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Bonstingl L, Skofler C, Ulz C, Zinnegger M, Sallinger K, Schönberger J, Schuch K, Pankratz K, Borrás-Cherrier A, Somodi V, Abuja PM, Oberauner-Wappis L, Moser T, Heitzer E, Bauernhofer T, Kroneis T, El-Heliebi A. Clinical Application of ISO and CEN/TS Standards for Liquid Biopsies-Information Everybody Wants but Nobody Wants to Pay For. Clin Chem 2024:hvae079. [PMID: 38958115 DOI: 10.1093/clinchem/hvae079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/09/2024] [Indexed: 07/04/2024]
Abstract
BACKGROUND Liquid biopsies are emerging as valuable clinical biomarkers for cancer monitoring. Although International Organization for Standards (ISO) and Technical Specifications from the European Committee for Standardization (CEN/TS) standardized workflows exist, their implementation in clinical practice is underdeveloped. We aimed to assess the applicability of ISO and CEN/TS standards in a real-world clinical setting, with a particular focus on evaluating the impact of preanalytical parameters and hemolysis on liquid biopsy analysis. METHODS We evaluated 659 peripheral blood samples from advanced prostate cancer patients against ISO and CEN/TS standards and documented all essential criteria, including tube draw order, filling level, temperature, and time tracking from blood draw to storage. We assessed hemolysis and its effect on circulating tumor DNA (ctDNA) and circulating tumor cell (CTC) analysis. RESULTS Our results demonstrated a high compliance rate, with 96.2% (634/659) of samples meeting essential ISO and CEN/TS criteria. We did not observe a significant impact on ctDNA or CTC detection rates between hemolytic and nonhemolytic samples. Hemolysis was identified in 12.9% (40/311) of plasma samples from our advanced prostate cancer cohort, and within the draw order of 5 blood collection tubes, hemolysis did not significantly increase from tube 1 to 5. In total, 83.8% (552/659) of blood collection tubes had high fill levels above 80% of nominal filling level. CONCLUSIONS Our study demonstrates the feasibility and benefits of adhering to ISO and CEN/TS standards in a clinical liquid biopsy study. The standards revealed that hemolysis occurred frequently but did not impair downstream ctDNA and CTC analysis in our cohort of advanced prostate cancer patients.
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Affiliation(s)
- Lilli Bonstingl
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
- CBmed, Center for Biomarker Research in Medicine, Graz, Austria
- ELBS, European Liquid Biopsy Society, Hamburg, Germany
| | - Christina Skofler
- CBmed, Center for Biomarker Research in Medicine, Graz, Austria
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Christine Ulz
- CBmed, Center for Biomarker Research in Medicine, Graz, Austria
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | | | - Katja Sallinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
- CBmed, Center for Biomarker Research in Medicine, Graz, Austria
| | - Julia Schönberger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Katharina Schuch
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Karin Pankratz
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Anatol Borrás-Cherrier
- Diagnostic and Research Center for Molecular BioMedicine, Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Visnja Somodi
- Diagnostic and Research Center for Molecular BioMedicine, Institute of Human Genetics, Medical University of Graz, Graz, Austria
| | - Peter M Abuja
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Lisa Oberauner-Wappis
- CBmed, Center for Biomarker Research in Medicine, Graz, Austria
- Diagnostic and Research Center for Molecular BioMedicine, Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Tina Moser
- Diagnostic and Research Center for Molecular BioMedicine, Institute of Human Genetics, Medical University of Graz, Graz, Austria
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Diagnostic and Research Center for Molecular BioMedicine, Institute of Human Genetics, Medical University of Graz, Graz, Austria
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Thomas Bauernhofer
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Thomas Kroneis
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Amin El-Heliebi
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
- CBmed, Center for Biomarker Research in Medicine, Graz, Austria
- ELBS, European Liquid Biopsy Society, Hamburg, Germany
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2
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Stitz R, Stoiber F, Silye R, Vlachos G, Andaloro S, Rebhan E, Dunzinger M, Pühringer F, Gallo C, El-Heliebi A, Heitzer E, Hauser-Kronberger C. Clinical Implementation of a Noninvasive, Multi-Analyte Droplet Digital PCR Test to Screen for Androgen Receptor Alterations. J Mol Diagn 2024; 26:467-478. [PMID: 38522838 DOI: 10.1016/j.jmoldx.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 01/14/2024] [Accepted: 02/13/2024] [Indexed: 03/26/2024] Open
Abstract
Alterations of the androgen receptor (AR) are associated with resistance to AR-directed therapy in prostate cancer. Thus, it is crucial to develop robust detection methods for AR alterations as predictive biomarkers to enable applicability in clinical practice. We designed and validated five multiplex droplet digital PCR assays for reliable detection of 12 AR targets including AR amplification, AR splice variant 7, and 10 AR hotspot mutations, as well as AR and KLK3 gene expression from plasma-derived cell-free DNA and cell-free RNA. The assays demonstrated excellent analytical sensitivity and specificity ranging from 95% to 100% (95% CI, 75% to 100%). Intrarun and interrun variation analyses revealed a high level of repeatability and reproducibility. The developed assays were applied further in peripheral blood samples from 77 patients with advanced prostate cancer to assess their feasibility in a real-world scenario. Optimizing the reverse transcription of RNA increased the yield of plasma-derived cell-free RNA by 30-fold. Among 23 patients with castration-resistant prostate cancer, 6 patients (26.1%) had one or a combination of several AR alterations, whereas only 2 of 54 patients (3.7%) in the hormone-sensitive stage showed AR alterations. These findings were consistent with other studies and suggest that implementation of comprehensive AR status detection in clinical practice is feasible and can support the treatment decision-making process.
