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Bátai B, Kiss L, Varga L, Nagy Á, Househam J, Baker AM, László T, Udvari A, Horváth R, Nagy T, Csomor J, Szakonyi J, Schneider T, Graham TA, Alpár D, Fitzgibbon J, Szepesi Á, Bödör C. Profiling of Copy Number Alterations Using Low-Coverage Whole-Genome Sequencing Informs Differential Diagnosis and Prognosis in Primary Cutaneous Follicle Center Lymphoma. Mod Pathol 2024; 37:100465. [PMID: 38460675 DOI: 10.1016/j.modpat.2024.100465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 02/21/2024] [Accepted: 03/01/2024] [Indexed: 03/11/2024]
Abstract
Primary cutaneous follicle center lymphoma (PCFCL) has an excellent prognosis using local treatment, whereas nodal follicular lymphoma (nFL), occasionally presenting with cutaneous spread, often requires systemic therapy. Distinction of the 2 diseases based on histopathology alone might be challenging. Copy number alterations (CNAs) have scarcely been explored on a genome-wide scale in PCFCL; however, they might serve as potential biomarkers during differential diagnosis and risk stratification. Low-coverage whole-genome sequencing is a robust, high-throughput method for genome-wide copy number profiling. In this study, we analyzed 28 PCFCL samples from 20 patients and compared the copy number profiles with a cohort of diagnostic samples of 64 nFL patients. Although the copy number profile of PCFCL was similar to that of nFL, PCFCL lacked amplifications of 18q, with the frequency peaking at 18q21.33 in nFL cases involving the BCL2 locus (PCFCL: 5.0% vs nFL: 31.3%, P = .018, Fisher exact test). Development of distant cutaneous spread was significantly associated with higher genomic instability including the proportion of genome altered (0.02 vs 0.13, P = .033) and number of CNAs (2 vs 9 P = .017), as well as the enrichment of 2p22.2-p15 amplification involving REL and XPO1 (6.3% vs 60.0%, P = .005), 3q23-q24 amplification (0.0% vs 50.0%, P = .004), 6q16.1-q23.3 deletion (6.3% vs 50.0%, P = .018), and 9p21.3 deletion covering CDKN2A and CDKN2B loci (0.0% vs 40.0%, P = .014, all Fisher exact test) in PCFCL. Analysis of sequential tumor samples in 2 cases harboring an unfavorable clinical course pointed to the acquisition of 2p amplification in the earliest common progenitor underlining its pivotal role in malignant transformation. By performing genome-wide copy number profiling on the largest patient cohort to date, we identified distinctive CNA alterations conceivably facilitating the differential diagnosis of PCFCL and secondary cutaneous involvement of nFL and potentially aiding the risk stratification of patients with PCFCL in the future.
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Affiliation(s)
- Bence Bátai
- HCEMM-SU Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary; Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Laura Kiss
- HCEMM-SU Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Luca Varga
- HCEMM-SU Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Ákos Nagy
- HCEMM-SU Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary; Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Jacob Househam
- Genomics and Evolutionary Dynamics Team, Centre for Evolution and Cancer, The Institute for Cancer Research, London, UK
| | - Ann-Marie Baker
- Genomics and Evolutionary Dynamics Team, Centre for Evolution and Cancer, The Institute for Cancer Research, London, UK
| | - Tamás László
- HCEMM-SU Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Anna Udvari
- HCEMM-SU Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Róbert Horváth
- HCEMM-SU Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Tibor Nagy
- HCEMM-SU Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary; Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Judit Csomor
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - József Szakonyi
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, Hungary
| | - Tamás Schneider
- Department of Hematology and Lymphoma, National Institute of Oncology, Budapest, Hungary
| | - Trevor A Graham
- Genomics and Evolutionary Dynamics Team, Centre for Evolution and Cancer, The Institute for Cancer Research, London, UK
| | - Donát Alpár
- HCEMM-SU Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Jude Fitzgibbon
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Ágota Szepesi
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary.
| | - Csaba Bödör
- HCEMM-SU Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary.
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Lakatos E, Gunasri V, Zapata L, Househam J, Heide T, Trahearn N, Swinyard O, Cisneros L, Lynn C, Mossner M, Kimberley C, Spiteri I, Cresswell GD, Llibre-Palomar G, Mitchison M, Maley CC, Jansen M, Rodriguez-Justo M, Bridgewater J, Baker AM, Sottoriva A, Graham TA. Epigenome and early selection determine the tumour-immune evolutionary trajectory of colorectal cancer. bioRxiv 2024:2024.02.12.579956. [PMID: 38405882 PMCID: PMC10888923 DOI: 10.1101/2024.02.12.579956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Immune system control is a major hurdle that cancer evolution must circumvent. The relative timing and evolutionary dynamics of subclones that have escaped immune control remain incompletely characterized, and how immune-mediated selection shapes the epigenome has received little attention. Here, we infer the genome- and epigenome-driven evolutionary dynamics of tumour-immune coevolution within primary colorectal cancers (CRCs). We utilise our existing CRC multi-region multi-omic dataset that we supplement with high-resolution spatially-resolved neoantigen sequencing data and highly multiplexed imaging of the tumour microenvironment (TME). Analysis of somatic chromatin accessibility alterations (SCAAs) reveals frequent somatic loss of accessibility at antigen presenting genes, and that SCAAs contribute to silencing of neoantigens. We observe that strong immune escape and exclusion occur at the outset of CRC formation, and that within tumours, including at the microscopic level of individual tumour glands, additional immune escape alterations have negligible consequences for the immunophenotype of cancer cells. Further minor immuno-editing occurs during local invasion and is associated with TME reorganisation, but that evolutionary bottleneck is relatively weak. Collectively, we show that immune evasion in CRC follows a "Big Bang" evolutionary pattern, whereby genetic, epigenetic and TME-driven immune evasion acquired by the time of transformation defines subsequent cancer-immune evolution.
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Affiliation(s)
- Eszter Lakatos
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Vinaya Gunasri
- UCL Cancer Institute, University College London, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Jacob Househam
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Timon Heide
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Nicholas Trahearn
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Ottilie Swinyard
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Luis Cisneros
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences Arizona State University, Tempe, USA
| | - Claire Lynn
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Maximilian Mossner
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Chris Kimberley
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - George D. Cresswell
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Gerard Llibre-Palomar
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Miriam Mitchison
- Histopathology Department, University College London Hospitals NHS Foundation Trust, London, UK
| | - Carlo C. Maley
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences Arizona State University, Tempe, USA
| | - Marnix Jansen
- UCL Cancer Institute, University College London, London, UK
| | | | | | - Ann-Marie Baker
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Trevor A. Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
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3
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Whiting FJH, Househam J, Baker AM, Sottoriva A, Graham TA. Phenotypic noise and plasticity in cancer evolution. Trends Cell Biol 2023:S0962-8924(23)00206-4. [PMID: 37968225 DOI: 10.1016/j.tcb.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 11/17/2023]
Abstract
Non-genetic alterations can produce changes in a cell's phenotype. In cancer, these phenomena can influence a cell's fitness by conferring access to heritable, beneficial phenotypes. Herein, we argue that current discussions of 'phenotypic plasticity' in cancer evolution ignore a salient feature of the original definition: namely, that it occurs in response to an environmental change. We suggest 'phenotypic noise' be used to distinguish non-genetic changes in phenotype that occur independently from the environment. We discuss the conceptual and methodological techniques used to identify these phenomena during cancer evolution. We propose that the distinction will guide efforts to define mechanisms of phenotype change, accelerate translational work to manipulate phenotypes through treatment, and, ultimately, improve patient outcomes.
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Affiliation(s)
| | - Jacob Househam
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Ann-Marie Baker
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
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Gatenbee CD, Baker AM, Prabhakaran S, Swinyard O, Slebos RJC, Mandal G, Mulholland E, Andor N, Marusyk A, Leedham S, Conejo-Garcia JR, Chung CH, Robertson-Tessi M, Graham TA, Anderson ARA. Virtual alignment of pathology image series for multi-gigapixel whole slide images. Nat Commun 2023; 14:4502. [PMID: 37495577 PMCID: PMC10372014 DOI: 10.1038/s41467-023-40218-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/13/2023] [Indexed: 07/28/2023] Open
Abstract
Interest in spatial omics is on the rise, but generation of highly multiplexed images remains challenging, due to cost, expertise, methodical constraints, and access to technology. An alternative approach is to register collections of whole slide images (WSI), generating spatially aligned datasets. WSI registration is a two-part problem, the first being the alignment itself and the second the application of transformations to huge multi-gigapixel images. To address both challenges, we developed Virtual Alignment of pathoLogy Image Series (VALIS), software which enables generation of highly multiplexed images by aligning any number of brightfield and/or immunofluorescent WSI, the results of which can be saved in the ome.tiff format. Benchmarking using publicly available datasets indicates VALIS provides state-of-the-art accuracy in WSI registration and 3D reconstruction. Leveraging existing open-source software tools, VALIS is written in Python, providing a free, fast, scalable, robust, and easy-to-use pipeline for registering multi-gigapixel WSI, facilitating downstream spatial analyses.
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Affiliation(s)
- Chandler D Gatenbee
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA.
| | - Ann-Marie Baker
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Sandhya Prabhakaran
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Ottilie Swinyard
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Robbert J C Slebos
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, CSB 6, Tampa, FL, USA
| | - Gunjan Mandal
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, MRC, Tampa, FL, 336122, USA
| | - Eoghan Mulholland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX37BN, UK
| | - Noemi Andor
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Andriy Marusyk
- Department of Cancer Physiology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, USA
| | - Simon Leedham
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX37BN, UK
| | - Jose R Conejo-Garcia
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, MRC, Tampa, FL, 336122, USA
| | - Christine H Chung
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, CSB 6, Tampa, FL, USA
| | - Mark Robertson-Tessi
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Alexander R A Anderson
- Department of Integrated Mathematical Oncology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA.
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5
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Hockings H, Lakatos E, Huang W, Mossner M, Khan MA, Metcalf S, Nicolini F, Smith K, Baker AM, Graham TA, Lockley M. Adaptive therapy achieves long-term control of chemotherapy resistance in high grade ovarian cancer. bioRxiv 2023:2023.07.21.549688. [PMID: 37546942 PMCID: PMC10401956 DOI: 10.1101/2023.07.21.549688] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Drug resistance results in poor outcomes for most patients with metastatic cancer. Adaptive Therapy (AT) proposes to address this by exploiting presumed fitness costs incurred by drug-resistant cells when drug is absent, and prescribing dose reductions to allow fitter, sensitive cells to re-grow and re-sensitise the tumour. However, empirical evidence for treatment-induced fitness change is lacking. We show that fitness costs in chemotherapy-resistant ovarian cancer cause selective decline and apoptosis of resistant populations in low-resource conditions. Moreover, carboplatin AT caused fluctuations in sensitive/resistant tumour population size in vitro and significantly extended survival of tumour-bearing mice. In sequential blood-derived cell-free DNA and tumour samples obtained longitudinally from ovarian cancer patients during treatment, we inferred resistant cancer cell population size through therapy and observed it correlated strongly with disease burden. These data have enabled us to launch a multicentre, phase 2 randomised controlled trial (ACTOv) to evaluate AT in ovarian cancer.
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Affiliation(s)
- Helen Hockings
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Eszter Lakatos
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Weini Huang
- School of Mathematical Sciences, Queen Mary University of London, London, UK
| | - Maximilian Mossner
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Mohammed Ateeb Khan
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Stephen Metcalf
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Francesco Nicolini
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Kane Smith
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Ann-Marie Baker
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Trevor A. Graham
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Michelle Lockley
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
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Barroux M, Househam J, Lakatos E, Ronel T, Baker AM, Salié H, Mossner M, Smith K, Kimberley C, Nowinski S, Berner A, Gunasri V, Jansen M, Caravagna G, Steiger K, Slotta-Huspenina J, Weichert W, Alberstmeier M, Chain B, Friess H, Bengsch B, Schmid R, Siveke J, Quante M, Graham T. Evolutionary and immune microenvironment dynamics during neoadjuvant treatment of oesophagael adenocarcinoma. Res Sq 2023:rs.3.rs-2738048. [PMID: 37090678 PMCID: PMC10120745 DOI: 10.21203/rs.3.rs-2738048/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Locally advanced oesophageal adenocarcinoma (EAC) remains difficult to treat because of common resistance to neoadjuvant therapy and high recurrence rates. The ecological and evolutionary dynamics responsible for treatment failure are incompletely understood. Here, we performed a comprehensive multi-omic analysis of samples collected from EAC patients in the MEMORI clinical trial, revealing major changes in gene expression profiles and immune microenvironment composition that did not appear to be driven by changes in clonal composition. Multi-region multi-timepoint whole exome (300x depth) and paired transcriptome sequencing was performed on 27 patients pre-, during and after neoadjuvant treatment. EAC showed major transcriptomic changes during treatment with upregulation of immune and stromal pathways and oncogenic pathways such as KRAS, Hedgehog and WNT. However, genetic data revealed that clonal sweeps were rare, suggesting that gene expression changes were not clonally driven. Additional longitudinal image mass cytometry was performed in a subset of 15 patients and T-cell receptor sequencing in 10 patients, revealing remodelling of the T-cell compartment during treatment and other shifts in microenvironment composition. The presence of immune escape mechanisms and a lack of clonal T-cell expansions were linked to poor clinical treatment response. This study identifies profound transcriptional changes during treatment with limited evidence that clonal replacement is the cause, suggesting phenotypic plasticity and immune dynamics as mechanisms for therapy resistance with pharmacological relevance.
