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Janssen FW, Lak NSM, Janda CY, Kester LA, Meister MT, Merks JHM, van den Heuvel-Eibrink MM, van Noesel MM, Zsiros J, Tytgat GAM, Looijenga LHJ. A comprehensive overview of liquid biopsy applications in pediatric solid tumors. NPJ Precis Oncol 2024; 8:172. [PMID: 39097671 PMCID: PMC11297996 DOI: 10.1038/s41698-024-00657-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/15/2024] [Indexed: 08/05/2024] Open
Abstract
Liquid biopsies are emerging as an alternative source for pediatric cancer biomarkers with potential applications during all stages of patient care, from diagnosis to long-term follow-up. While developments within this field are reported, these mainly focus on dedicated items such as a specific liquid biopsy matrix, analyte, and/or single tumor type. To the best of our knowledge, a comprehensive overview is lacking. Here, we review the current state of liquid biopsy research for the most common non-central nervous system pediatric solid tumors. These include neuroblastoma, renal tumors, germ cell tumors, osteosarcoma, Ewing sarcoma, rhabdomyosarcoma and other soft tissue sarcomas, and liver tumors. Within this selection, we discuss the most important or recent studies involving liquid biopsy-based biomarkers, anticipated clinical applications, and the current challenges for success. Furthermore, we provide an overview of liquid biopsy-based biomarker publication output for each tumor type based on a comprehensive literature search between 1989 and 2023. Per study identified, we list the relevant liquid biopsy-based biomarkers, matrices (e.g., peripheral blood, bone marrow, or cerebrospinal fluid), analytes (e.g., circulating cell-free and tumor DNA, microRNAs, and circulating tumor cells), methods (e.g., digital droplet PCR and next-generation sequencing), the involved pediatric patient cohort, and proposed applications. As such, we identified 344 unique publications. Taken together, while the liquid biopsy field in pediatric oncology is still behind adult oncology, potentially relevant publications have increased over the last decade. Importantly, steps towards clinical implementation are rapidly gaining ground, notably through validation of liquid biopsy-based biomarkers in pediatric clinical trials.
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Affiliation(s)
| | | | | | | | - Michael T Meister
- Princess Máxima Center, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Johannes H M Merks
- Princess Máxima Center, Utrecht, the Netherlands
- Division of Imaging and Oncology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - Marry M van den Heuvel-Eibrink
- Princess Máxima Center, Utrecht, the Netherlands
- Wilhelmina Children's Hospital-Division of CHILDHEALTH, University Medical Center Utrech, University of Utrecht, Utrecht, the Netherlands
| | - Max M van Noesel
- Princess Máxima Center, Utrecht, the Netherlands
- Division of Imaging and Oncology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | | | - Godelieve A M Tytgat
- Princess Máxima Center, Utrecht, the Netherlands
- Department of Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - Leendert H J Looijenga
- Princess Máxima Center, Utrecht, the Netherlands.
- Department of Pathology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands.
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2
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Modarresi Chahardehi A, Afrooghe A, Emtiazi N, Rafiei S, Rezaei NJ, Dahmardeh S, Farz F, Naderi Z, Arefnezhad R, Motedayyen H. MicroRNAs and angiosarcoma: are there promising reports? Front Oncol 2024; 14:1385632. [PMID: 38826780 PMCID: PMC11143796 DOI: 10.3389/fonc.2024.1385632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/06/2024] [Indexed: 06/04/2024] Open
Abstract
In recent years, microRNAs (miRNAs) have garnered increasing attention for their potential implications in cancer pathogenesis, functioning either as oncogenes or tumor suppressors. Notably, angiosarcoma, along with various other cardiovascular tumors such as lipomas, rhabdomyomas, hemangiomas, and myxomas, has shown variations in the expression of specific miRNA subtypes. A substantial body of evidence underscores the pivotal involvement of miRNAs in the genesis of angiosarcoma and certain cardiovascular tumors. This review aims to delve into the current literature on miRNAs and their prospective applications in cardiovascular malignancies, with a specific focus on angiosarcoma. It comprehensively covers diagnostic methods, prognostic evaluations, and potential treatments while providing a recapitulation of angiosarcoma's risk factors and molecular pathogenesis, with an emphasis on the role of miRNAs. These insights can serve as the groundwork for designing randomized control trials, ultimately facilitating the translation of these findings into clinical applications. Moving forward, it is imperative for studies to thoroughly scrutinize the advantages and disadvantages of miRNAs compared to current diagnostic and prognostic approaches in angiosarcoma and other cardiovascular tumors. Closing these knowledge gaps will be crucial for harnessing the full potential of miRNAs in the realm of angiosarcoma and cardiovascular tumor research.
