1
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Wang H, Tian S, Secreto CR, Sinha S, Shi M, Call T, Wang Y, Parikh SA, Kenderian SS, He R, Leis JF, VanDyke DL, Klee EW, Slager SL, Braggio E, Yan H, Ding W. Clonal dynamics of Richter transformation in chronic lymphocytic leukemia. Hematol Oncol 2024; 42:e3282. [PMID: 38852069 DOI: 10.1002/hon.3282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2024]
Affiliation(s)
- Hanyin Wang
- Division of Hospital Internal Medicine, Mayo Clinic Health System, Mankato, Minnesota, USA
| | - Shulan Tian
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Sutapa Sinha
- Division of Hematology, Mayo Clinic, Rochester, Minnesota, USA
| | - Min Shi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Timothy Call
- Division of Hematology, Mayo Clinic, Rochester, Minnesota, USA
| | - Yucai Wang
- Division of Hematology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sameer A Parikh
- Division of Hematology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Rong He
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jose F Leis
- Division of Hematology and Medical Oncology, Mayo Clinic, Phoenix, Arizona, USA
| | - Daniel L VanDyke
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Eric W Klee
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Susan L Slager
- Division of Hematology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Computational Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Esteban Braggio
- Division of Hematology and Medical Oncology, Mayo Clinic, Phoenix, Arizona, USA
| | - Huihuang Yan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Wei Ding
- Division of Hematology, Mayo Clinic, Rochester, Minnesota, USA
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2
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Rathgeber AC, Ludwig LS, Penter L. Single-cell genomics-based immune and disease monitoring in blood malignancies. Clin Hematol Int 2024; 6:62-84. [PMID: 38884110 PMCID: PMC11180218 DOI: 10.46989/001c.117961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 12/25/2023] [Indexed: 06/18/2024] Open
Abstract
Achieving long-term disease control using therapeutic immunomodulation is a long-standing concept with a strong tradition in blood malignancies. Besides allogeneic hematopoietic stem cell transplantation that continues to provide potentially curative treatment for otherwise challenging diagnoses, recent years have seen impressive progress in immunotherapies for leukemias and lymphomas with immune checkpoint blockade, bispecific monoclonal antibodies, and CAR T cell therapies. Despite their success, non-response, relapse, and immune toxicities remain frequent, thus prioritizing the elucidation of the underlying mechanisms and identifying predictive biomarkers. The increasing availability of single-cell genomic tools now provides a system's immunology view to resolve the molecular and cellular mechanisms of immunotherapies at unprecedented resolution. Here, we review recent studies that leverage these technological advancements for tracking immune responses, the emergence of immune resistance, and toxicities. As single-cell immune monitoring tools evolve and become more accessible, we expect their wide adoption for routine clinical applications to catalyze more precise therapeutic steering of personal immune responses.
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Affiliation(s)
- Anja C Rathgeber
- Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine
- Department of Hematology, Oncology, and Tumorimmunology Charité - Universitätsmedizin Berlin
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin
| | - Leif S Ludwig
- Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin
| | - Livius Penter
- Department of Hematology, Oncology, and Tumorimmunology Charité - Universitätsmedizin Berlin
- BIH Biomedical Innovation Academy Berlin Institute of Health at Charité - Universitätsmedizin Berlin
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3
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Salcedo A, Tarabichi M, Buchanan A, Espiritu SMG, Zhang H, Zhu K, Ou Yang TH, Leshchiner I, Anastassiou D, Guan Y, Jang GH, Mootor MFE, Haase K, Deshwar AG, Zou W, Umar I, Dentro S, Wintersinger JA, Chiotti K, Demeulemeester J, Jolly C, Sycza L, Ko M, Wedge DC, Morris QD, Ellrott K, Van Loo P, Boutros PC. Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction. Nat Biotechnol 2024:10.1038/s41587-024-02250-y. [PMID: 38862616 DOI: 10.1038/s41587-024-02250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 04/17/2024] [Indexed: 06/13/2024]
Abstract
Subclonal reconstruction algorithms use bulk DNA sequencing data to quantify parameters of tumor evolution, allowing an assessment of how cancers initiate, progress and respond to selective pressures. We launched the ICGC-TCGA (International Cancer Genome Consortium-The Cancer Genome Atlas) DREAM Somatic Mutation Calling Tumor Heterogeneity and Evolution Challenge to benchmark existing subclonal reconstruction algorithms. This 7-year community effort used cloud computing to benchmark 31 subclonal reconstruction algorithms on 51 simulated tumors. Algorithms were scored on seven independent tasks, leading to 12,061 total runs. Algorithm choice influenced performance substantially more than tumor features but purity-adjusted read depth, copy-number state and read mappability were associated with the performance of most algorithms on most tasks. No single algorithm was a top performer for all seven tasks and existing ensemble strategies were unable to outperform the best individual methods, highlighting a key research need. All containerized methods, evaluation code and datasets are available to support further assessment of the determinants of subclonal reconstruction accuracy and development of improved methods to understand tumor evolution.
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Affiliation(s)
- Adriana Salcedo
- Department of Human Genetics, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
- Institute for Precision Health, University of California, Los Angeles, CA, USA.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
| | - Maxime Tarabichi
- The Francis Crick Institute, London, UK.
- Wellcome Sanger Institute, Hinxton, UK.
- Institute for Interdisciplinary Research, Université Libre de Bruxelles, Brussels, Belgium.
| | - Alex Buchanan
- Oregon Health and Sciences University, Portland, OR, USA
| | | | - Hongjiu Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Kaiyi Zhu
- Department of Systems Biology, Columbia University, New York, NY, USA
- Center for Cancer Systems Therapeutics, Columbia University, New York, NY, USA
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Tai-Hsien Ou Yang
- Department of Systems Biology, Columbia University, New York, NY, USA
- Center for Cancer Systems Therapeutics, Columbia University, New York, NY, USA
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | | | - Dimitris Anastassiou
- Department of Systems Biology, Columbia University, New York, NY, USA
- Center for Cancer Systems Therapeutics, Columbia University, New York, NY, USA
- Department of Electrical Engineering, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Electronic Engineering and Computer Science, University of Michigan, Ann Arbor, MI, USA
| | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Mohammed F E Mootor
- Department of Human Genetics, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
- Institute for Precision Health, University of California, Los Angeles, CA, USA
| | | | - Amit G Deshwar
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - William Zou
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Imaad Umar
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Stefan Dentro
- The Francis Crick Institute, London, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Jeff A Wintersinger
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Kami Chiotti
- Oregon Health and Sciences University, Portland, OR, USA
| | - Jonas Demeulemeester
- The Francis Crick Institute, London, UK
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | | | - Lesia Sycza
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Minjeong Ko
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - David C Wedge
- Big Data Institute, University of Oxford, Oxford, UK
- Manchester Cancer Research Center, University of Manchester, Manchester, UK
| | - Quaid D Morris
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kyle Ellrott
- Oregon Health and Sciences University, Portland, OR, USA.
| | - Peter Van Loo
- The Francis Crick Institute, London, UK.
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
- Institute for Precision Health, University of California, Los Angeles, CA, USA.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada.
- Department of Urology, University of California, Los Angeles, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA.
- California NanoSystems Institute, University of California, Los Angeles, CA, USA.
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4
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Bertilaccio MTS, Chen SS. Mouse models of chronic lymphocytic leukemia and Richter transformation: what we have learnt and what we are missing. Front Immunol 2024; 15:1376660. [PMID: 38903501 PMCID: PMC11186982 DOI: 10.3389/fimmu.2024.1376660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/16/2024] [Indexed: 06/22/2024] Open
Abstract
Although the chronic lymphocytic leukemia (CLL) treatment landscape has changed dramatically, unmet clinical needs are emerging, as CLL in many patients does not respond, becomes resistant to treatment, relapses during treatment, or transforms into Richter. In the majority of cases, transformation evolves the original leukemia clone into a diffuse large B-cell lymphoma (DLBCL). Richter transformation (RT) represents a dreadful clinical challenge with limited therapeutic opportunities and scarce preclinical tools. CLL cells are well known to highly depend on survival signals provided by the tumor microenvironment (TME). These signals enhance the frequency of immunosuppressive cells with protumor function, including regulatory CD4+ T cells and tumor-associated macrophages. T cells, on the other hand, exhibit features of exhaustion and profound functional defects. Overall immune dysfunction and immunosuppression are common features of patients with CLL. The interaction between malignant cells and TME cells can occur during different phases of CLL development and transformation. A better understanding of in vivo CLL and RT biology and the availability of adequate mouse models that faithfully recapitulate the progression of CLL and RT within their microenvironments are "conditio sine qua non" to develop successful therapeutic strategies. In this review, we describe the xenograft and genetic-engineered mouse models of CLL and RT, how they helped to elucidate the pathophysiology of the disease progression and transformation, and how they have been and might be instrumental in developing innovative therapeutic approaches to finally eradicate these malignancies.
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MESH Headings
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Animals
- Tumor Microenvironment/immunology
- Humans
- Mice
- Disease Models, Animal
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/therapy
- Lymphoma, Large B-Cell, Diffuse/pathology
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Affiliation(s)
| | - Shih-Shih Chen
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
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5
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Luque LM, Carlevaro CM, Rodriguez-Lomba E, Lomba E. In silico study of heterogeneous tumour-derived organoid response to CAR T-cell therapy. Sci Rep 2024; 14:12307. [PMID: 38811838 PMCID: PMC11137006 DOI: 10.1038/s41598-024-63125-5] [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: 02/19/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024] Open
Abstract
Chimeric antigen receptor (CAR) T-cell therapy is a promising immunotherapy for treating cancers. This method consists in modifying the patients' T-cells to directly target antigen-presenting cancer cells. One of the barriers to the development of this type of therapies, is target antigen heterogeneity. It is thought that intratumour heterogeneity is one of the leading determinants of therapeutic resistance and treatment failure. While understanding antigen heterogeneity is important for effective therapeutics, a good therapy strategy could enhance the therapy efficiency. In this work we introduce an agent-based model (ABM), built upon a previous ABM, to rationalise the outcomes of different CAR T-cells therapies strategies over heterogeneous tumour-derived organoids. We found that one dose of CAR T-cell therapy should be expected to reduce the tumour size as well as its growth rate, however it may not be enough to completely eliminate it. Moreover, the amount of free CAR T-cells (i.e. CAR T-cells that did not kill any cancer cell) increases as we increase the dosage, and so does the risk of side effects. We tested different strategies to enhance smaller dosages, such as enhancing the CAR T-cells long-term persistence and multiple dosing. For both approaches an appropriate dosimetry strategy is necessary to produce "effective yet safe" therapeutic results. Moreover, an interesting emergent phenomenon results from the simulations, namely the formation of a shield-like structure of cells with low antigen expression. This shield turns out to protect cells with high antigen expression. Finally we tested a multi-antigen recognition therapy to overcome antigen escape and heterogeneity. Our studies suggest that larger dosages can completely eliminate the organoid, however the multi-antigen recognition increases the risk of side effects. Therefore, an appropriate small dosages dosimetry strategy is necessary to improve the outcomes. Based on our results, it is clear that a proper therapeutic strategy could enhance the therapies outcomes. In that direction, our computational approach provides a framework to model treatment combinations in different scenarios and to explore the characteristics of successful and unsuccessful treatments.
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Affiliation(s)
- Luciana Melina Luque
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK.
| | - Carlos Manuel Carlevaro
- Instituto de Física de Líquidos y Sistemas Biológicos, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900, La Plata, Argentina
- Departamento de Ingeniería Mecánica, Universidad Tecnológica Nacional, Facultad Regional La Plata, 1900, La Plata, Argentina
| | | | - Enrique Lomba
- Instituto de Química Física Blas Cabrera, Consejo Superior de Investigaciones Científicas, 28006, Madrid, Spain
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6
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Yuan DJ, Zinno J, Botella T, Dhingra D, Wang S, Hawkins A, Swett A, Sotelo J, Raviram R, Hughes C, Potenski C, Yokoyama A, Kakiuchi N, Ogawa S, Landau DA. Genotype-to-phenotype mapping of somatic clonal mosaicism via single-cell co-capture of DNA mutations and mRNA transcripts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595241. [PMID: 38826366 PMCID: PMC11142212 DOI: 10.1101/2024.05.22.595241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Somatic mosaicism is a hallmark of malignancy that is also pervasively observed in human physiological aging, with clonal expansions of cells harboring mutations in recurrently mutated driver genes. Bulk sequencing of tissue microdissection captures mutation frequencies, but cannot distinguish which mutations co-occur in the same clones to reconstruct clonal architectures, nor phenotypically profile clonal populations to delineate how driver mutations impact cellular behavior. To address these challenges, we developed single-cell Genotype-to-Phenotype sequencing (scG2P) for high-throughput, highly-multiplexed, single-cell joint capture of recurrently mutated genomic regions and mRNA phenotypic markers in cells or nuclei isolated from solid tissues. We applied scG2P to aged esophagus samples from five individuals with high alcohol and tobacco exposure and observed a clonal landscape dominated by a large number of clones with a single driver event, but only rare clones with two driver mutations. NOTCH1 mutants dominate the clonal landscape and are linked to stunted epithelial differentiation, while TP53 mutants and double-driver mutants promote clonal expansion through both differentiation biases and increased cell cycling. Thus, joint single-cell highly multiplexed capture of somatic mutations and mRNA transcripts enables high resolution reconstruction of clonal architecture and associated phenotypes in solid tissue somatic mosaicism.
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Affiliation(s)
- Dennis J Yuan
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - John Zinno
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Theo Botella
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | | | | | - Allegra Hawkins
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Ariel Swett
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Jesus Sotelo
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Ramya Raviram
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Clayton Hughes
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Catherine Potenski
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
| | - Akira Yokoyama
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- Department of Medical Oncology, Kyoto University, Kyoto, Japan
| | - Nobuyuki Kakiuchi
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- The Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
| | - Dan A Landau
- New York Genome Center, New York, NY
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY
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7
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Malcikova J, Pavlova S, Baliakas P, Chatzikonstantinou T, Tausch E, Catherwood M, Rossi D, Soussi T, Tichy B, Kater AP, Niemann CU, Davi F, Gaidano G, Stilgenbauer S, Rosenquist R, Stamatopoulos K, Ghia P, Pospisilova S. ERIC recommendations for TP53 mutation analysis in chronic lymphocytic leukemia-2024 update. Leukemia 2024:10.1038/s41375-024-02267-x. [PMID: 38755420 DOI: 10.1038/s41375-024-02267-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024]
Abstract
In chronic lymphocytic leukemia (CLL), analysis of TP53 aberrations (deletion and/or mutation) is a crucial part of treatment decision-making algorithms. Technological and treatment advances have resulted in the need for an update of the last recommendations for TP53 analysis in CLL, published by ERIC, the European Research Initiative on CLL, in 2018. Based on the current knowledge of the relevance of low-burden TP53-mutated clones, a specific variant allele frequency (VAF) cut-off for reporting TP53 mutations is no longer recommended, but instead, the need for thorough method validation by the reporting laboratory is emphasized. The result of TP53 analyses should always be interpreted within the context of available laboratory and clinical information, treatment indication, and therapeutic options. Methodological aspects of introducing next-generation sequencing (NGS) in routine practice are discussed with a focus on reliable detection of low-burden clones. Furthermore, potential interpretation challenges are presented, and a simplified algorithm for the classification of TP53 variants in CLL is provided, representing a consensus based on previously published guidelines. Finally, the reporting requirements are highlighted, including a template for clinical reports of TP53 aberrations. These recommendations are intended to assist diagnosticians in the correct assessment of TP53 mutation status, but also physicians in the appropriate understanding of the lab reports, thus decreasing the risk of misinterpretation and incorrect management of patients in routine practice whilst also leading to improved stratification of patients with CLL in clinical trials.
