1
|
Baxter MA, Spender LC, Cairns D, Walsh S, Oparka R, Porter RJ, Bray S, Skinner G, King S, Turbitt J, Collinson D, Miedzybrodzka ZH, Jellema G, Logan G, Kennedy RD, Turkington RC, McLean MH, Swinson D, Grabsch HI, Lord S, Seymour MJ, Hall PS, Petty RD. An investigation of the clinical impact and therapeutic relevance of a DNA damage immune response (DDIR) signature in patients with advanced gastroesophageal adenocarcinoma. ESMO Open 2024; 9:103450. [PMID: 38744099 PMCID: PMC11108838 DOI: 10.1016/j.esmoop.2024.103450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND An improved understanding of which gastroesophageal adenocarcinoma (GOA) patients respond to both chemotherapy and immune checkpoint inhibitors (ICI) is needed. We investigated the predictive role and underlying biology of a 44-gene DNA damage immune response (DDIR) signature in patients with advanced GOA. MATERIALS AND METHODS Transcriptional profiling was carried out on pretreatment tissue from 252 GOA patients treated with platinum-based chemotherapy (three dose levels) within the randomized phase III GO2 trial. Cross-validation was carried out in two independent GOA cohorts with transcriptional profiling, immune cell immunohistochemistry and epidermal growth factor receptor (EGFR) fluorescent in situ hybridization (FISH) (n = 430). RESULTS In the GO2 trial, DDIR-positive tumours had a greater radiological response (51.7% versus 28.5%, P = 0.022) and improved overall survival in a dose-dependent manner (P = 0.028). DDIR positivity was associated with a pretreatment inflamed tumour microenvironment (TME) and increased expression of biomarkers associated with ICI response such as CD274 (programmed death-ligand 1, PD-L1) and a microsatellite instability RNA signature. Consensus pathway analysis identified EGFR as a potential key determinant of the DDIR signature. EGFR amplification was associated with DDIR negativity and an immune cold TME. CONCLUSIONS Our results indicate the importance of the GOA TME in chemotherapy response, its relationship to DNA damage repair and EGFR as a targetable driver of an immune cold TME. Chemotherapy-sensitive inflamed GOAs could benefit from ICI delivered in combination with standard chemotherapy. Combining EGFR inhibitors and ICIs warrants further investigation in patients with EGFR-amplified tumours.
Collapse
Affiliation(s)
- M A Baxter
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee; Tayside Cancer Centre, Ninewells Hospital and Medical School, NHS Tayside, Dundee.
| | - L C Spender
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee
| | - D Cairns
- Leeds Cancer Research UK Clinical Trials Unit, Leeds Institute of Clinical Trials Research, University of Leeds, Leeds
| | - S Walsh
- Department of Pathology, Ninewells Hospital and Medical School, NHS Tayside, Dundee
| | - R Oparka
- Department of Pathology, Ninewells Hospital and Medical School, NHS Tayside, Dundee
| | - R J Porter
- Department of Pathology, CRUK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh
| | - S Bray
- Tayside Biorepository, University of Dundee, Dundee
| | - G Skinner
- Tayside Biorepository, University of Dundee, Dundee
| | - S King
- Tayside Biorepository, University of Dundee, Dundee
| | - J Turbitt
- Genetics and Molecular Pathology Laboratory Services, NHS Grampian, Aberdeen
| | - D Collinson
- Genetics and Molecular Pathology Laboratory Services, NHS Grampian, Aberdeen
| | - Z H Miedzybrodzka
- Genetics and Molecular Pathology Laboratory Services, NHS Grampian, Aberdeen; School of Medicine, Medical Sciences, Nutrition and Dentistry, Polwarth Building, University of Aberdeen, Aberdeen
| | - G Jellema
- Almac Diagnostic Services, Craigavon
| | - G Logan
- Almac Diagnostic Services, Craigavon
| | - R D Kennedy
- Almac Diagnostic Services, Craigavon; Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast
| | - R C Turkington
- Almac Diagnostic Services, Craigavon; Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast
| | - M H McLean
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee; Tayside Cancer Centre, Ninewells Hospital and Medical School, NHS Tayside, Dundee
| | - D Swinson
- St James's University Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - H I Grabsch
- Department of Pathology, GROW School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, The Netherlands; Division of Pathology and Data Analytics, Leeds Institute of Medical Research at St James's University, University of Leeds, Leeds
| | - S Lord
- Department of Oncology, University of Oxford, Oxford
| | - M J Seymour
- Leeds Cancer Research UK Clinical Trials Unit, Leeds Institute of Clinical Trials Research, University of Leeds, Leeds; St James's University Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - P S Hall
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh, UK
| | - R D Petty
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee; Tayside Cancer Centre, Ninewells Hospital and Medical School, NHS Tayside, Dundee.
| |
Collapse
|
2
|
Sharma P, Stecklein SR, Yoder R, Staley JM, Schwensen K, O’Dea A, Nye L, Satelli D, Crane G, Madan R, O’Neil MF, Wagner J, Larson KE, Balanoff C, Kilgore L, Phadnis MA, Godwin AK, Salgado R, Khan QJ, O’Shaughnessy J. Clinical and Biomarker Findings of Neoadjuvant Pembrolizumab and Carboplatin Plus Docetaxel in Triple-Negative Breast Cancer: NeoPACT Phase 2 Clinical Trial. JAMA Oncol 2024; 10:227-235. [PMID: 37991778 PMCID: PMC10666040 DOI: 10.1001/jamaoncol.2023.5033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/22/2023] [Indexed: 11/23/2023]
Abstract
Importance Addition of pembrolizumab to anthracycline-based chemotherapy improves pathologic complete response (pCR) and event-free survival (EFS) in triple-negative breast cancer (TNBC). The efficacy of anthracycline-free chemoimmunotherapy in TNBC has not been assessed. Objective To assess the efficacy of the anthracycline-free neoadjuvant regimen of carboplatin and docetaxel plus pembrolizumab in TNBC. Design, Setting, and Participants This was an open-label phase 2 clinical trial including a single group of patients with stage I to III TNBC enrolled at 2 sites who received neoadjuvant carboplatin and docetaxel plus pembrolizumab every 21 days for 6 cycles. Participants were enrolled from 2018 to 2022. Intervention or Exposure Carboplatin (with an area under the free carboplatin plasma concentration vs time curve of 6) and docetaxel (75 mg/m2) plus pembrolizumab (200 mg) every 21 days for 6 cycles. Myeloid growth factor support was administered with all cycles. Main Outcomes and Measures Primary end point was pathologic complete response (pCR) defined as no evidence of invasive tumor in breast and axilla. The secondary end points were residual cancer burden, EFS, toxicity, and immune biomarkers. RNA isolated from pretreatment tumor tissue was subjected to next-generation sequencing. Specimens were classified as positive or negative for the 44-gene DNA damage immune response (DDIR) signature and for the 27-gene tumor immune microenvironment (TIM; DetermaIO) signature using predefined cutoffs. Stromal tumor-infiltrating lymphocytes (sTILs) were evaluated using standard criteria. Programmed cell death-ligand 1 (PD-L1) testing was performed using a standard immunohistochemical assay. Results Among the eligible study population of 115 female patients (median [range] age, 50 [27-70] years) who enrolled from September 2018 to January 2022, 39% had node-positive disease. pCR and residual cancer burden 0 + 1 rates were 58% (95% CI, 48%-67%) and 69% (95% CI, 60%-78%), respectively. Grade 3 or higher immune-mediated adverse events were observed in 3.5% of patients. sTILs, PD-L1, DDIR, and TIM were each predictive of pCR in multivariable analyses. The areas under curve for pCR were 0.719, 0.740, 0.699, and 0.715 for sTILs, PD-L1, DDIR, and TIM, respectively. Estimated 3-year EFS was 86% in all patients; 98% in pCR group and 68% in no-pCR group. Conclusions and Relevance The findings of the phase 2 clinical trial indicate that neoadjuvant carboplatin and docetaxel plus pembrolizumab shows encouraging pCR and 3-year EFS. The regimen was well tolerated, and immune enrichment as identified by various biomarkers was independently predictive of pCR. These results provide data on an alternative anthracycline-free chemoimmunotherapy regimen for patients who are not eligible for anthracycline-based regimens and support further evaluation of this regimen as a chemotherapy de-escalation strategy in randomized studies for TNBC. Trial Registration ClinicalTrials.gov Identifier: NCT03639948.
Collapse
Affiliation(s)
- Priyanka Sharma
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
| | - Shane R. Stecklein
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City
| | - Rachel Yoder
- The University of Kansas Cancer Center, Kansas City
| | | | - Kelsey Schwensen
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
| | - Anne O’Dea
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
| | - Lauren Nye
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
| | - Deepti Satelli
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
| | - Gregory Crane
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
| | - Rashna Madan
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City
| | - Maura F. O’Neil
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City
| | - Jamie Wagner
- Department of Surgery, University of Kansas Medical Center, Kansas City
| | - Kelsey E. Larson
- Department of Surgery, University of Kansas Medical Center, Kansas City
| | - Christa Balanoff
- Department of Surgery, University of Kansas Medical Center, Kansas City
| | - Lyndsey Kilgore
- Department of Surgery, University of Kansas Medical Center, Kansas City
| | - Milind A. Phadnis
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City
| | - Andrew K. Godwin
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City
- The University of Kansas Cancer Center, Kansas City
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter Mac Callum Canter Centre, Melbourne, Australia
| | - Qamar J. Khan
- Department of Internal Medicine, University of Kansas Medical Center, Westwood
| | | |
Collapse
|
3
|
Tsukamoto Y, Kurogi S, Fujishima H, Shibata T, Fumoto S, Nishiki K, Suzuki K, Etoh T, Shiraishi N, Fuchino T, Hirashita Y, Nakada C, Uchida T, Inomata M, Moriyama M, Hijiya N. Association of immune-related expression profile with sensitivity to chemotherapy in esophageal squamous cell carcinoma. Cancer Sci 2023; 114:4459-4474. [PMID: 37715346 PMCID: PMC10637075 DOI: 10.1111/cas.15942] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/22/2023] [Accepted: 08/04/2023] [Indexed: 09/17/2023] Open
Abstract
Neoadjuvant chemotherapy (NAC) followed by surgery is one of the standard therapeutic approaches in Japan for patients with locally advanced esophageal carcinoma. Recently, the JCOG1109 study revealed that NAC with docetaxel, cisplatin and 5-fluorouracil (5-FU) (DCF-NAC) is superior to NAC with cisplatin and 5-FU, and has now become the standard preoperative chemotherapy. Using a microarray system, we have previously investigated the expression profiles of endoscopic biopsy samples from patients with esophageal squamous cell carcinoma (ESCC) before DCF-NAC (preNAC) and identified 17 molecules as biomarkers predictive of a pathologically complete response to DCF-NAC. Here, we re-grouped our previous dataset based on the histopathological response grade with the addition of several microarray profiles and conducted a re-analysis using bioinformatic web tools including DAVID, GSEA, UALCAN, and CIBERSORTx. We identified 204 genes that were differentially expressed between the highly resistant and sensitive groups. Some of these differentially expressed genes (DEGs) were related to the immune response and showed higher expression in the sensitive group. UALCAN showed that high expression of 28 of the top 50 DEGs was associated with a favorable prognosis (p < 0.25), and that this reached a significant (p < 0.05) level for 18 of them, suggesting that patients with high expression of these genes might have benefited from chemotherapy and thus had a better outcome. In preNAC biopsy tissues from a DCF-sensitive case, we demonstrated the presence of cells expressing mRNA for CXCL9, one of the prognosis-related DEGs. Our results highlight the association of immune-related expression profile in preNAC ESCC with the DCF-NAC efficacy.
Collapse
Affiliation(s)
- Yoshiyuki Tsukamoto
- Department of Molecular Pathology, Faculty of MedicineOita UniversityOitaJapan
| | - Shusaku Kurogi
- Department of Molecular Pathology, Faculty of MedicineOita UniversityOitaJapan
| | - Hajime Fujishima
- Department of Gastroenterological and Pediatric Surgery, Faculty of MedicineOita UniversityOitaJapan
| | - Tomotaka Shibata
- Department of Gastroenterological and Pediatric Surgery, Faculty of MedicineOita UniversityOitaJapan
| | | | - Kohei Nishiki
- Department of SurgeryOita Nakamura HospitalOitaJapan
| | - Kosuke Suzuki
- Department of Gastroenterological and Pediatric Surgery, Faculty of MedicineOita UniversityOitaJapan
| | - Tsuyoshi Etoh
- Department of Gastroenterological and Pediatric Surgery, Faculty of MedicineOita UniversityOitaJapan
| | - Norio Shiraishi
- Comprehensive Surgery for Community Medicine, Oita University Faculty of MedicineOita UniversityOitaJapan
| | - Takafumi Fuchino
- Department of Molecular Pathology, Faculty of MedicineOita UniversityOitaJapan
- Department of Gastroenterology, Faculty of MedicineOita UniversityOitaJapan
| | - Yuka Hirashita
- Department of Molecular Pathology, Faculty of MedicineOita UniversityOitaJapan
- Department of Gastroenterology, Faculty of MedicineOita UniversityOitaJapan
| | - Chisato Nakada
- Department of Molecular Pathology, Faculty of MedicineOita UniversityOitaJapan
- Department of Urology, Faculty of MedicineOita UniversityOitaJapan
| | - Tomohisa Uchida
- Department of Molecular Pathology, Faculty of MedicineOita UniversityOitaJapan
| | - Masafumi Inomata
- Department of Gastroenterological and Pediatric Surgery, Faculty of MedicineOita UniversityOitaJapan
| | - Masatsugu Moriyama
- Department of Molecular Pathology, Faculty of MedicineOita UniversityOitaJapan
| | - Naoki Hijiya
- Department of Molecular Pathology, Faculty of MedicineOita UniversityOitaJapan
| |
Collapse
|
4
|
Tovey H, Sipos O, Parker JS, Hoadley KA, Quist J, Kernaghan S, Kilburn L, Salgado R, Loi S, Kennedy RD, Roxanis I, Gazinska P, Pinder SE, Bliss J, Perou CM, Haider S, Grigoriadis A, Tutt A, Cheang MCU. Integrated Multimodal Analyses of DNA Damage Response and Immune Markers as Predictors of Response in Metastatic Triple-Negative Breast Cancer in the TNT Trial (NCT00532727). Clin Cancer Res 2023; 29:3691-3705. [PMID: 37574209 PMCID: PMC10502473 DOI: 10.1158/1078-0432.ccr-23-0370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/23/2023] [Accepted: 07/24/2023] [Indexed: 08/15/2023]
Abstract
PURPOSE The TNT trial (NCT00532727) showed no evidence of carboplatin superiority over docetaxel in metastatic triple-negative breast cancer (mTNBC), but carboplatin benefit was observed in the germline BRCA1/2 mutation subgroup. Broader response-predictive biomarkers are needed. We explored the predictive ability of DNA damage response (DDR) and immune markers. EXPERIMENTAL DESIGN Tumor-infiltrating lymphocytes were evaluated for 222 of 376 patients. Primary tumors (PT) from 186 TNT participants (13 matched recurrences) were profiled using total RNA sequencing. Four transcriptional DDR-related and 25 immune-related signatures were evaluated. We assessed their association with objective response rate (ORR) and progression-free survival (PFS). Conditional inference forest clustering was applied to integrate multimodal data. The biology of subgroups was characterized by 693 gene expression modules and other markers. RESULTS Transcriptional DDR-related biomarkers were not predictive of ORR to either treatment overall. Changes from PT to recurrence were demonstrated; in chemotherapy-naïve patients, transcriptional DDR markers separated carboplatin responders from nonresponders (P values = 0.017; 0.046). High immune infiltration was associated with docetaxel ORR (interaction P values < 0.05). Six subgroups were identified; the immune-enriched cluster had preferential docetaxel response [62.5% (D) vs. 29.4% (C); P = 0.016]. The immune-depleted cluster had preferential carboplatin response [8.0% (D) vs. 40.0% (C); P = 0.011]. DDR-related subgroups were too small to assess ORR. CONCLUSIONS High immune features predict docetaxel response, and high DDR signature scores predict carboplatin response in treatment-naïve mTNBC. Integrating multimodal DDR and immune-related markers identifies subgroups with differential treatment sensitivity. Treatment options for patients with immune-low and DDR-proficient tumors remains an outstanding need. Caution is needed using PT-derived transcriptional signatures to direct treatment in mTNBC, particularly DDR-related markers following prior chemotherapy.