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Affiliation(s)
- Melissa Barroux
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University of Munich
| | | | | | - Tahel Ronel
- Barts Cancer Institute, Queen Mary University of London
| | | | | | | | | | | | | | - Alison Berner
- Barts Cancer Institute, Queen Mary University of London
| | | | - Mamix Jansen
- UCL Cancer Institute: University College London Cancer Institute
| | | | - Katja Steiger
- Institute of Pathology, School of Medicine, Technical University of Munich
| | | | | | | | | | - Helmut Friess
- Department of Surgery, Klinikum rechts der Isar, Technical University of Munich
| | | | - Roland Schmid
- Medizinische Klinik und Poliklinik II, Klinikum rechts der Isar, Technische Universität München
| | - Jens Siveke
- German Cancer Consortium (DKTK) partner site Essen and Institute for Developmental Cancer Therapeutics (BIT), University Hospital Essen at the University Duisburg-Essen, Germany
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Baker AM, Berner A, Ronel T, Trahearn N, Bravi B, Bridgewater J, Chain B, Graham TA. Abstract 5934: Tracking T cell clonal dynamics across time and space in metastatic colorectal cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-5934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Here we tracked T cell dynamics in 15 metastatic colorectal cancer (mCRC) patients who had multiple resections (median: 3, range: 2-7) over a period of >7 years (median: 10 years, range: 7-16 years), using a novel T cell receptor sequencing (TCRseq) method. These samples had been previously characterized for DNA and methylation alterations and gene expression, enabling an integrated analysis to determine potential cellular and molecular drivers and consequences of immune dynamics. This multi-region, multi-timepoint dataset presents a unique opportunity to study the co-evolution of mCRC and the T cell response over time, across metastatic sites and in response to therapy.
T cell antigen specificity is defined by the TCR - a highly diverse sequence that enables tracking of specific T cell expansions across time and space. TCRseq quantifies the abundance of T cell clones and maps the dynamics of the TCR repertoire, however little is known about how these are altered in different metastatic sites, and post-chemotherapy. We developed and validated a new FFPE-compatible TCRseq method and sequenced 216 longitudinal samples representing the mCRC cohort described above.
We detected a median of 348 unique TCRs per sample (range 69-9700), and revealed high levels of intra-tumor spatial heterogeneity. No significant difference was detected in the number of T cell clones or the TCR clonality between primary tumors (n=40), lung metastases (n=30) and liver metastases (n=50). Furthermore, these were not significantly different between tumor regions (n=139) and surrounding stroma (n=38). We found that compared to chemo-naïve tumors (n=36), those that had been exposed to recent chemotherapy (n=41) had a significant increase in both the number of unique T cell clones and Simpson’s evenness, likely reflecting a broad T cell response to DNA-damaging agents. After more than a year had passed without chemotherapy (n=64) these returned to pre-chemotherapy levels.
In most cases the 10 most abundant TCR sequences in the primary tumor represented 15-40% of the total repertoire. We tracked these expanded clones through metastases, identifying ubiquitous clones which persisted across metastatic sites and through therapy. We found other expanded clones which were no longer present in metastases lesions, although some of these were found to expand again in later metastases. Finally, we examined correlations with tumor genomics, finding evidence in some patients that the TCR repertoire tracks closely with tumor clones even through metastasis and chemotherapy.
In summary, this project represents the first comprehensive analysis of T cell dynamics through colorectal cancer metastasis, highlighting the changing T cell landscape post-chemotherapy and correlating the TCR repertoire with tumor genomics. Our results could have important clinical implications for mCRC immunotherapy and the design of personalized T cell-based therapy.
Citation Format: Ann-Marie Baker, Alison Berner, Tahel Ronel, Nick Trahearn, Barbara Bravi, John Bridgewater, Benny Chain, Trevor A. Graham. Tracking T cell clonal dynamics across time and space in metastatic colorectal cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5934.
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Affiliation(s)
| | - Alison Berner
- 2Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Tahel Ronel
- 2Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Nick Trahearn
- 1The Institute of Cancer Research, Sutton, United Kingdom
| | | | | | - Benny Chain
- 4University College London, London, United Kingdom
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Haughey MJ, Bassolas A, Sousa S, Baker AM, Graham TA, Nicosia V, Huang W. First passage time analysis of spatial mutation patterns reveals sub-clonal evolutionary dynamics in colorectal cancer. PLoS Comput Biol 2023; 19:e1010952. [PMID: 36913406 PMCID: PMC10035892 DOI: 10.1371/journal.pcbi.1010952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 03/23/2023] [Accepted: 02/14/2023] [Indexed: 03/14/2023] Open
Abstract
The signature of early cancer dynamics on the spatial arrangement of tumour cells is poorly understood, and yet could encode information about how sub-clones grew within the expanding tumour. Novel methods of quantifying spatial tumour data at the cellular scale are required to link evolutionary dynamics to the resulting spatial architecture of the tumour. Here, we propose a framework using first passage times of random walks to quantify the complex spatial patterns of tumour cell population mixing. First, using a simple model of cell mixing we demonstrate how first passage time statistics can distinguish between different pattern structures. We then apply our method to simulated patterns of mutated and non-mutated tumour cell population mixing, generated using an agent-based model of expanding tumours, to explore how first passage times reflect mutant cell replicative advantage, time of emergence and strength of cell pushing. Finally, we explore applications to experimentally measured human colorectal cancer, and estimate parameters of early sub-clonal dynamics using our spatial computational model. We infer a wide range of sub-clonal dynamics, with mutant cell division rates varying between 1 and 4 times the rate of non-mutated cells across our sample set. Some mutated sub-clones emerged after as few as 100 non-mutant cell divisions, and others only after 50,000 divisions. The majority were consistent with boundary driven growth or short-range cell pushing. By analysing multiple sub-sampled regions in a small number of samples, we explore how the distribution of inferred dynamics could inform about the initial mutational event. Our results demonstrate the efficacy of first passage time analysis as a new methodology in spatial analysis of solid tumour tissue, and suggest that patterns of sub-clonal mixing can provide insights into early cancer dynamics.
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Affiliation(s)
- Magnus J. Haughey
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
| | - Aleix Bassolas
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
| | - Sandro Sousa
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
| | - Ann-Marie Baker
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Trevor A. Graham
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Vincenzo Nicosia
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
| | - Weini Huang
- School of Mathematical Sciences, Queen Mary University of London, London, United Kingdom
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9
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Heide T, Househam J, Cresswell GD, Spiteri I, Lynn C, Mossner M, Kimberley C, Fernandez-Mateos J, Chen B, Zapata L, James C, Barozzi I, Chkhaidze K, Nichol D, Gunasri V, Berner A, Schmidt M, Lakatos E, Baker AM, Costa H, Mitchinson M, Piazza R, Jansen M, Caravagna G, Ramazzotti D, Shibata D, Bridgewater J, Rodriguez-Justo M, Magnani L, Graham TA, Sottoriva A. The co-evolution of the genome and epigenome in colorectal cancer. Nature 2022; 611:733-743. [PMID: 36289335 PMCID: PMC9684080 DOI: 10.1038/s41586-022-05202-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/05/2022] [Indexed: 12/13/2022]
Abstract
Colorectal malignancies are a leading cause of cancer-related death1 and have undergone extensive genomic study2,3. However, DNA mutations alone do not fully explain malignant transformation4-7. Here we investigate the co-evolution of the genome and epigenome of colorectal tumours at single-clone resolution using spatial multi-omic profiling of individual glands. We collected 1,370 samples from 30 primary cancers and 8 concomitant adenomas and generated 1,207 chromatin accessibility profiles, 527 whole genomes and 297 whole transcriptomes. We found positive selection for DNA mutations in chromatin modifier genes and recurrent somatic chromatin accessibility alterations, including in regulatory regions of cancer driver genes that were otherwise devoid of genetic mutations. Genome-wide alterations in accessibility for transcription factor binding involved CTCF, downregulation of interferon and increased accessibility for SOX and HOX transcription factor families, suggesting the involvement of developmental genes during tumourigenesis. Somatic chromatin accessibility alterations were heritable and distinguished adenomas from cancers. Mutational signature analysis showed that the epigenome in turn influences the accumulation of DNA mutations. This study provides a map of genetic and epigenetic tumour heterogeneity, with fundamental implications for understanding colorectal cancer biology.
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Affiliation(s)
- Timon Heide
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Jacob Househam
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - George D Cresswell
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Claire Lynn
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Maximilian Mossner
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Chris Kimberley
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Bingjie Chen
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Chela James
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, UK
- Centre for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Ketevan Chkhaidze
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Daniel Nichol
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Vinaya Gunasri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Alison Berner
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Melissa Schmidt
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Eszter Lakatos
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Ann-Marie Baker
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Helena Costa
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Miriam Mitchinson
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Marnix Jansen
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Giulio Caravagna
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Mathematics and Geosciences, University of Triest, Triest, Italy
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Darryl Shibata
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | | | | | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Computational Biology Research Centre, Human Technopole, Milan, Italy.
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10
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Househam J, Heide T, Cresswell GD, Spiteri I, Kimberley C, Zapata L, Lynn C, James C, Mossner M, Fernandez-Mateos J, Vinceti A, Baker AM, Gabbutt C, Berner A, Schmidt M, Chen B, Lakatos E, Gunasri V, Nichol D, Costa H, Mitchinson M, Ramazzotti D, Werner B, Iorio F, Jansen M, Caravagna G, Barnes CP, Shibata D, Bridgewater J, Rodriguez-Justo M, Magnani L, Sottoriva A, Graham TA. Phenotypic plasticity and genetic control in colorectal cancer evolution. Nature 2022; 611:744-753. [PMID: 36289336 PMCID: PMC9684078 DOI: 10.1038/s41586-022-05311-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/01/2022] [Indexed: 12/12/2022]
Abstract
Genetic and epigenetic variation, together with transcriptional plasticity, contribute to intratumour heterogeneity1. The interplay of these biological processes and their respective contributions to tumour evolution remain unknown. Here we show that intratumour genetic ancestry only infrequently affects gene expression traits and subclonal evolution in colorectal cancer (CRC). Using spatially resolved paired whole-genome and transcriptome sequencing, we find that the majority of intratumour variation in gene expression is not strongly heritable but rather 'plastic'. Somatic expression quantitative trait loci analysis identified a number of putative genetic controls of expression by cis-acting coding and non-coding mutations, the majority of which were clonal within a tumour, alongside frequent structural alterations. Consistently, computational inference on the spatial patterning of tumour phylogenies finds that a considerable proportion of CRCs did not show evidence of subclonal selection, with only a subset of putative genetic drivers associated with subclone expansions. Spatial intermixing of clones is common, with some tumours growing exponentially and others only at the periphery. Together, our data suggest that most genetic intratumour variation in CRC has no major phenotypic consequence and that transcriptional plasticity is, instead, widespread within a tumour.
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Affiliation(s)
- Jacob Househam
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Timon Heide
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - George D Cresswell
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Chris Kimberley
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Claire Lynn
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Chela James
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Maximilian Mossner
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | | | - Ann-Marie Baker
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Calum Gabbutt
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Alison Berner
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Melissa Schmidt
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Bingjie Chen
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Eszter Lakatos
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Vinaya Gunasri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Daniel Nichol
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Helena Costa
- UCL Cancer Institute, University College London, London, UK
| | - Miriam Mitchinson
- Histopathology Department, University College London Hospitals NHS Foundation Trust, London, UK
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Benjamin Werner
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Francesco Iorio
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Marnix Jansen
- UCL Cancer Institute, University College London, London, UK
| | - Giulio Caravagna
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Darryl Shibata
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | | | | | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Computational Biology Research Centre, Human Technopole, Milan, Italy.
