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Sessler T, Quinn GP, Wappett M, Rogan E, Sharkey D, Ahmaderaghi B, Lawler M, Longley DB, McDade SS. surviveR: a flexible shiny application for patient survival analysis. Sci Rep 2023; 13:22093. [PMID: 38086891 PMCID: PMC10716386 DOI: 10.1038/s41598-023-48894-9] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Kaplan-Meier (KM) survival analyses based on complex patient categorization due to the burgeoning volumes of genomic, molecular and phenotypic data, are an increasingly important aspect of the biomedical researcher's toolkit. Commercial statistics and graphing packages for such analyses are functionally limited, whereas open-source tools have a high barrier-to-entry in terms of understanding of methodologies and computational expertise. We developed surviveR to address this unmet need for a survival analysis tool that can enable users with limited computational expertise to conduct routine but complex analyses. surviveR is a cloud-based Shiny application, that addresses our identified unmet need for an easy-to-use web-based tool that can plot and analyse survival based datasets. Integrated customization options allows a user with limited computational expertise to easily filter patients to enable custom cohort generation, automatically calculate log-rank test and Cox hazard ratios. Continuous datasets can be integrated, such as RNA or protein expression measurements which can be then used as categories for survival plotting. We further demonstrate the utility through exemplifying its application to a clinically relevant colorectal cancer patient dataset. surviveR is a cloud-based web application available at https://generatr.qub.ac.uk/app/surviveR , that can be used by non-experts users to perform complex custom survival analysis.
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Affiliation(s)
- Tamas Sessler
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Gerard P Quinn
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Mark Wappett
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Emily Rogan
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - David Sharkey
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Baharak Ahmaderaghi
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Mark Lawler
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Daniel B Longley
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Simon S McDade
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK.
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Quinn GP, Sessler T, Ahmaderaghi B, Lambe S, VanSteenhouse H, Lawler M, Wappett M, Seligmann B, Longley DB, McDade SS. classifieR a flexible interactive cloud-application for functional annotation of cancer transcriptomes. BMC Bioinformatics 2022; 23:114. [PMID: 35361119 PMCID: PMC8974006 DOI: 10.1186/s12859-022-04641-x] [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: 01/18/2022] [Accepted: 03/18/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Transcriptionally informed predictions are increasingly important for sub-typing cancer patients, understanding underlying biology and to inform novel treatment strategies. For instance, colorectal cancers (CRCs) can be classified into four CRC consensus molecular subgroups (CMS) or five intrinsic (CRIS) sub-types that have prognostic and predictive value. Breast cancer (BRCA) has five PAM50 molecular subgroups with similar value, and the OncotypeDX test provides transcriptomic based clinically actionable treatment-risk stratification. However, assigning samples to these subtypes and other transcriptionally inferred predictions is time consuming and requires significant bioinformatics experience. There is no "universal" method of using data from diverse assay/sequencing platforms to provide subgroup classification using the established classifier sets of genes (CMS, CRIS, PAM50, OncotypeDX), nor one which in provides additional useful functional annotations such as cellular composition, single-sample Gene Set Enrichment Analysis, or prediction of transcription factor activity. RESULTS To address this bottleneck, we developed classifieR, an easy-to-use R-Shiny based web application that supports flexible rapid single sample annotation of transcriptional profiles derived from cancer patient samples form diverse platforms. We demonstrate the utility of the " classifieR" framework to applications focused on the analysis of transcriptional profiles from colorectal (classifieRc) and breast (classifieRb). Samples are annotated with disease relevant transcriptional subgroups (CMS/CRIS sub-types in classifieRc and PAM50/inferred OncotypeDX in classifieRb), estimation of cellular composition using MCP-counter and xCell, single-sample Gene Set Enrichment Analysis (ssGSEA) and transcription factor activity predictions with Discriminant Regulon Expression Analysis (DoRothEA). CONCLUSIONS classifieR provides a framework which enables labs without access to a dedicated bioinformation can get information on the molecular makeup of their samples, providing an insight into patient prognosis, druggability and also as a tool for analysis and discovery. Applications are hosted online at https://generatr.qub.ac.uk/app/classifieRc and https://generatr.qub.ac.uk/app/classifieRb after signing up for an account on https://generatr.qub.ac.uk .