Collapse
Affiliation(s)
- Holly Tovey
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Orsolya Sipos
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Joel S. Parker
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Katherine A. Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jelmar Quist
- The Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Sarah Kernaghan
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Lucy Kilburn
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
| | - Sherene Loi
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Ioannis Roxanis
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Patrycja Gazinska
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
- Biobank Research Group, Lukasiewicz Research Network – PORT Polish Center for Technology Development, Wroclaw, Poland
| | - Sarah E. Pinder
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Judith Bliss
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Charles M. Perou
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Syed Haider
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Anita Grigoriadis
- The Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Andrew Tutt
- Breast Cancer Now Toby Robinsons Research Centre, The Institute of Cancer Research, London, United Kingdom
- The Breast Cancer Now Unit, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
- School of Cancer and Pharmaceutical Sciences, King's College London Faculty of Life Sciences and Medicine, London, United Kingdom
| | - Maggie Chon U. Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London, United Kingdom
| |
Collapse
|
5
|
Stecklein SR, Barlow W, Pusztai L, Timms K, Kennedy R, Logan GE, Seitz R, Badve S, Gökmen-Polar Y, Porter P, Linden H, Tripathy D, Hortobagyi GN, Godwin AK, Thompson A, Hayes DF, Sharma P. Dual Prognostic Classification of Triple-Negative Breast Cancer by DNA Damage Immune Response and Homologous Recombination Deficiency. JCO Precis Oncol 2023; 7:e2300197. [PMID: 37972336 PMCID: PMC10681491 DOI: 10.1200/po.23.00197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/12/2023] [Accepted: 09/11/2023] [Indexed: 11/19/2023] Open
Abstract
PURPOSE Triple-negative breast cancer (TNBC) is a heterogeneous disease. We previously showed that homologous recombination deficiency (HRD) and the DNA damage immune response (DDIR) signature are prognostic in TNBC. We hypothesized that these biomarkers reflect related but not completely interdependent biological processes, that their combined use would be prognostic, and that simultaneous assessment of the immunologic microenvironment and susceptibility to DNA damaging therapies might be able to identify subgroups with distinct therapeutic vulnerabilities. METHODS We analyzed the dual DDIR/HRD classification in 341 patients with TNBC treated with adjuvant anthracycline-based chemotherapy on the SWOG S9313 trial and corroborated our findings in The Cancer Genome Atlas breast cancer data set. RESULTS DDIR/HRD classification is highly prognostic in TNBC and identifies biologically and immunologically distinct subgroups. Immune-enriched DDIR+/HRD+ TNBCs have the most favorable prognosis, and DDIR+/HRD- and DDIR-/HRD+ TNBCs have favorable intermediate prognosis, despite the latter being immune-depleted. DDIR-/HRD- TNBCs have the worst prognosis and represent an internally heterogeneous group of immune-depleted chemoresistant tumors. CONCLUSION Our findings propose DDIR/HRD classification as a potentially clinically relevant approach to categorize tumors on the basis of therapeutic vulnerabilities.
Collapse
Affiliation(s)
| | | | | | | | - Richard Kennedy
- Almac Diagnostic Services, Craigavon, Northern Ireland, United Kingdom
- Patrick G Johnston Centre for Cancer Research, Queen's University of Belfast, Belfast, United Kingdom
| | - Gemma E Logan
- Almac Diagnostic Services, Craigavon, Northern Ireland, United Kingdom
| | | | - Sunil Badve
- Emory University School of Medicine, Atlanta, GA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Lang JD, Nguyen TVV, Levin MK, Blas PE, Williams HL, Rodriguez ESR, Briones N, Mueller C, Selleck W, Moore S, Zismann VL, Hendricks WPD, Espina V, O'Shaughnessy J. Pilot clinical trial and phenotypic analysis in chemotherapy-pretreated, metastatic triple-negative breast cancer patients treated with oral TAK-228 and TAK-117 (PIKTOR) to increase DNA damage repair deficiency followed by cisplatin and nab paclitaxel. Biomark Res 2023; 11:73. [PMID: 37491309 PMCID: PMC10369813 DOI: 10.1186/s40364-023-00511-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/04/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND A subset of triple-negative breast cancers (TNBCs) have homologous recombination deficiency with upregulation of compensatory DNA repair pathways. PIKTOR, a combination of TAK-228 (TORC1/2 inhibitor) and TAK-117 (PI3Kα inhibitor), is hypothesized to increase genomic instability and increase DNA damage repair (DDR) deficiency, leading to increased sensitivity to DNA-damaging chemotherapy and to immune checkpoint blockade inhibitors. METHODS 10 metastatic TNBC patients received 4 mg TAK-228 and 200 mg TAK-117 (PIKTOR) orally each day for 3 days followed by 4 days off, weekly, until disease progression (PD), followed by intravenous cisplatin 75 mg/m2 plus nab paclitaxel 220 mg/m2 every 3 weeks for up to 6 cycles. Patients received subsequent treatment with pembrolizumab and/or chemotherapy. Primary endpoints were objective response rate with cisplatin/nab paclitaxel and safety. Biopsies of a metastatic lesion were collected prior to and at PD on PIKTOR. Whole exome and RNA-sequencing and reverse phase protein arrays (RPPA) were used to phenotype tumors pre- and post-PIKTOR for alterations in DDR, proliferation, and immune response. RESULTS With cisplatin/nab paclitaxel (cis/nab pac) therapy post PIKTOR, 3 patients had clinical benefit (1 partial response (PR) and 2 stable disease (SD) ≥ 6 months) and continued to have durable benefit in progression-free survival with pembrolizumab post-cis/nab pac for 1.2, 2, and 3.6 years. Their post-PIKTOR metastatic tissue displayed decreased mismatch repair (MMR), increased tumor mutation burden, and significantly lower levels of 53BP1, DAG Lipase β, GCN2, AKT Ser473, and PKCzeta Thr410/403 compared to pre-PIKTOR tumor tissue. CONCLUSIONS Priming patients' chemotherapy-pretreated metastatic TNBC with PIKTOR led to very prolonged response/disease control with subsequent cis/nab pac, followed by pembrolizumab, in 3 of 10 treated patients. Our multi-omics approach revealed a higher number of genomic alterations, reductions in MMR, and alterations in immune and stress response pathways post-PIKTOR in patients who had durable responses. TRIAL REGISTRATION This clinical trial was registered on June 21, 2017, at ClinicalTrials.gov using identifier NCT03193853.
Collapse
Affiliation(s)
- Jessica D Lang
- The Translational Genomics Research Institute (TGen), Integrated Cancer Genomics Division, Phoenix, AZ, 85004, USA
- Department of Pathology and Laboratory Medicine, Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Tuong Vi V Nguyen
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 22030, USA
| | - Maren K Levin
- Baylor Scott & White Research Institute, Dallas, TX, 75246, USA
| | - Page E Blas
- Baylor Scott & White Research Institute, Dallas, TX, 75246, USA
| | | | | | - Natalia Briones
- The Translational Genomics Research Institute (TGen), Integrated Cancer Genomics Division, Phoenix, AZ, 85004, USA
| | - Claudius Mueller
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 22030, USA
| | - William Selleck
- The Translational Genomics Research Institute (TGen), Integrated Cancer Genomics Division, Phoenix, AZ, 85004, USA
| | - Sarah Moore
- The Translational Genomics Research Institute (TGen), Integrated Cancer Genomics Division, Phoenix, AZ, 85004, USA
| | - Victoria L Zismann
- The Translational Genomics Research Institute (TGen), Integrated Cancer Genomics Division, Phoenix, AZ, 85004, USA
| | - William P D Hendricks
- The Translational Genomics Research Institute (TGen), Integrated Cancer Genomics Division, Phoenix, AZ, 85004, USA
| | - Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, 22030, USA
| | - Joyce O'Shaughnessy
- Baylor University Medical Center, Texas Oncology, 3410 Worth Street, Suite 400, Dallas, TX, 75246, USA.
| |
Collapse
|
7
|
A Clinical Prediction Model for Breast Cancer in Women Having Their First Mammogram. Healthcare (Basel) 2023; 11:healthcare11060856. [PMID: 36981513 PMCID: PMC10048653 DOI: 10.3390/healthcare11060856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/17/2023] Open
Abstract
Background: Digital mammography is the most efficient screening and diagnostic modality for breast cancer (BC). However, the technology is not widely available in rural areas. This study aimed to construct a prediction model for BC in women scheduled for their first mammography at a breast center to prioritize patients on waiting lists. Methods: This retrospective cohort study analyzed breast clinic data from January 2013 to December 2017. Clinical parameters that were significantly associated with a BC diagnosis were used to construct predictive models using stepwise multiple logistic regression. The models’ discriminative capabilities were compared using receiver operating characteristic curves (AUCs). Results: Data from 822 women were selected for analysis using an inverse probability weighting method. Significant risk factors were age, body mass index (BMI), family history of BC, and indicated symptoms (mass and/or nipple discharge). When these factors were used to construct a model, the model performance according to the Akaike criterion was 1387.9, and the AUC was 0.82 (95% confidence interval: 0.76–0.87). Conclusion: In a resource-limited setting, the priority for a first mammogram should be patients with mass and/or nipple discharge, asymptomatic patients who are older or have high BMI, and women with a family history of BC.
Collapse
|
8
|
Shapiro GI, Barry SM. Combining PARP Inhibition and Immunotherapy in BRCA-Associated Cancers. Cancer Treat Res 2023; 186:207-221. [PMID: 37978138 DOI: 10.1007/978-3-031-30065-3_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Poly (ADP-ribose) polymerase (PARP) inhibitors have significantly improved treatment outcomes of homologous recombination (HR) repair-deficient cancers. While the activity of these agents is largely linked to multiple mechanisms underlying the synthetic lethality of PARP inhibition and HR deficiency, emerging data suggest that their efficacy is also tied to their effects on the immune microenvironment and dependent upon cytotoxic T-cell activation. Effects observed in preclinical models are currently being validated in on-treatment biopsy samples procured from patients enrolled in clinical trials. Although this work has stimulated the development of combinations of PARP inhibitors with immunomodulatory agents, results to date have not demonstrated the superiority of combined PARP inhibition and immune checkpoint blockade compared with PARP inhibition alone. These results have stimulated a more comprehensive assessment of the immunosuppressive components of the tumor microenvironment that must be addressed so that the efficacy of PARP inhibitor agents can be maximized.
Collapse
Affiliation(s)
- Geoffrey I Shapiro
- Department of Medical Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA.
| | - Suzanne M Barry
- Department of Medical Oncology and Center for DNA Damage and Repair, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| |
Collapse
|
9
|
The DNA damage induced immune response: Implications for cancer therapy. DNA Repair (Amst) 2022; 120:103409. [DOI: 10.1016/j.dnarep.2022.103409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 11/18/2022]
|
10
|
Beirne JP, Gilmore A, McInerney CE, Roddy A, Glenn McCluggage W, Harley IJ, Abdullah Alvi M, Prise KM, McArt DG, Mullan PB. A bespoke target selection tool to guide biomarker discovery in tubo-ovarian cancer. Comput Struct Biotechnol J 2022; 20:3359-3371. [PMID: 35832628 PMCID: PMC9260242 DOI: 10.1016/j.csbj.2022.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/26/2022] Open
Abstract
Introduction Cancers presenting at advanced stages inherently have poor prognosis. High grade serous carcinoma (HGSC) is the most common and aggressive form of tubo-ovarian cancer. Clinical tests to accurately diagnose and monitor this condition are lacking. Hence, development of disease-specific tests are urgently required. Methods The molecular profile of HGSC during disease progression was investigated in a unique patient cohort. A bespoke data browser was developed to analyse gene expression and DNA methylation datasets for biomarker discovery. The Ovarian Cancer Data Browser (OCDB) is built in C# with a.NET framework using an integrated development environment of Microsoft Visual Studio and fast access files (.faf). The graphical user interface is easy to navigate between four analytical modes (gene expression; methylation; combined gene expression and methylation data; methylation clusters), with a rapid query response time. A user should first define a disease progression trend for prioritising results. Single or multiomics data are then mined to identify probes, genes and methylation clusters that exhibit the desired trend. A unique scoring system based on the percentage change in expression/methylation between disease stages is used. Results are filtered and ranked using weighting and penalties. Results The OCDB’s utility for biomarker discovery is demonstrated with the identified target OSR2. Trends in OSR2 repression and hypermethylation with HGSC disease progression were confirmed in the browser samples and an independent cohort using bioassays. The OSR2 methylation biomarker could discriminate HGSC with high specificity (95%) and sensitivity (93.18%). Conclusions The OCDB has been refined and validated to be an integral part of a unique biomarker discovery pipeline. It may also be used independently to aid identification of novel targets. It carries the potential to identify further biomarker assays that can reduce type I and II errors within clinical diagnostics.
