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Mareboina M, Deng E, Mouratidis I, Yee NS, Pitteloud N, Georgakopoulos-Soares I, Chartoumpekis DV. A review on cell-free RNA profiling: Insights into metabolic diseases and predictive value for bariatric surgery outcomes. Mol Metab 2024; 87:101987. [PMID: 38977131 DOI: 10.1016/j.molmet.2024.101987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/25/2024] [Accepted: 07/04/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND The advent of liquid biopsies presents a novel, minimally invasive methodology for the detection of disease biomarkers, offering a significant advantage over traditional biopsy techniques. Particularly, the analysis of cell-free RNA (cfRNA) has garnered interest due to its dynamic expression profiles and the capability to study various RNA species, including messenger RNA (mRNA) and long non-coding RNA (lncRNA). These attributes position cfRNA as a versatile biomarker with broad potential applications in clinical research and diagnostics. SCOPE OF REVIEW This review delves into the utility of cfRNA biomarkers as prognostic tools for obesity-related comorbidities, such as diabetes, dyslipidemia, and non-alcoholic fatty liver disease. MAJOR CONCLUSIONS We evaluate the efficacy of cfRNA in forecasting metabolic outcomes associated with obesity and in identifying patients likely to experience favorable clinical outcomes following bariatric surgery. Additionally, this review synthesizes evidence from studies examining circulating cfRNA across different physiological and pathological states, with a focus on its role in diabetes, including disease progression monitoring and treatment efficacy assessment. Through this exploration, we underscore the emerging relevance of cfRNA signatures in the context of obesity and its comorbidities, setting the stage for future investigative efforts in this rapidly advancing domain.
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Affiliation(s)
- Manvita Mareboina
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Elen Deng
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Ioannis Mouratidis
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Nelson S Yee
- Division of Hematology-Oncology, Department of Medicine, Penn State Health Milton S. Hershey Medical Center, Next-Generation Therapies Program, Penn State Cancer Institute, Hershey, PA, USA
| | - Nelly Pitteloud
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital and University of Lausanne, CH-1011, Lausanne, Switzerland
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA.
| | - Dionysios V Chartoumpekis
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital and University of Lausanne, CH-1011, Lausanne, Switzerland.
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Schmithals C, Kakoschky B, Denk D, von Harten M, Klug JH, Hintermann E, Dropmann A, Hamza E, Jacomin AC, Marquardt JU, Zeuzem S, Schirmacher P, Herrmann E, Christen U, Vogl TJ, Waidmann O, Dooley S, Finkelmeier F, Piiper A. Tumour-specific activation of a tumour-blood transport improves the diagnostic accuracy of blood tumour markers in mice. EBioMedicine 2024; 105:105178. [PMID: 38889481 PMCID: PMC11237870 DOI: 10.1016/j.ebiom.2024.105178] [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: 09/14/2023] [Revised: 04/12/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND The accuracy of blood-based early tumour recognition is compromised by signal production at non-tumoral sites, low amount of signal produced by small tumours, and variable tumour production. Here we examined whether tumour-specific enhancement of vascular permeability by the particular tumour homing peptide, iRGD, which carries dual function of binding to integrin receptors overexpressed in the tumour vasculature and is known to promote extravasation via neuropilin-1 receptor upon site-specific cleavage, might be useful to improve blood-based tumour detection by inducing a yet unrecognised vice versa tumour-to-blood transport. METHODS To detect an iRGD-induced tumour-to-blood transport, we examined the effect of intravenously injected iRGD on blood levels of α-fetoprotein (AFP) and autotaxin in several mouse models of hepatocellular carcinoma (HCC) or in mice with chronic liver injury without HCC, and on prostate-specific antigen (PSA) levels in mice with prostate cancer. FINDINGS Intravenously injected iRGD rapidly and robustly elevated the blood levels of AFP in several mouse models of HCC, but not in mice with chronic liver injury. The effect was primarily seen in mice with small tumours and normal basal blood AFP levels, was attenuated by an anti-neuropilin-1 antibody, and depended on the concentration gradient between tumour and blood. iRGD treatment was also able to increase blood levels of autotaxin in HCC mice, and of PSA in mice with prostate cancer. INTERPRETATION We conclude that iRGD induces a tumour-to-blood transport in a tumour-specific fashion that has potential of improving diagnosis of early stage cancer. FUNDING Deutsche Krebshilfe, DKTK, LOEWE-Frankfurt Cancer Institute.
