasis. Additionally, piRNAs have been used as biomarkers for cancer diagnosis and prognosis and have great potential for clinical utility. However, research on the underlying mechanisms of piRNAs in cancer is limited. Here, we systematically reviewed recent advances in the biogenesis and biological functions of piRNAs and relevant bioinformatics databases with the aim of providing insights into cancer diagnosis and clinical applications. We also focused on some cancer hallmarks rarely reported to be related to piRNAs, which can promote in-depth research of piRNAs in molecular biology and facilitate their clinical translation into cancer treatment.
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Affiliation(s)
- Silu Chen
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, People's Republic of China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuai Ben
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Junyi Xin
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Shuwei Li
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Rui Zheng
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hao Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Lulu Fan
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Mulong Du
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,Department of Biostatistics, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, Jiangsu, People's Republic of China. .,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China. .,Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China. .,Suzhou Municipal Hospital, Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Nanjing, China.
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Druce P, Calanzani N, Snudden C, Milley K, Boscott R, Behiyat D, Martinez-Gutierrez J, Saji S, Oberoi J, Funston G, Messenger M, Walter FM, Emery J. Identifying Novel Biomarkers Ready for Evaluation in Low-Prevalence Populations for the Early Detection of Lower Gastrointestinal Cancers: A Systematic Review and Meta-Analysis. Adv Ther 2021; 38:3032-3065. [PMID: 33907946 PMCID: PMC8078393 DOI: 10.1007/s12325-021-01645-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/30/2021] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Lower gastrointestinal (GI) cancers are a major cause of cancer deaths worldwide. Prognosis improves with earlier diagnosis, and non-invasive biomarkers have the potential to aid with early detection. Substantial investment has been made into the development of biomarkers; however, studies are often carried out in specialist settings and few have been evaluated for low-prevalence populations. METHODS We aimed to identify novel biomarkers for the detection of lower GI cancers that have the potential to be evaluated for use in primary care. MEDLINE, Embase, Emcare and Web of Science were systematically searched for studies published in English from January 2000 to October 2019. Reference lists of included studies were also assessed. Studies had to report on measures of diagnostic performance for biomarkers (single or in panels) used to detect colorectal or anal cancers. We included all designs and excluded studies with fewer than 50 cases/controls. Data were extracted from published studies on types of biomarkers, populations and outcomes. Narrative synthesis was used, and measures of specificity and sensitivity were meta-analysed where possible. RESULTS We identified 142 studies reporting on biomarkers for lower GI cancers, for 24,844 cases and 45,374 controls. A total of 378 unique biomarkers were identified. Heterogeneity of study design, population type and sample source precluded meta-analysis for all markers except methylated septin 9 (mSEPT9) and pyruvate kinase type tumour M2 (TuM2-PK). The estimated sensitivity and specificity of mSEPT9 was 80.6% (95% CI 76.6-84.0%) and 88.0% (95% CI 79.1-93.4%) respectively; TuM2-PK had an estimated sensitivity of 81.6% (95% CI 75.2-86.6%) and specificity of 80.1% (95% CI 76.7-83.0%). CONCLUSION Two novel biomarkers (mSEPT9 and TuM2-PK) were identified from the literature with potential for use in lower-prevalence populations. Further research is needed to validate these biomarkers in primary care for screening and assessment of symptomatic patients.
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Affiliation(s)
- Paige Druce
- Centre for Cancer Research and Department of General Practice, University of Melbourne, Melbourne, VIC, Australia.
