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Stokes T, Cen HH, Kapranov P, Gallagher IJ, Pitsillides AA, Volmar C, Kraus WE, Johnson JD, Phillips SM, Wahlestedt C, Timmons JA. Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq. ADVANCED GENETICS (HOBOKEN, N.J.) 2023; 4:2200024. [PMID: 37288167 PMCID: PMC10242409 DOI: 10.1002/ggn2.202200024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Indexed: 06/09/2023]
Abstract
Sequencing the human genome empowers translational medicine, facilitating transcriptome-wide molecular diagnosis, pathway biology, and drug repositioning. Initially, microarrays are used to study the bulk transcriptome; but now short-read RNA sequencing (RNA-seq) predominates. Positioned as a superior technology, that makes the discovery of novel transcripts routine, most RNA-seq analyses are in fact modeled on the known transcriptome. Limitations of the RNA-seq methodology have emerged, while the design of, and the analysis strategies applied to, arrays have matured. An equitable comparison between these technologies is provided, highlighting advantages that modern arrays hold over RNA-seq. Array protocols more accurately quantify constitutively expressed protein coding genes across tissue replicates, and are more reliable for studying lower expressed genes. Arrays reveal long noncoding RNAs (lncRNA) are neither sparsely nor lower expressed than protein coding genes. Heterogeneous coverage of constitutively expressed genes observed with RNA-seq, undermines the validity and reproducibility of pathway analyses. The factors driving these observations, many of which are relevant to long-read or single-cell sequencing are discussed. As proposed herein, a reappreciation of bulk transcriptomic methods is required, including wider use of the modern high-density array data-to urgently revise existing anatomical RNA reference atlases and assist with more accurate study of lncRNAs.
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Affiliation(s)
- Tanner Stokes
- Faculty of ScienceMcMaster UniversityHamiltonL8S 4L8Canada
| | - Haoning Howard Cen
- Life Sciences InstituteUniversity of British ColumbiaVancouverV6T 1Z3Canada
| | | | - Iain J Gallagher
- School of Applied SciencesEdinburgh Napier UniversityEdinburghEH11 4BNUK
| | | | | | | | - James D. Johnson
- Life Sciences InstituteUniversity of British ColumbiaVancouverV6T 1Z3Canada
| | | | | | - James A. Timmons
- Miller School of MedicineUniversity of MiamiMiamiFL33136USA
- William Harvey Research InstituteQueen Mary University LondonLondonEC1M 6BQUK
- Augur Precision Medicine LTDStirlingFK9 5NFUK
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2
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Lashen A, Toss MS, Green AR, Mongan NP, Rakha E. Ki67 assessment in invasive luminal breast cancer: a comparative study between different scoring methods. Histopathology 2022; 81:786-798. [PMID: 35997652 PMCID: PMC9826086 DOI: 10.1111/his.14781] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/09/2022] [Accepted: 08/21/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Ki67 reflects the proliferation activity in breast cancer (BC). However, an optimal method for its assessment in clinical settings has yet to be robustly defined. In this study we compared several methods to score Ki67 to identify a reliable and reproducible method for routine practice. METHODS Sections from luminal BC cohort (n = 1662) were immunohistochemically stained with Ki67 and were assessed for the percentage, pattern, and intensity of expression. Ki67 positivity was evaluated using three methods: (i) quantification of Ki67-positive cells among 1000 invasive tumour cells within hotspot, (ii) average estimation of Ki67 within a defined hotspot, and (iii) average estimation of Ki67 positivity within the whole section. Time required for scoring, interobserver agreement and association with outcome were determined. RESULTS The mean percentage of Ki67 expression per 1000 cells method was 16%, while the mean value of Ki67 scores using the average estimation within hotspot and whole slide were 14% and 12%, respectively. Quantification of Ki67-positive cells within 1000 cells had the highest degree of consistency between observers, and the highest hazard ratio predicting patient outcome when compared to using different common Ki67 cutoffs, which was independent of the other two methods. Granular pattern of Ki67 expression was associated with poorer outcome as compared to the other patterns. CONCLUSION Assessment of Ki67 expression using quantification positive cells among 1000 tumour cells is an optimal method to achieve high reliability and reproducibility. Comment on the predominant Ki67 expression pattern would add prognostic and predictive value in luminal BC.
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Affiliation(s)
- Ayat Lashen
- Academic Unit for Translational Medical Sciences, School of MedicineUniversity of NottinghamNottinghamUK,Department of Pathology, Faculty of MedicineMenoufia UniversityShebin El KomEgypt,Nottingham Breast Cancer Research CentreUniversity of NottinghamNottinghamUK
| | - Michael S Toss
- Academic Unit for Translational Medical Sciences, School of MedicineUniversity of NottinghamNottinghamUK,Nottingham Breast Cancer Research CentreUniversity of NottinghamNottinghamUK,Department of HistopathologySheffield Teaching Hospitals NHS Foundation Trust SheffieldUK
| | - Andrew R Green
- Academic Unit for Translational Medical Sciences, School of MedicineUniversity of NottinghamNottinghamUK,Nottingham Breast Cancer Research CentreUniversity of NottinghamNottinghamUK
| | - Nigel P Mongan
- School of Veterinary Medicine and SciencesUniversity of NottinghamNottinghamUK,Department of PharmacologyWeill Cornell MedicineNew YorkUSA
| | - Emad Rakha
- Academic Unit for Translational Medical Sciences, School of MedicineUniversity of NottinghamNottinghamUK,Department of Pathology, Faculty of MedicineMenoufia UniversityShebin El KomEgypt,Nottingham Breast Cancer Research CentreUniversity of NottinghamNottinghamUK
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3
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Buus R, Szijgyarto Z, Schuster EF, Xiao H, Haynes BP, Sestak I, Cuzick J, Paré L, Seguí E, Chic N, Prat A, Dowsett M, Cheang MCU. Development and validation for research assessment of Oncotype DX® Breast Recurrence Score, EndoPredict® and Prosigna®. NPJ Breast Cancer 2021; 7:15. [PMID: 33579961 PMCID: PMC7881187 DOI: 10.1038/s41523-021-00216-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/17/2020] [Indexed: 12/22/2022] Open
Abstract
Multi-gene prognostic signatures including the Oncotype® DX Recurrence Score (RS), EndoPredict® (EP) and Prosigna® (Risk Of Recurrence, ROR) are widely used to predict the likelihood of distant recurrence in patients with oestrogen-receptor-positive (ER+), HER2-negative breast cancer. Here, we describe the development and validation of methods to recapitulate RS, EP and ROR scores from NanoString expression data. RNA was available from 107 tumours from postmenopausal women with early-stage, ER+, HER2- breast cancer from the translational Arimidex, Tamoxifen, Alone or in Combination study (TransATAC) where previously these signatures had been assessed with commercial methodology. Gene expression was measured using NanoString nCounter. For RS and EP, conversion factors to adjust for cross-platform variation were estimated using linear regression. For ROR, the steps to perform subgroup-specific normalisation of the gene expression data and calibration factors to calculate the 46-gene ROR score were assessed and verified. Training with bootstrapping (n = 59) was followed by validation (n = 48) using adjusted, research use only (RUO) NanoString-based algorithms. In the validation set, there was excellent concordance between the RUO scores and their commercial counterparts (rc(RS) = 0.96, 95% CI 0.93-0.97 with level of agreement (LoA) of -7.69 to 8.12; rc(EP) = 0.97, 95% CI 0.96-0.98 with LoA of -0.64 to 1.26 and rc(ROR) = 0.97 (95% CI 0.94-0.98) with LoA of -8.65 to 10.54). There was also a strong agreement in risk stratification: (RS: κ = 0.86, p < 0.0001; EP: κ = 0.87, p < 0.0001; ROR: κ = 0.92, p < 0.001). In conclusion, the calibrated algorithms recapitulate the commercial RS and EP scores on individual biopsies and ROR scores on samples based on subgroup-centreing method using NanoString expression data.