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Affiliation(s)
- Gerard P Quinn
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Tamas Sessler
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Baharak Ahmaderaghi
- Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, UK
| | - Shauna Lambe
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | | | - Mark Lawler
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Mark Wappett
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | | | - Daniel B Longley
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Simon S McDade
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK.
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Crawford N, Stott KJ, Sessler T, McCann C, McDaid W, Lees A, Latimer C, Fox JP, Munck JM, Smyth T, Shah A, Martins V, Lawler M, Dunne PD, Kerr EM, McDade SS, Coyle VM, Longley DB. Clinical Positioning of the IAP Antagonist Tolinapant (ASTX660) in Colorectal Cancer. Mol Cancer Ther 2021; 20:1627-1639. [PMID: 34389694 PMCID: PMC7611622 DOI: 10.1158/1535-7163.mct-20-1050] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 12/09/2020] [Revised: 02/25/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022]
Abstract
Inhibitors of apoptosis proteins (IAPs) are intracellular proteins, with important roles in regulating cell death, inflammation, and immunity. Here, we examined the clinical and therapeutic relevance of IAPs in colorectal cancer. We found that elevated expression of cIAP1 and cIAP2 (but not XIAP) significantly correlated with poor prognosis in patients with microsatellite stable (MSS) stage III colorectal cancer treated with 5-fluorouracil (5FU)-based adjuvant chemotherapy, suggesting their involvement in promoting chemoresistance. A novel IAP antagonist tolinapant (ASTX660) potently and rapidly downregulated cIAP1 in colorectal cancer models, demonstrating its robust on-target efficacy. In cells co-cultured with TNFα to mimic an inflammatory tumor microenvironment, tolinapant induced caspase-8-dependent apoptosis in colorectal cancer cell line models; however, the extent of apoptosis was limited because of inhibition by the caspase-8 paralogs FLIP and, unexpectedly, caspase-10. Importantly, tolinapant-induced apoptosis was augmented by FOLFOX in human colorectal cancer and murine organoid models in vitro and in vivo, due (at least in part) to FOLFOX-induced downregulation of class I histone deacetylases (HDAC), leading to acetylation of the FLIP-binding partner Ku70 and downregulation of FLIP. Moreover, the effects of FOLFOX could be phenocopied using the clinically relevant class I HDAC inhibitor, entinostat, which also induced acetylation of Ku70 and FLIP downregulation. Further analyses revealed that caspase-8 knockout RIPK3-positive colorectal cancer models were sensitive to tolinapant-induced necroptosis, an effect that could be exploited in caspase-8-proficient models using the clinically relevant caspase inhibitor emricasan. Our study provides evidence for immediate clinical exploration of tolinapant in combination with FOLFOX in poor prognosis MSS colorectal cancer with elevated cIAP1/2 expression.
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Affiliation(s)
- Nyree Crawford
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Katie J Stott
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Tamas Sessler
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Christopher McCann
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - William McDaid
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Andrea Lees
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Cheryl Latimer
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Jennifer P Fox
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | | | - Tomoko Smyth
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | - Alpesh Shah
- Astex Pharmaceuticals, Cambridge, United Kingdom
| | | | - Mark Lawler
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Philip D Dunne
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Emma M Kerr
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Simon S McDade
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Vicky M Coyle
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | - Daniel B Longley
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom.
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Abstract
The p53 tumour suppressor is best known for its canonical role as "guardian of the genome", activating cell cycle arrest and DNA repair in response to DNA damage which, if irreparable or sustained, triggers activation of cell death. However, despite an enormous amount of work identifying the breadth of the gene regulatory networks activated directly and indirectly in response to p53 activation, how p53 activation results in different cell fates in response to different stress signals in homeostasis and in response to p53 activating anti-cancer treatments remains relatively poorly understood. This is likely due to the complex interaction between cell death mechanisms in which p53 has been activated, their neighbouring stressed or unstressed cells and the local stromal and immune microenvironment in which they reside. In this review, we evaluate our understanding of the burgeoning number of cell death pathways affected by p53 activation and how these may paradoxically suppress cell death to ensure tissue integrity and organismal survival. We also discuss how these functions may be advantageous to tumours that maintain wild-type p53, the understanding of which may provide novel opportunity to enhance treatment efficacy.
