1
|
Campo A, Aliquò F, Velletri T, Scuruchi M, Avenoso A, Campo GM, D'Ascola A, Campo S, De Pasquale M. Involvement of selected circulating ncRNAs in the regulation of cognitive dysfunction induced by anesthesia. Gene 2024; 928:148806. [PMID: 39074643 DOI: 10.1016/j.gene.2024.148806] [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: 03/19/2024] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 07/31/2024]
Abstract
Post-operative cognitive dysfunction (POCD) refers to the functional impairment of the nervous system caused by prolonged exposure to anesthetics. It is known that prolonged exposure to anesthetics may increase the risk for the development of several cognitive impairments. The drugs used to induce general anesthesia are generally safe, owing to the CNS's direct and/or indirect self-protective activity against drug-induced damages. Non-coding RNAs have recently started to gain attention to better understand the mechanism of gene regulation correlated to cellular physiology and pathology. In order to provide new insights for the neuroprotective function of highly expressed ncRNAs in the central nervous system, we investigated their expression profile in the circulating exosomes of patients exposed to anesthesia vs healthy controls. The experimental design envisaged the recruitment of 30 adult patients undergoing general anesthesia and healthy controls. The effects of anesthetics have been evaluated on miR-34a and miR-124, on the lncRNAs MALAT-1, HOTAIR, GAS5, BLACAT1, HULC, PANDA, and on YRNAs. NcRNAs miR-34a, miR-124, MALAT-1, HOTAIR, GAS5, BLACAT1, and YRNA1 are significantly overexpressed following anesthesia, while YRNA5 is significantly down regulated. Some of them have neuroprotective function, while other correlate with neurological dysfunctions. Our data suggests that, during anesthesia, the toxic action of some non-coding RNAs could be compensated by other non-coding RNAs, both synthesized by the CNS or also transported into neurons from other tissues. It is reasonable to suppose a mutual action of these molecules likely to secure the CNS from anesthetics, that drive a convoluted cascade of ncRNA-dependent biological counter-responses. Our findings are novel in the field of brain dysfunction, indicating that some of the analyzed ncRNAs, although several of their functions still need to be addressed, could be suggested as potential biomarkers and therapeutic targets in post-operative cognitive dysfunction-related processes.
Collapse
Affiliation(s)
- Adele Campo
- Department of Clinical and Experimental Medicine, University of Messina, Policlinico Universitario, via Consolare Valeria, 1, 98125 Messina, Italy
| | - Federica Aliquò
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, Policlinico Universitario, via Consolare Valeria, 1, 98125 Messina, Italy
| | - Tania Velletri
- Department of Human Pathology of Adult and Childhood "Gaetano Barresi", University of Messina, Policlinico Universitario, via Consolare Valeria, 1, 98125 Messina, Italy
| | - Michele Scuruchi
- Department of Clinical and Experimental Medicine, University of Messina, Policlinico Universitario, via Consolare Valeria, 1, 98125 Messina, Italy
| | - Angela Avenoso
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, Policlinico Universitario, via Consolare Valeria, 1, 98125 Messina, Italy
| | - Giuseppe Maurizio Campo
- Department of Clinical and Experimental Medicine, University of Messina, Policlinico Universitario, via Consolare Valeria, 1, 98125 Messina, Italy
| | - Angela D'Ascola
- Department of Clinical and Experimental Medicine, University of Messina, Policlinico Universitario, via Consolare Valeria, 1, 98125 Messina, Italy
| | - Salvatore Campo
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, Policlinico Universitario, via Consolare Valeria, 1, 98125 Messina, Italy.
| | - Maria De Pasquale
- Department of Human Pathology of Adult and Childhood "Gaetano Barresi", University of Messina, Policlinico Universitario, via Consolare Valeria, 1, 98125 Messina, Italy
| |
Collapse
|
2
|
Fuller RN, Morcos A, Bustillos JG, Molina DC, Wall NR. Small non-coding RNAs and pancreatic ductal adenocarcinoma: Linking diagnosis, pathogenesis, drug resistance, and therapeutic potential. Biochim Biophys Acta Rev Cancer 2024; 1879:189153. [PMID: 38986720 DOI: 10.1016/j.bbcan.2024.189153] [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: 01/22/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024]
Abstract
This review comprehensively investigates the intricate interplay between small non-coding RNAs (sncRNAs) and pancreatic ductal adenocarcinoma (PDAC), a devastating malignancy with limited therapeutic options. Our analysis reveals the pivotal roles of sncRNAs in various facets of PDAC biology, spanning diagnosis, pathogenesis, drug resistance, and therapeutic strategies. sncRNAs have emerged as promising biomarkers for PDAC, demonstrating distinct expression profiles in diseased tissues. sncRNA differential expression patterns, often detectable in bodily fluids, hold potential for early and minimally invasive diagnostic approaches. Furthermore, sncRNAs exhibit intricate involvement in PDAC pathogenesis, regulating critical cellular processes such as proliferation, apoptosis, and metastasis. Additionally, mechanistic insights into sncRNA-mediated pathogenic pathways illuminate novel therapeutic targets and interventions. A significant focus of this review is dedicated to unraveling sncRNA mechanisms underlying drug resistance in PDAC. Understanding these mechanisms at the molecular level is imperative for devising strategies to overcome drug resistance. Exploring the therapeutic landscape, we discuss the potential of sncRNAs as therapeutic agents themselves as their ability to modulate gene expression with high specificity renders them attractive candidates for targeted therapy. In summary, this review integrates current knowledge on sncRNAs in PDAC, offering a holistic perspective on their diagnostic, pathogenic, and therapeutic relevance. By elucidating the roles of sncRNAs in PDAC biology, this review provides valuable insights for the development of novel diagnostic tools and targeted therapeutic approaches, crucial for improving the prognosis of PDAC patients.
Collapse
Affiliation(s)
- Ryan N Fuller
- Department of Basic Science, Division of Biochemistry, Center for Health Disparity and Mol. Med., Loma Linda University, Loma Linda, CA 92350, USA; Department of Radiation Medicine, James M. Slater, MD Proton Treatment and Research Center, Loma Linda University, Loma Linda, CA 92350, USA
| | - Ann Morcos
- Department of Basic Science, Division of Biochemistry, Center for Health Disparity and Mol. Med., Loma Linda University, Loma Linda, CA 92350, USA; Department of Radiation Medicine, James M. Slater, MD Proton Treatment and Research Center, Loma Linda University, Loma Linda, CA 92350, USA
| | - Joab Galvan Bustillos
- Department of Basic Science, Division of Biochemistry, Center for Health Disparity and Mol. Med., Loma Linda University, Loma Linda, CA 92350, USA; Division of Surgical Oncology, Department of Surgery, Loma Linda University, Loma Linda, CA 92350, USA
| | - David Caba Molina
- Division of Surgical Oncology, Department of Surgery, Loma Linda University, Loma Linda, CA 92350, USA
| | - Nathan R Wall
- Department of Basic Science, Division of Biochemistry, Center for Health Disparity and Mol. Med., Loma Linda University, Loma Linda, CA 92350, USA; Department of Radiation Medicine, James M. Slater, MD Proton Treatment and Research Center, Loma Linda University, Loma Linda, CA 92350, USA.
| |
Collapse
|
3
|
Shaker FH, Sanad EF, Elghazaly H, Hsia SM, Hamdy NM. piR-823 tale as emerging cancer-hallmark molecular marker in different cancer types: a step-toward ncRNA-precision. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03308-z. [PMID: 39102033 DOI: 10.1007/s00210-024-03308-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 07/16/2024] [Indexed: 08/06/2024]
Abstract
PIWI-interacting RNAs (piRNAs) have received a lot of attention for their functions in cancer research. This class of short non-coding RNAs (ncRNA) has roles in genomic stability, chromatin remodeling, messenger RNA (mRNA) integrity, and genome structure. We summarized the mechanisms underlying the biogenesis and regulatory molecular functions of piRNAs. Among all piRNAs studied in cancer, this review offers a comprehensive analysis of the emerging roles of piR-823 in various types of cancer, including colorectal, gastric, liver, breast, and renal cancers, as well as multiple myeloma. piR-823 has emerged as a crucial modulator of various cancer hallmarks through regulating multiple pathways. In the current review, we analyzed several databases and conducted an extensive literature search to explore the influence of piR-823 in carcinogenesis in addition to describing the potential application of piR-823 as prognostic and diagnostic markers as well as the therapeutic potential toward ncRNA precision.
Collapse
Affiliation(s)
- Fatma H Shaker
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Abassia, 11566, Egypt
| | - Eman F Sanad
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Abassia, 11566, Egypt
| | - Hesham Elghazaly
- Department of Clinical Oncology, Faculty of Medicine, Ain Shams University, Cairo, Abassia, 11566, Egypt
| | - Shih-Min Hsia
- School of Food and Safety, Nutrition Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, 110301, Taiwan
- Graduate Institute of Metabolism and Obesity Sciences, College of Nutrition, Taipei Medical University, Taipei, 110301, Taiwan
| | - Nadia M Hamdy
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Abassia, 11566, Egypt.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Leng X, Zhang M, Xu Y, Wang J, Ding N, Yu Y, Sun S, Dai W, Xue X, Li N, Yang Y, Shi Z. Non-coding RNAs as therapeutic targets in cancer and its clinical application. J Pharm Anal 2024; 14:100947. [PMID: 39149142 PMCID: PMC11325817 DOI: 10.1016/j.jpha.2024.02.001] [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: 10/27/2023] [Revised: 01/12/2024] [Accepted: 02/01/2024] [Indexed: 08/17/2024] Open
Abstract
Cancer genomics has led to the discovery of numerous oncogenes and tumor suppressor genes that play critical roles in cancer development and progression. Oncogenes promote cell growth and proliferation, whereas tumor suppressor genes inhibit cell growth and division. The dysregulation of these genes can lead to the development of cancer. Recent studies have focused on non-coding RNAs (ncRNAs), including circular RNA (circRNA), long non-coding RNA (lncRNA), and microRNA (miRNA), as therapeutic targets for cancer. In this article, we discuss the oncogenes and tumor suppressor genes of ncRNAs associated with different types of cancer and their potential as therapeutic targets. Here, we highlight the mechanisms of action of these genes and their clinical applications in cancer treatment. Understanding the molecular mechanisms underlying cancer development and identifying specific therapeutic targets are essential steps towards the development of effective cancer treatments.
Collapse
Affiliation(s)
- Xuejiao Leng
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Mengyuan Zhang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yujing Xu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jingjing Wang
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Ning Ding
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yancheng Yu
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shanliang Sun
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Weichen Dai
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xin Xue
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Nianguang Li
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Ye Yang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zhihao Shi
- Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, Nanjing, 211198, China
| |
Collapse
|
6
|
Zhang H, Li Y. Potential roles of PIWI-interacting RNAs in breast cancer, a new therapeutic strategy. Pathol Res Pract 2024; 257:155318. [PMID: 38688203 DOI: 10.1016/j.prp.2024.155318] [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: 03/27/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Breast cancer (BC) has been the focus of numerous studies aimed at identifying novel biological markers for its early detection. PIWI-interacting RNAs (piRNAs), a subset of small non-coding RNAs, have emerged as potential markers due to their aberrant expression in various cancers. PiRNAs have recently gained attention due to their aberrant expression in various cancers, including BC. PiRNAs, exhibit diverse biological activities, such as epigenetic regulation of gene and protein expression and their association with cell proliferation and metastasis has been well-established. As the field of non-coding RNAs rapidly evolves, there is great anticipation that therapies targeting piRNAs will advance swiftly. This review will delve into the various biological functions of piRNAs, such as gene suppression, transposon silencing, and epigenetic regulation of genes. The review will also highlight the role of piRNAs as either progenitors or suppressors in cancers, with a particular focus on BC. Lastly, it will touch upon the potential of piRNAs as biomarkers and therapeutic targets for BC.