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Affiliation(s)
- Richard Buus
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Zsolt Szijgyarto
- Clinical Trials and Statistics Unit (ICR-CTSU), Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Eugene F Schuster
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Hui Xiao
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Ben P Haynes
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | | | | | - Laia Paré
- Department of Medical Oncology, Hospital Clinic, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Elia Seguí
- Department of Medical Oncology, Hospital Clinic, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Nuria Chic
- Department of Medical Oncology, Hospital Clinic, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Aleix Prat
- Department of Medical Oncology, Hospital Clinic, Barcelona, Spain
- Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Mitch Dowsett
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK
| | - Maggie Chon U Cheang
- Clinical Trials and Statistics Unit (ICR-CTSU), Division of Clinical Studies, The Institute of Cancer Research, London, UK.
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4
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Harnan S, Tappenden P, Cooper K, Stevens J, Bessey A, Rafia R, Ward S, Wong R, Stein RC, Brown J. Tumour profiling tests to guide adjuvant chemotherapy decisions in early breast cancer: a systematic review and economic analysis. Health Technol Assess 2020; 23:1-328. [PMID: 31264581 DOI: 10.3310/hta23300] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Breast cancer and its treatment can have an impact on health-related quality of life and survival. Tumour profiling tests aim to identify whether or not women need chemotherapy owing to their risk of relapse. OBJECTIVES To conduct a systematic review of the effectiveness and cost-effectiveness of the tumour profiling tests oncotype DX® (Genomic Health, Inc., Redwood City, CA, USA), MammaPrint® (Agendia, Inc., Amsterdam, the Netherlands), Prosigna® (NanoString Technologies, Inc., Seattle, WA, USA), EndoPredict® (Myriad Genetics Ltd, London, UK) and immunohistochemistry 4 (IHC4). To develop a health economic model to assess the cost-effectiveness of these tests compared with clinical tools to guide the use of adjuvant chemotherapy in early-stage breast cancer from the perspective of the NHS and Personal Social Services. DESIGN A systematic review and health economic analysis were conducted. REVIEW METHODS The systematic review was partially an update of a 2013 review. Nine databases were searched in February 2017. The review included studies assessing clinical effectiveness in people with oestrogen receptor-positive, human epidermal growth factor receptor 2-negative, stage I or II cancer with zero to three positive lymph nodes. The economic analysis included a review of existing analyses and the development of a de novo model. RESULTS A total of 153 studies were identified. Only one completed randomised controlled trial (RCT) using a tumour profiling test in clinical practice was identified: Microarray In Node-negative Disease may Avoid ChemoTherapy (MINDACT) for MammaPrint. Other studies suggest that all the tests can provide information on the risk of relapse; however, results were more varied in lymph node-positive (LN+) patients than in lymph node-negative (LN0) patients. There is limited and varying evidence that oncotype DX and MammaPrint can predict benefit from chemotherapy. The net change in the percentage of patients with a chemotherapy recommendation or decision pre/post test ranged from an increase of 1% to a decrease of 23% among UK studies and a decrease of 0% to 64% across European studies. The health economic analysis suggests that the incremental cost-effectiveness ratios for the tests versus current practice are broadly favourable for the following scenarios: (1) oncotype DX, for the LN0 subgroup with a Nottingham Prognostic Index (NPI) of > 3.4 and the one to three positive lymph nodes (LN1-3) subgroup (if a predictive benefit is assumed); (2) IHC4 plus clinical factors (IHC4+C), for all patient subgroups; (3) Prosigna, for the LN0 subgroup with a NPI of > 3.4 and the LN1-3 subgroup; (4) EndoPredict Clinical, for the LN1-3 subgroup only; and (5) MammaPrint, for no subgroups. LIMITATIONS There was only one completed RCT using a tumour profiling test in clinical practice. Except for oncotype DX in the LN0 group with a NPI score of > 3.4 (clinical intermediate risk), evidence surrounding pre- and post-test chemotherapy probabilities is subject to considerable uncertainty. There is uncertainty regarding whether or not oncotype DX and MammaPrint are predictive of chemotherapy benefit. The MammaPrint analysis uses a different data source to the other four tests. The Translational substudy of the Arimidex, Tamoxifen, Alone or in Combination (TransATAC) study (used in the economic modelling) has a number of limitations. CONCLUSIONS The review suggests that all the tests can provide prognostic information on the risk of relapse; results were more varied in LN+ patients than in LN0 patients. There is limited and varying evidence that oncotype DX and MammaPrint are predictive of chemotherapy benefit. Health economic analyses indicate that some tests may have a favourable cost-effectiveness profile for certain patient subgroups; all estimates are subject to uncertainty. More evidence is needed on the prediction of chemotherapy benefit, long-term impacts and changes in UK pre-/post-chemotherapy decisions. STUDY REGISTRATION This study is registered as PROSPERO CRD42017059561. FUNDING The National Institute for Health Research Health Technology Assessment programme.
