1
|
Wen RM, Qiu Z, Marti GEW, Peterson EE, Marques FJG, Bermudez A, Wei Y, Nolley R, Lam N, Polasko AL, Chiu CL, Zhang D, Cho S, Karageorgos GM, McDonough E, Chadwick C, Ginty F, Jung KJ, Machiraju R, Mallick P, Crowley L, Pollack JR, Zhao H, Pitteri SJ, Brooks JD. AZGP1 deficiency promotes angiogenesis in prostate cancer. J Transl Med 2024; 22:383. [PMID: 38659028 PMCID: PMC11044612 DOI: 10.1186/s12967-024-05183-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Loss of AZGP1 expression is a biomarker associated with progression to castration resistance, development of metastasis, and poor disease-specific survival in prostate cancer. However, high expression of AZGP1 cells in prostate cancer has been reported to increase proliferation and invasion. The exact role of AZGP1 in prostate cancer progression remains elusive. METHOD AZGP1 knockout and overexpressing prostate cancer cells were generated using a lentiviral system. The effects of AZGP1 under- or over-expression in prostate cancer cells were evaluated by in vitro cell proliferation, migration, and invasion assays. Heterozygous AZGP1± mice were obtained from European Mouse Mutant Archive (EMMA), and prostate tissues from homozygous knockout male mice were collected at 2, 6 and 10 months for histological analysis. In vivo xenografts generated from AZGP1 under- or over-expressing prostate cancer cells were used to determine the role of AZGP1 in prostate cancer tumor growth, and subsequent proteomics analysis was conducted to elucidate the mechanisms of AZGP1 action in prostate cancer progression. AZGP1 expression and microvessel density were measured in human prostate cancer samples on a tissue microarray of 215 independent patient samples. RESULT Neither the knockout nor overexpression of AZGP1 exhibited significant effects on prostate cancer cell proliferation, clonal growth, migration, or invasion in vitro. The prostates of AZGP1-/- mice initially appeared to have grossly normal morphology; however, we observed fibrosis in the periglandular stroma and higher blood vessel density in the mouse prostate by 6 months. In PC3 and DU145 mouse xenografts, over-expression of AZGP1 did not affect tumor growth. Instead, these tumors displayed decreased microvessel density compared to xenografts derived from PC3 and DU145 control cells, suggesting that AZGP1 functions to inhibit angiogenesis in prostate cancer. Proteomics profiling further indicated that, compared to control xenografts, AZGP1 overexpressing PC3 xenografts are enriched with angiogenesis pathway proteins, including YWHAZ, EPHA2, SERPINE1, and PDCD6, MMP9, GPX1, HSPB1, COL18A1, RNH1, and ANXA1. In vitro functional studies show that AZGP1 inhibits human umbilical vein endothelial cell proliferation, migration, tubular formation and branching. Additionally, tumor microarray analysis shows that AZGP1 expression is negatively correlated with blood vessel density in human prostate cancer tissues. CONCLUSION AZGP1 is a negative regulator of angiogenesis, such that loss of AZGP1 promotes angiogenesis in prostate cancer. AZGP1 likely exerts heterotypical effects on cells in the tumor microenvironment, such as stromal and endothelial cells. This study sheds light on the anti-angiogenic characteristics of AZGP1 in the prostate and provides a rationale to target AZGP1 to inhibit prostate cancer progression.
Collapse
Affiliation(s)
- Ru M Wen
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Zhengyuan Qiu
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - G Edward W Marti
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Eric E Peterson
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Fernando Jose Garcia Marques
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Abel Bermudez
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Yi Wei
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Rosalie Nolley
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Nathan Lam
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alex LaPat Polasko
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chun-Lung Chiu
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Dalin Zhang
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sanghee Cho
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA
| | | | | | - Chrystal Chadwick
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA
| | - Fiona Ginty
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA
| | - Kyeong Joo Jung
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Raghu Machiraju
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Parag Mallick
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Laura Crowley
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Jonathan R Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hongjuan Zhao
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Sharon J Pitteri
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| |
Collapse
|
2
|