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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11
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Berner AM, Gabbutt C, Nowinski S, Househam J, Trahearn N, Cresswell GD, Nadhamuni VS, Kimberley C, Fassan M, Baker AM, Sottoriva A, Thirlwell C, Bridgewater J, Graham T. Abstract A045: Multiple roles for plasticity in metastasis and therapy resistance in long-term survivors of metastatic colorectal cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.evodyn22-a045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Long-term survivors (LS) of metastatic colorectal cancer (mCRC) who experience multiple recurrences with resectable oligometastatic disease provide an opportunity to explore co-evolution of the tumor and immune microenvironment. We profiled 16 LS of mCRC with a median follow-up of 9.3 years and median of 3 biopsies/resections per patient (range 2-7). We performed multi-omic profiling of 56 primary and 176 metastatic samples from formalin-fixed paraffin-embedded tissue using low pass whole genome sequencing, 3’ RNA sequencing and DNA methylation arrays. A machine learning cell classifier was used to quantify immune cell and fibroblast infiltration from hematoxylin and eosin staining. Copy number profiling showed that the fraction of genome altered remained relatively stable across time and tissue type but that already-altered segments underwent progressive fragmentation. Inter-timepoint divergence of copy number alterations was significantly higher than intra-timepoint divergence, and intra-timepoint divergence was lower for liver and lung metastases than for primary tumors. Chemotherapy treatment did not significantly affect either divergence type. Differential expression and gene set enrichment analysis (GSEA) revealed common pathways dysregulated in metastases compared to primaries, including reductions in E2F (important in G1/S checkpoint) and G2M checkpoint, suggestive of the onset of senescence in metastases. Tumors underwent progressive hypomethylation over time and analysis of genes with concordant changes in promoter methylation and expression revealed dysregulation in pathways related to endocytosis, cell adhesion and migration. This suggests an important role for phenotypic plasticity in driving the metastatic phenotype. There were transient increases in the proportion of macrophages, lymphocytes and neutrophils in tumors that had undergone neoadjuvant chemotherapy in the 6 months prior to resection and slight increases in M1 macrophage activity (by GSEA) in tumors that were previously therapy naïve. There were concordant transient increases in pathways associated with immune response (MYC V1 and MTORC1), as well as xenobiotic metabolism. The latter is a known mechanism of drug resistance to both the platinum- and fluoropyridine-based therapies used in CRC. There were also more sustained increases post-chemotherapy in inflammatory and immune pathways associated with the adaptive immune response and tissue injury and repair. These findings were corroborated by concordant changes in promoter methylation. These data suggest that there is a threshold level of aneuploidy required to facilitate CRC metastasis but the migratory phenotype and adaptation to the metastatic niche are driven by plasticity. Chemotherapy induces differing short-term and long-term anti-tumor immune responses in the local microenvironment. We see evidence that mCRCs are able to mount plastic pro-survival mechanisms in response to chemotherapy.
Citation Format: Alison May Berner, Calum Gabbutt, Salpie Nowinski, Jacob Househam, Nick Trahearn, George D. Cresswell, Vinaya Srirangam Nadhamuni, Christopher Kimberley, Matteo Fassan, Ann-Marie Baker, Andrea Sottoriva, Christina Thirlwell, John Bridgewater, Trevor Graham. Multiple roles for plasticity in metastasis and therapy resistance in long-term survivors of metastatic colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A045.
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Affiliation(s)
- Alison May Berner
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom,
| | - Calum Gabbutt
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom,
| | - Salpie Nowinski
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom,
| | - Jacob Househam
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom,
| | - Nick Trahearn
- Institute of Cancer Research, London, United Kingdom,
| | | | | | | | | | - Ann-Marie Baker
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom,
| | | | | | | | - Trevor Graham
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom,
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12
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Gatenbee CD, Baker AM, Schenck RO, Strobl M, West J, Robertson-Tessi M, Graham TA, Anderson AR. Abstract PR008: Immunosuppressive niche engineering at the onset of human colorectal cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.evodyn22-pr008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The evolutionary dynamics of tumor initiation remain undetermined, and the interplay between neoplastic cells and the immune system is hypothesized to be critical in transformation. Colorectal cancer (CRC) presents a unique opportunity to study the transition to malignancy as pre-cancers (adenomas) and early-stage cancers are frequently detected and surgically removed. Here, we demonstrate a key role for the immune response in tumor initiation by studying tumor-immune eco-evolutionary dynamics from pre-cancer to carcinoma using a computational model, ecological analysis of digital pathology data, and multi-region exome sequencing and neoantigen prediction in a total of 62 patient samples. Modelling indicates there are several potential routes to malignancy, each of which uniquely sculpts tumor ecology and intra-tumor antigenic heterogeneity (aITH). In patient samples, the immune microenvironment was characterized using the spatial distribution of 17 markers across registered whole-slide images, as well as patterns of intra-lesion aITH measured using multi-region exome sequencing and neoantigen prediction. The patient data were best described by a model where adenomas that become immunogenic early on do not progress to CRC because they are under immune control; progression therefore proceeds in adenomas with low immunogenicity. In these tumors, immune suppression is initially low, but gradually an immunosuppressive niche that is depleted in CD8+ cytotoxic T cells expands. There was little evidence for immune blockade (PD-L1 expression) in tumor initiation or progression. These results suggest that re-engineering the immunosuppressive niche may prove to be an effective immunotherapy in CRC.
Citation Format: Chandler D. Gatenbee, Ann-Marie Baker, Ryan O. Schenck, Maximilian Strobl, Jeffrey West, Mark Robertson-Tessi, Trevor A. Graham, Alexander R.A. Anderson. Immunosuppressive niche engineering at the onset of human colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr PR008.
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13
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Gatenbee CD, Baker AM, Schenck RO, Strobl M, West J, Robertson-Tessi M, Graham TA, Anderson AR. Abstract B033: Immunosuppressive niche engineering at the onset of human colorectal cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.evodyn22-b033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
This abstract is being presented as a short talk in the scientific program. A full abstract is available in the Proffered Abstracts section (PR0081) of the Conference Proceedings.
Citation Format: Chandler D. Gatenbee, Ann-Marie Baker, Ryan O. Schenck, Maximilian Strobl, Jeffrey West, Mark Robertson-Tessi, Trevor A. Graham, Alexander R.A. Anderson. Immunosuppressive niche engineering at the onset of human colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr B033.
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14
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Gatenbee CD, Baker AM, Schenck RO, Strobl M, West J, Neves MP, Hasan SY, Lakatos E, Martinez P, Cross WCH, Jansen M, Rodriguez-Justo M, Whelan CJ, Sottoriva A, Leedham S, Robertson-Tessi M, Graham TA, Anderson ARA. Immunosuppressive niche engineering at the onset of human colorectal cancer. Nat Commun 2022; 13:1798. [PMID: 35379804 PMCID: PMC8979971 DOI: 10.1038/s41467-022-29027-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/24/2022] [Indexed: 12/13/2022] Open
Abstract
The evolutionary dynamics of tumor initiation remain undetermined, and the interplay between neoplastic cells and the immune system is hypothesized to be critical in transformation. Colorectal cancer (CRC) presents a unique opportunity to study the transition to malignancy as pre-cancers (adenomas) and early-stage cancers are frequently resected. Here, we examine tumor-immune eco-evolutionary dynamics from pre-cancer to carcinoma using a computational model, ecological analysis of digital pathology data, and neoantigen prediction in 62 patient samples. Modeling predicted recruitment of immunosuppressive cells would be the most common driver of transformation. As predicted, ecological analysis reveals that progressed adenomas co-localized with immunosuppressive cells and cytokines, while benign adenomas co-localized with a mixed immune response. Carcinomas converge to a common immune "cold" ecology, relaxing selection against immunogenicity and high neoantigen burdens, with little evidence for PD-L1 overexpression driving tumor initiation. These findings suggest re-engineering the immunosuppressive niche may prove an effective immunotherapy in CRC.
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Affiliation(s)
- Chandler D Gatenbee
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA.
| | - Ann-Marie Baker
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Ryan O Schenck
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX37BN, UK
| | - Maximilian Strobl
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Jeffrey West
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Margarida P Neves
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Sara Yakub Hasan
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Eszter Lakatos
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Pierre Martinez
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
- Lyon Cancer Institute, Lyon, France
| | - William C H Cross
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Marnix Jansen
- Department of Pathology, University College London Hospital, London, UK
| | | | - Christopher J Whelan
- Cancer Physiology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
- Department of Biological Sciences, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL, 60607, USA
| | - Andrea Sottoriva
- Center for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Simon Leedham
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX37BN, UK
| | - Mark Robertson-Tessi
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Alexander R A Anderson
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA.
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15
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Schmidt M, Hackett RJ, Baker AM, McDonald SAC, Quante M, Graham TA. Evolutionary dynamics in Barrett oesophagus: implications for surveillance, risk stratification and therapy. Nat Rev Gastroenterol Hepatol 2022; 19:95-111. [PMID: 34728819 DOI: 10.1038/s41575-021-00531-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 12/13/2022]
Abstract
Cancer development is a dynamic evolutionary process characterized by marked intratumoural heterogeneity at the genetic, epigenetic and phenotypic levels. Barrett oesophagus, the pre-malignant condition to oesophageal adenocarcinoma (EAC), is an exemplary system to longitudinally study the evolution of malignancy. Evidence has emerged of Barrett oesophagus lesions pre-programmed for progression to EAC many years before clinical detection, indicating a considerable window for therapeutic intervention. In this Review, we explore the mechanisms underlying clonal expansion and contraction that establish the Barrett oesophagus clonal mosaicism over time and space and discuss intrinsic genotypic and extrinsic environmental drivers that direct the evolutionary trajectory of Barrett oesophagus towards a malignant phenotype. We propose that understanding and exploiting the evolutionary dynamics of Barrett oesophagus will identify novel therapeutic targets, improve prognostic tools and offer the opportunity for personalized surveillance programmes geared to prevent progression to EAC.
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Affiliation(s)
- Melissa Schmidt
- Evolution and Cancer Laboratory, 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
- Department of Medicine II, Klinikum rechts der Isar, Technical University Munich (TUM), München, Germany
| | - Richard J Hackett
- Clonal Dynamics in Epithelia Group; 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
| | - Ann-Marie Baker
- Evolution and Cancer Laboratory, 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
| | - Stuart A C McDonald
- Clonal Dynamics in Epithelia Group; 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
| | - Michael Quante
- Department of Medicine II, Klinikum rechts der Isar, Technical University Munich (TUM), München, Germany
- Department of Medicine II, Universitaetsklinikum Freiburg, Freiburg, Germany
| | - Trevor A Graham
- Evolution and Cancer Laboratory, 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.
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16
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Yalchin M, Baker AM, Graham TA, Hart A. Predicting Colorectal Cancer Occurrence in IBD. Cancers (Basel) 2021; 13:2908. [PMID: 34200768 PMCID: PMC8230430 DOI: 10.3390/cancers13122908] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022] Open
Abstract
Patients with colonic inflammatory bowel disease (IBD) are at an increased risk of developing colorectal cancer (CRC), and are therefore enrolled into a surveillance programme aimed at detecting dysplasia or early cancer. Current surveillance programmes are guided by clinical, endoscopic or histological predictors of colitis-associated CRC (CA-CRC). We have seen great progress in our understanding of these predictors of disease progression, and advances in endoscopic technique and management, along with improved medical care, has been mirrored by the falling incidence of CA-CRC over the last 50 years. However, more could be done to improve our molecular understanding of CA-CRC progression and enable better risk stratification for patients with IBD. This review summarises the known risk factors associated with CA-CRC and explores the molecular landscape that has the potential to complement and optimise the existing IBD surveillance programme.
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Affiliation(s)
- Mehmet Yalchin
- Inflammatory Bowel Disease Department, St. Mark’s Hospital, Watford R.d., Harrow HA1 3UJ, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse S.q., London EC1M 6BQ, UK; (A.-M.B.); (T.A.G.)
| | - Ann-Marie Baker
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse S.q., London EC1M 6BQ, UK; (A.-M.B.); (T.A.G.)
| | - Trevor A. Graham
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse S.q., London EC1M 6BQ, UK; (A.-M.B.); (T.A.G.)
| | - Ailsa Hart
- Inflammatory Bowel Disease Department, St. Mark’s Hospital, Watford R.d., Harrow HA1 3UJ, UK
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17
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Abstract
BACKGROUND Latent tuberculosis infection (LTBI) is an asymptomatic condition that may progress to active tuberculosis (TB), sometimes decades after exposure. Most people with active TB in Australia have not had recent contact and have been unaware of their risk. Tests for LTBI are available, allowing for diagnosis and preventive therapy to avoid active disease. OBJECTIVE The aim of this article is to review current approaches to the diagnosis and management of LTBI, with particular focus on the Australian general practice setting. Groups at elevated risk of having LTBI and progressing to active disease are outlined. Recent research into the prevalence and distribution of LTBI in Australia is reviewed, and Australian guidelines for testing and treatment are summarised. DISCUSSION LTBI occurs in an estimated 5% of all Australian residents. However, this is a particular issue for those born in TB-endemic countries. Approximately 17% of all overseas-born Australian residents, but only 0.4% of Australian-born residents, have LTBI. Appropriate diagnosis and management is an important long-term health promotion activity, and many people with LTBI can be managed safely and effectively in Australian general practice settings.