| | - Natalia Calanzani
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Claudia Snudden
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kristi Milley
- Centre for Cancer Research and Department of General Practice, University of Melbourne, Melbourne, VIC, Australia
| | - Rachel Boscott
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dawnya Behiyat
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Javiera Martinez-Gutierrez
- Department of Family Medicine, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Smiji Saji
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jasmeen Oberoi
- Centre for Cancer Research and Department of General Practice, University of Melbourne, Melbourne, VIC, Australia
| | - Garth Funston
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Mike Messenger
- Leeds Institute of Health Sciences, University of Leeds, Leeds, UK
| | - Fiona M Walter
- Centre for Cancer Research and Department of General Practice, University of Melbourne, Melbourne, VIC, Australia
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jon Emery
- Centre for Cancer Research and Department of General Practice, University of Melbourne, Melbourne, VIC, Australia
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
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He J, Wu F, Han Z, Hu M, Lin W, Li Y, Cao M. Biomarkers (mRNAs and Non-Coding RNAs) for the Diagnosis and Prognosis of Colorectal Cancer - From the Body Fluid to Tissue Level. Front Oncol 2021; 11:632834. [PMID: 33996548 PMCID: PMC8118670 DOI: 10.3389/fonc.2021.632834] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/09/2021] [Indexed: 12/24/2022] Open
Abstract
In recent years, the diagnosis and treatment of colorectal cancer (CRC) have been continuously improved, but the mortality rate continues to be high, especially in advanced patients. CRC patients usually have no obvious symptoms in the early stage and are already in the advanced stage when they are diagnosed. The 5-year survival rate is only 10%. The blood markers currently used to screen for CRC, such as carcinoembryonic antigen and carbohydrate antigen 19-9, have low sensitivity and specificity, whereas other methods are invasive or too expensive. As a result, recent research has shifted to the development of minimally invasive or noninvasive biomarkers in the form of body fluid biopsies. Non-coding RNA molecules are composed of microRNAs, long non-coding RNAs, small nucleolar RNAs, and circular RNAs, which have important roles in the occurrence and development of diseases and can be utilized for the early diagnosis and prognosis of tumors. In this review, we focus on the latest findings of mRNA-ncRNA as biomarkers for the diagnosis and prognosis of CRC, from fluid to tissue level.
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Affiliation(s)
- Jinhua He
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, China
| | - Feifeng Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Zeping Han
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, China
| | - Min Hu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Weida Lin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yuguang Li
- Department of Laboratory Medicine, Central Hospital of Panyu District, Guangzhou, China
| | - Mingrong Cao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
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PIWIL1 interacting RNA piR-017061 inhibits pancreatic cancer growth via regulating EFNA5. Hum Cell 2021; 34:550-563. [PMID: 33389678 DOI: 10.1007/s13577-020-00463-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022]
Abstract
PIWI (P element induced wimpy testis) integrating RNAs (piRNAs) are small non-coding RNAs with the length of approximately 30 nucleotides that plays crucial roles in germ cells and adult stem cells. Recently, accumulating data have shown that piRNA and PIWI proteins are involved in tumorigenesis. However, the roles of PIWI proteins and piRNAs in pancreatic cancer are still elusive. Here, we showed that piR-017061 is significantly downregulated in pancreatic cancer patients' samples and pancreatic cancer cell lines. Furthermore, we studied the function of piR-017061 in pancreatic cancer and our data revealed that piR-017061 inhibits pancreatic cancer cell growth in vitro and in vivo. Moreover, we analyzed the genomic loci around piR-017061 and identified EFNA5 as a novel target of piR-017061. Importantly, our data further revealed a direct binding between piR-017061 and EFNA5 mRNA mediated by PIWIL1. Mechanically, piR-017061 cooperates with PIWIL1 to facilitate EFNA5 mRNA degradation and loss of piR-017061 results in accumulation of EFNA5 which facilitates pancreatic cancer development. Hence, our data provided novel insights into PIWI/piRNA-mediated gene regulation and their function in pancreatic cancer. Since PIWI proteins and piRNA predominately express in germline and cancer cells, our study provided novel therapeutic strategy for pancreatic cancer treatment.