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Affiliation(s)
| | - Arya Afrooghe
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Nikoo Emtiazi
- Department of Pathology, Firoozgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Sajjad Rafiei
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences, Birjand, Iran
| | | | - Sarvin Dahmardeh
- Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Farz
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Zahra Naderi
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Reza Arefnezhad
- Coenzyme R Research Institute, Tehran, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hossein Motedayyen
- Autoimmune Diseases Research Center, Kashan University of Medical Sciences, Kashan, Iran
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Berkholz J, Schmitt A, Fragasso A, Schmid AC, Munz B. Smyd1: Implications for novel approaches in rhabdomyosarcoma therapy. Exp Cell Res 2024; 434:113863. [PMID: 38097153 DOI: 10.1016/j.yexcr.2023.113863] [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: 10/28/2022] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/19/2023]
Abstract
Rhabdomyosarcoma (RMS), a tumor that consists of poorly differentiated skeletal muscle cells, is the most common soft-tissue sarcoma in children. Despite considerable progress within the last decades, therapeutic options are still limited, warranting the need for novel approaches. Recent data suggest deregulation of the Smyd1 protein, a sumoylation target as well as H3K4me2/3 methyltransferase and transcriptional regulator in myogenesis, and its binding partner skNAC, in RMS cells. Here, we show that despite the fact that most RMS cells express at least low levels of Smyd1 and skNAC, failure to upregulate expression of these genes in reaction to differentiation-promoting signals can always be observed. While overexpression of the Smyd1 gene enhances many aspects of RMS cell differentiation and inhibits proliferation rate and metastatic potential of these cells, functional integrity of the putative Smyd1 sumoylation motif and its SET domain, the latter being crucial for HMT activity, appear to be prerequisites for most of these effects. Based on these findings, we explored the potential for novel RMS therapeutic strategies, employing small-molecule compounds to enhance Smyd1 activity. In particular, we tested manipulation of (a) Smyd1 sumoylation, (b) stability of H3K4me2/3 marks, and (c) calpain activity, with calpains being important targets of Smyd1 in myogenesis. We found that specifically the last strategy might represent a promising approach, given that suitable small-molecule compounds will be available for clinical use in the future.
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Affiliation(s)
- Janine Berkholz
- Charité - University Medicine Berlin, Institute of Physiology, Charitéplatz 1, D-10117, Berlin, Germany
| | - Angelika Schmitt
- University Hospital Tübingen, Medical Clinic, Department of Sports Medicine, Hoppe-Seyler-Str. 6, D-72076, Tübingen, Germany
| | - Annunziata Fragasso
- University Hospital Tübingen, Medical Clinic, Department of Sports Medicine, Hoppe-Seyler-Str. 6, D-72076, Tübingen, Germany
| | - Anna-Celina Schmid
- University Hospital Tübingen, Medical Clinic, Department of Sports Medicine, Hoppe-Seyler-Str. 6, D-72076, Tübingen, Germany
| | - Barbara Munz
- University Hospital Tübingen, Medical Clinic, Department of Sports Medicine, Hoppe-Seyler-Str. 6, D-72076, Tübingen, Germany; Interfaculty Research Institute for Sport and Physical Activity, Eberhard Karls University of Tübingen, D-72074 / D-72076, Tübingen, Germany.
