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Zhang XY, Hong LL, Ling ZQ. MUC16/CA125 in cancer: new advances. Clin Chim Acta 2024; 565:119981. [PMID: 39368688 DOI: 10.1016/j.cca.2024.119981] [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: 02/08/2024] [Revised: 09/27/2024] [Accepted: 09/29/2024] [Indexed: 10/07/2024]
Abstract
MUC16/CA125 is a common diagnostic marker for many types of cancer. However, due to the widespread expression of MUC16 in cancer, its specificity and sensitivity as a target are poor, which severely limits its clinical application. In recent years, various studies have shown that the clinical application potential of MUC16/CA125 has been greatly improved. The update of detection technology improves the accuracy and range of detection, and improves the early diagnosis rate of cancer. Targeting MUC16/CA125 is an important strategy for tumor therapy. Targeting residual amino acids, n-glycoylation structures or other targets on the surface of MUC16 cells can greatly improve the accuracy of detection and therapy. The new drug delivery method broke through the original technical shackles, targeted MUC16 positive cells more specifically and improved the drug efficacy. In this paper, the technological advances in detecting and identifying MUC16 targets and the great progress in cancer screening and treatment based on MUC16 as a target are described in detail, revealing the great potential of MUC16 as a target in cancer screening and treatment, and illustrating the potential clinical application value of MUC16.
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Affiliation(s)
- Xin-Yu Zhang
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, No. 1 Banshan East Rd., Gongshu District, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; The Second Clinical Medical College of Zhejiang Chinese Medicine University, Hangzhou 310053, People's Republic of China
| | - Lian-Lian Hong
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, No. 1 Banshan East Rd., Gongshu District, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
| | - Zhi-Qiang Ling
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, No. 1 Banshan East Rd., Gongshu District, Hangzhou, Zhejiang 310022, China; Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China.
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2
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van Schaik LF, Engelhardt EG, Wilthagen EA, Steeghs N, Fernández Coves A, Joore MA, van Harten WH, Retèl VP. Factors for a broad technology assessment of comprehensive genomic profiling in advanced cancer, a systematic review. Crit Rev Oncol Hematol 2024; 202:104441. [PMID: 39002790 DOI: 10.1016/j.critrevonc.2024.104441] [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: 04/15/2024] [Revised: 06/12/2024] [Accepted: 07/06/2024] [Indexed: 07/15/2024] Open
Abstract
Comprehensive Genomic Profiling (CGP) allows for the identification of many targets. Reimbursement decision-making is, however, challenging because besides the health benefits of on-label treatments and costs, other factors related to diagnostic and treatment pathways may also play a role. The aim of this study was to identify which other factors are relevant for the technology assessment of CGP and to summarize the available evidence for these factors. After a scoping search and two expert sessions, five factors were identified: feasibility, test journey, wider implications of diagnostic results, organisation of laboratories, and "scientific spillover". Subsequently, a systematic search identified 83 studies collecting mainly evidence for the factors "test journey" and "wider implications of diagnostic results". Its nature was, however, of limited value for decision-making. We recommend the use of comparative strategies, uniformity in outcome definitions, and the inclusion of a comprehensive set of factors in future evidence generation.
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Affiliation(s)
- L F van Schaik
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, P.O. Box 90103, Amsterdam 1006 BE, the Netherlands; Erasmus School of Health Policy and Management, Erasmus University Rotterdam, Rotterdam, the Netherlands.
| | - E G Engelhardt
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, P.O. Box 90103, Amsterdam 1006 BE, the Netherlands.
| | - E A Wilthagen
- Scientific Information Service, Netherlands Cancer Institute, Antoni van Leeuwenhoek, Plesmanlaan 121, Amsterdam CX 1066, the Netherlands.
| | - N Steeghs
- Department of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam CX 1066, the Netherlands.
| | - A Fernández Coves
- Department of Clinical Epidemiology and Medical Technology Assessment (KEMTA), P. Debyelaan 25, Oxford Building, P.O. Box 5800a, Maastricht, Limburg, the Netherlands; Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, The Netherlands.
| | - M A Joore
- Department of Clinical Epidemiology and Medical Technology Assessment (KEMTA), P. Debyelaan 25, Oxford Building, P.O. Box 5800a, Maastricht, Limburg, the Netherlands; Care and Public Health Research Institute (CAPHRI), Maastricht University, Maastricht, The Netherlands.
| | - W H van Harten
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, P.O. Box 90103, Amsterdam 1006 BE, the Netherlands; Department of Health Technology and Services Research, University of Twente, Enschede, the Netherlands.
| | - V P Retèl
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute, P.O. Box 90103, Amsterdam 1006 BE, the Netherlands; Erasmus School of Health Policy and Management, Erasmus University Rotterdam, Rotterdam, the Netherlands.
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3
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Andersen L, Christensen DS, Kjær A, Knudsen M, Andersen AK, Laursen MB, Ahrenfeldt J, Laursen BE, Birkbak NJ. Exploring the molecular landscape of cancer of unknown primary: A comparative analysis with other metastatic cancers. Mol Oncol 2024; 18:2393-2406. [PMID: 38750007 PMCID: PMC11459033 DOI: 10.1002/1878-0261.13664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/01/2024] [Accepted: 05/03/2024] [Indexed: 10/09/2024] Open
Abstract
Cancer of unknown primary (CUP) tumors are biologically very heterogeneous, which complicates stratification of patients for treatment. Consequently, these patients face limited treatment options and a poor prognosis. With this study, we aim to expand on the current knowledge of CUP biology by analyzing two cohorts: a well-characterized cohort of 44 CUP patients, and 213 metastatic patients with known primary. These cohorts were treated at the same institution and characterized by identical molecular assessments. Through comparative analysis of genomic and transcriptomic data, we found that CUP tumors were characterized by high expression of immune-related genes and pathways compared to other metastatic tumors. Moreover, CUP tumors uniformly demonstrated high levels of tumor-infiltrating leukocytes and circulating T cells, indicating a strong immune response. Finally, the genetic landscape of CUP tumors resembled that of other metastatic cancers and demonstrated mutations in established cancer genes. In conclusion, CUP tumors possess a distinct immunophenotype that distinguishes them from other metastatic cancers. These results may suggest an immune response in CUP that facilitates metastatic tumor growth while limiting growth of the primary tumor.
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Affiliation(s)
- Laura Andersen
- Department of Molecular MedicineAarhus University HospitalDenmark
- Department of Clinical MedicineAarhus UniversityDenmark
- Bioinformatics Research CenterAarhus UniversityDenmark
| | - Ditte S. Christensen
- Department of Molecular MedicineAarhus University HospitalDenmark
- Department of Clinical MedicineAarhus UniversityDenmark
- Department of OncologyAarhus University HospitalDenmark
| | - Asbjørn Kjær
- Department of Molecular MedicineAarhus University HospitalDenmark
- Department of Clinical MedicineAarhus UniversityDenmark
- Bioinformatics Research CenterAarhus UniversityDenmark
| | - Michael Knudsen
- Department of Molecular MedicineAarhus University HospitalDenmark
- Department of Clinical MedicineAarhus UniversityDenmark
| | | | - Maria B. Laursen
- Department of Molecular MedicineAarhus University HospitalDenmark
- Department of Clinical MedicineAarhus UniversityDenmark
| | - Johanne Ahrenfeldt
- Department of Molecular MedicineAarhus University HospitalDenmark
- Department of Clinical MedicineAarhus UniversityDenmark
- Bioinformatics Research CenterAarhus UniversityDenmark
| | - Britt E. Laursen
- Department of Molecular MedicineAarhus University HospitalDenmark
- Department of Clinical MedicineAarhus UniversityDenmark
- Department of OncologyAarhus University HospitalDenmark
| | - Nicolai J. Birkbak
- Department of Molecular MedicineAarhus University HospitalDenmark
- Department of Clinical MedicineAarhus UniversityDenmark
- Bioinformatics Research CenterAarhus UniversityDenmark
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4
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De Velasco MA, Sakai K, Mitani S, Kura Y, Minamoto S, Haeno T, Hayashi H, Nishio K. A machine learning-based method for feature reduction of methylation data for the classification of cancer tissue origin. Int J Clin Oncol 2024:10.1007/s10147-024-02617-w. [PMID: 39292320 DOI: 10.1007/s10147-024-02617-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 08/28/2024] [Indexed: 09/19/2024]
Abstract
BACKGROUND Genome DNA methylation profiling is a promising yet costly method for cancer classification, involving substantial data. We developed an ensemble learning model to identify cancer types using methylation profiles from a limited number of CpG sites. METHODS Analyzing methylation data from 890 samples across 10 cancer types from the TCGA database, we utilized ANOVA and Gain Ratio to select the most significant CpG sites, then employed Gradient Boosting to reduce these to just 100 sites. RESULTS This approach maintained high accuracy across multiple machine learning models, with classification accuracy rates between 87.7% and 93.5% for methods including Extreme Gradient Boosting, CatBoost, and Random Forest. This method effectively minimizes the number of features needed without losing performance, helping to classify primary organs and uncover subgroups within specific cancers like breast and lung. CONCLUSIONS Using a gradient boosting feature selector shows potential for streamlining methylation-based cancer classification.
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Affiliation(s)
- Marco A De Velasco
- Department of Genome Biology, Faculty of Medicine, Kindai University, Ohnohigashi 377-2, Osaka-Sayama, 589-9511, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Faculty of Medicine, Kindai University, Ohnohigashi 377-2, Osaka-Sayama, 589-9511, Japan
| | - Seiichiro Mitani
- Department of Medical Oncology, Faculty of Medicine, Kindai University, Osaka-Sayama, Japan
| | - Yurie Kura
- Department of Genome Biology, Faculty of Medicine, Kindai University, Ohnohigashi 377-2, Osaka-Sayama, 589-9511, Japan
| | - Shuji Minamoto
- Department of Molecular Tumor Pathobiology, Kindai University Graduate School of Medical Sciences, Osaka-Sayama, Japan
| | - Takahiro Haeno
- Department of Molecular Tumor Pathobiology, Kindai University Graduate School of Medical Sciences, Osaka-Sayama, Japan
| | - Hidetoshi Hayashi
- Department of Medical Oncology, Faculty of Medicine, Kindai University, Osaka-Sayama, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Faculty of Medicine, Kindai University, Ohnohigashi 377-2, Osaka-Sayama, 589-9511, Japan.