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Affiliation(s)
- Andrea Lees
- Patrick G Johnston Centre for Cancer Research, Queen’s University, Belfast BT9 7AE, UK;
| | | | - Simon McDade
- Patrick G Johnston Centre for Cancer Research, Queen’s University, Belfast BT9 7AE, UK;
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McCann C, Matveeva A, McAllister K, Van Schaeybroeck S, Sessler T, Fichtner M, Carberry S, Rehm M, Prehn JHM, Longley DB. Development of a protein signature to enable clinical positioning of IAP inhibitors in colorectal cancer. FEBS J 2021; 288:5374-5388. [PMID: 33660894 DOI: 10.1111/febs.15801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 12/11/2020] [Revised: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 12/18/2022]
Abstract
Resistance to chemotherapy-induced cell death is a major barrier to effective treatment of solid tumours such as colorectal cancer, CRC. Herein, we present a study aimed at developing a proteomics-based predictor of response to standard-of-care (SoC) chemotherapy in combination with antagonists of IAPs (inhibitors of apoptosis proteins), which have been implicated as mediators of drug resistance in CRC. We quantified the absolute expression of 19 key apoptotic proteins at baseline in a panel of 12 CRC cell lines representative of the genetic diversity seen in this disease to identify which proteins promote resistance or sensitivity to a model IAP antagonist [birinapant (Bir)] alone and in combination with SoC chemotherapy (5FU plus oxaliplatin). Quantitative western blotting demonstrated heterogeneous expression of IAP interactome proteins across the CRC cell line panel, and cell death analyses revealed a widely varied response to Bir/chemotherapy combinations. Baseline protein expression of cIAP1, caspase-8 and RIPK1 expression robustly correlated with response to Bir/chemotherapy combinations. Classifying cell lines into 'responsive', 'intermediate' and 'resistant' groups and using linear discriminant analysis (LDA) enabled the identification of a 12-protein signature that separated responders to Bir/chemotherapy combinations in the CRC cell line panel with 100% accuracy. Moreover, the LDA model was able to predict response accurately when cells were cocultured with Tumour necrosis factor-alpha to mimic a pro-inflammatory tumour microenvironment. Thus, our study provides the starting point for a proteomics-based companion diagnostic that predicts response to IAP antagonist/SoC chemotherapy combinations in CRC.
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Affiliation(s)
- Christopher McCann
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Anna Matveeva
- Department of Physiology & Medical Physics and Centre for Systems Medicine, Royal College of Surgeons in Ireland (RCSI) University of Medicine and Health Sciences, Dublin, Ireland
| | | | | | - Tamas Sessler
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Michael Fichtner
- Department of Physiology & Medical Physics and Centre for Systems Medicine, Royal College of Surgeons in Ireland (RCSI) University of Medicine and Health Sciences, Dublin, Ireland
| | - Steven Carberry
- Department of Physiology & Medical Physics and Centre for Systems Medicine, Royal College of Surgeons in Ireland (RCSI) University of Medicine and Health Sciences, Dublin, Ireland
| | - Markus Rehm
- Institute of Cell Biology and Immunology, University of Stuttgart, Germany
| | - Jochen H M Prehn
- Department of Physiology & Medical Physics and Centre for Systems Medicine, Royal College of Surgeons in Ireland (RCSI) University of Medicine and Health Sciences, Dublin, Ireland
| | - Daniel B Longley
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
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Fichtner M, Bozkurt E, Salvucci M, McCann C, McAllister KA, Halang L, Düssmann H, Kinsella S, Crawford N, Sessler T, Longley DB, Prehn JHM. Molecular subtype-specific responses of colon cancer cells to the SMAC mimetic Birinapant. Cell Death Dis 2020; 11:1020. [PMID: 33257690 PMCID: PMC7705699 DOI: 10.1038/s41419-020-03232-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 02/12/2020] [Revised: 11/07/2020] [Accepted: 11/10/2020] [Indexed: 12/24/2022]