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Kjær EKR, Vase CB, Rossing M, Ahlborn LB, Hjalgrim LL. Detection of circulating tumor-derived material in peripheral blood of pediatric sarcoma patients: A systematic review. Transl Oncol 2023; 34:101690. [PMID: 37201250 DOI: 10.1016/j.tranon.2023.101690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND Detection of circulating tumor-derived material (cTM) in the peripheral blood (PB) of cancer patients has been shown to be useful in early diagnosis, prediction of prognosis, and disease monitoring. However, it has not yet been thoroughly evaluated for pediatric sarcoma patients. METHODS We searched the PubMed and EMBASE databases for studies reporting the detection of circulating tumor cells, circulating tumor DNA, and circulating RNA in PB of pediatric sarcoma patients. Data on performance in identifying cTM and its applicability in diagnosis, and evaluation of tumor characteristics, prognostic factors, and treatment response was extracted from publications. RESULTS A total of 79 studies were assigned for the present systematic review, including detection of circulating tumor cells (116 patients), circulating tumor DNA (716 patients), and circulating RNA (2887 patients). Circulating tumor cells were detected in 76% of patients. Circulating DNA was detected in 63% by targeted NGS, 66% by shallow WGS, and 79% by digital droplet PCR. Circulating RNA was detected in 37% of patients. CONCLUSION Of the cTM from Ewing's sarcoma and rhabdomyosarcoma ctDNA proved to be the best target for clinical application including diagnosis, tumor characterization, prognosis, and monitoring of disease progression and treatment response. For osteosarcoma the most promising targets are copy number alterations or patient specific micro RNAs, however, further investigations are needed to obtain consensus on clinical utility.
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Affiliation(s)
- Eva Kristine Ruud Kjær
- Department of Paediatrics and Adolescent Medicine, Paediatric Oncology Research Laboratory (Bonkolab), Copenhagen University Hospital Rigshospitalet, 5704, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| | - Christian Bach Vase
- Department of Paediatrics and Adolescent Medicine, Paediatric Oncology Research Laboratory (Bonkolab), Copenhagen University Hospital Rigshospitalet, 5704, Blegdamsvej 9, Copenhagen DK-2100, Denmark
| | - Maria Rossing
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark; Center for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Lise Barlebo Ahlborn
- Center for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Lisa Lyngsie Hjalgrim
- Department of Paediatrics and Adolescent Medicine, Paediatric Oncology Research Laboratory (Bonkolab), Copenhagen University Hospital Rigshospitalet, 5704, Blegdamsvej 9, Copenhagen DK-2100, Denmark.
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Teo AYT, Lim VY, Yang VS. MicroRNAs in the Pathogenesis, Prognostication and Prediction of Treatment Resistance in Soft Tissue Sarcomas. Cancers (Basel) 2023; 15:cancers15030577. [PMID: 36765536 PMCID: PMC9913386 DOI: 10.3390/cancers15030577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023] Open
Abstract
Soft tissue sarcomas are highly aggressive malignant neoplasms of mesenchymal origin, accounting for less than 1% of adult cancers, but comprising over 20% of paediatric solid tumours. In locally advanced, unresectable, or metastatic disease, outcomes from even the first line of systemic treatment are invariably poor. MicroRNAs (miRNAs), which are short non-coding RNA molecules, target and modulate multiple dysregulated target genes and/or signalling pathways within cancer cells. Accordingly, miRNAs demonstrate great promise for their utility in diagnosing, prognosticating and improving treatment for soft tissue sarcomas. This review aims to provide an updated discussion on the known roles of specific miRNAs in the pathogenesis of sarcomas, and their potential use in prognosticating outcomes and prediction of therapeutic resistance.