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Affiliation(s)
- Sue Harnan
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Paul Tappenden
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Katy Cooper
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - John Stevens
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Alice Bessey
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Rachid Rafia
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Sue Ward
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Ruth Wong
- Health Economics and Decision Science, School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Robert C Stein
- University College London Hospitals Biomedical Research Centre, London, UK.,Research Department of Oncology, University College London, London, UK
| | - Janet Brown
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
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5
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Lu Y, Tong Y, Huang J, Lin L, Wu J, Fei X, Huang O, He J, Zhu L, Chen W, Li Y, Chen X, Shen K. Primary 21-Gene Recurrence Score and Disease Outcome in Loco-Regional and Distant Recurrent Breast Cancer Patients. Front Oncol 2020; 10:1315. [PMID: 32850415 PMCID: PMC7412719 DOI: 10.3389/fonc.2020.01315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
Background: The 21-gene recurrence score (RS) assay has been proven prognostic and predictive for hormone receptor-positive/HER2-negative, node-negative early breast cancer patients. However, whether primary 21-gene RS can predict prognosis in recurrent breast cancer patients remained unknown. Patients and Methods: Consecutive breast cancer patients operated in Comprehensive Breast Health Center, Shanghai Ruijin Hospital between January 2009 and December 2018 were retrospectively analyzed. Patients with available 21-gene RS result for the primary tumor and reporting disease recurrence during follow-up were included. Association of 21-gene RS and overall survival (OS), post-recurrence overall survival (PR-OS), post-recurrence progression-free survival (PR-PFS), and first-line systemic treatment after recurrence were compared among different groups. Results: A total of 74 recurrent patients were included, with 10, 27, 37 patients in the RS <18, 18–30, and ≥ 31 groups, respectively. Recurrent patients with RS ≥ 31 were more likely to receive chemotherapy as their first-line treatment compared to those with RS <31 (P = 0.025). Compared to those with RS <31, patients with RS ≥ 31 had significantly worse OS (P = 0.025), worse PR-OS (P = 0.026), and a trend of inferior PR-PFS (P = 0.106). Multivariate analysis demonstrated that primary ER expression level (OS: P = 0.009; PR-OS: P = 0.017) and histological grade (OS: P = 0.003; PR-OS: P = 0.009), but not primary 21-gene RS (OS: P = 0.706; PR-OS: P = 0.120), were independently associated with worse OS and PR-OS. Conclusions: High primary 21-gene RS tended to be associated with worse disease outcome in loco-regional and distant recurrent breast cancer patients, which could influence the first-line systemic treatment after relapse, warranting further clinical evaluation.
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Affiliation(s)
- Yujie Lu
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiwei Tong
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiahui Huang
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Lin
- Department of Clinical Laboratory, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jiayi Wu
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaochun Fei
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ou Huang
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianrong He
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Zhu
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiguo Chen
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yafen Li
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaosong Chen
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kunwei Shen
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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6
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Lundberg A, Lindström LS, Parker JS, Löverli E, Perou CM, Bergh J, Tobin NP. A pan-cancer analysis of the frequency of DNA alterations across cell cycle activity levels. Oncogene 2020; 39:5430-5440. [PMID: 32581248 DOI: 10.1038/s41388-020-1367-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/04/2020] [Accepted: 06/10/2020] [Indexed: 01/22/2023]
Abstract
Pan-cancer genomic analyses based on the magnitude of pathway activity are currently lacking. Focusing on the cell cycle, we examined the DNA mutations and chromosome arm-level aneuploidy within tumours with low, intermediate and high cell-cycle activity in 9515 pan-cancer patients with 32 different tumour types. Boxplots showed that cell-cycle activity varied broadly across and within all cancers. TP53 and PIK3CA mutations were common in all cell cycle score (CCS) tertiles but with increasing frequency as cell-cycle activity levels increased (P < 0.001). Mutations in BRAF and gains in 16p were less frequent in CCS High tumours (P < 0.001). In Kaplan-Meier analysis, patients whose tumours were CCS Low had a longer Progression Free Interval (PFI) relative to Intermediate or High (P < 0.001) and this significance remained in multivariable analysis (CCS Intermediate: HR = 1.37; 95% CI 1.17-1.60, CCS High: 1.54; 1.29-1.84, CCS Low = Ref). These results demonstrate that whilst similar DNA alterations can be found at all cell-cycle activity levels, some notable exceptions exist. Moreover, independent prognostic information can be derived on a pan-cancer level from a simple measure of cell-cycle activity.
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Affiliation(s)
- Arian Lundberg
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Linda S Lindström
- Department of Biosciences and Nutrition, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Joel S Parker
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elinor Löverli
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Charles M Perou
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonas Bergh
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden.,Department of Public Health, Oxford University, Oxford, UK
| | - Nicholas P Tobin
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden.