Collapse
Affiliation(s)
- Hongpeng Zhang
- The Second Clinical College, China Medical University, Shenyang 110122, China
| | - Yanshu Li
- School of Life Sciences, China Medical University, Shenyang 110122, China.
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Wei J, Dai J, Shi X, Zhao R, Fu G, Li R, Xia C, Zhang L, Zhou T, Wang H, Shi Y. Cadmium disrupts spermatogenic cell cycle via piRNA-DQ717867/p53 pathway. Reprod Toxicol 2024; 125:108554. [PMID: 38331007 DOI: 10.1016/j.reprotox.2024.108554] [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: 12/01/2023] [Revised: 01/17/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024]
Abstract
Cadmium (Cd) is a harmful environmental pollutant that disrupts public health, including respiratory, digestive, and reproductive systems. In this study, male rats were exposed to CdCl2 at a dose of 3 mg/kg by oral for 28 days to investigate the impact on spermatogenesis. Testis tissue samples were collected after sacrifice, and piRNA expression levels were measured using piRNA microarray and qPCR. PiRNAs, specialized molecules involved in spermatogenesis, were examined. CdCl2 exposure led to disrupted piRNA expression, particularly in piRNA-DQ759395 in rats. This piRNA was found to have a binding site with p53, and a similar piRNA-DQ717867 was discovered in mice. In GC-2spd cells, CdCl2 exposure increased piRNA-DQ717867 expression, which resulted in cell cycle arrest and abnormal expression of cell cycle-related proteins. The activation of p53-related pathways and disruptions in cell cycle regulation were also observed. Antagomir-717867 transfections and PFT-a pretreatment in GC-2spd cells supported the involvement of piRNA-DQ717867 in regulating cell cycle-related proteins. This study suggests that Cd exposure induces abnormal expression of piRNA-DQ759395 in rat testis and that piRNA-DQ717867 may regulate p53, causing cell cycle abnormalities in GC-2spd cells. These findings help understand the mechanisms of male reproductive toxicity caused by Cd exposure and emphasize the role of piRNAs in cell cycle regulation and male reproductive health.
Collapse
Affiliation(s)
- Jiaoyang Wei
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, China
| | - Juan Dai
- Wuhan centers for Disease Prevention and Control, China
| | - Xiaofan Shi
- Qinghai centers for Disease Prevention and Control, China
| | - Ruixue Zhao
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, China
| | | | - Rui Li
- Central China Normal University, China
| | - Chao Xia
- Ezhou centers for Disease Prevention and Control, China
| | - Ling Zhang
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, China
| | - Ting Zhou
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, China
| | - Huaiji Wang
- Wuhan centers for Disease Prevention and Control, China.
| | - Yuqin Shi
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, China.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Mi T, Tan X, Wang Z, Zhang Z, Jin L, Wang J, Li M, Wu X, He D. Activation of the p53 signaling pathway by piRNA-MW557525 overexpression induces a G0/G1 phase arrest thus inhibiting neuroblastoma growth. Eur J Med Res 2023; 28:503. [PMID: 37941038 PMCID: PMC10631185 DOI: 10.1186/s40001-023-01493-w] [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: 07/31/2023] [Accepted: 11/01/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Neuroblastoma (NB) is the most common extracranial malignant solid tumor in children. Due to drug resistance to radiotherapy and chemotherapy, mainly due to the existence of cancer stem cells (CSCs), some children still have a poor prognosis. Therefore, researchers have focused their attention on CSCs. Our research group successfully constructed cancer stem cell-like cells named Piwil2-iCSCs by reprogramming human preputial fibroblasts (FBs) with the PIWIL2 gene in the early stage, and Piwil2-iCSCs were confirmed to induce the formation of embryonic tumors. PiRNAs, noncoding small RNAs that interact with PIWI proteins, play important roles in a variety of tumors. Therefore, our study aimed to explore the role of differentially expressed (DE) piRNAs derived from sequencing of Piwil2-iCSCs in NB. METHODS The DE piRNAs in Piwil2-iCSCs were screened using high-throughput sequencing and further verified in NB tissues and cells. An unknown piRNA, named piRNA-MW557525, showed obvious downregulation in NB. Thus we studied the effect of piRNA-MW557525 on the biological behavior of NB through in vitro and in vivo experiments. On this basis, we successfully constructed a stably transfected NB cell line overexpressing piRNA-MW557525 and performed transcriptome sequencing to further explore the mechanism of piRNA-MW557525 in NB. RESULTS In vitro, piRNA-MW557525 inhibited NB cell proliferation, migration and invasion and induced apoptosis; in vivo, piRNA-MW557525 significantly reduced the volume and weight of tumors and inhibited their proliferation, migration and invasion. piRNA-MW557525 overexpression induced G0/G1 phase arrest in NB cells via activation of the P53-P21-CDK2-Cyclin E signaling pathway thus inhibiting NB growth. CONCLUSIONS Our findings show that piRNA-MW557525 functions as a tumor suppressor gene in NB and may serve as an innovative biomarker and possible therapeutic target for NB.
Collapse
Affiliation(s)
- Tao Mi
- Department of Urology; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation Base of Child Development and Critical Disorders; Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Xiaojun Tan
- Department of Urology; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation Base of Child Development and Critical Disorders; Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Yuzhong District, Chongqing, 400014, People's Republic of China
- Department of Urology, Nanchong Central Hospital, The Second Clinical Medical College, North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Zhang Wang
- Department of Urology; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation Base of Child Development and Critical Disorders; Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Zhaoxia Zhang
- Department of Urology; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation Base of Child Development and Critical Disorders; Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Yuzhong District, Chongqing, 400014, People's Republic of China
| | | | - Jinkui Wang
- Department of Urology; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation Base of Child Development and Critical Disorders; Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Mujie Li
- Department of Urology; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation Base of Child Development and Critical Disorders; Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Xin Wu
- Department of Urology; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation Base of Child Development and Critical Disorders; Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Yuzhong District, Chongqing, 400014, People's Republic of China
| | - Dawei He
- Department of Urology; Chongqing Key Laboratory of Children Urogenital Development and Tissue Engineering; Ministry of Education Key Laboratory of Child Development and Disorders; National Clinical Research Center for Child Health and Disorders; China International Science and Technology Cooperation Base of Child Development and Critical Disorders; Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Yuzhong District, Chongqing, 400014, People's Republic of China.
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Wu YJ, Wang J, Zhang P, Yuan LX, Ju LL, Wang HX, Chen L, Cao YL, Cai WH, Ni Y, Li M. PIWIL1 interacting RNA piR-017724 inhibits proliferation, invasion, and migration, and inhibits the development of HCC by silencing PLIN3. Front Oncol 2023; 13:1203821. [PMID: 37503320 PMCID: PMC10369847 DOI: 10.3389/fonc.2023.1203821] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) accounts for the majority of primary liver cancers. Worldwide, liver cancer is the fourth most common cause of cancer-related death. Recent studies have found that PIWI-interacting RNAs (piRNAs) participate in the occurrence and development of various tumors and are closely related to the growth, invasion, metastasis and prognosis of malignant tumors. Studies on the role and functional mechanism of piRNAs in HCC development and progression are limited. Methods Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) were used to detect the expression of piR-017724 in both HCC tissues and cells. Based on the clinical data of HCC patients, the clinical and prognostic value of piR-017724 was further analyzed. Then, targeted silencing and overexpressing of piR-017724 in HCC cells was further used to examine the biological functions of piR-017724. In addition, the downstream target protein of piR-017724 was predicted and validated through high-throughput sequencing and public databases. Results The piR-017724 was significantly downregulated in HCC tissues and cells, and the downregulation of piR-017724 was associated with tumor stage and poor prognosis in HCC. The piR-017724 inhibitor promoted the proliferation, migration and invasion of HCC cells, while the piR-017724 mimic had the opposite effect. However, the piR-017724 did not affect apoptosis of HCC cells. High-throughput sequencing and qRT-PCR confirmed a reciprocal relationship between piR-017724 and PLIN3. Therefore, we speculate that piR-017724 may inhibit the development and progression of HCC by affecting the downstream protein PLIN3. Conclusions Our study shows that piR-017724, which is lowly expressed in HCC, inhibits the proliferation, migration and invasion of HCC cells and may affect the development of hepatocellular liver cancer through PLIN3, which provides new insights into the clinical application of piR-017724 in the treatment of hepatocellular carcinoma.
Collapse
Affiliation(s)
- Yi-Jing Wu
- Medical School of Nantong University, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China
| | - Jie Wang
- Medical School of Nantong University, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China
| | - Peng Zhang
- Nantong Institute of Liver Disease, Department of Hepatobiliary Surgery, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China
| | - Liu-Xia Yuan
- Nantong Institute of Liver Disease, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China
| | - Lin-Ling Ju
- Nantong Institute of Liver Disease, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China
| | - Hui-Xuan Wang
- Nantong Institute of Liver Disease, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China
| | - Lin Chen
- Nantong Institute of Liver Disease, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China
| | - Ya-Li Cao
- Preventive Health Department, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China
| | - Wei-Hua Cai
- Department of Hepatobiliary Surgery, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China
| | - Yi Ni
- Thyroid and Breast Surgery, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China
| | - Min Li
- Integrating Traditional Chinese Medicine with Hepatology, Nantong Third People’s Hospital, Affiliated Nantong Hospital 3 of Nantong University, Nantong, China
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Zheng K, Zhang XL, Wang L, You ZH, Ji BY, Liang X, Li ZW. SPRDA: a link prediction approach based on the structural perturbation to infer disease-associated Piwi-interacting RNAs. Brief Bioinform 2023; 24:6850564. [PMID: 36445194 DOI: 10.1093/bib/bbac498] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/30/2022] Open
Abstract
piRNA and PIWI proteins have been confirmed for disease diagnosis and treatment as novel biomarkers due to its abnormal expression in various cancers. However, the current research is not strong enough to further clarify the functions of piRNA in cancer and its underlying mechanism. Therefore, how to provide large-scale and serious piRNA candidates for biological research has grown up to be a pressing issue. In this study, a novel computational model based on the structural perturbation method is proposed to predict potential disease-associated piRNAs, called SPRDA. Notably, SPRDA belongs to positive-unlabeled learning, which is unaffected by negative examples in contrast to previous approaches. In the 5-fold cross-validation, SPRDA shows high performance on the benchmark dataset piRDisease, with an AUC of 0.9529. Furthermore, the predictive performance of SPRDA for 10 diseases shows the robustness of the proposed method. Overall, the proposed approach can provide unique insights into the pathogenesis of the disease and will advance the field of oncology diagnosis and treatment.