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Affiliation(s)
- Regina Stitz
- Department of Pathology, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria; Doctoral Program Medical Science, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Franz Stoiber
- Department of Urology Medicine, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Renè Silye
- Department of Pathology, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Georgios Vlachos
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Silvia Andaloro
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Elisabeth Rebhan
- Department of Pathology, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Michael Dunzinger
- Department of Urology Medicine, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Franz Pühringer
- Department of Pathology, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Caroline Gallo
- Department of Pathology, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria
| | - Amin El-Heliebi
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Centre, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria.
| | - Cornelia Hauser-Kronberger
- Department of Pathology, Salzkammergutklinikum Vöcklabruck, Vöcklabruck, Austria; Department of Anatomy and Cell Biology, Paracelsus Medical University Salzburg, Salzburg, Austria.
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3
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Nicolò E, Gianni C, Pontolillo L, Serafini MS, Munoz-Arcos LS, Andreopoulou E, Curigliano G, Reduzzi C, Cristofanilli M. Circulating tumor cells et al.: towards a comprehensive liquid biopsy approach in breast cancer. TRANSLATIONAL BREAST CANCER RESEARCH : A JOURNAL FOCUSING ON TRANSLATIONAL RESEARCH IN BREAST CANCER 2024; 5:10. [PMID: 38751670 PMCID: PMC11093063 DOI: 10.21037/tbcr-23-55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/21/2024] [Indexed: 05/18/2024]
Abstract
Liquid biopsy has emerged as a crucial tool in managing breast cancer (BC) patients, offering a minimally invasive approach to detect circulating tumor biomarkers. Until recently, the majority of the studies in BC focused on evaluating a single liquid biopsy analyte, primarily circulating tumor DNA and circulating tumor cells (CTCs). Despite the proven prognostic and predictive value of CTCs, their low abundance when detected using enrichment methods, especially in the early stages, poses a significant challenge. It is becoming evident that combining diverse circulating biomarkers, each representing different facets of tumor biology, has the potential to enhance the management of patients with BC. This article emphasizes the importance of considering these biomarkers as complementary/synergistic rather than competitive, recognizing their ability to contribute to a comprehensive disease profile. The review provides an overview of the clinical significance of simultaneously analyzing CTCs and other biomarkers, including cell-free circulating DNA, extracellular vesicles, non-canonical CTCs, cell-free RNAs, and non-malignant cells. Such a comprehensive liquid biopsy approach holds promise not only in BC but also in other cancer types, offering opportunities for early detection, prognostication, and therapy monitoring. However, addressing associated challenges, such as refining detection methods and establishing standardized protocols, is crucial for realizing the full potential of liquid biopsy in transforming our understanding and approach to BC. As the field evolves, collaborative efforts will be instrumental in unlocking the revolutionary impact of liquid biopsy in BC research and management.
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Affiliation(s)
- Eleonora Nicolò
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
- Division of Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy
| | - Caterina Gianni
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
- Department of Medical Oncology, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Meldola, Italy
| | - Letizia Pontolillo
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
- Medical Oncology Department, Catholic University of Sacred Heart, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Mara Serena Serafini
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Laura Sofia Munoz-Arcos
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Eleni Andreopoulou
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Giuseppe Curigliano
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
- Division of Early Drug Development, European Institute of Oncology IRCCS, Milan, Italy
| | - Carolina Reduzzi
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Massimo Cristofanilli
- Department of Medicine, Division of Hematology-Oncology, Weill Cornell Medicine, New York, NY, USA
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Batool SM, Yekula A, Khanna P, Hsia T, Gamblin AS, Ekanayake E, Escobedo AK, You DG, Castro CM, Im H, Kilic T, Garlin MA, Skog J, Dinulescu DM, Dudley J, Agrawal N, Cheng J, Abtin F, Aberle DR, Chia D, Elashoff D, Grognan T, Krysan K, Oh SS, Strom C, Tu M, Wei F, Xian RR, Skates SJ, Zhang DY, Trinh T, Watson M, Aft R, Rawal S, Agarwal A, Kesmodel SB, Yang C, Shen C, Hochberg FH, Wong DTW, Patel AA, Papadopoulos N, Bettegowda C, Cote RJ, Srivastava S, Lee H, Carter BS, Balaj L. The Liquid Biopsy Consortium: Challenges and opportunities for early cancer detection and monitoring. Cell Rep Med 2023; 4:101198. [PMID: 37716353 PMCID: PMC10591039 DOI: 10.1016/j.xcrm.2023.101198] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 12/01/2022] [Accepted: 08/22/2023] [Indexed: 09/18/2023]
Abstract
The emerging field of liquid biopsy stands at the forefront of novel diagnostic strategies for cancer and other diseases. Liquid biopsy allows minimally invasive molecular characterization of cancers for diagnosis, patient stratification to therapy, and longitudinal monitoring. Liquid biopsy strategies include detection and monitoring of circulating tumor cells, cell-free DNA, and extracellular vesicles. In this review, we address the current understanding and the role of existing liquid-biopsy-based modalities in cancer diagnostics and monitoring. We specifically focus on the technical and clinical challenges associated with liquid biopsy and biomarker development being addressed by the Liquid Biopsy Consortium, established through the National Cancer Institute. The Liquid Biopsy Consortium has developed new methods/assays and validated existing methods/technologies to capture and characterize tumor-derived circulating cargo, as well as addressed existing challenges and provided recommendations for advancing biomarker assays.