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7
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Chen J, Zheng Y, Chen Z, Fan F, Wang Y. Clinical presentation and long-term outcome of primary spinal intradural malignant peripheral nerve sheath tumors. Clin Neurol Neurosurg 2019; 185:105484. [PMID: 31421588 DOI: 10.1016/j.clineuro.2019.105484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 07/29/2019] [Accepted: 08/08/2019] [Indexed: 01/24/2023]
Abstract
OBJECTIVE Primary spinal intradural malignant peripheral nerve sheath tumors (MPNSTs) are exceedingly rare, and there is limited published information regarding these lesions. The purpose of this study was to analyze the clinical course, treatment, and outcome of primary spinal intradural MPNSTs. PATIENTS AND METHODS A retrospective study was performed on 8 patients with primary spinal intradural MPNSTs who were surgically treated and pathologically confirmed in our institution between 2007 and 2018. RESULTS There were 3 females and 5 males, with a median age of 46.5 years (range, 21-68 years). Limb weakness was the most common clinical symptom (5/8, 62.5%). The radiological diagnosis was meningioma or schwannoma in most patients (7/8, 87.5%). Malignancies were graded high in 5 cases (62.5%) and low in 3 cases (37.5%). Gross total resection (GTR) was performed in 5 cases, while subtotal resection (STR) was achieved in 3 cases. The mean follow-up period was 48.9 months (range, 10-160 months). During follow-up, local recurrence occurred in 6/8 cases (75.0%) and distant metastasis occurred in 2/8 cases (25.0%). The median survival time (MST) of these 8 patients was 21.0 months. The overall 1-year, 2-year, and 5-year survival rates were 87.5% (7/8), 50.0% (4/8), and 25.0% (2/8), respectively. CONCLUSIONS Primary spinal intradural MPNST is a challenging clinical entity given its high local relapse rate. Primary spinal intradural MPNSTs radiologically present themselves heterogeneous and thus difficult to distinguish from schwannomas or meningiomas. Surgical resection, especially GTR, is the preferential treatment for primary spinal intradural MPNSTs.
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Affiliation(s)
- Jun Chen
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yifeng Zheng
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Zirong Chen
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Fanfan Fan
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yu Wang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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8
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Lundberg A, Lindström LS, Harrell JC, Falato C, Carlson JW, Wright PK, Foukakis T, Perou CM, Czene K, Bergh J, Tobin NP. Gene Expression Signatures and Immunohistochemical Subtypes Add Prognostic Value to Each Other in Breast Cancer Cohorts. Clin Cancer Res 2017; 23:7512-7520. [PMID: 28972043 PMCID: PMC5822691 DOI: 10.1158/1078-0432.ccr-17-1535] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/22/2017] [Accepted: 09/25/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Gene signatures and Ki67 stratify the same breast tumor into opposing good/poor prognosis groups in approximately 20% of patients. Given this discrepancy, we hypothesized that the combination of a clinically relevant signature and IHC markers may provide more prognostic information than either classifier alone.Experimental Design: We assessed Ki67 alone or combined with ER, PR and HER2 (forming IHC subtypes), and the research versions of the Genomic Grade Index, 70-gene, cell-cycle score, recurrence score (RS), and PAM50 signatures on matching TMA/whole tumor sections and microarray data in two Swedish breast cancer cohorts of 379 and 209 patients, with median follow-up of 12.4 and 12.5 years, respectively. First, we fit Cox proportional hazards models and used the change in likelihood ratio (Δ LR) to determine the additional prognostic information provided by signatures beyond that of (i) Ki67 and (ii) IHC subtypes. Second and uniquely, we then assessed whether signatures could compete well with pathology-based IHC classifiers by calculating the additional prognostic information of Ki67/IHC subtypes beyond signatures.Results: In cohort 1, only RS and PAM50 provided additional prognostic information beyond Ki67 and IHC subtypes (Δ LR-χ2 Ki67: RS = 12.8, PAM50 = 20.7, IHC subtypes: RS = 12.9, PAM50 = 11.7). Conversely, IHC subtypes added prognostic information beyond all signatures except PAM50. Similar results were observed in cohort 2.Conclusions: RS and PAM50 provided more prognostic information than the IHC subtypes in all breast cancer patients; however, the IHC subtypes did not add any prognostic information to PAM50. Clin Cancer Res; 23(24); 7512-20. ©2017 AACR.
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Affiliation(s)
- Arian Lundberg
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Linda S Lindström
- Department of Biosciences and Nutrition, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Claudette Falato
- Department of Oncology and Pathology, Karolinska Institutet, Radiumhemmet, Karolinska University Hospital, Stockholm, Sweden
| | - Joseph W Carlson
- Department of Pathology and Cytology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Paul K Wright
- Department of Adult Histopathology and Manchester Cytology Centre, Manchester Royal Infirmary, Manchester, United Kingdom
| | - Theodoros Foukakis
- Department of Oncology and Pathology, Karolinska Institutet, Radiumhemmet, Karolinska University Hospital, Stockholm, Sweden
| | - Charles M Perou
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Jonas Bergh
- Department of Oncology and Pathology, Karolinska Institutet, Radiumhemmet, Karolinska University Hospital, Stockholm, Sweden
- Department of Public Health, Oxford University, Oxford, United Kingdom
| | - Nicholas P Tobin
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden.
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9
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Tobin NP, Lundberg A, Lindström LS, Harrell JC, Foukakis T, Carlsson L, Einbeigi Z, Linderholm BK, Loman N, Malmberg M, Fernö M, Czene K, Perou CM, Bergh J, Hatschek T. PAM50 Provides Prognostic Information When Applied to the Lymph Node Metastases of Advanced Breast Cancer Patients. Clin Cancer Res 2017; 23:7225-7231. [PMID: 28972041 DOI: 10.1158/1078-0432.ccr-17-2301] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 08/29/2017] [Accepted: 09/25/2017] [Indexed: 11/16/2022]
Abstract
Purpose: Transcriptional pathway activity and the molecular subtypes of breast cancer metastases have been shown to significantly influence patient postrelapse survival. Here, we further determine the relevance of clinically employed gene signatures in the advanced breast cancer (ABC) setting.Experimental Design: Sufficient RNA for expression profiling was obtained from distant metastatic or inoperable loco-regional relapse tissue by fine-needle aspiration from 109 patients of the Swedish TEX clinical trial. Gene signatures (GGI, 70 gene, recurrence score, cell-cycle score, risk of recurrence score, and PAM50) were applied to all metastases, and their relationship to long- (5-year) and short-term (1.5-year) postrelapse survival at all and locoregional lymph nodes (n = 40) versus other metastatic sites (n = 69) combined was assessed using Kaplan-Meier and/or multivariate Cox regression analyses.Results: The majority of metastases were classified into intermediate or high-risk groups by all signatures, and a significant association was found between metastatic signature subgroups and primary tumor estrogen receptor status and histologic grade (P < 0.05). When considering all sites of metastasis, only PAM50 was statistically significant in Kaplan-Meier analysis (Log-rank P = 0.008 and 0.008 for long- and short-term postrelapse breast cancer-specific survival, respectively). This significance remained in both uni- and multivariate models when restricting analyses to lymph node metastases only, and a similar trend was observed in other metastatic sites combined, but did not reach formal significance.Conclusions: Our findings are the first to demonstrate that the PAM50 signature can provide prognostic information from the lymph node metastases of ABC patients. Clin Cancer Res; 23(23); 7225-31. ©2017 AACR.