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Tamtaji OR, Behnam M, Pourattar MA, Hamblin MR, Mahjoubin-Tehran M, Mirzaei H, Asemi Z. PIWI-interacting RNAs and PIWI proteins in glioma: molecular pathogenesis and role as biomarkers. Cell Commun Signal 2020; 18:168. [PMID: 33109195 PMCID: PMC7590611 DOI: 10.1186/s12964-020-00657-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 09/06/2020] [Indexed: 12/12/2022] Open
Abstract
Glioma is the most common primary brain tumor, and is a major health problem throughout the world. Today, researchers have discovered many risk factors that are associated with the initiation and progression of gliomas. Studies have shown that PIWI-interacting RNAs (piRNAs) and PIWI proteins are involved in tumorigenesis by epigenetic mechanisms. Hence, it seems that piRNAs and PIWI proteins may be potential prognostic, diagnostic or therapeutic biomarkers in the treatment of glioma. Previous studies have demonstrated a relationship between piRNAs and PIWI proteins and some of the molecular and cellular pathways in glioma. Here, we summarize recent evidence and evaluate the molecular mechanisms by which piRNAs and PIWI proteins are involved in glioma. Video abstract
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Affiliation(s)
- Omid Reza Tamtaji
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | | | | | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, 2028, South Africa
| | - Maryam Mahjoubin-Tehran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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Gan X, Wang T, Chen ZY, Zhang KH. Blood-derived molecular signatures as biomarker panels for the early detection of colorectal cancer. Mol Biol Rep 2020; 47:8159-8168. [DOI: 10.1007/s11033-020-05838-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/10/2020] [Indexed: 12/24/2022]
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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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45
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Jing Z, Xi Y, Yin J, Shuwen H. Biological roles of piRNAs in colorectal cancer. Gene 2020; 769:145063. [PMID: 32827685 DOI: 10.1016/j.gene.2020.145063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 08/17/2020] [Indexed: 12/25/2022]
Abstract
Colorectal cancer (CRC) is one of the most common malignancies worldwide and a major cause of cancer-related deaths. Numerous studies have suggested that piwi-interacting RNAs (piRNAs), a new type of non-coding RNA (ncRNA), are closely related to the occurrence and development of cancer. piRNAs have been shown to regulate the occurrence of CRC by modulating multiple molecular signaling pathways. Here, the roles of piRNAs in CRC were reviewed to provide evidence for their potential as molecular targets for CRC.
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Affiliation(s)
- Zhuang Jing
- Graduate School of Nursing, Huzhou University, Zhejiang, No. 1 Bachelor Road, Huzhou, Zhejiang Province 313000, PR China
| | - Yang Xi
- Department of Oncology, Huzhou Cent Hospital, Affiliated Cent Hospital HuZhou University, 198 Hongqi Rd, Huzhou, Zhejiang 313000, PR China
| | - Jin Yin
- Department of Laboratory Medicine, Huzhou Cent Hospital, Affiliated Cent Hospital HuZhou University, 198 Hongqi Rd, Huzhou, Zhejiang 313000, PR China
| | - Han Shuwen
- Department of Oncology, Huzhou Cent Hospital, Affiliated Cent Hospital HuZhou University, 198 Hongqi Rd, Huzhou, Zhejiang 313000, PR China.
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Hallal S, Ebrahim Khani S, Wei H, Lee MYT, Sim HW, Sy J, Shivalingam B, Buckland ME, Alexander-Kaufman KL. Deep Sequencing of Small RNAs from Neurosurgical Extracellular Vesicles Substantiates miR-486-3p as a Circulating Biomarker that Distinguishes Glioblastoma from Lower-Grade Astrocytoma Patients. Int J Mol Sci 2020; 21:ijms21144954. [PMID: 32668808 PMCID: PMC7404297 DOI: 10.3390/ijms21144954] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/01/2020] [Accepted: 07/07/2020] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) play key roles in glioblastoma (GBM; astrocytoma grade IV) biology and are novel sources of biomarkers. EVs released from GBM tumors can cross the blood-brain-barrier into the periphery carrying GBM molecules, including small non-coding RNA (sncRNA). Biomarkers cargoed in circulating EVs have shown great promise for assessing the molecular state of brain tumors in situ. Neurosurgical aspirate fluids captured during tumor resections are a rich source of GBM-EVs isolated directly from tumor microenvironments. Using density gradient ultracentrifugation, EVs were purified from cavitron ultrasonic surgical aspirate (CUSA) washings from GBM (n = 12) and astrocytoma II-III (GII-III, n = 5) surgeries. The sncRNA contents of surgically captured EVs were profiled using the Illumina® NextSeqTM 500 NGS System. Differential expression analysis identified 27 miRNA and 10 piRNA species in GBM relative to GII-III CUSA-EVs. Resolved CUSA-EV sncRNAs could discriminate serum-EV sncRNA profiles from GBM and GII-III patients and healthy controls and 14 miRNAs (including miR-486-3p and miR-106b-3p) and cancer-associated piRNAs (piR_016658, _016659, _020829 and _204090) were also significantly expressed in serum-EVs. Circulating EV markers that correlate with histological, neuroradiographic and clinical parameters will provide objective measures of tumor activity and improve the accuracy of GBM tumor surveillance.