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Affiliation(s)
- Jitka Malcikova
- Department of Internal Medicine, Hematology and Oncology, and Institute of Medical Genetics and Genomics, University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine, Hematology and Oncology, and Institute of Medical Genetics and Genomics, University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Eugen Tausch
- Division of CLL, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Mark Catherwood
- Haematology Department, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Davide Rossi
- Hematology, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Thierry Soussi
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Hematopoietic and Leukemic Development, UMRS_938, Sorbonne University, Paris, France
| | - Boris Tichy
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Arnon P Kater
- Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | | | - Frederic Davi
- Sorbonne Université, Paris, France
- Department of Hematology, Hôpital Pitié-Salpêtière, AP-HP, Paris, France
| | - Gianluca Gaidano
- Division of Haematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Stephan Stilgenbauer
- Division of CLL, Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Paolo Ghia
- Università Vita-Salute San Raffaele, Milan, Italy.
- Strategic Research Program on CLL, Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy.
| | - Sarka Pospisilova
- Department of Internal Medicine, Hematology and Oncology, and Institute of Medical Genetics and Genomics, University Hospital Brno and Medical Faculty, Masaryk University, Brno, Czech Republic.
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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8
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Acton OJ, Sheppard D, Kunzelmann S, Caswell SJ, Nans A, Burgess AJO, Kelly G, Morris ER, Rosenthal PB, Taylor IA. Platform-directed allostery and quaternary structure dynamics of SAMHD1 catalysis. Nat Commun 2024; 15:3775. [PMID: 38710701 PMCID: PMC11074143 DOI: 10.1038/s41467-024-48237-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/25/2024] [Indexed: 05/08/2024] Open
Abstract
SAMHD1 regulates cellular nucleotide homeostasis, controlling dNTP levels by catalysing their hydrolysis into 2'-deoxynucleosides and triphosphate. In differentiated CD4+ macrophage and resting T-cells SAMHD1 activity results in the inhibition of HIV-1 infection through a dNTP blockade. In cancer, SAMHD1 desensitizes cells to nucleoside-analogue chemotherapies. Here we employ time-resolved cryogenic-EM imaging and single-particle analysis to visualise assembly, allostery and catalysis by this multi-subunit enzyme. Our observations reveal how dynamic conformational changes in the SAMHD1 quaternary structure drive the catalytic cycle. We capture five states at high-resolution in a live catalytic reaction, revealing how allosteric activators support assembly of a stable SAMHD1 tetrameric core and how catalysis is driven by the opening and closing of active sites through pairwise coupling of active sites and order-disorder transitions in regulatory domains. This direct visualisation of enzyme catalysis dynamics within an allostery-stabilised platform sets a precedent for mechanistic studies into the regulation of multi-subunit enzymes.
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Affiliation(s)
- Oliver J Acton
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- AstraZeneca, The Discovery Centre, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Devon Sheppard
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sarah J Caswell
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- AstraZeneca, The Discovery Centre, 1 Francis Crick Avenue, Cambridge, CB2 0AA, UK
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ailidh J O Burgess
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Geoff Kelly
- The Medical Research Council Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Elizabeth R Morris
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Biosciences, University of Durham, Durham, DH1 3LE, UK
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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9
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Sánchez-Beato M, Méndez M, Guirado M, Pedrosa L, Sequero S, Yanguas-Casás N, de la Cruz-Merino L, Gálvez L, Llanos M, García JF, Provencio M. A genetic profiling guideline to support diagnosis and clinical management of lymphomas. Clin Transl Oncol 2024; 26:1043-1062. [PMID: 37672206 PMCID: PMC11026206 DOI: 10.1007/s12094-023-03307-1] [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: 06/27/2023] [Accepted: 08/09/2023] [Indexed: 09/07/2023]
Abstract
The new lymphoma classifications (International Consensus Classification of Mature Lymphoid Neoplasms, and 5th World Health Organization Classification of Lymphoid Neoplasms) include genetics as an integral part of lymphoma diagnosis, allowing better lymphoma subclassification, patient risk stratification, and prediction of treatment response. Lymphomas are characterized by very few recurrent and disease-specific mutations, and most entities have a heterogenous genetic landscape with a long tail of recurrently mutated genes. Most of these occur at low frequencies, reflecting the clinical heterogeneity of lymphomas. Multiple studies have identified genetic markers that improve diagnostics and prognostication, and next-generation sequencing is becoming an essential tool in the clinical laboratory. This review provides a "next-generation sequencing" guide for lymphomas. It discusses the genetic alterations of the most frequent mature lymphoma entities with diagnostic, prognostic, and predictive potential and proposes targeted sequencing panels to detect mutations and copy-number alterations for B- and NK/T-cell lymphomas.
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Affiliation(s)
- Margarita Sánchez-Beato
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain.
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain.
| | - Miriam Méndez
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - María Guirado
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Hospital General Universitario de Elche, Alicante, Spain
| | - Lucía Pedrosa
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - Silvia Sequero
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Hospital Universitario San Cecilio, Granada, Spain
| | - Natalia Yanguas-Casás
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
| | - Luis de la Cruz-Merino
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Facultad de Medicina, Hospital Universitario Virgen Macarena, Universidad de Sevilla, Instituto de Biomedicina de Sevilla (IBID)/CSIC, Seville, Spain
| | - Laura Gálvez
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Unidad de Gestión Clínica Intercentros de Oncología Médica, Hospitales Universitarios Regional y Virgen de la Victoria, Málaga, Spain
| | - Marta Llanos
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Hospital Universitario de Canarias, La Laguna, Sta. Cruz de Tenerife, Spain
| | - Juan Fernando García
- Servicio de Anatomía Patológica, Hospital MD Anderson Cancer Center, Madrid, Spain
| | - Mariano Provencio
- Servicio de Oncología Médica, Grupo de Investigación en Linfomas, Hospital Universitario Puerta de Hierro-Majadahonda, IDIPHISA, Madrid, Spain
- Grupo Oncológico para el Tratamiento y Estudio de los Linfomas-GOTEL, Madrid, Spain
- Servicio de Oncología Médica, Departamento de Medicina, Facultad de Medicina, Hospital Universitario Puerta de Hierro-Majadahonda, Universidad Autónoma de Madrid, IDIPHISA, Madrid, Spain
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10
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Sciaccotta R, Gangemi S, Penna G, Giordano L, Pioggia G, Allegra A. Potential New Therapies "ROS-Based" in CLL: An Innovative Paradigm in the Induction of Tumor Cell Apoptosis. Antioxidants (Basel) 2024; 13:475. [PMID: 38671922 PMCID: PMC11047475 DOI: 10.3390/antiox13040475] [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: 03/18/2024] [Revised: 04/09/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
Chronic lymphocytic leukemia, in spite of recent advancements, is still an incurable disease; the majority of patients eventually acquire resistance to treatment through relapses. In all subtypes of chronic lymphocytic leukemia, the disruption of normal B-cell homeostasis is thought to be mostly caused by the absence of apoptosis. Consequently, apoptosis induction is crucial to the management of this illness. Damaged biological components can accumulate as a result of the oxidation of intracellular lipids, proteins, and DNA by reactive oxygen species. It is possible that cancer cells are more susceptible to apoptosis because of their increased production of reactive oxygen species. An excess of reactive oxygen species can lead to oxidative stress, which can harm biological elements like DNA and trigger apoptotic pathways that cause planned cell death. In order to upset the balance of oxidative stress in cells, recent therapeutic treatments in chronic lymphocytic leukemia have focused on either producing reactive oxygen species or inhibiting it. Examples include targets created in the field of nanomedicine, natural extracts and nutraceuticals, tailored therapy using biomarkers, and metabolic targets. Current developments in the complex connection between apoptosis, particularly ferroptosis and its involvement in epigenomics and alterations, have created a new paradigm.
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Affiliation(s)
- Raffaele Sciaccotta
- Hematology Unit, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (R.S.); (G.P.); (L.G.)
| | - Sebastiano Gangemi
- Allergy and Clinical Immunology Unit, Department of Clinical and Experimental Medicine, University of Messina, Via Consolare Valeria, 98125 Messina, Italy;
| | - Giuseppa Penna
- Hematology Unit, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (R.S.); (G.P.); (L.G.)
| | - Laura Giordano
- Hematology Unit, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (R.S.); (G.P.); (L.G.)
| | - Giovanni Pioggia
- Institute for Biomedical Research and Innovation (IRIB), National Research Council of Italy (CNR), 98164 Messina, Italy;
| | - Alessandro Allegra
- Hematology Unit, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, Via Consolare Valeria, 98125 Messina, Italy; (R.S.); (G.P.); (L.G.)
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11
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Nesic M, Rasmussen MH, Henriksen TV, Demuth C, Frydendahl A, Nordentoft I, Dyrskjøt L, Andersen CL. Beyond basics: Key mutation selection features for successful tumor-informed ctDNA detection. Int J Cancer 2024. [PMID: 38623608 DOI: 10.1002/ijc.34964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/17/2024]
Abstract
Tumor-informed mutation-based approaches are frequently used for detection of circulating tumor DNA (ctDNA). Not all mutations make equally effective ctDNA markers. The objective was to explore if prioritizing mutations using mutational features-such as cancer cell fraction (CCF), multiplicity, and error rate-would improve the success rate of tumor-informed ctDNA analysis. Additionally, we aimed to develop a practical and easily implementable analysis pipeline for identifying and prioritizing candidate mutations from whole-exome sequencing (WES) data. We analyzed WES and ctDNA data from three tumor-informed ctDNA studies, one on bladder cancer (Cohort A) and two on colorectal cancer (Cohorts I and N). The studies included 390 patients. For each patient, a unique set of mutations (median mutations/patient: 6, interquartile 13, range: 1-46, total n = 4023) were used as markers of ctDNA. The tool PureCN was used to assess the CCF and multiplicity of each mutation. High-CCF mutations were detected more frequently than low-CCF mutations (Cohort A: odds ratio [OR] 20.6, 95% confidence interval [CI] 5.72-173, p = 1.73e-12; Cohort I: OR 2.24, 95% CI 1.44-3.52, p = 1.66e-04; and Cohort N: OR 1.78, 95% CI 1.14-2.79, p = 7.86e-03). The detection-likelihood was additionally improved by selecting mutations with multiplicity of two or above (Cohort A: OR 1.55, 95% CI 1. 14-2.11, p = 3.85e-03; Cohort I: OR 1.78, 95% CI 1.23-2.56, p = 1.34e-03; and Cohort N: OR 1.94, 95% CI 1.63-2.31, p = 2.83e-14). Furthermore, selecting the mutations for which the ctDNA detection method had the lowest error rates, additionally improved the detection-likelihood, particularly evident when plasma cell-free DNA tumor fractions were below 0.1% (p = 2.1e-07). Selecting mutational markers with high CCF, high multiplicity, and low error rate significantly improve ctDNA detection likelihood. We provide free access to the analysis pipeline enabling others to perform qualified prioritization of mutations for tumor-informed ctDNA analysis.
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Affiliation(s)
- Marijana Nesic
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Mads H Rasmussen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Tenna V Henriksen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Christina Demuth
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Amanda Frydendahl
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Claus L Andersen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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12
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Chen SS. Mouse models of CLL: In vivo modeling of disease initiation, progression, and transformation to Richter transformation. Semin Hematol 2024:S0037-1963(24)00056-8. [PMID: 38755077 DOI: 10.1053/j.seminhematol.2024.03.003] [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: 12/30/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 05/18/2024]
Abstract
Chronic lymphocytic leukemia (CLL) is a highly complex disease characterized by the proliferation of CD5+ B cells in lymphoid tissues. Current modern treatments have brought significant clinical benefits to CLL patients. However, there are still unmet needs. Patients relapse on Bruton's tyrosine kinase inhibitors and BCL2 inhibitors and often develop more aggressive diseases including Richter transformation (RT), an incurable complication of up to ∼10% patients. This evidence underscores the need for improved immunotherapies, combination treatment strategies, and predictive biomarkers. A mouse model that can recapitulate human CLL disease and certain components of the tumor immune microenvironment represents a promising preclinical tool for such purposes. In this review, we provide an overview of CRISPR-engineered and xenograft mouse models utilizing either cell lines, or primary CLL cells suitable for studies of key events driving the disease onset, progression and transformation of CLL. We also review how CRISPR/Cas9 established mouse models carrying loss-of-function lesions allow one to study key mutations driving disease progression. Finally, we discuss how next generation humanized mice might improve to generation of faithful xenograft mouse models of human CLL.
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Affiliation(s)
- Shih-Shih Chen
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, New York.
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13
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Appin CL, Hong C, Suwala AK, Hilz S, Mathur R, Solomon DA, Smirnov IV, Stevers NO, Shai A, Wang A, Berger MS, Chang SM, Phillips JJ, Costello JF. Whole tumor analysis reveals early origin of the TERT promoter mutation and intercellular heterogeneity in TERT expression. Neuro Oncol 2024; 26:640-652. [PMID: 38141254 PMCID: PMC10995505 DOI: 10.1093/neuonc/noad231] [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: 06/13/2023] [Indexed: 12/25/2023] Open
Abstract
BACKGROUND The TERT promoter mutation (TPM) is acquired in most IDH-wildtype glioblastomas (GBM) and IDH-mutant oligodendrogliomas (OD) enabling tumor cell immortality. Previous studies on TPM clonality show conflicting results. This study was performed to determine whether TPM is clonal on a tumor-wide scale. METHODS We investigated TPM clonality in relation to presumed early events in 19 IDH-wildtype GBM and 10 IDH-mutant OD using 3-dimensional comprehensive tumor sampling. We performed Sanger sequencing on 264 tumor samples and deep amplicon sequencing on 187 tumor samples. We obtained tumor purity and copy number estimates from whole exome sequencing. TERT expression was assessed by RNA-seq and RNAscope. RESULTS We detected TPM in 100% of tumor samples with quantifiable tumor purity (219 samples). Variant allele frequencies (VAF) of TPM correlate positively with chromosome 10 loss in GBM (R = 0.85), IDH1 mutation in OD (R = 0.87), and with tumor purity (R = 0.91 for GBM; R = 0.90 for OD). In comparison, oncogene amplification was tumor-wide for MDM4- and most EGFR-amplified cases but heterogeneous for MYCN and PDGFRA, and strikingly high in low-purity samples. TPM VAF was moderately correlated with TERT expression (R = 0.52 for GBM; R = 0.65 for OD). TERT expression was detected in a subset of cells, solely in TPM-positive samples, including samples equivocal for tumor. CONCLUSIONS On a tumor-wide scale, TPM is among the earliest events in glioma evolution. Intercellular heterogeneity of TERT expression, however, suggests dynamic regulation during tumor growth. TERT expression may be a tumor cell-specific biomarker.
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Affiliation(s)
- Christina L Appin
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Abigail K Suwala
- Department of Neurological Surgery, University of California, San Francisco, California, USA
- Department of Neuropathology, University of Heidelberg, Institute of Pathology, Heidelberg, Germany
| | - Stephanie Hilz
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Radhika Mathur
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - David A Solomon
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Ivan V Smirnov
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Nicholas O Stevers
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Albert Wang
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, California, USA
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14
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Sud A, Parry EM, Wu CJ. The molecular map of CLL and Richter's syndrome. Semin Hematol 2024; 61:73-82. [PMID: 38368146 DOI: 10.1053/j.seminhematol.2024.01.009] [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: 10/31/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 02/19/2024]
Abstract
Clonal expansion of B-cells, from the early stages of monoclonal B-cell lymphocytosis through to chronic lymphocytic leukemia (CLL), and then in some cases to Richter's syndrome (RS) provides a comprehensive model of cancer evolution, notable for the marked morphological transformation and distinct clinical phenotypes. High-throughput sequencing of large cohorts of patients and single-cell studies have generated a molecular map of CLL and more recently, of RS, yielding fundamental insights into these diseases and of clonal evolution. A selection of CLL driver genes have been functionally interrogated to yield novel insights into the biology of CLL. Such findings have the potential to impact patient care through risk stratification, treatment selection and drug discovery. However, this molecular map remains incomplete, with extant questions concerning the origin of the B-cell clone, the role of the TME, inter- and intra-compartmental heterogeneity and of therapeutic resistance mechanisms. Through the application of multi-modal single-cell technologies across tissues, disease states and clinical contexts, these questions can now be addressed with the answers holding great promise of generating translatable knowledge to improve patient care.