Collapse
|
11
|
Parkes EE, Savage KI, Lioe T, Boyd C, Halliday S, Walker SM, Lowry K, Knight L, Buckley NE, Grogan A, Logan GE, Clayton A, Hurwitz J, Kirk SJ, Xu J, Sidi FA, Humphries MP, Bingham V, James JA, James CR, Paul Harkin D, Kennedy RD, McIntosh SA. Activation of a cGAS-STING-mediated immune response predicts response to neoadjuvant chemotherapy in early breast cancer. Br J Cancer 2022; 126:247-258. [PMID: 34728791 PMCID: PMC8770594 DOI: 10.1038/s41416-021-01599-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 09/21/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The DNA-damage immune-response (DDIR) signature is an immune-driven gene expression signature retrospectively validated as predicting response to anthracycline-based therapy. This feasibility study prospectively evaluates the use of this assay to predict neoadjuvant chemotherapy response in early breast cancer. METHODS This feasibility study assessed the integration of a novel biomarker into clinical workflows. Tumour samples were collected from patients receiving standard of care neoadjuvant chemotherapy (FEC + /-taxane and anti-HER2 therapy as appropriate) at baseline, mid- and post-chemotherapy. Baseline DDIR signature scores were correlated with pathological treatment response. RNA sequencing was used to assess chemotherapy/response-related changes in biologically linked gene signatures. RESULTS DDIR signature reports were available within 14 days for 97.8% of 46 patients (13 TNBC, 16 HER2 + ve, 27 ER + HER2-ve). Positive scores predicted response to treatment (odds ratio 4.67 for RCB 0-1 disease (95% CI 1.13-15.09, P = 0.032)). DDIR positivity correlated with immune infiltration and upregulated immune-checkpoint gene expression. CONCLUSIONS This study validates the DDIR signature as predictive of response to neoadjuvant chemotherapy which can be integrated into clinical workflows, potentially identifying a subgroup with high sensitivity to anthracycline chemotherapy. Transcriptomic data suggest induction with anthracycline-containing regimens in immune restricted, "cold" tumours may be effective for immune priming. TRIAL REGISTRATION Not applicable (non-interventional study). CRUK Internal Database Number 14232.
Collapse
Affiliation(s)
- Eileen E Parkes
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Kienan I Savage
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Tong Lioe
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Clinton Boyd
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Sophia Halliday
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Steven M Walker
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Keith Lowry
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Laura Knight
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Niamh E Buckley
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Andrena Grogan
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Gemma E Logan
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Alison Clayton
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Jane Hurwitz
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - Stephen J Kirk
- South Eastern Health and Social Care Trust, Ulster Hospital, Upper Newtownards Road, BT 16 1RH, Dundonald, UK
| | - Jiamei Xu
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Fatima Abdullahi Sidi
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Matthew P Humphries
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Victoria Bingham
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Jaqueline A James
- Precision Medicine Centre, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
| | - Colin R James
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK
| | - D Paul Harkin
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Richard D Kennedy
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK
- Almac Diagnostic Services, Almac Group, 19 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK
| | - Stuart A McIntosh
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, UK.
- Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast, BT9 7AB, UK.
| |
Collapse
|
12
|
Bieńkowski M, Tomasik B, Braun M, Jassem J. PARP inhibitors for metastatic castration-resistant prostate cancer: Biological rationale and current evidence. Cancer Treat Rev 2022; 104:102359. [DOI: 10.1016/j.ctrv.2022.102359] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 12/27/2022]
|
13
|
Imyanitov EN, Iyevleva AG. Molecular tests for prediction of tumor sensitivity to cytotoxic drugs. Cancer Lett 2022; 526:41-52. [PMID: 34808283 DOI: 10.1016/j.canlet.2021.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/15/2021] [Accepted: 11/16/2021] [Indexed: 11/15/2022]
Abstract
Chemotherapy constitutes the backbone of cancer treatment. Several predictive assays assist personalized administration of cytotoxic drugs and are recommended for use in a clinical setting. The deficiency of DNA repair by homologous recombination (HRD), which is caused by inactivation of BRCA1/2 genes or other genetic events, is associated with high tumor responsiveness to platinum compounds, bifunctional alkylating agents and topoisomerase II poisons. Low activity of MGMT predicts the efficacy of nitrosoureas and tetrazines. Some clinically established pharmacogenetic tests allow for the adjustment of drug dosage, for example, the analysis of DPYD allelic variants for administration of fluoropyrimidines and UGT1A1 genotyping for the use of irinotecan. While there are promising molecular predictors of tumor sensitivity to pemetrexed, gemcitabine and taxanes, they remain in the investigational stage and require additional validation. Comprehensive molecular analysis of tumors obtained from drug responders and non-responders is likely to reveal new clinically useful predictive markers for cytotoxic therapy.
Collapse
Affiliation(s)
- Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg, 194100, Russia; Department of Oncology, I.I. Mechnikov North-Western Medical University, St.-Petersburg, 191015, Russia.
| | - Aglaya G Iyevleva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg, 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg, 194100, Russia
| |
Collapse
|
14
|
When breaks get hot: inflammatory signaling in BRCA1/2-mutant cancers. Trends Cancer 2022; 8:174-189. [PMID: 35000881 DOI: 10.1016/j.trecan.2021.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/24/2022]
Abstract
Genomic instability and inflammation are intricately connected hallmark features of cancer. DNA repair defects due to BRCA1/2 mutation instigate immune signaling through the cGAS/STING pathway. The subsequent inflammatory signaling provides both tumor-suppressive as well as tumor-promoting traits. To prevent clearance by the immune system, genomically instable cancer cells need to adapt to escape immune surveillance. Currently, it is unclear how genomically unstable cancers, including BRCA1/2-mutant tumors, are rewired to escape immune clearance. Here, we summarize the mechanisms by which genomic instability triggers inflammatory signaling and describe adaptive mechanisms by which cancer cells can 'fly under the radar' of the immune system. Additionally, we discuss how therapeutic activation of the immune system may improve treatment of genomically instable cancers.
Collapse
|
15
|
Hsiao YW, Lu TP. Race-Specific Genetic Profiles of Homologous Recombination Deficiency in Multiple Cancers. J Pers Med 2021; 11:1287. [PMID: 34945758 PMCID: PMC8705317 DOI: 10.3390/jpm11121287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Abstract
Homologous recombination deficiency (HRD) has been used to predict both cancer prognosis and the response to DNA-damaging therapies in many cancer types. HRD has diverse manifestations in different cancers and even in different populations. Many screening strategies have been designed for detecting the sensitivity of a patient's HRD status to targeted therapies. However, these approaches suffer from low sensitivity, and are not specific to each cancer type and population group. Therefore, identifying race-specific and targetable HRD-related genes is of clinical importance. Here, we conducted analyses using genomic sequencing data that was generated by the Pan-Cancer Atlas. Collapsing non-synonymous variants with functional damage to HRD-related genes, we analyzed the association between these genes and race within cancer types using the optimal sequencing kernel association test (SKAT-O). We have identified race-specific mutational patterns of curated HRD-related genes across cancers. Overall, more significant mutation sites were found in ATM, BRCA2, POLE, and TOP2B in both the 'White' and 'Asian' populations, whereas PTEN, EGFG, and RIF1 mutations were observed in both the 'White' and 'African American/Black' populations. Furthermore, supported by pathogenic tendency databases and previous reports, in the 'African American/Black' population, several associations, including BLM with breast invasive carcinoma, ERCC5 with ovarian serous cystadenocarcinoma, as well as PTEN with stomach adenocarcinoma, were newly described here. Although several HRD-related genes are common across cancers, many of them were found to be specific to race. Further studies, using a larger cohort of diverse populations, are necessary to identify HRD-related genes that are specific to race, for guiding gene testing methods.
Collapse
Affiliation(s)
- Yi-Wen Hsiao
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan;
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan;
- Bioinformatics and Biostatistics Core, Center of Genomic and Precision Medicine, National Taiwan University, Taipei 100, Taiwan
| |
Collapse
|
16
|
Bronger H. Immunology and Immune Checkpoint Inhibition in Ovarian Cancer - Current Aspects. Geburtshilfe Frauenheilkd 2021; 81:1128-1144. [PMID: 34629492 PMCID: PMC8494520 DOI: 10.1055/a-1475-4335] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/05/2021] [Indexed: 12/17/2022] Open
Abstract
In the last decade immunotherapies such as immune checkpoint blockade (ICB) against the PD-1/PD-L1 system have revolutionised the treatment of numerous entities. To date, ovarian cancer has benefited very little from this success story. Possible causes include a rather low mutational burden compared to other tumour types, inadequate presentation of (neo-)antigens, and increased infiltration with immunosuppressive immune cells such as regulatory T cells and tumour-associated macrophages. In the clinical trials completed to date, the response rates to PD-1/PD-L1 checkpoint inhibitors have therefore been disappointingly low as well, although isolated long-term remissions have also been observed in ovarian cancer. The task now is to find suitable predictive biomarkers as well as to identify combination partners for ICB therapy that can increase the immunogenicity of ovarian cancer or overcome immunosuppressive resistance mechanisms. This paper provides an overview of the immune milieu in ovarian cancer, its impact on the effect of ICB, and summarises the clinical trial data available to date on ICB in ovarian cancer.
Collapse
Affiliation(s)
- Holger Bronger
- Klinik und Poliklinik für Frauenheilkunde, Klinikum rechts der Isar, Technische Universität München, München, Germany.,Deutsches Konsortium für Translationale Krebsforschung (DKTK), Partnerstandort München und Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| |
Collapse
|
17
|
Yang C, Zhang Z, Tang X, Zhang X, Chen Y, Hu T, Zhang H, Guan M, Zhang X, Wu Z. Pan-cancer analysis reveals homologous recombination deficiency score as a predictive marker for immunotherapy responders. Hum Cell 2021; 35:199-213. [PMID: 34628623 DOI: 10.1007/s13577-021-00630-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/02/2021] [Indexed: 02/07/2023]
Abstract
The immune context of the tumor microenvironment (TME) is critical for effective immunotherapy. Nonetheless, DNA-based biomarkers for the immune-sensitive TME and the identification of immune checkpoint inhibitor (ICI) responders are under-explored. This study aims to comprehensively landscape the homologous recombination deficiency (HRD) score, an emerging hallmark for tumor genome instability that triggers immune responsiveness across major cancer types, and to unveil their link to the TME and immunotherapeutic response. The HRD-associated genomic scars were characterized in 9088 tumor samples across 32 cancer types from TCGA. We evaluated the HRD score's performance in classifying ICI responders using an independent breast cancer cohort (GSE87049) and 11 in vivo murine mammary tumor models treated with anti-PD1/CTLA4 regimen (GSE124821). This study revealed a broad association between HRD-high genotype and neoantigenesis in the major cancer types including bladder cancer, breast cancer, head and neck squamous carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, ovarian cancer, and sarcoma. Tumors with high HRD score bears increased leukocyte infiltration and lymphocyte fraction and demonstrated immune-sensitive microenvironment. The tumor immune dysfunction and exclusion (TIDE) model further confirmed HRD score-high genotype as a potential predictor for ICI immunotherapy responders in breast cancer. In conclusion, tumors with high HRD score exhibit an immune-sensitive TME. The HRD-high genotype is a promising marker for identifying ICI therapy responders among breast cancer patients.
Collapse
Affiliation(s)
- Can Yang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Zijing Zhang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Xuemei Tang
- Central Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China
| | - Xinju Zhang
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yuming Chen
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Tingting Hu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Huating Zhang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
- Central Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China.
- Clinical Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
| | - Xiuming Zhang
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, 518002, China.
| | - Zhiyuan Wu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
- Central Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
- Clinical Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
| |
Collapse
|
18
|
Russo A, Incorvaia L, Malapelle U, Del Re M, Capoluongo E, Vincenzi B, Chiari R, Cortesi L, Danesi R, Florena AM, Fontanini G, Gori S, Marchetti A, Normanno N, Pinto C, Sangiolo D, Silvestris N, Tagliaferri P, Tallini G, Cinieri S, Beretta GD. The Tumor-Agnostic Treatment For Patients with Solid Tumors: a Position Paper on behalf of the AIOM- SIAPEC/IAP-SIBIOC-SIF Italian Scientific Societies. Crit Rev Oncol Hematol 2021; 165:103436. [PMID: 34371157 DOI: 10.1016/j.critrevonc.2021.103436] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/04/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
The personalized medicine is in a rapidly evolving scenario. The identification of actionable mutations is revolutionizing the therapeutic landscape of tumors. The morphological and histological tumor features are enriched by the extensive genomic profiling, and the first tumor-agnostic drugs have been approved regardless of tumor histology, guided by predictive and druggable genetic alterations. This new paradigm of "mutational oncology", presents a great potential to change the oncologic therapeutic scenario, but also some critical aspects need to be underlined. A process governance is mandatory to ensure the genomic testing accuracy and homogeneity, the economic sustainability, and the regulatory issues, ultimately granting the possibility of translating this model in the "real world". In this position paper, based on experts' opinion, the AIOM-SIAPEC-IAP-SIBIOC-SIF Italian Scientific Societies revised the new agnostic biomarkers, the diagnostic technologies available, the current availability of agnostic drugs and their present indication.