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Affiliation(s)
- Justin Denholm
- BMed, MBioethics, MPHTM, PhD, FRACP, Medical Director, Victorian Tuberculosis Program, Vic
| | - Ann-Marie Baker
- RN, Grad Dip Community Health, Clinical Nurse Consultant, Victorian Tuberculosis Program, Vic
| | - Mark Timlin
- MBBS, MPH, MBE, General Practitioner, Member Refugee Health Special Interest Group, Vic
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18
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Tempest N, Jansen M, Baker AM, Hill CJ, Hale M, Magee D, Treanor D, Wright NA, Hapangama DK. Histological 3D reconstruction and in vivo lineage tracing of the human endometrium. J Pathol 2020; 251:440-451. [PMID: 32476144 DOI: 10.1002/path.5478] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/30/2020] [Accepted: 05/20/2020] [Indexed: 12/13/2022]
Abstract
Regular menstrual shedding and repair of the endometrial functionalis is unique to humans and higher-order primates. The current consensus postulates endometrial glands to have a single-tubular architecture, where multi-potential stem cells reside in the blind-ending glandular-bases. Utilising fixed samples from patients, we have studied the three-dimensional (3D) micro-architecture of the human endometrium. We demonstrate that some non-branching, single, vertical functionalis glands originate from a complex horizontally interconnecting network of basalis glands. The existence of a multipotent endometrial epithelial stem cell capable of regenerating the entire complement of glandular lineages was demonstrated by in vivo lineage tracing, using naturally occurring somatic mitochondrial DNA mutations as clonal markers. Vertical tracking of mutated clones showed that at least one stem-cell population resides in the basalis glands. These novel findings provide insight into the efficient and scar-less regenerative potential of the human endometrium. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Nicola Tempest
- Liverpool Women's Hospital NHS Foundation Trust, member of the Liverpool Health partnership, Liverpool, UK
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, member of the Liverpool Health partnership, Liverpool, UK
| | - Marnix Jansen
- UCL Cancer Institute, University College London, London, UK
| | - Ann-Marie Baker
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Christopher J Hill
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, member of the Liverpool Health partnership, Liverpool, UK
| | - Mike Hale
- Pathology and Tumour Biology, University of Leeds, Leeds, UK
| | - Derek Magee
- School of Computing, University of Leeds, Leeds, UK
- Heterogenius Ltd, Leeds, UK
| | - Darren Treanor
- Pathology and Tumour Biology, University of Leeds, Leeds, UK
- Pathology department, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- Pathology department, Linköping University, Linköping, Sweden
| | - Nicholas A Wright
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Dharani K Hapangama
- Liverpool Women's Hospital NHS Foundation Trust, member of the Liverpool Health partnership, Liverpool, UK
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, member of the Liverpool Health partnership, Liverpool, UK
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19
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Demircioglu F, Wang J, Candido J, Costa ASH, Casado P, de Luxan Delgado B, Reynolds LE, Gomez-Escudero J, Newport E, Rajeeve V, Baker AM, Roy-Luzarraga M, Graham TA, Foster J, Wang Y, Campbell JJ, Singh R, Zhang P, Schall TJ, Balkwill FR, Sosabowski J, Cutillas PR, Frezza C, Sancho P, Hodivala-Dilke K. Cancer associated fibroblast FAK regulates malignant cell metabolism. Nat Commun 2020; 11:1290. [PMID: 32157087 PMCID: PMC7064590 DOI: 10.1038/s41467-020-15104-3] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/18/2020] [Indexed: 12/19/2022] Open
Abstract
Emerging evidence suggests that cancer cell metabolism can be regulated by cancer-associated fibroblasts (CAFs), but the mechanisms are poorly defined. Here we show that CAFs regulate malignant cell metabolism through pathways under the control of FAK. In breast and pancreatic cancer patients we find that low FAK expression, specifically in the stromal compartment, predicts reduced overall survival. In mice, depletion of FAK in a subpopulation of CAFs regulates paracrine signals that increase malignant cell glycolysis and tumour growth. Proteomic and phosphoproteomic analysis in our mouse model identifies metabolic alterations which are reflected at the transcriptomic level in patients with low stromal FAK. Mechanistically we demonstrate that FAK-depletion in CAFs increases chemokine production, which via CCR1/CCR2 on cancer cells, activate protein kinase A, leading to enhanced malignant cell glycolysis. Our data uncover mechanisms whereby stromal fibroblasts regulate cancer cell metabolism independent of genetic mutations in cancer cells.
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Affiliation(s)
- Fevzi Demircioglu
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Jun Wang
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Juliana Candido
- Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Ana S H Costa
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Pedro Casado
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Beatriz de Luxan Delgado
- Centre for Stem Cells in Cancer and Ageing, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Louise E Reynolds
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Jesus Gomez-Escudero
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Emma Newport
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Vinothini Rajeeve
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Ann-Marie Baker
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Marina Roy-Luzarraga
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Trevor A Graham
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Julie Foster
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Yu Wang
- ChemoCentryx Inc., 850 Maude Ave, Mountain View, CA94043, USA
| | | | - Rajinder Singh
- ChemoCentryx Inc., 850 Maude Ave, Mountain View, CA94043, USA
| | - Penglie Zhang
- ChemoCentryx Inc., 850 Maude Ave, Mountain View, CA94043, USA
| | - Thomas J Schall
- ChemoCentryx Inc., 850 Maude Ave, Mountain View, CA94043, USA
| | - Frances R Balkwill
- Centre for Cancer and Inflammation, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Jane Sosabowski
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Pedro R Cutillas
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Patricia Sancho
- Centre for Stem Cells in Cancer and Ageing, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
- IIS Aragon, Hospital Universitario Miguel Servet, Zaragoza, 50009, Spain
| | - Kairbaan Hodivala-Dilke
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK.
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20
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Saunderson EA, Baker AM, Williams M, Curtius K, Jones JL, Graham TA, Ficz G. A novel use of random priming-based single-strand library preparation for whole genome sequencing of formalin-fixed paraffin-embedded tissue samples. NAR Genom Bioinform 2020; 2:lqz017. [PMID: 31867579 PMCID: PMC6919645 DOI: 10.1093/nargab/lqz017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/18/2019] [Accepted: 12/06/2019] [Indexed: 01/23/2023] Open
Abstract
The desire to analyse limited amounts of biological material, historic samples and rare cell populations has collectively driven the need for efficient methods for whole genome sequencing (WGS) of limited amounts of poor quality DNA. Most protocols are designed to recover double-stranded DNA (dsDNA) by ligating sequencing adaptors to dsDNA with or without subsequent polymerase chain reaction amplification of the library. While this is sufficient for many applications, limited DNA requires a method that can recover both single-stranded DNA (ssDNA) and dsDNA. Here, we present a WGS library preparation method, called 'degraded DNA adaptor tagging' (DDAT), adapted from a protocol designed for whole genome bisulfite sequencing. This method uses two rounds of random primer extension to recover both ssDNA and dsDNA. We show that by using DDAT we can generate WGS data from formalin-fixed paraffin-embedded (FFPE) samples using as little as 2 ng of highly degraded DNA input. Furthermore, DDAT WGS data quality was higher for all FFPE samples tested compared to data produced using a standard WGS library preparation method. Therefore, the DDAT method has potential to unlock WGS data from DNA previously considered impossible to sequence, broadening opportunities to understand the role of genetics in health and disease.
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Affiliation(s)
- Emily A Saunderson
- Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Ann-Marie Baker
- Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Marc Williams
- Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Kit Curtius
- Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - J Louise Jones
- Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Trevor A Graham
- Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Gabriella Ficz
- Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
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21
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Baker AM, Gabbutt C, Williams MJ, Cereser B, Jawad N, Rodriguez-Justo M, Jansen M, Barnes CP, Simons BD, McDonald SA, Graham TA, Wright NA. Crypt fusion as a homeostatic mechanism in the human colon. Gut 2019; 68:1986-1993. [PMID: 30872394 PMCID: PMC6839731 DOI: 10.1136/gutjnl-2018-317540] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/24/2019] [Accepted: 02/22/2019] [Indexed: 12/19/2022]
Abstract
OBJECTIVE The crypt population in the human intestine is dynamic: crypts can divide to produce two new daughter crypts through a process termed crypt fission, but whether this is balanced by a second process to remove crypts, as recently shown in mouse models, is uncertain. We examined whether crypt fusion (the process of two neighbouring crypts fusing into a single daughter crypt) occurs in the human colon. DESIGN We used somatic alterations in the gene cytochrome c oxidase (CCO) as lineage tracing markers to assess the clonality of bifurcating colon crypts (n=309 bifurcating crypts from 13 patients). Mathematical modelling was used to determine whether the existence of crypt fusion can explain the experimental data, and how the process of fusion influences the rate of crypt fission. RESULTS In 55% (21/38) of bifurcating crypts in which clonality could be assessed, we observed perfect segregation of clonal lineages to the respective crypt arms. Mathematical modelling showed that this frequency of perfect segregation could not be explained by fission alone (p<10-20). With the rates of fission and fusion taken to be approximately equal, we then used the distribution of CCO-deficient patch size to estimate the rate of crypt fission, finding a value of around 0.011 divisions/crypt/year. CONCLUSIONS We have provided the evidence that human colonic crypts undergo fusion, a potential homeostatic process to regulate total crypt number. The existence of crypt fusion in the human colon adds a new facet to our understanding of the highly dynamic and plastic phenotype of the colonic epithelium.
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Affiliation(s)
- Ann-Marie Baker
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Calum Gabbutt
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Marc J Williams
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Biancastella Cereser
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Noor Jawad
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Marnix Jansen
- Histopathology, University College London, London, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Benjamin D Simons
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Stuart Ac McDonald
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Trevor A Graham
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Nicholas A Wright
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
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22
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Cox TR, Bird D, Baker AM, Barker HE, Ho MWY, Lang G, Erler JT. Editor's Note: LOX-Mediated Collagen Cross-linking Is Responsible for Fibrosis-Enhanced Metastasis. Cancer Res 2019; 79:5124. [PMID: 31575632 DOI: 10.1158/0008-5472.can-19-2419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Chkhaidze K, Heide T, Werner B, Williams MJ, Huang W, Caravagna G, Baker AM, Graham TA, Sottoriva A. Abstract 4232: Spatially constrained tumor growth affects the patterns of clonal selection and neutral drift in cancer genomic data. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Quantification of the effect of spatial tumor sampling on the patterns of mutations detected in next-generation sequencing data is largely lacking. Here we use a spatial stochastic cellular automaton model of tumor growth that accounts for somatic mutations, selection, drift and spatial constrains, to simulate multi-region sequencing data derived from spatial sampling of a neoplasm. We show that the spatial structure of a solid cancer has a major impact on the detection of clonal selection and genetic drift from bulk sequencing data and single-cell sequencing data. Our results indicate that spatial constrains can introduce significant sampling biases when performing multi- region bulk sampling and that such bias becomes a major confounding factor for the measurement of the evolutionary dynamics of human tumors. We present a statistical inference framework that takes into account the spatial effects of a growing tumor and allows inferring the evolutionary dynamics from patient genomic data. Our analysis shows that measuring cancer evolution using next-generation sequencing while accounting for the numerous confounding factors requires a mechanistic model-based approach that captures the sources of noise in the data.
Citation Format: Kate Chkhaidze, Timon Heide, Benjamin Werner, Marc J. Williams, Weini Huang, Giulio Caravagna, Ann-Marie Baker, Trevor A. Graham, Andrea Sottoriva. Spatially constrained tumor growth affects the patterns of clonal selection and neutral drift in cancer genomic data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4232.
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Affiliation(s)
| | - Timon Heide
- 1Institute of Cancer Research, London, United Kingdom
| | | | - Marc J. Williams
- 2Barts Cancer Institute, Queen Mary University, London, United Kingdom
| | - Weini Huang
- 2Barts Cancer Institute, Queen Mary University, London, United Kingdom
| | | | - Ann-Marie Baker
- 2Barts Cancer Institute, Queen Mary University, London, United Kingdom
| | - Trevor A. Graham
- 2Barts Cancer Institute, Queen Mary University, London, United Kingdom
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24
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Baker AM, Graham TA. Concurrent in situ analysis of point mutations and immune infiltrate in FFPE cancers. Methods Enzymol 2019; 636:287-297. [PMID: 32178822 DOI: 10.1016/bs.mie.2019.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Existing methodology for analysis of genetic heterogeneity generally involves digestion of the tumor tissue, followed by bulk DNA extraction or single cell preparation. Such methods destroy the tissue morphology, and therefore opportunities to analyze tumor heterogeneity and clonal architecture within the native spatial context are lost. Thus, there is a clear need for the development of generally applicable methods of in situ mutation detection (ISMD), in which tumor cells can be genetically analyzed in the context of their cellular microenvironment, including immune infiltrate. Furthermore, protocols in which ISMD can be combined with immunohistochemical analysis are highly sought after, as the combination of these two techniques enables insight not only into genetic heterogeneity, but is also permissive of genotype-phenotype analysis, whilst preserving tissue morphology and spatial context. Here we describe a novel method for in situ point mutation detection using commercially available BaseScope reagents, followed by immunohistochemical detection of immune infiltrate on the same tissue section.
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Affiliation(s)
- Ann-Marie Baker
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom.
| | - Trevor A Graham
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom.