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Affiliation(s)
- Amit Sud
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Department of Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Erin M Parry
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA.
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Department of Medicine, Brigham and Women's Hospital, Boston, MA
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15
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Eichhorst B, Ten Hacken E. Special issue on chronic lymphocytic leukemia: Prognostication and therapeutic options introductory editorial. Semin Hematol 2024; 61:69-72. [PMID: 38599948 DOI: 10.1053/j.seminhematol.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Affiliation(s)
- Barbara Eichhorst
- Department for Internal Medicine and Center für Integrated Oncology Aachen, Bonn, Cologne, Duesseldorf, University of Cologne, Cologne, Germany.
| | - Elisa Ten Hacken
- Department of Medicine, Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY.
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16
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Imodoye SO, Adedokun KA, Bello IO. From complexity to clarity: unravelling tumor heterogeneity through the lens of tumor microenvironment for innovative cancer therapy. Histochem Cell Biol 2024; 161:299-323. [PMID: 38189822 DOI: 10.1007/s00418-023-02258-6] [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] [Accepted: 12/06/2023] [Indexed: 01/09/2024]
Abstract
Despite the tremendous clinical successes recorded in the landscape of cancer therapy, tumor heterogeneity remains a formidable challenge to successful cancer treatment. In recent years, the emergence of high-throughput technologies has advanced our understanding of the variables influencing tumor heterogeneity beyond intrinsic tumor characteristics. Emerging knowledge shows that drivers of tumor heterogeneity are not only intrinsic to cancer cells but can also emanate from their microenvironment, which significantly favors tumor progression and impairs therapeutic response. Although much has been explored to understand the fundamentals of the influence of innate tumor factors on cancer diversity, the roles of the tumor microenvironment (TME) are often undervalued. It is therefore imperative that a clear understanding of the interactions between the TME and other tumor intrinsic factors underlying the plastic molecular behaviors of cancers be identified to develop patient-specific treatment strategies. This review highlights the roles of the TME as an emerging factor in tumor heterogeneity. More particularly, we discuss the role of the TME in the context of tumor heterogeneity and explore the cutting-edge diagnostic and therapeutic approaches that could be used to resolve this recurring clinical conundrum. We conclude by speculating on exciting research questions that can advance our understanding of tumor heterogeneity with the goal of developing customized therapeutic solutions.
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Affiliation(s)
- Sikiru O Imodoye
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA.
| | - Kamoru A Adedokun
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14263, USA
| | - Ibrahim O Bello
- Department of Oral Medicine and Diagnostic Sciences, College of Dentistry, King Saud University, Riyadh, Saudi Arabia.
- Department of Pathology, University of Helsinki, Haartmaninkatu 3, 00014, Helsinki, Finland.
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17
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Gómez Tejeda Zañudo J, Barroso-Sousa R, Jain E, Jin Q, Li T, Buendia-Buendia JE, Pereslete A, Abravanel DL, Ferreira AR, Wrabel E, Helvie K, Hughes ME, Partridge AH, Overmoyer B, Lin NU, Tayob N, Tolaney SM, Wagle N. Exemestane plus everolimus and palbociclib in metastatic breast cancer: clinical response and genomic/transcriptomic determinants of resistance in a phase I/II trial. Nat Commun 2024; 15:2446. [PMID: 38503755 PMCID: PMC10951222 DOI: 10.1038/s41467-024-45835-6] [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] [Received: 10/09/2022] [Accepted: 02/02/2024] [Indexed: 03/21/2024] Open
Abstract
The landscape of cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) resistance is still being elucidated and the optimal subsequent therapy to overcome resistance remains uncertain. Here we present the final results of a phase Ib/IIa, open-label trial (NCT02871791) of exemestane plus everolimus and palbociclib for CDK4/6i-resistant metastatic breast cancer. The primary objective of phase Ib was to evaluate safety and tolerability and determine the maximum tolerated dose/recommended phase II dose (100 mg palbociclib, 5 mg everolimus, 25 mg exemestane). The primary objective of phase IIa was to determine the clinical benefit rate (18.8%, n = 6/32), which did not meet the predefined endpoint (65%). Secondary objectives included pharmacokinetic profiling (phase Ib), objective response rate, disease control rate, duration of response, and progression free survival (phase IIa), and correlative multi-omics analysis to investigate biomarkers of resistance to CDK4/6i. All participants were female. Multi-omics data from the phase IIa patients (n = 24 tumor/17 blood biopsy exomes; n = 27 tumor transcriptomes) showed potential mechanisms of resistance (convergent evolution of HER2 activation, BRAFV600E), identified joint genomic/transcriptomic resistance features (ESR1 mutations, high estrogen receptor pathway activity, and a Luminal A/B subtype; ERBB2/BRAF mutations, high RTK/MAPK pathway activity, and a HER2-E subtype), and provided hypothesis-generating results suggesting that mTOR pathway activation correlates with response to the trial's therapy. Our results illustrate how genome and transcriptome sequencing may help better identify patients likely to respond to CDK4/6i therapies.
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Affiliation(s)
- Jorge Gómez Tejeda Zañudo
- Cancer Program, Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Romualdo Barroso-Sousa
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Oncology Center, Hospital Sírio-Libanês, Brasília, Brazil
| | - Esha Jain
- Cancer Program, Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Repare Therapeutics, Cambridge, MA, USA
| | - Qingchun Jin
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, MA, USA
| | - Tianyu Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, MA, USA
| | - Jorge E Buendia-Buendia
- Cancer Program, Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cellarity, Somerville, MA, USA
| | | | - Daniel L Abravanel
- Cancer Program, Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Arlindo R Ferreira
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Unit, Champalimaud Clinical Centre, Champalimaud Foundation, Lisbon, Portugal
| | - Eileen Wrabel
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Karla Helvie
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Ann H Partridge
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Beth Overmoyer
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nancy U Lin
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nabihah Tayob
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, MA, USA
| | - Sara M Tolaney
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nikhil Wagle
- Cancer Program, Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Genentech, South San Francisco, CA, USA.
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18
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Skotheim RI, Bogaard M, Carm KT, Axcrona U, Axcrona K. Prostate cancer: Molecular aspects, consequences, and opportunities of the multifocal nature. Biochim Biophys Acta Rev Cancer 2024; 1879:189080. [PMID: 38272101 DOI: 10.1016/j.bbcan.2024.189080] [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: 07/05/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 01/27/2024]
Abstract
Prostate cancer is unique compared to other major cancers due to the presence of multiple primary malignant foci in the majority of patients at the time of diagnosis. Each malignant focus has distinct somatic mutations and gene expression patterns, which represents a challenge for the development of prognostic tests for localized prostate cancer. Additionally, the molecular heterogeneity of advanced prostate cancer has important implications for management, particularly for patients with metastatic and locally recurrent cancer. Studies have shown that prostate cancers with mutations in DNA damage response genes are more sensitive to drugs inhibiting the poly ADP-ribose polymerase (PARP) enzyme. However, testing for such mutations should consider both spatial and temporal heterogeneity. Here, we summarize studies where multiregional genomics and transcriptomics analyses have been performed for primary prostate cancer. We further discuss the vast interfocal heterogeneity and how prognostic biomarkers and a molecular definition of the index tumor should be developed. The concept of focal treatments in prostate cancer has been evolving as a demand from patients and clinicians and is one example where there is a need for defining an index tumor. Here, biomarkers must have proven value for individual malignant foci. The potential discovery and implementation of biomarkers that are agnostic to heterogeneity are also explored as an alternative to multisample testing. Thus, deciding upon whole-organ treatment, such as radical prostatectomy, should depend on information from biomarkers which are informative for the whole organ.
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Affiliation(s)
- Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
| | - Mari Bogaard
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Kristina T Carm
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Ulrika Axcrona
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Karol Axcrona
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Department of Urology, Akershus University Hospital, Lørenskog, Norway
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19
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Bonni S, Brindley DN, Chamberlain MD, Daneshvar-Baghbadorani N, Freywald A, Hemmings DG, Hombach-Klonisch S, Klonisch T, Raouf A, Shemanko CS, Topolnitska D, Visser K, Vizeacoumar FJ, Wang E, Gibson SB. Breast Tumor Metastasis and Its Microenvironment: It Takes Both Seed and Soil to Grow a Tumor and Target It for Treatment. Cancers (Basel) 2024; 16:911. [PMID: 38473273 DOI: 10.3390/cancers16050911] [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: 01/09/2024] [Revised: 02/12/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Metastasis remains a major challenge in treating breast cancer. Breast tumors metastasize to organ-specific locations such as the brain, lungs, and bone, but why some organs are favored over others remains unclear. Breast tumors also show heterogeneity, plasticity, and distinct microenvironments. This contributes to treatment failure and relapse. The interaction of breast cancer cells with their metastatic microenvironment has led to the concept that primary breast cancer cells act as seeds, whereas the metastatic tissue microenvironment (TME) is the soil. Improving our understanding of this interaction could lead to better treatment strategies for metastatic breast cancer. Targeted treatments for different subtypes of breast cancers have improved overall patient survival, even with metastasis. However, these targeted treatments are based upon the biology of the primary tumor and often these patients' relapse, after therapy, with metastatic tumors. The advent of immunotherapy allowed the immune system to target metastatic tumors. Unfortunately, immunotherapy has not been as effective in metastatic breast cancer relative to other cancers with metastases, such as melanoma. This review will describe the heterogeneic nature of breast cancer cells and their microenvironments. The distinct properties of metastatic breast cancer cells and their microenvironments that allow interactions, especially in bone and brain metastasis, will also be described. Finally, we will review immunotherapy approaches to treat metastatic breast tumors and discuss future therapeutic approaches to improve treatments for metastatic breast cancer.
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Affiliation(s)
- Shirin Bonni
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 4N1, Canada
- The Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - David N Brindley
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - M Dean Chamberlain
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada
- Saskatchewan Cancer Agency, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Nima Daneshvar-Baghbadorani
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada
- Saskatchewan Cancer Agency, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Andrew Freywald
- Department of Pathology, Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Denise G Hemmings
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Obstetrics and Gynecology, University of Alberta, Edmonton, AB T6G 2S2, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Sabine Hombach-Klonisch
- Department of Human Anatomy and Cell Science, Faculty of Health Sciences, College of Medicine, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Thomas Klonisch
- Department of Human Anatomy and Cell Science, Faculty of Health Sciences, College of Medicine, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Afshin Raouf
- Department of Immunology, Faculty of Medicine, University of Manitoba, Winnipeg, MB R3E OT5, Canada
- Cancer Care Manitoba Research Institute, Cancer Care Manitoba, Winnipeg, MB R3E OV9, Canada
| | - Carrie Simone Shemanko
- The Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - Diana Topolnitska
- Department of Immunology, Faculty of Medicine, University of Manitoba, Winnipeg, MB R3E OT5, Canada
- Cancer Care Manitoba Research Institute, Cancer Care Manitoba, Winnipeg, MB R3E OV9, Canada
| | - Kaitlyn Visser
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Obstetrics and Gynecology, University of Alberta, Edmonton, AB T6G 2S2, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
| | - Franco J Vizeacoumar
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 0W8, Canada
- Saskatchewan Cancer Agency, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
| | - Edwin Wang
- Department of Biochemistry and Molecular Biology, Medical Genetics, and Oncology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Spencer B Gibson
- Department of Oncology, University of Alberta, Edmonton, AB T6G 2R3, Canada
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20
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Bennett R, Seymour JF. Update on the management of relapsed/refractory chronic lymphocytic leukemia. Blood Cancer J 2024; 14:33. [PMID: 38378673 PMCID: PMC10879527 DOI: 10.1038/s41408-024-01001-1] [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: 12/19/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/22/2024] Open
Abstract
Chronic lymphocytic leukemia (CLL) predominantly affects older adults, characterized by a relapsing and remitting pattern with sequential treatments available for many patients. Identification of progressive/relapsed CLL should prompt close monitoring and early discussion about the next therapies when treatment indications are present. The intervening period represents an opportunity to optimize patient health, including establishing adequate vaccination and surveillance for second primary malignancies, and treating non-CLL-related comorbidities which may impact well-being and CLL therapy. We now see patients with relapsed/refractory (RR) CLL in the clinic who have been previously treated with chemoimmunotherapy (CIT) and/or one or more novel therapies. Continuous covalent inhibitors of Bruton's tyrosine kinase (cBTKi) and fixed-duration venetoclax (Ven)-anti-CD20 monoclonal antibody (mAb) are preferred over CIT given the survival advantages associated with these therapies, although have never been evaluated head-to-head. While both classes are effective for RR CLL, potential side effects and the logistics of administration differ. Few randomized data demonstrate the sequential use of cBTKi and fixed-duration Ven-anti-CD20 mAb; however, they may be used in either sequence. Newer non-covalent BTKi, active against BTK C481 resistance mutations emerging with continuous cBTKi exposure, and novel approaches such as BTK degraders, bispecific antibodies, and chimeric antigen receptor T-cell therapies demonstrate impressive efficacy. In this review of RR CLL we explore relevant investigations, consideration of broader CLL- and non-CLL-related health needs, and evidence for efficacy and safety of B-cell receptor inhibitors and Ven, including available data to support drug sequencing or switching. We describe novel approaches to RR CLL, including rechallenging with fixed-duration therapies, allogeneic stem cell transplant indications in the novel therapy era, and highlight early data supporting the use of T-cell directing therapies and novel drug targets.
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Affiliation(s)
- Rory Bennett
- Department of Clinical Haematology, Royal Melbourne Hospital and Peter MacCallum Cancer Centre, 305 Grattan St, Parkville, Melbourne, VIC, 3000, Australia
| | - John F Seymour
- Department of Clinical Haematology, Royal Melbourne Hospital and Peter MacCallum Cancer Centre, 305 Grattan St, Parkville, Melbourne, VIC, 3000, Australia.
- University of Melbourne, Grattan St, Parkville, Melbourne, VIC, 3010, Australia.
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21
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Blanco-Heredia J, Souza CA, Trincado JL, Gonzalez-Cao M, Gonçalves-Ribeiro S, Gil SR, Pravdyvets D, Cedeño S, Callari M, Marra A, Gazzo AM, Weigelt B, Pareja F, Vougiouklakis T, Jungbluth AA, Rosell R, Brander C, Tresserra F, Reis-Filho JS, Tiezzi DG, de la Iglesia N, Heyn H, De Mattos-Arruda L. Converging and evolving immuno-genomic routes toward immune escape in breast cancer. Nat Commun 2024; 15:1302. [PMID: 38383522 PMCID: PMC10882008 DOI: 10.1038/s41467-024-45292-1] [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: 08/21/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
The interactions between tumor and immune cells along the course of breast cancer progression remain largely unknown. Here, we extensively characterize multiple sequential and parallel multiregion tumor and blood specimens of an index patient and a cohort of metastatic triple-negative breast cancers. We demonstrate that a continuous increase in tumor genomic heterogeneity and distinct molecular clocks correlated with resistance to treatment, eventually allowing tumors to escape from immune control. TCR repertoire loses diversity over time, leading to convergent evolution as breast cancer progresses. Although mixed populations of effector memory and cytotoxic single T cells coexist in the peripheral blood, defects in the antigen presentation machinery coupled with subdued T cell recruitment into metastases are observed, indicating a potent immune avoidance microenvironment not compatible with an effective antitumor response in lethal metastatic disease. Our results demonstrate that the immune responses against cancer are not static, but rather follow dynamic processes that match cancer genomic progression, illustrating the complex nature of tumor and immune cell interactions.