- Department of Molecular Tumor Pathobiology, Kindai University Graduate School of Medical Sciences, Osaka-Sayama, Japan.
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5
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Krebs M, Haller F, Spörl S, Gerhard-Hartmann E, Utpatel K, Maurus K, Kunzmann V, Chatterjee M, Venkataramani V, Maatouk I, Bittrich M, Einwag T, Meidenbauer N, Tögel L, Hirsch D, Dietmaier W, Keil F, Scheiter A, Immel A, Heudobler D, Einhell S, Kaiser U, Sedlmeier AM, Maurer J, Schenkirsch G, Jordan F, Schmutz M, Dintner S, Rosenwald A, Hartmann A, Evert M, Märkl B, Bargou R, Mackensen A, Beckmann MW, Pukrop T, Herr W, Einsele H, Trepel M, Goebeler ME, Claus R, Kerscher A, Lüke F. The WERA cancer center matrix: Strategic management of patient access to precision oncology in a large and mostly rural area of Germany. Eur J Cancer 2024; 207:114144. [PMID: 38852290 DOI: 10.1016/j.ejca.2024.114144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
Abstract
PURPOSE Providing patient access to precision oncology (PO) is a major challenge of clinical oncologists. Here, we provide an easily transferable model from strategic management science to assess the outreach of a cancer center. METHODS As members of the German WERA alliance, the cancer centers in Würzburg, Erlangen, Regensburg and Augsburg merged care data regarding their geographical impact. Specifically, we examined the provenance of patients from WERA´s molecular tumor boards (MTBs) between 2020 and 2022 (n = 2243). As second dimension, we added the provenance of patients receiving general cancer care by WERA. Clustering our catchment area along these two dimensions set up a four-quadrant matrix consisting of postal code areas with referrals towards WERA. These areas were re-identified on a map of the Federal State of Bavaria. RESULTS The WERA matrix overlooked an active screening area of 821 postal code areas - representing about 50 % of Bavaria´s spatial expansion and more than six million inhabitants. The WERA matrix identified regions successfully connected to our outreach structures in terms of subsidiarity - with general cancer care mainly performed locally but PO performed in collaboration with WERA. We also detected postal code areas with a potential PO backlog - characterized by high levels of cancer care performed by WERA and low levels or no MTB representation. CONCLUSIONS The WERA matrix provided a transparent portfolio of postal code areas, which helped assessing the geographical impact of our PO program. We believe that its intuitive principle can easily be transferred to other cancer centers.
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Affiliation(s)
- Markus Krebs
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany; Department of Urology and Pediatric Urology, University Hospital Würzburg, 97080 Würzburg, Germany.
| | - Florian Haller
- Institute of Pathology, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, 91054 Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Silvia Spörl
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany; Department of Medicine V, Hematology and Oncology, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Elena Gerhard-Hartmann
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany; Institute of Pathology, University of Würzburg, 97080 Würzburg, Germany
| | - Kirsten Utpatel
- Institute of Pathology, University of Regensburg, 93053 Regensburg, Germany; Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany
| | - Katja Maurus
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany; Institute of Pathology, University of Würzburg, 97080 Würzburg, Germany
| | - Volker Kunzmann
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany; Department of Internal Medicine II, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Manik Chatterjee
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Vivek Venkataramani
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Imad Maatouk
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany; Department of Internal Medicine II, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Max Bittrich
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany; Department of Internal Medicine II, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Tatjana Einwag
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Norbert Meidenbauer
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany; Department of Medicine V, Hematology and Oncology, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Lars Tögel
- Institute of Pathology, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, 91054 Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Daniela Hirsch
- Institute of Pathology, University of Regensburg, 93053 Regensburg, Germany; Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany
| | - Wolfgang Dietmaier
- Institute of Pathology, University of Regensburg, 93053 Regensburg, Germany; Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany
| | - Felix Keil
- Institute of Pathology, University of Regensburg, 93053 Regensburg, Germany; Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany
| | - Alexander Scheiter
- Institute of Pathology, University of Regensburg, 93053 Regensburg, Germany; Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany
| | - Alexander Immel
- Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany
| | - Daniel Heudobler
- Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany; Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Sabine Einhell
- Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany; Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Ulrich Kaiser
- Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany; Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Anja M Sedlmeier
- Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany; Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Julia Maurer
- Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany
| | | | - Frank Jordan
- Comprehensive Cancer Center Augsburg, 86156 Augsburg, Germany; Department of Hematology and Clinical Oncology, Medical Faculty, University of Augsburg, 86156 Augsburg, Germany
| | - Maximilian Schmutz
- Comprehensive Cancer Center Augsburg, 86156 Augsburg, Germany; Department of Hematology and Clinical Oncology, Medical Faculty, University of Augsburg, 86156 Augsburg, Germany; Institute of Digital Medicine (IDM), Medical Faculty, University of Augsburg, 86156 Augsburg, Germany
| | - Sebastian Dintner
- Comprehensive Cancer Center Augsburg, 86156 Augsburg, Germany; Institute of Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, 86156 Augsburg, Germany
| | - Andreas Rosenwald
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany; Institute of Pathology, University of Würzburg, 97080 Würzburg, Germany
| | - Arndt Hartmann
- Institute of Pathology, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, 91054 Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany
| | - Matthias Evert
- Institute of Pathology, University of Regensburg, 93053 Regensburg, Germany; Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany
| | - Bruno Märkl
- Comprehensive Cancer Center Augsburg, 86156 Augsburg, Germany; Institute of Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, 86156 Augsburg, Germany
| | - Ralf Bargou
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany; Bavarian Cancer Research Center (BZKF), 91052 Erlangen, Germany
| | - Andreas Mackensen
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany; Department of Medicine V, Hematology and Oncology, University Hospital Erlangen, 91054 Erlangen, Germany; Bavarian Cancer Research Center (BZKF), 91052 Erlangen, Germany
| | - Matthias W Beckmann
- Comprehensive Cancer Center Erlangen-EMN, 91054 Erlangen, Germany; Bavarian Cancer Research Center (BZKF), 91052 Erlangen, Germany; Department of Gynecology and Obstetrics, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Tobias Pukrop
- Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany; Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, 93053 Regensburg, Germany; Bavarian Cancer Research Center (BZKF), 91052 Erlangen, Germany; Division of Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine, 93053 Regensburg, Germany
| | - Wolfgang Herr
- Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany; Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, 97080 Würzburg, Germany; Bavarian Cancer Research Center (BZKF), 91052 Erlangen, Germany
| | - Martin Trepel
- Comprehensive Cancer Center Augsburg, 86156 Augsburg, Germany; Department of Hematology and Clinical Oncology, Medical Faculty, University of Augsburg, 86156 Augsburg, Germany; Bavarian Cancer Research Center (BZKF), 91052 Erlangen, Germany
| | - Maria-Elisabeth Goebeler
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany; Department of Internal Medicine II, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Rainer Claus
- Comprehensive Cancer Center Augsburg, 86156 Augsburg, Germany; Department of Hematology and Clinical Oncology, Medical Faculty, University of Augsburg, 86156 Augsburg, Germany; Institute of Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, 86156 Augsburg, Germany
| | - Alexander Kerscher
- Comprehensive Cancer Center Mainfranken, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Florian Lüke
- Comprehensive Cancer Center Ostbayern, 93053 Regensburg, Germany; Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, 93053 Regensburg, Germany; Division of Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine, 93053 Regensburg, Germany
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6
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Jacquin N, Flippot R, Masliah-Planchon J, Grisay G, Brillet R, Dupain C, Kamal M, Guillou I, Gruel N, Servant N, Gestraud P, Wong J, Cockenpot V, Goncalves A, Selves J, Blons H, Rouleau E, Delattre O, Gervais C, Le Tourneau C, Bièche I, Allory Y, Albigès L, Watson S. Metastatic renal cell carcinoma with occult primary: a multicenter prospective cohort. NPJ Precis Oncol 2024; 8:147. [PMID: 39025947 PMCID: PMC11258290 DOI: 10.1038/s41698-024-00648-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024] Open
Abstract
Metastatic carcinoma of presumed renal origin (rCUP) has recently emerged as a new entity within the heterogeneous entity of Cancers of Unknown Primary (CUP) but their biological features and optimal therapeutic management remain unknown. We report the molecular characteristics and clinical outcome of a series of 25 rCUP prospectively identified within the French National Multidisciplinary Tumor Board for CUP. This cohort strongly suggests that rCUP share similarities with common RCC subtypes and benefit from renal-tailored systemic treatment. This study highlights the importance of integrating clinical and molecular data for optimal diagnosis and management of CUP.
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Affiliation(s)
- Nicolas Jacquin
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France
- Department of Medical Oncology, Institut Godinot, Reims, France
| | - Ronan Flippot
- Department of Cancer Medicine, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | | | - Guillaume Grisay
- Department of Cancer Medicine, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Riwan Brillet
- Clinical Bioinformatic Unit, Department of Diagnostic and Theragnostic Medicine, Institut Curie Hospital, Paris, France
| | - Célia Dupain
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Maud Kamal
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Isabelle Guillou
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
| | - Nadège Gruel
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France
- Department of Translational Research, Institut Curie Hospital, Paris, France
| | - Nicolas Servant
- INSERM U900, CBIO-Centre for Computational Biology, Institut Curie Research Center, Mines ParisTech, Paris, France
| | - Pierre Gestraud
- INSERM U900, CBIO-Centre for Computational Biology, Institut Curie Research Center, Mines ParisTech, Paris, France
| | - Jennifer Wong
- Somatic Genetic Unit, Department of Genetics, Institut Curie Hospital, Paris, France
| | | | | | - Janick Selves
- Department of Pathology, University Hospital of Toulouse (IUCT), Toulouse, France
| | - Hélène Blons
- Department of Biochemistry, Pharmacogenetics and Molecular Oncology, Georges Pompidou European Hospital, APHP, Paris, France
| | - Etienne Rouleau
- PRISM Center for personalized medicine, Gustave Roussy Cancer Center, Villejuif, France
| | - Olivier Delattre
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France
- Somatic Genetic Unit, Department of Genetics, Institut Curie Hospital, Paris, France
| | - Claire Gervais
- Department of Medical Oncology, Georges Pompidou European Hospital, APHP, Paris, France
| | - Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, Paris, France
- INSERM U900, Institut Curie, Saint-Cloud, France
- Paris-Saclay University, Paris, France
| | - Ivan Bièche
- Department of Genetics, Institut Curie Hospital, INSERM U1016, Université Paris Cité, Paris, France
| | - Yves Allory
- Department of Pathology, Institut Curie Hospital, Saint-Cloud, France.