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Affiliation(s)
| | - Anudeep Yekula
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Prerna Khanna
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tiffaney Hsia
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Austin S Gamblin
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Emil Ekanayake
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ana K Escobedo
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Dong Gil You
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Cesar M Castro
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Hyungsoon Im
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tugba Kilic
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Johan Skog
- Exosome Diagnostics Inc., Waltham, MA, USA
| | | | - Jonathan Dudley
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Jordan Cheng
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | - David Chia
- University of California Los Angeles, Los Angeles, CA, USA
| | - David Elashoff
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | - Scott S Oh
- University of California Los Angeles, Los Angeles, CA, USA
| | - Charles Strom
- University of California Los Angeles, Los Angeles, CA, USA
| | - Michael Tu
- Liquid Diagnostics LLC., Los Angeles, CA, USA
| | - Fang Wei
- University of California Los Angeles, Los Angeles, CA, USA
| | - Rena R Xian
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Steven J Skates
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Thi Trinh
- Yale University School of Medicine, New Haven, CT, USA
| | - Mark Watson
- Washington University School of Medicine, St. Louis, MO, USA
| | - Rebecca Aft
- Washington University School of Medicine, St. Louis, MO, USA
| | - Siddarth Rawal
- Washington University School of Medicine, St. Louis, MO, USA; Circulogix Inc., St. Louis, MO, USA
| | | | | | | | - Cheng Shen
- California Institute of Technology, Pasadena, CA, USA
| | | | - David T W Wong
- University of California Los Angeles, Los Angeles, CA, USA
| | | | | | | | - Richard J Cote
- Washington University School of Medicine, St. Louis, MO, USA; Circulogix Inc., St. Louis, MO, USA
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, USA
| | - Hakho Lee
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Bob S Carter
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Leonora Balaj
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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5
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Li W, Li D, Ma Q, Chen Y, Hu Z, Bai Y, Xie L. Targeted inhibition of mTOR by BML-275 induces mitochondrial-mediated apoptosis and autophagy in prostate cancer. Eur J Pharmacol 2023; 957:176035. [PMID: 37657741 DOI: 10.1016/j.ejphar.2023.176035] [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: 04/21/2023] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Prostate cancer (PCa) is the most frequently diagnosed cancer among men and the second leading cause of death in Western countries. Clinically, screening drugs and develop developing new therapeutics to treat PCa is of great significance. In this study, BML-275 was demonstrated to exert potent antitumor effects in PCa by antagonizing mTOR activity. In cultured PCa cells, BML-275 treatment reduced the expression levels of c-Myc and survivin, promoted the activation of p53, and thereby induced p21/cyclin D1/CDK4/6-dependent cell cycle G1/S arrest. As a result, BML-275 inhibited cellular proliferation and induced mitochondrial-mediated apoptosis. In addition, BML-275 treatment triggered autophagy. Interestingly, EACC-mediated suppression of autophagy did not affect BML-275-induced proliferation and apoptosis. Nude mouse tumorigenic experiments also confirmed that BML-275 inhibited PCa growth, induced PCa cell apoptosis and autophagy. Mechanistically, the activities of PI3K/AKT and AMPK pathways were downregulated by BML-275 treatment in vitro and in vivo. Importantly, mTOR, a common downstream negative protein of PI3K/AKT and AMPK signaling, was induced to inactivate, which may be associated with the induction of apoptosis and autophagy. The pharmacological activation of mTOR by MHY1485 abolished the induction of apoptosis and autophagy of BML-275. Molecular docking results showed that BML-275 can bind to the FKRP12-rapamycin binding site on mTOR protein, and thereby may have the same inhibitory activity on mTOR as rapamycin. Thus, these findings indicated that BML-275 induces mitochondrial-mediated apoptosis and autophagy in PCa by targeting mTOR inhibition. BML-275 may be a potential candidate for the treatment of PCa.