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Affiliation(s)
- Andrea York Tiang Teo
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Vivian Yujing Lim
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Valerie Shiwen Yang
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore 169857, Singapore
- Correspondence:
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Chellini L, Palombo R, Riccioni V, Paronetto MP. Oncogenic Dysregulation of Circulating Noncoding RNAs: Novel Challenges and Opportunities in Sarcoma Diagnosis and Treatment. Cancers (Basel) 2022; 14:cancers14194677. [PMID: 36230599 PMCID: PMC9562196 DOI: 10.3390/cancers14194677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/07/2022] [Accepted: 09/17/2022] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Body fluids contain different classes of RNA molecules such as protein-coding messenger RNAs (mRNA) and noncoding RNAs, including microRNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). These circulating RNAs can travel naked or packed into extracellular vesicles and display valuable potential as non-invasive biomarkers of sarcoma malignancy. In this review, we summarize current knowledge on the possible functions of these circulating RNAs and discuss their possible exploitation as novel markers to improve sarcoma diagnosis and prognosis. Despite the recent advance in technological tools have improved protocols for the extraction and detection of circulating RNA, many aspects related to the biology of these molecules remain to be elucidated. In particular, the lack of standardization in the assessment of these markers makes difficult their adoption into clinical practice. Abstract Sarcomas comprise a heterogeneous group of rare mesenchymal malignancies. Sarcomas can be grouped into two categories characterized by different prognosis and treatment approaches: soft tissue sarcoma and primary bone sarcoma. In the last years, research on novel diagnostic, prognostic or predictive biomarkers in sarcoma management has been focused on circulating tumor-derived molecules as valuable tools. Liquid biopsies that measure various tumor components, including circulating cell-free DNA and RNA, circulating tumor cells, tumor extracellular vesicles and exosomes, are gaining attention as methods for molecular screening and early diagnosis. Compared with traditional tissue biopsies, liquid biopsies are minimally invasive and blood samples can be collected serially over time to monitor cancer progression. This review will focus on circulating noncoding RNA molecules from liquid biopsies that are dysregulated in sarcoma malignancies and discuss advantages and current limitations of their employment as biomarkers in the management of sarcomas. It will also explore their utility in the evaluation of the clinical response to treatments and of disease relapse. Moreover, it will explore state-of-the-art techniques that allow for the early detection of these circulating biomarkers. Despite the huge potential, current reports highlight poor sensitivity, specificity, and survival benefit of these methods, that are therefore still insufficient for routine screening purposes.
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Affiliation(s)
- Lidia Chellini
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Ramona Palombo
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
- Department of Movement, Human and Health Sciences, Università degli Studi di Roma “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
| | - Veronica Riccioni
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
| | - Maria Paola Paronetto
- Laboratory of Molecular and Cellular Neurobiology, IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
- Department of Movement, Human and Health Sciences, Università degli Studi di Roma “Foro Italico”, Piazza Lauro de Bosis, 15, 00135 Rome, Italy
- Correspondence:
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7
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Ramadan F, Saab R, Hussein N, Clézardin P, Cohen PA, Ghayad SE. Non-coding RNA in rhabdomyosarcoma progression and metastasis. Front Oncol 2022; 12:971174. [PMID: 36033507 PMCID: PMC9403786 DOI: 10.3389/fonc.2022.971174] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/25/2022] [Indexed: 12/12/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is a soft tissue sarcoma of skeletal muscle differentiation, with a predominant occurrence in children and adolescents. One of the major challenges facing treatment success is the presence of metastatic disease at the time of diagnosis, commonly associated with the more aggressive fusion-positive subtype. Non-coding RNA (ncRNA) can regulate gene transcription and translation, and their dysregulation has been associated with cancer development and progression. MicroRNA (miRNA) are short non-coding nucleic acid sequences involved in the regulation of gene expression that act by targeting messenger RNA (mRNA), and their aberrant expression has been associated with both RMS initiation and progression. Other ncRNA including long non-coding RNA (lncRNA), circular RNA (circRNA) and ribosomal RNA (rRNA) have also been associated with RMS revealing important mechanistic roles in RMS biology, but these studies are still limited and require further investigation. In this review, we discuss the established roles of ncRNA in RMS differentiation, growth and progression, highlighting their potential use in RMS prognosis, as therapeutic agents or as targets of treatment.