- Université Versailles St-Quentin, Université Paris-Saclay, Montigny-le-Bretonneux, France.
| | - Laurence Albigès
- Department of Cancer Medicine, Institut Gustave Roussy, Université Paris-Saclay, Villejuif, France.
| | - Sarah Watson
- INSERM U830, Diversity and Plasticity of Childhood Tumors Lab, PSL Research University, Institut Curie Research Center, Paris, France.
- Department of Medical Oncology, Institut Curie Hospital, Paris, France.
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7
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Mosele MF, Westphalen CB, Stenzinger A, Barlesi F, Bayle A, Bièche I, Bonastre J, Castro E, Dienstmann R, Krämer A, Czarnecka AM, Meric-Bernstam F, Michiels S, Miller R, Normanno N, Reis-Filho J, Remon J, Robson M, Rouleau E, Scarpa A, Serrano C, Mateo J, André F. Recommendations for the use of next-generation sequencing (NGS) for patients with advanced cancer in 2024: a report from the ESMO Precision Medicine Working Group. Ann Oncol 2024; 35:588-606. [PMID: 38834388 DOI: 10.1016/j.annonc.2024.04.005] [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: 02/20/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Advancements in the field of precision medicine have prompted the European Society for Medical Oncology (ESMO) Precision Medicine Working Group to update the recommendations for the use of tumour next-generation sequencing (NGS) for patients with advanced cancers in routine practice. METHODS The group discussed the clinical impact of tumour NGS in guiding treatment decision using the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT) considering cost-effectiveness and accessibility. RESULTS As for 2020 recommendations, ESMO recommends running tumour NGS in advanced non-squamous non-small-cell lung cancer, prostate cancer, colorectal cancer, cholangiocarcinoma, and ovarian cancer. Moreover, it is recommended to carry out tumour NGS in clinical research centres and under specific circumstances discussed with patients. In this updated report, the consensus within the group has led to an expansion of the recommendations to encompass patients with advanced breast cancer and rare tumours such as gastrointestinal stromal tumours, sarcoma, thyroid cancer, and cancer of unknown primary. Finally, ESMO recommends carrying out tumour NGS to detect tumour-agnostic alterations in patients with metastatic cancers where access to matched therapies is available. CONCLUSION Tumour NGS is increasingly expanding its scope and application within oncology with the aim of enhancing the efficacy of precision medicine for patients with cancer.
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Affiliation(s)
- M F Mosele
- INSERM U981, Gustave Roussy, Villejuif; Department of Cancer Medicine, Gustave Roussy, Villejuif, France
| | - C B Westphalen
- Comprehensive Cancer Center Munich & Department of Medicine III, University Hospital, LMU Munich, Munich
| | - A Stenzinger
- Institute of Pathology, University Hospital Heidelberg and Center for Personalized Medicine (ZPM), Heidelberg, Germany
| | - F Barlesi
- INSERM U981, Gustave Roussy, Villejuif; Department of Cancer Medicine, Gustave Roussy, Villejuif, France; Faculty of Medicine, Université Paris-Saclay, Kremlin Bicêtre
| | - A Bayle
- Faculty of Medicine, Université Paris-Saclay, Kremlin Bicêtre; Drug Development Department (DITEP), Gustave Roussy, Villejuif; Oncostat U1018, Inserm, Université Paris-Saclay, labeled Ligue Contre le Cancer, Villejuif; Service de Biostatistique et Epidémiologie, Gustave Roussy, Villejuif
| | - I Bièche
- Department of Genetics, Institut Curie, INSERM U1016, Université Paris Cité, Paris, France
| | - J Bonastre
- Oncostat U1018, Inserm, Université Paris-Saclay, labeled Ligue Contre le Cancer, Villejuif; Service de Biostatistique et Epidémiologie, Gustave Roussy, Villejuif
| | - E Castro
- Department of Medical Oncology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre, Madrid
| | - R Dienstmann
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona; University of Vic-Central University of Catalonia, Vic, Spain; Oncoclínicas, São Paulo, Brazil
| | - A Krämer
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ), Heidelberg; Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - A M Czarnecka
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw; Department of Experimental Pharmacology, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - F Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Michiels
- Oncostat U1018, Inserm, Université Paris-Saclay, labeled Ligue Contre le Cancer, Villejuif; Service de Biostatistique et Epidémiologie, Gustave Roussy, Villejuif
| | - R Miller
- Department of Medical Oncology, University College London, London; Department of Medical Oncology, St Bartholomew's Hospital, London, UK
| | - N Normanno
- Scientific Directorate, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - J Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York
| | - J Remon
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France
| | - M Robson
- Breast Medicine and Clinical Genetics Services, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - E Rouleau
- Tumor Genetics Service, Medical Biology and Pathology Department, Gustave Roussy, Villejuif, France
| | - A Scarpa
- Section of Pathology, Department of Diagnostics and Public Health, University of Verona-School of Medicine, Verona, Italy
| | - C Serrano
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona
| | - J Mateo
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona
| | - F André
- INSERM U981, Gustave Roussy, Villejuif; Department of Cancer Medicine, Gustave Roussy, Villejuif, France; Faculty of Medicine, Université Paris-Saclay, Kremlin Bicêtre.
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8
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Junior JNA, Preto DD'A, Lazarini MEZN, de Lima MA, Bonatelli M, Berardinelli GN, da Silva VD, Pinheiro C, Reis RM, Cárcano FM. PD-L1 expression and microsatellite instability (MSI) in cancer of unknown primary site. Int J Clin Oncol 2024; 29:726-734. [PMID: 38528294 PMCID: PMC11130030 DOI: 10.1007/s10147-024-02494-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/18/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND Cancer of unknown primary site (CUP) is a heterogeneous group of tumors for which the origin remains unknown. Clinical outcomes might be influenced by regulatory processes in its microenvironment. Microsatellite instability (MSI) is a predictive biomarker for cancer immunotherapy and its status, as well as co-occurrence with PD-L1 expression, is poorly evaluated. We aim to evaluate the expression of PD-L1 and the status of MSI in CUP and their possible associations with clinical-pathological features. METHODS The combined positive score (CPS) PD-L1 expression was evaluated by immunohistochemistry. MSI status was assessed using a hexa-plex marker panel by polymerase chain reaction followed by fragment analysis. RESULTS Among the 166 cases, MSI analysis was conclusive in 120, with two cases being MSI positive (1.6%). PD-L1 expression was positive in 18.3% of 109 feasible cases. PD-L1 expression was significantly associated with non-visceral metastasis and a dominance of nodal metastasis. The median overall survival (mOS) was 3.7 (95% CI 1.6-5.8) months and patients who expressed PD-L1 achieved a better mOS compared to those who did not express PD-L1 (18.7 versus 3.0 months, p-value: < .001). ECOG-PS equal to or more than two and PD-L1 expression were independent prognostic factors in multivariate analysis (2.37 and 0.42, respectively). CONCLUSION PD-L1 is expressed in a subset (1/5) of patients with CUP and associated with improved overall survival, while MSI is a rare event. There is a need to explore better the tumor microenvironment as well as the role of immunotherapy to change such a bad clinical outcome.
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Affiliation(s)
| | - Daniel D 'Almeida Preto
- Department of Clinical Oncology, Barretos Cancer Hospital, Barretos, Brazil
- Barretos School of Health Sciences Dr. Paulo Prata - FACISB, Barretos, Brazil
| | | | | | - Murilo Bonatelli
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | - Céline Pinheiro
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Barretos School of Health Sciences Dr. Paulo Prata - FACISB, Barretos, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Medical School, Life and Health Sciences Research Institute (ICVS), University of Minho, Braga, Portugal
- 3ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
| | - Flavio Mavignier Cárcano
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.
- Oncoclinicas & Co - Medica Scientia Innovation Research (MEDSIR), Sao Paulo, Brazil.
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9
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Metzger P, Boerries M. [The collaborative project "Personalized medicine for oncology" (PM4Onco) as part of the Medical Informatics Initiative (MII)]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2024; 67:668-675. [PMID: 38739266 PMCID: PMC11166753 DOI: 10.1007/s00103-024-03886-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2024] [Indexed: 05/14/2024]
Abstract
The collaborative project Personalized Medicine for Oncology (PM4Onco) was launched in 2023 as part of the National Decade against Cancer (NKD) and is executed within the Medical Informatics Initiative (MII). Its aim is to establish a sustainable infrastructure for the integration and use of data from clinical and biomedical research and therefore combines the experience and preliminary work of all four consortia of the MII and the leading oncology centers in Germany. The data provided by PM4Onco will be prepared in a suitable form to support decision making in molecular tumor boards. This concept and infrastructure will be extended to 23 participating partner sites and thus improve access to targeted therapies based on clinical information and analysis of molecular genetic alterations in tumors at different stages of the disease. This will help to improve the treatment and prognosis of tumor diseases.Clinical cancer registries are involved in the project to improve data quality through standardized documentation routines. Clinical experts advise on the expansion of the core datasets for personalized medicine (PM). Information on quality of life and treatment outcomes reported by patients in questionnaires, which is rarely collected outside of clinical trials, will make a significant contribution. Patient representatives are involved from the onset to ensure that the important perspective of patients is taken into account in the decision-making process. PM4Onco thus creates an alliance between the MII, oncological centers of excellence, clinical cancer registries, young scientists, patients, and citizens to strengthen and advance PM in cancer therapy.
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Affiliation(s)
- Patrick Metzger
- Institut für Medizinische Bioinformatik und Systemmedizin (IBSM), Universitätsklinikum Freiburg, Medizinische Fakultät, Universität Freiburg, Breisacher Straße 153, 79110, Freiburg, Deutschland
| | - Melanie Boerries
- Institut für Medizinische Bioinformatik und Systemmedizin (IBSM), Universitätsklinikum Freiburg, Medizinische Fakultät, Universität Freiburg, Breisacher Straße 153, 79110, Freiburg, Deutschland.
- Deutsches Konsortium für Translationale Krebsforschung (DKTK), Standort Freiburg, Kooperation zwischen DKFZ und Universitätsklinikum Freiburg, Universität Freiburg, Freiburg, Deutschland.