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25
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Baker AM, Cross W, Curtius K, Al Bakir I, Choi CHR, Davis HL, Temko D, Biswas S, Martinez P, Williams MJ, Lindsay JO, Feakins R, Vega R, Hayes SJ, Tomlinson IPM, McDonald SAC, Moorghen M, Silver A, East JE, Wright NA, Wang LM, Rodriguez-Justo M, Jansen M, Hart AL, Leedham SJ, Graham TA. Evolutionary history of human colitis-associated colorectal cancer. Gut 2019; 68:985-995. [PMID: 29991641 PMCID: PMC6580738 DOI: 10.1136/gutjnl-2018-316191] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE IBD confers an increased lifetime risk of developing colorectal cancer (CRC), and colitis-associated CRC (CA-CRC) is molecularly distinct from sporadic CRC (S-CRC). Here we have dissected the evolutionary history of CA-CRC using multiregion sequencing. DESIGN Exome sequencing was performed on fresh-frozen multiple regions of carcinoma, adjacent non-cancerous mucosa and blood from 12 patients with CA-CRC (n=55 exomes), and key variants were validated with orthogonal methods. Genome-wide copy number profiling was performed using single nucleotide polymorphism arrays and low-pass whole genome sequencing on archival non-dysplastic mucosa (n=9), low-grade dysplasia (LGD; n=30), high-grade dysplasia (HGD; n=13), mixed LGD/HGD (n=7) and CA-CRC (n=19). Phylogenetic trees were reconstructed, and evolutionary analysis used to reveal the temporal sequence of events leading to CA-CRC. RESULTS 10/12 tumours were microsatellite stable with a median mutation burden of 3.0 single nucleotide alterations (SNA) per Mb, ~20% higher than S-CRC (2.5 SNAs/Mb), and consistent with elevated ageing-associated mutational processes. Non-dysplastic mucosa had considerable mutation burden (median 47 SNAs), including mutations shared with the neighbouring CA-CRC, indicating a precancer mutational field. CA-CRCs were often near triploid (40%) or near tetraploid (20%) and phylogenetic analysis revealed that copy number alterations (CNAs) began to accrue in non-dysplastic bowel, but the LGD/HGD transition often involved a punctuated 'catastrophic' CNA increase. CONCLUSIONS Evolutionary genomic analysis revealed precancer clones bearing extensive SNAs and CNAs, with progression to cancer involving a dramatic accrual of CNAs at HGD. Detection of the cancerised field is an encouraging prospect for surveillance, but punctuated evolution may limit the window for early detection.
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Affiliation(s)
- Ann-Marie Baker
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - William Cross
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Kit Curtius
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ibrahim Al Bakir
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Inflammatory Bowel Disease Unit, St Mark’s Hospital, London, UK
| | - Chang-Ho Ryan Choi
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Inflammatory Bowel Disease Unit, St Mark’s Hospital, London, UK
| | | | - Daniel Temko
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Department of Computer Science, University College London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Sujata Biswas
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Pierre Martinez
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Marc J Williams
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
- Department of Cell and Developmental Biology, University College London, London, UK
| | - James O Lindsay
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Roger Feakins
- Department of Histopathology, The Royal London Hospital, London, UK
| | - Roser Vega
- Department of Gastroenterology, University College London Hospital, London, UK
| | - Stephen J Hayes
- Department of Histopathology, Salford Royal NHS Foundation Trust, University of Manchester, Manchester, UK
| | - Ian P M Tomlinson
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Stuart A C McDonald
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Morgan Moorghen
- Inflammatory Bowel Disease Unit, St Mark’s Hospital, London, UK
| | - Andrew Silver
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - James E East
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Nicholas A Wright
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Lai Mun Wang
- Cellular Pathology, John Radcliffe Hospital, Oxford, UK
| | | | - Marnix Jansen
- Department of Histopathology, University College London Hospital, London, UK
| | - Ailsa L Hart
- Inflammatory Bowel Disease Unit, St Mark’s Hospital, London, UK
| | - Simon J Leedham
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Trevor A Graham
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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Baker AM, Cereser B, Melton S, Fletcher AG, Rodriguez-Justo M, Tadrous PJ, Humphries A, Elia G, McDonald SAC, Wright NA, Simons BD, Jansen M, Graham TA. Quantification of Crypt and Stem Cell Evolution in the Normal and Neoplastic Human Colon. Cell Rep 2019; 27:2524. [PMID: 31116993 PMCID: PMC6533202 DOI: 10.1016/j.celrep.2019.05.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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27
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Tempest N, Baker AM, Wright NA, Hapangama DK. Does human endometrial LGR5 gene expression suggest the existence of another hormonally regulated epithelial stem cell niche? Hum Reprod 2019; 33:1052-1062. [PMID: 29648645 PMCID: PMC5972618 DOI: 10.1093/humrep/dey083] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 03/27/2018] [Indexed: 12/21/2022] Open
Abstract
STUDY QUESTION Is human endometrial leucine-rich repeat-containing G-protein-coupled receptor 5 (LGR5) gene expression limited to the postulated epithelial stem cell niche, stratum basalis glands, and is it hormonally regulated? SUMMARY ANSWER LGR5 expressing cells are not limited to the postulated stem cell niche but LGR5 expression is hormonally regulated. WHAT IS KNOWN ALREADY The human endometrium is a highly regenerative tissue; however, endometrial epithelial stem cell markers are yet to be confirmed. LGR5 is a marker of stem cells in various epithelia. STUDY DESIGN, SIZE, DURATION The study was conducted at a University Research Institute. Endometrial samples from 50 healthy women undergoing benign gynaecological surgery with no endometrial pathology at the Liverpool Women's hospital were included and analysed in the following six sub-categories; proliferative, secretory phases of menstrual cycle, postmenopausal, those using oral and local progestagens and samples for in vitro explant culture. PARTICIPANTS/MATERIALS, SETTING, METHODS In this study, we used the gold standard method, in situ hybridisation (ISH) along with qPCR and a systems biology approach to study the location of LGR5 gene expression in full thickness human endometrium and Fallopian tubes. The progesterone regulation of endometrial LGR5 was examined in vivo and in short-term cultured endometrial tissue explants in vitro. LGR5 expression was correlated with epithelial proliferation (Ki67), and expression of previously reported epithelia progenitor markers (SOX9 and SSEA-1) immunohistochemistry (IHC). MAIN RESULTS AND THE ROLE OF CHANCE LGR5 gene expression was significantly higher in the endometrial luminal epithelium than in all other epithelial compartments in the healthy human endometrium, including the endometrial stratum basalis (P < 0.05). The strongest SSEA-1 and SOX9 staining was observed in the stratum basalis glands, but the general trend of SOX9 and SSEA-1 expression followed the same cyclical pattern of expression as LGR5. Stratum functionalis epithelial Ki67-LI and LGR5 expression levels correlated significantly (r = 0.74, P = 0.01), however, they did not correlate in luminal and stratum basalis epithelium (r = 0.5 and 0.13, respectively). Endometrial LGR5 demonstrates a dynamic spatiotemporal expression pattern, suggesting hormonal regulation. Oral and local progestogens significantly reduced endometrial LGR5 mRNA levels compared with women not on hormonal treatment (P < 0.01). Our data were in agreement with in silico analysis of published endometrial microarrays. LARGE SCALE DATA We did not generate our own large scale data but interrogated publically available large scale data sets. LIMITATIONS, REASONS FOR CAUTION In the absence of reliable antibodies for human LGR5 protein and validated lineage markers for the various epithelial populations that potentially exist within the endometrium, our study does not formally characterise or examine the functional ability of the resident LGR5+ cells as multipotent. WIDER IMPLICATIONS OF THE FINDINGS These data will facilitate future lineage tracing studies in the human endometrial epithelium; to identify the location of stem cells and further complement the in vitro functional studies, to confirm if the LGR5 expressing epithelial cells indeed represent the epithelial stem cell population. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by funding from the Wellbeing of Women project grant (RTF510) and Cancer Research UK (A14895). None of the authors have any conflicts of interest to disclose.
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Affiliation(s)
- N Tempest
- Liverpool Women's Hospital NHS Foundation Trust, Liverpool L8 7SS, UK.,Department of Women's and Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool L8 7SS, UK
| | - A M Baker
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - N A Wright
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - D K Hapangama
- Liverpool Women's Hospital NHS Foundation Trust, Liverpool L8 7SS, UK.,Department of Women's and Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool L8 7SS, UK
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28
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Cross W, Kovac M, Mustonen V, Temko D, Davis H, Baker AM, Biswas S, Arnold R, Chegwidden L, Gatenbee C, Anderson AR, Koelzer VH, Martinez P, Jiang X, Domingo E, Woodcock DJ, Feng Y, Kovacova M, Maughan T, Jansen M, Rodriguez-Justo M, Ashraf S, Guy R, Cunningham C, East JE, Wedge DC, Wang LM, Palles C, Heinimann K, Sottoriva A, Leedham SJ, Graham TA, Tomlinson IPM. The evolutionary landscape of colorectal tumorigenesis. Nat Ecol Evol 2018; 2:1661-1672. [PMID: 30177804 PMCID: PMC6152905 DOI: 10.1038/s41559-018-0642-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/12/2018] [Indexed: 01/19/2023]
Abstract
The evolutionary events that cause colorectal adenomas (benign) to progress to carcinomas (malignant) remain largely undetermined. Using multi-region genome and exome sequencing of 24 benign and malignant colorectal tumours, we investigate the evolutionary fitness landscape occupied by these neoplasms. Unlike carcinomas, advanced adenomas frequently harbour sub-clonal driver mutations-considered to be functionally important in the carcinogenic process-that have not swept to fixation, and have relatively high genetic heterogeneity. Carcinomas are distinguished from adenomas by widespread aneusomies that are usually clonal and often accrue in a 'punctuated' fashion. We conclude that adenomas evolve across an undulating fitness landscape, whereas carcinomas occupy a sharper fitness peak, probably owing to stabilizing selection.
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Affiliation(s)
- William Cross
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Michal Kovac
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Bone Tumour Reference Center at the Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland
| | - Daniel Temko
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- CoMPLEX, Department of Computer Science, University College London, London, UK
| | - Hayley Davis
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ann-Marie Baker
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sujata Biswas
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Roland Arnold
- Cancer Bioinfomatics Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Laura Chegwidden
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Chandler Gatenbee
- Integrated Mathematical Oncology Department, Moffitt Comprehensive Cancer Centre, Tampa, FL, USA
| | - Alexander R Anderson
- Integrated Mathematical Oncology Department, Moffitt Comprehensive Cancer Centre, Tampa, FL, USA
| | - Viktor H Koelzer
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Pierre Martinez
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Xiaowei Jiang
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Enric Domingo
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Yun Feng
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Monika Kovacova
- Institute of Mathematics and Physics, Faculty of Mechanical Engineering, Slovak University of Technology in Bratislava, Bratislava, Slovakia
| | - Tim Maughan
- Department of Oncology, University of Oxford, Oxford, UK
| | - Marnix Jansen
- Department of Research Pathology, Cancer Institute, University College London, London, UK
| | - Manuel Rodriguez-Justo
- Department of Research Pathology, Cancer Institute, University College London, London, UK
| | - Shazad Ashraf
- Department of Surgery, University Hospitals Birmingham, Birmingham, UK
| | - Richard Guy
- Department of Colorectal Surgery, Cancer Centre, Churchill Hospital, Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Christopher Cunningham
- Department of Colorectal Surgery, Cancer Centre, Churchill Hospital, Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - James E East
- Translational Gastroenterology Unit, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - David C Wedge
- Big Data Institute, University of Oxford, Oxford, UK
| | - Lai Mun Wang
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Claire Palles
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Karl Heinimann
- Institute for Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Simon J Leedham
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Ian P M Tomlinson
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
- Department of Histopathology, University Hospitals Birmingham, Birmingham, UK.
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29
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Fearon AE, Carter EP, Clayton NS, Wilkes EH, Baker AM, Kapitonova E, Bakhouche BA, Tanner Y, Wang J, Gadaleta E, Chelala C, Moore KM, Marshall JF, Chupin J, Schmid P, Jones JL, Lockley M, Cutillas PR, Grose RP. PHLDA1 Mediates Drug Resistance in Receptor Tyrosine Kinase-Driven Cancer. Cell Rep 2018; 22:2469-2481. [PMID: 29490281 PMCID: PMC5848852 DOI: 10.1016/j.celrep.2018.02.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 11/09/2017] [Accepted: 02/06/2018] [Indexed: 11/09/2022] Open
Abstract
Development of resistance causes failure of drugs targeting receptor tyrosine kinase (RTK) networks and represents a critical challenge for precision medicine. Here, we show that PHLDA1 downregulation is critical to acquisition and maintenance of drug resistance in RTK-driven cancer. Using fibroblast growth factor receptor (FGFR) inhibition in endometrial cancer cells, we identify an Akt-driven compensatory mechanism underpinned by downregulation of PHLDA1. We demonstrate broad clinical relevance of our findings, showing that PHLDA1 downregulation also occurs in response to RTK-targeted therapy in breast and renal cancer patients, as well as following trastuzumab treatment in HER2+ breast cancer cells. Crucially, knockdown of PHLDA1 alone was sufficient to confer de novo resistance to RTK inhibitors and induction of PHLDA1 expression re-sensitized drug-resistant cancer cells to targeted therapies, identifying PHLDA1 as a biomarker for drug response and highlighting the potential of PHLDA1 reactivation as a means of circumventing drug resistance.