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Affiliation(s)
- Farah Ramadan
- Department of Biology, Faculty of Science II, Lebanese University, Beirut, Lebanon
- Université Claude Bernard Lyon 1, Lyon, France
- INSERM, Unit 1033, LYOS, Lyon, France
- Department of Chemistry and Biochemistry, Laboratory of Cancer Biology and Molecular Immunology, Faculty of Science I, Lebanese University, Hadat, Lebanon
| | - Raya Saab
- Department of Anatomy, Cell Biology and Physiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Department of Pediatric and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Nader Hussein
- Department of Chemistry and Biochemistry, Laboratory of Cancer Biology and Molecular Immunology, Faculty of Science I, Lebanese University, Hadat, Lebanon
| | - Philippe Clézardin
- Université Claude Bernard Lyon 1, Lyon, France
- INSERM, Unit 1033, LYOS, Lyon, France
| | - Pascale A. Cohen
- Université Claude Bernard Lyon 1, Lyon, France
- INSERM, Unit 1033, LYOS, Lyon, France
| | - Sandra E. Ghayad
- Department of Biology, Faculty of Science II, Lebanese University, Beirut, Lebanon
- Aix-Marseille University, INSERM 1263, INRAE 1260, C2VN, Marseille, France
- *Correspondence: Sandra E. Ghayad,
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8
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Hettmer S, Linardic CM, Kelsey A, Rudzinski ER, Vokuhl C, Selfe J, Ruhen O, Shern JF, Khan J, Kovach AR, Lupo PJ, Gatz SA, Schäfer BW, Volchenboum S, Minard-Colin V, Koscielniak E, Hawkins DS, Bisogno G, Sparber-Sauer M, Venkatramani R, Merks JHM, Shipley J. Molecular testing of rhabdomyosarcoma in clinical trials to improve risk stratification and outcome: A consensus view from European paediatric Soft tissue sarcoma Study Group, Children's Oncology Group and Cooperative Weichteilsarkom-Studiengruppe. Eur J Cancer 2022; 172:367-386. [PMID: 35839732 DOI: 10.1016/j.ejca.2022.05.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/27/2022] [Accepted: 05/22/2022] [Indexed: 02/07/2023]
Abstract
Rhabdomyosarcomas (RMSs) are the most common soft tissue sarcomas in children/adolescents less than 18 years of age with an annual incidence of 1-2/million. Inter/intra-tumour heterogeneity raise challenges in clinical, pathological and biological research studies. Risk stratification in European and North American clinical trials previously relied on clinico-pathological features, but now, incorporates PAX3/7-FOXO1-fusion gene status in the place of alveolar histology. International working groups propose a coordinated approach through the INternational Soft Tissue SaRcoma ConsorTium to evaluate the specific genetic abnormalities and generate and integrate molecular and clinical data related to patients with RMS across different trial settings. We review relevant data and present a consensus view on what molecular features should be assessed. In particular, we recommend the assessment of the MYOD1-LR122R mutation for risk escalation, as it has been associated with poor outcomes in spindle/sclerosing RMS and rare RMS with classic embryonal histopathology. The prospective analyses of rare fusion genes beyond PAX3/7-FOXO1 will generate new data linked to outcomes and assessment of TP53 mutations and CDK4 amplification may confirm their prognostic value. Pathogenic/likely pathogenic germline variants in TP53 and other cancer predisposition genes should also be assessed. DNA/RNA profiling of tumours at diagnosis/relapse and serial analyses of plasma samples is recommended where possible to validate potential molecular biomarkers, identify new biomarkers and assess how liquid biopsy analyses can have the greatest benefit. Together with the development of new molecularly-derived therapeutic strategies that we review, a synchronised international approach is expected to enhance progress towards improved treatment assignment, management and outcomes for patients with RMS.