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Affiliation(s)
- Nicholas P Tobin
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden.
| | - Arian Lundberg
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Linda S Lindström
- Department of Biosciences and Nutrition, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Theodoros Foukakis
- Department of Oncology and Pathology, Karolinska Institutet, Radiumhemmet, Karolinska Oncology, University Hospital, Stockholm, Sweden
| | - Lena Carlsson
- Department of Oncology, Sundsvall General Hospital, Sundsvall, Sweden
| | - Zakaria Einbeigi
- Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Barbro K Linderholm
- Department of Oncology and Pathology, Cancer Center Karolinska, Karolinska Institutet and University Hospital, Stockholm, Sweden.,Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Niklas Loman
- Department of Oncology, Skåne University Hospital, Lund, Sweden
| | - Martin Malmberg
- Department of Oncology, Skåne University Hospital, Helsingborg, Sweden
| | - Mårten Fernö
- Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Medicon Village, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Charles M Perou
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jonas Bergh
- Department of Oncology and Pathology, Karolinska Institutet, Radiumhemmet, Karolinska Oncology, University Hospital, Stockholm, Sweden.,Department of Public Health, Oxford University, Oxford, United Kingdom
| | - Thomas Hatschek
- Department of Oncology and Pathology, Karolinska Institutet, Radiumhemmet, Karolinska Oncology, University Hospital, Stockholm, Sweden
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Fredholm H, Magnusson K, Lindström LS, Tobin NP, Lindman H, Bergh J, Holmberg L, Pontén F, Frisell J, Fredriksson I. Breast cancer in young women and prognosis: How important are proliferation markers? Eur J Cancer 2017; 84:278-289. [PMID: 28844016 DOI: 10.1016/j.ejca.2017.07.044] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 07/26/2017] [Accepted: 07/27/2017] [Indexed: 01/03/2023]
Abstract
AIM Compared to middle-aged women, young women with breast cancer have a higher risk of systemic disease. We studied expression of proliferation markers in relation to age and subtype and their association with long-term prognosis. METHODS Distant disease-free survival (DDFS) was studied in 504 women aged <40 years and 383 women aged ≥40 years from a population-based cohort. Information on patient characteristics, treatment and follow-up was collected from medical records. Tissue microarrays were produced for analysis of oestrogen receptor, progesterone receptor (PR), Her2, Ki-67 and cyclins. RESULTS Young women with luminal tumours had significantly higher expression of Ki-67 and cyclins. Proliferation markers were prognostic only within this subtype. Ki-67 was a prognostic indicator only in young women with luminal PR+ tumours. The optimal cut-off for Ki-67 varied by age. High expression of cyclin E1 conferred a better DDFS in women aged <40 years with luminal PR- tumours (hazard ratio [HR] 0.47 [0.24-0.92]). Age <40 years was an independent risk factor of DDFS exclusively in women with luminal B PR+ tumours (HR 2.35 [1.22-4.50]). Young women with luminal B PR- tumours expressing low cyclin E1 had a six-fold risk of distant disease compared with luminal A (HR 6.21 [2.17-17.6]). CONCLUSIONS The higher expression of proliferation markers in young women does not have a strong impact on prognosis. Ki-67 is only prognostic in the subgroup of young women with luminal PR+ tumours. The only cyclin adding prognostic value beyond subtype is cyclin E1. Age is an independent prognostic factor only in women with luminal B PR+ tumours.
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Affiliation(s)
- Hanna Fredholm
- Karolinska Institutet, Department of Molecular Medicine and Surgery, Stockholm, Sweden; Department of Breast- and Endocrine Surgery, Karolinska University Hospital, Stockholm, Sweden.
| | - Kristina Magnusson
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala, Sweden
| | - Linda S Lindström
- Karolinska Institutet, Department of Biosciences and Nutrition, Stockholm, Sweden
| | - Nicholas P Tobin
- Karolinska Institutet, Department of Oncology and Pathology, Cancer Center Karolinska, Stockholm, Sweden
| | - Henrik Lindman
- Uppsala University, Department of Radiology, Oncology and Radiation Science, Uppsala University Hospital, Uppsala, Sweden
| | - Jonas Bergh
- Karolinska Institutet, Department of Oncology and Pathology, Cancer Center Karolinska, Stockholm, Sweden; Karolinska Oncology, Radiumhemmet, Karolinska University Hospital, Stockholm, Sweden
| | - Lars Holmberg
- Uppsala University, Department of Surgical Sciences, Regional Cancer Center, Uppsala University Hospital, Uppsala, Sweden; King's College London, Faculty of Life Sciences and Medicine, Division of Cancer Studies, London, UK
| | - Fredrik Pontén
- Uppsala University, Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala, Sweden
| | - Jan Frisell
- Karolinska Institutet, Department of Molecular Medicine and Surgery, Stockholm, Sweden; Department of Breast- and Endocrine Surgery, Karolinska University Hospital, Stockholm, Sweden
| | - Irma Fredriksson
- Karolinska Institutet, Department of Molecular Medicine and Surgery, Stockholm, Sweden; Department of Breast- and Endocrine Surgery, Karolinska University Hospital, Stockholm, Sweden
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Lal S, McCart Reed AE, de Luca XM, Simpson PT. Molecular signatures in breast cancer. Methods 2017; 131:135-146. [PMID: 28669865 DOI: 10.1016/j.ymeth.2017.06.032] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 06/26/2017] [Accepted: 06/28/2017] [Indexed: 12/12/2022] Open
Abstract
The use of molecular signatures to add value to standard clinical and pathological parameters has impacted clinical practice in many cancer types, but perhaps most notably in the breast cancer field. This is, in part, due to the considerable complexity of the disease at the clinical, morphological and molecular levels. The adoption of molecular profiling of DNA, RNA and protein continues to reveal important differences in the intrinsic biology between molecular subtypes and has begun to impact the way patients are managed. Several bioinformatic tools have been developed using DNA or RNA-based signatures to stratify the disease into biologically and/or clinically meaningful subgroups. Here, we review the approaches that have been used to develop gene expression signatures into currently available diagnostic assays (e.g., OncotypeDX® and Mammaprint®), plus we describe the latest work on genome sequencing, the methodologies used in the discovery process of mutational signatures, and the potential of these signatures to impact the clinic.