Collapse
Affiliation(s)
- Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy.
| | - Lorena Incorvaia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Medical Oncology, University of Palermo, 90127, Palermo, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, 80138, Naples, Italy
| | - Marzia Del Re
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Ettore Capoluongo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, Via Pansini 5, 80131, Naples, Italy; CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80131, Naples, Italy
| | - Bruno Vincenzi
- Department of Medical Oncology, Campus Bio-Medico University, 00128, Rome, Italy
| | - Rita Chiari
- Medical Oncology, AULSS 6 Euganea, South Padova Hospital, Monselice, PD, Italy
| | - Laura Cortesi
- Department of Oncology and Hematology, Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology and Pharmacogenetics, Department of Clinical and Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Ada Maria Florena
- Pathologic Anatomy Unit, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Stefania Gori
- Department of Oncology, IRCCS Ospedale Sacro Cuore Don Calabria, Negrar di Valpolicella, Italy
| | - Antonio Marchetti
- Center of Predictive Molecular Medicine, University-Foundation, CeSI Biotech Chieti, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131, Naples, Italy
| | - Carmine Pinto
- Medical Oncology Unit, Clinical Cancer Centre, IRCCS-AUSL di Reggio Emilia, Reggio Emilia, Italy
| | - Dario Sangiolo
- Department of Oncology, University of Torino, Turin, Italy; Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Nicola Silvestris
- Medical Oncology Unit, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy; Department of Biomedical Sciences and Human Oncology, Department of Internal Medicine and Oncology (DIMO), University of Bari, Bari, Italy
| | - Pierosandro Tagliaferri
- Medical and Translational Oncology Unit, Department of Experimental and Clinical Medicine, Magna Graecia University, 88100, Catanzaro, Italy
| | - Giovanni Tallini
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna School of Medicine, Bologna, Italy
| | - Saverio Cinieri
- Medical Oncology Division and Breast Unit, Senatore Antonio Perrino Hospital, ASL Brindisi, Brindisi, Italy
| | | |
Collapse
|
19
|
Turner PG, Jain S, Cole A, Grey A, Mitchell D, Prise KM, Hounsell AR, McGarry CK, Biggart S, O'Sullivan JM. Toxicity and Efficacy of Concurrent Androgen Deprivation Therapy, Pelvic Radiotherapy, and Radium-223 in Patients with De Novo Metastatic Hormone-Sensitive Prostate Cancer. Clin Cancer Res 2021; 27:4549-4556. [PMID: 34187853 DOI: 10.1158/1078-0432.ccr-21-0685] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/08/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Radium-223 is an alpha-emitting radionuclide associated with overall survival (OS) improvement in metastatic castration-resistant prostate cancer (mCRPC). External beam radiotherapy (EBRT) to prostate extends OS in men with metastatic hormone-sensitive prostate cancer (mHSPC) limited to less than 4 metastases. We hypothesized that combination radium-223 + pelvic EBRT could safely deliver maximal radiotherapy doses to primary and metastatic prostate cancer and may improve disease control. PATIENTS AND METHODS Thirty patients with de novo bone metastatic mHSPC who had commenced androgen deprivation therapy (ADT) and docetaxel were recruited to this single-arm, open-label, prospective clinical trial: Neo-adjuvant Androgen Deprivation Therapy, Pelvic Radiotherapy and RADium-223 (ADRRAD; for new presentation T1-4 N0-1 M1B adenocarcinoma of prostate). Study treatments were: ADT, 6 cycles of radium-223 q28 days, conventionally fractionated prostate radiotherapy (74 Gy) and simultaneous integrated boost to pelvic lymph nodes (60 Gy). RESULTS No grade 4/5 toxicity was observed. Three patients experienced grade 3 leukopenia, and 1 each experienced grade 3 neutropenia and thrombocytopenia; all were asymptomatic. One patient each experienced grade 3 dysuria and grade 3 urinary infection. No grade 3 gastrointestinal (GI) toxicity was observed. On treatment completion, there was a signal of efficacy; 24 (80%) patients had whole-body MRI evidence of tumor response or stability. Twenty-seven (90%) patients showed a reduction in alkaline phosphatase (ALP) compared with pretreatment levels. Median progression-free survival was 20.5 months. CONCLUSIONS This is the first trial of combination ADT, radium-223, and EBRT to pelvis, post docetaxel. The combination was safe, with an efficacy signal. Multicenter randomized controlled trials (RCT) are warranted.
Collapse
Affiliation(s)
- Philip G Turner
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom. .,The Northern Ireland Cancer Centre, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Suneil Jain
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom.,The Northern Ireland Cancer Centre, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Aidan Cole
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom.,The Northern Ireland Cancer Centre, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Arthur Grey
- The Northern Ireland Cancer Centre, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Darren Mitchell
- The Northern Ireland Cancer Centre, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Kevin M Prise
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Alan R Hounsell
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom.,The Northern Ireland Cancer Centre, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Conor K McGarry
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom.,The Northern Ireland Cancer Centre, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Sandra Biggart
- The Northern Ireland Cancer Centre, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Joe M O'Sullivan
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom.,The Northern Ireland Cancer Centre, Belfast Health and Social Care Trust, Belfast, United Kingdom
| |
Collapse
|
20
|
Parkes EE, Humphries MP, Gilmore E, Sidi FA, Bingham V, Phyu SM, Craig S, Graham C, Miller J, Griffin D, Salto-Tellez M, Madden SF, Kennedy RD, Bakhoum SF, McQuaid S, Buckley NE. The clinical and molecular significance associated with STING signaling in breast cancer. NPJ Breast Cancer 2021; 7:81. [PMID: 34172750 PMCID: PMC8233333 DOI: 10.1038/s41523-021-00283-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 05/27/2021] [Indexed: 12/22/2022] Open
Abstract
STING signaling in cancer is a crucial component of response to immunotherapy and other anti-cancer treatments. Currently, there is no robust method of measuring STING activation in cancer. Here, we describe an immunohistochemistry-based assay with digital pathology assessment of STING in tumor cells. Using this novel approach in estrogen receptor-positive (ER+) and ER- breast cancer, we identify perinuclear-localized expression of STING (pnSTING) in ER+ cases as an independent predictor of good prognosis, associated with immune cell infiltration and upregulation of immune checkpoints. Tumors with low pnSTING are immunosuppressed with increased infiltration of "M2"-polarized macrophages. In ER- disease, pnSTING does not appear to have a significant prognostic role with STING uncoupled from interferon responses. Importantly, a gene signature defining low pnSTING expression is predictive of poor prognosis in independent ER+ datasets. Low pnSTING is associated with chromosomal instability, MYC amplification and mTOR signaling, suggesting novel therapeutic approaches for this subgroup.
Collapse
Affiliation(s)
- Eileen E Parkes
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK.
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, UK.
| | - Matthew P Humphries
- Precision Medicine Centre of Excellence, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Elaine Gilmore
- Precision Medicine Centre of Excellence, Queen's University Belfast, Belfast, Northern Ireland, UK
- School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Fatima A Sidi
- Precision Medicine Centre of Excellence, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Victoria Bingham
- Precision Medicine Centre of Excellence, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Su M Phyu
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, UK
| | - Stephanie Craig
- Precision Medicine Centre of Excellence, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Catherine Graham
- Precision Medicine Centre of Excellence, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Joseph Miller
- Precision Medicine Centre of Excellence, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Daryl Griffin
- Precision Medicine Centre of Excellence, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Manuel Salto-Tellez
- Precision Medicine Centre of Excellence, Queen's University Belfast, Belfast, Northern Ireland, UK
- Department of Cellular Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
- Integrated Pathology Programme, Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Stephen F Madden
- Data Science Centre, RCSI University of Medicine and Health Sciences, Dublin, Ireland, UK
| | - Richard D Kennedy
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephen McQuaid
- Precision Medicine Centre of Excellence, Queen's University Belfast, Belfast, Northern Ireland, UK
- Department of Cellular Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
- Northern Ireland Biobank, Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Niamh E Buckley
- School of Pharmacy, Queen's University Belfast, Belfast, Northern Ireland, UK.
| |
Collapse
|
21
|
Foley KG, Lavery A, Napier E, Campbell D, Eatock MM, Kennedy RD, Bradley KM, Turkington RC. A DNA-damage immune response assay combined with PET biomarkers predicts response to neo-adjuvant chemotherapy and survival in oesophageal adenocarcinoma. Sci Rep 2021; 11:13061. [PMID: 34158588 PMCID: PMC8219719 DOI: 10.1038/s41598-021-92545-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 06/07/2021] [Indexed: 11/24/2022] Open
Abstract
18F-fluorodeoxyglucose PET-CT may guide treatment decisions in patients with oesophageal adenocarcinoma (OAC). This study evaluated the added value of maximum standardised uptake value (SUVmax) to a novel DNA-damage immune response (DDIR) assay to improve pathological response prediction. The diagnostic accuracy of PET response and the prognostic significance of PET metrics for recurrence-free survival (RFS) and overall survival (OS) were assessed. This was a retrospective, single-centre study of OAC patients treated with neo-adjuvant chemotherapy from 2003 to 2014. SUVmax was recorded from baseline and repeat PET-CT after completion of pre-operative chemotherapy. Logistic regression models tested the additional predictive value of PET metrics combined with the DDIR assay for pathological response. Cox regression models tested the prognostic significance of PET metrics for RFS and OS. In total, 113 patients were included; 25 (22.1%) were DDIR positive and 88 (77.9%) were DDIR negative. 69 (61.1%) were PET responders (SUVmax reduction of 35%) and 44 (38.9%) were PET non-responders. After adding PET metrics to DDIR status, post-chemotherapy SUVmax (hazard ratio (HR) 0.75, p = 0.02), SUVmax change (HR 1.04, p = 0.003) and an optimum SUVmax reduction of 46.5% (HR 4.36, p = 0.021) showed additional value for predicting pathological response. The optimised SUVmax threshold was independently significant for RFS (HR 0.47, 95% CI 0.26–0.85, p = 0.012) and OS (HR 0.51, 95% CI 0.26–0.99, p = 0.047). This study demonstrated the additional value of PET metrics, when combined with a novel DDIR assay, to predict pathological response in OAC patients treated with neo-adjuvant chemotherapy. Furthermore, an optimised SUVmax reduction threshold for pathological response was calculated and was independently significant for RFS and OS.
Collapse
Affiliation(s)
| | | | - Eoin Napier
- Belfast Health and Social Care Trust, Belfast, UK
| | | | - Martin M Eatock
- Queen's University Belfast, Belfast, UK.,Belfast Health and Social Care Trust, Belfast, UK
| | | | - Kevin M Bradley
- Wales Research & Diagnostic Positron Emission Tomography Imaging Centre (PETIC), Cardiff University, Cardiff, UK
| | | |
Collapse
|
22
|
Gallon J, Loomis E, Curry E, Martin N, Brody L, Garner I, Brown R, Flanagan JM. Chromatin accessibility changes at intergenic regions are associated with ovarian cancer drug resistance. Clin Epigenetics 2021; 13:122. [PMID: 34090482 PMCID: PMC8180030 DOI: 10.1186/s13148-021-01105-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background Resistance to DNA damaging chemotherapies leads to cancer treatment failure and poor patient prognosis. We investigated how genomic distribution of accessible chromatin sites is altered during acquisition of cisplatin resistance using matched ovarian cell lines from high grade serous ovarian cancer (HGSOC) patients before and after becoming clinically resistant to platinum-based chemotherapy. Results Resistant lines show altered chromatin accessibility at intergenic regions, but less so at gene promoters. Clusters of cis-regulatory elements at these intergenic regions show chromatin changes that are associated with altered expression of linked genes, with enrichment for genes involved in the Fanconi anemia/BRCA DNA damage response pathway. Further, genome-wide distribution of platinum adducts associates with the chromatin changes observed and distinguish sensitive from resistant lines. In the resistant line, we observe fewer adducts around gene promoters and more adducts at intergenic regions.
Conclusions Chromatin changes at intergenic regulators of gene expression are associated with in vivo derived drug resistance and Pt-adduct distribution in patient-derived HGSOC drug resistance models. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01105-6.
Collapse
Affiliation(s)
- John Gallon
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK
| | - Erick Loomis
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK
| | - Edward Curry
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK
| | - Nicholas Martin
- Trace Element Laboratory, Charing Cross Hospital, Imperial College NHS Trust, London, UK
| | - Leigh Brody
- Desktop Genetics, 28 Hanbury St, London, E1 6QR, UK
| | - Ian Garner
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK
| | - Robert Brown
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK. .,Institute of Cancer Research, Sutton, London, SM2 5NG, UK.
| | - James M Flanagan
- Department of Surgery and Cancer, Ovarian Cancer Action Research Centre, Imperial College London, London, W12 8EE, UK.
| |
Collapse
|
23
|
Weberpals JI, Pugh TJ, Marco-Casanova P, Goss GD, Andrews Wright N, Rath P, Torchia J, Fortuna A, Jones GN, Roudier MP, Bernard L, Lo B, Torti D, Leon A, Marsh K, Hodgson D, Duciaume M, Howat WJ, Lukashchuk N, Lazic SE, Whelan D, Sekhon HS. Tumor genomic, transcriptomic, and immune profiling characterizes differential response to first-line platinum chemotherapy in high grade serous ovarian cancer. Cancer Med 2021; 10:3045-3058. [PMID: 33811746 PMCID: PMC8085970 DOI: 10.1002/cam4.3831] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/09/2021] [Indexed: 01/01/2023] Open
Abstract
Background In high grade serous ovarian cancer (HGSOC), there is a spectrum of sensitivity to first line platinum‐based chemotherapy. This study molecularly characterizes HGSOC patients from two distinct groups of chemotherapy responders (good vs. poor). Methods Following primary debulking surgery and intravenous carboplatin/paclitaxel, women with stage III–IV HGSOC were grouped by response. Patients in the good response (GR) and poor response (PR) groups respectively had a progression‐free intervals (PFI) of ≥12 and ≤6 months. Analysis of surgical specimens interrogated genomic and immunologic features using whole exome sequencing. RNA‐sequencing detected gene expression outliers and inference of immune infiltrate, with validation by targeted NanoString arrays. PD‐L1 expression was scored by immunohistochemistry (IHC). Results A total of 39 patient samples were analyzed (GR = 20; PR = 19). Median PFI for GR and PR patient cohorts was 32 and 3 months, respectively. GR tumors were enriched for loss‐of‐function BRCA2 mutations and had a significantly higher nonsynonymous mutation rate compared to PR tumors (p = 0.001). Samples from the PR cohort were characterized by mutations in MGA and RAD51B and trended towards a greater rate of amplification of PIK3CA, MECOM, and ATR in comparison to GR tumors. Gene expression analysis by NanoString correlated increased PARP4 with PR and increased PD‐L1 and EMSY with GR. There was greater tumor immune cell infiltration and higher immune cell PD‐L1 protein expression in the GR group. Conclusions Our research demonstrates that tumors from HGSOC patients responding poorly to first line chemotherapy have a distinct molecular profile characterized by actionable drug targets including PARP4.