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Affiliation(s)
- Simone Hettmer
- Division of Pediatric Hematology and Oncology, Department of Pediatric and Adolescent Medicine, University Medical Center Freiburg, University of Freiburg, Germany
| | - Corinne M Linardic
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA; Department of Pharmacology and Cancer Biology; Duke University of Medicine, Durham, NC, USA
| | - Anna Kelsey
- Department of Paediatric Histopathology, Royal Manchester Children's Hospital, Manchester Foundation Trust, Manchester, UK
| | - Erin R Rudzinski
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Department of Laboratories, Seattle Children's Hospital, Seattle, WA, USA
| | - Christian Vokuhl
- Section of Pediatric Pathology, Department of Pathology, University Hospital Bonn, Germany
| | - Joanna Selfe
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Olivia Ruhen
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Jack F Shern
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA; Pediatric Oncology Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Javed Khan
- Genetics Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Alexander R Kovach
- Department of Pharmacology and Cancer Biology; Duke University of Medicine, Durham, NC, USA
| | - Philip J Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Susanne A Gatz
- Institute of Cancer and Genomic Sciences, Cancer Research UK Clinical Trials Unit (CRCTU), University of Birmingham, Birmingham, UK
| | - Beat W Schäfer
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | | | | | - Ewa Koscielniak
- Klinikum der Landeshauptstadt Stuttgart GKAöR, Olgahospital, Stuttgart Cancer Center, Zentrum für Kinder-, Jugend- und Frauenmedizin, Pädiatrie 5 (Pädiatrische Onkologie, Hämatologie, Immunologie), Stuttgart, Germany; Medizinische Fakultät, University of Tübingen, Germany
| | - Douglas S Hawkins
- Seattle Children's Hospital, University of Washington, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gianni Bisogno
- Hematology Oncology Division, Department of Women's and Children's Health, University of Padova, Padua, Italy
| | - Monika Sparber-Sauer
- Klinikum der Landeshauptstadt Stuttgart GKAöR, Olgahospital, Stuttgart Cancer Center, Zentrum für Kinder-, Jugend- und Frauenmedizin, Pädiatrie 5 (Pädiatrische Onkologie, Hämatologie, Immunologie), Stuttgart, Germany; Medizinische Fakultät, University of Tübingen, Germany
| | - Rajkumar Venkatramani
- Department of Pediatrics, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | | | - Janet Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK.
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9
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Liu T, Li H, Li Y, Wang L, Chen G, Pu G, Guo X, Cho WC, Fasihi Harandi M, Zheng Y, Luo X. Integrative Analysis of RNA Expression and Regulatory Networks in Mice Liver Infected by Echinococcus multilocularis. Front Cell Dev Biol 2022; 10:798551. [PMID: 35399512 PMCID: PMC8989267 DOI: 10.3389/fcell.2022.798551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/17/2022] [Indexed: 11/13/2022] Open
Abstract
The larvae of Echinococcus multilocularis causes alveolar echinococcosis, which poses a great threat to the public health. However, the molecular mechanisms underlying the host and parasite interactions are still unclear. Exploring the transcriptomic maps of mRNA, miRNA and lncRNA expressed in the liver in response to E. multilocularis infection will help us to understand its pathogenesis. Using liver perfusion, different cell populations including the hepatic cells, hepatic stellate cells and Kupffer cells were isolated from mice interperitoneally inoculated with protoscoleces. Their transcriptional profiles including lncRNAs, miRNAs and mRNAs were done by RNA-seq. Among these cell populations, the most differentially-expressed (DE) mRNA, lncRNAs and miRNAs were annotated and may involve in the pathological processes, mainly including metabolic disorders, immune responses and liver fibrosis. Following the integrative analysis of 38 differentially-expressed DEmiRNAs and 8 DElncRNAs, the lncRNA-mRNA-miRNA networks were constructed, including F63-miR-223-3p-Fbxw7/ZFP36/map1b, F63-miR-27-5p-Tdrd6/Dip2c/Wdfy4 and IFNgAS1-IFN-γ. These results unveil the presence of several potential lncRNA-mRNA-miRNA axes during E. multilocularis infection, and further exploring of these axes may contribute to better understanding of the pathogenic mechanisms.