Collapse
Affiliation(s)
- Kai Zheng
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China.,College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277100, China
| | - Xin-Lu Zhang
- Civil Product General Research Institute, The 36th Research Institute of China Electronics Technology Group Corporation, Jiaxing, 314000, China
| | - Lei Wang
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277100, China.,Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Zhu-Hong You
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning, 530007, China
| | - Bo-Ya Ji
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410006, China
| | - Xiao Liang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | - Zheng-Wei Li
- College of Information Science and Engineering, Zaozhuang University, Zaozhuang 277100, China.,Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning, 530007, China
| |
Collapse
|
15
|
Zheng K, Zhang XL, Wang L, You ZH, Zhan ZH, Li HY. Line graph attention networks for predicting disease-associated Piwi-interacting RNAs. Brief Bioinform 2022; 23:6748487. [PMID: 36198846 DOI: 10.1093/bib/bbac393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/08/2022] [Accepted: 08/12/2022] [Indexed: 12/14/2022] Open
Abstract
PIWI proteins and Piwi-Interacting RNAs (piRNAs) are commonly detected in human cancers, especially in germline and somatic tissues, and correlate with poorer clinical outcomes, suggesting that they play a functional role in cancer. As the problem of combinatorial explosions between ncRNA and disease exposes gradually, new bioinformatics methods for large-scale identification and prioritization of potential associations are therefore of interest. However, in the real world, the network of interactions between molecules is enormously intricate and noisy, which poses a problem for efficient graph mining. Line graphs can extend many heterogeneous networks to replace dichotomous networks. In this study, we present a new graph neural network framework, line graph attention networks (LGAT). And we apply it to predict PiRNA disease association (GAPDA). In the experiment, GAPDA performs excellently in 5-fold cross-validation with an AUC of 0.9038. Not only that, it still has superior performance compared with methods based on collaborative filtering and attribute features. The experimental results show that GAPDA ensures the prospect of the graph neural network on such problems and can be an excellent supplement for future biomedical research.
Collapse
Affiliation(s)
- Kai Zheng
- College of Information Science and Engineering, Zaozhuang University, Shandong 277100, China.,Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | | | - Lei Wang
- College of Information Science and Engineering, Zaozhuang University, Shandong 277100, China.,Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning 530007, China
| | - Zhu-Hong You
- Big Data and Intelligent Computing Research Center, Guangxi Academy of Sciences, Nanning 530007, China
| | - Zhao-Hui Zhan
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Hao-Yuan Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| |
Collapse
|
16
|
Chattopadhyay T, Gupta P, Nayak R, Mallick B. Genome-wide profiling of dysregulated piRNAs and their target genes implicated in oncogenicity of Tongue Squamous Cell Carcinoma. Gene 2022; 849:146919. [PMID: 36179965 DOI: 10.1016/j.gene.2022.146919] [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: 06/12/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are single-stranded, 23-36 nucleotide long RNAs that regulate gene expression in the germline but are also detected in some cancers. However, there are no reports yet on piRNA expression in tongue squamous cell carcinoma (TSCC), the most common oral cancer (80-90% percent of all oral cancers). We performed small RNA and whole transcriptome sequencing in H357 tongue cancer and HOK cells (GEO database accession numbers: GSE196674 and GSE196688). We also examined nine published sets of gene expression array data of TSCC tissues from the GEO database to decode piRNAs and their putative targets that may be involved in tumorigenesis. We identified a pool of 16058 and 25677 piRNAs in H357 and HOK, respectively, among which 406 are differentially expressed. We also found that 2094 protein-coding genes are differentially expressed in either TSCC tissues or cell lines. We performed target predictions for these piRNA, pathway and disease function (DF) analyses, as well as qRT-PCR validation of piRNA-target pairs. These experiments revealed one up-regulated (FDFT1) and four down-regulated (OGA, BDH1, TAT, HYAL4) target genes that are enriched in 11 canonical pathways (CPs), with postulated roles in the initiation and progression of TSCC. Downregulation of piR-33422 is predicted to upregulate the FDFT1 gene, which encodes a mevalonate/cholesterol-pathway related farnesyl-diphosphate farnesyltransferase. The FDFT1 appears to be involved in the largest number of oncogenesis-related processes and is interacting with statins, which is a classical cancer drug. This study provides the first evidence of the piRNome of TSCC, which could be investigated further to decode piRNA-mediated gene regulations in malignancy and potential drug targets, such as FDFT1.
Collapse
Affiliation(s)
- Trisha Chattopadhyay
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Pooja Gupta
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Rojalin Nayak
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
| |
Collapse
|
17
|
Wang C, Zhang C, Fu Q, Zhang N, Ding M, Zhou Z, Chen X, Zhang F, Zhang C, Zhang CY, Wang JJ. Increased serum piwi-interacting RNAs as a novel potential diagnostic tool for brucellosis. Front Cell Infect Microbiol 2022; 12:992775. [PMID: 36189348 PMCID: PMC9519857 DOI: 10.3389/fcimb.2022.992775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Background Piwi-interacting RNAs (piRNAs) have emerged as potential novel indicators for various diseases; however, their diagnostic value for brucellosis remains unclear. This study aimed to evaluate the diagnostic potential of altered serum piRNAs in patients with brucellosis. Methods Illumina sequencing via synthesis (SBS) technology was used to screen the serum piRNA profile in brucellosis patients, and markedly dysregulated piRNAs were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR) assay in two sets from a cohort of 73 brucellosis patients and 65 controls. Results Illumina SBS technology results showed that seven piRNAs were markedly elevated in brucellosis patients compared to normal controls. The seven upregulated piRNAs were further validated individually by qRT-PCR, of which three piRNAs (piR-000753, piR-001312, and piR-016742) were confirmed to be significantly and steadily increased in the patients (> 2-fold, P < 0.01). The area under the receiver operating characteristic (ROC) curve (AUCs) for the three piRNAs ranged from 0.698 to 0.783. The AUC for the three piRNAs combination was 0.772, with a specificity of 86% and a positive predictive value of 90%, respectively. Conclusions The three-piRNA panel identified in this study has potential as a novel blood-based auxiliary tool for brucellosis detection.
Collapse
Affiliation(s)
- Cheng Wang
- Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Cuiping Zhang
- Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
- Department of Prenatal Diagnosis, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Quan Fu
- Department of Microbiology, Harbin Medical University, Harbin, China
- Department of Clinical Laboratory, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Nan Zhang
- Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
| | - Meng Ding
- Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Zhen Zhou
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xi Chen
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
| | - Fengmin Zhang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Chunni Zhang
- Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
- *Correspondence: Jun-Jun Wang, ; Chunni Zhang, ; Chen-Yu Zhang,
| | - Chen-Yu Zhang
- Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
- *Correspondence: Jun-Jun Wang, ; Chunni Zhang, ; Chen-Yu Zhang,
| | - Jun-Jun Wang
- Department of Clinical Laboratory, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science, NJU Advanced Institute for Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, China
- Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, Chinese Academy of Medical Sciences Research Unit of Extracellular RNA, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, China
- *Correspondence: Jun-Jun Wang, ; Chunni Zhang, ; Chen-Yu Zhang,
| |
Collapse
|
18
|
Zheng K, Liang Y, Liu YY, Yasir M, Wang P. A decision support system based on multi-sources information to predict piRNA–disease associations using stacked autoencoder. Soft comput 2022. [DOI: 10.1007/s00500-022-07396-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
19
|
Ali SD, Tayara H, Chong KT. Identification of piRNA disease associations using deep learning. Comput Struct Biotechnol J 2022; 20:1208-1217. [PMID: 35317234 PMCID: PMC8908038 DOI: 10.1016/j.csbj.2022.02.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/24/2022] [Accepted: 02/26/2022] [Indexed: 01/09/2023] Open
Abstract
Piwi-interacting RNAs (piRNAs) play a pivotal role in maintaining genome integrity by repression of transposable elements, gene stability, and association with various disease progressions. Cost-efficient computational methods for the identification of piRNA disease associations promote the efficacy of disease-specific drug development. In this regard, we developed a simple, robust, and efficient deep learning method for identifying the piRNA disease associations known as piRDA. The proposed architecture extracts the most significant and abstract information from raw sequences represented in a simplicated piRNA disease pair without any involvement of features engineering. Two-step positive unlabeled learning and bootstrapping technique are utilized to abstain from the false-negative and biased predictions dealing with positive unlabeled data. The performance of proposed method piRDA is evaluated using k-fold cross-validation. The piRDA is significantly improved in all the performance evaluation measures for the identification of piRNA disease associations in comparison to state-of-the-art method. Moreover, it is thus projected conclusively that the proposed computational method could play a significant role as a supportive and practical tool for primitive disease mechanisms and pharmaceutical research such as in academia and drug design. Eventually, the proposed model can be accessed using publicly available and user-friendly web tool athttp://nsclbio.jbnu.ac.kr/tools/piRDA/.
Collapse
Affiliation(s)
- Syed Danish Ali
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- The University of Azad Jammu and Kashmir, Muzaffarabad 13100, Pakistan
| | - Hilal Tayara
- School of International Engineering and Science, Jeonbuk National University, Jeonju 54896, South Korea
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju 54896, South Korea
- Advanced Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, South Korea
| |
Collapse
|
20
|
Ameli Mojarad M, Ameli Mojarad M, Shojaee B, Nazemalhosseini-Mojarad E. piRNA: A promising biomarker in early detection of gastrointestinal cancer. Pathol Res Pract 2021; 230:153757. [PMID: 34998210 DOI: 10.1016/j.prp.2021.153757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 01/02/2023]
Abstract
Gastrointestinal (GI) cancer has become the primary concern of today's society due to its aggressive nature and poor prognosis. PIWI-interacting RNAs (piRNAs), a subgroup of non-coding RNAs, are mainly expressed in the germline and have emerged as a critical regulator in gene expression and the epigenetic silencing of DNA transposable elements by interacting with PIWI proteins. piRNAs' dysregulations were reported to promote or suppress the initiation and development of different malignancies, especially gastrointestinal cancers. Recently, several studies suggested the use of piRNAs as potential cancer biomarkers associated with the progression and chemoresistance of GI cancer. Hence, this review article aims to focus on the role of piRNAs in GI cancer progression, metastasis, and their molecular mechanisms as therapeutic markers for GI cancer patients.
Collapse
Affiliation(s)
- Melika Ameli Mojarad
- Department of Biology Faculty of Basics Science, Kharazmi University, Tehran, Iran.
| | | | - Bahador Shojaee
- Gastroenterology and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
21
|
Bartos M, Siegl F, Kopkova A, Radova L, Oppelt J, Vecera M, Kazda T, Jancalek R, Hendrych M, Hermanova M, Kasparova P, Pleskacova Z, Vybihal V, Fadrus P, Smrcka M, Lakomy R, Lipina R, Cesak T, Slaby O, Sana J. Small RNA Sequencing Identifies PIWI-Interacting RNAs Deregulated in Glioblastoma-piR-9491 and piR-12488 Reduce Tumor Cell Colonies In Vitro. Front Oncol 2021; 11:707017. [PMID: 34485142 PMCID: PMC8415021 DOI: 10.3389/fonc.2021.707017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/20/2021] [Indexed: 11/24/2022] Open
Abstract
Glioblastoma (GBM) is the most frequently occurring primary malignant brain tumor of astrocytic origin. To change poor prognosis, it is necessary to deeply understand the molecular mechanisms of gliomagenesis and identify new potential biomarkers and therapeutic targets. PIWI-interacting RNAs (piRNAs) help in maintaining genome stability, and their deregulation has already been observed in many tumors. Recent studies suggest that these molecules could also play an important role in the glioma biology. To determine GBM-associated piRNAs, we performed small RNA sequencing analysis in the discovery set of 19 GBM and 11 non-tumor brain samples followed by TaqMan qRT-PCR analyses in the independent set of 77 GBM and 23 non-tumor patients. Obtained data were subsequently bioinformatically analyzed. Small RNA sequencing revealed 58 significantly deregulated piRNA molecules in GBM samples in comparison with non-tumor brain tissues. Deregulation of piR-1849, piR-9491, piR-12487, and piR-12488 was successfully confirmed in the independent groups of patients and controls (all p < 0.0001), and piR-9491 and piR-12488 reduced GBM cells’ ability to form colonies in vitro. In addition, piR-23231 was significantly associated with the overall survival of the GBM patients treated with Stupp regimen (p = 0.007). Our results suggest that piRNAs could be a novel promising diagnostic and prognostic biomarker in GBM potentially playing important roles in gliomagenesis.