Azimi M, Cho S, Bozkurt E, McDonough E, Kisakol B, Matveeva A, Salvucci M, Dussmann H, McDade S, Firat C, Urganci N, Shia J, Longley DB, Ginty F, Prehn JHM. Spatial Effects of Infiltrating T cells on Neighbouring Cancer Cells and Prognosis in Stage III CRC patients. bioRxiv 2024:2024.01.30.577720. [PMID: 38352309 PMCID: PMC10862776 DOI: 10.1101/2024.01.30.577720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Colorectal cancer (CRC) is one of the most frequently occurring cancers, but prognostic biomarkers identifying patients at risk of recurrence are still lacking. In this study, we aimed to investigate in more detail the spatial relationship between intratumoural T cells, cancer cells, and cancer cell hallmarks, as prognostic biomarkers in stage III colorectal cancer patients. We conducted multiplexed imaging of 56 protein markers at single cell resolution on resected fixed tissue from stage III CRC patients who received adjuvant 5-fluorouracil-based chemotherapy. Images underwent segmentation for tumour, stroma and immune cells, and cancer cell 'state' protein marker expression was quantified at a cellular level. We developed a Python package for estimation of spatial proximity, nearest neighbour analysis focusing on cancer cell - T cell interactions at single-cell level. In our discovery cohort (MSK), we processed 462 core samples (total number of cells: 1,669,228) from 221 adjuvant 5FU-treated stage III patients. The validation cohort (HV) consisted of 272 samples (total number of cells: 853,398) from 98 stage III CRC patients. While there were trends for an association between percentage of cytotoxic T cells (across the whole cancer core), it did not reach significance (Discovery cohort: p = 0.07, Validation cohort: p = 0.19). We next utilized our region-based nearest neighbourhood approach to determine the spatial relationships between cytotoxic T cells, helper T cells and cancer cell clusters. In the both cohorts, we found that lower distance between cytotoxic T cells, T helper cells and cancer cells was significantly associated with increased disease-free survival. An unsupervised trained model that clustered patients based on the median distance between immune cells and cancer cells, as well as protein expression profiles, successfully classified patients into low-risk and high-risk groups (Discovery cohort: p = 0.01, Validation cohort: p = 0.003).
Collapse
Affiliation(s)
- Mohammadreza Azimi
- Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Sanghee Cho
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA (formerly GE Research Center)
| | - Emir Bozkurt
- Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Elizabeth McDonough
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA (formerly GE Research Center)
| | - Batuhan Kisakol
- Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Anna Matveeva
- Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Heiko Dussmann
- Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| | - Simon McDade
- School of Medicine, Dentistry and Biomedical Sciences, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | | | | | - Jinru Shia
- Memorial Sloan Kettering Cancer Centre, NY
| | - Daniel B Longley
- School of Medicine, Dentistry and Biomedical Sciences, Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Fiona Ginty
- GE HealthCare Technology and Innovation Center, Niskayuna, NY, 12309, USA (formerly GE Research Center)
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, Dublin 2, Ireland
| |
Collapse
|
3
|
Kisakol B, Matveeva A, Salvucci M, Kel A, McDonough E, Ginty F, Longley DB, Prehn JHM. Identification of unique rectal cancer-specific subtypes. Br J Cancer 2024:10.1038/s41416-024-02656-0. [PMID: 38532103 DOI: 10.1038/s41416-024-02656-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Existing colorectal cancer subtyping methods were generated without much consideration of potential differences in expression profiles between colon and rectal tissues. Moreover, locally advanced rectal cancers at resection often have received neoadjuvant chemoradiotherapy which likely has a significant impact on gene expression. METHODS We collected mRNA expression profiles for rectal and colon cancer samples (n = 2121). We observed that (i) Consensus Molecular Subtyping (CMS) had a different prognosis in treatment-naïve rectal vs. colon cancers, and (ii) that neoadjuvant chemoradiotherapy exposure produced a strong shift in CMS subtypes in rectal cancers. We therefore clustered 182 untreated rectal cancers to find rectal cancer-specific subtypes (RSSs). RESULTS We identified three robust subtypes. We observed that RSS1 had better, and RSS2 had worse disease-free survival. RSS1 showed high expression of MYC target genes and low activity of angiogenesis genes. RSS2 exhibited low regulatory T cell abundance, strong EMT and angiogenesis signalling, and high activation of TGF-β, NF-κB, and TNF-α signalling. RSS3 was characterised by the deactivation of EGFR, MAPK and WNT pathways. CONCLUSIONS We conclude that RSS subtyping allows for more accurate prognosis predictions in rectal cancers than CMS subtyping and provides new insight into targetable disease pathways within these subtypes.
Collapse
Affiliation(s)
- Batuhan Kisakol
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, 2, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, 2, Ireland
| | - Anna Matveeva
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, 2, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, 2, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, 2, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, 2, Ireland
| | | | | | | | - Daniel B Longley
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, 2, Ireland.