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Affiliation(s)
- Tingli Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, China
| | - Hong Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, China
| | - Yanping Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, China
| | - Liqun Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, China
| | - Guoliang Chen
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, China
| | - Guiting Pu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, China
| | - Xiaola Guo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, China
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
| | - Majid Fasihi Harandi
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Yadong Zheng
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection and Internet Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology and College of Veterinary Medicine of Zhejiang A&F University, Hangzhou, China
- *Correspondence: Xuenong Luo, ; Yadong Zheng,
| | - Xuenong Luo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, China
- *Correspondence: Xuenong Luo, ; Yadong Zheng,
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Olmedillas-López S, Olivera-Salazar R, García-Arranz M, García-Olmo D. Current and Emerging Applications of Droplet Digital PCR in Oncology: An Updated Review. Mol Diagn Ther 2021; 26:61-87. [PMID: 34773243 DOI: 10.1007/s40291-021-00562-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2021] [Indexed: 12/14/2022]
Abstract
In the era of personalized medicine and targeted therapies for the management of patients with cancer, ultrasensitive detection methods for tumor genotyping, such as next-generation sequencing or droplet digital polymerase chain reaction (ddPCR), play a significant role. In the search for less invasive strategies for diagnosis, prognosis and disease monitoring, the number of publications regarding liquid biopsy approaches using ddPCR has increased substantially in recent years. There is a long list of malignancies in which ddPCR provides a reliable and accurate tool for detection of nucleic acid-based markers derived from cell-free DNA, cell-free RNA, circulating tumor cells, extracellular vesicles or exosomes when isolated from whole blood, plasma and serum, helping to anticipate tumor relapse or unveil intratumor heterogeneity and clonal evolution in response to treatment. This updated review describes recent developments in ddPCR platforms and provides a general overview about the major applications of liquid biopsy in blood, including its utility for molecular response and minimal residual disease monitoring in hematological malignancies or the therapeutic management of patients with colorectal or lung cancer, particularly for the selection and monitoring of treatment with tyrosine kinase inhibitors. Although plasma is the main source of genetic material for tumor genomic profiling, liquid biopsy by ddPCR is being investigated in a wide variety of biologic fluids, such as cerebrospinal fluid, urine, stool, ocular fluids, sputum, saliva, bronchoalveolar lavage, pleural effusion, mucin, peritoneal fluid, fine needle aspirate, bile or pancreatic juice. The present review focuses on these "alternative" sources of genetic material and their analysis by ddPCR in different kinds of cancers.
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Affiliation(s)
- Susana Olmedillas-López
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.
| | - Rocío Olivera-Salazar
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain
| | - Mariano García-Arranz
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain
| | - Damián García-Olmo
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Avda. Reyes Católicos, 2, 28040, Madrid, Spain.,Department of Surgery, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029, Madrid, Spain.,Department of Surgery, Fundación Jiménez Díaz University Hospital (FJD), 28040, Madrid, Spain
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11
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Tewari RS, Ala U, Accornero P, Baratta M, Miretti S. Circulating skeletal muscle related microRNAs profile in Piedmontese cattle during different age. Sci Rep 2021; 11:15815. [PMID: 34349188 PMCID: PMC8339070 DOI: 10.1038/s41598-021-95137-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/14/2021] [Indexed: 02/07/2023] Open
Abstract
Piedmontese cattle is known for double-muscle phenotype. MicroRNAs (miRNAs) play important role as regulators in skeletal muscle physiological processes, and we hypothesize that plasma miRNAs expression profiles could be affected by skeletal muscle growth status related to age. Plasma samples of cattle were collected during four different ages from first week of life until the time of commercial end of the fattening period before slaughter. Small-RNA sequencing data analysis revealed the presence of 40% of muscle-related miRNAs among the top 25 highly expressed miRNAs and, 19 miRNAs showed differential expression too. Using qRT-PCR, we validated in a larger bovine population, miRNAs involved in skeletal muscle physiology pathways. Comparing new-born with the other age groups, miR-10b, miR-126-5p, miR-143 and miR-146b were significantly up-regulated, whereas miR-21-5p, miR-221, miR-223 and miR-30b-5p were significantly down-regulated. High expression levels of miR-23a in all the groups were found. Myostatin, a negative regulator of skeletal muscle hypertrophy, was predicted as the target gene for miR-23a and miR-126-5p and we demonstrated their direct binding. Correlation analysis revealed association between miRNAs expression profiles and animals’ weights along the age. Circulating miRNAs could be promising for future studies on their biomarker potentialities to beef cattle selection.
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Affiliation(s)
- Rupal S Tewari
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - Ugo Ala
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - Paolo Accornero
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - Mario Baratta
- Department of Veterinary Sciences, University of Turin, Turin, Italy
| | - Silvia Miretti
- Department of Veterinary Sciences, University of Turin, Turin, Italy.
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