Collapse
Affiliation(s)
- Michael Bartos
- Department of Neurosurgery, University Hospital Hradec Kralove, Hradec Kralove, Czechia
| | - Frantisek Siegl
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Alena Kopkova
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Lenka Radova
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Jan Oppelt
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Marek Vecera
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Tomas Kazda
- Department of Radiation Oncology, Masaryk Memorial Cancer Institute and Medical Faculty, Masaryk University, Brno, Czechia
| | - Radim Jancalek
- Department of Neurosurgery, St. Anne's University Hospital and Medical Faculty, Masaryk University, Brno, Czechia
| | - Michal Hendrych
- 1st Department of Pathology, St. Anne's University Hospital and Medical Faculty, Masaryk University, Brno, Czechia
| | - Marketa Hermanova
- 1st Department of Pathology, St. Anne's University Hospital and Medical Faculty, Masaryk University, Brno, Czechia
| | - Petra Kasparova
- The Fingerland Department of Pathology, University Hospital Hradec Kralove, Hradec Kralove, Czechia
| | - Zuzana Pleskacova
- Department of Oncology and Radiotherapy, University Hospital Hradec Kralove, Hradec Kralove, Czechia
| | - Vaclav Vybihal
- Department of Neurosurgery, University Hospital Brno, Brno, Czechia
| | - Pavel Fadrus
- Department of Neurosurgery, University Hospital Brno, Brno, Czechia
| | - Martin Smrcka
- Department of Neurosurgery, University Hospital Brno, Brno, Czechia
| | - Radek Lakomy
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czechia
| | - Radim Lipina
- Department of Neurosurgery, University Hospital Ostrava, Ostrava, Czechia
| | - Tomas Cesak
- Department of Neurosurgery, University Hospital Hradec Kralove, Hradec Kralove, Czechia
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czechia.,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czechia.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Jiri Sana
- Central European Institute of Technology, Masaryk University, Brno, Czechia.,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czechia.,Department of Pathology, University Hospital Brno, Brno, Czechia
| |
Collapse
|
22
|
Kunnummal M, Angelin M, Das AV. PIWI proteins and piRNAs in cervical cancer: a propitious dart in cancer stem cell-targeted therapy. Hum Cell 2021; 34:1629-1641. [PMID: 34374035 DOI: 10.1007/s13577-021-00590-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/02/2021] [Indexed: 11/27/2022]
Abstract
Any form of cancer is a result of uncontrolled cell growth caused by mutations and/or epigenetic alterations, implying that a balance of chromatin remodeling activities and epigenetic regulators is crucial to prevent the transformation of a normal cell to a cancer cell. Many of the chromatin remodelers do not recognize any specific sites on their targets and require guiding molecules to reach the respective targets. PIWI proteins and their interacting small non-coding RNAs (piRNAs) have proved to act as a guiding signal for such molecules. While epigenetic alterations lead to tumorigenesis, the stemness of cancer cells contributes to recurrence and metastasis of cancer. Various studies have propounded that the PIWI-piRNA complex also promotes stemness of cancer cells, providing new doors for target-mediated anti-cancer therapies. Despite the progress in diagnosis and development of vaccines, cervical cancer remains to be the second most prevalent cancer among women, due to the lack of cost-effective and accessible diagnostic and prevention methods. With the emergence of liquid biopsy, there is a significant demand for the ideal biomarker in the diagnosis of cancer. PIWI and piRNAs have been recommended to serve as prognostic and diagnostic markers, to differentiate early and later stages of cancer, including cervical cancer. This review discusses how PIWIs and piRNAs are involved in disease progression as well as their potential role in diagnostics and therapeutics in cervical cancer.
Collapse
Affiliation(s)
- Midhunaraj Kunnummal
- Cancer Research Program-12, Rajiv Gandhi Centre for Biotechnology, Thycaud, Thiruvananthapuram, Kerala, P.O. 695 014, India
- Manipal Academy of Higher Education, Tiger Circle Road, Madhav Nagar, Manipal, Karnataka, 576104, India
| | - Mary Angelin
- Cancer Research Program-12, Rajiv Gandhi Centre for Biotechnology, Thycaud, Thiruvananthapuram, Kerala, P.O. 695 014, India
| | - Ani V Das
- Cancer Research Program-12, Rajiv Gandhi Centre for Biotechnology, Thycaud, Thiruvananthapuram, Kerala, P.O. 695 014, India.
| |
Collapse
|
23
|
Zivarpour P, Asemi Z, Jamilian H, Hallajzadeh J. PiRNAs and PIWI proteins as new biomarkers for diagnosis and treatment of liver cancer. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
24
|
Kärkkäinen E, Heikkinen S, Tengström M, Kosma VM, Mannermaa A, Hartikainen JM. The debatable presence of PIWI-interacting RNAs in invasive breast cancer. Cancer Med 2021; 10:3593-3603. [PMID: 33960684 PMCID: PMC8178507 DOI: 10.1002/cam4.3915] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 12/16/2020] [Accepted: 03/29/2021] [Indexed: 01/27/2023] Open
Abstract
Numerous factors influence breast cancer (BC) prognosis, thus complicating the prediction of outcome. By identifying biomarkers that would distinguish the cases with poorer response to therapy already at the time of diagnosis, the rate of survival could be improved. Lately, Piwi-interacting RNAs (piRNAs) have been introduced as potential cancer biomarkers, however, due to the recently raised challenges in piRNA annotations, further evaluation of piRNAs' involvement in cancer is required. We performed small RNA sequencing in 227 fresh-frozen breast tissue samples from the Eastern Finnish Kuopio Breast Cancer Project material to study the presence of piRNAs in BC and their associations with the clinicopathological features and outcome of BC patients. We observed the presence of three small RNAs annotated as piRNA database entries (DQ596932, DQ570994, and DQ571955) in our samples. The actual species of these RNAs however remain uncertain. All three small RNAs were upregulated in grade III tumors and DQ596932 additionally in estrogen receptor negative tumors. Furthermore, patients with estrogen receptor positive BC and higher DQ571955 had shorter relapse-free survival and poorer BC-specific survival, thus indicating DQ571955 as a candidate predictive marker for radiotherapy response in estrogen receptor positive BC. DQ596932 showed possible prognostic value in BC, whereas DQ570994 was identified as a candidate predictive marker for tamoxifen and chemotherapy response. These three small RNAs appear as candidate biomarkers for BC, which could after further investigation provide novel approaches for the treatment of therapy resistant BC. Overall, our results indicate that the prevalence of piRNAs in cancer is most likely not as comprehensive as has been previously thought.
Collapse
Affiliation(s)
- Emmi Kärkkäinen
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
| | - Sami Heikkinen
- School of Medicine, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.,School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Maria Tengström
- School of Medicine, Institute of Clinical Medicine, Oncology, and Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland.,Cancer Center, Kuopio University Hospital, Kuopio, Finland
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland.,Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland.,Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Jaana M Hartikainen
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, and Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
| |
Collapse
|
25
|
Le P, Romano G, Nana-Sinkam P, Acunzo M. Non-Coding RNAs in Cancer Diagnosis and Therapy: Focus on Lung Cancer. Cancers (Basel) 2021; 13:cancers13061372. [PMID: 33803619 PMCID: PMC8003033 DOI: 10.3390/cancers13061372] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/03/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023] Open
Abstract
Over the last several decades, clinical evaluation and treatment of lung cancers have largely improved with the classification of genetic drivers of the disease, such as EGFR, ALK, and ROS1. There are numerous regulatory factors that exert cellular control over key oncogenic pathways involved in lung cancers. In particular, non-coding RNAs (ncRNAs) have a diversity of regulatory roles in lung cancers such that they have been shown to be involved in inducing proliferation, suppressing apoptotic pathways, increasing metastatic potential of cancer cells, and acquiring drug resistance. The dysregulation of various ncRNAs in human cancers has prompted preclinical studies examining the therapeutic potential of restoring and/or inhibiting these ncRNAs. Furthermore, ncRNAs demonstrate tissue-specific expression in addition to high stability within biological fluids. This makes them excellent candidates as cancer biomarkers. This review aims to discuss the relevance of ncRNAs in cancer pathology, diagnosis, and therapy, with a focus on lung cancer.
Collapse
|
26
|
|
27
|
Ding L, Jiang M, Wang R, Shen D, Wang H, Lu Z, Zheng Q, Wang L, Xia L, Li G. The emerging role of small non-coding RNA in renal cell carcinoma. Transl Oncol 2020; 14:100974. [PMID: 33395751 PMCID: PMC7719974 DOI: 10.1016/j.tranon.2020.100974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/14/2020] [Accepted: 11/24/2020] [Indexed: 12/12/2022] Open
Abstract
SncRNAs contribute to the progress of renal cell carcinoma. SncRNAs are promising biomarkers for diagnosis and prognosis of renal cell carcinoma. Despite the potential of sncRNA-based cancer therapy, some obstacles remain, including several severe adverse effect.
Noncoding RNAs are transcribed in the most regions of the human genome, divided into small noncoding RNAs (less than 200 nt) and long noncoding RNAs (more than 200 nt) according to their size. Compelling evidences suggest that small noncoding RNAs play critical roles in tumorigenesis and tumor progression, especially in renal cell carcinoma. MiRNA, the most famous small noncoding RNA, has been comprehensively explored for its fundamental role in cancer. And several miRNA-based therapeutic strategies have been applied to several ongoing clinical trials. However, piRNAs and tsRNAs, have not received as much research attention, because of several technological limitations. Nevertheless, some studies have revealed the presence of aberration of piRNAs and tsRNAs in renal cell carcinoma, highlighting a potentially novel mechanism for tumor onset and progression. In this review, we provide an overview of three classes of small noncoding RNA: miRNAs, piRNAs and tsRNAs, that have been reported dysregulation in renal cell carcinoma and have the potential for advancing diagnosis, prognosis and therapeutic applications of this disease.