- Comprehensive Cancer Center Freiburg (CCCF), Universitätsklinikum Freiburg, Universität Freiburg, Freiburg, Deutschland.
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10
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Zhang XY, Hong LL, Ling ZQ. MUC16: clinical targets with great potential. Clin Exp Med 2024; 24:101. [PMID: 38758220 PMCID: PMC11101557 DOI: 10.1007/s10238-024-01365-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 04/29/2024] [Indexed: 05/18/2024]
Abstract
Mucin 16 (MUC16) is a membrane-bound mucin that is abnormally expressed or mutated in a variety of diseases, especially tumors, while being expressed in normal body epithelium. MUC16 and its extracellular components are often important cancer-related biomarkers. Abnormal expression of MUC16 promotes tumor progression through mesenchymal protein, PI3K/AKT pathway, JAK2/STAT3 pathway, ERK/FBW7/c-Myc, and other mechanisms, and plays an important role in the occurrence and development of tumors. In addition, MUC16 also helps tumor immune escape by inhibiting T cells and NK cells. Many drugs and trials targeting MUC16 have been developed, and MUC16 may be a new direction for future treatments. In this paper, the mechanism of action of MUC16 in the development of cancer, especially in the immune escape of tumor, is introduced in detail, indicating the potential of MUC16 in clinical treatment.
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Affiliation(s)
- Xin-Yu Zhang
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, No.1 Banshan East Rd., Gongshu District, Hangzhou, 310022, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China
- The Second Clinical Medical College of Zhejiang, Chinese Medicine University, Hangzhou, 310053, China
| | - Lian-Lian Hong
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, No.1 Banshan East Rd., Gongshu District, Hangzhou, 310022, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China
| | - Zhi-Qiang Ling
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, No.1 Banshan East Rd., Gongshu District, Hangzhou, 310022, Zhejiang, China.
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China.
- The Second Clinical Medical College of Zhejiang, Chinese Medicine University, Hangzhou, 310053, China.
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11
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Conway AM, Pearce SP, Clipson A, Hill SM, Chemi F, Slane-Tan D, Ferdous S, Hossain ASMM, Kamieniecka K, White DJ, Mitchell C, Kerr A, Krebs MG, Brady G, Dive C, Cook N, Rothwell DG. A cfDNA methylation-based tissue-of-origin classifier for cancers of unknown primary. Nat Commun 2024; 15:3292. [PMID: 38632274 PMCID: PMC11024142 DOI: 10.1038/s41467-024-47195-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Cancers of Unknown Primary (CUP) remains a diagnostic and therapeutic challenge due to biological heterogeneity and poor responses to standard chemotherapy. Predicting tissue-of-origin (TOO) molecularly could help refine this diagnosis, with tissue acquisition barriers mitigated via liquid biopsies. However, TOO liquid biopsies are unexplored in CUP cohorts. Here we describe CUPiD, a machine learning classifier for accurate TOO predictions across 29 tumour classes using circulating cell-free DNA (cfDNA) methylation patterns. We tested CUPiD on 143 cfDNA samples from patients with 13 cancer types alongside 27 non-cancer controls, with overall sensitivity of 84.6% and TOO accuracy of 96.8%. In an additional cohort of 41 patients with CUP CUPiD predictions were made in 32/41 (78.0%) cases, with 88.5% of the predictions clinically consistent with a subsequent or suspected primary tumour diagnosis, when available (23/26 patients). Combining CUPiD with cfDNA mutation data demonstrated potential diagnosis re-classification and/or treatment change in this hard-to-treat cancer group.
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Affiliation(s)
- Alicia-Marie Conway
- Nucleic Acid Biomarker Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester and The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Simon P Pearce
- Bioinformatics and Biostatistics Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK
| | - Alexandra Clipson
- Nucleic Acid Biomarker Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK
| | - Steven M Hill
- Bioinformatics and Biostatistics Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK
| | - Francesca Chemi
- Nucleic Acid Biomarker Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK
| | - Dan Slane-Tan
- Nucleic Acid Biomarker Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK
| | - Saba Ferdous
- Bioinformatics and Biostatistics Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK
| | - A S Md Mukarram Hossain
- Bioinformatics and Biostatistics Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK
| | - Katarzyna Kamieniecka
- Bioinformatics and Biostatistics Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK
| | - Daniel J White
- Nucleic Acid Biomarker Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK
| | | | - Alastair Kerr
- Bioinformatics and Biostatistics Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK
| | - Matthew G Krebs
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester and The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Gerard Brady
- Nucleic Acid Biomarker Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK
| | - Caroline Dive
- Nucleic Acid Biomarker Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK.
- Bioinformatics and Biostatistics Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK.
| | - Natalie Cook
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester and The Christie NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK.
| | - Dominic G Rothwell
- Nucleic Acid Biomarker Team, Cancer Research UK National Biomarker Centre, The University of Manchester, Manchester, UK.
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12
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Stark L, Kasajima A, Stögbauer F, Schmidl B, Rinecker J, Holzmann K, Färber S, Pfarr N, Steiger K, Wollenberg B, Ruland J, Winter C, Wirth M. Head and neck cancer of unknown primary: unveiling primary tumor sites through machine learning on DNA methylation profiles. Clin Epigenetics 2024; 16:47. [PMID: 38528631 PMCID: PMC10964705 DOI: 10.1186/s13148-024-01657-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/13/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND The unknown tissue of origin in head and neck cancer of unknown primary (hnCUP) leads to invasive diagnostic procedures and unspecific and potentially inefficient treatment options for patients. The most common histologic subtype, squamous cell carcinoma, can stem from various tumor primary sites, including the oral cavity, oropharynx, larynx, head and neck skin, lungs, and esophagus. DNA methylation profiles are highly tissue-specific and have been successfully used to classify tissue origin. We therefore developed a support vector machine (SVM) classifier trained with publicly available DNA methylation profiles of commonly cervically metastasizing squamous cell carcinomas (n = 1103) in order to identify the primary tissue of origin of our own cohort of squamous cell hnCUP patient's samples (n = 28). Methylation analysis was performed with Infinium MethylationEPIC v1.0 BeadChip by Illumina. RESULTS The SVM algorithm achieved the highest overall accuracy of tested classifiers, with 87%. Squamous cell hnCUP samples on DNA methylation level resembled squamous cell carcinomas commonly metastasizing into cervical lymph nodes. The most frequently predicted cancer localization was the oral cavity in 11 cases (39%), followed by the oropharynx and larynx (both 7, 25%), skin (2, 7%), and esophagus (1, 4%). These frequencies concord with the expected distribution of lymph node metastases in epidemiological studies. CONCLUSIONS On DNA methylation level, hnCUP is comparable to primary tumor tissue cancer types that commonly metastasize to cervical lymph nodes. Our SVM-based classifier can accurately predict these cancers' tissues of origin and could significantly reduce the invasiveness of hnCUP diagnostics and enable a more precise therapy after clinical validation.
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Affiliation(s)
- Leonhard Stark
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich, Munich, Germany.
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine and Health, Technical University of Munich, Munich, Germany.
| | - Atsuko Kasajima
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Fabian Stögbauer
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Benedikt Schmidl
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Jakob Rinecker
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Katharina Holzmann
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Sarah Färber
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Nicole Pfarr
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Katja Steiger
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Barbara Wollenberg
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
- Partner Site Munich and German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Jürgen Ruland
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine and Health, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research, TranslaTUM, Technical University of Munich, Munich, Germany
- Partner Site Munich and German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christof Winter
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine and Health, Technical University of Munich, Munich, Germany
- Center for Translational Cancer Research, TranslaTUM, Technical University of Munich, Munich, Germany
- Partner Site Munich and German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Markus Wirth
- Department of Otolaryngology, Head and Neck Surgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
- Partner Site Munich and German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
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13
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Boys EL, Gao B, Grimison P, Sutherland S, MacKenzie KL, Reddel RR, Liu J. Retrospective analysis of clinical characteristics and outcomes of patients with carcinoma of unknown primary from three tertiary centers in Australia. Cancer Med 2024; 13:e7052. [PMID: 38523552 PMCID: PMC10961596 DOI: 10.1002/cam4.7052] [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: 10/18/2023] [Revised: 02/08/2024] [Accepted: 02/16/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND Carcinoma of unknown primary (CUP) remains an important tumor entity and a disproportionate cause of cancer mortality. Little is known about the contemporary clinical characteristics, treatment patterns, and outcomes of CUP patients based on updated international classification guidelines. We evaluated a contemporary CUP cohort to provide insight into current clinical practice and the impact of tissue of origin assignment, site-specific and empirical therapy in a real-world setting. METHODS We conducted a retrospective cohort study of CUP patients, as defined by the updated European Society of Medical Oncology (ESMO) 2023 guidelines, across three tertiary referral centers in Australia between 2015 and 2022. We analyzed clinical characteristics, treatment patterns, and survival outcomes using the Kaplan-Meier method and Cox regression proportional hazard model between favorable and unfavorable risk groups. RESULTS We identified a total of 123 CUP patients (n = 86 unfavorable, n = 37 favorable risk as per the 2023 ESMO guidelines). Sixty-four patients (52%) were assigned a tissue of origin by the treating clinician. Median progression free survival (PFS) was 6.8 (95% confidence interval (CI) 5.1-12.1) months and overall survival (OS) 10.2 (95% CI 6.0-18.5) months. Unfavorable risk (hazard ratio [HR] 2.9, p = 0.006), poor performance status (HR 2.8, p < 0.001), and non-squamous histology (HR 2.5, p < 0.05) were associated with poor survival outcome. A total of 70 patients (57%) proceeded to systemic therapy. In patients with non-squamous histology and unfavorable risk, site-specific therapy compared to empirical chemotherapy did not improve outcome (median OS 8.2 vs. 11.8 months, p = 0.7). CONCLUSIONS In this real-world cohort, CUP presentations were heterogenous. Overall survival and rates of systemic treatment were poor. Poor performance status and unfavorable risk were associated with worse survival. For most patients, site-specific therapy did not improve survival outcome. Improved and timely access to diagnostic tests and therapeutics for this group of patients is urgently required.