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Affiliation(s)
- Samir Lal
- The University of Queensland, Centre for Clinical Research, Faculty of Medicine, Herston, QLD 4029, Australia
| | - Amy E McCart Reed
- The University of Queensland, Centre for Clinical Research, Faculty of Medicine, Herston, QLD 4029, Australia
| | - Xavier M de Luca
- The University of Queensland, Centre for Clinical Research, Faculty of Medicine, Herston, QLD 4029, Australia
| | - Peter T Simpson
- The University of Queensland, Centre for Clinical Research, Faculty of Medicine, Herston, QLD 4029, Australia.
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12
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Wan W, Lou Y, Hu Z, Wang T, Li J, Tang Y, Wu Z, Xu L, Yang X, Song D, Xiao J. Factors affecting survival outcomes of patients with non-metastatic Ewing’s sarcoma family tumors in the spine: a retrospective analysis of 63 patients in a single center. J Neurooncol 2016; 131:313-320. [DOI: 10.1007/s11060-016-2295-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 10/09/2016] [Indexed: 12/28/2022]
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14
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Falato C, Tobin NP, Lorent J, Lindström LS, Bergh J, Foukakis T. Intrinsic subtypes and genomic signatures of primary breast cancer and prognosis after systemic relapse. Mol Oncol 2016; 10:517-25. [PMID: 26651914 PMCID: PMC5423143 DOI: 10.1016/j.molonc.2015.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/04/2015] [Accepted: 11/06/2015] [Indexed: 02/08/2023] Open
Abstract
Molecular subtypes and gene expression signatures are widely used in early breast cancer but their role in metastatic disease is less explored. Two hundred-twenty patients diagnosed with primary breast cancer and subsequent relapse in Stockholm, Sweden between 1997 and 2006 were identified and their primary tumor was assessed for immunohistochemistry (IHC)- and PAM50-based subtypes, risk of recurrence (ROR-S) score, 21-gene and 70-gene signatures using research-based microarray expression profiles. Clinical and pathological data were retrospectively collected. Post-relapse survival within intrinsic subtypes and genomic signatures was investigated by Kaplan-Meier and Cox regression methods. ROR weighted for proliferation index (ROR-P) was explored and the prognostic contribution provided when combined to a clinical model estimated as change in LR- χ(2). IHC classified 27%, 24%, 36% and 13% of the tumors as luminal A, luminal B, HER2+ and triple negative, respectively. PAM50 categorized 22%, 24%, 26%, 22%, 6% of the tumors as luminal A, luminal B, HER2-enriched, basal-like and normal-like. Triple negative and basal tumors had a significantly shorter median post-relapse survival in comparison with luminal. Overall, neither IHC nor PAM50 subtypes, 21- and 70- gene profiles were prognostic in multivariable models. Low and medium ROR-S had a longer survival compared with the high-risk group (23 vs 10 months; p = 0.04). ROR-P independently correlated with post-relapse survival (p = 0.002) and provided the most significant prognostic information when added to a clinical model. ROR score from primary tumor represents an independent prognostic factor of post-relapse survival beyond classical clinical and pathological variables.
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Affiliation(s)
- Claudette Falato
- Department of Oncology and Pathology, Karolinska Institute and University Hospital, Stockholm, Sweden.
| | - Nicholas P Tobin
- Department of Oncology and Pathology, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Julie Lorent
- Department of Oncology and Pathology, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Linda S Lindström
- Department of Bioscience and Nutrition, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Jonas Bergh
- Department of Oncology and Pathology, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Theodoros Foukakis
- Department of Oncology and Pathology, Karolinska Institute and University Hospital, Stockholm, Sweden
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15
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Tobin NP, Wennmalm K, Lindström LS, Foukakis T, He L, Genové G, Östman A, Landberg G, Betsholtz C, Bergh J. An Endothelial Gene Signature Score Predicts Poor Outcome in Patients with Endocrine-Treated, Low Genomic Grade Breast Tumors. Clin Cancer Res 2016; 22:2417-26. [PMID: 26769751 DOI: 10.1158/1078-0432.ccr-15-1691] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/02/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE The ability of vascular genes to provide treatment predictive information in breast cancer patients remains unclear. As such, we assessed the expression of genes representative of normal endothelial microvasculature (MV) in relation to treatment-specific patient subgroups. EXPERIMENTAL DESIGN We used expression data from 993 breast tumors to assess 57 MV genes (summarized to yield an MV score) as well as the genomic grade index (GGI) and PAM50 signatures. MV score was compared with CD31 staining by correlation and gene ontology (GO) analysis, along with clinicopathologic characteristics and PAM50 subtypes. Uni-, multivariate, and/or t-test analyses were performed in all and treatment-specific subgroups, along with a clinical trial cohort of patients with metastatic breast cancer, seven of whom received antiangiogenic therapy. RESULTS MV score did not correlate with microvessel density (correlation = 0.096), but displayed enrichment for angiogenic GO terms, and was lower in Luminal B tumors. In endocrine-treated patients, a high MV score was associated with decreased risk of metastasis [HR 0.58; 95% confidence interval (CI), 0.38-0.89], even after adjusting for histologic grade, but not GGI or PAM50. Subgroup analysis showed the prognostic strength of the MV score resided in low genomic grade tumors and MV score was significantly increased in metastatic breast tumors after treatment with sunitinib + docetaxel (P = 0.031). CONCLUSIONS MV score identifies two groups of better and worse survival in low-risk endocrine-treated breast cancer patients. We also show normalization of tumor vasculature on a transcriptional level in response to an angiogenic inhibitor in human breast cancer samples. Clin Cancer Res; 22(10); 2417-26. ©2016 AACR.