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Affiliation(s)
- Susannah Hallal
- Department of Neurosurgical Services, Chris O’Brien Lifehouse, Camperdown 2050, Australia; (S.H.); (B.S.)
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Camperdown 2006, Australia; (S.E.K.); (M.E.B.)
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Saeideh Ebrahim Khani
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Camperdown 2006, Australia; (S.E.K.); (M.E.B.)
| | - Heng Wei
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Maggie Yuk Ting Lee
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Hao-Wen Sim
- Department of Medical Oncology and NHMRC Clinical Trials Centre, Chris O’Brien Lifehouse, Camperdown 2050, Australia;
- Central Clinical School, The University of Sydney, Camperdown 2006, Australia
- The Kinghorn Cancer Centre, St Vincent’s Hospital, Darlinghurst 2010, Australia
| | - Joanne Sy
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Brindha Shivalingam
- Department of Neurosurgical Services, Chris O’Brien Lifehouse, Camperdown 2050, Australia; (S.H.); (B.S.)
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
| | - Michael E. Buckland
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Camperdown 2006, Australia; (S.E.K.); (M.E.B.)
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
| | - Kimberley L. Alexander-Kaufman
- Department of Neurosurgical Services, Chris O’Brien Lifehouse, Camperdown 2050, Australia; (S.H.); (B.S.)
- Discipline of Pathology, School of Medical Sciences, The University of Sydney, Camperdown 2006, Australia; (S.E.K.); (M.E.B.)
- Brainstorm Brain Cancer Research, Brain and Mind Centre, The University of Sydney, Camperdown 2050, Australia; (H.W.); (M.Y.T.L.)
- Neuropathology Department, Royal Prince Alfred Hospital, Camperdown 2050, Australia;
- Correspondence: ; Tel.: +61-2-8514-0675
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Song W, Ren J, Wang C, Ge Y, Fu T. Analysis of Circular RNA-Related Competing Endogenous RNA Identifies the Immune-Related Risk Signature for Colorectal Cancer. Front Genet 2020; 11:505. [PMID: 32582276 PMCID: PMC7283524 DOI: 10.3389/fgene.2020.00505] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/24/2020] [Indexed: 12/24/2022] Open
Abstract
Background Recent papers have described circular RNAs (circRNAs) playing important roles in the development and progression of colorectal cancer (CRC). However, the expression profiles of circRNAs and their functions in CRC have rarely been studied. The objective was to identify circRNAs involved in the carcinogenesis and progression of CRC and to explore potential molecular mechanisms as a competitive endogenous RNA (ceRNA). Moreover, we aimed to establish an immune-related gene signature for predicting the overall survival (OS) of CRC. Methods The expression patterns of circRNA, miRNA, mRNA, and clinicopathological data were collected from the GEO and TCGA databases. A ceRNA network would be established, and the functional enrichment analyses were performed. The protein-protein interaction network (PPI) was constructed, and hub genes were identified using a cytohub plugin. Subsequently, an immune-related signature was developed based on mRNAs in the ceRNA network. In addition, OS-nomogram was constructed by combining an immune-related signature and clinicopathological characterization to predict the OS. Results We established a circRNA-miRNA-mRNA ceRNA network. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the mRNAs were mainly enriched in neuroactive ligand-receptor interaction, Wnt signaling pathway, cell adhesion molecules (CAMs), and renin secretion. PPI network and module analysis identified 10 hub genes, and the circRNA-miRNA hub gene regulatory modules was established. After univariate and multivariate analysis, seven immune-related genes in the ceRNA network were used to construct the immune-related signature. Patients were divided into low-risk and high-risk groups, and there were significant differences in the OS. The ROC of the nomogram indicated the satisfactory accuracy and predictive power. Furthermore, we established a prognostic nomogram based on immune-related risk score and clinical characterization. The ROC and calibration curves revealed the accuracy of the nomogram. In addition, the high-risk score was positively correlated with six immune infiltrating cells (P < 0.05). Conclusion We screened the key genes and established a circRNA-related ceRNA network involved in CRC, which will assist in understanding the molecular mechanisms underlying the carcinogenesis and progression. Moreover, our proposed immune-based signature may predict survival and reflect the immune status of CRC patients.