Collapse
Affiliation(s)
- Johanne I Weberpals
- Department of Obstetrics and Gynecology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Trevor J Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Glenwood D Goss
- Ottawa Hospital Research Institute, Ottawa, ON, Canada.,Department of Medicine, Division of Medical Oncology, University of Ottawa, Ottawa, ON, Canada
| | | | - Prisni Rath
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | | | - Gemma N Jones
- Translational Medicine, R&D Oncology, AstraZeneca, Cambridge, UK
| | | | - Laurence Bernard
- Department of Obstetrics and Gynecology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Bryan Lo
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, ON, Canada
| | - Dax Torti
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Alberto Leon
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kayla Marsh
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Darren Hodgson
- Translational Medicine, R&D Oncology, AstraZeneca, Cambridge, UK
| | - Marc Duciaume
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - William J Howat
- Translational Medicine, R&D Oncology, AstraZeneca, Cambridge, UK
| | | | - Stanley E Lazic
- Quantitative Biology, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Doreen Whelan
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Harmanjatinder S Sekhon
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, Ottawa, ON, Canada.,Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada
| |
Collapse
|
24
|
Malla SB, Fisher DJ, Domingo E, Blake A, Hassanieh S, Redmond KL, Richman SD, Youdell M, Walker SM, Logan GE, Chatzipli A, Amirkhah R, Humphries MP, Craig SG, McDermott U, Seymour MT, Morton DG, Quirke P, West NP, Salto-Tellez M, Kennedy RD, Johnston PG, Tomlinson I, Koelzer VH, Campo L, Kaplan RS, Longley DB, Lawler M, Maughan TS, Brown LC, Dunne PD. In-depth Clinical and Biological Exploration of DNA Damage Immune Response as a Biomarker for Oxaliplatin Use in Colorectal Cancer. Clin Cancer Res 2021; 27:288-300. [PMID: 33028592 PMCID: PMC7614625 DOI: 10.1158/1078-0432.ccr-20-3237] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/01/2020] [Accepted: 10/01/2020] [Indexed: 12/24/2022]
Abstract
PURPOSE The DNA damage immune response (DDIR) assay was developed in breast cancer based on biology associated with deficiencies in homologous recombination and Fanconi anemia pathways. A positive DDIR call identifies patients likely to respond to platinum-based chemotherapies in breast and esophageal cancers. In colorectal cancer, there is currently no biomarker to predict response to oxaliplatin. We tested the ability of the DDIR assay to predict response to oxaliplatin-based chemotherapy in colorectal cancer and characterized the biology in DDIR-positive colorectal cancer. EXPERIMENTAL DESIGN Samples and clinical data were assessed according to DDIR status from patients who received either 5-fluorouracil (5-FU) or 5FUFA (bolus and infusion 5-FU with folinic acid) plus oxaliplatin (FOLFOX) within the FOCUS trial (n = 361, stage IV), or neoadjuvant FOLFOX in the FOxTROT trial (n = 97, stage II/III). Whole transcriptome, mutation, and IHC data of these samples were used to interrogate the biology of DDIR in colorectal cancer. RESULTS Contrary to our hypothesis, DDIR-negative patients displayed a trend toward improved outcome for oxaliplatin-based chemotherapy compared with DDIR-positive patients. DDIR positivity was associated with microsatellite instability (MSI) and colorectal molecular subtype 1. Refinement of the DDIR signature, based on overlapping IFN-related chemokine signaling associated with DDIR positivity across colorectal cancer and breast cancer cohorts, further confirmed that the DDIR assay did not have predictive value for oxaliplatin-based chemotherapy in colorectal cancer. CONCLUSIONS DDIR positivity does not predict improved response following oxaliplatin treatment in colorectal cancer. However, data presented here suggest the potential of the DDIR assay in identifying immune-rich tumors that may benefit from immune checkpoint blockade, beyond current use of MSI status.
Collapse
Affiliation(s)
- Sudhir B Malla
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - David J Fisher
- MRC Clinical Trials Unit, University College London, London, United Kingdom
| | - Enric Domingo
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Andrew Blake
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Sylvana Hassanieh
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Keara L Redmond
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Susan D Richman
- Pathology and data analytics, School of Medicine, University of Leeds, Leeds, United Kingdom
| | - Michael Youdell
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | | | - Gemma E Logan
- Almac Diagnostic Services, Craigavon, United Kingdom
| | - Aikaterina Chatzipli
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Raheleh Amirkhah
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Matthew P Humphries
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Stephanie G Craig
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Ultan McDermott
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, United Kingdom
- AstraZeneca, United Kingdom
| | | | - Dion G Morton
- University of Birmingham, Birmingham, United Kingdom
| | - Philip Quirke
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Nicholas P West
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Manuel Salto-Tellez
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Richard D Kennedy
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Patrick G Johnston
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | | | | | - Letitia Campo
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Richard S Kaplan
- MRC Clinical Trials Unit, University College London, London, United Kingdom
| | - Daniel B Longley
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Mark Lawler
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, United Kingdom
| | - Timothy S Maughan
- MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom.
| | - Louise C Brown
- MRC Clinical Trials Unit, University College London, London, United Kingdom
| | | |
Collapse
|
25
|
Ali RMM, McIntosh SA, Savage KI. Homologous recombination deficiency in breast cancer: Implications for risk, cancer development, and therapy. Genes Chromosomes Cancer 2020; 60:358-372. [DOI: 10.1002/gcc.22921] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 12/19/2022] Open
Affiliation(s)
- Rayhaan M. M. Ali
- Patrick G Johnston Centre for Cancer Research Queen's University Belfast Belfast UK
| | - Stuart A. McIntosh
- Patrick G Johnston Centre for Cancer Research Queen's University Belfast Belfast UK
| | - Kienan I. Savage
- Patrick G Johnston Centre for Cancer Research Queen's University Belfast Belfast UK
| |
Collapse
|
26
|
Bodily WR, Shirts BH, Walsh T, Gulsuner S, King MC, Parker A, Roosan M, Piccolo SR. Effects of germline and somatic events in candidate BRCA-like genes on breast-tumor signatures. PLoS One 2020; 15:e0239197. [PMID: 32997669 PMCID: PMC7526916 DOI: 10.1371/journal.pone.0239197] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/02/2020] [Indexed: 11/19/2022] Open
Abstract
Mutations in BRCA1 and BRCA2 cause deficiencies in homologous recombination repair (HR), resulting in repair of DNA double-strand breaks by the alternative non-homologous end-joining pathway, which is more error prone. HR deficiency of breast tumors is important because it is associated with better responses to platinum salt therapies and PARP inhibitors. Among other consequences of HR deficiency are characteristic somatic-mutation signatures and gene-expression patterns. The term "BRCA-like" (or "BRCAness") describes tumors that harbor an HR defect but have no detectable germline mutation in BRCA1 or BRCA2. A better understanding of the genes and molecular events associated with tumors being BRCA-like could provide mechanistic insights and guide development of targeted treatments. Using data from The Cancer Genome Atlas (TCGA) for 1101 breast-cancer patients, we identified individuals with a germline mutation, somatic mutation, homozygous deletion, and/or hypermethylation event in BRCA1, BRCA2, and 59 other cancer-predisposition genes. Based on the assumption that BRCA-like events would have similar downstream effects on tumor biology as BRCA1/BRCA2 germline mutations, we quantified these effects based on somatic-mutation signatures and gene-expression profiles. We reduced the dimensionality of the somatic-mutation signatures and expression data and used a statistical resampling approach to quantify similarities among patients who had a BRCA1/BRCA2 germline mutation, another type of aberration in BRCA1 or BRCA2, or any type of aberration in one of the other genes. Somatic-mutation signatures of tumors having a non-germline aberration in BRCA1/BRCA2 (n = 80) were generally similar to each other and to tumors from BRCA1/BRCA2 germline carriers (n = 44). Additionally, somatic-mutation signatures of tumors with germline or somatic events in ATR (n = 16) and BARD1 (n = 8) showed high similarity to tumors from BRCA1/BRCA2 carriers. Other genes (CDKN2A, CTNNA1, PALB2, PALLD, PRSS1, SDHC) also showed high similarity but only for a small number of events or for a single event type. Tumors with germline mutations or hypermethylation of BRCA1 had relatively similar gene-expression profiles and overlapped considerably with the Basal-like subtype; but the transcriptional effects of the other events lacked consistency. Our findings confirm previously known relationships between molecular signatures and germline or somatic events in BRCA1/BRCA2. Our methodology represents an objective way to identify genes that have similar downstream effects on molecular signatures when mutated, deleted, or hypermethylated.
Collapse
Affiliation(s)
- Weston R. Bodily
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| | - Brian H. Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Tom Walsh
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Suleyman Gulsuner
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Alyssa Parker
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| | - Moom Roosan
- Pharmacy Practice Department, Chapman University School of Pharmacy, Irvine, CA, United States of America
| | - Stephen R. Piccolo
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| |
Collapse
|
27
|
Ho AY, Wright JL, Blitzblau RC, Mutter RW, Duda DG, Norton L, Bardia A, Spring L, Isakoff SJ, Chen JH, Grassberger C, Bellon JR, Beriwal S, Khan AJ, Speers C, Dunn SA, Thompson A, Santa-Maria CA, Krop IE, Mittendorf E, King TA, Gupta GP. Optimizing Radiation Therapy to Boost Systemic Immune Responses in Breast Cancer: A Critical Review for Breast Radiation Oncologists. Int J Radiat Oncol Biol Phys 2020; 108:227-241. [PMID: 32417409 PMCID: PMC7646202 DOI: 10.1016/j.ijrobp.2020.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/24/2020] [Accepted: 05/07/2020] [Indexed: 12/13/2022]
Abstract
Immunotherapy using immune checkpoint blockade has revolutionized the treatment of many types of cancer. Radiation therapy (RT)-particularly when delivered at high doses using newer techniques-may be capable of generating systemic antitumor effects when combined with immunotherapy in breast cancer. These systemic effects might be due to the local immune-priming effects of RT resulting in the expansion and circulation of effector immune cells to distant sites. Although this concept merits further exploration, several challenges need to be overcome. One is an understanding of how the heterogeneity of breast cancers may relate to tumor immunogenicity. Another concerns the need to develop knowledge and expertise in delivery, sequencing, and timing of RT with immunotherapy. Clinical trials addressing these issues are under way. We here review and discuss the particular opportunities and issues regarding this topic, including the design of informative clinical and translational studies.
Collapse
Affiliation(s)
- Alice Y Ho
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts.
| | - Jean L Wright
- Department of Radiation Oncology, Johns Hopkins Cancer Center, Brooklandville, Maryland
| | - Rachel C Blitzblau
- Department of Radiation Oncology, Duke Cancer Center, Durham, North Carolina
| | - Robert W Mutter
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Dan G Duda
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Larry Norton
- Department of Medical Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aditya Bardia
- Department of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Laura Spring
- Department of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Steven J Isakoff
- Department of Medical Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jonathan H Chen
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Clemens Grassberger
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jennifer R Bellon
- Department of Radiation Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Sushil Beriwal
- Department of Radiation Oncology, University of Pittsburgh Cancer Center, Pittsburgh, Pennslyvania
| | - Atif J Khan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Corey Speers
- Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan
| | - Samantha A Dunn
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Alastair Thompson
- Department of Surgical Oncology, Baylor College of Medicine Medical Center, Houston, Texas
| | - Cesar A Santa-Maria
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ian E Krop
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Elizabeth Mittendorf
- Department of Surgical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Tari A King
- Department of Surgical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Gaorav P Gupta
- Department of Radiation Oncology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| |
Collapse
|
28
|
Tovey H, Cheang MCU. Identifying Biomarkers to Pair with Targeting Treatments within Triple Negative Breast Cancer for Improved Patient Stratification. Cancers (Basel) 2019; 11:E1864. [PMID: 31769425 PMCID: PMC6966447 DOI: 10.3390/cancers11121864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/07/2019] [Accepted: 11/18/2019] [Indexed: 12/24/2022] Open
Abstract
The concept of precision medicine has been around for many years and recent advances in high-throughput sequencing techniques are enabling this to become reality. Within the field of breast cancer, a number of signatures have been developed to molecularly sub-classify tumours. Notable examples recently approved by National Institute for Health and Care Excellence in the UK to guide treatment decisions for oestrogen receptors (ER)+ human epidermal growth factor receptor 2 (HER2)- patients include Prosigna test, EndoPredict, and Oncotype DX. However, a population of still unmet need are those with triple negative breast cancer (TNBC). Accounting for 15-20% of patients, this population has comparatively poor prognosis and as yet no targeted treatment options. Studies have shown that some patients with TNBC respond favourably to DNA damaging drugs (carboplatin) or agents which inhibit DNA damage response (poly ADP ribose polymerase (PARP) inhibitors). Known to be a heterogeneous population, there is a need to identify further TNBC patients who may benefit from these treatments. A number of signatures have been identified based on association with treatment response or specific genetic features/pathways however many of these were not restricted to TNBC patients and as of yet are not common practice in the clinic.
Collapse
Affiliation(s)
- Holly Tovey
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London SM2 5NG, UK
| | - Maggie Chon U. Cheang
- Clinical Trials and Statistics Unit, The Institute of Cancer Research, London SM2 5NG, UK
| |
Collapse
|
29
|
Turkington RC, Knight LA, Blayney JK, Secrier M, Douglas R, Parkes EE, Sutton EK, Stevenson L, McManus D, Halliday S, McCavigan AM, Logan GE, Walker SM, Steele CJ, Perner J, Bornschein J, MacRae S, Miremadi A, McCarron E, McQuaid S, Arthur K, James JA, Eatock MM, O'Neill R, Noble F, Underwood TJ, Harkin DP, Salto-Tellez M, Fitzgerald RC, Kennedy RD. Immune activation by DNA damage predicts response to chemotherapy and survival in oesophageal adenocarcinoma. Gut 2019; 68:1918-1927. [PMID: 30852560 PMCID: PMC6839732 DOI: 10.1136/gutjnl-2018-317624] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/13/2019] [Accepted: 02/15/2019] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Current strategies to guide selection of neoadjuvant therapy in oesophageal adenocarcinoma (OAC) are inadequate. We assessed the ability of a DNA damage immune response (DDIR) assay to predict response following neoadjuvant chemotherapy in OAC. DESIGN Transcriptional profiling of 273 formalin-fixed paraffin-embedded prechemotherapy endoscopic OAC biopsies was performed. All patients were treated with platinum-based neoadjuvant chemotherapy and resection between 2003 and 2014 at four centres in the Oesophageal Cancer Clinical and Molecular Stratification consortium. CD8 and programmed death ligand 1 (PD-L1) immunohistochemical staining was assessed in matched resection specimens from 126 cases. Kaplan-Meier and Cox proportional hazards regression analysis were applied according to DDIR status for recurrence-free survival (RFS) and overall survival (OS). RESULTS A total of 66 OAC samples (24%) were DDIR positive with the remaining 207 samples (76%) being DDIR negative. DDIR assay positivity was associated with improved RFS (HR: 0.61; 95% CI 0.38 to 0.98; p=0.042) and OS (HR: 0.52; 95% CI 0.31 to 0.88; p=0.015) following multivariate analysis. DDIR-positive patients had a higher pathological response rate (p=0.033), lower nodal burden (p=0.026) and reduced circumferential margin involvement (p=0.007). No difference in OS was observed according to DDIR status in an independent surgery-alone dataset.DDIR-positive OAC tumours were also associated with the presence of CD8+ lymphocytes (intratumoural: p<0.001; stromal: p=0.026) as well as PD-L1 expression (intratumoural: p=0.047; stromal: p=0.025). CONCLUSION The DDIR assay is strongly predictive of benefit from DNA-damaging neoadjuvant chemotherapy followed by surgical resection and is associated with a proinflammatory microenvironment in OAC.