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Affiliation(s)
- Christian Schmithals
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany
| | - Bianca Kakoschky
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany
| | - Dominic Denk
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, University Hospital, Frankfurt am Main, Germany
| | - Maike von Harten
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany
| | - Jan Henrik Klug
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany
| | - Edith Hintermann
- Pharmazentrum Frankfurt / ZAFES, Goethe University Frankfurt, University Hospital, Frankfurt am Main, Germany
| | - Anne Dropmann
- Molecular Hepatology-Alcohol Associated Diseases, Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Germany
| | - Eman Hamza
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany; Suez University, Faculty of Science, Zoology Department, Suez, Egypt
| | - Anne Claire Jacomin
- Frankfurt Cancer Institute, Goethe University Frankfurt, University Hospital, Frankfurt am Main, Germany; Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Jens U Marquardt
- Department of Medicine I, University Medical Centre Schleswig-Holstein - Campus Lübeck, Lübeck, Germany
| | - Stefan Zeuzem
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/M., a Partnership Between DKFZ and University Hospital Frankfurt/M., Germany
| | | | - Eva Herrmann
- Goethe University Frankfurt, University Hospital, Institute of Biostatistics and Mathematical Modelling, Germany
| | - Urs Christen
- Pharmazentrum Frankfurt / ZAFES, Goethe University Frankfurt, University Hospital, Frankfurt am Main, Germany
| | - Thomas J Vogl
- Goethe University Frankfurt, University Hospital, Institute for Diagnostic and Interventional Radiology, Germany
| | - Oliver Waidmann
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany; Centrum für Hämatologie und Onkologie Bethanien, Frankfurt/Main, Germany
| | - Steven Dooley
- Molecular Hepatology-Alcohol Associated Diseases, Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Germany
| | - Fabian Finkelmeier
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, University Hospital, Frankfurt am Main, Germany
| | - Albrecht Piiper
- Goethe University Frankfurt, University Hospital, Medical Clinic 1, Frankfurt am Main, Germany; Frankfurt Cancer Institute, Goethe University Frankfurt, University Hospital, Frankfurt am Main, Germany; German Cancer Consortium (DKTK), Partner Site Frankfurt/M., a Partnership Between DKFZ and University Hospital Frankfurt/M., Germany.
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3
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Liu X, Tao Y, Cai Z, Bao P, Ma H, Li K, Li M, Zhu Y, Lu ZJ. Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data. Bioinformatics 2024; 40:btae316. [PMID: 38741230 PMCID: PMC11139513 DOI: 10.1093/bioinformatics/btae316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/29/2024] [Accepted: 05/11/2024] [Indexed: 05/16/2024] Open
Abstract
MOTIVATION Multi-omics data provide a comprehensive view of gene regulation at multiple levels, which is helpful in achieving accurate diagnosis of complex diseases like cancer. However, conventional integration methods rarely utilize prior biological knowledge and lack interpretability. RESULTS To integrate various multi-omics data of tissue and liquid biopsies for disease diagnosis and prognosis, we developed a biological pathway informed Transformer, Pathformer. It embeds multi-omics input with a compacted multi-modal vector and a pathway-based sparse neural network. Pathformer also leverages criss-cross attention mechanism to capture the crosstalk between different pathways and modalities. We first benchmarked Pathformer with 18 comparable methods on multiple cancer datasets, where Pathformer outperformed all the other methods, with an average improvement of 6.3%-14.7% in F1 score for cancer survival prediction, 5.1%-12% for cancer stage prediction, and 8.1%-13.6% for cancer drug response prediction. Subsequently, for cancer prognosis prediction based on tissue multi-omics data, we used a case study to demonstrate the biological interpretability of Pathformer by identifying key pathways and their biological crosstalk. Then, for cancer early diagnosis based on liquid biopsy data, we used plasma and platelet datasets to demonstrate Pathformer's potential of clinical applications in cancer screening. Moreover, we revealed deregulation of interesting pathways (e.g. scavenger receptor pathway) and their crosstalk in cancer patients' blood, providing potential candidate targets for cancer microenvironment study. AVAILABILITY AND IMPLEMENTATION Pathformer is implemented and freely available at https://github.com/lulab/Pathformer.