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Affiliation(s)
- Wei Song
- Department of Gastrointestinal Surgery II, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jun Ren
- Department of Gastrointestinal Surgery II, Renmin Hospital of Wuhan University, Wuhan, China
| | - Chuntao Wang
- Department of Gastrointestinal Surgery II, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuhang Ge
- Department of Gastrointestinal Surgery II, Renmin Hospital of Wuhan University, Wuhan, China
| | - Tao Fu
- Department of Gastrointestinal Surgery II, Renmin Hospital of Wuhan University, Wuhan, China
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Mentis AFA, Dardiotis E, Romas NA, Papavassiliou AG. PIWI family proteins as prognostic markers in cancer: a systematic review and meta-analysis. Cell Mol Life Sci 2020; 77:2289-2314. [PMID: 31814070 PMCID: PMC11104808 DOI: 10.1007/s00018-019-03403-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND P-element-induced-wimpy-testis-(PIWI)-like proteins are implicated in germ cells' regulation and detected in numerous cancer types. In this meta-analysis, we aimed to associate, for the first time, the prognosis in cancer patients with intratumoral expression of PIWI family proteins. METHODS PubMed, Embase, and Web of Knowledge databases were searched, and studies investigating the association between intratumoral mRNA or protein expression of different PIWI family proteins and survival, metastasis, or recurrence of various cancer types were reviewed. Study qualities were assessed using the REMARK criteria. Studies' heterogeneity was evaluated using I2 index and Cochran Q test. Publication bias was assessed by funnel plots and Egger's regression. Pooled hazard ratios (HR) with 95% confidence intervals (95% CIs) were calculated for different PIWI family proteins separately. Specifically, log of calculated HR was pooled using random-effects model. RESULTS Twenty-six studies (4299 participants) were included. The pooled HR of mortality in high versus low expression of PIWIL1, PIWIL2, and PIWIL4 was 1.87 (95% CI: 1.31-2.66, p < 0.05), 1.09 (95% CI: 0.58-2.07, p = 0.79), and 0.44 (95% CI: 0.25-0.76, p < 0.05), respectively. The pooled HR of recurrence in high versus low expression of PIWIL1 and PIWIL2 was 1.72 (95% CI: 1.20-2.49, p < 0.05) and 1.98 (95% CI: 0.65-5.98, p = 0.23), respectively. CONCLUSIONS Highly variable results were observed for different cancer types. Higher PIWIL1 and lower piwil4 and PIWIL4 expression levels could potentially indicate worse prognosis in cancer. These proteins' expressions could be used for personalized prognosis and treatment in the future.
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Affiliation(s)
- Alexios-Fotios A Mentis
- Public Health Laboratories, Hellenic Pasteur Institute, Athens, Greece
- Department of Microbiology, University Hospital of Thessaly, Larissa, Greece
| | | | - Nicholas A Romas
- Department of Urology, Columbia University Medical Center, Vagelos College of Physicians and Surgeons, New York, USA
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street - Bldg. 16, 11527, Athens, Greece.