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Affiliation(s)
- Emma L. Boys
- ProCan®, Children's Medical Research InstituteWestmeadNew South WalesAustralia
- Faculty of Medicine and HealthThe University of SydneySydneyNew South WalesAustralia
- Department of Medical OncologyCrown Princess Mary Cancer CentreWestmeadNew South WalesAustralia
- Blacktown Cancer and Haematology Centre, Blacktown HospitalBlacktownNew South WalesAustralia
| | - Bo Gao
- Faculty of Medicine and HealthThe University of SydneySydneyNew South WalesAustralia
- Department of Medical OncologyCrown Princess Mary Cancer CentreWestmeadNew South WalesAustralia
- Blacktown Cancer and Haematology Centre, Blacktown HospitalBlacktownNew South WalesAustralia
| | - Peter Grimison
- Faculty of Medicine and HealthThe University of SydneySydneyNew South WalesAustralia
- Chris O'Brien LifehouseSydneyNew South WalesAustralia
| | - Sarah Sutherland
- Faculty of Medicine and HealthThe University of SydneySydneyNew South WalesAustralia
- Chris O'Brien LifehouseSydneyNew South WalesAustralia
| | - Karen L. MacKenzie
- ProCan®, Children's Medical Research InstituteWestmeadNew South WalesAustralia
- School of Medical Science, Faculty of Medicine and HealthThe University of SydneySydneyNew South WalesAustralia
| | - Roger R. Reddel
- ProCan®, Children's Medical Research InstituteWestmeadNew South WalesAustralia
- Sydney Medical School, Faculty of Medicine and HealthThe University of SydneySydneyNew South WalesAustralia
| | - Jia Liu
- ProCan®, Children's Medical Research InstituteWestmeadNew South WalesAustralia
- The Kinghorn Cancer Centre, St Vincent's HospitalDarlinghurstNew South WalesAustralia
- School of Clinical Medicine, St Vincent's CampusUniversity of New South WalesSydneyNew South WalesAustralia
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14
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Liu X, Jiang H, Wang X. Advances in Cancer Research: Current and Future Diagnostic and Therapeutic Strategies. BIOSENSORS 2024; 14:100. [PMID: 38392019 PMCID: PMC10886776 DOI: 10.3390/bios14020100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Cancers of unknown primary (CUP) exhibit significant cellular heterogeneity and malignancy, which poses significant challenges for diagnosis and treatment. Recent years have seen deeper insights into the imaging, pathology, and genetic characteristics of CUP, driven by interdisciplinary collaboration and the evolution of diagnostic and therapeutic strategies. However, due to their insidious onset, lack of evidence-based medicine, and limited clinical understanding, diagnosing and treating CUP remain a significant challenge. To inspire more creative and fantastic research, herein, we report and highlight recent advances in the diagnosis and therapeutic strategies of CUP. Specifically, we discuss advanced diagnostic technologies, including 12-deoxy-2-[fluorine-18]fluoro-D-glucose integrated with computed tomography (18F-FDG PET/CT) or 68Ga-FAPI (fibroblast activation protein inhibitor) PET/CT, liquid biopsy, molecular diagnostics, self-assembling nanotechnology, and artificial intelligence (AI). In particular, the discussion will extend to the effective treatment techniques currently available, such as targeted therapies, immunotherapies, and bio-nanotechnology-based therapeutics. Finally, a novel perspective on the challenges and directions for future CUP diagnostic and therapeutic strategies is discussed.
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Affiliation(s)
- Xiaohui Liu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Hui Jiang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xuemei Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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15
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Satomi K, Ichimura K, Shibahara J. Decoding the DNA methylome of central nervous system tumors: An emerging modality for integrated diagnosis. Pathol Int 2024; 74:51-67. [PMID: 38224248 DOI: 10.1111/pin.13402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/16/2024]
Abstract
The definitive diagnosis and classification of individual cancers are crucial for patient care and cancer research. To achieve a robust diagnosis of central nervous system (CNS) tumors, a genotype-phenotype integrated diagnostic approach was introduced in recent versions of the World Health Organization classification, followed by the incorporation of a genome-wide DNA methylome-based classification. Microarray-based platforms are widely used to obtain DNA methylome data, and the German Cancer Research Center (Deutsches Krebsforschungszentrum [DKFZ]) has a webtool for a DNA methylation-based classifier (DKFZ classifier). Integration of DNA methylome will further enhance the precision of CNS tumor classification, especially in diagnostically challenging cases. However, in the clinical application of DNA methylome-based classification, challenges related to data interpretation persist, in addition to technical caveats, regulations, and limited accessibility. Dimensionality reduction (DMR) can complement integrated diagnosis by visualizing a profile and comparing it with other known samples. Therefore, DNA methylome-based classification is a highly useful research tool for auxiliary analysis in challenging diagnostic and rare disease cases, and for establishing novel tumor concepts. Decoding the DNA methylome, especially by DMR in addition to DKFZ classifier, emphasizes the capability of grasping the fundamental biological principles that provide new perspectives on CNS tumors.
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Affiliation(s)
- Kaishi Satomi
- Department of Pathology, Kyorin University Faculty of Medicine, Tokyo, Japan
| | - Koichi Ichimura
- Department of Brain Disease Translational Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Junji Shibahara
- Department of Pathology, Kyorin University Faculty of Medicine, Tokyo, Japan
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16
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Ghag R, Kaushal M, Nwanne G, Knoten A, Kiryluk K, Rosenberg A, Menez S, Bagnasco SM, Sperati CJ, Atta MG, Gaut JP, Williams JC, El-Achkar TM, Arend LJ, Parikh CR, Jain S. Single Nucleus RNA Sequencing of Remnant Kidney Biopsies and Urine Cell RNA Sequencing Reveal Cell Specific Markers of Covid-19 Acute Kidney Injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.10.566497. [PMID: 37986991 PMCID: PMC10659401 DOI: 10.1101/2023.11.10.566497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Acute kidney injury (AKI) in COVID-19 patients is associated with high mortality and morbidity. Critically ill COVID-19 patients are at twice the risk of in-hospital mortality compared to non-COVID AKI patients. We know little about the cell-specific mechanism in the kidney that contributes to worse clinical outcomes in these patients. New generation single cell technologies have the potential to provide insights into physiological states and molecular mechanisms in COVID-AKI. One of the key limitations is that these patients are severely ill posing significant risks in procuring additional biopsy tissue. We recently generated single nucleus RNA-sequencing data using COVID-AKI patient biopsy tissue as part of the human kidney atlas. Here we describe this approach in detail and report deeper comparative analysis of snRNAseq of 4 COVID-AKI, 4 reference, and 6 non-COVID-AKI biopsies. We also generated and analyzed urine transcriptomics data to find overlapping COVID-AKI-enriched genes and their corresponding cell types in the kidney from snRNA-seq data. We identified all major and minor cell types and states by using by using less than a few cubic millimeters of leftover tissue after pathological workup in our approach. Differential expression analysis of COVID-AKI biopsies showed pathways enriched in viral response, WNT signaling, kidney development, and cytokines in several nephron epithelial cells. COVID-AKI profiles showed a much higher proportion of altered TAL cells than non-COVID AKI and the reference samples. In addition to kidney injury and fibrosis markers indicating robust remodeling we found that, 17 genes overlap between urine cell COVID-AKI transcriptome and the snRNA-seq data from COVID-AKI biopsies. A key feature was that several of the distal nephron and collecting system cell types express these markers. Some of these markers have been previously observed in COVID-19 studies suggesting a common mechanism of injury and potentially the kidney as one of the sources of soluble factors with a potential role in disease progression. Translational Statement The manuscript describes innovation, application and discovery that impact clinical care in kidney disease. First, the approach to maximize use of remnant frozen clinical biopsies to inform on clinically relevant molecular features can augment existing pathological workflow for any frozen tissue without much change in the protocol. Second, this approach is transformational in medical crises such as pandemics where mechanistic insights are needed to evaluate organ injury, targets for drug therapy and diagnostic and prognostic markers. Third, the cell type specific and soluble markers identified and validated can be used for diagnoses or prognoses in AKI due to different etiologies and in multiorgan injury.
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17
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Le Tourneau C, André F, Helland Å, Mileshkin L, Minnaard W, Schiel A, Taskén K, Thomas DM, Veronese ML, Durán-Pacheco G, Leyens L, Rufibach K, Thomas M, Krämer A. Modified study designs to expand treatment options in personalised oncology: a multistakeholder view. Eur J Cancer 2023; 194:113278. [PMID: 37820553 DOI: 10.1016/j.ejca.2023.113278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 10/13/2023]
Abstract
Personalised oncology, whereby patients are given therapies based on their molecular tumour profile, is rapidly becoming an essential part of optimal clinical care, at least partly facilitated by recent advances in next-generation sequencing-based technology using liquid- and tissue-based biopsies. Consequently, clinical trials have shifted in approach, from traditional studies evaluating cytotoxic chemotherapy in largely histology-based populations to modified, biomarker-driven studies (e.g. basket, umbrella, platform) of molecularly guided therapies and cancer immunotherapies in selected patient subsets. Such modified study designs may assess, within the same trial structure, multiple cancer types and treatments, and should incorporate a multistakeholder perspective. This is key to generating complementary, fit-for-purpose and timely evidence for molecularly guided therapies that can be used as proof-of-concept to inform further study designs, lead to approval by regulatory authorities and be used as confirmation of clinical benefit for health technology assessment bodies. In general, the future of cancer clinical trials requires a framework for the application of innovative technologies and dynamic design methodologies, in order to efficiently transform scientific discoveries into clinical utility. Next-generation, modified studies that involve the joint efforts of all key stakeholders will offer individualised strategies that ultimately contribute to globalised knowledge and collective learning. In this review, we outline the background and purpose of such modified study designs and detail key aspects from a multistakeholder perspective. We also provide methodological considerations for designing the studies and highlight how insights from already-ongoing studies may address current challenges and opportunities in the era of personalised oncology.
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Affiliation(s)
- Christophe Le Tourneau
- Department of Drug Development and Innovation (D3i), Institut Curie, INSERM U900 Research Unit, Paris-Saclay University, Paris, France
| | | | - Åslaug Helland
- Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Linda Mileshkin
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | | | | | - Kjetil Taskén
- Division of Cancer Medicine, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - David M Thomas
- Garvan Institute of Medical Research, Darlinghurst, Australia
| | | | | | - Lada Leyens
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | | | | | - Alwin Krämer
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany.