Abstract
Colorectal cancer is a molecularly heterogeneous disease. Responses to genotoxic chemotherapy in the adjuvant or palliative setting vary greatly between patients, and colorectal cancer cells often resist chemotherapy by evading apoptosis. Antagonists of an inhibitor of apoptosis proteins (IAPs) can restore defective apoptosis signaling by degrading cIAP1 and cIAP2 proteins and by inhibition of XIAP. Due to the multiple molecular mechanisms-of-action of these targets, responses to IAP antagonist may differ between molecularly distinct colon cancer cells. In this study, responses to the IAP antagonist Birinapant and oxaliplatin/5-fluorouracil (5-FU) were investigated in 14 colon cancer cell lines, representing the consensus molecular subtypes (CMS). Treatment with Birinapant alone did not result in a substantial increase in apoptotic cells in this cell line panel. Annexin-V/PI assays quantified by flow cytometry and high-content screening showed that Birinapant increased responses of CMS1 and partially CMS3 cell lines to oxaliplatin/5-FU, whereas CMS2 cells were not effectively sensitized. FRET-based imaging of caspase-8 and -3 activation validated these differences at the single-cell level, with CMS1 cells displaying sustained activation of caspase-8-like activity during Birinapant and oxaliplatin/5-FU co-treatment, ultimately activating the intrinsic mitochondrial apoptosis pathway. In CMS2 cell lines, Birinapant exhibited synergistic effects in combination with TNFα, suggesting that Birinapant can restore extrinsic apoptosis signaling in the context of inflammatory signals in this subtype. To explore this further, we co-cultured CMS2 and CMS1 colon cancer cells with peripheral blood mononuclear cells. We observed increased cell death during Birinapant single treatment in these co-cultures, which was abrogated by anti-TNFα-neutralizing antibodies. Collectively, our study demonstrates that IAP inhibition is a promising modulator of response to oxaliplatin/5-FU in colorectal cancers of the CMS1 subtype, and may show promise as in the CMS2 subtype, suggesting that molecular subtyping may aid as a patient stratification tool for IAP antagonists in this disease.
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Affiliation(s)
- Michael Fichtner
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Emir Bozkurt
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Balcova, Izmir, Turkey
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Christopher McCann
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | | | - Luise Halang
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Heiko Düssmann
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sinéad Kinsella
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland.,Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nyree Crawford
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Tamas Sessler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Daniel B Longley
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland.
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Sessler T, Falcone F, Gallagher P, Wright T, Savage K, Longley DB, McDade SS. Abstract 1386: 5-FU-induces PD-L1 in the absence of p53 via ATM dependent activation of STAT3. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1386] [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
Background: 5-Fluorouracil (5-FU) is an antimetabolite DNA damaging chemotherapeutics that forms the backbone for treatment of colorectal cancer (CRC) and currently it is the most commonly used anti-cancer drug. Despite the central role played by p53 in regulating DNA-damage response, its role in regulating response to 5-FU remains unclear.
Methods: To better understand how p53 status differentially affects response to 5-FU, we conducted a detailed phenotypic analysis of the effects of 5FU alone or in combination with Oxaliplatin on cell cycle, DNA damage, cell death, DNA repair and consequent signaling across a panel of p53 isogenic, null and mutant CRC cell lines.