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Affiliation(s)
- Wangjian Li
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China; Department of Urology, The Central Hospital Affiliated to Shaoxing University, Shaoxing, 312030, China
| | - Dongzhang Li
- Department of Urology, The Central Hospital Affiliated to Shaoxing University, Shaoxing, 312030, China
| | - Quan Ma
- Department of Urology, The Central Hospital Affiliated to Shaoxing University, Shaoxing, 312030, China
| | - Yongliang Chen
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Zujian Hu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Yongheng Bai
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Liping Xie
- Department of Urology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, China.
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Mugoni V, Ciani Y, Quaini O, Tomasini S, Notarangelo M, Vannuccini F, Marinelli A, Leonardi E, Pontalti S, Martinelli A, Rossetto D, Pesce I, Mansy SS, Barbareschi M, Ferro A, Caffo O, Attard G, Di Vizio D, D'Agostino VG, Nardella C, Demichelis F. Integrating extracellular vesicle and circulating cell-free DNA analysis using a single plasma aliquot improves the detection of HER2 positivity in breast cancer patients. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e108. [PMID: 38046436 PMCID: PMC10688391 DOI: 10.1002/jex2.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/19/2023] [Accepted: 08/11/2023] [Indexed: 12/05/2023]
Abstract
Multi-analyte liquid biopsies represent an emerging opportunity for non-invasive cancer assessment. We developed ONCE (One Aliquot for Circulating Elements), an approach for the isolation of extracellular vesicles (EV) and cell-free DNA (cfDNA) from a single aliquot of blood. We assessed ONCE performance to classify HER2-positive early-stage breast cancer (BrCa) patients by combining EV-associated RNA (EV-RNA) and cfDNA signals on n = 64 healthy donors (HD) and non-metastatic BrCa patients. Specifically, we isolated EV-enriched samples by a charge-based (CB) method and investigated EV-RNA and cfDNA by next-generation sequencing (NGS) and by digital droplet PCR (ddPCR). Sequencing of cfDNA and EV-RNA from HER2- and HER2+ patients demonstrated concordance with in situ molecular analyses of matched tissues. Combined analysis of the two circulating analytes by ddPCR showed increased sensitivity in ERBB2/HER2 detection compared to single nucleic acid components. Multi-analyte liquid biopsy prediction performance was comparable to tissue-based sequencing results from TCGA. Also, imaging flow cytometry analysis revealed HER2 protein on the surface of EV isolated from the HER2+ BrCa plasma, thus corroborating the potential relevance of studying EV as companion analyte to cfDNA. This data confirms the relevance of combining cfDNA and EV-RNA for HER2 cancer assessment and supports ONCE as a valuable tool for multi-analytes liquid biopsies' clinical implementation.
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Affiliation(s)
- Vera Mugoni
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Yari Ciani
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Orsetta Quaini
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Simone Tomasini
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Michela Notarangelo
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Federico Vannuccini
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Alessia Marinelli
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Elena Leonardi
- Unit of Surgical Pathology, Santa Chiara Hospital, APSSTrentoItaly
| | - Stefano Pontalti
- Department of Medical OncologySanta Chiara Hospital, APSSTrentoItaly
| | - Angela Martinelli
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Daniele Rossetto
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Isabella Pesce
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Sheref S. Mansy
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | | | - Antonella Ferro
- Department of Medical OncologySanta Chiara Hospital, APSSTrentoItaly
| | - Orazio Caffo
- Department of Medical OncologySanta Chiara Hospital, APSSTrentoItaly
| | | | - Dolores Di Vizio
- Department of Surgery, Division of Cancer Biology and TherapeuticsCedars‐Sinai Medical CenterLos AngelesCaliforniaUSA
| | | | - Caterina Nardella
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative BiologyUniversity of TrentoTrentoItaly
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7
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Noor J, Chaudhry A, Noor R, Batool S. Advancements and Applications of Liquid Biopsies in Oncology: A Narrative Review. Cureus 2023; 15:e42731. [PMID: 37654932 PMCID: PMC10466971 DOI: 10.7759/cureus.42731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2023] [Indexed: 09/02/2023] Open
Abstract
According to the World Health Organization (WHO), nearly 10 million people died from cancer worldwide in 2020, making it the leading cause of mortality. Liquid biopsies, which provide non-invasive and real-time monitoring of tumor dynamics, have evolved into innovative diagnostic techniques in the field of oncology. Liquid biopsies offer important insights into tumor heterogeneity, treatment response, minimum residual disease identification, and personalized treatment of cancer through the analysis of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), extracellular vesicles, and microRNAs. They offer several advantages over traditional tissue biopsies, such as being less invasive, more convenient, more representative of tumor heterogeneity and dynamics, and more informative for guiding personalized treatment decisions. Liquid biopsies are being utilized increasingly in clinical oncology, particularly for patients with metastatic disease who require ongoing monitoring and treatment modification. In this narrative review article, we review the latest developments of liquid biopsy technologies, their applications and limitations, and their potential to transform diagnosis, prognosis, and management of cancer patients.