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18
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Mock A, Teleanu MV, Kreutzfeldt S, Heilig CE, Hüllein J, Möhrmann L, Jahn A, Hanf D, Kerle IA, Singh HM, Hutter B, Uhrig S, Fröhlich M, Neumann O, Hartig A, Brückmann S, Hirsch S, Grund K, Dikow N, Lipka DB, Renner M, Bhatti IA, Apostolidis L, Schlenk RF, Schaaf CP, Stenzinger A, Schröck E, Hübschmann D, Heining C, Horak P, Glimm H, Fröhling S. NCT/DKFZ MASTER handbook of interpreting whole-genome, transcriptome, and methylome data for precision oncology. NPJ Precis Oncol 2023; 7:109. [PMID: 37884744 PMCID: PMC10603123 DOI: 10.1038/s41698-023-00458-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
Analysis of selected cancer genes has become an important tool in precision oncology but cannot fully capture the molecular features and, most importantly, vulnerabilities of individual tumors. Observational and interventional studies have shown that decision-making based on comprehensive molecular characterization adds significant clinical value. However, the complexity and heterogeneity of the resulting data are major challenges for disciplines involved in interpretation and recommendations for individualized care, and limited information exists on how to approach multilayered tumor profiles in clinical routine. We report our experience with the practical use of data from whole-genome or exome and RNA sequencing and DNA methylation profiling within the MASTER (Molecularly Aided Stratification for Tumor Eradication Research) program of the National Center for Tumor Diseases (NCT) Heidelberg and Dresden and the German Cancer Research Center (DKFZ). We cover all relevant steps of an end-to-end precision oncology workflow, from sample collection, molecular analysis, and variant prioritization to assigning treatment recommendations and discussion in the molecular tumor board. To provide insight into our approach to multidimensional tumor profiles and guidance on interpreting their biological impact and diagnostic and therapeutic implications, we present case studies from the NCT/DKFZ molecular tumor board that illustrate our daily practice. This manual is intended to be useful for physicians, biologists, and bioinformaticians involved in the clinical interpretation of genome-wide molecular information.
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Affiliation(s)
- Andreas Mock
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany
| | - Maria-Veronica Teleanu
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology, Oncology and Rheumatology, Heidelberg Unversity Hospital, Heidelberg, Germany
| | - Simon Kreutzfeldt
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph E Heilig
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jennifer Hüllein
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Lino Möhrmann
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Arne Jahn
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Technische Universität Dresden and Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
| | - Dorothea Hanf
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Irina A Kerle
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Hans Martin Singh
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - Barbara Hutter
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Sebastian Uhrig
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Martina Fröhlich
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Olaf Neumann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas Hartig
- Institute of Pathology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Sascha Brückmann
- Institute of Pathology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Steffen Hirsch
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Kerstin Grund
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel B Lipka
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Translational Cancer Epigenomics, Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Marcus Renner
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Irfan Ahmed Bhatti
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - Leonidas Apostolidis
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
| | - Richard F Schlenk
- Department of Hematology, Oncology and Rheumatology, Heidelberg Unversity Hospital, Heidelberg, Germany
- Department of Medical Oncology, NCT Heidelberg and Heidelberg University Hospital, Heidelberg, Germany
- NCT Trial Center, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Christian P Schaaf
- Institute of Human Genetics, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Evelin Schröck
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus, Technische Universität Dresden and Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
| | - Daniel Hübschmann
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Christoph Heining
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Peter Horak
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hanno Glimm
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Department of Translational Medical Oncology, National Center for Tumor Diseases/University Cancer Center (NCT/UCC) Dresden, Dresden, Germany
- DKFZ, Heidelberg, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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19
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Wurm AA, Brilloff S, Kolovich S, Schäfer S, Rahimian E, Kufrin V, Bill M, Carrero ZI, Drukewitz S, Krüger A, Hüther M, Uhrig S, Oster S, Westphal D, Meier F, Pfütze K, Hübschmann D, Horak P, Kreutzfeldt S, Richter D, Schröck E, Baretton G, Heining C, Möhrmann L, Fröhling S, Ball CR, Glimm H. Signaling-induced systematic repression of miRNAs uncovers cancer vulnerabilities and targeted therapy sensitivity. Cell Rep Med 2023; 4:101200. [PMID: 37734378 PMCID: PMC10591033 DOI: 10.1016/j.xcrm.2023.101200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 06/21/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023]
Abstract
Targeted therapies are effective in treating cancer, but success depends on identifying cancer vulnerabilities. In our study, we utilize small RNA sequencing to examine the impact of pathway activation on microRNA (miRNA) expression patterns. Interestingly, we discover that miRNAs capable of inhibiting key members of activated pathways are frequently diminished. Building on this observation, we develop an approach that integrates a low-miRNA-expression signature to identify druggable target genes in cancer. We train and validate our approach in colorectal cancer cells and extend it to diverse cancer models using patient-derived in vitro and in vivo systems. Finally, we demonstrate its additional value to support genomic and transcriptomic-based drug prediction strategies in a pan-cancer patient cohort from the National Center for Tumor Diseases (NCT)/German Cancer Consortium (DKTK) Molecularly Aided Stratification for Tumor Eradication (MASTER) precision oncology trial. In conclusion, our strategy can predict cancer vulnerabilities with high sensitivity and accuracy and might be suitable for future therapy recommendations in a variety of cancer subtypes.
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Affiliation(s)
- Alexander A Wurm
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; German Cancer Consortium (DKTK), Dresden, Germany.
| | - Silke Brilloff
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Sofia Kolovich
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Silvia Schäfer
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Elahe Rahimian
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Vida Kufrin
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Marius Bill
- Mildred Scheel Early Career Center, National Center for Tumor Diseases (NCT/UCC) Dresden, Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; German Cancer Consortium (DKTK), Dresden, Germany; Department of Internal Medicine I, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Zunamys I Carrero
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; German Cancer Consortium (DKTK), Dresden, Germany
| | - Stephan Drukewitz
- German Cancer Consortium (DKTK), Dresden, Germany; Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Institute of Human Genetics, University of Leipzig, Leipzig, Germany
| | - Alexander Krüger
- German Cancer Consortium (DKTK), Dresden, Germany; Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Melanie Hüther
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Sebastian Uhrig
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg, a partnership between DKFZ and University Hospital Heidelberg, Heidelberg, Germany
| | - Sandra Oster
- German Cancer Consortium (DKTK), Dresden, Germany; Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Dana Westphal
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Friedegund Meier
- Department of Dermatology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; Skin Cancer Center at the University Cancer Centre Dresden and National Center for Tumor Diseases, Dresden, Germany
| | - Katrin Pfütze
- German Cancer Consortium (DKTK), Heidelberg, Germany; Sample Processing Laboratory, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg, a partnership between DKFZ and University Hospital Heidelberg, Heidelberg, Germany
| | - Daniel Hübschmann
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) Heidelberg, a partnership between DKFZ and University Hospital Heidelberg, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
| | - Peter Horak
- German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, a partnership between DKFZ and University Hospital Heidelberg, Heidelberg, Germany
| | - Simon Kreutzfeldt
- German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, a partnership between DKFZ and University Hospital Heidelberg, Heidelberg, Germany
| | - Daniela Richter
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; German Cancer Consortium (DKTK), Dresden, Germany
| | - Evelin Schröck
- German Cancer Consortium (DKTK), Dresden, Germany; Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Institute for Clinical Genetics, University Hospital Carl Gustav Carus at Technische Universität Dresden, Dresden, Germany; ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
| | - Gustavo Baretton
- German Cancer Consortium (DKTK), Dresden, Germany; Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany
| | - Christoph Heining
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; German Cancer Consortium (DKTK), Dresden, Germany
| | - Lino Möhrmann
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; German Cancer Consortium (DKTK), Dresden, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), Heidelberg, Germany; Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, a partnership between DKFZ and University Hospital Heidelberg, Heidelberg, Germany
| | - Claudia R Ball
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; German Cancer Consortium (DKTK), Dresden, Germany; Technische Universität Dresden, Faculty of Biology, Dresden, Germany
| | - Hanno Glimm
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT/UCC) Dresden, a partnership between DKFZ, Faculty of Medicine of the Technische Universität Dresden, University Hospital Carl Gustav Carus Dresden, and Helmholtz-Zentrum Dresden - Rossendorf (HZDR), Dresden, Germany; Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany; German Cancer Consortium (DKTK), Dresden, Germany; Translational Functional Cancer Genomics, National Center for Tumor Diseases (NCT) Heidelberg, a partnership between DKFZ and University Hospital Heidelberg, Heidelberg, Germany
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20
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Huey RW, Shah AT, Reddi HV, Dasari P, Topham JT, Hwang H, Dhillon N, Willett A, Smaglo BG, Estrella JS, Rashid A, Matamoros A, Overman MJ, Choquette L, Omerza G, Kelly K, Wang X, Loree JM, Rueter J, Varadhachary GR, Raghav K. Feasibility and value of genomic profiling in cancer of unknown primary: real-world evidence from prospective profiling study. J Natl Cancer Inst 2023; 115:994-997. [PMID: 37202363 PMCID: PMC10407690 DOI: 10.1093/jnci/djad095] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/13/2023] [Accepted: 05/16/2023] [Indexed: 05/20/2023] Open
Abstract
Real-world evidence regarding the value of integrating genomic profiling (GP) in managing cancer of unknown primary (CUP) is limited. We assessed this clinical utility using a prospective trial of 158 patients with CUP (October 2016-September 2019) who underwent GP using next-generation sequencing designed to identify genomic alterations (GAs). Only 61 (38.6%) patients had sufficient tissue for successful profiling. GAs were seen in 55 (90.2%) patients of which GAs with US Food and Drug Administration-approved genomically matched therapy were seen in 25 (40.9%) patients. A change in therapy was recommended and implemented (primary endpoint of the study) in 16 (10.1%) and 4 (2.5%) patients of the entire study cohort, respectively. The most common reason for inability to implement the profiling-guided therapy was worsening of performance status (56.3%). Integrating GP in management of CUP is feasible but challenging because of paucity of tissue and aggressive natural history of the disease and requires innovative precision strategies.