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Affiliation(s)
- Abbie E Fearon
- Centre for Tumour Biology, Barts Cancer Institute-a CRUK Centre of Excellence, Queen Mary University of London, London EC1M 6BQ, UK
| | - Edward P Carter
- Centre for Tumour Biology, Barts Cancer Institute-a CRUK Centre of Excellence, Queen Mary University of London, London EC1M 6BQ, UK
| | - Natasha S Clayton
- Centre for Tumour Biology, Barts Cancer Institute-a CRUK Centre of Excellence, Queen Mary University of London, London EC1M 6BQ, UK
| | - Edmund H Wilkes
- Integrative Cell Signalling and Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, London EC1M 6BQ, UK
| | - Ann-Marie Baker
- Centre for Tumour Biology, Barts Cancer Institute-a CRUK Centre of Excellence, Queen Mary University of London, London EC1M 6BQ, UK
| | - Ekaterina Kapitonova
- Centre for Tumour Biology, Barts Cancer Institute-a CRUK Centre of Excellence, Queen Mary University of London, London EC1M 6BQ, UK
| | - Bakhouche A Bakhouche
- Centre for Tumour Biology, Barts Cancer Institute-a CRUK Centre of Excellence, Queen Mary University of London, London EC1M 6BQ, UK
| | - Yasmine Tanner
- Centre for Tumour Biology, Barts Cancer Institute-a CRUK Centre of Excellence, Queen Mary University of London, London EC1M 6BQ, UK
| | - Jun Wang
- Centre for Molecular Oncology, Barts Cancer Institute, London EC1M 6BQ, UK
| | - Emanuela Gadaleta
- Centre for Molecular Oncology, Barts Cancer Institute, London EC1M 6BQ, UK
| | - Claude Chelala
- Centre for Molecular Oncology, Barts Cancer Institute, London EC1M 6BQ, UK
| | - Kate M Moore
- Centre for Tumour Biology, Barts Cancer Institute-a CRUK Centre of Excellence, Queen Mary University of London, London EC1M 6BQ, UK
| | - John F Marshall
- Centre for Tumour Biology, Barts Cancer Institute-a CRUK Centre of Excellence, Queen Mary University of London, London EC1M 6BQ, UK
| | - Juliette Chupin
- Centre for Experimental Cancer Medicine, Barts Cancer Institute, London EC1M 6BQ, UK
| | - Peter Schmid
- Centre for Experimental Cancer Medicine, Barts Cancer Institute, London EC1M 6BQ, UK
| | - J Louise Jones
- Centre for Tumour Biology, Barts Cancer Institute-a CRUK Centre of Excellence, Queen Mary University of London, London EC1M 6BQ, UK
| | - Michelle Lockley
- Centre for Molecular Oncology, Barts Cancer Institute, London EC1M 6BQ, UK
| | - Pedro R Cutillas
- Integrative Cell Signalling and Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, London EC1M 6BQ, UK
| | - Richard P Grose
- Centre for Tumour Biology, Barts Cancer Institute-a CRUK Centre of Excellence, Queen Mary University of London, London EC1M 6BQ, UK.
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30
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Baker AM, Huang W, Wang XMM, Jansen M, Ma XJ, Kim J, Anderson CM, Wu X, Pan L, Su N, Luo Y, Domingo E, Heide T, Sottoriva A, Lewis A, Beggs AD, Wright NA, Rodriguez-Justo M, Park E, Tomlinson I, Graham TA. Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution. Nat Commun 2017; 8:1998. [PMID: 29222441 PMCID: PMC5722928 DOI: 10.1038/s41467-017-02295-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 11/17/2017] [Indexed: 01/15/2023] Open
Abstract
Intra-tumor heterogeneity (ITH) is a major underlying cause of therapy resistance and disease recurrence, and is a read-out of tumor growth. Current genetic ITH analysis methods do not preserve spatial context and may not detect rare subclones. Here, we address these shortfalls by developing and validating BaseScope-a novel mutation-specific RNA in situ hybridization assay. We target common point mutations in the BRAF, KRAS and PIK3CA oncogenes in archival colorectal cancer samples to precisely map the spatial and morphological context of mutant subclones. Computational modeling suggests that subclones must arise sufficiently early, or carry a considerable fitness advantage, to form large or spatially disparate subclones. Examples of putative treatment-resistant cells isolated in small topographical areas are observed. The BaseScope assay represents a significant technical advance for in situ mutation detection that provides new insight into tumor evolution, and could have ramifications for selecting patients for treatment.
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Affiliation(s)
- Ann-Marie Baker
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.
| | - Weini Huang
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | | | - Marnix Jansen
- Department of Histopathology, University College London Hospital, London, WC1E 6JJ, UK
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Xiao-Jun Ma
- Advanced Cell Diagnostics, Newark, CA, 94560, USA
| | - Jeffrey Kim
- Advanced Cell Diagnostics, Newark, CA, 94560, USA
| | | | - Xingyong Wu
- Advanced Cell Diagnostics, Newark, CA, 94560, USA
| | - Liuliu Pan
- Advanced Cell Diagnostics, Newark, CA, 94560, USA
| | - Nan Su
- Advanced Cell Diagnostics, Newark, CA, 94560, USA
| | - Yuling Luo
- Advanced Cell Diagnostics, Newark, CA, 94560, USA
| | - Enric Domingo
- Department of Oncology, Old Road Campus Research Building, University of Oxford, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Timon Heide
- Centre for Evolution and Cancer, The Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, 15 Cotswold Road, Sutton, London, SM2 5NG, UK
| | - Annabelle Lewis
- Cancer Gene Regulation Laboratory, Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Andrew D Beggs
- Surgical Research Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Nicholas A Wright
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | | | - Emily Park
- Advanced Cell Diagnostics, Newark, CA, 94560, USA
| | - Ian Tomlinson
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Trevor A Graham
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.
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31
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Sundaresan S, Meininger CA, Kang AJ, Photenhauer AL, Hayes MM, Sahoo N, Grembecka J, Cierpicki T, Ding L, Giordano TJ, Else T, Madrigal DJ, Low MJ, Campbell F, Baker AM, Xu H, Wright NA, Merchant JL. Gastrin Induces Nuclear Export and Proteasome Degradation of Menin in Enteric Glial Cells. Gastroenterology 2017; 153:1555-1567.e15. [PMID: 28859856 PMCID: PMC5705278 DOI: 10.1053/j.gastro.2017.08.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 07/31/2017] [Accepted: 08/13/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND & AIMS The multiple endocrine neoplasia, type 1 (MEN1) locus encodes the nuclear protein and tumor suppressor menin. MEN1 mutations frequently cause neuroendocrine tumors such as gastrinomas, characterized by their predominant duodenal location and local metastasis at time of diagnosis. Diffuse gastrin cell hyperplasia precedes the appearance of MEN1 gastrinomas, which develop within submucosal Brunner's glands. We investigated how menin regulates expression of the gastrin gene and induces generation of submucosal gastrin-expressing cell hyperplasia. METHODS Primary enteric glial cultures were generated from the VillinCre:Men1FL/FL:Sst-/- mice or C57BL/6 mice (controls), with or without inhibition of gastric acid by omeprazole. Primary enteric glial cells from C57BL/6 mice were incubated with gastrin and separated into nuclear and cytoplasmic fractions. Cells were incubated with forskolin and H89 to activate or inhibit protein kinase A (a family of enzymes whose activity depends on cellular levels of cyclic AMP). Gastrin was measured in blood, tissue, and cell cultures using an ELISA. Immunoprecipitation with menin or ubiquitin was used to demonstrate post-translational modification of menin. Primary glial cells were incubated with leptomycin b and MG132 to block nuclear export and proteasome activity, respectively. We obtained human duodenal, lymph node, and pancreatic gastrinoma samples, collected from patients who underwent surgery from 1996 through 2007 in the United States or the United Kingdom. RESULTS Enteric glial cells that stained positive for glial fibrillary acidic protein (GFAP+) expressed gastrin de novo through a mechanism that required PKA. Gastrin-induced nuclear export of menin via cholecystokinin B receptor (CCKBR)-mediated activation of PKA. Once exported from the nucleus, menin was ubiquitinated and degraded by the proteasome. GFAP and other markers of enteric glial cells (eg, p75 and S100B), colocalized with gastrin in human duodenal gastrinomas. CONCLUSIONS MEN1-associated gastrinomas, which develop in the submucosa, might arise from enteric glial cells through hormone-dependent PKA signaling. This pathway disrupts nuclear menin function, leading to hypergastrinemia and associated sequelae.
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Affiliation(s)
- Sinju Sundaresan
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan
| | - Cameron A Meininger
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan
| | - Anthony J Kang
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan
| | - Amanda L Photenhauer
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan
| | - Michael M Hayes
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan
| | - Nirakar Sahoo
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Lin Ding
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan
| | - Thomas J Giordano
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Tobias Else
- Division of Metabolism Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan
| | - David J Madrigal
- Endocrine Oncology Program, University of Michigan, Ann Arbor, Michigan
| | - Malcolm J Low
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Fiona Campbell
- Department of Pathology, Royal Liverpool University Hospital, Liverpool, United Kingdom
| | - Ann-Marie Baker
- Center for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Haoxing Xu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Nicholas A Wright
- Center for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Juanita L Merchant
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan; Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan.
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32
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Cioffi M, Trabulo SM, Vallespinos M, Raj D, Kheir TB, Lin ML, Begum J, Baker AM, Amgheib A, Saif J, Perez M, Soriano J, Desco M, Gomez-Gaviro MV, Cusso L, Megias D, Aicher A, Heeschen C. The miR-25-93-106b cluster regulates tumor metastasis and immune evasion via modulation of CXCL12 and PD-L1. Oncotarget 2017; 8:21609-21625. [PMID: 28423491 PMCID: PMC5400610 DOI: 10.18632/oncotarget.15450] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 01/10/2017] [Indexed: 12/14/2022] Open
Abstract
The stromal microenvironment controls response to injury and inflammation, and is also an important determinant of cancer cell behavior. However, our understanding of its modulation by miRNA (miR) and their respective targets is still sparse. Here, we identified the miR-25-93-106b cluster and two new target genes as critical drivers for metastasis and immune evasion of cancer cells. Using miR-25-93-106b knockout mice or antagomiRs, we demonstrated regulation of the production of the chemoattractant CXCL12 controlling bone marrow metastasis. Moreover, we identified the immune checkpoint PD-L1 (CD274) as a novel miR-93/106b target playing a central role in diminishing tumor immunity. Eventually, upregulation of miR-93 and miR-106b via miR-mimics or treatment with an epigenetic reader domain (BET) inhibitor resulted in diminished expression of CXCL12 and PD-L1. These data suggest a potential new therapeutic rationale for use of BET inhibitors for dual targeting of cancers with strong immunosuppressive and metastatic phenotypes.
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Affiliation(s)
- Michele Cioffi
- Stem Cells & Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Sara M Trabulo
- Stem Cells & Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Stem Cells in Cancer & Ageing, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Mireia Vallespinos
- Stem Cells & Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Deepak Raj
- Stem Cells in Cancer & Ageing, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Tony Bou Kheir
- Stem Cells in Cancer & Ageing, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Meng-Lay Lin
- Stem Cells in Cancer & Ageing, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Julfa Begum
- Stem Cells in Cancer & Ageing, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Ann-Marie Baker
- Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Ala Amgheib
- Stem Cells in Cancer & Ageing, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Jaimy Saif
- School of Clinical Sciences, University of Bristol, Bristol, UK
| | - Manuel Perez
- Confocal Microscopy Unit, Centro Nacional de Investigaciones Oncológicas, Spain
| | - Joaquim Soriano
- Confocal Microscopy Unit, Centro Nacional de Investigaciones Oncológicas, Spain
| | - Manuel Desco
- Departamento de Ingenieria Biomedica e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Leganés, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain
| | - Maria Victoria Gomez-Gaviro
- Departamento de Ingenieria Biomedica e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Leganés, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain
| | - Lorena Cusso
- Departamento de Ingenieria Biomedica e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Leganés, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain
| | - Diego Megias
- Confocal Microscopy Unit, Centro Nacional de Investigaciones Oncológicas, Spain
| | - Alexandra Aicher
- Stem Cells & Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Stem Cells in Cancer & Ageing, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Christopher Heeschen
- Stem Cells & Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Stem Cells in Cancer & Ageing, Barts Cancer Institute, Queen Mary University of London, London, UK
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Moyo N, Trauer J, Trevan P, Baker AM, Musemburi J, McGrath K, Nolan A, McIntyre E, Hulls J, Denholm JT. Tuberculosis screening in an aged care residential facility in a low-incidence setting. Commun Dis Intell (2018) 2017; 41:E209-E211. [PMID: 29720065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Tuberculosis (TB) remains a disease of high morbidity in Australia, with implications for both public health and the individual. Cost analyses is relevant for programmatic evaluation of TB. There is minimal published TB cost data in the Australian setting. Patients with drug sensitive active pulmonary TB (DS-PTB) and latent TB (LTBI) were enrolled in a single tertiary referral centre to evaluate healthcare provider costs. The median cost of treating drug susceptible pulmonary TB in this case series was 11,538 AUD. Approximately 50% of total costs is derived from inpatient hospitalisation bed days. In comparison, the average cost of managing latent TB was 582 AUD per completed course. We find the median provider cost of our DS-PTB treatment group comparable to costs from other regions globally with similar economic profiles. A program designed to detect and treat LTBI to prevent subsequent disease may be cost effective in appropriately selected patients and warrants further study.