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Affiliation(s)
- Jawad Noor
- Internal Medicine, St. Dominic Hospital, Jackson, USA
| | | | - Riwad Noor
- Medicine/Public Health, Nishtar Hospital, Multan, PAK
| | - Saima Batool
- Pathology, Nishtar Medical University, Multan, PAK
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8
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Eickelschulte S, Riediger AL, Angeles AK, Janke F, Duensing S, Sültmann H, Görtz M. Biomarkers for the Detection and Risk Stratification of Aggressive Prostate Cancer. Cancers (Basel) 2022; 14:cancers14246094. [PMID: 36551580 PMCID: PMC9777028 DOI: 10.3390/cancers14246094] [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: 11/17/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Current strategies for the clinical management of prostate cancer are inadequate for a precise risk stratification between indolent and aggressive tumors. Recently developed tissue-based molecular biomarkers have refined the risk assessment of the disease. The characterization of tissue biopsy components and subsequent identification of relevant tissue-based molecular alterations have the potential to improve the clinical decision making and patient outcomes. However, tissue biopsies are invasive and spatially restricted due to tumor heterogeneity. Therefore, there is an urgent need for complementary diagnostic and prognostic options. Liquid biopsy approaches are minimally invasive with potential utility for the early detection, risk stratification, and monitoring of tumors. In this review, we focus on tissue and liquid biopsy biomarkers for early diagnosis and risk stratification of prostate cancer, including modifications on the genomic, epigenomic, transcriptomic, and proteomic levels. High-risk molecular alterations combined with orthogonal clinical parameters can improve the identification of aggressive tumors and increase patient survival.
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Affiliation(s)
- Samaneh Eickelschulte
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Anja Lisa Riediger
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Arlou Kristina Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Stefan Duensing
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Magdalena Görtz
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-42-2603
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9
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Hydroxymethylation profile of cell-free DNA is a biomarker for early colorectal cancer. Sci Rep 2022; 12:16566. [PMID: 36195648 PMCID: PMC9532421 DOI: 10.1038/s41598-022-20975-1] [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: 11/15/2021] [Accepted: 09/21/2022] [Indexed: 12/03/2022] Open
Abstract
Early detection of cancer will improve survival rates. The blood biomarker 5-hydroxymethylcytosine has been shown to discriminate cancer. In a large covariate-controlled study of over two thousand individual blood samples, we created, tested and explored the properties of a 5-hydroxymethylcytosine-based classifier to detect colorectal cancer (CRC). In an independent validation sample set, the classifier discriminated CRC samples from controls with an area under the receiver operating characteristic curve (AUC) of 90% (95% CI [87, 93]). Sensitivity was 55% at 95% specificity. Performance was similar for early stage 1 (AUC 89%; 95% CI [83, 94]) and late stage 4 CRC (AUC 94%; 95% CI [89, 98]). The classifier could detect CRC even when the proportion of tumor DNA in blood was undetectable by other methods. Expanding the classifier to include information about cell-free DNA fragment size and abundance across the genome led to gains in sensitivity (63% at 95% specificity), with similar overall performance (AUC 91%; 95% CI [89, 94]). We confirm that 5-hydroxymethylcytosine can be used to detect CRC, even in early-stage disease. Therefore, the inclusion of 5-hydroxymethylcytosine in multianalyte testing could improve sensitivity for the detection of early-stage cancer.
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10
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A Systematic Review of Circulating Tumor Cells Clinical Application in Prostate Cancer Diagnosis. Cancers (Basel) 2022; 14:cancers14153802. [PMID: 35954464 PMCID: PMC9367494 DOI: 10.3390/cancers14153802] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Cell-dependent and cell-independent information drawn from the blood stream were merged into the attractive term “liquid biopsy” and tentatively applied to most segments of cancer management: detection, risk-stratification, personalization of care and follow-up. However, the robust science behind liquid biopsies has not been widely used, thereby remaining a latent and possibly undervalued instrument. Here, we conducted a systematic review of CTCs in prostate cancer management to summarize their use in clinical practice. Abstract The purpose of the review is to summarize the recent data on circulating tumor cells (CTC) use in clinical practice. We performed a systematic literature search using two databases (Medline and Scopus) over the past five years and the following terms: (CTC OR “circulating tumor cells” OR “liquid biopsy”) AND prostate. The primary outcome was CTC predictive value for prostate cancer (PC) progression and survival. The secondary outcomes were the CTC predictive value for therapy response and the results of CTC detection depending on the assessment method. In metastatic PC, the CTC count showed itself to be a prognostic marker in terms of clinically important features, namely survival rates and response to treatment. CTC concentration was significantly associated with the overall survival and progression-free survival rates. A strong association between the overall survival or progression-free survival rate and CTC concentration could be observed. Variant-7 androgen receptors-positive (AR-V7-positive) patients showed a poor response to androgen receptor signaling (ARS) inhibitors, but this did not compromise their response to taxanes. In localized PC, only positive Cluster of Differentiantion 82 protein (CD82+) correlated with a higher survival rate. CTC count and AR-V7 expression showed itself to be a valuable biomarker for survival in metastatic PC and response to ARS-inhibitors. CTC diagnostic performance for localized PC or for screening and early detection is not high enough to show additional value over the other biomarkers.