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Gu X, Wang C, Deng H, Qing C, Liu R, Liu S, Xue X. Exosomal piRNA profiling revealed unique circulating piRNA signatures of cholangiocarcinoma and gallbladder carcinoma. Acta Biochim Biophys Sin (Shanghai) 2020; 52:475-484. [PMID: 32369104 DOI: 10.1093/abbs/gmaa028] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/21/2020] [Accepted: 03/13/2020] [Indexed: 01/02/2023] Open
Abstract
Cholangiocarcinoma (CCA) and gallbladder carcinoma (GBC) are biliary tract cancers with poor five-year survival and high recurrence rates. Both CCA and GBC patients suffer from lack of circulating diagnostic biomarkers at the early stage. Extracellular vesicles, especially exosomes, have been emerged as promising diagnostic sources for cancers due to easy and quick accessibility. Hence, identification of exosomal biomarkers provides a novel strategy for CCA and GBC diagnosis. Here, five CCA patients and four GBC patients were enrolled for exosomal small RNA sequencing. Our data showed that exosomal piwi-interacting RNA (piRNA) populations were altered in the plasma of CCA and GBC patients. In comparison to healthy individuals, 694 and 323 piRNAs were upregulated in CCA and GBC, respectively, while 36 and 191 piRNAs were downregulated. Interestingly, sequencing results predicted that piR-2660989, piR-10506469, piR-20548188, piR-10822895, piR-hsa-23209, and piR-18044111 were upregulated in both CCA and GBC plasma. Importantly, we further included blood samples from 50 health individuals, 40 CCA patients, and 25 GBC patients and found that piR-10506469 were significantly increased in the exosomes of plasma from both CCA and GBC patients. Moreover, we analyzed the expression levels of differentially expressed exosomal piRNAs in the plasma of CCA and GBC patient before and after surgeries and found that piR-10506469 and piR-20548188 were significantly decreased in patients underwent surgeries. Taken together, our data revealed that exosomal piRNAs those are differentially expressed in CCA and GBC plasma may serve as potential biomarkers for the diagnosis of CCA and GBC.
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Affiliation(s)
- Xinjin Gu
- Department of Hepatobiliary and Pancreatic Surgical Oncology, Chinese People’s Liberation Army General Hospital, Medical School of Chinese People’s Liberation Army, Beijing 100853, China
| | - Chen Wang
- Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Hui Deng
- Department of Respiratory and Critical Care, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Chong Qing
- Department of Respiratory and Critical Care, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Rong Liu
- Department of Hepatobiliary and Pancreatic Surgical Oncology, Chinese People’s Liberation Army General Hospital, Medical School of Chinese People’s Liberation Army, Beijing 100853, China
| | - Sanhong Liu
- Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Xinying Xue
- Department of Respiratory and Critical Care, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
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Wu X, Pan Y, Fang Y, Zhang J, Xie M, Yang F, Yu T, Ma P, Li W, Shu Y. The Biogenesis and Functions of piRNAs in Human Diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:108-120. [PMID: 32516734 PMCID: PMC7283962 DOI: 10.1016/j.omtn.2020.05.023] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/17/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are a novel type of small noncoding RNAs, which are 26-30 nt in length and bind to Piwi proteins. These short RNAs were originally discovered in germline cells and are considered as key regulators for germline maintenance. A growing body of evidence has now extended our views into piRNA biological significance showing that they can also regulate gene expression in somatic cells through transposon silencing, epigenetic programming, DNA rearrangements, mRNA turnover, and translational control. Mounting studies have revealed that the dysregulation of piRNAs may cause epigenetic changes and contribute to diverse diseases. This review illustrates piRNA biogenesis, mechanisms behind piRNA-mediated gene regulation, and changes of piRNAs in different diseases, especially in cancers.
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Affiliation(s)
- Xi Wu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Yutian Pan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Yuan Fang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Jingxin Zhang
- Department of General Surgery, The Affiliated People's Hospital of Jiangsu University, Zhenjiang 212002, People's Republic of China
| | - Mengyan Xie
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Fengming Yang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Tao Yu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Pei Ma
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China.
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China; Department of Oncology, Affiliated Sir Run Run Hospital of Nanjing Medical University, Nanjing 211166, People's Republic of China.
| | - Yongqian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China; Department of Oncology, Affiliated Sir Run Run Hospital of Nanjing Medical University, Nanjing 211166, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China.
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