Collapse
Affiliation(s)
- Lifeng Ding
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Minxiao Jiang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Ruyue Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Danyang Shen
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Huan Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Zeyi Lu
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Qiming Zheng
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Liya Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Liqun Xia
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Gonghui Li
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China.
| |
Collapse
|
28
|
Vinasco-Sandoval T, Moreira FC, F. Vidal A, Pinto P, Ribeiro-dos-Santos AM, Cruz RLS, Fonseca Cabral G, Anaissi AKM, Lopes KDP, Ribeiro-dos-Santos A, Demachki S, de Assumpção PP, Ribeiro-dos-Santos Â, Santos S. Global Analyses of Expressed Piwi-Interacting RNAs in Gastric Cancer. Int J Mol Sci 2020; 21:E7656. [PMID: 33081152 PMCID: PMC7593925 DOI: 10.3390/ijms21207656] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/07/2020] [Accepted: 08/18/2020] [Indexed: 12/15/2022] Open
Abstract
Gastric cancer (GC) represents a notable amount of morbidity and mortality worldwide. Understanding the molecular basis of CG will offer insight into its pathogenesis in an attempt to identify new molecular biomarkers to early diagnose this disease. Therefore, studies involving small non-coding RNAs have been widely explored. Among these, PIWI-interacting RNAs (piRNAs) are an emergent class that can play important roles in carcinogenesis. In this study, small-RNA sequencing was used to identify the global piRNAs expression profile (piRNome) of gastric cancer patients. We found 698 piRNAs in gastric tissues, 14 of which were differentially expressed (DE) between gastric cancer (GC), adjacent to gastric cancer (ADJ), and non-cancer tissues (NC). Moreover, three of these DE piRNAs (piR-48966*, piR-49145, piR-31335*) were differently expressed in both GC and ADJ samples in comparison to NC samples, indicating that the tumor-adjacent tissue was molecularly altered and should not be considered as a normal control. These three piRNAs are potential risk biomarkers for GC, especially piR-48966* and piR-31335*. Furthermore, an in-silico search for mRNAs targeted by the differentially expressed piRNAs revealed that these piRNAs may regulate genes that participate in cancer-related pathways, suggesting that these small non-coding RNAs may be directly and indirectly involved in gastric carcinogenesis.
Collapse
Affiliation(s)
- Tatiana Vinasco-Sandoval
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Fabiano Cordeiro Moreira
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Amanda F. Vidal
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Pablo Pinto
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - André M. Ribeiro-dos-Santos
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Rebecca L. S. Cruz
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Gleyce Fonseca Cabral
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Ana K. M. Anaissi
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Katia de Paiva Lopes
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Arthur Ribeiro-dos-Santos
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
| | - Samia Demachki
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Paulo Pimentel de Assumpção
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Ândrea Ribeiro-dos-Santos
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| | - Sidney Santos
- Graduate Program in Genetics and Molecular Biology, Laboratory of Human and Medical Genetics, Federal University of Pará, Belém, Pará 66075-110, Brazil; (T.V.-S.); (F.C.M.); (A.F.V.); (P.P.); (A.M.R.-d.-S.); (R.L.S.C.); (G.F.C.); (K.d.P.L.); (A.R.-d.-S.); (Â.R.-d.-S.)
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Research, Federal University of Pará, Belém, Pará 66063-023, Brazil; (A.K.M.A.); (S.D.); (P.P.d.A.)
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Abstract
Targeted cancer therapy aims to achieve specific elimination of cancerous but not normal cells. Recently, PIWI proteins, a subfamily of the PAZ-PIWI domain (PPD) protein family, have emerged as promising candidates for targeted cancer therapy. PPD proteins are essential for small noncoding RNA pathways. The Argonaute subfamily partners with microRNA and small interfering RNA, whereas the PIWI subfamily partners with PIWI-interacting RNA (piRNA). Both PIWI proteins and piRNA are mostly expressed in the germline and best known for their function in transposon silencing, with no detectable function in mammalian somatic tissues. However, PIWI proteins become aberrantly expressed in multiple types of somatic cancers, thus gaining interest in targeted therapy. Despite this, little is known about the regulatory mechanism of PIWI proteins in cancer. Here we report that one of the four PIWI proteins in humans, PIWIL1, is highly expressed in gastric cancer tissues and cell lines. Knocking out the PIWIL1 gene (PIWIL1-KO) drastically reduces gastric cancer cell proliferation, migration, metastasis, and tumorigenesis. RNA deep sequencing of gastric cancer cell line SNU-1 reveals that KO significantly changes the transcriptome, causing the up-regulation of most of its associated transcripts. Surprisingly, few bona fide piRNAs exist in gastric cancer cells. Furthermore, abolishing the piRNA-binding activity of PIWIL1 does not affect its oncogenic function. Thus, PIWIL1 function in gastric cancer cells is independent of piRNA. This piRNA-independent regulation involves interaction with the UPF1-mediated nonsense-mediated mRNA decay (NMD) mechanism. Altogether, our findings reveal a piRNA-independent function of PIWIL1 in promoting gastric cancer.
Collapse
|
31
|
Abstract
Liver cancer is one of the most common and deadly cancers in the world. In recent years, non-coding RNA has been a hot topic in liver cancer research. piRNAs (PIWI-interacting RNAs) are a new type of small non-coding RNA, which are formed by the PIWI proteins interacting with RNA. The latest research shows that piRNA and PIWI proteins are abnormally expressed in various cancers, including pancreatic, colorectal, breast, etc. piRNA plays an important regulatory role in liver cancer. In this review, we discuss the biological function of piRNAs and new progress in the development of liver cancer, and new targets and ideas for piRNA and PIWI proteins in the diagnosis and treatment of liver cancer.
Collapse
Affiliation(s)
- Jiamin Xu
- Graduate School of Nursing, Huzhou University, Huzhou, China
| | - Xi Yang
- Department of Oncology, Huzhou Cent Hosp, Affiliated Cent Hops Huzhou University, Huzhou, China
| | - Qing Zhou
- Department of Critical Care Medicine, Huzhou Cent Hosp, Affiliated Cent Hops Huzhou University, Huzhou, China
| | - Jing Zhuang
- Graduate School of Nursing, Huzhou University, Huzhou, China
| | - Shuwen Han
- Department of Oncology, Huzhou Cent Hosp, Affiliated Cent Hops Huzhou University, Huzhou, China
| |
Collapse
|
32
|
Mai D, Zheng Y, Guo H, Ding P, Bai R, Li M, Ye Y, Zhang J, Huang X, Liu D, Sui Q, Pan L, Su J, Deng J, Wu G, Li R, Deng S, Bai Y, Ligu Y, Tan W, Wu C, Wu T, Zheng J, Lin D. Serum piRNA-54265 is a New Biomarker for early detection and clinical surveillance of Human Colorectal Cancer. Am J Cancer Res 2020; 10:8468-8478. [PMID: 32754257 PMCID: PMC7392023 DOI: 10.7150/thno.46241] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/28/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Our previous study has demonstrated an oncogenic role of PIWI-interacting RNA-54265 (piR-54265) in colorectal cancer (CRC). Here, we investigate whether it can be a blood biomarker for population screening and clinical applications. Methods: Serum piR-54265 levels were determined by a digital PCR method in 209 cancer-free healthy controls, 725 patients with CRC, 1303 patients with other types of digestive cancer and 192 patients with benign colorectal tumors. A prospective case-control analysis was conducted to assess the predictive value of serum piR-54265 for future CRC diagnosis. Receiver operating characteristic (ROC) curve was constructed to quantify the diagnostic performance of serum piR-54265 levels by assessing its sensitivity, specificity and respective areas under curve (AUC). The odds ratios (ORs) were computed using multivariate logistic regression models. Results: Serum piR-54265 levels were significantly elevated only in patients with CRC compared with controls and patients with other cancer types. The AUC for recognizing CRC was 0.896 (95% CI, 0.874-0.914), with a sensitivity and specificity being 85.7% and 65.1% at 1500 copies/µL as a cut-off value. The serum piR-54265 levels in patients declined substantially after surgery but increased significantly again when tumor relapses. The prediagnostic serum piR-54265 levels were significantly associated with future CRC diagnosis, with the ORs of 7.23, 2.80, 2.45, and 1.24 for those whose CRC was diagnosed within 1, 2, 3 and >3 years. Serum piR-54265 test is more sensitive than other blood CRC markers. Conclusion: Serum piR-54265 may serve as a valuable biomarker for CRC screening, early detection and clinical surveillance.
Collapse
|
33
|
Boukelia A, Boucheham A, Belguidoum M, Batouche M, Zehraoui F, Tahi F. A Novel Integrative Approach for Non-coding RNA Classification Based on Deep Learning. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191105160633] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background:
Molecular biomarkers show new ways to understand many disease
processes. Noncoding RNAs as biomarkers play a crucial role in several cellular activities, which
are highly correlated to many human diseases especially cancer. The classification and the
identification of ncRNAs have become a critical issue due to their application, such as biomarkers
in many human diseases.
Objective:
Most existing computational tools for ncRNA classification are mainly used for
classifying only one type of ncRNA. They are based on structural information or specific known
features. Furthermore, these tools suffer from a lack of significant and validated features.
Therefore, the performance of these methods is not always satisfactory.
Methods:
We propose a novel approach named imCnC for ncRNA classification based on
multisource deep learning, which integrates several data sources such as genomic and epigenomic
data to identify several ncRNA types. Also, we propose an optimization technique to visualize the
extracted features pattern from the multisource CNN model to measure the epigenomics features
of each ncRNA type.
Results:
The computational results using a dataset of 16 human ncRNA classes downloaded from
RFAM show that imCnC outperforms the existing tools. Indeed, imCnC achieved an accuracy of
94,18%. In addition, our method enables to discover new ncRNA features using an optimization
technique to measure and visualize the features pattern of the imCnC classifier.
Collapse
Affiliation(s)
- Abdelbasset Boukelia
- Computer Science Department, Faculty NTIC, University Abdelhamid Mehri Constantine 2, Constantine 25000, Algeria
| | - Anouar Boucheham
- University Salah Boubnider Constantine 3, Constantine 25000, Algeria
| | - Meriem Belguidoum
- Computer Science Department, Faculty NTIC, University Abdelhamid Mehri Constantine 2, Constantine 25000, Algeria
| | - Mohamed Batouche
- IT Department, CCIS - RC, Princess Nourah University, Riyadh, Saudi Arabia
| | - Farida Zehraoui
- IBISC, University Evry, University Paris-Saclay, Evry, France
| | - Fariza Tahi
- IBISC, University Evry, University Paris-Saclay, Evry, France
| |
Collapse
|
34
|
Esmaeili M, Keshani M, Vakilian M, Esmaeili M, Peymani M, Seyed Forootan F, Chau TL, Göktuna SI, Zaker SR, Nasr Esfahani MH, Ghaedi K. Role of non-coding RNAs as novel biomarkers for detection of colorectal cancer progression through interaction with the cell signaling pathways. Gene 2020; 753:144796. [PMID: 32450203 DOI: 10.1016/j.gene.2020.144796] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/06/2020] [Accepted: 05/19/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is one of the most common types of cancer which affects the colon and the rectum. Approximately one third of annual CRC mortality occurs due to the late detection of this type of cancer. Therefore, there is an urgent need for more powerful diagnostic and prognostic tools for identification and treatment of colorectal tumorigenesis. Non-coding RNAs (ncRNAs) have been implicated in the pathology of CRC and also linked to metastasis, proliferation, differentiation, migration, angiogenesis and apoptosis in numerous cancers. Recently, attention has turned towards ncRNAs as specific targets for diagnosis, prognosis and treatment of various types of cancers, including CRC. In this review, we have tried to outline the roles of ncRNAs, and their involvement in signaling pathways responsible for the progression of CRC.