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Affiliation(s)
- Juan Blanco-Heredia
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carla Anjos Souza
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Juan L Trincado
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | | | | | - Sara Ruiz Gil
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | | | - Samandhy Cedeño
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
| | - Maurizio Callari
- Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, UK
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea M Gazzo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Theodore Vougiouklakis
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Achim A Jungbluth
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rafael Rosell
- Dexeus Institute of Oncology, Quironsalud Group, Barcelona, Spain
| | - Christian Brander
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain
- ICREA, Passeig de Lluís Companys, 23, Barcelona, Spain
- Universitat de Vic-Universitat Central de Catalunya, Catalunya, Spain
| | | | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Guimarães Tiezzi
- Department of Gynecology and Obstetrics - Breast Disease Division and Laboratory for Translational Data Science, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
- Advanced Research Center in Medicine (CEPAM), Union of the Colleges of the Great Lakes (UNILAGO), São José do Rio Preto, Brazil
| | | | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- Omniscope, Barcelona, Spain
| | - Leticia De Mattos-Arruda
- IrsiCaixa, Germans Trias i Pujol University Hospital, Badalona, Spain.
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain.
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22
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Zhang SM, Paulin CB, Shu H, Yagüe-Capilla M, Michel M, Marttila P, Ortis F, Bwanika HC, Dirks C, Venkatram RP, Wiita E, Jemth AS, Almlöf I, Loseva O, Hormann FM, Koolmeister T, Linde E, Lee S, Llona-Minguez S, Haraldsson M, Axelsson H, Strömberg K, Homan EJ, Scobie M, Lundbäck T, Helleday T, Rudd SG. Identification and evaluation of small-molecule inhibitors against the dNTPase SAMHD1 via a comprehensive screening funnel. iScience 2024; 27:108907. [PMID: 38318365 PMCID: PMC10839966 DOI: 10.1016/j.isci.2024.108907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 09/05/2023] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
SAMHD1 is a dNTP triphosphohydrolase governing nucleotide pool homeostasis and can detoxify chemotherapy metabolites controlling their clinical responses. To understand SAMHD1 biology and investigate the potential of targeting SAMHD1 as neoadjuvant to current chemotherapies, we set out to discover selective small-molecule inhibitors. Here, we report a discovery pipeline encompassing a biochemical screening campaign and a set of complementary biochemical, biophysical, and cell-based readouts for rigorous characterization of the screen output. The identified small molecules, TH6342 and analogs, accompanied by inactive control TH7126, demonstrated specific, low μM potency against both physiological and oncology-drug-derived substrates. By coupling kinetic studies with thermal shift assays, we reveal the inhibitory mechanism of TH6342 and analogs, which engage pre-tetrameric SAMHD1 and deter oligomerization and allosteric activation without occupying nucleotide-binding pockets. Altogether, our study diversifies inhibitory modes against SAMHD1, and the discovery pipeline reported herein represents a thorough framework for future SAMHD1 inhibitor development.
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Affiliation(s)
- Si Min Zhang
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Cynthia B.J. Paulin
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Huazhang Shu
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Miriam Yagüe-Capilla
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Maurice Michel
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Petra Marttila
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Florian Ortis
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Henri Colyn Bwanika
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Christopher Dirks
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Rajagopal Papagudi Venkatram
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Elisée Wiita
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Ann-Sofie Jemth
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Ingrid Almlöf
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Olga Loseva
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Femke M. Hormann
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Tobias Koolmeister
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Erika Linde
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Sun Lee
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Sabin Llona-Minguez
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Martin Haraldsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Hanna Axelsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Kia Strömberg
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Evert J. Homan
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Martin Scobie
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
| | - Sean G. Rudd
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
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23
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Dopeso H, Gazzo AM, Derakhshan F, Brown DN, Selenica P, Jalali S, Da Cruz Paula A, Marra A, da Silva EM, Basili T, Gusain L, Colon-Cartagena L, Bhaloo SI, Green H, Vanderbilt C, Oesterreich S, Grabenstetter A, Kuba MG, Ross D, Giri D, Wen HY, Zhang H, Brogi E, Weigelt B, Pareja F, Reis-Filho JS. Genomic and epigenomic basis of breast invasive lobular carcinomas lacking CDH1 genetic alterations. NPJ Precis Oncol 2024; 8:33. [PMID: 38347189 PMCID: PMC10861500 DOI: 10.1038/s41698-024-00508-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 12/14/2023] [Indexed: 02/15/2024] Open
Abstract
CDH1 (E-cadherin) bi-allelic inactivation is the hallmark alteration of breast invasive lobular carcinoma (ILC), resulting in its discohesive phenotype. A subset of ILCs, however, lack CDH1 genetic/epigenetic inactivation, and their genetic underpinning is unknown. Through clinical targeted sequencing data reanalysis of 364 primary ILCs, we identified 25 ILCs lacking CDH1 bi-allelic genetic alterations. CDH1 promoter methylation was frequent (63%) in these cases. Targeted sequencing reanalysis revealed 3 ILCs harboring AXIN2 deleterious fusions (n = 2) or loss-of-function mutation (n = 1). Whole-genome sequencing of 3 cases lacking bi-allelic CDH1 genetic/epigenetic inactivation confirmed the AXIN2 mutation and no other cell-cell adhesion genetic alterations but revealed a new CTNND1 (p120) deleterious fusion. AXIN2 knock-out in MCF7 cells resulted in lobular-like features, including increased cellular migration and resistance to anoikis. Taken together, ILCs lacking CDH1 genetic/epigenetic alterations are driven by inactivating alterations in other cell adhesion genes (CTNND1 or AXIN2), endorsing a convergent phenotype in ILC.
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Affiliation(s)
- Higinio Dopeso
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea M Gazzo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fatemeh Derakhshan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - David N Brown
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sahar Jalali
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edaise M da Silva
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thais Basili
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laxmi Gusain
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorraine Colon-Cartagena
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shirin Issa Bhaloo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hunter Green
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chad Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steffi Oesterreich
- Department of Pharmacology & Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Anne Grabenstetter
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Gabriela Kuba
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dara Ross
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dilip Giri
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hannah Y Wen
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hong Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edi Brogi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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24
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Cristian M, Așchie M, Mitroi AF, Deacu M, Boșoteanu M, Bălțătescu GI, Stoica AG, Nicolau AA, Enciu M, Crețu AM, Caloian AD, Orășanu CI, Poinăreanu I. The impact of MYD88 and PIM1 in mature large B-cell non-Hodgkin lymphomas: Defining element of their evolution and prognosis. Medicine (Baltimore) 2024; 103:e36269. [PMID: 38335426 PMCID: PMC10860999 DOI: 10.1097/md.0000000000036269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 02/12/2024] Open
Abstract
Sequence studies of the entire exome and transcriptome of lymphoma tissues have identified MYD88 and PIM1 as involved in the development and oncogenic signaling. We aimed to determine the frequency of MYD88 and PIM1 mutations, as well as their expressions in conjunction with the clinicopathological parameters identified in mature large B-cell non-Hodgkin lymphomas. The ten-year retrospective study included 50 cases of mature large B-cell lymphoma, diagnosed at the Pathology Department of the Emergency County Hospital of Constanţa and Săcele County Hospital of Brasov. They were statistically analyzed by demographic, clinicopathological, and morphogenetic characteristics. We used a real-time polymerase chain reaction technique to identify PIM1 and MYD88 mutations as well as an immunohistochemical technique to evaluate the expressions of the 2 genes. Patients with lymphoma in the small bowel, spleen, brain, and testis had a low-performance status Eastern Cooperative Oncology Group (P = .001). The Eastern Cooperative Oncology Group performance status represented an independent risk factor predicting mortality (HR = 9.372, P < .001). An increased lactate dehydrogenase value was associated with a low survival (P = .002). The international prognostic index score represents a negative risk factor in terms of patient survival (HR = 4.654, P < .001). In cases of diffuse large B-cell lymphoma (DLBCL), immunopositivity of MYD88 is associated with non-germinal center B-cell origin (P < .001). The multivariate analysis observed the association between high lactate dehydrogenase value and the immunohistochemical expression of PIM1 or with the mutant status of the PIM1 gene representing negative prognostic factors (HR = 2.066, P = .042, respectively HR = 3.100, P = .004). In conclusion, our preliminary data suggest that the oncogenic mutations of PIM1 and MYD88 in our DLBCL cohort may improve the diagnosis and prognosis of DLBCL patients in an advanced stage.
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Affiliation(s)
- Miruna Cristian
- Faculty of Medicine, “Ovidius” University of Constanta, Constanța, Romania
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology – CEDMOG, “Ovidius” University of Constanta, Constanța, Romania
- Department of Clinical Pathology, “Sf. Apostol Andrei” Emergency County Hospital, Constanta, Romania
| | - Mariana Așchie
- Faculty of Medicine, “Ovidius” University of Constanta, Constanța, Romania
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology – CEDMOG, “Ovidius” University of Constanta, Constanța, Romania
- Department of Clinical Pathology, “Sf. Apostol Andrei” Emergency County Hospital, Constanta, Romania
- Academy of Medical Sciences, Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
| | - Anca-Florentina Mitroi
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology – CEDMOG, “Ovidius” University of Constanta, Constanța, Romania
- Department of Clinical Pathology, “Sf. Apostol Andrei” Emergency County Hospital, Constanta, Romania
| | - Mariana Deacu
- Faculty of Medicine, “Ovidius” University of Constanta, Constanța, Romania
- Department of Clinical Pathology, “Sf. Apostol Andrei” Emergency County Hospital, Constanta, Romania
| | - Mădălina Boșoteanu
- Faculty of Medicine, “Ovidius” University of Constanta, Constanța, Romania
- Department of Clinical Pathology, “Sf. Apostol Andrei” Emergency County Hospital, Constanta, Romania
| | - Gabriela-Izabela Bălțătescu
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology – CEDMOG, “Ovidius” University of Constanta, Constanța, Romania
- Department of Clinical Pathology, “Sf. Apostol Andrei” Emergency County Hospital, Constanta, Romania
| | - Andreea-Georgiana Stoica
- Faculty of Medicine, “Ovidius” University of Constanta, Constanța, Romania
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology – CEDMOG, “Ovidius” University of Constanta, Constanța, Romania
- Department of Hematology, “Sf. Apostol Andrei” Emergency County Hospital, Constanta, Romania
| | - Anca-Antonela Nicolau
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology – CEDMOG, “Ovidius” University of Constanta, Constanța, Romania
- Department of Clinical Pathology, “Sf. Apostol Andrei” Emergency County Hospital, Constanta, Romania
| | - Manuela Enciu
- Faculty of Medicine, “Ovidius” University of Constanta, Constanța, Romania
- Department of Clinical Pathology, “Sf. Apostol Andrei” Emergency County Hospital, Constanta, Romania
| | - Ana-Maria Crețu
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology – CEDMOG, “Ovidius” University of Constanta, Constanța, Romania
- Department of Clinical Pathology, “Sf. Apostol Andrei” Emergency County Hospital, Constanta, Romania
| | - Andreea-Daniela Caloian
- Faculty of Medicine, “Ovidius” University of Constanta, Constanța, Romania
- Department of Hemato-Oncology, “Ovidius” Clinical Hospital, Constanta, Romania
| | - Cristian-Ionuț Orășanu
- Faculty of Medicine, “Ovidius” University of Constanta, Constanța, Romania
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology – CEDMOG, “Ovidius” University of Constanta, Constanța, Romania
- Department of Clinical Pathology, “Sf. Apostol Andrei” Emergency County Hospital, Constanta, Romania
| | - Ionuț Poinăreanu
- Faculty of Medicine, “Ovidius” University of Constanta, Constanța, Romania
- Department of Pathology, Săcele Municipal Hospital, Brasov, Romania
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25
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Antonello A, Bergamin R, Calonaci N, Househam J, Milite S, Williams MJ, Anselmi F, d'Onofrio A, Sundaram V, Sosinsky A, Cross WCH, Caravagna G. Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc. Genome Biol 2024; 25:38. [PMID: 38297376 PMCID: PMC10832148 DOI: 10.1186/s13059-024-03170-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-tumor heterogeneity. Here, we present CNAqc, an evolution-inspired method to perform the computational validation of clonal and subclonal CNAs detected from bulk DNA sequencing. CNAqc is validated using single-cell data and simulations, is applied to over 4000 TCGA and PCAWG samples, and is incorporated into the validation process for the clinically accredited bioinformatics pipeline at Genomics England. CNAqc is designed to support automated quality control procedures for tumor somatic data validation.
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Affiliation(s)
- Alice Antonello
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Riccardo Bergamin
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Nicola Calonaci
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Jacob Househam
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Salvatore Milite
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
- Centre for Computational Biology, Human Technopole, Milan, Italy
| | - Marc J Williams
- Department of Computational Oncology, Memorial Sloan Kettering, New York, USA
| | - Fabio Anselmi
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Alberto d'Onofrio
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | | | | | - William C H Cross
- Department of Research Pathology, UCL Cancer Institute, University College London, London, UK
| | - Giulio Caravagna
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy.
- Evolutionary Genomics and Modelling Team, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
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26
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László T, Kotmayer L, Fésüs V, Hegyi L, Gróf S, Nagy Á, Kajtár B, Balogh A, Weisinger J, Masszi T, Nagy Z, Farkas P, Demeter J, Istenes I, Szász R, Gergely L, Sulák A, Borbényi Z, Lévai D, Schneider T, Pettendi P, Bodai E, Szerafin L, Rejtő L, Bátai Á, Dömötör MÁ, Sánta H, Plander M, Szendrei T, Hamed A, Lázár Z, Pauker Z, Radványi G, Kiss A, Körösmezey G, Jakucs J, Dombi PJ, Simon Z, Klucsik Z, Gurzó M, Tiboly M, Vidra T, Ilonczai P, Bors A, Andrikovics H, Egyed M, Székely T, Masszi A, Alpár D, Matolcsy A, Bödör C. Low-burden TP53 mutations represent frequent genetic events in CLL with an increased risk for treatment initiation. J Pathol Clin Res 2024; 10:e351. [PMID: 37987115 PMCID: PMC10766018 DOI: 10.1002/cjp2.351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/21/2023] [Accepted: 10/25/2023] [Indexed: 11/22/2023]
Abstract
TP53 aberrations predict chemoresistance and represent a contraindication for the use of standard chemoimmunotherapy in chronic lymphocytic leukaemia (CLL). Recent next-generation sequencing (NGS)-based studies have identified frequent low-burden TP53 mutations with variant allele frequencies below 10%, but the clinical impact of these low-burden TP53 mutations is still a matter of debate. In this study, we aimed to scrutinise the subclonal architecture and clinical impact of TP53 mutations using a sensitive, NGS-based mutation analysis in a 'real-world' cohort of 901 patients with CLL. In total, 225 TP53 mutations were identified in 17.5% (158/901) of the patients; 48% of these alterations represented high-burden mutations, while 52% were low-burden TP53 mutations. Low-burden mutations as sole alterations were identified in 39% (62/158) of all mutated cases with 82% (51/62) of these being represented by a single low-burden TP53 mutation. Patients harbouring low-burden TP53 mutations had significantly lower time to first treatment compared to patients with wild-type TP53. Our study has expanded the knowledge on the frequency, clonal architecture, and clinical impact of low-burden TP53 mutations. By demonstrating that patients with sole low-burden TP53 variants represent more than one-third of patients with TP53 mutations and have an increased risk for treatment initiation, our findings strengthen the need to redefine the threshold of TP53 variant reporting to below 10% in the routine diagnostic setting.