Collapse
Affiliation(s)
- Richard C Turkington
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | | | - Jaine K Blayney
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Maria Secrier
- Genetics Institute, University College London, London, UK
| | - Rosalie Douglas
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Eileen E Parkes
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Eilis K Sutton
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Leanne Stevenson
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Damian McManus
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | - Sophia Halliday
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | | | | | | | | | - Juliane Perner
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Jan Bornschein
- Translational Gastroenterology Unit, John Radcliffe Hospital Oxford University Hospitals NHS Trust, Oxford, UK
| | | | - Ahmad Miremadi
- Department of Histopathology, Addenbrookes Hospital, Cambridge, UK
| | - Eamon McCarron
- Department of Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | - Stephen McQuaid
- Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, Belfast, UK
| | - Kenneth Arthur
- Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, Belfast, UK
| | - Jacqueline A James
- Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, Belfast, UK
| | - Martin M Eatock
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
- Department of Medical Oncology, Belfast Health and Social Care Trust, Belfast, UK
| | - Robert O'Neill
- Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, UK
| | - Fergus Noble
- Department of Surgery, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | | | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | | | - Richard D Kennedy
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
- Almac Diagnostics Ltd, Craigavon, UK
| |
Collapse
|
30
|
Sharma P, Barlow WE, Godwin AK, Parkes EE, Knight LA, Walker SM, Kennedy RD, Harkin DP, Logan GE, Steele CJ, Lambe SM, Badve S, Gökmen-Polar Y, Pathak HB, Isakova K, Linden HM, Porter P, Pusztai L, Thompson AM, Tripathy D, Hortobagyi GN, Hayes DF. Validation of the DNA Damage Immune Response Signature in Patients With Triple-Negative Breast Cancer From the SWOG 9313c Trial. J Clin Oncol 2019; 37:3484-3492. [PMID: 31657982 DOI: 10.1200/jco.19.00693] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
PURPOSE To independently validate two biomarkers, a 44-gene DNA damage immune response (DDIR) signature and stromal tumor-infiltrating lymphocytes (sTILs), as prognostic markers in patients with triple-negative breast cancer (TNBC) treated with adjuvant doxorubicin (A) and cyclophosphamide (C) in SWOG 9313. METHODS Four hundred twenty-five centrally determined patient cases with TNBC from S9313 were identified. DDIR signature was performed on RNA isolated from formalin-fixed paraffin-embedded tumor tissue, and samples were classified as DDIR negative or positive using predefined cutoffs. Evaluation of sTILs was performed as described previously. Markers were tested for prognostic value for disease-free survival (DFS) and overall survival (OS) using Cox regression models adjusted for treatment assignment, nodal status, and tumor size. RESULTS Among 425 patients with TNBC, 33% were node positive. DDIR was tested successfully in 90% of patients (381 of 425), 62% of which were DDIR signature positive. DDIR signature positivity was associated with improved DFS (hazard ratio [HR], 0.67; 95% CI, 0.48 to 0.92; P = .015) and OS (HR, 0.61; 95% CI, 0.43 to 0.89; P = .010). sTILs density assessment was available in 99% of patients and was associated with improved DFS (HR, 0.70; 95% CI, 0.51 to 0.96; P = .026 for sTILs density ≥ 20% v < 20%) and OS (HR, 0.59; 95% CI, 0.41 to 0.85; P = .004 for sTILs density ≥ 20% v < 20%). DDIR signature score and sTILs density were moderately correlated (r = 0.60), which precluded statistical significance for DFS in a joint model. Three-year DFS and OS in a subgroup of patients with DDIR positivity and T1c/T2N0 disease were 88% and 94%, respectively. CONCLUSION The prognostic role of sTILs and DDIR in early-stage TNBC was confirmed. DDIR signature conferred improved prognosis in two thirds of patients with TNBC treated with adjuvant AC. DDIR signature has the potential to stratify outcome and to identify patients with less projected benefit after AC chemotherapy.
Collapse
Affiliation(s)
| | | | | | | | - Laura A Knight
- Queen's University Belfast, Belfast, UK.,Almac Group, Craigavon, UK
| | - Steven M Walker
- Queen's University Belfast, Belfast, UK.,Almac Group, Craigavon, UK
| | | | - Denis P Harkin
- Queen's University Belfast, Belfast, UK.,Almac Group, Craigavon, UK
| | | | | | | | - Sunil Badve
- Indiana University School of Medicine, Indianapolis, IN
| | | | | | | | - Hannah M Linden
- University of Washington, Seattle, WA.,Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Peggy Porter
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | - Debu Tripathy
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | |
Collapse
|
31
|
Hoppe MM, Sundar R, Tan DSP, Jeyasekharan AD. Biomarkers for Homologous Recombination Deficiency in Cancer. J Natl Cancer Inst 2019; 110:704-713. [PMID: 29788099 DOI: 10.1093/jnci/djy085] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/06/2018] [Indexed: 12/11/2022] Open
Abstract
Defective DNA repair is a common hallmark of cancer. Homologous recombination is a DNA repair pathway of clinical interest due to the sensitivity of homologous recombination-deficient cells to poly-ADP ribose polymerase (PARP) inhibitors. The measurement of homologous recombination deficiency (HRD) in cancer is therefore vital to the appropriate design of clinical trials incorporating PARP inhibitors. However, methods to identify HRD in tumors are varied and controversial. Understanding existing and new methods to measure HRD is important to their appropriate use in clinical trials and practice. The aim of this review is to summarize the biology and clinical validation of current methods to measure HRD, to aid decision-making for patient stratification and translational research in PARP inhibitor trials. We discuss the current clinical development of PARP inhibitors, along with established indicators for HRD such as germline BRCA1/2 mutation status and clinical response to platinum-based therapy. We then examine newer assays undergoing clinical validation, including 1) somatic mutations in homologous recombination genes, 2) "genomic scar" assays using array-based comparative genomic hybridization (aCGH), single nucleotide polymorphism (SNP) analysis or mutational signatures derived from next-generation sequencing, 3) transcriptional profiles of HRD, and 4) phenotypic or functional assays of protein expression and localization. We highlight the strengths and weaknesses of each of these assays, for consideration during the design of studies involving PARP inhibitors.
Collapse
Affiliation(s)
- Michal M Hoppe
- Cancer Science Institute of Singapore, National University Hospital, Singapore
| | - Raghav Sundar
- Department of Haematology-Oncology, National University Hospital, Singapore
| | - David S P Tan
- Cancer Science Institute of Singapore, National University Hospital, Singapore.,Department of Haematology-Oncology, National University Hospital, Singapore
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University Hospital, Singapore.,Department of Haematology-Oncology, National University Hospital, Singapore
| |
Collapse
|
32
|
A Novel Role for Cathepsin S as a Potential Biomarker in Triple Negative Breast Cancer. JOURNAL OF ONCOLOGY 2019; 2019:3980273. [PMID: 31346333 PMCID: PMC6620839 DOI: 10.1155/2019/3980273] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/04/2019] [Indexed: 12/31/2022]
Abstract
Cathepsin S (CTSS) has previously been implicated in a number of cancer types, where it is associated with poor clinical features and outcome. To date, patient outcome in breast cancer has not been examined with respect to this protease. Here, we carried out immunohistochemical (IHC) staining of CTSS using a breast cancer tissue microarray in patients who received adjuvant therapy. We scored CTSS expression in the epithelial and stromal compartments and evaluated the association of CTSS expression with matched clinical outcome data. We observed differences in outcome based on CTSS expression, with stromal-derived CTSS expression correlating with a poor outcome and epithelial CTSS expression associated with an improved outcome. Further subtype characterisation revealed high epithelial CTSS expression in TNBC patients with improved outcome, which remained consistent across two independent TMA cohorts. Further in silico gene expression analysis, using both in-house and publicly available datasets, confirmed these observations and suggested high CTSS expression may also be beneficial to outcome in ER-/HER2+ cancer. Furthermore, high CTSS expression was associated with the BL1 Lehmann subgroup, which is characterised by defects in DNA damage repair pathways and correlates with improved outcome. Finally, analysis of matching IHC analysis reveals an increased M1 (tumour destructive) polarisation in macrophage in patients exhibiting high epithelial CTSS expression. In conclusion, our observations suggest epithelial CTSS expression may be prognostic of improved outcome in TNBC. Improved outcome observed with HER2+ at the gene expression level furthermore suggests CTSS may be prognostic of improved outcome in ER- cancers as a whole. Lastly, from the context of these patients receiving adjuvant therapy and as a result of its association with BL1 subgroup CTSS may be elevated in patients with defects in DNA damage repair pathways, indicating it may be predictive of tumour sensitivity to DNA damaging agents.
Collapse
|
33
|
DNA Repair Deficiency in Breast Cancer: Opportunities for Immunotherapy. JOURNAL OF ONCOLOGY 2019; 2019:4325105. [PMID: 31320901 PMCID: PMC6607732 DOI: 10.1155/2019/4325105] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/04/2019] [Accepted: 05/29/2019] [Indexed: 12/19/2022]
Abstract
Historically the development of anticancer treatments has been focused on their effect on tumor cells alone. However, newer treatments have shifted attention to targets on immune cells, resulting in dramatic responses. The effect of DNA repair deficiency on the microenvironment remains an area of key interest. Moreover, established therapies such as DNA damaging treatments such as chemotherapy and PARP inhibitors further modify the tumor microenvironment. Here we describe DNA repair pathways in breast cancer and activation of innate immune pathways in DNA repair deficiency, in particular, the STING (STimulator of INterferon Genes) pathway. Breast tumors with DNA repair deficiency are associated with upregulation of immune checkpoints including PD-L1 (Programmed Death Ligand-1) and may represent a target population for single agent or combination immunotherapy treatment.
Collapse
|
34
|
Belli C, Duso BA, Ferraro E, Curigliano G. Homologous recombination deficiency in triple negative breast cancer. Breast 2019; 45:15-21. [PMID: 30818144 DOI: 10.1016/j.breast.2019.02.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/08/2019] [Accepted: 02/15/2019] [Indexed: 01/09/2023] Open
Abstract
Triple negative breast cancer (TNBC) represents a heterogeneous subtype of breast cancer characterized by an unfavorable prognosis due to its aggressive biology. The median overall survival (OS) for patients with metastatic TNBC is around 9-12 months with conventional cytotoxic agents. Considering this suboptimal outcome, which is induced despite of medical treatment, new therapeutic strategies would be urgently needed. The ultimate goal of precision medicine is to identify specific molecular alterations that permit considering effective targeted drug(s). Germline BRCA mutations occur in 10-20% of TNBC patients while somatic mutations occur in 3-5% of them. Alterations in the homologous recombination (HR) system are typical of BRCA mutant tumors, but can also be identified in tumors that do not carry this mutation, defining a subgroup of patients referred to as BRCAness. In this review, we focus on the role of homologous recombination deficiency (HRD) as both predictive and prognostic factor in different settings of TNBC patients treated with DNA damaging drugs and poly ADP ribose polymerase (PARP) inhibitors.
Collapse
Affiliation(s)
- Carmen Belli
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, via Ripamonti 435, 20141, Milan, Italy.
| | - Bruno Achutti Duso
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, via Ripamonti 435, 20141, Milan, Italy
| | - Emanuela Ferraro
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, via Ripamonti 435, 20141, Milan, Italy
| | - Giuseppe Curigliano
- Division of Early Drug Development for Innovative Therapies, European Institute of Oncology IRCCS, Milan, via Ripamonti 435, 20141, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, via Festa del Perdono 7, 20122, Milan, Italy
| |
Collapse
|
35
|
Suh KJ, Ryu HS, Lee KH, Kim H, Min A, Kim TY, Yang Y, Lee HB, Moon HG, Han SW, Oh DY, Han W, Park IA, Noh DY, Im SA. Prognostic effects of abnormal DNA damage response protein expression in breast cancer. Breast Cancer Res Treat 2019; 175:117-127. [DOI: 10.1007/s10549-019-05128-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 01/01/2019] [Indexed: 12/20/2022]
|
36
|
Humphries MP, Hynes S, Bingham V, Cougot D, James J, Patel-Socha F, Parkes EE, Blayney JK, O'Rorke MA, Irwin GW, McArt DG, Kennedy RD, Mullan PB, McQuaid S, Salto-Tellez M, Buckley NE. Automated Tumour Recognition and Digital Pathology Scoring Unravels New Role for PD-L1 in Predicting Good Outcome in ER-/HER2+ Breast Cancer. JOURNAL OF ONCOLOGY 2018; 2018:2937012. [PMID: 30651729 PMCID: PMC6311859 DOI: 10.1155/2018/2937012] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 10/30/2018] [Accepted: 11/15/2018] [Indexed: 12/31/2022]
Abstract
The role of PD-L1 as a prognostic and predictive biomarker is an area of great interest. However, there is a lack of consensus on how to deliver PD-L1 as a clinical biomarker. At the heart of this conundrum is the subjective scoring of PD-L1 IHC in most studies to date. Current standard scoring systems involve separation of epithelial and inflammatory cells and find clinical significance in different percentages of expression, e.g., above or below 1%. Clearly, an objective, reproducible and accurate approach to PD-L1 scoring would bring a degree of necessary consistency to this landscape. Using a systematic comparison of technologies and the application of QuPath, a digital pathology platform, we show that high PD-L1 expression is associated with improved clinical outcome in Triple Negative breast cancer in the context of standard of care (SoC) chemotherapy, consistent with previous findings. In addition, we demonstrate for the first time that high PD-L1 expression is also associated with better outcome in ER- disease as a whole including HER2+ breast cancer. We demonstrate the influence of antibody choice on quantification and clinical impact with the Ventana antibody (SP142) providing the most robust assay in our hands. Through sampling different regions of the tumour, we show that tumour rich regions display the greatest range of PD-L1 expression and this has the most clinical significance compared to stroma and lymphoid rich areas. Furthermore, we observe that both inflammatory and epithelial PD-L1 expression are associated with improved survival in the context of chemotherapy. Moreover, as seen with PD-L1 inhibitor studies, a low threshold of PD-L1 expression stratifies patient outcome. This emphasises the importance of using digital pathology and precise biomarker quantitation to achieve accurate and reproducible scores that can discriminate low PD-L1 expression.