Collapse
Affiliation(s)
- Mohadeseh Esmaeili
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran.
| | - Maryam Keshani
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran.
| | - Mehrdad Vakilian
- Department of Cell Regeneration and Advanced Therapies, Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Pablo de Olavide-University of Seville-CSIC, Sevilla, Spain; Department of Cellular Biology, Genetics and Physiology, Faculty of Science, University of Malaga (UMA), Málaga, Spain.
| | - Maryam Esmaeili
- Department of Cellular Biotechnology, Cell Science Research Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran; Department of Cellular Biotechnology, Cell Science Research Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Farzad Seyed Forootan
- Department of Cellular Biotechnology, Cell Science Research Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran; Legal Medicine Research Centre, Legal Medicine Organization, Tehran, Iran.
| | - Tieu Lan Chau
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey.
| | - Serkan Ismail Göktuna
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara, Turkey; National Nanotechnology Research Institute (UNAM), Bilkent University, Ankara, Turkey.
| | - Sayed Rasoul Zaker
- Department of Plant and Animal Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Mohammad Hossein Nasr Esfahani
- Department of Cellular Biotechnology, Cell Science Research Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran; Department of Cellular Biotechnology, Cell Science Research Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran.
| |
Collapse
|
35
|
Valkov N, Das S. Y RNAs: Biogenesis, Function and Implications for the Cardiovascular System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1229:327-342. [PMID: 32285422 DOI: 10.1007/978-981-15-1671-9_20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In recent years, progress in the field of high-throughput sequencing technology and its application to a wide variety of biological specimens has greatly advanced the discovery and cataloging of a diverse set of non-coding RNAs (ncRNAs) that have been found to have unexpected biological functions. Y RNAs are an emerging class of highly conserved, small ncRNAs. There is a growing number of reports in the literature demonstrating that Y RNAs and their fragments are not just random degradation products but are themselves bioactive molecules. This review will outline what is currently known about Y RNA including biogenesis, structure and functional roles. In addition, we will provide an overview of studies reporting the presence and functions attributed to Y RNAs in the cardiovascular system.
Collapse
Affiliation(s)
- Nedyalka Valkov
- Cardiovascular Research Center of Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Saumya Das
- Cardiovascular Research Center of Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
36
|
Lin Y, Qian F, Shen L, Chen F, Chen J, Shen B. Computer-aided biomarker discovery for precision medicine: data resources, models and applications. Brief Bioinform 2020; 20:952-975. [PMID: 29194464 DOI: 10.1093/bib/bbx158] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 10/17/2017] [Indexed: 12/21/2022] Open
Abstract
Biomarkers are a class of measurable and evaluable indicators with the potential to predict disease initiation and progression. In contrast to disease-associated factors, biomarkers hold the promise to capture the changeable signatures of biological states. With methodological advances, computer-aided biomarker discovery has now become a burgeoning paradigm in the field of biomedical science. In recent years, the 'big data' term has accumulated for the systematical investigation of complex biological phenomena and promoted the flourishing of computational methods for systems-level biomarker screening. Compared with routine wet-lab experiments, bioinformatics approaches are more efficient to decode disease pathogenesis under a holistic framework, which is propitious to identify biomarkers ranging from single molecules to molecular networks for disease diagnosis, prognosis and therapy. In this review, the concept and characteristics of typical biomarker types, e.g. single molecular biomarkers, module/network biomarkers, cross-level biomarkers, etc., are explicated on the guidance of systems biology. Then, publicly available data resources together with some well-constructed biomarker databases and knowledge bases are introduced. Biomarker identification models using mathematical, network and machine learning theories are sequentially discussed. Based on network substructural and functional evidences, a novel bioinformatics model is particularly highlighted for microRNA biomarker discovery. This article aims to give deep insights into the advantages and challenges of current computational approaches for biomarker detection, and to light up the future wisdom toward precision medicine and nation-wide healthcare.
Collapse
Affiliation(s)
- Yuxin Lin
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
| | - Fuliang Qian
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
| | - Li Shen
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
| | - Feifei Chen
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
| | - Jiajia Chen
- School of Chemistry, Biology and Material Engineering, Suzhou University of Science and Technology, China
| | - Bairong Shen
- Center for Systems Biology, Soochow University, Suzhou, Jiangsu, China
| |
Collapse
|
37
|
Fonseca Cabral G, Azevedo dos Santos Pinheiro J, Vidal AF, Santos S, Ribeiro-dos-Santos Â. piRNAs in Gastric Cancer: A New Approach Towards Translational Research. Int J Mol Sci 2020; 21:ijms21062126. [PMID: 32204558 PMCID: PMC7139476 DOI: 10.3390/ijms21062126] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/11/2020] [Accepted: 02/18/2020] [Indexed: 12/12/2022] Open
Abstract
Background: Gastric cancer is currently the third leading cause of cancer-related deaths worldwide, usually diagnosed at late stages. The development of new biomarkers to improve its prevention and patient management is critical for disease control. piRNAs are small regulatory RNAs important for gene silencing mechanisms, mainly associated with the silencing of transposable elements. piRNA pathways may also be involved in gene regulation and the deregulation of piRNAs may be an important factor in carcinogenic processes. Thus, several studies suggest piRNAs as potential cancer biomarkers. Translational studies suggest that piRNAs may regulate key genes and pathways associated with gastric cancer progression, though there is no functional annotation in piRNA databases. The impacts of genetic variants in piRNA genes and their influence in gastric cancer development remains elusive, highlighting the gap in piRNA regulatory mechanisms knowledge. Here, we discuss the current state of understanding of piRNA-mediated regulation and piRNA functions and suggest that genetic alterations in piRNA genes may affect their functionality, thus, it may be associated with gastric carcinogenesis. Conclusions: In the era of precision medicine, investigations about genetic and epigenetic mechanisms are essential to further comprehend gastric carcinogenesis and the role of piRNAs as potential biomarkers for translational research.
Collapse
Affiliation(s)
- Gleyce Fonseca Cabral
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
| | - Jhully Azevedo dos Santos Pinheiro
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
| | - Amanda Ferreira Vidal
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
| | - Sidney Santos
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
- Programa de Pós-Graduacão em Oncologia e Ciências Médicas, Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66.073-000, PA, Brazil
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Pará, Belém 66.075-110, PA, Brazil; (G.F.C.); (J.A.d.S.P.); (A.F.V.); (S.S.)
- Programa de Pós-Graduacão em Oncologia e Ciências Médicas, Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66.073-000, PA, Brazil
- Correspondence: ; Tel.: +55-091-3201-7843
| |
Collapse
|
38
|
Das B, Jain N, Mallick B. piR‐39980 promotes cell proliferation, migration and invasion, and inhibits apoptosis via repression of SERPINB1 in human osteosarcoma. Biol Cell 2020; 112:73-91. [DOI: 10.1111/boc.201900063] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/14/2019] [Accepted: 12/16/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Basudeb Das
- RNAi and Functional Genomics LaboratoryDepartment of Life ScienceNational Institute of Technology Rourkela 769008 Odisha India
| | - Neha Jain
- RNAi and Functional Genomics LaboratoryDepartment of Life ScienceNational Institute of Technology Rourkela 769008 Odisha India
| | - Bibekanand Mallick
- RNAi and Functional Genomics LaboratoryDepartment of Life ScienceNational Institute of Technology Rourkela 769008 Odisha India
| |
Collapse
|
39
|
Kamalidehghan B, Habibi M, Afjeh SS, Shoai M, Alidoost S, Almasi Ghale R, Eshghifar N, Pouresmaeili F. The Importance of Small Non-Coding RNAs in Human Reproduction: A Review Article. APPLICATION OF CLINICAL GENETICS 2020; 13:1-11. [PMID: 32021379 PMCID: PMC6956659 DOI: 10.2147/tacg.s207491] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 12/04/2019] [Indexed: 12/14/2022]
Abstract
Background MicroRNAs (miRNA) play a key role in the regulation of gene expression through the translational suppression and control of post-transcriptional modifications. Aim Previous studies demonstrated that miRNAs conduct the pathways involved in human reproduction including maintenance of primordial germ cells (PGCs), spermatogenesis, oocyte maturation, folliculogenesis and corpus luteum function. The association of miRNA expression with infertility, polycystic ovary syndrome (PCOS), premature ovarian failure (POF), and repeated implantation failure (RIF) was previously revealed. Furthermore, there are evidences of the importance of miRNAs in embryonic development and implantation. Piwi-interacting RNAs (piRNAs) and miRNAs play an important role in the post-transcriptional regulatory processes of germ cells. Indeed, the investigation of small RNAs including miRNAs and piRNAs increase our understanding of the mechanisms involved in fertility. In this review, the current knowledge of microRNAs in embryogenesis and fertility is discussed. Conclusion Further research is necessary to provide new insights into the application of small RNAs in the diagnosis and therapeutic approaches to infertility.
Collapse
Affiliation(s)
- Behnam Kamalidehghan
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Habibi
- Central Laboratory, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sara S Afjeh
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Shoai
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Saeideh Alidoost
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Rouzbeh Almasi Ghale
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Nahal Eshghifar
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran and Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Farkhondeh Pouresmaeili
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
40
|
Martinez VG, Munera-Maravilla E, Bernardini A, Rubio C, Suarez-Cabrera C, Segovia C, Lodewijk I, Dueñas M, Martínez-Fernández M, Paramio JM. Epigenetics of Bladder Cancer: Where Biomarkers and Therapeutic Targets Meet. Front Genet 2019; 10:1125. [PMID: 31850055 PMCID: PMC6902278 DOI: 10.3389/fgene.2019.01125] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022] Open
Abstract
Bladder cancer (BC) is the most common neoplasia of the urothelial tract. Due to its high incidence, prevalence, recurrence and mortality, it remains an unsolved clinical and social problem. The treatment of BC is challenging and, although immunotherapies have revealed potential benefit in a percentage of patients, it remains mostly an incurable disease at its advanced state. Epigenetic alterations, including aberrant DNA methylation, altered chromatin remodeling and deregulated expression of non-coding RNAs are common events in BC and can be driver events in BC pathogenesis. Accordingly, these epigenetic alterations are now being used as potential biomarkers for these disorders and are being envisioned as potential therapeutic targets for the future management of BC. In this review, we summarize the recent findings in these emerging and exciting new aspects paving the way for future clinical treatment of this disease.