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Affiliation(s)
- Xiaofan Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Yuhuan Tao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Zilin Cai
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pengfei Bao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Hongli Ma
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
| | - Kexing Li
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Mengtao Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), MST State Key Laboratory of Complex Severe and Rare Diseases, MOE Key Laboratory of Rheumatology and Clinical Immunology, Beijing 100730, China
| | - Yunping Zhu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Institute for Precision Medicine, Tsinghua University, Beijing 100084, China
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4
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Lehrich BM, Zhang J, Monga SP, Dhanasekaran R. Battle of the biopsies: Role of tissue and liquid biopsy in hepatocellular carcinoma. J Hepatol 2024; 80:515-530. [PMID: 38104635 PMCID: PMC10923008 DOI: 10.1016/j.jhep.2023.11.030] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/27/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
The diagnosis and management of hepatocellular carcinoma (HCC) have improved significantly in recent years. With the introduction of immunotherapy-based combination therapy, there has been a notable expansion in treatment options for patients with unresectable HCC. Simultaneously, innovative molecular tests for early detection and management of HCC are emerging. This progress prompts a key question: as liquid biopsy techniques rise in prominence, will they replace traditional tissue biopsies, or will both techniques remain relevant? Given the ongoing challenges of early HCC detection, including issues with ultrasound sensitivity, accessibility, and patient adherence to surveillance, the evolution of diagnostic techniques is more relevant than ever. Furthermore, the accurate stratification of HCC is limited by the absence of reliable biomarkers which can predict response to therapies. While the advantages of molecular diagnostics are evident, their potential has not yet been fully harnessed, largely because tissue biopsies are not routinely performed for HCC. Liquid biopsies, analysing components such as circulating tumour cells, DNA, and extracellular vesicles, provide a promising alternative, though they are still associated with challenges related to sensitivity, cost, and accessibility. The early results from multi-analyte liquid biopsy panels are promising and suggest they could play a transformative role in HCC detection and management; however, comprehensive clinical validation is still ongoing. In this review, we explore the challenges and potential of both tissue and liquid biopsy, highlighting that these diagnostic methods, while distinct in their approaches, are set to jointly reshape the future of HCC management.
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Affiliation(s)
- Brandon M Lehrich
- Department of Pathology and Pittsburgh Liver Institute, University of Pittsburgh, School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Josephine Zhang
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Staford, CA, 94303, USA
| | - Satdarshan P Monga
- Department of Pathology and Pittsburgh Liver Institute, University of Pittsburgh, School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA.
| | - Renumathy Dhanasekaran
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University, Staford, CA, 94303, USA.
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5
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Wang AE, Leven EA, Grinspan LT, Villanueva A. Novel biomarkers and strategies for HCC diagnosis and care. Clin Liver Dis (Hoboken) 2024; 23:e0152. [PMID: 38707238 PMCID: PMC11068134 DOI: 10.1097/cld.0000000000000152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/04/2024] [Indexed: 05/07/2024] Open
Affiliation(s)
- Allison E. Wang
- Department of Medicine, Division of Gastroenterology, Mount Sinai Morningside-West, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emily A. Leven
- Department of Medicine, Division of Gastroenterology, Mount Sinai Hospital, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lauren T. Grinspan
- Department of Medicine, Division of Liver Diseases, Recanati/Miller Transplantation Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Augusto Villanueva
- Department of Medicine, Divisions of Liver Disease and Hematology/Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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