Collapse
Affiliation(s)
- Matthew P. Humphries
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Sean Hynes
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Victoria Bingham
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Delphine Cougot
- Horizon Discovery Ltd, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, UK
| | - Jacqueline James
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Farah Patel-Socha
- Horizon Discovery Ltd, 8100 Cambridge Research Park, Waterbeach, Cambridge, CB25 9TL, UK
| | - Eileen E. Parkes
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Jaine K. Blayney
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Michael A. O'Rorke
- College of Public Health, The University of Iowa, Iowa City, IA 52242, USA
| | - Gareth W. Irwin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Darragh G. McArt
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Richard D. Kennedy
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Paul B. Mullan
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Stephen McQuaid
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Niamh E. Buckley
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
- School of Pharmacy, Queen's University Belfast, Belfast, UK
| |
Collapse
|
37
|
Sharma P, López-Tarruella S, García-Saenz JA, Khan QJ, Gómez HL, Prat A, Moreno F, Jerez-Gilarranz Y, Barnadas A, Picornell AC, Monte-Millán MD, González-Rivera M, Massarrah T, Pelaez-Lorenzo B, Palomero MI, González Del Val R, Cortés J, Fuentes-Rivera H, Morales DB, Márquez-Rodas I, Perou CM, Lehn C, Wang YY, Klemp JR, Mammen JV, Wagner JL, Amin AL, O'Dea AP, Heldstab J, Jensen RA, Kimler BF, Godwin AK, Martín M. Pathological Response and Survival in Triple-Negative Breast Cancer Following Neoadjuvant Carboplatin plus Docetaxel. Clin Cancer Res 2018; 24:5820-5829. [PMID: 30061361 PMCID: PMC6279513 DOI: 10.1158/1078-0432.ccr-18-0585] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 05/21/2018] [Accepted: 07/24/2018] [Indexed: 12/16/2022]
Abstract
PURPOSE Prognostic value of pathologic complete response (pCR) and extent of pathologic response attained with anthracycline-free platinum plus taxane neoadjuvant chemotherapy (NAC) in triple-negative breast cancer (TNBC) is unknown. We report recurrence-free survival (RFS) and overall survival (OS) according to degree of pathologic response in patients treated with carboplatin plus docetaxel NAC. PATIENTS AND METHODS One-hundred and ninety patients with stage I-III TNBC were treated with neoadjuvant carboplatin (AUC6) plus docetaxel (75 mg/m2) every 21 days × 6 cycles. pCR (no evidence of invasive tumor in breast and axilla) and Residual cancer burden (RCB) were evaluated. Patients were followed for recurrence and survival. Extent of pathologic response was associated with RFS and OS using the Kaplan-Meier method. RESULTS Median age was 51 years, and 52% were node-positive. pCR and RCB I rates were 55% and 13%, respectively. Five percent of pCR patients, 0% of RCB I patients, and 58% of RCB II/III patients received adjuvant anthracyclines. Three-year RFS and OS were 79% and 87%, respectively. Three-year RFS was 90% in patients with pCR and 66% in those without pCR [HR = 0.30; 95% confidence interval (CI), 0.14-0.62; P = 0.0001]. Three-year OS was 94% in patients with pCR and 79% in those without pCR (HR = 0.25; 95% CI, 0.10-0.63; P = 0.001). Patients with RCB I demonstrated 3-year RFS (93%) and OS (100%) similar to those with pCR. On multivariable analysis, higher tumor stage, node positivity, and RCB II/III were associated with worse RFS. CONCLUSIONS Neoadjuvant carboplatin plus docetaxel yields encouraging efficacy in TNBC. Patients achieving pCR or RCB I with this regimen demonstrate excellent 3-year RFS and OS without adjuvant anthracycline.
Collapse
Affiliation(s)
- Priyanka Sharma
- Division of Medical Oncology, University of Kansas Medical Center, Westwood, Kansas.
| | - Sara López-Tarruella
- Department of Medical Oncology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, CIBERONC, GEICAM, Madrid, Spain
| | | | - Qamar J Khan
- Division of Medical Oncology, University of Kansas Medical Center, Westwood, Kansas
| | - Henry L Gómez
- Department of Medical Oncology, Instituto Nacional de Enfermedades Neoplásicas, Lima, Perú
| | - Aleix Prat
- Department of Medical Oncology, Hospital Clinic of Barcelona, Barcelona, Spain
- Translational Genomics and Targeted Therapeutics in Solid Tumors, Institut d'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Fernando Moreno
- Department of Medical Oncology, Hospital Clínico San Carlos, Madrid, Spain
| | - Yolanda Jerez-Gilarranz
- Department of Medical Oncology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, CIBERONC, GEICAM, Madrid, Spain
| | - Agustí Barnadas
- Department of Medical Oncology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Antoni C Picornell
- Department of Medical Oncology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, CIBERONC, GEICAM, Madrid, Spain
| | - María Del Monte-Millán
- Department of Medical Oncology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, CIBERONC, GEICAM, Madrid, Spain
| | - Milagros González-Rivera
- Laboratory of Translational Oncology, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain
| | - Tatiana Massarrah
- Department of Medical Oncology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, CIBERONC, GEICAM, Madrid, Spain
| | | | - María Isabel Palomero
- Department of Medical Oncology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, CIBERONC, GEICAM, Madrid, Spain
| | - Ricardo González Del Val
- Department of Medical Oncology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, CIBERONC, GEICAM, Madrid, Spain
| | - Javier Cortés
- Department of Oncology, Ramón y Cajal University Hospital, Madrid, Spain. Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Hugo Fuentes-Rivera
- Department of Medical Oncology, Instituto Nacional de Enfermedades Neoplásicas, Lima, Perú
| | - Denisse Bretel Morales
- Department of Medical Oncology, Instituto Nacional de Enfermedades Neoplásicas, Lima, Perú
| | - Iván Márquez-Rodas
- Department of Medical Oncology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, CIBERONC, GEICAM, Madrid, Spain
| | - Charles M Perou
- Departments of Genetics and Pathology & Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Carolyn Lehn
- Division of Medical Oncology, University of Kansas Medical Center, Westwood, Kansas
| | - Yen Y Wang
- Division of Medical Oncology, University of Kansas Medical Center, Westwood, Kansas
| | - Jennifer R Klemp
- Division of Medical Oncology, University of Kansas Medical Center, Westwood, Kansas
| | - Joshua V Mammen
- Division of Medical Oncology, University of Kansas Medical Center, Westwood, Kansas
| | - Jamie L Wagner
- Division of Medical Oncology, University of Kansas Medical Center, Westwood, Kansas
| | - Amanda L Amin
- Division of Medical Oncology, University of Kansas Medical Center, Westwood, Kansas
| | - Anne P O'Dea
- Division of Medical Oncology, University of Kansas Medical Center, Westwood, Kansas
| | - Jaimie Heldstab
- Division of Medical Oncology, University of Kansas Medical Center, Westwood, Kansas
| | - Roy A Jensen
- Division of Medical Oncology, University of Kansas Medical Center, Westwood, Kansas
| | - Bruce F Kimler
- Division of Medical Oncology, University of Kansas Medical Center, Westwood, Kansas
| | - Andrew K Godwin
- Division of Medical Oncology, University of Kansas Medical Center, Westwood, Kansas
| | - Miguel Martín
- Department of Medical Oncology, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, CIBERONC, GEICAM, Madrid, Spain.
| |
Collapse
|
38
|
Induction of HRR genes and inhibition of DNMT1 is associated with anthracycline anti-tumor antibiotic-tolerant breast carcinoma cells. Mol Cell Biochem 2018; 453:163-178. [DOI: 10.1007/s11010-018-3442-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/30/2018] [Indexed: 12/30/2022]
|
39
|
Zhao EY, Shen Y, Pleasance E, Kasaian K, Leelakumari S, Jones M, Bose P, Ch'ng C, Reisle C, Eirew P, Corbett R, Mungall KL, Thiessen N, Ma Y, Schein JE, Mungall AJ, Zhao Y, Moore RA, Den Brok W, Wilson S, Villa D, Shenkier T, Lohrisch C, Chia S, Yip S, Gelmon K, Lim H, Renouf D, Sun S, Schrader KA, Young S, Bosdet I, Karsan A, Laskin J, Marra MA, Jones SJM. Homologous Recombination Deficiency and Platinum-Based Therapy Outcomes in Advanced Breast Cancer. Clin Cancer Res 2018; 23:7521-7530. [PMID: 29246904 DOI: 10.1158/1078-0432.ccr-17-1941] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/14/2017] [Accepted: 09/26/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Recent studies have identified mutation signatures of homologous recombination deficiency (HRD) in over 20% of breast cancers, as well as pancreatic, ovarian, and gastric cancers. There is an urgent need to understand the clinical implications of HRD signatures. Whereas BRCA1/2 mutations confer sensitivity to platinum-based chemotherapies, it is not yet clear whether mutation signatures can independently predict platinum response.Experimental Design: In this observational study, we sequenced tumor whole genomes (100× depth) and matched normals (60×) of 93 advanced-stage breast cancers (33 platinum-treated). We computed a published metric called HRDetect, independently trained to predict BRCA1/2 status, and assessed its capacity to predict outcomes on platinum-based chemotherapies. Clinical endpoints were overall survival (OS), total duration on platinum-based therapy (TDT), and radiographic evidence of clinical improvement (CI).Results: HRDetect predicted BRCA1/2 status with an area under the curve (AUC) of 0.94 and optimal threshold of 0.7. Elevated HRDetect was also significantly associated with CI on platinum-based therapy (AUC = 0.89; P = 0.006) with the same optimal threshold, even after adjusting for BRCA1/2 mutation status and treatment timing. HRDetect scores over 0.7 were associated with a 3-month extended median TDT (P = 0.0003) and 1.3-year extended median OS (P = 0.04).Conclusions: Our findings not only independently validate HRDetect, but also provide the first evidence of its association with platinum response in advanced breast cancer. We demonstrate that HRD mutation signatures may offer clinically relevant information independently of BRCA1/2 mutation status and hope this work will guide the development of clinical trials. Clin Cancer Res; 23(24); 7521-30. ©2017 AACR.
Collapse
Affiliation(s)
- Eric Y Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Katayoon Kasaian
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Sreeja Leelakumari
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Martin Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Pinaki Bose
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Carolyn Ch'ng
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Caralyn Reisle
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Peter Eirew
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Richard Corbett
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Nina Thiessen
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Jacqueline E Schein
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Wendie Den Brok
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Sheridan Wilson
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Diego Villa
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Tamara Shenkier
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Caroline Lohrisch
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Stephen Chia
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Karen Gelmon
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Howard Lim
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Daniel Renouf
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Sophie Sun
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Kasmintan A Schrader
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean Young
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Ian Bosdet
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Aly Karsan
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada.,Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada. .,Department of Medical Genetics, The University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
40
|
Minchom A, Aversa C, Lopez J. Dancing with the DNA damage response: next-generation anti-cancer therapeutic strategies. Ther Adv Med Oncol 2018; 10:1758835918786658. [PMID: 30023007 PMCID: PMC6047242 DOI: 10.1177/1758835918786658] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/08/2018] [Indexed: 01/01/2023] Open
Abstract
Maintenance of genomic stability is a critical determinant of cell survival and relies on the coordinated action of the DNA damage response (DDR), which orchestrates a network of cellular processes, including DNA replication, DNA repair and cell-cycle progression. In cancer, the critical balance between the loss of genomic stability in malignant cells and the DDR provides exciting therapeutic opportunities. Drugs targeting DDR pathways taking advantage of clinical synthetic lethality have already shown therapeutic benefit - for example, the PARP inhibitor olaparib has shown benefit in BRCA-mutant ovarian and breast cancer. Olaparib has also shown benefit in metastatic prostate cancer in DDR-defective patients, expanding the potential biomarker of response beyond BRCA. Other agents and combinations aiming to block the DDR while pushing damaged DNA through the cell cycle, including PARP, ATR, ATM, CHK and DNA-PK inhibitors, are in development. Emerging work is also uncovering how the DDR interacts intimately with the host immune response, including by activating the innate immune response, further suggesting that clinical applications together with immunotherapy may be beneficial. Here, we review recent considerations related to the DDR from a clinical standpoint, providing a framework to address future directions and clinical opportunities.
Collapse
Affiliation(s)
- Anna Minchom
- Drug Development Unit at Royal Marsden Hospital/ Institute of Cancer Research, Sutton, UK
| | - Caterina Aversa
- Drug Development Unit at Royal Marsden Hospital/ Institute of Cancer Research, Sutton, UK
| | - Juanita Lopez
- Drug Development Unit at Royal Marsden Hospital/Institute of Cancer Research, Downs Rd, Sutton, SM2 5PT, UK
| |
Collapse
|
41
|
MacGregor TP, Carter R, Gillies RS, Findlay JM, Kartsonaki C, Castro-Giner F, Sahgal N, Wang LM, Chetty R, Maynard ND, Cazier JB, Buffa F, McHugh PJ, Tomlinson I, Middleton MR, Sharma RA. Translational study identifies XPF and MUS81 as predictive biomarkers for oxaliplatin-based peri-operative chemotherapy in patients with esophageal adenocarcinoma. Sci Rep 2018; 8:7265. [PMID: 29739952 PMCID: PMC5940885 DOI: 10.1038/s41598-018-24232-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 02/09/2018] [Indexed: 02/06/2023] Open
Abstract
Oxaliplatin-based chemotherapy is used to treat patients with esophageal adenocarcinoma (EAC), but no biomarkers are currently available for patient selection. We performed a prospective, clinical trial to identify potential biomarkers associated with clinical outcomes. Tumor tissue was obtained from 38 patients with resectable EAC before and after 2 cycles of oxaliplatin-fluorouracil chemotherapy. Pre-treatment mRNA expression of 280 DNA repair (DNAR) genes was tested for association with histopathological regression at surgery, disease-free survival (DFS) and overall survival (OS). High expression of 13 DNA damage repair genes was associated with DFS less than one year (P < 0.05); expression of 11 DNAR genes were associated with worse OS (P < 0.05). From clinical associations with outcomes, two genes, ERCC1 and EME1, were identified as candidate biomarkers. In cell lines in vitro, we showed the mechanism of action related to repair of oxaliplatin-induced DNA damage by depletion and knockout of protein binding partners of the candidate biomarkers, XPF and MUS81 respectively. In clinical samples from the clinical trial, pre-treatment XPF protein levels were associated with pathological response, and MUS81 protein was associated with 1-year DFS. XPF and MUS81 merit further validation in prospective clinical trials as biomarkers that may predict clinical response of EAC to oxaliplatin-based chemotherapy.