Collapse
Affiliation(s)
- Victor G. Martinez
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Ester Munera-Maravilla
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Alejandra Bernardini
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Carolina Rubio
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Cristian Suarez-Cabrera
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Cristina Segovia
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Iris Lodewijk
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
| | - Marta Dueñas
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Mónica Martínez-Fernández
- Genomes & Disease Lab, CiMUS (Center for Research in Molecular Medicine and Chronic Diseases), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jesus Maria Paramio
- Biomedical Research Institute I + 12, University Hospital 12 de Octubre, Madrid, Spain
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| |
Collapse
|
41
|
Yao H, Wang X, Song J, Wang Y, Song Q, Han J. Coxsackievirus B3 infection induces changes in the expression of numerous piRNAs. Arch Virol 2019; 165:105-114. [PMID: 31741095 DOI: 10.1007/s00705-019-04451-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 09/26/2019] [Indexed: 01/02/2023]
Abstract
Piwi-interacting RNAs (piRNAs) play pivotal roles in spermatogenesis and are widely distributed among somatic tissues. However, little is known about piRNAs in HeLa cells infected with coxsackievirus B3 (CVB3). In this study, we systematically investigated changes in piRNA expression in HeLa cells infected with CVB3 using high-throughput sequencing technology. piRNA expression profiles in CVB3-infected HeLa cells were examined at 3, 6 and 9 h postinfection (pi). Of the 32,826 piRNAs that were annotated in the NCBI database, 151,571, 89,698 and 76,626 piRNAs were detected in CVB3-infected HeLa cells at 3, 6 and 9 h pi, respectively. Compared with normal cells, 211, 72 and 94 piRNAs were differentially expressed in CVB3-infected HeLa cells at 3, 6 and 9 h pi, respectively. Thirteen piRNAs, including four novel piRNAs, exhibited concurrent changes in CVB3-infected HeLa cells. The changes in the expression of these 13 piRNAs was confirmed in CVB3-infected HeLa cells and 293T cells by stem-loop RT-qPCR at 3, 6 and 9 h pi. The target genes of 13 piRNAs were predicted. The four novel piRNAs were associated with LTR/ERV, LINE/L1 and LTR/ERVK repetitive elements located on different chromosomes. These findings may promote a better understanding of the regulatory mechanism of pathophysiological changes induced by CVB3 infection.
Collapse
Affiliation(s)
- Hailan Yao
- Molecular Immunology Laboratory, Capital Institute of Pediatrics, 2 YaBao Rd, Beijing, 100020, China
| | - Xinling Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 155 Changbai Rd, Beijing, 102206, China
| | - Juan Song
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 155 Changbai Rd, Beijing, 102206, China
| | - Yanhai Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 155 Changbai Rd, Beijing, 102206, China
| | - Qinqin Song
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 155 Changbai Rd, Beijing, 102206, China
| | - Jun Han
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 155 Changbai Rd, Beijing, 102206, China.
| |
Collapse
|
42
|
Jia R, He X, Ma W, Lei Y, Cheng H, Sun H, Huang J, Wang K. Aptamer-Functionalized Activatable DNA Tetrahedron Nanoprobe for PIWI-Interacting RNA Imaging and Regulating in Cancer Cells. Anal Chem 2019; 91:15107-15113. [PMID: 31691558 DOI: 10.1021/acs.analchem.9b03819] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
It has been reported that PIWI-interacting RNAs (piRNAs) play critical roles in activating invasion and metastasis, evading growth suppressors, and sustaining proliferative signaling of cancer and can be regarded as a novel biomarker candidate. Thus, it is necessary to develop an effective method for imaging and regulating cancer-related piRNAs to diagnose and treat cancers. Herein, we designed aptamer-functionalized activatable DNA tetrahedron nanoprobes (apt-ADTNs) to image and regulate endogenous piRNAs in cancer cells. As proof of concept, overexpressed piRNA-36026 in MCF-7 cells was used for this study. In brief, aptamer AS1411 and piRNA-36026 antisequence with Cy5 fluorescent dye are appended from the DNA tetrahedron; then, a short oligonucleotide with black hole quencher 2 (Q-oligo) is complementary with piRNA-36026 antisequence to quench the fluorescence of Cy5. The apt-ADTNs can recognize the MCF-7 cells through aptamer AS1411, and then enter the cells. Q-oligo is detached from the apt-ADTNs because of the binding between apt-ADTNs and piRNA-36026, leading to the recovery of the Cy5 fluorescence signal. Meanwhile, the hybridization of apt-ADTNs and piRNA-36026 results in down-regulating of dissociative piRNA-36026 in cytoplasm and the subsequent apoptosis of MCF-7 cells. As the achievement of synchronously imaging and regulating piRNA-36026 in MCF-7 cells, we believe that this design holds great promise in application of diagnosis and therapy for cancer.
Collapse
Affiliation(s)
- Ruichen Jia
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
| | - Xiaoxiao He
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
| | - Wenjie Ma
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
| | - Yanli Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
| | - Hong Cheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
| | - Huanhuan Sun
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering , Hunan University, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province , Changsha 410082 , China
| |
Collapse
|
43
|
Zuo Y, Liang Y, Zhang J, Hao Y, Li M, Wen Z, Zhao Y. Transcriptome Analysis Identifies Piwi-Interacting RNAs as Prognostic Markers for Recurrence of Prostate Cancer. Front Genet 2019; 10:1018. [PMID: 31695724 PMCID: PMC6817565 DOI: 10.3389/fgene.2019.01018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 09/24/2019] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer remains the second leading cause of male cancer death, and there is an unmet need for biomarkers to identify patients with such aggressive disease. Piwi-inteacting RNAs (piRNAs) have been classified as transcriptional and posttranscriptional regulators in somatic cells. In this study, we discovered three piRNAs as novel prognostic markers and their association with prostate cancer biochemical recurrence was confirmed in validation data set. To obtain a better understanding of piRNA expression patterns in prostate cancer and to find gene coexpression with piRNAs, we performed weighted gene coexpression network analysis. Target genes of three piRNAs have also been predicted based on base complementarity and expression correlativity. Functional analysis revealed the relationships between target genes and prostate cancer. Our work also identified differential expression of piRNAs between Gleason stage 3 + 4 and 4 + 3 prostate cancer. Overall, this study may explain the roles and demonstrate the potential clinical utility of piRNAs in prostate cancer in a way.
Collapse
Affiliation(s)
- Yuanli Zuo
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yu Liang
- College of Chemistry, Sichuan University, Chengdu, China
| | - Jiting Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yingyi Hao
- College of Chemistry, Sichuan University, Chengdu, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, China
| | - Zhining Wen
- College of Chemistry, Sichuan University, Chengdu, China.,Medical Big Data Center, Sichuan University, Chengdu, China
| | - Yun Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| |
Collapse
|
44
|
Yu Y, Xiao J, Hann SS. The emerging roles of PIWI-interacting RNA in human cancers. Cancer Manag Res 2019; 11:5895-5909. [PMID: 31303794 PMCID: PMC6612017 DOI: 10.2147/cmar.s209300] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/14/2019] [Indexed: 12/17/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) are a type of non-coding RNAs that interact with PIWI proteins, which are members of the argonaute family. Originally described in the germline, piRNAs are also expressed in human somatic cells in a tissue-specific manner. piRNAs are involved in spermatogenesis, germ stem-cell maintenance, silencing of transposon, epigenetic and genomic regulation and rearrangement. A large number of studies have demonstrated that expression of piRNAs is involved in many kinds of disease, including cancer. Abnormal expression of piRNAs is emerging as a critical player in cancer cell proliferation, apoptosis, invasion, and migration in vitro and in vivo. Functionally, piRNAs maintain genomic integrity by repressing the mobilization of transposable elements, and regulate the expression of downstream target genes via transcriptional or post-transcriptional mechanisms. Furthermore, altered expression of piRNAs in cancer is linked to clinical outcome, highlighting the important role that they may play as novel diagnostic and prognostic biomarkers, and as therapeutic targets for cancer therapy. In this review, we focus on the biogenesis and the functional roles of piRNAs in cancers, discuss emerging insights into the roles of piRNAs in the occurrence, progression, and treatment of cancers, reveal various mechanisms underlying piRNAs-mediated gene regulation, and highlight their potential clinical utilities as biomarkers as well as potential targets for cancer treatment.
Collapse
Affiliation(s)
- Yaya Yu
- Laboratory of Tumor Biology, The Second Clinical College of Guangzhou University of Chinese Medicine , Guangzhou, Guangdong Province, 510120, People's Republic of China
| | - Jing Xiao
- Department of Gynecology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, People's Republic of China
| | - Swei Sunny Hann
- Laboratory of Tumor Biology, The Second Clinical College of Guangzhou University of Chinese Medicine , Guangzhou, Guangdong Province, 510120, People's Republic of China.,Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, 510120, People's Republic of China
| |
Collapse
|
45
|
Klimenko OV, Sidorov A. The full recovery of mice (Mus Musculus C57BL/6 strain) from virus-induced sarcoma after treatment with a complex of DDMC delivery system and sncRNAs. Noncoding RNA Res 2019; 4:69-78. [PMID: 31193489 PMCID: PMC6531865 DOI: 10.1016/j.ncrna.2019.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/22/2019] [Accepted: 03/22/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Virus-induced cellular genetic modifications result in the development of many human cancers. METHODS In our experiments, we used the RVP3 cell line, which produce primary mouse virus-induced sarcoma in 100% of cases. Inbreed 4-week-old female C57BL/6 mice were injected subcutaneously in the interscapular region with RVP3 cells. Three groups of mice were used. For treatment, one and/or two intravenous injections of a complex of small non-coding RNAs (sncRNAs) a-miR-155, piR-30074, and miR-125b with a 2-diethylaminoethyl-dextran methyl methacrylate copolymer (DDMC) delivery system were used. The first group consisted of untreated animals (control). The second group was treated with one injection of complex DDMC/sncRNAs (1st group). The third group was treated with two injections of complex DDMC/sncRNAs (2nd group). The tumors were removed aseptically, freed of necrotic material, and used with spleen and lungs for subsequent RT-PCR and immunofluorescence experiments, or stained with Leishman-Romanowski dye. RESULTS As a result, the mice fully recovered from virus-induced sarcoma after two treatments with a complex including the DDMC vector and a-miR-155, piR-30074, and miR-125b. In vitro studies showed genetic and morphological transformations of murine cancer cells after the injections. CONCLUSIONS Treatment of virus-induced sarcoma of mice with a-miR-155, piR-30074, and miR-125b as active component of anti-cancer complex and DDMC vector as delivery system due to epigenetic-regulated transformation of cancer cells into cells with non-cancerous physiology and morphology and full recovery of disease.
Collapse
Affiliation(s)
- Oxana V. Klimenko
- SID ALEX GROUP, Ltd., Kyselova 1185/2, Prague, 182 00, Czech Republic
| | | |
Collapse
|
46
|
Qu A, Wang W, Yang Y, Zhang X, Dong Y, Zheng G, Wu Q, Zou M, Du L, Wang Y, Wang C. A serum piRNA signature as promising non-invasive diagnostic and prognostic biomarkers for colorectal cancer. Cancer Manag Res 2019; 11:3703-3720. [PMID: 31118791 PMCID: PMC6500438 DOI: 10.2147/cmar.s193266] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 03/06/2019] [Indexed: 12/21/2022] Open
Abstract
Purpose: Piwi-interacting RNAs (piRNAs) are a novel class of small non-coding RNAs, which are not easily degraded but detectable in human body fluids. Recent studies have shown that aberrant piRNA expression is a signature feature across multiple tumor types. However, the expressions of piRNAs in serum of tumor patients and their potential clinical values remain largely unclear. Patients and methods: High-throughput sequencing was performed to investigate the serum piRNA profiles, followed by evaluations in serum samples of 220 colorectal cancer (CRC) patients and 220 healthy controls using reverse transcription quantitative real-time PCR (RT-qPCR). Biomarker panels including piRNA-based Panel I and carcinoembryonic antigen (CEA)-based Panel II, were developed by logistic regression model, and their diagnostic potentials were compared. Fagan's nomogram was plotted to promote clinical application. Results: We identified five differentially expressed serum piRNAs (piR-001311, piR-004153, piR-017723, piR-017724 and piR-020365), which, when combined in the piRNA-based Panel I, outperformed the CEA-based Panel II (P<0.001) and could detect CRC with an area under the receiver operating characteristic curve of 0.867. In addition, Kaplan-Meier analysis showed that patients with low serum piR-017724 level had worse overall survival (OS) and progression-free survival (PFS). In multivariate Cox regression analysis, serum piR-017724 was an independent prognostic factor for OS and PFS (P<0.05). Conclusion: Our findings suggest serum piRNA expression signatures have potential for use as biomarkers for CRC detection and to predict prognosis at the time of diagnosis.