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, 2, Ireland.
| |
Collapse
|
4
|
Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, Börner K, Snyder MP. Author Correction: Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol 2024:10.1038/s41556-024-01384-0. [PMID: 38429479 DOI: 10.1038/s41556-024-01384-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Affiliation(s)
- Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Liming Pei
- Center for Mitochondrial and Epigenomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology and the Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Michael Angelo
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - James P Carson
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Joana P Gonçalves
- Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - James S Hagood
- Department of Pediatrics (Pulmonology) and Program for Rare and Interstitial Lung Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John W Hickey
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Neil L Kelleher
- Departments of Medicine, Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Shin Lin
- Division of Cardiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Yiing Lin
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Huiping Liu
- Departments of Pharmacology, Medicine (Hematology and Oncology), Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Andrea Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Brent R Stockwell
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Ioannis S Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Katy Börner
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
| |
Collapse
|
5
|
Karageorgos GM, Cho S, McDonough E, Chadwick C, Ghose S, Owens J, Jung KJ, Machiraju R, West R, Brooks JD, Mallick P, Ginty F. Deep learning-based automated pipeline for blood vessel detection and distribution analysis in multiplexed prostate cancer images. Front Bioinform 2024; 3:1296667. [PMID: 38323039 PMCID: PMC10844485 DOI: 10.3389/fbinf.2023.1296667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/18/2023] [Indexed: 02/08/2024] Open
Abstract
Introduction: Prostate cancer is a highly heterogeneous disease, presenting varying levels of aggressiveness and response to treatment. Angiogenesis is one of the hallmarks of cancer, providing oxygen and nutrient supply to tumors. Micro vessel density has previously been correlated with higher Gleason score and poor prognosis. Manual segmentation of blood vessels (BVs) In microscopy images is challenging, time consuming and may be prone to inter-rater variabilities. In this study, an automated pipeline is presented for BV detection and distribution analysis in multiplexed prostate cancer images. Methods: A deep learning model was trained to segment BVs by combining CD31, CD34 and collagen IV images. In addition, the trained model was used to analyze the size and distribution patterns of BVs in relation to disease progression in a cohort of prostate cancer patients (N = 215). Results: The model was capable of accurately detecting and segmenting BVs, as compared to ground truth annotations provided by two reviewers. The precision (P), recall (R) and dice similarity coefficient (DSC) were equal to 0.93 (SD 0.04), 0.97 (SD 0.02) and 0.71 (SD 0.07) with respect to reviewer 1, and 0.95 (SD 0.05), 0.94 (SD 0.07) and 0.70 (SD 0.08) with respect to reviewer 2, respectively. BV count was significantly associated with 5-year recurrence (adjusted p = 0.0042), while both count and area of blood vessel were significantly associated with Gleason grade (adjusted p = 0.032 and 0.003 respectively). Discussion: The proposed methodology is anticipated to streamline and standardize BV analysis, offering additional insights into the biology of prostate cancer, with broad applicability to other cancers.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Kyeong Joo Jung
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, United States
| | - Raghu Machiraju
- Department of Computer Science and Engineering, The Ohio State University, Columbus, OH, United States
| | - Robert West
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - James D. Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States
| | - Parag Mallick
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Stanford, CA, United States
| | | |
Collapse
|
6
|
Chadwick C, De Jesus M, Ginty F, Martinez JS. Pathobiology of Candida auris infection analyzed by multiplexed imaging and single cell analysis. PLoS One 2024; 19:e0293011. [PMID: 38232081 DOI: 10.1371/journal.pone.0293011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 10/03/2023] [Indexed: 01/19/2024] Open
Abstract
Fungal organisms contribute to significant human morbidity and mortality and Candida auris (C. auris) infections are of utmost concern due to multi-drug resistant strains and persistence in critical care and hospital settings. Pathogenesis and pathology of C. auris is still poorly understood and in this study, we demonstrate how the use of multiplex immunofluorescent imaging (MxIF) and single-cell analysis can contribute to a deeper understanding of fungal infections within organs. We used two different neutrophil depletion murine models (treated with either 1A8-an anti-Ly6G antibody, or RB6-8C5-an anti-Ly6G/Ly6C antibody; both 1A8 and RB6-8C5 antibodies have been shown to deplete neutrophils) and compared to wildtype, non-neutropenic mice. Following pathologist assessment, fixed samples underwent MxIF imaging using a C. albicans antibody (shown to be cross-reactive to C. auris) and immune cell biomarkers-CD3 (T cells), CD68 (macrophages), B220 (B cells), CD45 (monocytes), and Ly6G (neutrophils) to quantify organ specific immune niches. MxIF analysis highlighted the heterogenous distribution of C. auris infection within heart, kidney, and brain 7 days post-infection. Size and number of fungal abscesses was greatest in the heart and lowest in brain. Infected mice had an increased count of CD3+, CD68+, B220+, and CD45+ immune cells, concentrated around C. auris abscesses. CD68+ cells were predominant in wildtype (non-neutropenic mice) and CD3+/CD45+ cells were predominant in neutropenic mice, with B cells being the least abundant. These findings suggest a Th2 driven immune response in neutropenic C. auris infection mice models. This study demonstrates the value of MxIF to broaden understanding of C. auris pathobiology, and mechanistic understanding of fungal infections.