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Affiliation(s)
- Tamás László
- HCEMM‐SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
| | - Lili Kotmayer
- HCEMM‐SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
| | - Viktória Fésüs
- HCEMM‐SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
- Kaposi Mór University Teaching Hospital of County SomogyKaposvárHungary
| | - Lajos Hegyi
- HCEMM‐SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
| | - Stefánia Gróf
- HCEMM‐SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
| | - Ákos Nagy
- HCEMM‐SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
| | - Béla Kajtár
- Department of PathologyUniversity of Pécs Medical SchoolPécsHungary
| | - Alexandra Balogh
- Department of Internal Medicine and HematologySemmelweis UniversityBudapestHungary
| | - Júlia Weisinger
- Department of Internal Medicine and HematologySemmelweis UniversityBudapestHungary
| | - Tamás Masszi
- Department of Internal Medicine and HematologySemmelweis UniversityBudapestHungary
| | - Zsolt Nagy
- Department of Internal Medicine and HematologySemmelweis UniversityBudapestHungary
| | - Péter Farkas
- Department of Internal Medicine and HematologySemmelweis UniversityBudapestHungary
| | - Judit Demeter
- Department of Internal Medicine and OncologySemmelweis UniversityBudapestHungary
| | - Ildikó Istenes
- Department of Internal Medicine and OncologySemmelweis UniversityBudapestHungary
| | - Róbert Szász
- Division of Hematology, Department of Internal MedicineUniversity of DebrecenDebrecenHungary
| | - Lajos Gergely
- Division of Hematology, Department of Internal MedicineUniversity of DebrecenDebrecenHungary
| | - Adrienn Sulák
- 2nd Department of Internal Medicine and Cardiology CenterUniversity of SzegedSzegedHungary
| | - Zita Borbényi
- 2nd Department of Internal Medicine and Cardiology CenterUniversity of SzegedSzegedHungary
| | - Dóra Lévai
- Hematology and Lymphoma UnitNational Institute of OncologyBudapestHungary
| | - Tamás Schneider
- Hematology and Lymphoma UnitNational Institute of OncologyBudapestHungary
| | - Piroska Pettendi
- Hetényi Géza Hospital and Clinic of County Jász‐Nagykun‐SzolnokSzolnokHungary
| | - Emese Bodai
- Hetényi Géza Hospital and Clinic of County Jász‐Nagykun‐SzolnokSzolnokHungary
| | - László Szerafin
- Hospitals of County Szabolcs‐Szatmár‐Bereg and University Teaching HospitalNyíregyházaHungary
| | - László Rejtő
- Hospitals of County Szabolcs‐Szatmár‐Bereg and University Teaching HospitalNyíregyházaHungary
| | - Árpád Bátai
- Fejér County Szent György University Teaching HospitalSzékesfehérvárHungary
| | - Mária Á Dömötör
- Fejér County Szent György University Teaching HospitalSzékesfehérvárHungary
| | - Hermina Sánta
- Fejér County Szent György University Teaching HospitalSzékesfehérvárHungary
| | - Márk Plander
- Markusovszky University Teaching HospitalSzombathelyHungary
| | - Tamás Szendrei
- Markusovszky University Teaching HospitalSzombathelyHungary
| | - Aryan Hamed
- Petz Aladár University Teaching HospitalGyőrHungary
| | - Zsolt Lázár
- Petz Aladár University Teaching HospitalGyőrHungary
| | - Zsolt Pauker
- Borsod‐Abaúj‐Zemplén County Hospital and University Teaching HospitalMiskolcHungary
| | - Gáspár Radványi
- Borsod‐Abaúj‐Zemplén County Hospital and University Teaching HospitalMiskolcHungary
| | - Adrienn Kiss
- Military Hospital – State Health CentreBudapestHungary
| | | | | | | | | | - Zsolt Klucsik
- Bács‐Kiskun County Teaching HospitalKecskemétHungary
| | - Mihály Gurzó
- Bács‐Kiskun County Teaching HospitalKecskemétHungary
| | | | - Tímea Vidra
- Soproni Erzsébet Teaching Hospital and Rehabilitation InstituteSopronHungary
| | | | - András Bors
- Central Hospital of Southern Pest – National Institute of Hematology and InfectologyBudapestHungary
| | - Hajnalka Andrikovics
- Central Hospital of Southern Pest – National Institute of Hematology and InfectologyBudapestHungary
| | - Miklós Egyed
- Kaposi Mór University Teaching Hospital of County SomogyKaposvárHungary
| | - Tamás Székely
- HCEMM‐SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
| | - András Masszi
- Department of Internal Medicine and HematologySemmelweis UniversityBudapestHungary
- Hematology and Lymphoma UnitNational Institute of OncologyBudapestHungary
| | - Donát Alpár
- HCEMM‐SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
| | - András Matolcsy
- HCEMM‐SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
- Department of Laboratory MedicineKarolinska InstituteSolnaSweden
| | - Csaba Bödör
- HCEMM‐SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer ResearchSemmelweis UniversityBudapestHungary
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Aref S, Mansour M, Abdel-Aziz S, Sabry M, Aref M, El Dosoky W. Cytogenetic Subclone Burden: A New Biomarker Predicting Chronic Lymphocytic Leukemia Patients Outcome. Asian Pac J Cancer Prev 2024; 25:65-72. [PMID: 38285768 PMCID: PMC10911707 DOI: 10.31557/apjcp.2024.25.1.65] [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: 05/02/2023] [Accepted: 01/19/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Chronic lymphocytic leukemia is the most prevalent adult leukemia that occurs in older patients and presents a variable course of the disease. Risk stratification of CLL is a matter of continuous improvement. Thus, this study aimed to assess the impact of the quantification of 17p del and 11q del cytogenetic subclones on the outcome of patients with chronic lymphocytic leukemia. PATIENTS AND METHODS This is a prospective study that involved 100 subjects with CLL. For all included patients; assessment of the cytogenetic subclones burden for 17p del and 11q del using the FISH technique was carried out. RESULTS CLL patients with a high 17p del (>33%) cytogenetic subclone burden showed significantly shorter lymphocyte doubling time (LDT), time to first treatment (TTFT), and progression free survival (PFS) compared to those with a lower burden. On contrary 11q del subclone(>30%) burden had an insignificant impact on LDT, TTFT and PFS. CONCLUSION Quantification of 17pdel burden (>vs.≤33%) could be used for refining risk stratification of CLL patients.
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Affiliation(s)
- Salah Aref
- Hematology Unit, Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt.
| | - Mona Mansour
- Hematology Unit, Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt.
| | - Sherin Abdel-Aziz
- Hematology Unit, Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt.
| | - Mohammed Sabry
- Hematology Unit, Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt.
| | - Mohamed Aref
- Internal Medicine Department, Mansoura Faculty of Medicine, Mansoura University, Mansoura, Egypt.
| | - Wesam El Dosoky
- Hematology Unit, Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt.
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28
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Navrkalova V, Plevova K, Radova L, Porc J, Pal K, Malcikova J, Pavlova S, Doubek M, Panovska A, Kotaskova J, Pospisilova S. Integrative NGS testing reveals clonal dynamics of adverse genomic defects contributing to a natural progression in treatment-naïve CLL patients. Br J Haematol 2024; 204:240-249. [PMID: 38062779 DOI: 10.1111/bjh.19191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/17/2023] [Accepted: 10/25/2023] [Indexed: 01/11/2024]
Abstract
Large-scale next-generation sequencing (NGS) studies revealed extensive genetic heterogeneity, driving a highly variable clinical course of chronic lymphocytic leukaemia (CLL). The evolution of subclonal populations contributes to diverse therapy responses and disease refractoriness. Besides, the dynamics and impact of subpopulations before therapy initiation are not well understood. We examined changes in genomic defects in serial samples of 100 untreated CLL patients, spanning from indolent to aggressive disease. A comprehensive NGS panel LYNX, which provides targeted mutational analysis and genome-wide chromosomal defect assessment, was employed. We observed dynamic changes in the composition and/or proportion of genomic aberrations in most patients (62%). Clonal evolution of gene variants prevailed over the chromosomal alterations. Unsupervised clustering based on aberration dynamics revealed four groups of patients with different clinical behaviour. An adverse cluster was associated with fast progression and early therapy need, characterized by the expansion of TP53 defects, ATM mutations, and 18p- alongside dynamic SF3B1 mutations. Our results show that clonal evolution is active even without therapy pressure and that repeated genetic testing can be clinically relevant during long-term patient monitoring. Moreover, integrative NGS testing contributes to the consolidated evaluation of results and accurate assessment of individual patient prognosis.
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Affiliation(s)
- Veronika Navrkalova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Lenka Radova
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jakub Porc
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Karol Pal
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jitka Malcikova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jana Kotaskova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
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29
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Kamran SC, Zhou Y, Otani K, Drumm M, Otani Y, Wu S, Wu CL, Feldman AS, Wszolek M, Lee RJ, Saylor PJ, Lennerz J, Van Allen E, Willers H, Hong TS, Liu Y, Davicioni E, Gibb EA, Shipley WU, Mouw KW, Efstathiou JA, Miyamoto DT. Genomic Tumor Correlates of Clinical Outcomes Following Organ-Sparing Chemoradiation Therapy for Bladder Cancer. Clin Cancer Res 2023; 29:5116-5127. [PMID: 37870965 PMCID: PMC10722135 DOI: 10.1158/1078-0432.ccr-23-0792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/20/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
PURPOSE There is an urgent need for biomarkers of radiation response in organ-sparing therapies. Bladder preservation with trimodality therapy (TMT), consisting of transurethral tumor resection followed by chemoradiation, is an alternative to radical cystectomy for muscle-invasive bladder cancer (MIBC), but molecular determinants of response are poorly understood. EXPERIMENTAL DESIGN We characterized genomic and transcriptomic features correlated with long-term response in a single institution cohort of patients with MIBC homogeneously treated with TMT. Pretreatment tumors from 76 patients with MIBC underwent whole-exome sequencing; 67 underwent matched transcriptomic profiling. Molecular features were correlated with clinical outcomes including modified bladder-intact event-free survival (mBI-EFS), a composite endpoint that reflects long-term cancer control with bladder preservation. RESULTS With a median follow-up of 74.6 months in alive patients, 37 patients had favorable long-term response to TMT while 39 had unfavorable long-term response. Tumor mutational burden was not associated with outcomes after TMT. DNA damage response gene alterations were associated with improved locoregional control and mBI-EFS. Of these alterations, somatic ERCC2 mutations stood out as significantly associated with favorable long-term outcomes; patients with ERCC2 mutations had significantly improved mBI-EFS [HR, 0.15; 95% confidence interval (CI), 0.06-0.37; P = 0.030] and improved BI-EFS, an endpoint that includes all-cause mortality (HR, 0.33; 95% CI, 0.15-0.68; P = 0.044). ERCC2 mutant bladder cancer cell lines were significantly more sensitive to concurrent cisplatin and radiation treatment in vitro than isogenic ERCC2 wild-type cells. CONCLUSIONS Our data identify ERCC2 mutation as a candidate biomarker associated with sensitivity and long-term response to chemoradiation in MIBC. These findings warrant validation in independent cohorts.
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Affiliation(s)
- Sophia C. Kamran
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Yuzhen Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Keisuke Otani
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Michael Drumm
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Yukako Otani
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Shulin Wu
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Chin-Lee Wu
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Adam S. Feldman
- Harvard Medical School, Boston, Massachusetts
- Department of Urology, Massachusetts General Hospital, Boston, Massachusetts
| | - Matthew Wszolek
- Harvard Medical School, Boston, Massachusetts
- Department of Urology, Massachusetts General Hospital, Boston, Massachusetts
| | - Richard J. Lee
- Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Philip J. Saylor
- Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jochen Lennerz
- Harvard Medical School, Boston, Massachusetts
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Eliezer Van Allen
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Department of Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Henning Willers
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Theodore S. Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Yang Liu
- Veracyte, San Francisco, California
| | | | | | - William U. Shipley
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Kent W. Mouw
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jason A. Efstathiou
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - David T. Miyamoto
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts
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30
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Hortal AM, Villanueva A, Arellano I, Prieto C, Mendoza P, Bustelo XR, Alarcón B. Mice Overexpressing Wild-Type RRAS2 Are a Novel Model for Preclinical Testing of Anti-Chronic Lymphocytic Leukemia Therapies. Cancers (Basel) 2023; 15:5817. [PMID: 38136362 PMCID: PMC10742337 DOI: 10.3390/cancers15245817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
B-cell chronic lymphocytic leukemia (B-CLL) is the most common type of leukemia in the Western world. Mutation in different genes, such as TP53 and ATM, and deletions at specific chromosomic regions, among which are 11q or 17p, have been described to be associated to worse disease prognosis. Recent research from our group has demonstrated that, contrary to what is the usual cancer development process through missense mutations, B-CLL is driven by the overexpression of the small GTPase RRAS2 in its wild-type form without activating mutations. Some mouse models of this disease have been developed to date and are commonly used in B-CLL research, but they present different disadvantages such as the long waiting period until the leukemia fully develops, the need to do cell engraftment or, in some cases, the fact that the model does not recapitulate the alterations found in human patients. We have recently described Rosa26-RRAS2fl/flxmb1-Cre as a new mouse model of B-CLL with a full penetrance of the disease. In this work, we have validated this mouse model as a novel tool for the development of new therapies for B-CLL, by testing two of the most broadly applied targeted agents: ibrutinib and venetoclax. This also opens the door to new targeted agents against R-RAS2 itself, an approach not yet explored in the clinic.
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Affiliation(s)
- Alejandro M. Hortal
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.V.); (I.A.); (C.P.); (P.M.)
| | - Ana Villanueva
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.V.); (I.A.); (C.P.); (P.M.)
| | - Irene Arellano
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.V.); (I.A.); (C.P.); (P.M.)
| | - Cristina Prieto
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.V.); (I.A.); (C.P.); (P.M.)
| | - Pilar Mendoza
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.V.); (I.A.); (C.P.); (P.M.)
| | - Xosé R. Bustelo
- Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer and Centro de Investigación Biomédica en Red de Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Balbino Alarcón
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, 28049 Madrid, Spain; (A.V.); (I.A.); (C.P.); (P.M.)
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31
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Lacuna M, Hortal AM, Cifuentes C, Gonzalo T, Alcoceba M, Bastos M, Bustelo XR, González M, Alarcón B. Characterization of Three Somatic Mutations in the 3'UTR of RRAS2 and Their Inverse Correlation with Lymphocytosis in Chronic Lymphocytic Leukemia. Cells 2023; 12:2687. [PMID: 38067115 PMCID: PMC10705375 DOI: 10.3390/cells12232687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a hematologic malignancy characterized by progressive accumulation of a rare population of CD5+ B-lymphocytes in peripheral blood, bone marrow, and lymphoid tissues. CLL exhibits remarkable clinical heterogeneity, with some patients presenting with indolent disease and others progressing rapidly to aggressive CLL. The significant heterogeneity of CLL underscores the importance of identifying novel prognostic markers. Recently, the RAS-related gene RRAS2 has emerged as both a driver oncogene and a potential marker for CLL progression, with higher RRAS2 expression associated with poorer disease prognosis. Although missense somatic mutations in the coding sequence of RRAS2 have not been described in CLL, this study reports the frequent detection of three somatic mutations in the 3' untranslated region (3'UTR) affecting positions +26, +53, and +180 downstream of the stop codon in the mRNA. An inverse relationship was observed between these three somatic mutations and RRAS2 mRNA expression, which correlated with lower blood lymphocytosis. These findings highlight the importance of RRAS2 overexpression in CLL development and prognosis and point to somatic mutations in its 3'UTR as novel mechanistic clues. Our results may contribute to the development of targeted therapeutic strategies and improved risk stratification for CLL patients.