Collapse
Affiliation(s)
- T P MacGregor
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK
| | - R Carter
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK
| | - R S Gillies
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK
- Department of Upper GI Surgery, Churchill Hospital, Oxford, UK
| | - J M Findlay
- Department of Upper GI Surgery, Churchill Hospital, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - C Kartsonaki
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit (MRC PHRU) at the University of Oxford, Oxford, UK
| | - F Castro-Giner
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - N Sahgal
- Ludwig Institute for Cancer Research, University of Oxford, Nuffield Department of Medicine, Oxford, UK
| | - L M Wang
- NIHR Oxford Biomedical Research Centre/Department of Cellular Pathology/Radcliffe Department of Medicine, Oxford University Hospitals and University of Oxford, Oxford, UK
- Department of Laboratory Medicine, Changi General Hospital, Singapore, Singapore
| | - R Chetty
- Laboratory Medicine Programme, University Health Network, Toronto, Canada
| | - N D Maynard
- Department of Upper GI Surgery, Churchill Hospital, Oxford, UK
| | - J B Cazier
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - F Buffa
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK
| | - P J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - I Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M R Middleton
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK
| | - R A Sharma
- NIHR Oxford Biomedical Research Centre, Department of Oncology, University of Oxford, Oxford, UK.
- NIHR University College London Hospitals Biomedical Research Centre, UCL Cancer Institute, University College London, London, UK.
| |
Collapse
|
42
|
Telli ML, Stover DG, Loi S, Aparicio S, Carey LA, Domchek SM, Newman L, Sledge GW, Winer EP. Homologous recombination deficiency and host anti-tumor immunity in triple-negative breast cancer. Breast Cancer Res Treat 2018; 171:21-31. [PMID: 29736741 DOI: 10.1007/s10549-018-4807-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 04/30/2018] [Indexed: 12/21/2022]
Abstract
PURPOSE Triple-negative breast cancer (TNBC) is associated with worse outcomes relative to other breast cancer subtypes. Chemotherapy remains the standard-of-care systemic therapy for patients with localized or metastatic disease, with few biomarkers to guide benefit. METHODS We will discuss recent advances in our understanding of two key biological processes in TNBC, homologous recombination (HR) DNA repair deficiency and host anti-tumor immunity, and their intersection. RESULTS Recent advances in our understanding of homologous recombination (HR) deficiency, including FDA approval of PARP inhibitor olaparib for BRCA1 or BRCA2 mutation carriers, and host anti-tumor immunity in TNBC offer potential for new and biomarker-driven approaches to treat TNBC. Assays interrogating HR DNA repair capacity may guide treatment with agents inducing or targeting DNA damage repair. Tumor infiltrating lymphocytes (TILs) are associated with improved prognosis in TNBC and recent efforts to characterize infiltrating immune cell subsets and activate host anti-tumor immunity offer promise, yet challenges remain particularly in tumors lacking pre-existing immune infiltrates. Advances in these fields provide potential biomarkers to stratify patients with TNBC and guide therapy: induction of DNA damage in HR-deficient tumors and activation of existing or recruitment of host anti-tumor immune cells. Importantly, these advances provide an opportunity to guide use of existing therapies and development of novel therapies for TNBC. Efforts to combine therapies that exploit HR deficiency to enhance the activity of immune-directed therapies offer promise. CONCLUSIONS HR deficiency remains an important biomarker target and potentially effective adjunct to enhance immunogenicity of 'immune cold' TNBCs.
Collapse
Affiliation(s)
- M L Telli
- Stanford University School of Medicine, Stanford, CA, USA
| | - D G Stover
- Ohio State University Comprehensive Cancer Center, Columbus, OH, USA. .,Ohio State University Comprehensive Cancer Center, Biomedical Research Tower, Room 512, 460 West 12th Ave, Columbus, OH, 43210, USA.
| | - S Loi
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - S Aparicio
- University of British Columbia, Vancouver, BC, Canada
| | - L A Carey
- University of North Carolina, Chapel Hill, NC, USA
| | - S M Domchek
- University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - L Newman
- Henry Ford Hospital, Detroit, MI, USA
| | - G W Sledge
- Stanford University School of Medicine, Stanford, CA, USA
| | - E P Winer
- Dana Farber Cancer Institute, Boston, MA, USA
| |
Collapse
|
43
|
Carboplatin in BRCA1/2-mutated and triple-negative breast cancer BRCAness subgroups: the TNT Trial. Nat Med 2018; 24:628-637. [PMID: 29713086 DOI: 10.1038/s41591-018-0009-7] [Citation(s) in RCA: 555] [Impact Index Per Article: 92.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/02/2018] [Indexed: 12/25/2022]
Abstract
Germline mutations in BRCA1/2 predispose individuals to breast cancer (termed germline-mutated BRCA1/2 breast cancer, gBRCA-BC) by impairing homologous recombination (HR) and causing genomic instability. HR also repairs DNA lesions caused by platinum agents and PARP inhibitors. Triple-negative breast cancers (TNBCs) harbor subpopulations with BRCA1/2 mutations, hypothesized to be especially platinum-sensitive. Cancers in putative 'BRCAness' subgroups-tumors with BRCA1 methylation; low levels of BRCA1 mRNA (BRCA1 mRNA-low); or mutational signatures for HR deficiency and those with basal phenotypes-may also be sensitive to platinum. We assessed the efficacy of carboplatin and another mechanistically distinct therapy, docetaxel, in a phase 3 trial in subjects with unselected advanced TNBC. A prespecified protocol enabled biomarker-treatment interaction analyses in gBRCA-BC and BRCAness subgroups. The primary endpoint was objective response rate (ORR). In the unselected population (376 subjects; 188 carboplatin, 188 docetaxel), carboplatin was not more active than docetaxel (ORR, 31.4% versus 34.0%, respectively; P = 0.66). In contrast, in subjects with gBRCA-BC, carboplatin had double the ORR of docetaxel (68% versus 33%, respectively; biomarker, treatment interaction P = 0.01). Such benefit was not observed for subjects with BRCA1 methylation, BRCA1 mRNA-low tumors or a high score in a Myriad HRD assay. Significant interaction between treatment and the basal-like subtype was driven by high docetaxel response in the nonbasal subgroup. We conclude that patients with advanced TNBC benefit from characterization of BRCA1/2 mutations, but not BRCA1 methylation or Myriad HRD analyses, to inform choices on platinum-based chemotherapy. Additionally, gene expression analysis of basal-like cancers may also influence treatment selection.
Collapse
|
44
|
Abstract
OPINION STATEMENT Triple-negative breast cancer (TNBC) accounts for 15% of all breast cancers and is associated with poor long-term outcomes compared to other breast cancer subtypes. Currently, chemotherapy remains the main modality of treatment for early-stage TNBC, as there is no approved targeted therapy for this subtype. The biologic heterogeneity of TNBC has hindered the development and evaluation of novel agents, but recent advancements in subclassifying TNBC have paved the way for further investigation of more effective systemic therapies, including cytotoxic and targeted agents. TNBC is enriched for germline BRCA mutation and for somatic deficiencies in homologous recombination DNA repair, the so-called "BRCAness" phenotype. Together, germline BRCA mutations and BRCAness are promising biomarkers of susceptibility to DNA-damaging therapy. Various investigational approaches are consequently being investigated in early-stage TNBC, including immune checkpoint inhibitors, platinum compounds, PI3K pathway inhibitors, and androgen receptor inhibitors. Due to the biological diversity found within TNBC, patient selection based on molecular biomarkers could aid the design of early-phase clinical trials, ultimately accelerating the clinical application of effective new agents. TNBC is an aggressive breast cancer subtype, for which multiple targeted approaches will likely be required for patient outcomes to be substantially improved.
Collapse
|
45
|
O’Kane GM, Connor AA, Gallinger S. Characterization, Detection, and Treatment Approaches for Homologous Recombination Deficiency in Cancer. Trends Mol Med 2017; 23:1121-1137. [DOI: 10.1016/j.molmed.2017.10.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 02/07/2023]
|
46
|
A BRCA1 deficient, NFκB driven immune signal predicts good outcome in triple negative breast cancer. Oncotarget 2017; 7:19884-96. [PMID: 26943587 PMCID: PMC4991425 DOI: 10.18632/oncotarget.7865] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 02/18/2016] [Indexed: 12/31/2022] Open
Abstract
Triple negative (TNBCs) and the closely related Basal-like (BLBCs) breast cancers are a loosely defined collection of cancers with poor clinical outcomes. Both show strong similarities with BRCA1-mutant breast cancers and BRCA1 dysfunction, or ‘BRCAness’, is observed in a large proportion of sporadic BLBCs. BRCA1 expression and function has been shown in vitro to modulate responses to radiation and chemotherapy. Exploitation of this knowledge in the treatment of BRCA1-mutant patients has had varying degrees of success. This reflects the significant problem of accurately detecting those patients with BRCA1 dysfunction. Moreover, not all BRCA1 mutations/loss of function result in the same histology/pathology or indeed have similar effects in modulating therapeutic responses. Given the poor clinical outcomes and lack of targeted therapy for these subtypes, a better understanding of the biology underlying these diseases is required in order to develop novel therapeutic strategies. We have discovered a consistent NFκB hyperactivity associated with BRCA1 dysfunction as a consequence of increased Reactive Oxygen Species (ROS). This biology is found in a subset of BRCA1-mutant and triple negative breast cancer cases and confers good outcome. The increased NFκB signalling results in an anti-tumour microenvironment which may allow CD8+ cytotoxic T cells to suppress tumour progression. However, tumours lacking this NFκB-driven biology have a more tumour-promoting environment and so are associated with poorer prognosis. Tumour-derived gene expression data and cell line models imply that these tumours may benefit from alternative treatment strategies such as reprogramming the microenvironment and targeting the IGF and AR signalling pathways.
Collapse
|
47
|
Alvi MA, Wilson RH, Salto-Tellez M. Rare cancers: the greatest inequality in cancer research and oncology treatment. Br J Cancer 2017; 117:1255-1257. [PMID: 28934760 PMCID: PMC5672935 DOI: 10.1038/bjc.2017.321] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Muhammad A Alvi
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Northern Ireland BT9 7AE, UK
| | - Richard H Wilson
- Colorectal Cancer Focus Group, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Northern Ireland BT9 7AE, UK
| | - Manuel Salto-Tellez
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Northern Ireland BT9 7AE, UK
- Tissue Pathology Department, Belfast Health and Social Care Trust, Northern Ireland BT12 6BA, UK
| |
Collapse
|
48
|
Affiliation(s)
- Thaiz Rivera Vargas
- Centre de Recherche; INSERM U1231; Facultés de Médecine et de Pharmacie; Dijon France
- Faculté de Médecine; Université de Bourgogne Franche comté; Dijon France
| | - Lionel Apetoh
- Centre de Recherche; INSERM U1231; Facultés de Médecine et de Pharmacie; Dijon France
- Faculté de Médecine; Université de Bourgogne Franche comté; Dijon France
- Centre Georges François Leclerc; Dijon France
| |
Collapse
|
49
|
Thomas SN, Chen L, Liu Y, Höti N, Zhang H. Targeted Proteomic Analyses of Histone H4 Acetylation Changes Associated with Homologous-Recombination-Deficient High-Grade Serous Ovarian Carcinomas. J Proteome Res 2017; 16:3704-3710. [PMID: 28866885 DOI: 10.1021/acs.jproteome.7b00405] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Approximately 20% of high-grade serous ovarian cancers are homologous-recombination (HR)-deficient due to genetic and epigenetic mutations of HR pathway genes including the tumor suppressor genes BRCA1 and 2. HR deficiency (HRD) compromises cells' ability to efficiently repair DNA damage, but it also increases sensitivity to chemotherapeutic treatment strategies; however, not all ovarian cancer patients with HRD tumors exhibit positive responses to chemotherapy. Our previous iTRAQ-based comprehensive proteomic characterization of high-grade serous ovarian carcinomas found that lower levels of histone H4 acetylation at Lys12 and Lys16 (H4-K12acK16ac) were associated with HRD tumors compared with non-HRD tumors. In the current study, we developed and validated an H4-K12acK16ac parallel-reaction-monitoring (PRM)-targeted mass-spectrometry-based assay to analyze acetylation changes of histone H4 and to determine the association of these changes with total H4, histone acetyltransferase, and histone deacetylase (HDAC) levels. Whereas the levels of H4 and histone acetyltransferases were stable irrespective of HRD status, the levels of histone H4 acetylation and one HDAC, HDAC6, were elevated in the HRD tumors. Relative H4 acetylation levels were also analyzed by an antibody-based approach in additional ovarian tumors. It is possible that specific H4 acetylation at Lys12 and Lys16 associated with HRD could inform chemotherapeutic treatment modalities to improve ovarian cancer patients' treatment response.
Collapse
Affiliation(s)
- Stefani N Thomas
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine , Baltimore, Maryland 21231, United States
| | - Lijun Chen
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine , Baltimore, Maryland 21231, United States
| | - Yang Liu
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine , Baltimore, Maryland 21231, United States
| | - Naseruddin Höti
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine , Baltimore, Maryland 21231, United States
| | - Hui Zhang
- Department of Pathology, Clinical Chemistry Division, Johns Hopkins University School of Medicine , Baltimore, Maryland 21231, United States
| |
Collapse
|
50
|
Mouw KW, Goldberg MS, Konstantinopoulos PA, D'Andrea AD. DNA Damage and Repair Biomarkers of Immunotherapy Response. Cancer Discov 2017; 7:675-693. [PMID: 28630051 PMCID: PMC5659200 DOI: 10.1158/2159-8290.cd-17-0226] [Citation(s) in RCA: 463] [Impact Index Per Article: 66.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/05/2017] [Accepted: 05/18/2017] [Indexed: 12/16/2022]
Abstract
DNA-damaging agents are widely used in clinical oncology and exploit deficiencies in tumor DNA repair. Given the expanding role of immune checkpoint blockade as a therapeutic strategy, the interaction of tumor DNA damage with the immune system has recently come into focus, and it is now clear that the tumor DNA repair landscape has an important role in driving response to immune checkpoint blockade. Here, we summarize the mechanisms by which DNA damage and genomic instability have been found to shape the antitumor immune response and describe clinical efforts to use DNA repair biomarkers to guide use of immune-directed therapies.Significance: Only a subset of patients respond to immune checkpoint blockade, and reliable predictive biomarkers of response are needed to guide therapy decisions. DNA repair deficiency is common among tumors, and emerging experimental and clinical evidence suggests that features of genomic instability are associated with response to immune-directed therapies. Cancer Discov; 7(7); 675-93. ©2017 AACR.
Collapse
Affiliation(s)
- Kent W Mouw
- Department of Radiation Oncology, Brigham & Women's Hospital/Dana-Farber Cancer Institute, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts
| | - Michael S Goldberg
- Harvard Medical School, Boston, Massachusetts
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Panagiotis A Konstantinopoulos
- Harvard Medical School, Boston, Massachusetts
- Medical Gynecology Oncology Program, Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alan D D'Andrea
- Department of Radiation Oncology, Brigham & Women's Hospital/Dana-Farber Cancer Institute, Boston, Massachusetts.
- Harvard Medical School, Boston, Massachusetts
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, Massachusetts
| |
Collapse
|