Results: This revealed that while 5-FU induce both p53 dependent and independent cell death, the effects on cell cycle are profoundly different, with p53 deficient cells accumulating in S-phase with prolongated double strand breaks. This is not observed in p53 proficient cells, which are protected from these effects by induction of the p53 target gene p21/CDKN1A limiting cell cycle and enforcing suppression of cell cycle genes. Notably in both p53 or p21 deficient cells 5-FU results in sustained DNA damage-signaling through ATR and ATM in p53 deficient cells which preferentially arrest in S-phase. Importantly, these cells exhibit significant induction of cell surface expression of programmed death ligand-1 (PD-L1), which is enhanced by ATR inhibition concomitant with increased ATM activation. Further analysis indicates that transcriptional induction of PD-L1 is mediated through STAT3 in an interferon independent manner.
Conclusion: This work adds significantly to our understanding of how p53 status impacts 5FU induced cell cycle arrest and response in CRC patients and have important implications for understanding 5-FU response, particularly in future combinations with immune checkpoint inhibitors.
Citation Format: Tamas Sessler, Fiammetta Falcone, Peter Gallagher, Timothy Wright, Kienan Savage, Daniel B. Longley, Simon S. McDade. 5-FU-induces PD-L1 in the absence of p53 via ATM dependent activation of STAT3 [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1386.
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Lees A, McIntyre AJ, Crawford NT, Falcone F, McCann C, Holohan C, Quinn GP, Roberts JZ, Sessler T, Gallagher PF, Gregg GMA, McAllister K, McLaughlin KM, Allen WL, Egan LJ, Ryan AE, Labonte-Wilson MJ, Dunne PD, Wappett M, Coyle VM, Johnston PG, Kerr EM, Longley DB, McDade SS. The pseudo-caspase FLIP(L) regulates cell fate following p53 activation. Proc Natl Acad Sci U S A 2020; 117:17808-17819. [PMID: 32661168 PMCID: PMC7395556 DOI: 10.1073/pnas.2001520117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 12/20/2022] Open
Abstract
p53 is the most frequently mutated, well-studied tumor-suppressor gene, yet the molecular basis of the switch from p53-induced cell-cycle arrest to apoptosis remains poorly understood. Using a combination of transcriptomics and functional genomics, we unexpectedly identified a nodal role for the caspase-8 paralog and only human pseudo-caspase, FLIP(L), in regulating this switch. Moreover, we identify FLIP(L) as a direct p53 transcriptional target gene that is rapidly up-regulated in response to Nutlin-3A, an MDM2 inhibitor that potently activates p53. Genetically or pharmacologically inhibiting expression of FLIP(L) using siRNA or entinostat (a clinically relevant class-I HDAC inhibitor) efficiently promoted apoptosis in colorectal cancer cells in response to Nutlin-3A, which otherwise predominantly induced cell-cycle arrest. Enhanced apoptosis was also observed when entinostat was combined with clinically relevant, p53-activating chemotherapy in vitro, and this translated into enhanced in vivo efficacy. Mechanistically, FLIP(L) inhibited p53-induced apoptosis by blocking activation of caspase-8 by the TRAIL-R2/DR5 death receptor; notably, this activation was not dependent on receptor engagement by its ligand, TRAIL. In the absence of caspase-8, another of its paralogs, caspase-10 (also transcriptionally up-regulated by p53), induced apoptosis in Nutlin-3A-treated, FLIP(L)-depleted cells, albeit to a lesser extent than in caspase-8-proficient cells. FLIP(L) depletion also modulated transcription of canonical p53 target genes, suppressing p53-induced expression of the cell-cycle regulator p21 and enhancing p53-induced up-regulation of proapoptotic PUMA. Thus, even in the absence of caspase-8/10, FLIP(L) silencing promoted p53-induced apoptosis by enhancing PUMA expression. Thus, we report unexpected, therapeutically relevant roles for FLIP(L) in determining cell fate following p53 activation.