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Affiliation(s)
- Marta Lacuna
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.L.); (A.M.H.); (C.C.); (T.G.)
| | - Alejandro M. Hortal
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.L.); (A.M.H.); (C.C.); (T.G.)
| | - Claudia Cifuentes
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.L.); (A.M.H.); (C.C.); (T.G.)
| | - Tania Gonzalo
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.L.); (A.M.H.); (C.C.); (T.G.)
| | - Miguel Alcoceba
- Departamento de Hematología, Hospital Universitario de Salamanca (HUS-IBSAL), 37007 Salamanca, Spain; (M.A.); (M.B.); (M.G.)
- Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer and Centro de Investigación Biomédica en Red de Cáncer, CSIC, Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Miguel Bastos
- Departamento de Hematología, Hospital Universitario de Salamanca (HUS-IBSAL), 37007 Salamanca, Spain; (M.A.); (M.B.); (M.G.)
- Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer and Centro de Investigación Biomédica en Red de Cáncer, CSIC, Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Xosé R. Bustelo
- Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer and Centro de Investigación Biomédica en Red de Cáncer, CSIC, Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Marcos González
- Departamento de Hematología, Hospital Universitario de Salamanca (HUS-IBSAL), 37007 Salamanca, Spain; (M.A.); (M.B.); (M.G.)
- Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer and Centro de Investigación Biomédica en Red de Cáncer, CSIC, Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Balbino Alarcón
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.L.); (A.M.H.); (C.C.); (T.G.)
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32
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López-Oreja I, Gohr A, Playa-Albinyana H, Giró A, Arenas F, Higashi M, Tripathi R, López-Guerra M, Irimia M, Aymerich M, Valcárcel J, Bonnal S, Colomer D. SF3B1 mutation-mediated sensitization to H3B-8800 splicing inhibitor in chronic lymphocytic leukemia. Life Sci Alliance 2023; 6:e202301955. [PMID: 37562845 PMCID: PMC10415613 DOI: 10.26508/lsa.202301955] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
Splicing factor 3B subunit 1 (SF3B1) is involved in pre-mRNA branch site recognition and is the target of antitumor-splicing inhibitors. Mutations in SF3B1 are observed in 15% of patients with chronic lymphocytic leukemia (CLL) and are associated with poor prognosis, but their pathogenic mechanisms remain poorly understood. Using deep RNA-sequencing data from 298 CLL tumor samples and isogenic SF3B1 WT and K700E-mutated CLL cell lines, we characterize targets and pre-mRNA sequence features associated with the selection of cryptic 3' splice sites upon SF3B1 mutation, including an event in the MAP3K7 gene relevant for activation of NF-κB signaling. Using the H3B-8800 splicing modulator, we show, for the first time in CLL, cytotoxic effects in vitro in primary CLL samples and in SF3B1-mutated isogenic CLL cell lines, accompanied by major splicing changes and delayed leukemic infiltration in a CLL xenotransplant mouse model. H3B-8800 displayed preferential lethality towards SF3B1-mutated cells and synergism with the BCL2 inhibitor venetoclax, supporting the potential use of SF3B1 inhibitors as a novel therapeutic strategy in CLL.
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Affiliation(s)
- Irene López-Oreja
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - André Gohr
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Heribert Playa-Albinyana
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Ariadna Giró
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Fabian Arenas
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Morihiro Higashi
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Rupal Tripathi
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Mònica López-Guerra
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Marta Aymerich
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Sophie Bonnal
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
- Hematopathology Section, Department of Pathology, Hospital Clínic, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncologia, Madrid, Spain
- Universitat Barcelona, Barcelona, Spain
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33
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Jondreville L, Dehgane L, Doualle C, Smagghe L, Grange B, Davi F, Lerner LK, Garnier D, Bravetti C, Tournilhac O, Roos-Weil D, Boubaya M, Chapiro E, Susin SA, Nguyen-Khac F. del(8p) and TNFRSF10B loss are associated with a poor prognosis and resistance to fludarabine in chronic lymphocytic leukemia. Leukemia 2023; 37:2221-2230. [PMID: 37752286 DOI: 10.1038/s41375-023-02035-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 08/22/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023]
Abstract
Chronic lymphocytic leukemia (CLL) is a heterogeneous disease, the prognosis of which varies according to the cytogenetic group. We characterized a rare chromosomal abnormality (del(8p), deletion of the short arm of chromosome 8) in the context of CLL. By comparing the largest cohort of del(8p) CLL to date (n = 57) with a non-del(8p) cohort (n = 155), del(8p) was significantly associated with a poor prognosis, a shorter time to first treatment, worse overall survival (OS), and a higher risk of Richter transformation. For patients treated with fludarabine-based regimens, the next-treatment-free survival and the OS were shorter in del(8p) cases (including those with mutated IGHV). One copy of the TNFRSF10B gene (coding a pro-apoptotic receptor activated by TRAIL) was lost in 91% of del(8p) CLL. TNFRSF10B was haploinsufficient in del(8p) CLL, and was involved in the modulation of fludarabine-induced cell death - as confirmed by our experiments in primary cells and in CRISPR-edited TNFRSF10B knock-out CLL cell lines. Lastly, del(8p) abrogated the synergy between fludarabine and TRAIL-induced apoptosis. Our results highlight del(8p)'s value as a prognostic marker and suggest that fit CLL patients (i.e. with mutated IGHV and no TP53 disruption) should be screened for del(8p) before the initiation of fludarabine-based treatment.
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Affiliation(s)
- Ludovic Jondreville
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS 1138, Drug Resistance in Hematological Malignancies Team, F-75006, Paris, France
| | - Lea Dehgane
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS 1138, Drug Resistance in Hematological Malignancies Team, F-75006, Paris, France
| | - Cecile Doualle
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS 1138, Drug Resistance in Hematological Malignancies Team, F-75006, Paris, France
| | - Luce Smagghe
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS 1138, Drug Resistance in Hematological Malignancies Team, F-75006, Paris, France
| | - Beatrice Grange
- Service d'Hématologie Biologique, Hôpital Pitié-Salpêtrière, Sorbonne Université, AP-HP, Paris, France
| | - Frederic Davi
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS 1138, Drug Resistance in Hematological Malignancies Team, F-75006, Paris, France
- Service d'Hématologie Biologique, Hôpital Pitié-Salpêtrière, Sorbonne Université, AP-HP, Paris, France
| | - Leticia K Lerner
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS 1138, Drug Resistance in Hematological Malignancies Team, F-75006, Paris, France
| | - Delphine Garnier
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS 1138, Drug Resistance in Hematological Malignancies Team, F-75006, Paris, France
| | - Clotilde Bravetti
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS 1138, Drug Resistance in Hematological Malignancies Team, F-75006, Paris, France
- Service d'Hématologie Biologique, Hôpital Pitié-Salpêtrière, Sorbonne Université, AP-HP, Paris, France
| | - Olivier Tournilhac
- Service d'Hématologie Clinique, CHU Estaing, 1 place Lucie et Raymond Aubrac, 63003, Clermont-Ferrand, France
| | - Damien Roos-Weil
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS 1138, Drug Resistance in Hematological Malignancies Team, F-75006, Paris, France
- Service d'Hématologie Clinique, Hôpital Pitié-Salpêtrière, AP-HP, Paris, France
| | - Marouane Boubaya
- Unité de Recherche Clinique, Hôpitaux Universitaires Paris Seine-Saint-Denis, AP-HP, Bobigny, France
| | - Elise Chapiro
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS 1138, Drug Resistance in Hematological Malignancies Team, F-75006, Paris, France.
- Service d'Hématologie Biologique, Hôpital Pitié-Salpêtrière, Sorbonne Université, AP-HP, Paris, France.
| | - Santos A Susin
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS 1138, Drug Resistance in Hematological Malignancies Team, F-75006, Paris, France.
| | - Florence Nguyen-Khac
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS 1138, Drug Resistance in Hematological Malignancies Team, F-75006, Paris, France.
- Service d'Hématologie Biologique, Hôpital Pitié-Salpêtrière, Sorbonne Université, AP-HP, Paris, France.
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Parrondo RD, Iqbal M, Von Roemeling R, Von Roemeling C, Tun HW. IRAK-4 inhibition: emavusertib for the treatment of lymphoid and myeloid malignancies. Front Immunol 2023; 14:1239082. [PMID: 37954584 PMCID: PMC10637517 DOI: 10.3389/fimmu.2023.1239082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
Several studies have identified mutations in the MYD88L265P gene as a key driver mutation in several B-cell lymphomas. B-cell lymphomas that harbor the MYD88L265P mutation form a complex with phosphorylated Bruton's tyrosine kinase (BTK) and are responsive to BTK inhibition. However, BTK inhibition in B-cell lymphomas rarely results in a complete response and most patients experience eventual disease relapse. Persistent survival signaling though downstream molecules such as interleukin 1 receptor-associated kinase 4 (IRAK-4), an integral part of the "myddosome" complex, has been shown to be constitutively active in B-cell lymphoma patients treated with BTK inhibitors. Emerging evidence is demonstrating the therapeutic benefit of IRAK-4 inhibition in B-cell lymphomas, along with possibly reversing BTK inhibitor resistance. While MYD88 gene mutations are not present in myeloid malignancies, downstream overexpression of the oncogenic long form of IRAK-4 has been found in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), particularly in AML and MDS that harbor mutations in splicing factors U2AF1 and SF3B1. These data suggest that the anti-leukemic activity of IRAK-4 inhibition can be exploited in relapsed/refractory (R/R) AML/MDS. In this review article, we discuss the currently available pre-clinical and clinical data of emavusertib, a selective, orally bioavailable IRAK-4 inhibitor in the treatment of R/R B-cell lymphomas and myeloid malignancies.
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Affiliation(s)
- Ricardo D. Parrondo
- Department of Hematology-Oncology, Mayo Clinic Cancer Center, Jacksonville, FL, United States
| | - Madiha Iqbal
- Department of Hematology-Oncology, Mayo Clinic Cancer Center, Jacksonville, FL, United States
| | | | | | - Han W. Tun
- Department of Hematology-Oncology, Mayo Clinic Cancer Center, Jacksonville, FL, United States
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35
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Yang LP, Jiang TJ, He MM, Ling YH, Wang ZX, Wu HX, Zhang Z, Xu RH, Wang F, Yuan SQ, Zhao Q. Comprehensive genomic characterization of sporadic synchronous colorectal cancer: Implications for treatment optimization and clinical outcome. Cell Rep Med 2023; 4:101222. [PMID: 37794586 PMCID: PMC10591049 DOI: 10.1016/j.xcrm.2023.101222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 07/12/2023] [Accepted: 09/11/2023] [Indexed: 10/06/2023]
Abstract
Sporadic synchronous colorectal cancer (SCRC) refers to multiple primary CRC tumors detected simultaneously in an individual without predisposing hereditary conditions, which accounts for the majority of multiple CRCs while lacking a profound understanding of the genomic landscape and evolutionary dynamics to optimize its treatment. In this study, 103 primary tumor samples from 51 patients with SCRC undergo whole-exome sequencing. The germline and somatic mutations and evolutionary and clinical features are comprehensively investigated. Somatic genetic events are largely inconsistent between paired tumors. Compared with solitary CRC, SCRCs have higher prevalence of tumor mutation burden high (TMB-H; 33.3%) and microsatellite-instability high (MSI-H; 29.4%) and different mutation frequencies in oncogenic signaling pathways. Moreover, neutrally evolving SCRC tumors are associated with higher intratumoral heterogeneity and better prognosis. These findings unveil special molecular features, carcinogenesis, and prognosis of sporadic SCRC. Strategies for targeted therapy and immunotherapy should be optimized accordingly.
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Affiliation(s)
- Lu-Ping Yang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Teng-Jia Jiang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Ming-Ming He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China; Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, P.R. China
| | - Yi-Hong Ling
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Zi-Xian Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China; Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, P.R. China
| | - Hao-Xiang Wu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China; Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, P.R. China
| | - Zhen Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Rui-Hua Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China; Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou 510060, P.R. China
| | - Feng Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China
| | - Shu-Qiang Yuan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China.
| | - Qi Zhao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, P.R. China.
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36
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Bao C, Tourdot RW, Brunette GJ, Stewart C, Sun L, Baba H, Watanabe M, Agoston AT, Jajoo K, Davison JM, Nason KS, Getz G, Wang KK, Imamura Y, Odze R, Bass AJ, Stachler MD, Zhang CZ. Genomic signatures of past and present chromosomal instability in Barrett's esophagus and early esophageal adenocarcinoma. Nat Commun 2023; 14:6203. [PMID: 37794034 PMCID: PMC10550953 DOI: 10.1038/s41467-023-41805-6] [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] [Received: 08/01/2023] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations but how these alterations arise is poorly understood. Here we perform haplotype-specific analysis of chromosomal copy-number evolution in the progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) on multiregional whole-genome sequencing data of BE with dysplasia and microscopic EAC foci. We identify distinct patterns of copy-number evolution indicating multigenerational chromosomal instability that is initiated by cell division errors but propagated only after p53 loss. While abnormal mitosis, including whole-genome duplication, underlies chromosomal copy-number changes, segmental alterations display signatures of successive breakage-fusion-bridge cycles and chromothripsis of unstable dicentric chromosomes. Our analysis elucidates how multigenerational chromosomal instability generates copy-number variation in BE cells, precipitates complex alterations including DNA amplifications, and promotes their independent clonal expansion and transformation. In particular, we suggest sloping copy-number variation as a signature of ongoing chromosomal instability that precedes copy-number complexity. These findings suggest copy-number heterogeneity in advanced cancers originates from chromosomal instability in precancerous cells and such instability may be identified from the presence of sloping copy-number variation in bulk sequencing data.
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Affiliation(s)
- Chunyang Bao
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Richard W Tourdot
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
- Department of Biomedical Informatics, Blavatnik Institute of Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA
| | - Gregory J Brunette
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Department of Biomedical Informatics, Blavatnik Institute of Harvard Medical School, 10 Shattuck St, Boston, MA, 02115, USA
| | - Chip Stewart
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA
| | - Lili Sun
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Single-Cell Sequencing Program, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, 2 Chome-40-1 Kurokami, Chuo Ward, Kumamoto, Japan
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation of Cancer Research, 3-8-31 Ariake, Koto, Tokyo, Japan
| | - Agoston T Agoston
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Kunal Jajoo
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Jon M Davison
- Department of Pathology, University of Pittsburgh School of Medicine, 200 Lothrop Street, Pittsburgh, PA, 15213, USA
| | - Katie S Nason
- Department of Surgery, Baystate Medical Center, University of Massachusetts Medical School, 759 Chestnut St, Springfield, MA, 01107, USA
| | - Gad Getz
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Kenneth K Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Yu Imamura
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation of Cancer Research, 3-8-31 Ariake, Koto, Tokyo, Japan
| | - Robert Odze
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
- Department of Pathology and Lab Medicine, Tufts University School of Medicine, 145 Harrison Ave, Boston, MA, 02111, USA
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
| | - Matthew D Stachler
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
- Department of Pathology, University of California, San Francisco. 513 Parnassus Ave, San Francisco, CA, 94143, USA.
| | - Cheng-Zhong Zhang
- Department of Data Science, Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA.
- Department of Pathology, Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA.
- Cancer Program, Broad Institute of MIT and Harvard, 415 Main St, Cambridge, MA, 02142, USA.