Collapse
Affiliation(s)
- Ailin Qu
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, People's Republic of China
| | - Wenfei Wang
- Humanistic Medicine Research Center, Qilu Hospital, Shandong University, Jinan, Shandong 250012, People's Republic of China.,Humanistic Medicine Research Center, Shandong University, Jinan, Shandong 250012, People's Republic of China
| | - Yongmei Yang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong 250012, People's Republic of China
| | - Xin Zhang
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong 250012, People's Republic of China
| | - Yuhuan Dong
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong 250012, People's Republic of China
| | - Guixi Zheng
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong 250012, People's Republic of China
| | - Qiuyan Wu
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong 250012, People's Republic of China
| | - Mingjin Zou
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, Shandong 250012, People's Republic of China
| | - Lutao Du
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, People's Republic of China
| | - Yunshan Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, People's Republic of China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong 250033, People's Republic of China
| |
Collapse
|
47
|
The Roles of Human DNA Methyltransferases and Their Isoforms in Shaping the Epigenome. Genes (Basel) 2019; 10:genes10020172. [PMID: 30813436 PMCID: PMC6409524 DOI: 10.3390/genes10020172] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/16/2019] [Accepted: 02/19/2019] [Indexed: 12/20/2022] Open
Abstract
A DNA sequence is the hard copy of the human genome and it is a driving force in determining the physiological processes in an organism. Concurrently, the chemical modification of the genome and its related histone proteins is dynamically involved in regulating physiological processes and diseases, which overall constitutes the epigenome network. Among the various forms of epigenetic modifications, DNA methylation at the C-5 position of cytosine in the cytosine–guanine (CpG) dinucleotide is one of the most well studied epigenetic modifications. DNA methyltransferases (DNMTs) are a family of enzymes involved in generating and maintaining CpG methylation across the genome. In mammalian systems, DNA methylation is performed by DNMT1 and DNMT3s (DNMT3A and 3B). DNMT1 is predominantly involved in the maintenance of DNA methylation during cell division, while DNMT3s are involved in establishing de novo cytosine methylation and maintenance in both embryonic and somatic cells. In general, all DNMTs require accessory proteins, such as ubiquitin-like containing plant homeodomain (PHD) and really interesting new gene (RING) finger domain 1 (UHRF1) or DNMT3-like (DNMT3L), for their biological function. This review mainly focuses on the role of DNMT3B and its isoforms in de novo methylation and maintenance of DNA methylation, especially with respect to their role as an accessory protein.
Collapse
|
48
|
Calcagno DQ, Wisnieski F, Mota ERDS, Maia de Sousa SB, Costa da Silva JM, Leal MF, Gigek CO, Santos LC, Rasmussen LT, Assumpção PP, Burbano RR, Smith MAC. Role of histone acetylation in gastric cancer: implications of dietetic compounds and clinical perspectives. Epigenomics 2019; 11:349-362. [DOI: 10.2217/epi-2018-0081] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Histone modifications regulate the structural status of chromatin and thereby influence the transcriptional status of genes. These processes are controlled by the recruitment of different enzymes to a specific genomic site. Furthermore, obtaining an understanding of these mechanisms could help delineate alternative treatment and preventive strategies for cancer. For example, in gastric cancer, cholecalciferol, curcumin, resveratrol, quercetin, garcinol and sodium butyrate are natural regulators of acetylation and deacetylation enzyme activity that exert chemopreventive and anticancer effects. Here, we review the recent findings on histone acetylation in gastric cancer and discuss the effects of nutrients and bioactive compounds on histone acetylation and their potential role in the prevention and treatment of this type of cancer.
Collapse
Affiliation(s)
- Danielle Q Calcagno
- Programa de Pós-graduação em Oncologia e Ciências Médicas, Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
- Programa de Pós-graduação em Química Medicinal e Modelagem Molecular, Universidade Federal do Pará, Belém, PA, Brazil
- Residência Multiprofissional em Saúde/Oncologia, Hospital Universitário João de Barros Barreto, Universidade Federal do Pará, Belém, PA, Brazil
| | | | - Elizangela R da Silva Mota
- Programa de Pós-graduação em Química Medicinal e Modelagem Molecular, Universidade Federal do Pará, Belém, PA, Brazil
| | - Stefanie B Maia de Sousa
- Programa de Pós-graduação em Oncologia e Ciências Médicas, Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
| | | | - Mariana F Leal
- Programa de Pós-graduação em Oncologia e Ciências Médicas, Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
- Disciplina de Genética, Universidade Federal de São Paulo, SP, Brazil
| | - Carolina O Gigek
- Disciplina de Genética, Universidade Federal de São Paulo, SP, Brazil
- Departamento de Patologia, Universidade Federal de São Paulo, SP, Brazil
| | - Leonardo C Santos
- Disciplina de Genética, Universidade Federal de São Paulo, SP, Brazil
| | - Lucas T Rasmussen
- Disciplina de Genética, Universidade Federal de São Paulo, SP, Brazil
- Pró-Reitoria de Pesquisa e Pós-Graduação, Universidade do Sagrado Coração, Bauru, SP, Brazil
| | - Paulo P Assumpção
- Programa de Pós-graduação em Oncologia e Ciências Médicas, Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
| | - Rommel R Burbano
- Programa de Pós-graduação em Oncologia e Ciências Médicas, Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém, PA, Brazil
- Laboratório de Biologia Molecular, Hospital Ophir Loyola, Belém, PA, Brazil
| | - Marília AC Smith
- Disciplina de Genética, Universidade Federal de São Paulo, SP, Brazil
| |
Collapse
|
49
|
Araújo T, Khayat A, Quintana L, Calcagno D, Mourão R, Modesto A, Paiva J, Lima A, Moreira F, Oliveira E, Souza M, Othman M, Liehr T, Abdelhay E, Gomes R, Santos S, Assumpção P. Piwi like RNA-mediated gene silencing 1 gene as a possible major player in gastric cancer. World J Gastroenterol 2018; 24:5338-5350. [PMID: 30598579 PMCID: PMC6305533 DOI: 10.3748/wjg.v24.i47.5338] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/07/2018] [Accepted: 10/05/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To establish a permanent piwi like RNA-mediated gene silencing 1 (PIWIL1) gene knockout in AGP01 gastric cancer cell line using CRISPR-Cas9 system and analyze phenotypic modifications as well as gene expression alterations.
METHODS CRISPR-Cas9 system used was purchased from Dharmacon GE Life Sciences (Lafayette, CO, United States) and permanent knockout was performed according to manufacturer’s recommendations. Wound-healing assay was performed to investigate the effect of PIWIL1 knockout on migration capability of cells and Boyden chamber invasion assay was performed to investigate the effect on invasion capability. For the gene expression analysis, a one-color microarray-based gene expression analysis kit (Agilent Technologies, Santa Clara, CA, United States) was used according to the protocol provided by the manufacturer.
RESULTS PIWIL1 gene knockout caused a significant decrease in AGP01 migration capacity as well as a significant decrease in cell invasiveness. Moreover, functional analysis based on grouping of all differentially expressed mRNAs identified a total of 35 genes (5 up-regulated and 30 down-regulated) encoding proteins involved in cellular invasion and migration. According to current literature, 9 of these 35 genes (DOCK2, ZNF503, PDE4D, ABL1, ABL2, LPAR1, SMAD2, WASF3 and DACH1) are possibly related to the mechanisms used by PIWIL1 to promote carcinogenic effects related to migration and invasion, since their functions are consistent with the changes observed (being up- or down-regulated after knockout).
CONCLUSION Taken together, these data reinforce the idea that PIWIL1 plays a crucial role in the signaling pathway of gastric cancer, regulating several genes involved in migration and invasion processes; therefore, its use as a therapeutic target may generate promising results in the treatment of gastric cancer.
Collapse
Affiliation(s)
- Taíssa Araújo
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil
| | - André Khayat
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil
| | - Luciana Quintana
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil
| | - Danielle Calcagno
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil
| | - Ronald Mourão
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil
| | - Antônio Modesto
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil
| | - Juliana Paiva
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil
| | - Adhara Lima
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil
| | - Fabiano Moreira
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil
| | - Edivaldo Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, Instituto Evandro Chagas, Belém 66087-082, Brazil
| | - Michel Souza
- Laboratório de Cultura de Tecidos e Citogenética, Instituto Evandro Chagas, Belém 66087-082, Brazil
| | - Moneeb Othman
- Institute of Human Genetics, Universitätsklinikum Jena, Jena 07747, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Universitätsklinikum Jena, Jena 07747, Germany
| | - Eliana Abdelhay
- Laboratório de Célula Tronco, Centro de Transplante de Medula Óssea, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro 20230-130, Brazil
| | - Renata Gomes
- Laboratório de Célula Tronco, Centro de Transplante de Medula Óssea, Instituto Nacional de Câncer José Alencar Gomes da Silva, Rio de Janeiro 20230-130, Brazil
| | - Sidney Santos
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil
| | - Paulo Assumpção
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-000, Brazil
| |
Collapse
|
50
|
Non-coding RNAome of RPE cells under oxidative stress suggests unknown regulative aspects of Retinitis pigmentosa etiopathogenesis. Sci Rep 2018; 8:16638. [PMID: 30413775 PMCID: PMC6226517 DOI: 10.1038/s41598-018-35086-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/29/2018] [Indexed: 12/26/2022] Open
Abstract
The discovery of thousands of non-coding RNAs has revolutionized molecular biology, being implicated in several biological processes and diseases. To clarify oxidative stress role on Retinitis pigmentosa, a very heterogeneous and inherited ocular disorder group characterized by progressive retinal degeneration, we realized a comparative transcriptome analysis of human retinal pigment epithelium cells, comparing two groups, one treated with oxLDL and one untreated, in four time points (1 h, 2 h, 4 h, 6 h). Data analysis foresaw a complex pipeline, starting from CLC Genomics Workbench, STAR and TopHat2/TopHat-Fusion alignment comparisons, followed by transcriptomes assembly and expression quantification. We then filtered out non-coding RNAs and continued the computational analysis roadmap with specific tools and databases for long non-coding RNAs (FEELnc), circular RNAs (CIRCexplorer, UROBORUS, CIRI, KNIFE, CircInteractome) and piwi-interacting RNAs (piRNABank, piRNA Cluster, piRBase, PILFER). Finally, all detected non-coding RNAs underwent pathway analysis by Cytoscape software. Eight-hundred and fifty-four non-coding RNAs, between long non-coding RNAs and PIWI-interacting, were differentially expressed throughout all considered time points, in treated and untreated samples. These non-coding RNAs target host genes involved in several biochemical pathways are related to compromised response to oxidative stress, visual functions, synaptic impairment of retinal neurotransmission, impairment of the interphotoreceptor matrix and blood – retina barrier, all leading to retinal cell death. These data suggest that non-coding RNAs could play a relevant role in Retinitis pigmentosa etiopathogenesis.
Collapse
|