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Affiliation(s)
- Andrea Lees
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Alexander J McIntyre
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Nyree T Crawford
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Fiammetta Falcone
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Christopher McCann
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Caitriona Holohan
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Gerard P Quinn
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Jamie Z Roberts
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Tamas Sessler
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Peter F Gallagher
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Gemma M A Gregg
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Katherine McAllister
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Kirsty M McLaughlin
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Wendy L Allen
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Laurence J Egan
- Discipline of Pharmacology & Therapeutics, Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, National University of Ireland Galway, Galway, Ireland
| | - Aideen E Ryan
- Discipline of Pharmacology & Therapeutics, Lambe Institute for Translational Research, School of Medicine, College of Medicine, Nursing and Health Sciences, National University of Ireland Galway, Galway, Ireland
- Regenerative Medicine Institute, College of Medicine, Nursing and Health Sciences, National University of Ireland Galway, Galway, Ireland
| | - Melissa J Labonte-Wilson
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Philip D Dunne
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Mark Wappett
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Vicky M Coyle
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Patrick G Johnston
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Emma M Kerr
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom
| | - Daniel B Longley
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom;
| | - Simon S McDade
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland BT9 7BL, United Kingdom;
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Roberts JZ, Holohan C, Sessler T, Fox J, Crawford N, Riley JS, Khawaja H, Majkut J, Evergren E, Humphreys LM, Ferris J, Higgins C, Espona-Fiedler M, Moynagh P, McDade SS, Longley DB. The SCF Skp2 ubiquitin ligase complex modulates TRAIL-R2-induced apoptosis by regulating FLIP(L). Cell Death Differ 2020; 27:2726-2741. [PMID: 32313199 PMCID: PMC7429845 DOI: 10.1038/s41418-020-0539-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 12/04/2019] [Revised: 03/30/2020] [Accepted: 03/31/2020] [Indexed: 01/21/2023] Open
Abstract
TRAIL-R2 (DR5) is a clinically-relevant therapeutic target and a key target for immune effector cells. Herein, we identify a novel interaction between TRAIL-R2 and the Skp1-Cullin-1-F-box (SCF) Cullin-Ring E3 Ubiquitin Ligase complex containing Skp2 (SCFSkp2). We find that SCFSkp2 can interact with both TRAIL-R2’s pre-ligand association complex (PLAC) and ligand-activated death-inducing signalling complex (DISC). Moreover, Cullin-1 interacts with TRAIL-R2 in its active NEDDylated form. Inhibiting Cullin-1’s DISC recruitment using the NEDDylation inhibitor MLN4924 (Pevonedistat) or siRNA increased apoptosis induction in response to TRAIL. This correlated with enhanced levels of the caspase-8 regulator FLIP at the TRAIL-R2 DISC, particularly the long splice form, FLIP(L). We subsequently found that FLIP(L) (but not FLIP(S), caspase-8, nor the other core DISC component FADD) interacts with Cullin-1 and Skp2. Importantly, this interaction is enhanced when FLIP(L) is in its DISC-associated, C-terminally truncated p43-form. Prevention of FLIP(L) processing to its p43-form stabilises the protein, suggesting that by enhancing its interaction with SCFSkp2, cleavage to the p43-form is a critical step in FLIP(L) turnover. In support of this, we found that silencing any of the components of the SCFSkp2 complex inhibits FLIP ubiquitination, while overexpressing Cullin-1/Skp2 enhances its ubiquitination in a NEDDylation-dependent manner. DISC recruitment of TRAF2, previously identified as an E3 ligase for caspase-8 at the DISC, was also enhanced when Cullin-1’s recruitment was inhibited, although its interaction with Cullin-1 was found to be mediated indirectly via FLIP(L). Notably, the interaction of p43-FLIP(L) with Cullin-1 disrupts its ability to interact with FADD, caspase-8 and TRAF2. Collectively, our results suggest that processing of FLIP(L) to p43-FLIP(L) at the TRAIL-R2 DISC enhances its interaction with co-localised SCFSkp2, leading to disruption of p43-FLIP(L)’s interactions with other DISC components and promoting its ubiquitination and degradation, thereby modulating TRAIL-R2-mediated apoptosis.
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Affiliation(s)
- Jamie Z Roberts
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Caitriona Holohan
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Tamas Sessler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Jennifer Fox
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Nyree Crawford
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Joel S Riley
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Hajrah Khawaja
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Joanna Majkut
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Emma Evergren
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Luke M Humphreys
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Jennifer Ferris
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Catherine Higgins
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | | | - Paul Moynagh
- Department of Biology, National University of Ireland Maynooth, Kildare, Ireland.,Centre for Experimental Medicine, Queen's University Belfast, Belfast, UK
| | - Simon S McDade
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Daniel B Longley
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK.