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Nguyen-Khac F, Balogh Z, Chauzeix J, Veronese L, Chapiro E. Cytogenetics in the management of chronic lymphocytic leukemia: Guidelines from the Groupe Francophone de Cytogénétique Hématologique (GFCH). Curr Res Transl Med 2023; 71:103410. [PMID: 38039634 DOI: 10.1016/j.retram.2023.103410] [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: 07/05/2023] [Accepted: 09/14/2023] [Indexed: 12/03/2023]
Abstract
Chromosomal abnormalities are frequent in chronic lymphocytic leukemia (CLL), and most have prognostic value. In addition to the four well-known abnormalities (13q, 11q and 17p deletions, and trisomy 12), other recurrent aberrations have been linked to the disease outcome and/or drug resistance. Moreover, the complex karyotype has recently emerged as a prognostic marker for patients undergoing immunochemotherapy or targeted therapies. Here, we describe the main chromosomal abnormalities identified in CLL and related disorders (small lymphocytic lymphoma and monoclonal B-cell lymphocytosis) by reviewing the most recent literature and discussing their detection and clinical impact. Lastly, we provide technical guidelines and a strategy for the cytogenetic assessment of CLL.
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Affiliation(s)
- Florence Nguyen-Khac
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS 1138, Drug Resistance in Hematological Malignancies Team, F-75006 Paris, France; Sorbonne Université, Paris, France; Service d'Hématologie Biologique, Bâtiment Pharmacie, 3e étage, Pitié-Salpêtrière/Charles Foix University Hospital, AP-HP, 83 Bd de l'Hôpital, Paris F-75013, France.
| | - Zsofia Balogh
- Département d'Innovation Thérapeutique et des Essais Précoces, Gustave Roussy, Villejuif, France
| | - Jasmine Chauzeix
- Service d'Hématologie biologique, CHU de Limoges - CRIBL, UMR CNRS 7276/INSERM 1262, Limoges, France
| | - Lauren Veronese
- Service de Cytogénétique Médicale, CHU Estaing, 1 place Lucie et Raymond Aubrac, Clermont-Ferrand 63003, France
| | - Elise Chapiro
- Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Inserm UMRS 1138, Drug Resistance in Hematological Malignancies Team, F-75006 Paris, France; Sorbonne Université, Paris, France; Service d'Hématologie Biologique, Bâtiment Pharmacie, 3e étage, Pitié-Salpêtrière/Charles Foix University Hospital, AP-HP, 83 Bd de l'Hôpital, Paris F-75013, France
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38
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Andrade JR, Gallagher AD, Maharaj J, McClelland SE. Disentangling the roles of aneuploidy, chromosomal instability and tumour heterogeneity in developing resistance to cancer therapies. Chromosome Res 2023; 31:28. [PMID: 37721639 PMCID: PMC10506951 DOI: 10.1007/s10577-023-09737-5] [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: 05/01/2023] [Revised: 07/26/2023] [Accepted: 08/29/2023] [Indexed: 09/19/2023]
Abstract
Aneuploidy is defined as the cellular state of having a number of chromosomes that deviates from a multiple of the normal haploid chromosome number of a given organism. Aneuploidy can be present in a static state: Down syndrome individuals stably maintain an extra copy of chromosome 21 in their cells. In cancer cells, however, aneuploidy is usually present in combination with chromosomal instability (CIN) which leads to a continual generation of new chromosomal alterations and the development of intratumour heterogeneity (ITH). The prevalence of cells with specific chromosomal alterations is further shaped by evolutionary selection, for example, during the administration of cancer therapies. Aneuploidy, CIN and ITH have each been individually associated with poor prognosis in cancer, and a wealth of evidence suggests they contribute, either alone or in combination, to cancer therapy resistance by providing a reservoir of potential resistant states, or the ability to rapidly evolve resistance. A full understanding of the contribution and interplay between aneuploidy, CIN and ITH is required to tackle therapy resistance in cancer patients. However, these characteristics often co-occur and are intrinsically linked, presenting a major challenge to defining their individual contributions. Moreover, their accurate measurement in both experimental and clinical settings is a technical hurdle. Here, we attempt to deconstruct the contribution of the individual and combined roles of aneuploidy, CIN and ITH to therapy resistance in cancer, and outline emerging approaches to measure and disentangle their roles as a step towards integrating these principles into cancer therapeutic strategy.
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Affiliation(s)
- Joana Reis Andrade
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
| | - Annie Dinky Gallagher
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
| | - Jovanna Maharaj
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M6BQ, England
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39
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Burack WR, Li H, Adlowitz D, Spence JM, Rimsza LM, Shadman M, Spier CM, Kaminski MS, Leonard JP, Leblanc ML, Smith SM, Friedberg JW. Subclonal TP53 mutations are frequent and predict resistance to radioimmunotherapy in follicular lymphoma. Blood Adv 2023; 7:5082-5090. [PMID: 37379264 PMCID: PMC10471938 DOI: 10.1182/bloodadvances.2022009467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/12/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023] Open
Abstract
Although TP53 is commonly mutated in transformed follicular lymphoma, mutations are reported in <5% of pretreatment follicular lymphoma (FL) specimens. We assayed archival follicular B-cell non-Hodgkin lymphoma specimens from a completed clinical trial, Southwest Oncology Group S0016, a phase 3 randomized intergroup trial of CHOP (cyclophosphamide, hydroxydaunorubicin, oncovin, and prednisone) chemotherapy plus R-CHOP (rituximab-CHOP) compared with CHOP chemotherapy plus 131-iodine tositumomab (radioimmunotherapy [RIT]-CHOP). Subclonal TP53 mutations (median allele frequency 0.02) were found in 25% of diagnostic FL specimens and in 27% of a separate validation cohort. In the R-CHOP arm, pathogenic TP53 mutations were not associated with progression-free survival (PFS) (10-year PFS 43% vs 44%). In contrast, among patients with no detectable pathogenic TP53 mutation, RIT-CHOP was associated with a longer PFS than with R-CHOP (10-year PFS 67% vs 44%; hazard ratio = 0.49; P = .008). No relationship was detected between PFS and the extent of activation-induced cytidine deaminase (AICDA)-mediated heterogeneity. In summary, subclonal TP53 mutations are common in FL and are a distinct phenomenon from AICDA-mediated genetic heterogeneity. The absence of a detectable subclonal mutation in TP53 defined a population that particularly benefited from RIT.
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Affiliation(s)
- W. Richard Burack
- Department of Pathology, University of Rochester Medical Center, Rochester, NY
| | - Hongli Li
- Clinical Research Division, Fred Hutchison Cancer Research Center, Seattle, WA
| | - Diana Adlowitz
- Department of Pathology, University of Rochester Medical Center, Rochester, NY
| | - Janice M. Spence
- Department of Pathology, University of Rochester Medical Center, Rochester, NY
| | - Lisa M. Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic in Arizona, Phoenix, AZ
| | - Mazyar Shadman
- Clinical Research Division, Fred Hutchison Cancer Research Center, Seattle, WA
| | | | - Mark S. Kaminski
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - John P. Leonard
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Michael L. Leblanc
- Clinical Research Division, Fred Hutchison Cancer Research Center, Seattle, WA
| | - Sonali M. Smith
- Department of Medicine, University of Chicago School of Medicine, Chicago, IL
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40
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Haselager MV, van Driel BF, Perelaer E, de Rooij D, Lashgari D, Loos R, Kater AP, Moerland PD, Eldering E. In Vitro 3D Spheroid Culture System Displays Sustained T Cell-dependent CLL Proliferation and Survival. Hemasphere 2023; 7:e938. [PMID: 37637994 PMCID: PMC10448932 DOI: 10.1097/hs9.0000000000000938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/26/2023] [Indexed: 08/29/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) cells are highly dependent on microenvironmental cells and signals. The lymph node (LN) is the critical site of in vivo CLL proliferation and development of resistance to both chemotherapy and targeted agents. We present a new model that incorporates key aspects of the CLL LN, which enables investigation of CLL cells in the context of a protective niche. We describe a three-dimensional (3D) in vitro culture system using ultra-low attachment plates to create spheroids of CLL cells derived from peripheral blood. Starting from CLL:T cell ratios as observed in LN samples, CLL activation was induced by either direct stimulation and/or indirectly via T cells. Compared with two-dimensional cultures, 3D cultures promoted CLL proliferation in a T cell-dependent manner, and enabled expansion for up to 7 weeks, including the formation of follicle-like structures after several weeks of culture. This model enables high-throughput drug screening, of which we describe response to Btk inhibition, venetoclax resistance, and T cell-mediated cytotoxicity as examples. In summary, we present the first LN-mimicking in vitro 3D culture for primary CLL, which enables readouts such as real-time drug screens, kinetic growth assays, and spatial localization. This is the first in vitro CLL system that allows testing of response and resistance to venetoclax and Bruton's tyrosine kinase inhibitors in the context of the tumor microenvironment, thereby opening up new possibilities for clinically useful applications.
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Affiliation(s)
- Marco V. Haselager
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
- Lymphoma and Myeloma Center Amsterdam, LYMMCARE, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Cancer Immunology, Amsterdam, The Netherlands
| | - Bianca F. van Driel
- Department of Hematology, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
| | - Eduard Perelaer
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
| | - Dennis de Rooij
- Department of Hematology, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
| | - Danial Lashgari
- Amsterdam Institute for Infection and Immunity, Cancer Immunology, Amsterdam, The Netherlands
- Department of Epidemiology and Data Science, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
| | - Remco Loos
- Center for Innovation and Translational Research Europe, Bristol Myers Squibb, Sevilla, Spain
| | - Arnon P. Kater
- Lymphoma and Myeloma Center Amsterdam, LYMMCARE, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Cancer Immunology, Amsterdam, The Netherlands
- Department of Hematology, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
| | - Perry D. Moerland
- Department of Epidemiology and Data Science, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
- Amsterdam Institute for Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology Amsterdam, The Netherlands
| | - Eric Eldering
- Department of Experimental Immunology, Amsterdam UMC Location University of Amsterdam, Meibergdreef, The Netherlands
- Lymphoma and Myeloma Center Amsterdam, LYMMCARE, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Cancer Immunology, Amsterdam, The Netherlands
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41
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Li H, Yuan L, Wang P, Sheng Y, Fu Z, Peng H. Clonal architecture and single-cell transcriptome landscape in Richter's syndrome. Br J Haematol 2023; 202:1055-1060. [PMID: 37401149 DOI: 10.1111/bjh.18952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Affiliation(s)
- Heng Li
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Lingli Yuan
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
| | - Peilong Wang
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Yue Sheng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
| | - Zheng Fu
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
- MegaRobo Technologies Co., Ltd, Suzhou, China
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Institute of Molecular Hematology, Central South University, Changsha, Hunan, China
- Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan, China
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42
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Maffeo B, Panuzzo C, Moraca A, Cilloni D. A Leukemic Target with a Thousand Faces: The Mitochondria. Int J Mol Sci 2023; 24:13069. [PMID: 37685874 PMCID: PMC10487524 DOI: 10.3390/ijms241713069] [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: 07/21/2023] [Revised: 08/16/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
In the era of personalized medicine greatly improved by molecular diagnosis and tailor-made therapies, the survival rate of acute myeloid leukemia (AML) at 5 years remains unfortunately low. Indeed, the high heterogeneity of AML clones with distinct metabolic and molecular profiles allows them to survive the chemotherapy-induced changes, thus leading to resistance, clonal evolution, and relapse. Moreover, leukemic stem cells (LSCs), the quiescent reservoir of residual disease, can persist for a long time and activate the recurrence of disease, supported by significant metabolic differences compared to AML blasts. All these points highlight the relevance to develop combination therapies, including metabolism inhibitors to improve treatment efficacy. In this review, we summarized the metabolic differences in AML blasts and LSCs, the molecular pathways related to mitochondria and metabolism are druggable and targeted in leukemia therapies, with a distinct interest for Venetoclax, which has revolutionized the therapeutic paradigms of several leukemia subtype, unfit for intensive treatment regimens.
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Affiliation(s)
| | - Cristina Panuzzo
- Department of Clinical and Biological Sciences, University of Turin, 10043 Orbassano, Italy; (B.M.); (A.M.); (D.C.)
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43
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García-Sanz R, García-Álvarez M, Medina A, Askari E, González-Calle V, Casanova M, de la Torre-Loizaga I, Escalante-Barrigón F, Bastos-Boente M, Bárez A, Vidaña-Bedera N, Alonso JM, Sarasquete ME, González M, Chillón MC, Alcoceba M, Jiménez C. Clonal architecture and evolutionary history of Waldenström's macroglobulinemia at the single-cell level. Dis Model Mech 2023; 16:dmm050227. [PMID: 37493341 PMCID: PMC10461465 DOI: 10.1242/dmm.050227] [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: 04/04/2023] [Accepted: 07/19/2023] [Indexed: 07/27/2023] Open
Abstract
To provide insight into the subclonal architecture and co-dependency patterns of the alterations in Waldenström's macroglobulinemia (WM), we performed single-cell mutational and protein profiling of eight patients. A custom panel was designed to screen for mutations and copy number alterations at the single-cell level in samples taken from patients at diagnosis (n=5) or at disease progression (n=3). Results showed that in asymptomatic WM at diagnosis, MYD88L265P was the predominant clonal alteration; other events, if present, were secondary and subclonal to MYD88L265P. In symptomatic WM, clonal diversity was more evident, uncovering combinations of alterations that synergized to promote clonal expansion and dominance. At disease progression, a dominant clone was observed, sometimes accompanied by other less complex minor clones, which could be consistent with a clonal selection process. Clonal diversity was also reduced, probably due to the effect of treatment. Finally, we combined protein expression with mutational analysis to map somatic genotype with the immunophenotype. Our findings provide a comprehensive view of the clonality of tumor populations in WM and how clonal complexity can evolve and impact disease progression.
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Affiliation(s)
- Ramón García-Sanz
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - María García-Álvarez
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Alejandro Medina
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Elham Askari
- Hematology Department, Fundación Jiménez Díaz, Centro de Investigación Biomédica en Red-Cáncer, Madrid 28040, Spain
| | - Verónica González-Calle
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - María Casanova
- Hematology Department, Hospital Costa del Sol, Marbella 29603, Spain
| | - Igor de la Torre-Loizaga
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | | | - Miguel Bastos-Boente
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Abelardo Bárez
- Hematology Department, Complejo Asistencial de Ávila, Ávila 05071, Spain
| | - Nerea Vidaña-Bedera
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - José María Alonso
- Hematology Department, Complejo Asistencial Universitario de Palencia, Palencia 34005, Spain
| | - María Eugenia Sarasquete
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Marcos González
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - María Carmen Chillón
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Miguel Alcoceba
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
| | - Cristina Jiménez
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), Salamanca 37007, Spain
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44
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Bland P, Saville H, Wai PT, Curnow L, Muirhead G, Nieminuszczy J, Ravindran N, John MB, Hedayat S, Barker HE, Wright J, Yu L, Mavrommati I, Read A, Peck B, Allen M, Gazinska P, Pemberton HN, Gulati A, Nash S, Noor F, Guppy N, Roxanis I, Pratt G, Oldreive C, Stankovic T, Barlow S, Kalirai H, Coupland SE, Broderick R, Alsafadi S, Houy A, Stern MH, Pettit S, Choudhary JS, Haider S, Niedzwiedz W, Lord CJ, Natrajan R. SF3B1 hotspot mutations confer sensitivity to PARP inhibition by eliciting a defective replication stress response. Nat Genet 2023; 55:1311-1323. [PMID: 37524790 PMCID: PMC10412459 DOI: 10.1038/s41588-023-01460-5] [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: 03/09/2023] [Accepted: 06/26/2023] [Indexed: 08/02/2023]
Abstract
SF3B1 hotspot mutations are associated with a poor prognosis in several tumor types and lead to global disruption of canonical splicing. Through synthetic lethal drug screens, we identify that SF3B1 mutant (SF3B1MUT) cells are selectively sensitive to poly (ADP-ribose) polymerase inhibitors (PARPi), independent of hotspot mutation and tumor site. SF3B1MUT cells display a defective response to PARPi-induced replication stress that occurs via downregulation of the cyclin-dependent kinase 2 interacting protein (CINP), leading to increased replication fork origin firing and loss of phosphorylated CHK1 (pCHK1; S317) induction. This results in subsequent failure to resolve DNA replication intermediates and G2/M cell cycle arrest. These defects are rescued through CINP overexpression, or further targeted by a combination of ataxia-telangiectasia mutated and PARP inhibition. In vivo, PARPi produce profound antitumor effects in multiple SF3B1MUT cancer models and eliminate distant metastases. These data provide the rationale for testing the clinical efficacy of PARPi in a biomarker-driven, homologous recombination proficient, patient population.