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Affiliation(s)
- Nompilo Moyo
- Victorian Tuberculosis Program, Melbourne Health, Melbourne, Australia
| | - James Trauer
- Victorian Tuberculosis Program, Melbourne Health, Melbourne, Australia
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Peter Trevan
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Ann-Marie Baker
- Victorian Tuberculosis Program, Melbourne Health, Melbourne, Australia
| | - Joseph Musemburi
- Victorian Tuberculosis Program, Melbourne Health, Melbourne, Australia
| | - Kerry McGrath
- Victorian Tuberculosis Program, Melbourne Health, Melbourne, Australia
| | - Aine Nolan
- Victorian Tuberculosis Program, Melbourne Health, Melbourne, Australia
| | - Eamon McIntyre
- Victorian Tuberculosis Program, Melbourne Health, Melbourne, Australia
| | - Jane Hulls
- Victorian Tuberculosis Program, Melbourne Health, Melbourne, Australia
| | - Justin T Denholm
- Victorian Tuberculosis Program, Melbourne Health, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia
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Baker AM, Wang M, Ma XJ, Anderson C, Huang W, Domingo E, Lewis A, Bridgewater J, Jansen M, Wright NA, Rodriguez-Justo M, Park E, Tomlinson I, Graham TA. Abstract 3953: Visualization of treatment resistant subclones in colorectal cancer by mutation specific RNA in situ hybridization. Tumour Biol 2017. [DOI: 10.1158/1538-7445.am2017-3953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Affiliation(s)
- Ann-Marie Baker
- a Barts Cancer Institute, Barts and the London School of Medicine and Dentistry , Queen Mary University of London , London , UK
| | - Trevor A Graham
- a Barts Cancer Institute, Barts and the London School of Medicine and Dentistry , Queen Mary University of London , London , UK
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Martinez P, Timmer MR, Lau CT, Calpe S, Sancho-Serra MDC, Straub D, Baker AM, Meijer SL, Kate FJWT, Mallant-Hent RC, Naber AHJ, van Oijen AHAM, Baak LC, Scholten P, Böhmer CJM, Fockens P, Bergman JJGHM, Maley CC, Graham TA, Krishnadath KK. Dynamic clonal equilibrium and predetermined cancer risk in Barrett's oesophagus. Nat Commun 2016; 7:12158. [PMID: 27538785 PMCID: PMC4992167 DOI: 10.1038/ncomms12158] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 06/06/2016] [Indexed: 12/24/2022] Open
Abstract
Surveillance of Barrett's oesophagus allows us to study the evolutionary dynamics of a human neoplasm over time. Here we use multicolour fluorescence in situ hybridization on brush cytology specimens, from two time points with a median interval of 37 months in 195 non-dysplastic Barrett's patients, and a third time point in a subset of 90 patients at a median interval of 36 months, to study clonal evolution at single-cell resolution. Baseline genetic diversity predicts progression and remains in a stable dynamic equilibrium over time. Clonal expansions are rare, being detected once every 36.8 patient years, and growing at an average rate of 1.58 cm(2) (95% CI: 0.09-4.06) per year, often involving the p16 locus. This suggests a lack of strong clonal selection in Barrett's and that the malignant potential of 'benign' Barrett's lesions is predetermined, with important implications for surveillance programs.
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Affiliation(s)
- Pierre Martinez
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ London, UK
| | - Margriet R. Timmer
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Center for Experimental and Molecular Medicine, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Chiu T. Lau
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Center for Experimental and Molecular Medicine, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Silvia Calpe
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Center for Experimental and Molecular Medicine, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Maria del Carmen Sancho-Serra
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Center for Experimental and Molecular Medicine, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Danielle Straub
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Center for Experimental and Molecular Medicine, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Ann-Marie Baker
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ London, UK
| | - Sybren L. Meijer
- Department of Pathology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Fiebo J. W. ten Kate
- Department of Pathology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Rosalie C. Mallant-Hent
- Department of Gastroenterology and Hepatology, Flevoziekenhuis, 1300 EG Almere, The Netherlands
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
| | - Anton H. J. Naber
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Tergooiziekenhuizen, 1201 DA Hilversum, The Netherlands
| | - Arnoud H. A. M. van Oijen
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Medisch Centrum, 1800 AM Alkmaar, The Netherlands
| | - Lubbertus C. Baak
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Onze Lieve Vrouwe Gasthuis, 1091 AC Amsterdam, The Netherlands
| | - Pieter Scholten
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Sint Lucas Andreas Ziekenhuis, 1006 AE Amsterdam, The Netherlands
| | - Clarisse J. M. Böhmer
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Spaarne Ziekenhuis, 2134 TM Hoofddorp, The Netherlands
| | - Paul Fockens
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
| | - Jacques J. G. H. M. Bergman
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
| | - Carlo C. Maley
- Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, Arizona 85281, USA
| | - Trevor A. Graham
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ London, UK
| | - Kausilia K Krishnadath
- Department of Gastroenterology and Hepatology, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Center for Experimental and Molecular Medicine, Academic Medical Center—University of Amsterdam, 1100 DD Amsterdam, The Netherlands
- Gastroenterological Association, 1006 AE Amsterdam, The Netherlands
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Baker AM, Van Noorden S, Rodriguez-Justo M, Cohen P, Wright NA, Lampert IA. Distribution of the c-MYC gene product in colorectal neoplasia. Histopathology 2016; 69:222-9. [PMID: 26826706 PMCID: PMC4949543 DOI: 10.1111/his.12939] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/27/2016] [Indexed: 12/14/2022]
Abstract
AIMS Recent attempts to study MYC distribution in human samples have been confounded by a lack of agreement in immunohistochemical staining between antibodies targeting the N-terminus and those targeting the C-terminus of the MYC protein. The aim of this study was to use a novel in-situ hybridization (ISH) approach to detect MYC mRNA in clinically relevant samples, and thereby determine the reliability of MYC-targeting antibodies. METHODS AND RESULTS We performed immunohistochemistry on human formalin-fixed paraffin embedded normal colon (n = 15), hyperplastic polyp (n = 4) and neoplastic colon samples (n = 55), using the N-terminally directed antibody Y69, and the C-terminally directed antibody 9E10. The MYC protein distributions were then compared with the location of MYC mRNA, determined by ISH. We found that the localization of MYC mRNA correlated well with the protein distribution determined with the N-terminally directed antibody Y69, and was also associated with expression of the proliferation marker Ki67. The protein distribution determined with the C-terminally directed antibody 9E10 was not always associated with MYC mRNA, Y69, or Ki67, and indeed often showed a reciprocal pattern of expression, with staining being strongest in non-proliferating cells. CONCLUSIONS The observed discrepancy between the staining patterns suggests that the significance of 9E10 in immunohistochemical staining is currently uncertain, and therefore should be interpreted with caution.
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Affiliation(s)
- Ann-Marie Baker
- Centre for Tumour Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Susan Van Noorden
- Department of Histopathology, Imperial College London, Hammersmith Hospital, London, UK
| | | | - Patrizia Cohen
- Department of Cellular Pathology, Clarence Memorial Wing, St Mary's Hospital, London, UK
| | - Nicholas A Wright
- Centre for Tumour Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Irvin A Lampert
- Department of Histopathology, West Middlesex University Hospital, Isleworth, UK
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Abstract
The population of cells that make up a cancer are manifestly heterogeneous at the genetic, epigenetic, and phenotypic levels. In this mini-review, we summarise the extent of intra-tumour heterogeneity (ITH) across human malignancies, review the mechanisms that are responsible for generating and maintaining ITH, and discuss the ramifications and opportunities that ITH presents for cancer prognostication and treatment.
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Affiliation(s)
- Laura Gay
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Ann-Marie Baker
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Trevor A. Graham
- Evolution and Cancer Laboratory, Centre for Tumour Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
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Baker AM, Graham TA, Elia G, Wright NA, Rodriguez-Justo M. Characterization of LGR5 stem cells in colorectal adenomas and carcinomas. Sci Rep 2015; 5:8654. [PMID: 25728748 PMCID: PMC4345329 DOI: 10.1038/srep08654] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/23/2015] [Indexed: 12/20/2022] Open
Abstract
LGR5 is known to be a stem cell marker in the murine small intestine and colon, however the localization of LGR5 in human adenoma samples has not been examined in detail, and previous studies have been limited by the lack of specific antibodies. Here we used in situ hybridization to specifically examine LGR5 mRNA expression in a panel of human adenoma and carcinoma samples (n = 66). We found that a small number of cells express LGR5 at the base of normal colonic crypts. We then showed that conventional adenomas widely express high levels of LGR5, and there is no evidence of stereotypic cellular hierarchy. In contrast, serrated lesions display basal localization of LGR5, and the cellular hierarchy resembles that of a normal crypt. Moreover, ectopic crypts found in traditional serrated adenomas show basal LGR5 mRNA, indicating that they replicate the stem cell organization of normal crypts with the development of a cellular hierarchy. These data imply differences in the stem cell dynamics between the serrated and conventional pathways of colorectal carcinogenesis. Furthermore we noted high LGR5 expression in invading cells, with later development of a stem cell niche in adenocarcinomas of all stages.
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Affiliation(s)
- Ann-Marie Baker
- Centre for Tumor Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK, EC1M 6BQ
| | - Trevor A. Graham
- Centre for Tumor Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK, EC1M 6BQ
| | - George Elia
- Centre for Tumor Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK, EC1M 6BQ
| | - Nicholas A. Wright
- Centre for Tumor Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK, EC1M 6BQ
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Baker AM, Graham TA. Revealing human intestinal stem cell and crypt dynamics. Mol Cell Oncol 2014; 1:e970069. [PMID: 27308359 DOI: 10.4161/23723548.2014.970069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 09/04/2014] [Accepted: 09/06/2014] [Indexed: 11/19/2022]
Abstract
Stem cell and crypt dynamics in the human gut have been remarkably poorly characterized. We used random somatic mutations to trace stem cell lineages in the human intestine and coupled these data with mathematical modeling to infer the in vivo temporal dynamics of human intestinal stem cells.
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Affiliation(s)
- Ann-Marie Baker
- Evolution and Cancer Laboratory; Barts Cancer Institute; Barts and the London School of Medicine and Dentistry; Queen Mary University of London ; London, UK
| | - Trevor A Graham
- Evolution and Cancer Laboratory; Barts Cancer Institute; Barts and the London School of Medicine and Dentistry; Queen Mary University of London ; London, UK
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41
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Baker AM, Cereser B, Melton S, Fletcher AG, Rodriguez-Justo M, Tadrous PJ, Humphries A, Elia G, McDonald SAC, Wright NA, Simons BD, Jansen M, Graham TA. Quantification of crypt and stem cell evolution in the normal and neoplastic human colon. Cell Rep 2014; 8:940-7. [PMID: 25127143 PMCID: PMC4471679 DOI: 10.1016/j.celrep.2014.07.019] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/27/2014] [Accepted: 07/15/2014] [Indexed: 01/08/2023] Open
Abstract
Human intestinal stem cell and crypt dynamics remain poorly characterized because transgenic lineage-tracing methods are impractical in humans. Here, we have circumvented this problem by quantitatively using somatic mtDNA mutations to trace clonal lineages. By analyzing clonal imprints on the walls of colonic crypts, we show that human intestinal stem cells conform to one-dimensional neutral drift dynamics with a "functional" stem cell number of five to six in both normal patients and individuals with familial adenomatous polyposis (germline APC(-/+)). Furthermore, we show that, in adenomatous crypts (APC(-/-)), there is a proportionate increase in both functional stem cell number and the loss/replacement rate. Finally, by analyzing fields of mtDNA mutant crypts, we show that a normal colon crypt divides around once every 30-40 years, and the division rate is increased in adenomas by at least an order of magnitude. These data provide in vivo quantification of human intestinal stem cell and crypt dynamics.
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Affiliation(s)
- Ann-Marie Baker
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Biancastella Cereser
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Samuel Melton
- Cavendish Laboratory, Department of Physics, J.J. Thomson Avenue, University of Cambridge, Cambridge CB3 0HE, UK
| | - Alexander G Fletcher
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK
| | | | - Paul J Tadrous
- Cellular Pathology, Northwest London Hospitals NHS Trust, London HA1 3UJ, UK
| | | | - George Elia
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Stuart A C McDonald
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Nicholas A Wright
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Benjamin D Simons
- Cavendish Laboratory, Department of Physics, J.J. Thomson Avenue, University of Cambridge, Cambridge CB3 0HE, UK; The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; The Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Marnix Jansen
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK; Department of Pathology, Academic Medical Centre, Meibergdreef 9, 1105AZ Amsterdam, the Netherlands
| | - Trevor A Graham
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK; Center for Evolution and Cancer, 2340 Sutter Street, University of California, San Francisco, San Francisco, CA 94143, USA.