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Affiliation(s)
- Ryan W Huey
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aakash Tushar Shah
- Margaret M. and Albert B. Alkek Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Honey V Reddi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Priyadarsini Dasari
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Hyunsoo Hwang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nishat Dhillon
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anneleis Willett
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brandon G Smaglo
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeannelyn S Estrella
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Asif Rashid
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Aurelio Matamoros
- Department of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael J Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linda Choquette
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Greg Omerza
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin Kelly
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Xuemei Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jonathan M Loree
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Jens Rueter
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Gauri R Varadhachary
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kanwal Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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21
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Normanno N, De Luca A, Abate RE, Morabito A, Milella M, Tabbò F, Curigliano G, Masini C, Marchetti P, Pruneri G, Guarneri V, Frassineti GL, Fasola G, Adamo V, Daniele B, Berardi R, Feroce F, Maiello E, Pinto C. Current practice of genomic profiling of patients with advanced solid tumours in Italy: the Italian Register of Actionable Mutations (RATIONAL) study. Eur J Cancer 2023; 187:174-184. [PMID: 37167765 DOI: 10.1016/j.ejca.2023.03.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023]
Abstract
BACKGROUND The Italian Register of Actionable Mutations (RATIONAL) is a multicentric, observational study collecting next-generation sequencing (NGS)-based tumour profiling data of patients with advanced solid tumours. METHODS The study enrols patients who had available an NGS-based tumour profiling (Pathway-A) or undergo comprehensive genomic profiling (CGP) with FoundationOne CDx assays within the trial (Pathway-B). The primary endpoint was the rate of actionable mutations identified. RESULTS Sequencing data were available for 738 patients in Pathway-A (218) and -B (520). In Pathway-A, 154/218 (70.6%) tests were performed using NGS panels ≤52 genes, and genomic alterations (GAs) were found in 164/218 (75.2%) patients. In Pathway-B, CGP revealed GAs in 512/520 (98.5%) patients. Levels I/II/III actionable GAs according to the European Society of Medical Oncology Scale for Clinical Actionability of molecular Targets (ESCAT) were identified in 254/554 (45.8%) patients with non-small-cell lung cancer, cholangiocarcinoma, colorectal, gastric, pancreatic and breast cancer. The rate of patients with level I GAs was similar in Pathways A and B (69 versus 102). CGP in Pathway-B revealed a higher number of patients with level II/III GAs (99 versus 20) and potentially germline pathogenic/likely pathogenic variants (58 versus 15) as compared with standard testing in Pathway-A. In patients with cancer of unknown primary, CGP detected OncoKB levels 3B/4 GAs in 31/58 (53.4%) cases. Overall, 67/573 (11.7%) of patients received targeted therapy based on genomic testing. CONCLUSION The Italian Register of Actionable Mutations represents the first overview of genomic profiling in Italian current clinical practice and highlights the utility of CGP for identifying therapeutic targets in selected cancer patients.
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Affiliation(s)
- Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy.
| | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Alessandro Morabito
- Thoracic Department, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Michele Milella
- U.O.C. Oncology, Azienda Ospedaliera Universitaria Integrata, University and Hospital Trust of Verona, Verona, Italy
| | - Fabrizio Tabbò
- Department of Oncology, Università degli Studi di Torino, AOU San Luigi, Orbassano, Italy
| | - Giuseppe Curigliano
- Department of Oncology and Hemato-Oncology, University of Milano, Milano, Italy; Division of Early Drug Development, European Institute of Oncology IRCCS, Milano, Italy
| | - Cristina Masini
- Medical Oncology, Comprehensive Cancer Centre IRCCS - AUSL Reggio Emilia, Reggio Emilia, Italy
| | - Paolo Marchetti
- Istituto Dermopatico dell'Immacolata (IDI-IRCCS), Roma, Italy
| | - Giancarlo Pruneri
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milano, Italy
| | - Valentina Guarneri
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy; Oncology 2, Istituto Oncologico Veneto (IOV) IRCCS, Padova, Italy
| | - Giovanni L Frassineti
- Department of Medical Oncology-IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Gianpiero Fasola
- Department of Medical Oncology, University Hospital of Udine, Udine, Italy
| | - Vincenzo Adamo
- Scientific Direction Oncology Department, Papardo Hospital, Messina, Italy
| | | | | | - Florinda Feroce
- Surgical Pathology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Evaristo Maiello
- Oncology Unit, Fondazione Casa Sollievo della Sofferenza IRCCS, San Giovanni Rotondo, Italy
| | - Carmine Pinto
- Medical Oncology, Comprehensive Cancer Centre IRCCS - AUSL Reggio Emilia, Reggio Emilia, Italy
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22
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Loh JW, Lee JY, Lim AH, Guan P, Lim BY, Kannan B, Lee ECY, Gu NX, Ko TK, Ng CCY, Lim JCT, Yeong J, Lim JQ, Ong CK, Teh BT, Chan JY. Spatial transcriptomics reveal topological immune landscapes of Asian head and neck angiosarcoma. Commun Biol 2023; 6:461. [PMID: 37106027 PMCID: PMC10140281 DOI: 10.1038/s42003-023-04856-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
Angiosarcomas are rare malignant tumors of the endothelium, arising commonly from the head and neck region (AS-HN) and recently associated with ultraviolet (UV) exposure and human herpesvirus-7 infection. We examined 81 cases of angiosarcomas, including 47 cases of AS-HN, integrating information from whole genome sequencing, gene expression profiling and spatial transcriptomics (10X Visium). In the AS-HN cohort, we observed recurrent somatic mutations in CSMD3 (18%), LRP1B (18%), MUC16 (18%), POT1 (16%) and TP53 (16%). UV-positive AS-HN harbored significantly higher tumor mutation burden than UV-negative cases (p = 0.0294). NanoString profiling identified three clusters with distinct tumor inflammation signature scores (p < 0.001). Spatial transcriptomics revealed topological profiles of the tumor microenvironment, identifying dominant but tumor-excluded inflammatory signals in immune-hot cases and immune foci even in otherwise immune-cold cases. In conclusion, spatial transcriptomics reveal the tumor immune landscape of angiosarcoma, and in combination with multi-omic information, may improve implementation of treatment strategies.
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Affiliation(s)
- Jui Wan Loh
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Jing Yi Lee
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Abner Herbert Lim
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore
| | - Peiyong Guan
- Genome Institute of Singapore, Agency of Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Boon Yee Lim
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | - Bavani Kannan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Ning Xin Gu
- MGI Tech Singapore PTE LTD, Singapore, Singapore
| | - Tun Kiat Ko
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore
| | | | - Jeffrey Chun Tatt Lim
- Institute of Molecular and Cell Biology, Agency of Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Joe Yeong
- Institute of Molecular and Cell Biology, Agency of Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Choon Kiat Ong
- Lymphoma Genomic Translational Research Laboratory, Division of Cellular and Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Bin Tean Teh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Agency of Science, Technology and Research (ASTAR), Singapore, Singapore.
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.
| | - Jason Yongsheng Chan
- Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore.
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore.
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore.
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23
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Ni Y, Liu X, Simeneh ZM, Yang M, Li R. Benchmarking of Nanopore R10.4 and R9.4.1 flow cells in single-cell whole-genome amplification and whole-genome shotgun sequencing. Comput Struct Biotechnol J 2023; 21:2352-2364. [PMID: 37025654 PMCID: PMC10070092 DOI: 10.1016/j.csbj.2023.03.038] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 03/30/2023] Open
Abstract
Third-generation sequencing can be used in human cancer genomics and epigenomic research. Oxford Nanopore Technologies (ONT) recently released R10.4 flow cell, which claimed an improved read accuracy compared to R9.4.1 flow cell. To evaluate the benefits and defects of R10.4 flow cell for cancer cell profiling on MinION devices, we used the human non-small-cell lung-carcinoma cell line HCC78 to construct libraries for both single-cell whole-genome amplification (scWGA) and whole-genome shotgun sequencing. The R10.4 and R9.4.1 reads were benchmarked in terms of read accuracy, variant detection, modification calling, genome recovery rate and compared with the next generation sequencing (NGS) reads. The results highlighted that the R10.4 outperforms R9.4.1 reads, achieving a higher modal read accuracy of over 99.1%, superior variation detection, lower false-discovery rate (FDR) in methylation calling, and comparable genome recovery rate. To achieve high yields scWGA sequencing in the ONT platform as NGS, we recommended multiple displacement amplification with a modified T7 endonuclease Ⅰ cutting procedure as a promising method. In addition, we provided a possible solution to filter the likely false positive sites among the whole genome region with R10.4 by using scWGA sequencing result as a negative control. Our study is the first benchmark of whole genome single-cell sequencing using ONT R10.4 and R9.4.1 MinION flow cells by clarifying the capacity of genomic and epigenomic profiling within a single flow cell. A promising method for scWGA sequencing together with the methylation calling results can benefit researchers who work on cancer cell genomic and epigenomic profiling using third-generation sequencing.
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Affiliation(s)
- Ying Ni
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, China
- Department of Biomedical Sciences and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
| | - Xudong Liu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Zemenu Mengistie Simeneh
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, China
- Department of Biomedical Sciences and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
| | - Mengsu Yang
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, China
- Department of Biomedical Sciences and Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong, China
- Corresponding author at: Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, Guangdong, China.
| | - Runsheng Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- Corresponding author at: Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.
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24
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Roggia C, Armeanu-Ebinger S, Gschwind A, Seibel-Kelemen O, Hertler S, Faust U, Liebmann A, Haack TB, Neumann M, Bonzheim I, Forschner A, Kopp HG, Herster F, Hartkopf A, Bitzer M, Malek NP, Brecht IB, Ruhm K, Möller Y, Löwenheim H, Ossowski S, Rieß OH, Schroeder C. Germline findings in patients with advanced malignancies screened with paired blood-tumour testing for personalised treatment approaches. Eur J Cancer 2023; 179:48-55. [PMID: 36495689 DOI: 10.1016/j.ejca.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/18/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Sequencing of tumour tissue with comprehensive gene panels is increasingly used to guide treatment in precision oncology. Analysis of tumour-normal pairs allows in contrast to tumour-only assessment direct discrimination between somatic and germline alterations, which might have important implications not only for the patients but also their families. METHODS We performed tumour normal sequencing with a large gene panel in 1048 patients with advanced cancer to support treatment decision. Sequencing results were correlated with clinical and family data. RESULTS We identified 156 likely pathogenic or pathogenic (LP/P) germline variants in cancer predisposition genes (CPGs) in 144 cases (13.7%). Of all patients, 8.8% had a LP/P variant in autosomal-dominant cancer predisposition genes (AD-CPGs), most of them being genes with high or moderate penetrance (ATM, BRCA2, CHEK2 and BRCA1). In 48 cases, the P/LP variant matched the expected tumour spectrum. A second variant in tumour tissue was found in 31 patients with AD-CPG variants. Low frequency mutations in either TP53, ATM or DNMT3A in the normal sample indicated clonal haematopoiesis in five cases. CONCLUSIONS Tumour-normal testing for personalised treatment identifies germline LP/P variants in a relevant proportion of patients with cancer. The majority of them would not have been referred to genetic counselling based on family history. Indirect functional readouts of tumour-normal sequencing can provide novel links between CPGs and unexpected cancers. The interpretation of increasingly complex datasets in precision oncology is challenging and concepts of interdisciplinary personalised cancer prevention are needed to support patients and their families.