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Affiliation(s)
- Nicholas P Tobin
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden.
| | - Kristian Wennmalm
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Linda S Lindström
- Department of Surgery, University of California at San Francisco (UCSF), San Francisco, California. Department of Biosciences and Nutrition, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Theodoros Foukakis
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Liqun He
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Guillem Genové
- Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Arne Östman
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Göran Landberg
- Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden
| | - Christer Betsholtz
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden. Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jonas Bergh
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden
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16
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Tobin NP, Foukakis T, De Petris L, Bergh J. The importance of molecular markers for diagnosis and selection of targeted treatments in patients with cancer. J Intern Med 2015; 278:545-70. [PMID: 26373821 DOI: 10.1111/joim.12429] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The past 30 years have seen the introduction of a number of cancer therapies with the aim of restricting the growth and spread of primary and metastatic tumours. A shared commonality among these therapies is their targeting of various aspects of the cancer hallmarks, that is traits that are essential to successful tumour propagation and dissemination. The evolution of molecular-scale technology has been central to the identification of new cancer targets, and it is not a coincidence that improved therapies have emerged at the same time as gene expression arrays and DNA sequencing have enhanced our understanding of cancer genetics. Modern tumour pathology is now viewed at the molecular level ranging from IHC biomarkers, to gene signature classifiers and gene mutations, all of which provide crucial information about which patients will respond to targeted therapy regimens. In this review, we briefly discuss the general types of targeted therapies used in a clinical setting and provide a short background on immunohistochemical, gene expression and DNA sequencing technologies, before focusing on three tumour types: breast, lung and colorectal cancers. For each of these cancer types, we provide a background to the disease along with an overview of the current standard therapies and then focus on the relevant targeted therapies and the pathways they inhibit. Finally, we highlight several strategies that are pivotal to the successful development of targeted anti-cancer drugs.
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Affiliation(s)
- N P Tobin
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - T Foukakis
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - L De Petris
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - J Bergh
- Department of Oncology and Pathology, Karolinska Institutet and University Hospital, Stockholm, Sweden
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Christgen M, von Ahsen S, Christgen H, Länger F, Kreipe H. The region-of-interest size impacts on Ki67 quantification by computer-assisted image analysis in breast cancer. Hum Pathol 2015. [PMID: 26206765 DOI: 10.1016/j.humpath.2015.05.016] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Therapeutic decision-making in breast cancer depends on histopathologic biomarkers and is influenced by the Ki67 proliferation index. Computer-assisted image analysis (CAIA) promises to improve Ki67 quantification. Several commercial applications have been developed for semiautomated CAIA-based Ki67 quantification, many of which rely on measurements in user-defined regions of interest (ROIs). Because of intratumoral proliferative heterogeneity, definition of the ROI is an important step in the analytical procedure. This study explores the ROI size impacts on Ki67 quantification. Whole-slide sections of 100 breast cancers were immunostained with the anti-Ki67 antibody 30-9 and were analyzed on the iScan Coreo digital pathology platform using a Food and Drug Administration-cleared Ki67 quantification software version v5.3 (Virtuoso; Ventana, Tucson, TX). For each case, the Ki67 labeling index (LI) was determined in multiple ROIs of gradually increasing size centered around a high-proliferation area. The spatial Ki67 decline was modeled with nonlinear regression. Depending on the ROI size, the median Ki67 LI varied between 55% and 15%. The proportion of tumors classified as Ki67 low according to the St Gallen 2013/2015 cutoff increased from 2% to 56%, as the ROI size increased from 50 to 10,000 cells captured. The interrater reliability of conventional Ki67 assessment versus CAIA-based Ki67 quantification was also dependent on the ROI size and varied between slight and almost perfect agreement (Cohen κ = 0.06-0.85). In conclusion, the ROI size is a critically important parameter for semiautomated Ki67 quantification by CAIA. Ki67 LIs determined on platforms like iScan Coreo/Virtuoso require an ROI size adjustment, for which we offer a downloadable data transformation tool.
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Affiliation(s)
- Matthias Christgen
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany.
| | - Sabrina von Ahsen
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
| | | | - Florian Länger
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
| | - Hans Kreipe
- Institute of Pathology, Hannover Medical School, 30625 Hannover, Germany
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Wang T, Yin H, Han S, Yang X, Wang J, Huang Q, Yan W, Zhou W, Xiao J. Malignant peripheral nerve sheath tumor (MPNST) in the spine: a retrospective analysis of clinical and molecular prognostic factors. J Neurooncol 2015; 122:349-55. [PMID: 25598015 DOI: 10.1007/s11060-015-1721-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/12/2015] [Indexed: 01/23/2023]
Abstract
Spinal malignant peripheral nerve sheath tumors (MPNSTs) are relatively rare. There is little information published in the literature regarding this subject. The aim of this retrospective study was to evaluate factors that may affect the outcomes of patients with spinal MPNSTs by reviewing 43 patients with spinal MPNST who were treated in our hospital between 2001 and 2012. Univariate and multivariate analyses were performed to identify prognostic variables relative to patient and tumor characteristics, treatment modality and molecules. All 43 MPNST patients (25 men and 18 women; median age 49 years) underwent surgical resection, of whom 15 patients also underwent postoperative radiotherapy. Local recurrence was found in 21 (48.8 %) patients. Twenty-two (51.2 %) patients died during the follow-up periods with a median survival time of 49 months. The 5-year recurrence and survival rate was 53 and 44 % respectively. The statistical analyses suggested that high-grade malignancy and osteolytic destruction were closely associated with recurrence and death. A total of 38 cases accepted postoperative immunohistochemisty examine. S-100 was identified as an independent factor related to both recurrence and survival, adjusting for clinical factors. In conclusion, we confirmed that malignant grade and osteolytic destruction were the two independent factors for both recurrence and survival, while patients with S-100 protein negative had a higher recurrence rate and a lower survival rate.