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Baker AM, Graham TA, Wright NA. Pre-tumour clones, periodic selection and clonal interference in the origin and progression of gastrointestinal cancer: potential for biomarker development. J Pathol 2013; 229:502-14. [PMID: 23288692 DOI: 10.1002/path.4157] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 12/17/2012] [Accepted: 12/18/2012] [Indexed: 12/18/2022]
Abstract
Classically, the risk of cancer progression in premalignant conditions of the gastrointestinal tract is assessed by examining the degree of histological dysplasia. However, there are many putative pro-cancer genetic changes that have occurred in histologically normal tissue well before the onset of dysplasia. Here we summarize the evidence for such pre-tumour clones and the existing technology that can be used to locate these clones and characterize them at the genetic level. We also discuss the mechanisms by which pre-tumour clones may spread through large areas of normal tissue, and highlight emerging theories on how multiple clones compete and interact within the gastrointestinal mucosa. It is important to gain an understanding of these processes, as it is envisaged that certain pre-tumour changes may be powerful predictive markers, with the potential to identify patients at high risk of developing cancer at a much earlier stage.
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Affiliation(s)
- Ann-Marie Baker
- Centre for Tumour Biology, Barts and the London School of Medicine and Dentistry, London, UK.
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Cox TR, Bird D, Baker AM, Barker HE, Ho MWY, Lang G, Erler JT. LOX-mediated collagen crosslinking is responsible for fibrosis-enhanced metastasis. Cancer Res 2013; 73:1721-32. [PMID: 23345161 DOI: 10.1158/0008-5472.can-12-2233] [Citation(s) in RCA: 382] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Tumor metastasis is a highly complex, dynamic, and inefficient process involving multiple steps, yet it accounts for more than 90% of cancer-related deaths. Although it has long been known that fibrotic signals enhance tumor progression and metastasis, the underlying molecular mechanisms are still unclear. Identifying events involved in creating environments that promote metastatic colonization and growth are critical for the development of effective cancer therapies. Here, we show a critical role for lysyl oxidase (LOX) in establishing a milieu within fibrosing tissues that is favorable to growth of metastastic tumor cells. We show that LOX-dependent collagen crosslinking is involved in creating a growth-permissive fibrotic microenvironment capable of supporting metastatic growth by enhancing tumor cell persistence and survival. We show that therapeutic targeting of LOX abrogates not only the extent to which fibrosis manifests, but also prevents fibrosis-enhanced metastatic colonization. Finally, we show that the LOX-mediated collagen crosslinking directly increases tumor cell proliferation, enhancing metastatic colonization and growth manifesting in vivo as increased metastasis. This is the first time that crosslinking of collagen I has been shown to enhance metastatic growth. These findings provide an important link between ECM homeostasis, fibrosis, and cancer with important clinical implications for both the treatment of fibrotic disease and cancer.
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Affiliation(s)
- Thomas R Cox
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
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Baker AM, Bird D, Welti JC, Gourlaouen M, Lang G, Murray GI, Reynolds AR, Cox TR, Erler JT. Lysyl oxidase plays a critical role in endothelial cell stimulation to drive tumor angiogenesis. Cancer Res 2012. [PMID: 23188504 DOI: 10.1158/0008-5472.can-12-24470008-5472.can-12-2447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Identification of key molecules that drive angiogenesis is critical for the development of new modalities for the prevention of solid tumor progression. Using multiple models of colorectal cancer, we show that activity of the extracellular matrix-modifying enzyme lysyl oxidase (LOX) is essential for stimulating endothelial cells in vitro and angiogenesis in vivo. We show that LOX activates Akt through platelet-derived growth factor receptor β (PDGFRβ) stimulation, resulting in increased VEGF expression. LOX-driven angiogenesis can be abrogated through targeting LOX directly or using inhibitors of PDGFRβ, Akt, and VEGF signaling. Furthermore, we show that LOX is clinically correlated with VEGF expression and blood vessel formation in 515 colorectal cancer patient samples. Finally, we validate our findings in a breast cancer model, showing the universality of these observations. Taken together, our findings have broad clinical and therapeutic implications for a wide variety of solid tumor types.
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Affiliation(s)
- Ann-Marie Baker
- Hypoxia and Metastasis Team, The Institute of Cancer Research, London, UK
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Baker AM, Bird D, Welti JC, Gourlaouen M, Lang G, Murray GI, Reynolds AR, Cox TR, Erler JT. Lysyl oxidase plays a critical role in endothelial cell stimulation to drive tumor angiogenesis. Cancer Res 2012. [PMID: 23188504 DOI: 10.1158/0008-5472.can-12-2447] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Identification of key molecules that drive angiogenesis is critical for the development of new modalities for the prevention of solid tumor progression. Using multiple models of colorectal cancer, we show that activity of the extracellular matrix-modifying enzyme lysyl oxidase (LOX) is essential for stimulating endothelial cells in vitro and angiogenesis in vivo. We show that LOX activates Akt through platelet-derived growth factor receptor β (PDGFRβ) stimulation, resulting in increased VEGF expression. LOX-driven angiogenesis can be abrogated through targeting LOX directly or using inhibitors of PDGFRβ, Akt, and VEGF signaling. Furthermore, we show that LOX is clinically correlated with VEGF expression and blood vessel formation in 515 colorectal cancer patient samples. Finally, we validate our findings in a breast cancer model, showing the universality of these observations. Taken together, our findings have broad clinical and therapeutic implications for a wide variety of solid tumor types.
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Affiliation(s)
- Ann-Marie Baker
- Hypoxia and Metastasis Team, The Institute of Cancer Research, London, UK
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Castalanelli MA, Baker AM, Munyard KA, Grimm M, Groth DM. Molecular phylogeny supports the paraphyletic nature of the genus Trogoderma (Coleoptera: Dermestidae) collected in the Australasian ecozone. Bull Entomol Res 2012; 102:17-28. [PMID: 21749736 DOI: 10.1017/s0007485311000319] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
To date, a molecular phylogenetic approach has not been used to investigate the evolutionary structure of Trogoderma and closely related genera. Using two mitochondrial genes, Cytochrome Oxidase I and Cytochrome B, and the nuclear gene, 18S, the reported polyphyletic positioning of Trogoderma was examined. Paraphyly in Trogoderma was observed, with one Australian Trogoderma species reconciled as sister to all Dermestidae and the Anthrenocerus genus deeply nested within the Australian Trogoderma clade. In addition, time to most recent common ancestor for a number of Dermestidae was calculated. Based on these estimations, the Dermestidae origin exceeded 175 million years, placing the origins of this family in Pangaea.
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Affiliation(s)
- M A Castalanelli
- Cooperative Research Centre for National Plant Biosecurity, Deakin, ACT, Australia.
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Salam T, Collins M, Baker AM. All the World's a Stage: Integrating Theater and Medicine for Interprofessional Team Building in Physician and Nurse Residency Programs. Ochsner J 2012; 12:359-62. [PMID: 23267264 PMCID: PMC3527865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND To facilitate the delivery of excellent patient care, physician-nurse teams must work in a collaborative manner. We found that venues for the joint training of physician-nurse teams to foster collaboration are insufficient. METHODS We developed a novel interprofessional experience in which resident physicians and nurse residents practiced communication and collaboration skills involving a simulated alcohol withdrawal patient care scenario. Theater students portrayed the patients experiencing withdrawal. The team cared for each patient in a fully equipped and functioning hospital room in a simulation center. Together, they collaborated on interventions and a patient plan of care. After the 10-minute bedside scenario, physician and nurse educators facilitated a joint debriefing session for the physician-nurse learning team. RESULTS Learners noted an improvement in their ability to identify alcohol withdrawal (44% of participants preencounter to 94% of participants postencounter) and to communicate with team members (55% of participants preencounter to 81% of participants postencounter). CONCLUSION The learners felt the physician-nurse team training experience was exceptionally valuable for its authenticity.
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Affiliation(s)
| | - Michelle Collins
- Department of Nursing, Christiana Care Health System, Newark, DE
| | - Ann-Marie Baker
- Department of Nursing, Christiana Care Health System, Newark, DE
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Huey JA, Baker AM, Hughes JM. Evidence for multiple historical colonizations of an endoreic drainage basin by an Australian freshwater fish. J Fish Biol 2011; 79:1047-1067. [PMID: 21967589 DOI: 10.1111/j.1095-8649.2011.03088.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The contemporary and historical colonization capacity of an Australian freshwater fish, north-west glassfish Ambassis sp., was tested using mtDNA sequence data and six newly developed microsatellite loci in an endoreic basin in central Australia. Overall, Ambassis sp. exhibited weak genetic structure within catchments, suggesting some capacity to recolonize extirpated waterholes after disturbance. Genetic structure revealed that the historical pattern of connectivity among catchments in the Lake Eyre Basin was dramatically different from other species studied in this region. Two highly divergent clades were detected in separate catchments in the basin. mtDNA from individuals sampled in catchments north of the Lake Eyre Basin suggest that Ambassis sp. has colonized on two separate occasions from catchments in northern Australia, subsequently generating two highly divergent lineages.
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Affiliation(s)
- J A Huey
- Griffith University, Australian Rivers Institute, Griffith School of Environment, 170 Kessels Road, Nathan, Qld 4111, Australia.
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Castalanelli MA, Mikac KM, Baker AM, Munyard K, Grimm M, Groth DM. Multiple incursions and putative species revealed using a mitochondrial and nuclear phylogenetic approach to the Trogoderma variabile (Coleoptera: Dermestidae) trapping program in Australia. Bull Entomol Res 2011; 101:333-343. [PMID: 21226978 DOI: 10.1017/s0007485310000544] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The Warehouse beetle, Trogoderma variabile (Coleoptera: Dermestidae), is an internationally significant invasive pest of packed goods and stored grain. When it was first documented in Australia at Griffith, New South Wales, in 1977, an eradication campaign was initiated. After several years and considerable effort, the eradication campaign was abandoned. To monitor the presence and spread of T. variabile, surveys were carried out by government agencies in 1992 and 2002. When survey data was compared, it was concluded that the distribution of morphologically identified T. variabile had doubled in most Australian states. Here, we used samples from the 2002 survey to conduct a phylogenetic study using partial sequences of mitochondrial genes Cytochrome oxidase I and Cytochrome B, and the nuclear gene 18S, to examine the distribution and dispersal of T. variabile and detect the presence of misidentified species. Based on our molecular results, we show that only 47% of the samples analysed were T. variabile, and the remaining were a mixture of six putative species. In addition, T. variabile was found in only 78% of the trapping sites. We discuss the importance of correct diagnosis in relation to the eradication campaign.
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Affiliation(s)
- M A Castalanelli
- Cooperative Research Centre for National Plant Biosecurity, Deakin, ACT, Australia.
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Krosch MN, Baker AM, Mather PB, Cranston PS. Systematics and biogeography of the Gondwanan Orthocladiinae (Diptera: Chironomidae). Mol Phylogenet Evol 2011; 59:458-68. [PMID: 21402162 DOI: 10.1016/j.ympev.2011.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 01/31/2011] [Accepted: 03/03/2011] [Indexed: 10/18/2022]
Abstract
Restrictions to effective dispersal and gene flow caused by the fragmentation of ancient supercontinents are considered to have driven diversification and speciation on disjunct landmasses globally. Investigating the role that these processes have played in the development of diversity within and among taxa is crucial to understanding the origins and evolution of regional biotas. Within the chironomid (non-biting midge) subfamily Orthocladiinae (Diptera: Chironomidae), a group of genera that are distributed across the austral continents (Australia, New Zealand, South America) have been proposed to represent a relict Gondwanan clade. We used a molecular approach to resolve relationships among taxa with the aim to determine the relative roles that vicariance and dispersal may have played in the evolution of this group. Continental biotas did not form monophyletic groups, in accordance with expectations given existing morphological evidence. Patterns of phylogenetic relationships among taxa did not accord with expected patterns based on the geological sequence of break-up of the Gondwanan supercontinent. Likewise, divergence time estimates, particularly for New Zealand taxa, largely post-dated continental fragmentation and implied instead that several transoceanic dispersal events may have occurred post-vicariance. Passive dispersal of gravid female chironomid adults is the most likely mechanism for transoceanic movement, potentially facilitated by West Wind Drift or anti-cyclone fronts. Estimated timings of divergence among Australian and South American Botryocladius, on the other hand, were congruent with the proposed ages of separation of the two continents from Antarctica. Taken together, these data suggest that a complex relationship between both vicariance and dispersal may explain the evolution of this group. The sampling regime we implemented here was the most intensive yet performed for austral members of the Orthocladiinae and unsurprisingly revealed several novel taxa that will require formal description.
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Affiliation(s)
- M N Krosch
- Biogeosciences, Queensland University of Technology, 2 George St., Brisbane 4001, Australia.
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