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Affiliation(s)
- Philip Bland
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Harry Saville
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Patty T Wai
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Lucinda Curnow
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Gareth Muirhead
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Nivedita Ravindran
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Marie Beatrix John
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Somaieh Hedayat
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Holly E Barker
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - James Wright
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Lu Yu
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Ioanna Mavrommati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Abigail Read
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Barrie Peck
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Translational Cancer Metabolism Team, Centre for Tumour Biology, Barts Cancer Institute, Cancer Research UK Centre of Excellence, Queen Mary University of London, Charterhouse Square, London, UK
| | - Mark Allen
- Biological Services Unit, The Institute of Cancer Research, London, UK
| | - Patrycja Gazinska
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Helen N Pemberton
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Aditi Gulati
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Sarah Nash
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Farzana Noor
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Naomi Guppy
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Ioannis Roxanis
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Guy Pratt
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Ceri Oldreive
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Tatjana Stankovic
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Samantha Barlow
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Helen Kalirai
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Sarah E Coupland
- Liverpool Ocular Oncology Research Group, Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Ronan Broderick
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Samar Alsafadi
- Inserm U830, PSL University, Institut Curie, Paris, France
| | - Alexandre Houy
- Inserm U830, PSL University, Institut Curie, Paris, France
| | | | - Stephen Pettit
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Jyoti S Choudhary
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Syed Haider
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Christopher J Lord
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- The Cancer Research UK Gene Function Laboratory, The Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
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Smits HJG, Ruiter LN, Breimer GE, Willems SM, Philippens MEP. Using Intratumor Heterogeneity of Immunohistochemistry Biomarkers to Classify Laryngeal and Hypopharyngeal Tumors Based on Histologic Features. Mod Pathol 2023; 36:100199. [PMID: 37116830 DOI: 10.1016/j.modpat.2023.100199] [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: 11/03/2022] [Revised: 03/23/2023] [Accepted: 04/17/2023] [Indexed: 04/30/2023]
Abstract
Haralick texture features are used to quantify the spatial distribution of signal intensities within an image. In this study, the heterogeneity of proliferation (Ki-67 expression) and immune cells (CD45 expression) within tumors was quantified and used to classify histologic characteristics of larynx and hypopharynx carcinomas. Of 21 laryngectomy specimens, 74 whole-mount tumor slides were scored on histologic characteristics. Ki-67 and CD45 immunohistochemistry was performed, and all sections were digitized. The tumor area was annotated in QuPath. Haralick features independent of the diaminobenzidine intensity were extracted from the isolated diaminobenzidine signal to quantify intratumor heterogeneity. Haralick features from both Ki-67 and CD45 were used as input for a principal component analysis. A linear support vector machine was fitted to the first 4 principal components for classification and validated with a leave-one-patient-out cross-validation method. Significant differences in individual Haralick features were found between cohesive and noncohesive tumors for CD45 (angular second motion: P =.03, inverse difference moment: P =.009, and entropy: P =.02) and between the larynx and hypopharynx tumors for both CD45 (angular second motion: P =.03, inverse difference moment: P =.007, and entropy: P =.005) and Ki-67 (correlation: P =.003). Therefore, these features were used for classification. The linear classifier resulted in a classification accuracy of 85% for site of origin and 81% for growth pattern. A leave-one-patient-out cross-validation resulted in an error rate of 0.27 and 0.35 for both classifiers, respectively. In conclusion, we show a method to quantify intratumor heterogeneity of immunohistochemistry biomarkers using Haralick features. This study also shows the feasibility of using these features to classify tumors by histologic characteristics. The classifiers created in this study are a proof of concept because more data are needed to create robust classifiers, but the method shows potential for automated tumor classification.
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Affiliation(s)
- Hilde J G Smits
- Department of Radiotherapy, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Lilian N Ruiter
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gerben E Breimer
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Stefan M Willems
- Department of Pathology and Medical Biology, University Medical Center Groningen, Groningen, the Netherlands
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Aptullahoglu E, Wallis JP, Marr H, Marshall S, Bown N, Willmore E, Lunec J. SF3B1 Mutations Are Associated with Resistance to Non-Genotoxic MDM2 Inhibition in Chronic Lymphocytic Leukemia. Int J Mol Sci 2023; 24:11335. [PMID: 37511096 PMCID: PMC10379212 DOI: 10.3390/ijms241411335] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a genetically and clinically heterogeneous malignancy affecting older individuals. There are a number of current treatment options for CLL, including monoclonal antibodies, targeted drugs, chemotherapy, and different combinations of these. However, for those patients who are intrinsically treatment resistant, or relapse following initial responses, novel targeted therapies are still needed. Targeting the mouse double-minute-2 human homolog (MDM2), a primary negative regulator of p53, is an appealing therapeutic strategy for non-genotoxic reactivation of p53, since the TP53 gene is in its wild-type state at diagnosis in approximately 90% of patients. Mutated SF3B1 and TP53 are both associated with more aggressive disease, resistance to therapies and poorer overall survival for CLL. In this study, we performed a screen for SF3B1 and TP53 mutations and tested RG7388 (idasanutlin), a second-generation MDM2 inhibitor, in a cohort of CLL primary patient samples. SF3B1 mutations were detected in 24 of 195 cases (12.3%) and found associated with poor overall survival (hazard ratio [HR] 2.12, p = 0.032) and high CD38 expression (median CD38 (%) 32 vs. 5; p = 0.0087). The novel striking finding of this study was an independent link between SF3B1 mutational status and poor response to RG7388. Overall, SF3B1 mutations in CLL patient samples were associated with resistance to treatment with RG7388 ex vivo, and patients with the wild type for both SF3B1 and TP53 are more likely to benefit from treatment with MDM2 inhibitors.
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Affiliation(s)
- Erhan Aptullahoglu
- Medical Faculty, Newcastle University Cancer Centre, Newcastle upon Tyne NE2 4AD, UK
| | - Jonathan P Wallis
- Department of Haematology, Freeman Hospital, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Helen Marr
- Department of Haematology, Freeman Hospital, Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Scott Marshall
- Department of Haematology, City Hospitals Sunderland NHS Trust, Sunderland SR4 7TP, UK
| | - Nick Bown
- Northern Genetics Service, Institute of Genetic Medicine, Newcastle upon Tyne NE1 4EP, UK
| | - Elaine Willmore
- Medical Faculty, Newcastle University Cancer Centre, Newcastle upon Tyne NE2 4AD, UK
| | - John Lunec
- Medical Faculty, Newcastle University Cancer Centre, Newcastle upon Tyne NE2 4AD, UK
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47
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Maher N, Mouhssine S, Matti BF, Alwan AF, Gaidano G. Treatment Refractoriness in Chronic Lymphocytic Leukemia: Old and New Molecular Biomarkers. Int J Mol Sci 2023; 24:10374. [PMID: 37373521 DOI: 10.3390/ijms241210374] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common leukemia in adults. Despite its indolent clinical course, therapy refractoriness and disease progression still represent an unmet clinical need. Before the advent of pathway inhibitors, chemoimmunotherapy (CIT) was the commonest option for CLL treatment and is still widely used in areas with limited access to pathway inhibitors. Several biomarkers of refractoriness to CIT have been highlighted, including the unmutated status of immunoglobulin heavy chain variable genes and genetic lesions of TP53, BIRC3 and NOTCH1. In order to overcome resistance to CIT, targeted pathway inhibitors have become the standard of care for the treatment of CLL, with practice-changing results obtained through the inhibitors of Bruton tyrosine kinase (BTK) and BCL2. However, several acquired genetic lesions causing resistance to covalent and noncovalent BTK inhibitors have been reported, including point mutations of both BTK (e.g., C481S and L528W) and PLCG2 (e.g., R665W). Multiple mechanisms are involved in resistance to the BCL2 inhibitor venetoclax, including point mutations that impair drug binding, the upregulation of BCL2-related anti-apoptotic family members, and microenvironmental alterations. Recently, immune checkpoint inhibitors and CAR-T cells have been tested for CLL treatment, obtaining conflicting results. Potential refractoriness biomarkers to immunotherapy were identified, including abnormal levels of circulating IL-10 and IL-6 and the reduced presence of CD27+CD45RO- CD8+ T cells.
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Affiliation(s)
- Nawar Maher
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, 28100 Novara, Italy
| | - Samir Mouhssine
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, 28100 Novara, Italy
| | - Bassam Francis Matti
- Department of Hematology and Bone Marrow Transplant, Hematology and Bone Marrow Transplant Center, Baghdad 00964, Iraq
| | - Alaa Fadhil Alwan
- Department of Clinical Hematology, The National Center of Hematology, Mustansiriyah University, Baghdad 10015, Iraq
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, 28100 Novara, Italy
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48
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Challakkara MF, Chhabra R. snoRNAs in hematopoiesis and blood malignancies: A comprehensive review. J Cell Physiol 2023; 238:1207-1225. [PMID: 37183323 DOI: 10.1002/jcp.31032] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/29/2023] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNA molecules of highly variable size, usually ranging from 60 to 150 nucleotides. They are classified into H/ACA box snoRNAs, C/D box snoRNAs, and scaRNAs. Their functional profile includes biogenesis of ribosomes, processing of rRNAs, 2'-O-methylation and pseudouridylation of RNAs, alternative splicing and processing of mRNAs and the generation of small RNA molecules like miRNA. The snoRNAs have been observed to have an important role in hematopoiesis and malignant hematopoietic conditions including leukemia, lymphoma, and multiple myeloma. Blood malignancies arise in immune system cells or the bone marrow due to chromosome abnormalities. It has been estimated that annually over 1.25 million cases of blood cancer occur worldwide. The snoRNAs often show a differential expression profile in blood malignancies. Recent reports associate the abnormal expression of snoRNAs with the inhibition of apoptosis, uncontrolled cell proliferation, angiogenesis, and metastasis. This implies that targeting snoRNAs could be a potential way to treat hematologic malignancies. In this review, we describe the various functions of snoRNAs, their role in hematopoiesis, and the consequences of their dysregulation in blood malignancies. We also evaluate the potential of the dysregulated snoRNAs as biomarkers and therapeutic targets for blood malignancies.
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Affiliation(s)
- Mohamed Fahad Challakkara
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Ravindresh Chhabra
- Department of Biochemistry, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab, India
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49
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Sarmah D, Meredith WO, Weber IK, Price MR, Birtwistle MR. Predicting anti-cancer drug combination responses with a temporal cell state network model. PLoS Comput Biol 2023; 19:e1011082. [PMID: 37126527 PMCID: PMC10174488 DOI: 10.1371/journal.pcbi.1011082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 05/11/2023] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
Cancer chemotherapy combines multiple drugs, but predicting the effects of drug combinations on cancer cell proliferation remains challenging, even for simple in vitro systems. We hypothesized that by combining knowledge of single drug dose responses and cell state transition network dynamics, we could predict how a population of cancer cells will respond to drug combinations. We tested this hypothesis here using three targeted inhibitors of different cell cycle states in two different cell lines in vitro. We formulated a Markov model to capture temporal cell state transitions between different cell cycle phases, with single drug data constraining how drug doses affect transition rates. This model was able to predict the landscape of all three different pairwise drug combinations across all dose ranges for both cell lines with no additional data. While further application to different cell lines, more drugs, additional cell state networks, and more complex co-culture or in vivo systems remain, this work demonstrates how currently available or attainable information could be sufficient for prediction of drug combination response for single cell lines in vitro.
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Affiliation(s)
- Deepraj Sarmah
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, United States of America
| | - Wesley O. Meredith
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, United States of America
| | - Ian K. Weber
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, United States of America
- The University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Madison R. Price
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, United States of America
- College of Pharmacy, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Marc R. Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina, United States of America
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
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50
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Ravi A, Hellmann MD, Arniella MB, Holton M, Freeman SS, Naranbhai V, Stewart C, Leshchiner I, Kim J, Akiyama Y, Griffin AT, Vokes NI, Sakhi M, Kamesan V, Rizvi H, Ricciuti B, Forde PM, Anagnostou V, Riess JW, Gibbons DL, Pennell NA, Velcheti V, Digumarthy SR, Mino-Kenudson M, Califano A, Heymach JV, Herbst RS, Brahmer JR, Schalper KA, Velculescu VE, Henick BS, Rizvi N, Jänne PA, Awad MM, Chow A, Greenbaum BD, Luksza M, Shaw AT, Wolchok J, Hacohen N, Getz G, Gainor JF. Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer. Nat Genet 2023; 55:807-819. [PMID: 37024582 PMCID: PMC10181943 DOI: 10.1038/s41588-023-01355-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 02/24/2023] [Indexed: 04/08/2023]
Abstract
Anti-PD-1/PD-L1 agents have transformed the treatment landscape of advanced non-small cell lung cancer (NSCLC). To expand our understanding of the molecular features underlying response to checkpoint inhibitors in NSCLC, we describe here the first joint analysis of the Stand Up To Cancer-Mark Foundation cohort, a resource of whole exome and/or RNA sequencing from 393 patients with NSCLC treated with anti-PD-(L)1 therapy, along with matched clinical response annotation. We identify a number of associations between molecular features and outcome, including (1) favorable (for example, ATM altered) and unfavorable (for example, TERT amplified) genomic subgroups, (2) a prominent association between expression of inducible components of the immunoproteasome and response and (3) a dedifferentiated tumor-intrinsic subtype with enhanced response to checkpoint blockade. Taken together, results from this cohort demonstrate the complexity of biological determinants underlying immunotherapy outcomes and reinforce the discovery potential of integrative analysis within large, well-curated, cancer-specific cohorts.
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Affiliation(s)
- Arvind Ravi
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Monica B Arniella
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Mark Holton
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Samuel S Freeman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Center for the AIDS Programme for Research in South Africa, Durban, South Africa
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | - Chip Stewart
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Ignaty Leshchiner
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | - Yo Akiyama
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Aaron T Griffin
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Natalie I Vokes
- Department of Thoracic and Head and Neck Oncology, MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Mustafa Sakhi
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | - Vashine Kamesan
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | - Hira Rizvi
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Patrick M Forde
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valsamo Anagnostou
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Don L Gibbons
- Department of Thoracic and Head and Neck Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Nathan A Pennell
- Department of Hematology and Medical Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Vamsidhar Velcheti
- Department of Hematology and Oncology, NYU Langone Health, New York, NY, USA
| | - Subba R Digumarthy
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Mari Mino-Kenudson
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Andrea Califano
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, New York, NY, USA
| | - John V Heymach
- Department of Thoracic and Head and Neck Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Roy S Herbst
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Julie R Brahmer
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kurt A Schalper
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Victor E Velculescu
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brian S Henick
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andrew Chow
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Marta Luksza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alice T Shaw
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | | | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA.
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