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11
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Pietrasz D, Sereni E, Lancelotti F, Pea A, Luchini C, Innamorati G, Salvia R, Bassi C. Circulating tumour DNA: a challenging innovation to develop "precision onco-surgery" in pancreatic adenocarcinoma. Br J Cancer 2022; 126:1676-1683. [PMID: 35197581 PMCID: PMC9174156 DOI: 10.1038/s41416-022-01745-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 12/13/2021] [Accepted: 02/04/2022] [Indexed: 12/20/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is predicted to become the third leading cause of cancer-related mortality within the next decade. Management of PDAC remains challenging with limited effective treatment options and a dismal long-term prognosis. Liquid biopsy and circulating biomarkers seem to be promising to improve the multidisciplinary approach in PDAC treatment. Circulating tumour DNA (ctDNA) is the most studied blood liquid biopsy analyte and can provide insight into the molecular profile and individual characteristics of the tumour in real-time and in advance of standard imaging modalities. This could pave the way for identifying new therapeutic targets and markers of tumour response to supplement diagnostic and provide enhanced stratified treatment. Although its specificity seems excellent, the current sensitivity of ctDNA remains a limitation for clinical use, especially in patients with a low tumour burden. Increasing evidence suggests that ctDNA is a pertinent candidate biomarker to assess minimal residual disease after surgery but also a strong independent prognostic biomarker. This review explores the current knowledge and recent developments in ctDNA as a screening, diagnostic, prognostic and predictive biomarker in the management of resectable PDAC but also technical and analytical challenges that must be overcome to move toward "precision onco-surgery."
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Affiliation(s)
- Daniel Pietrasz
- APHP Hôpital Paul-Brousse, Centre Hépato-Biliaire, Université Paris-Saclay, 94800, Villejuif, France.
- Unit of General and Pancreatic Surgery, Department of Surgery and Oncology, University of Verona Hospital Trust, Verona, Italy.
| | - Elisabetta Sereni
- Unit of General and Pancreatic Surgery, Department of Surgery and Oncology, University of Verona Hospital Trust, Verona, Italy
| | - Francesco Lancelotti
- Unit of General and Pancreatic Surgery, Department of Surgery and Oncology, University of Verona Hospital Trust, Verona, Italy
| | - Antonio Pea
- Unit of General and Pancreatic Surgery, Department of Surgery and Oncology, University of Verona Hospital Trust, Verona, Italy
| | - Claudio Luchini
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Giulio Innamorati
- Unit of General and Pancreatic Surgery, Department of Surgery and Oncology, University of Verona Hospital Trust, Verona, Italy
| | - Roberto Salvia
- Unit of General and Pancreatic Surgery, Department of Surgery and Oncology, University of Verona Hospital Trust, Verona, Italy
| | - Claudio Bassi
- Unit of General and Pancreatic Surgery, Department of Surgery and Oncology, University of Verona Hospital Trust, Verona, Italy
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12
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Keup C, Kimmig R, Kasimir-Bauer S. Combinatorial Power of cfDNA, CTCs and EVs in Oncology. Diagnostics (Basel) 2022; 12:870. [PMID: 35453918 PMCID: PMC9031112 DOI: 10.3390/diagnostics12040870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 01/01/2023] Open
Abstract
Liquid biopsy is a promising technique for clinical management of oncological patients. The diversity of analytes circulating in the blood useable for liquid biopsy testing is enormous. Circulating tumor cells (CTCs), cell-free DNA (cfDNA) and extracellular vesicles (EVs), as well as blood cells and other soluble components in the plasma, were shown as liquid biopsy analytes. A few studies directly comparing two liquid biopsy analytes showed a benefit of one analyte over the other, while most authors concluded the benefit of the additional analyte. Only three years ago, the first studies to examine the value of a characterization of more than two liquid biopsy analytes from the same sample were conducted. We attempt to reflect on the recent development of multimodal liquid biopsy testing in this review. Although the analytes and clinical purposes of the published multimodal studies differed significantly, the additive value of the analytes was concluded in almost all projects. Thus, the blood components, as liquid biopsy reservoirs, are complementary rather than competitive, and orthogonal data sets were even shown to harbor synergistic effects. The unmistakable potential of multimodal liquid biopsy testing, however, is dampened by its clinical utility, which is yet to be proven, the lack of methodical standardization and insufficiently mature reimbursement, logistics and data handling.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
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13
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Systemic Effects Reflected in Specific Biomarker Patterns Are Instrumental for the Paradigm Change in Prostate Cancer Management: A Strategic Paper. Cancers (Basel) 2022; 14:cancers14030675. [PMID: 35158943 PMCID: PMC8833369 DOI: 10.3390/cancers14030675] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 12/11/2022] Open
Abstract
Prostate cancer (PCa) is reported as the most common malignancy and second leading cause of death in America. In Europe, PCa is considered the leading type of tumour in 28 European countries. The costs of treating PCa are currently increasing more rapidly than those of any other cancer. Corresponding economic burden is enormous, due to an overtreatment of slowly developing disease on one hand and underestimation/therapy resistance of particularly aggressive PCa subtypes on the other hand. The incidence of metastatic PCa is rapidly increasing that is particularly characteristic for young adults. PCa is a systemic multi-factorial disease resulting from an imbalanced interplay between risks and protective factors. Sub-optimal behavioural patterns, abnormal stress reactions, imbalanced antioxidant defence, systemic ischemia and inflammation, mitochondriopathies, aberrant metabolic pathways, gene methylation and damage to DNA, amongst others, are synergistically involved in pathomechanisms of PCa development and progression. To this end, PCa-relevant systemic effects are reflected in liquid biopsies such as blood patterns which are instrumental for predictive diagnostics, targeted prevention and personalisation of medical services (PPPM/3P medicine) as a new paradigm in the overall PCa management. This strategic review article highlights systemic effects in prostate cancer development and progression, demonstrates evident challenges in PCa management and provides expert recommendations in the framework of 3P medicine.