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Affiliation(s)
- Ting Wang
- Department of Bone Tumor Surgery, Changzheng Hospital, Second Military Medical University, 415 Fengyang Road, Shanghai, 200003, China
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Montes de Oca R, Gurard-Levin ZA, Berger F, Rehman H, Martel E, Corpet A, de Koning L, Vassias I, Wilson LOW, Meseure D, Reyal F, Savignoni A, Asselain B, Sastre-Garau X, Almouzni G. The histone chaperone HJURP is a new independent prognostic marker for luminal A breast carcinoma. Mol Oncol 2014; 9:657-74. [PMID: 25497280 DOI: 10.1016/j.molonc.2014.11.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/12/2014] [Accepted: 11/12/2014] [Indexed: 10/24/2022] Open
Abstract
BACKGROUND Breast cancer is a heterogeneous disease with different molecular subtypes that have varying responses to therapy. An ongoing challenge in breast cancer research is to distinguish high-risk patients from good prognosis patients. This is particularly difficult in the low-grade, ER-positive luminal A tumors, where robust diagnostic tools to aid clinical treatment decisions are lacking. Recent data implicating chromatin regulators in cancer initiation and progression offers a promising avenue to develop new tools to help guide clinical decisions. METHODS Here we exploit a published transcriptome dataset and an independent validation cohort to correlate the mRNA expression of selected chromatin regulators with respect to the four intrinsic breast cancer molecular subtypes. We then perform univariate and multivariate analyses to compare the prognostic value of a panel of chromatin regulators to Ki67, a currently utilized proliferation marker. RESULTS Unsupervised hierarchical clustering revealed a gene cluster containing several histone chaperones and histone variants highly-expressed in the proliferative subtypes (basal-like, HER2-positive, luminal B) but not in the luminal A subtype. Several chromatin regulators, including the histone chaperones CAF-1 (subunits p150 and p60), ASF1b, and HJURP, and the centromeric histone variant CENP-A, associated with local and metastatic relapse and poor patient outcome. Importantly, we find that HJURP can discriminate favorable and unfavorable outcome within the luminal A subtype, outperforming the currently utilized proliferation marker Ki67, as an independent prognostic marker for luminal A patients. CONCLUSIONS The integration of chromatin regulators as clinical biomarkers, in particular the histone chaperone HJURP, will help guide patient substratification and treatment options for low-risk luminal A breast carcinoma patients.
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Affiliation(s)
- Rocío Montes de Oca
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
| | - Zachary A Gurard-Levin
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
| | - Frédérique Berger
- Sorbonne University, PSL*, France; Institut Curie, U900, Paris F-75248, France; INSERM, U900, Mines Paris-Tech, Paris F-75248, France; Institut Curie, Department of Biostatistics, Paris F-75248, France.
| | - Haniya Rehman
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
| | - Elise Martel
- Institut Curie, Investigative Pathology Platform, Paris F-75248, France.
| | - Armelle Corpet
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
| | - Leanne de Koning
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
| | - Isabelle Vassias
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
| | - Laurence O W Wilson
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
| | - Didier Meseure
- Institut Curie, Investigative Pathology Platform, Paris F-75248, France.
| | - Fabien Reyal
- Institut Curie, Department of Surgery, Paris F-75248, France.
| | - Alexia Savignoni
- Institut Curie, U900, Paris F-75248, France; INSERM, U900, Mines Paris-Tech, Paris F-75248, France; Institut Curie, Department of Biostatistics, Paris F-75248, France.
| | - Bernard Asselain
- Institut Curie, U900, Paris F-75248, France; INSERM, U900, Mines Paris-Tech, Paris F-75248, France; Institut Curie, Department of Biostatistics, Paris F-75248, France.
| | | | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris F-75248, France; CNRS, UMR3664, Paris F-75248, France; Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris F-75248, France; UPMC, UMR3664, Paris F-75248, France; Sorbonne University, PSL*, France.
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Tobin NP, Lindström LS, Carlson JW, Bjöhle J, Bergh J, Wennmalm K. Multi-level gene expression signatures, but not binary, outperform Ki67 for the long term prognostication of breast cancer patients. Mol Oncol 2014; 8:741-52. [PMID: 24630985 PMCID: PMC5528643 DOI: 10.1016/j.molonc.2014.02.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/24/2014] [Accepted: 02/17/2014] [Indexed: 12/16/2022] Open
Abstract
Proliferation-related gene signatures have been proposed to aid breast cancer management by providing reproducible prognostic and predictive information on a patient-by-patient basis. It is unclear however, whether a less demanding assessment of cell division rate (as determined in clinical setting by expression of Ki67) can function in place of gene profiling. We investigated agreement between literature-, distribution-based, as well as signature-derived values for Ki67, relative to the genomic grade index (GGI), 70-gene signature, p53 signature, recurrence score (RS), and the molecular subtype models of Sorlie, Hu, and Parker in representative sets of 253 and 159 breast cancers with a median follow-up of 13 and 14.5 years, respectively. The relevance for breast cancer specific survival was also addressed in uni- and bivariate Cox models. Taking both cohorts into account, our broad approach identified ROC optimized Ki67 cutoffs in the range of 8-28%. With optimum signature-reproducing cutoffs, similarity in classification of individual tumors was higher for binary signatures (72-85%), than multi-level signatures (67-73%). Consistent with strong agreement, no prognostic superiority was noted for either Ki67 or the binary GGI, 70-gene and p53 signatures in the Uppsala dataset by bivariate analyses. In contrast, Ki67-independent prognostic capacity could be demonstrated for RS and molecular subtypes according to Sorlie, Hu and Parker in both datasets. Our results show that the added prognostic value of binary proliferation-related gene signatures is limited for Ki67-assessed breast cancers. More complex, multi-level descriptions have a greater potential in short- and long-term prognostication for biologically relevant breast cancer subgroups.
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Affiliation(s)
- Nicholas P Tobin
- Cancer Center Karolinska, Karolinska Institutet and University Hospital, S-171 76 Stockholm, Sweden.
| | - Linda S Lindström
- University of California at San Francisco (UCSF), Department of Surgery, 1600 Divisadero Street, 94117 San Francisco, CA, USA; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet and University Hospital, S-171 77 Stockholm, Sweden
| | - Joseph W Carlson
- Cancer Center Karolinska, Karolinska Institutet and University Hospital, S-171 76 Stockholm, Sweden
| | - Judith Bjöhle
- Cancer Center Karolinska, Karolinska Institutet and University Hospital, S-171 76 Stockholm, Sweden
| | - Jonas Bergh
- Honorary Professor, Manchester University, Manchester M20 4BX, England
| | - Kristian Wennmalm
- Cancer Center Karolinska, Karolinska Institutet and University Hospital, S-171 76 Stockholm, Sweden
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