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Affiliation(s)
- Cristiana Roggia
- Institute of Medical Genetics and Applied Genomics, University Hospital and Medical Faculty Tübingen, Tübingen, Germany.
| | - Sorin Armeanu-Ebinger
- Institute of Medical Genetics and Applied Genomics, University Hospital and Medical Faculty Tübingen, Tübingen, Germany
| | - Axel Gschwind
- Institute of Medical Genetics and Applied Genomics, University Hospital and Medical Faculty Tübingen, Tübingen, Germany
| | - Olga Seibel-Kelemen
- Institute of Medical Genetics and Applied Genomics, University Hospital and Medical Faculty Tübingen, Tübingen, Germany
| | - Sonja Hertler
- Institute of Medical Genetics and Applied Genomics, University Hospital and Medical Faculty Tübingen, Tübingen, Germany
| | - Ulrike Faust
- Institute of Medical Genetics and Applied Genomics, University Hospital and Medical Faculty Tübingen, Tübingen, Germany
| | - Alexandra Liebmann
- Institute of Medical Genetics and Applied Genomics, University Hospital and Medical Faculty Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University Hospital and Medical Faculty Tübingen, Tübingen, Germany
| | - Manuela Neumann
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Irina Bonzheim
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Andrea Forschner
- Department of Dermatology, University Hospital Tübingen, Tübingen, Germany
| | - Hans-Georg Kopp
- Robert Bosch Center for Tumor Diseases (RBCT) Robert Bosch Cancer Center, Stuttgart, Germany
| | - Franziska Herster
- Robert Bosch Center for Tumor Diseases (RBCT) Robert Bosch Cancer Center, Stuttgart, Germany
| | - Andreas Hartkopf
- Department of Gynecology, University Hospital Tübingen, Tübingen, Germany
| | - Michael Bitzer
- Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Nisar P Malek
- Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Ines B Brecht
- Department of General Pediatrics, Pediatric Hematology and Oncology, University Hospital Tübingen, Tübingen, Germany
| | - Kristina Ruhm
- Center for Personalized Medicine, University of Tübingen, Tübingen, Germany
| | - Yvonne Möller
- Center for Personalized Medicine, University of Tübingen, Tübingen, Germany
| | - Hubert Löwenheim
- Department of Otolaryngology-Head & Neck Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University Hospital and Medical Faculty Tübingen, Tübingen, Germany
| | - Olaf H Rieß
- Institute of Medical Genetics and Applied Genomics, University Hospital and Medical Faculty Tübingen, Tübingen, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University Hospital and Medical Faculty Tübingen, Tübingen, Germany
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25
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Schipper L, Samsom K, Snaebjornsson P, Battaglia T, Bosch L, Lalezari F, Priestley P, Shale C, van den Broek A, Jacobs N, Roepman P, van der Hoeven J, Steeghs N, Vollebergh M, Marchetti S, Cuppen E, Meijer G, Voest E, Monkhorst K. Complete genomic characterization in patients with cancer of unknown primary origin in routine diagnostics. ESMO Open 2022; 7:100611. [PMID: 36463731 PMCID: PMC9808446 DOI: 10.1016/j.esmoop.2022.100611] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND In ∼3%-5% of patients with metastatic disease, tumor origin remains unknown despite modern imaging techniques and extensive pathology work-up. With long diagnostic delays and limited and ineffective therapy options, the clinical outcome of patients with cancer of unknown primary (CUP) remains poor. Large-scale genome sequencing studies have revealed that tumor types can be predicted based on distinct patterns of somatic variants and other genomic characteristics. Moreover, actionable genomic events are present in almost half of CUP patients. This study investigated the clinical value of whole genome sequencing (WGS) in terms of primary tumor identification and detection of actionable events, in the routine diagnostic work-up of CUP patients. PATIENTS AND METHODS A WGS-based tumor type 'cancer of unknown primary prediction algorithm' (CUPPA) was developed based on previously described principles and validated on a large pan-cancer WGS database of metastatic cancer patients (>4000 samples) and 254 independent patients, respectively. We assessed the clinical value of this prediction algorithm as part of routine WGS-based diagnostic work-up for 72 CUP patients. RESULTS CUPPA correctly predicted the primary tumor type in 78% of samples in the independent validation cohort (194/254 patients). High-confidence predictions (>95% precision) were obtained for 162/254 patients (64%). When integrated in the diagnostic work-up of CUP patients, CUPPA could identify a primary tumor type for 49/72 patients (68%). Most common diagnoses included non-small-cell lung (n = 7), gastroesophageal (n = 4), pancreatic (n = 4), and colorectal cancer (n = 3). Actionable events with matched therapy options in clinical trials were identified in 47% of patients. CONCLUSIONS Genome-based tumor type prediction can predict cancer diagnoses with high accuracy when integrated in the routine diagnostic work-up of patients with metastatic cancer. With identification of the primary tumor type in the majority of patients and detection of actionable events, WGS is a valuable diagnostic tool for patients with CUP.
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Affiliation(s)
- L.J. Schipper
- Department of Molecular Oncology, Netherlands Cancer Institute, Amsterdam,Oncode Institute, Utrecht, The Netherlands
| | - K.G. Samsom
- Department of Pathology, Netherlands Cancer Institute, Amsterdam
| | - P. Snaebjornsson
- Department of Pathology, Netherlands Cancer Institute, Amsterdam
| | - T. Battaglia
- Department of Molecular Oncology, Netherlands Cancer Institute, Amsterdam
| | - L.J.W. Bosch
- Department of Pathology, Netherlands Cancer Institute, Amsterdam
| | - F. Lalezari
- Department of Radiology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - P. Priestley
- Hartwig Medical Foundation Australia, Sydney, Australia
| | - C. Shale
- Hartwig Medical Foundation Australia, Sydney, Australia
| | | | - N. Jacobs
- Hartwig Medical Foundation, Amsterdam
| | | | | | - N. Steeghs
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam
| | - M.A. Vollebergh
- Department of Gastroenterology, Netherlands Cancer Institute, Amsterdam
| | - S. Marchetti
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam
| | - E. Cuppen
- Oncode Institute, Utrecht, The Netherlands,Hartwig Medical Foundation, Amsterdam,Center for Molecular Medicine, UMC Utrecht, Utrecht
| | - G.A. Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam
| | - E.E. Voest
- Department of Molecular Oncology, Netherlands Cancer Institute, Amsterdam,Oncode Institute, Utrecht, The Netherlands,Department of Gastroenterology, Netherlands Cancer Institute, Amsterdam
| | - K. Monkhorst
- Department of Pathology, Netherlands Cancer Institute, Amsterdam,Correspondence to: Dr Kim Monkhorst, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands. Tel: +0205122948
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26
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Cuppen E, Elemento O, Rosenquist R, Nikic S, IJzerman M, Zaleski ID, Frederix G, Levin LÅ, Mullighan CG, Buettner R, Pugh TJ, Grimmond S, Caldas C, Andre F, Custers I, Campo E, van Snellenberg H, Schuh A, Nakagawa H, von Kalle C, Haferlach T, Fröhling S, Jobanputra V. Implementation of Whole-Genome and Transcriptome Sequencing Into Clinical Cancer Care. JCO Precis Oncol 2022; 6:e2200245. [PMID: 36480778 PMCID: PMC10166391 DOI: 10.1200/po.22.00245] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/30/2022] [Accepted: 09/21/2022] [Indexed: 12/13/2022] Open
Abstract
PURPOSE The combination of whole-genome and transcriptome sequencing (WGTS) is expected to transform diagnosis and treatment for patients with cancer. WGTS is a comprehensive precision diagnostic test that is starting to replace the standard of care for oncology molecular testing in health care systems around the world; however, the implementation and widescale adoption of this best-in-class testing is lacking. METHODS Here, we address the barriers in integrating WGTS for cancer diagnostics and treatment selection and answer questions regarding utility in different cancer types, cost-effectiveness and affordability, and other practical considerations for WGTS implementation. RESULTS We review the current studies implementing WGTS in health care systems and provide a synopsis of the clinical evidence and insights into practical considerations for WGTS implementation. We reflect on regulatory, costs, reimbursement, and incidental findings aspects of this test. CONCLUSION WGTS is an appropriate comprehensive clinical test for many tumor types and can replace multiple, cascade testing approaches currently performed. Decreasing sequencing cost, increasing number of clinically relevant aberrations and discovery of more complex biomarkers of treatment response, should pave the way for health care systems and laboratories in implementing WGTS into clinical practice, to transform diagnosis and treatment for patients with cancer.
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Affiliation(s)
- Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, the Netherlands
- Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, the Netherlands
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Svetlana Nikic
- Illumina Productos de España, S.L.U., Plaza Pablo Ruiz Picasso, Madrid, Spain
| | - Maarten IJzerman
- Erasmus School of Health Policy & Management, Erasmus University, Rotterdam, the Netherlands
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Isabelle Durand Zaleski
- Université de Paris, CRESS, INSERM, INRA, URCEco, AP-HP, Hôpital de l'Hôtel Dieu, Paris, France
| | - Geert Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center, Utrecht, the Netherlands
| | - Lars-Åke Levin
- Department of Health, Medicine and Caring Sciences (HMV), Linköping University, Linköping, Sweden
| | | | | | - Trevor J. Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Sean Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, Cambridge, United Kingdom
| | | | | | - Elias Campo
- Institut d’Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red, Cáncer (CIBERONC), Madrid, Spain
- Hematopathology Unit, Hospital Clínic of Barcelona, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | | | - Anna Schuh
- University of Oxford, Oxford, United Kingdom
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Christof von Kalle
- Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Clinical Study Center, Berlin, Germany
| | | | - Stefan Fröhling
- Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Vaidehi Jobanputra
- New York Genome Center; Department of Pathology, Columbia University Irving Medical Center, New York, NY
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