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14
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Krappinger JC, Bonstingl L, Pansy K, Sallinger K, Wreglesworth NI, Grinninger L, Deutsch A, El-Heliebi A, Kroneis T, Mcfarlane RJ, Sensen CW, Feichtinger J. Non-coding Natural Antisense Transcripts: Analysis and Application. J Biotechnol 2021; 340:75-101. [PMID: 34371054 DOI: 10.1016/j.jbiotec.2021.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/30/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022]
Abstract
Non-coding natural antisense transcripts (ncNATs) are regulatory RNA sequences that are transcribed in the opposite direction to protein-coding or non-coding transcripts. These transcripts are implicated in a broad variety of biological and pathological processes, including tumorigenesis and oncogenic progression. With this complex field still in its infancy, annotations, expression profiling and functional characterisations of ncNATs are far less comprehensive than those for protein-coding genes, pointing out substantial gaps in the analysis and characterisation of these regulatory transcripts. In this review, we discuss ncNATs from an analysis perspective, in particular regarding the use of high-throughput sequencing strategies, such as RNA-sequencing, and summarize the unique challenges of investigating the antisense transcriptome. Finally, we elaborate on their potential as biomarkers and future targets for treatment, focusing on cancer.
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Affiliation(s)
- Julian C Krappinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria
| | - Lilli Bonstingl
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Katrin Pansy
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Katja Sallinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Nick I Wreglesworth
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Lukas Grinninger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Austrian Biotech University of Applied Sciences, Konrad Lorenz-Straße 10, 3430 Tulln an der Donau, Austria
| | - Alexander Deutsch
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Amin El-Heliebi
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Thomas Kroneis
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Ramsay J Mcfarlane
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Christoph W Sensen
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria; Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria; HCEMM Kft., Római blvd. 21, 6723 Szeged, Hungary
| | - Julia Feichtinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria.
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15
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Keup C, Suryaprakash V, Hauch S, Storbeck M, Hahn P, Sprenger-Haussels M, Kolberg HC, Tewes M, Hoffmann O, Kimmig R, Kasimir-Bauer S. Integrative statistical analyses of multiple liquid biopsy analytes in metastatic breast cancer. Genome Med 2021; 13:85. [PMID: 34001236 PMCID: PMC8130163 DOI: 10.1186/s13073-021-00902-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 04/30/2021] [Indexed: 02/08/2023] Open
Abstract
Background Single liquid biopsy analytes (LBAs) have been utilized for therapy selection in metastatic breast cancer (MBC). We performed integrative statistical analyses to examine the clinical relevance of using multiple LBAs: matched circulating tumor cell (CTC) mRNA, CTC genomic DNA (gDNA), extracellular vesicle (EV) mRNA, and cell-free DNA (cfDNA). Methods Blood was drawn from 26 hormone receptor-positive, HER2-negative MBC patients. CTC mRNA and EV mRNA were analyzed using a multi-marker qPCR. Plasma from CTC-depleted blood was utilized for cfDNA isolation. gDNA from CTCs was isolated from mRNA-depleted CTC lysates. CTC gDNA and cfDNA were analyzed by targeted sequencing. Hierarchical clustering was performed within each analyte, and its results were combined into a score termed Evaluation of multiple Liquid biopsy analytes In Metastatic breast cancer patients All from one blood sample (ELIMA.score), which calculates the contribution of each analyte to the overall survival prediction. Singular value decomposition (SVD), mutual information calculation, k-means clustering, and graph-theoretic analysis were conducted to elucidate the dependence between individual analytes. Results A combination of two/three/four LBAs increased the prevalence of patients with actionable signals. Aggregating the results of hierarchical clustering of individual LBAs into the ELIMA.score resulted in a highly significant correlation with overall survival, thereby bolstering evidence for the additive value of using multiple LBAs. Computation of mutual information indicated that none of the LBAs is independent of the others, but the ability of a single LBA to describe the others is rather limited—only CTC gDNA could partially describe the other three LBAs. SVD revealed that the strongest singular vectors originate from all four LBAs, but a majority originated from CTC gDNA. After k-means clustering of patients based on parameters of all four LBAs, the graph-theoretic analysis revealed CTC ERBB2 variants only in patients belonging to one particular cluster. Conclusions The additional benefits of using all four LBAs were objectively demonstrated in this pilot study, which also indicated a relative dominance of CTC gDNA over the other LBAs. Consequently, a multi-parametric liquid biopsy approach deconvolutes the genomic and transcriptomic complexity and should be considered in clinical practice. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00902-1.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122, Essen, Germany.