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Abstract
Possessing structural homology with their active enzyme counterparts but lacking catalytic activity, pseudoenzymes have been identified for all major enzyme groups. Caspases are a family of cysteine‐dependent aspartate‐directed proteases that play essential roles in regulating cell death and inflammation. Here, we discuss the only human pseudo‐caspase, FLIP(L), a paralog of the apoptosis‐initiating caspases, caspase‐8 and caspase‐10. FLIP(L) has been shown to play a key role in regulating the processing and activity of caspase‐8, thereby modulating apoptotic signaling mediated by death receptors (such as TRAIL‐R1/R2), TNF receptor‐1 (TNFR1), and Toll‐like receptors. In this review, these canonical roles of FLIP(L) are discussed. Additionally, a range of nonclassical pseudoenzyme roles are described, in which FLIP(L) functions independently of caspase‐8. These nonclassical pseudoenzyme functions enable FLIP(L) to play key roles in the regulation of a wide range of biological processes beyond its canonical roles as a modulator of cell death.
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Affiliation(s)
- Peter Smyth
- The Patrick G Johnston Centre for Cancer Research, Queen's University, Belfast, UK
| | - Tamas Sessler
- The Patrick G Johnston Centre for Cancer Research, Queen's University, Belfast, UK
| | - Christopher J Scott
- The Patrick G Johnston Centre for Cancer Research, Queen's University, Belfast, UK
| | - Daniel B Longley
- The Patrick G Johnston Centre for Cancer Research, Queen's University, Belfast, UK
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11
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Humphreys LM, Fox JP, Higgins CA, Majkut J, Sessler T, McLaughlin K, McCann C, Roberts JZ, Crawford NT, McDade SS, Scott CJ, Harrison T, Longley DB. A revised model of TRAIL-R2 DISC assembly explains how FLIP(L) can inhibit or promote apoptosis. EMBO Rep 2020; 21:e49254. [PMID: 32009295 PMCID: PMC7054686 DOI: 10.15252/embr.201949254] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 09/10/2019] [Revised: 12/20/2019] [Accepted: 01/13/2020] [Indexed: 11/23/2022] Open
Abstract
The long FLIP splice form FLIP(L) can act as both an inhibitor and promoter of caspase‐8 at death‐inducing signalling complexes (DISCs) formed by death receptors such as TRAIL‐R2 and related intracellular complexes such as the ripoptosome. Herein, we describe a revised DISC assembly model that explains how FLIP(L) can have these opposite effects by defining the stoichiometry (with respect to caspase‐8) at which it converts from being anti‐ to pro‐apoptotic at the DISC. We also show that in the complete absence of FLIP(L), procaspase‐8 activation at the TRAIL‐R2 DISC has significantly slower kinetics, although ultimately the extent of apoptosis is significantly greater. This revised model of DISC assembly also explains why FLIP's recruitment to the TRAIL‐R2 DISC is impaired in the absence of caspase‐8 despite showing that it can interact with the DISC adaptor protein FADD and why the short FLIP splice form FLIP(S) is the more potent inhibitor of DISC‐mediated apoptosis.
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Affiliation(s)
- Luke M Humphreys
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Jennifer P Fox
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Catherine A Higgins
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Joanna Majkut
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Tamas Sessler
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Kirsty McLaughlin
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Christopher McCann
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Jamie Z Roberts
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Nyree T Crawford
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Simon S McDade
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Christopher J Scott
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Timothy Harrison
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Daniel B Longley
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
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Sessler T, Healy S, Samali A, Szegezdi E. Structural determinants of DISC function: new insights into death receptor-mediated apoptosis signalling. Pharmacol Ther 2013; 140:186-99. [PMID: 23845861 DOI: 10.1016/j.pharmthera.2013.06.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [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: 06/13/2013] [Accepted: 06/14/2013] [Indexed: 12/15/2022]
Abstract
Death receptors are members of the tumour necrosis factor (TNF) receptor superfamily characterised by an ~80 amino acid long alpha-helical fold, termed the death domain (DD). Death receptors diversified during early vertebrate evolution indicating that the DD fold has plasticity and specificity that can be easily adjusted to attain additional functions. Eight members of the death receptor family have been identified in humans, which can be divided into four structurally homologous groups or clades, namely: the p75(NTR) clade (consisting of ectodysplasin A receptor, death receptor 6 (DR6) and p75 neurotrophin (NTR) receptor); the tumour necrosis factor receptor 1 clade (TNFR1 and DR3), the CD95 clade (CD95/FAS) and the TNF-related apoptosis-inducing ligand receptor (TRAILR) clade (TRAILR1 and TRAILR2). Receptors in the same clade participate in similar processes indicating that structural diversification enabled functional specialisation. On the surface of nearly all human cells multiple death receptors are expressed, enabling the cell to respond to a plethora of external signals. Activation of different death receptors converges on the activation of three main signal transduction pathways: nuclear factor-κB-mediated differentiation or inflammation, mitogen-associated protein kinase-mediated stress response and caspase-mediated apoptosis. While the ability to induce cell death is true for nearly all DRs, the FAS and TRAILR clades have specialised in inducing cell death. Here we summarise recent discoveries about the molecular regulation and structural requirements of apoptosis induction by death receptors and discuss how this information can be used to better explain the biological functions, similarities and distinguishing features of death receptors.
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Affiliation(s)
- Tamas Sessler
- Apoptosis Research Centre, National University of Ireland, Galway, Ireland
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van Dijk M, Halpin-McCormick A, Sessler T, Samali A, Szegezdi E. Resistance to TRAIL in non-transformed cells is due to multiple redundant pathways. Cell Death Dis 2013; 4:e702. [PMID: 23828565 PMCID: PMC3730397 DOI: 10.1038/cddis.2013.214] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [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: 12/20/2012] [Revised: 04/03/2013] [Accepted: 04/05/2013] [Indexed: 11/09/2022]
Abstract
Tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) is a cytokine and a selective inducer of apoptosis in a range of tumour cells, but not in normal, untransformed cells. A large number of chemotherapeutics as well as biological agents are being tested for their potential to sensitise resistant tumour cells to TRAIL as a means to broaden the range of tumours treatable with TRAIL. However, because of the incomplete understanding of the mechanism(s) underlying TRAIL resistance in non-malignant cells, it is unpredictable whether the effect of these sensitisers will be restricted to tumour cells or they would also sensitise non-transformed cells causing unwanted toxicity. In this study, we carried out a systematic analysis of the mechanisms driving TRAIL resistance in non-transformed cells. We found that cellular FLICE-like inhibitory protein, anti-apoptotic B-cell lymphoma 2 proteins, and X-linked inhibitor of apoptosis protein were independently able to provide resistance to TRAIL. Deficiency of only one of these proteins was not sufficient to elicit TRAIL sensitivity, demonstrating that in non-transformed cells multiple pathways control TRAIL resistance and they act in a redundant manner. This is contrary to the resistance mechanisms found in tumour cell types, many of them tend to rely on a single mechanism of resistance. Supporting this notion we found that 76% of TRAIL-resistant cell lines (13 out of 17) expressed only one of the above-identified anti-apoptotic proteins at a high level (≥1.2-fold higher than the mean expression across all cell lines). Furthermore, inhibition or knockdown of the single overexpressed protein in these tumour cells was sufficient to trigger TRAIL sensitivity. Therefore, the redundancy in resistance pathways in non-transformed cells may offer a safe therapeutic window for TRAIL-based combination therapies where selective sensitisation of the tumour to TRAIL can be achieved by targeting the single non-redundant resistance pathway.
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Affiliation(s)
- M van Dijk
- Apoptosis Research Centre, School of Natural Sciences, National University of Ireland, Galway, Ireland
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