| | | | | | | | | | | | - Hans-Christian Kolberg
- Department of Gynecology and Obstetrics, Marienhospital Bottrop, 46236, Bottrop, Germany
| | - Mitra Tewes
- Department of Medical Oncology, University Hospital of Essen, 45122, Essen, Germany
| | - Oliver Hoffmann
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122, Essen, Germany
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16
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Nonn O, Fischer C, Geisberger S, El-Heliebi A, Kroneis T, Forstner D, Desoye G, Staff AC, Sugulle M, Dechend R, Pecks U, Kollmann M, Stern C, Cartwright JE, Whitley GS, Thilaganathan B, Wadsack C, Huppertz B, Herse F, Gauster M. Maternal Angiotensin Increases Placental Leptin in Early Gestation via an Alternative Renin-Angiotensin System Pathway: Suggesting a Link to Preeclampsia. Hypertension 2021; 77:1723-1736. [PMID: 33775117 DOI: 10.1161/hypertensionaha.120.16425] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Olivia Nonn
- From the Division of Cell Biology, Histology and Embryology (O.N., A.E.-H., T.K., D.F., B.H., M.G.), Medical University of Graz, Austria
| | - Cornelius Fischer
- Berlin Institute of Systems Biology, Max Delbrueck Centre for Molecular Medicine in the Helmholtz Association, Germany (C.F., S.G.)
| | - Sabrina Geisberger
- Berlin Institute of Systems Biology, Max Delbrueck Centre for Molecular Medicine in the Helmholtz Association, Germany (C.F., S.G.).,Experimental Clinical Research Centre, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association and Charité Berlin, Germany (S.G., R.D., F.H.).,DZHK (German Center for Cardiovascular Research), partner site Berlin, Germany (S.G.).,Berlin Institute of Health (BIH), Berlin, Germany (S.G.)
| | - Amin El-Heliebi
- From the Division of Cell Biology, Histology and Embryology (O.N., A.E.-H., T.K., D.F., B.H., M.G.), Medical University of Graz, Austria
| | - Thomas Kroneis
- From the Division of Cell Biology, Histology and Embryology (O.N., A.E.-H., T.K., D.F., B.H., M.G.), Medical University of Graz, Austria
| | - Désirée Forstner
- From the Division of Cell Biology, Histology and Embryology (O.N., A.E.-H., T.K., D.F., B.H., M.G.), Medical University of Graz, Austria
| | - Gernot Desoye
- Gottfried Schatz Research Centre and Department of Obstetrics and Gynecology (G.D., M.K., C.S., C.W.), Medical University of Graz, Austria
| | - Anne Cathrine Staff
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway (A.C.S., M.S.).,Division of Obstetrics and Gynecology, Oslo University Hospital, Norway (A.C.S., M.S.)
| | - Meryam Sugulle
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway (A.C.S., M.S.).,Division of Obstetrics and Gynecology, Oslo University Hospital, Norway (A.C.S., M.S.)
| | - Ralf Dechend
- Experimental Clinical Research Centre, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association and Charité Berlin, Germany (S.G., R.D., F.H.)
| | - Ulrich Pecks
- Division of Obstetrics and Gynecology, University Hospital Schleswig-Holstein, Kiel, Germany (U.P.)
| | - Martina Kollmann
- Gottfried Schatz Research Centre and Department of Obstetrics and Gynecology (G.D., M.K., C.S., C.W.), Medical University of Graz, Austria
| | - Christina Stern
- Gottfried Schatz Research Centre and Department of Obstetrics and Gynecology (G.D., M.K., C.S., C.W.), Medical University of Graz, Austria
| | - Judith E Cartwright
- Molecular and Clinical Sciences Research Institute, St George's, University of London, United Kingdom (J.E.C., G.S.W.)
| | - Guy S Whitley
- Molecular and Clinical Sciences Research Institute, St George's, University of London, United Kingdom (J.E.C., G.S.W.)
| | - Basky Thilaganathan
- Fetal Medicine Unit, St George's University Hospitals NHS Foundation Trust, London, United Kingdom (B.T.)
| | - Christian Wadsack
- Gottfried Schatz Research Centre and Department of Obstetrics and Gynecology (G.D., M.K., C.S., C.W.), Medical University of Graz, Austria
| | - Berthold Huppertz
- From the Division of Cell Biology, Histology and Embryology (O.N., A.E.-H., T.K., D.F., B.H., M.G.), Medical University of Graz, Austria
| | - Florian Herse
- Experimental Clinical Research Centre, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association and Charité Berlin, Germany (S.G., R.D., F.H.)
| | - Martin Gauster
- From the Division of Cell Biology, Histology and Embryology (O.N., A.E.-H., T.K., D.F., B.H., M.G.), Medical University of Graz, Austria
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