Collapse
Affiliation(s)
| | - Magdia De Jesus
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York, United States of America
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
| | - Fiona Ginty
- GE Research, Niskayuna, New York, United States of America
| | | |
Collapse
|
7
|
Zuhair R, Eastwood M, Jones M, Cross A, Hester J, Issa F, Ginty F, Sailem H. Decoding mTOR signalling heterogeneity in the tumour microenvironment using multiplexed imaging and graph convolutional networks. bioRxiv 2023:2023.12.30.573693. [PMID: 38234756 PMCID: PMC10793449 DOI: 10.1101/2023.12.30.573693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Evaluating the contribution of the tumour microenvironment (TME) in tumour progression has proven a complex challenge due to the intricate interactions within the TME. Multiplexed imaging is an emerging technology that allows concurrent assessment of multiple of these components simultaneously. Here we utilise a highly multiplexed dataset of 61 markers across 746 colorectal tumours to investigate how complex mTOR signalling in different tissue compartments influences patient prognosis. We found that the signalling of mTOR pathway can have heterogeneous activation patterns in tumour and immune compartments which correlate with patient prognosis. Using graph neural networks, we determined the most predictive features of mTOR activity in immune cells and identified relevant cellular subpopulations. We validated our observations using spatial transcriptomics data analysis in an independent patient cohort. Our work provides a framework for studying complex cell signalling and reveals important insights for developing mTOR-based therapies.
Collapse
|
8
|
Jain S, Pei L, Spraggins JM, Angelo M, Carson JP, Gehlenborg N, Ginty F, Gonçalves JP, Hagood JS, Hickey JW, Kelleher NL, Laurent LC, Lin S, Lin Y, Liu H, Naba A, Nakayasu ES, Qian WJ, Radtke A, Robson P, Stockwell BR, Van de Plas R, Vlachos IS, Zhou M, Börner K, Snyder MP. Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP). Nat Cell Biol 2023; 25:1089-1100. [PMID: 37468756 PMCID: PMC10681365 DOI: 10.1038/s41556-023-01194-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/22/2023] [Indexed: 07/21/2023]
Abstract
The Human BioMolecular Atlas Program (HuBMAP) aims to create a multi-scale spatial atlas of the healthy human body at single-cell resolution by applying advanced technologies and disseminating resources to the community. As the HuBMAP moves past its first phase, creating ontologies, protocols and pipelines, this Perspective introduces the production phase: the generation of reference spatial maps of functional tissue units across many organs from diverse populations and the creation of mapping tools and infrastructure to advance biomedical research.
Collapse
Affiliation(s)
- Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| | - Liming Pei
- Center for Mitochondrial and Epigenomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jeffrey M Spraggins
- Department of Cell and Developmental Biology and the Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Michael Angelo
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | - James P Carson
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, USA
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Joana P Gonçalves
- Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands
| | - James S Hagood
- Department of Pediatrics (Pulmonology) and Program for Rare and Interstitial Lung Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - John W Hickey
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Neil L Kelleher
- Departments of Medicine, Chemistry and Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Louise C Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Shin Lin
- Division of Cardiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Yiing Lin
- Department of Surgery, Washington University School of Medicine, St Louis, MO, USA
| | - Huiping Liu
- Departments of Pharmacology, Medicine (Hematology and Oncology), Lurie Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alexandra Naba
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Andrea Radtke
- Lymphocyte Biology Section and Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Brent R Stockwell
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA
| | - Raf Van de Plas
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Ioannis S Vlachos
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Department of Pathology, Beth Israel Deaconess Medical Center, and Harvard Medical School, Boston, MA, USA
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Katy Börner
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
| | - Michael P Snyder
- Department of Genetics, Stanford School of Medicine, Stanford, CA, USA.
| |
Collapse
|
9
|
Quardokus EM, Saunders DC, McDonough E, Hickey JW, Werlein C, Surrette C, Rajbhandari P, Casals AM, Tian H, Lowery L, Neumann EK, Björklund F, Neelakantan TV, Croteau J, Wiblin AE, Fisher J, Livengood AJ, Dowell KG, Silverstein JC, Spraggins JM, Pryhuber GS, Deutsch G, Ginty F, Nolan GP, Melov S, Jonigk D, Caldwell MA, Vlachos IS, Muller W, Gehlenborg N, Stockwell BR, Lundberg E, Snyder MP, Germain RN, Camarillo JM, Kelleher NL, Börner K, Radtke AJ. Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging. Nat Methods 2023; 20:1174-1178. [PMID: 37468619 PMCID: PMC10406602 DOI: 10.1038/s41592-023-01846-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/14/2023] [Indexed: 07/21/2023]
Abstract
Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Advances in the field now allow high-parameter data collection (>60 targets); however, considerable expertise and capital are needed to construct the antibody panels employed by these methods. Organ mapping antibody panels are community-validated resources that save time and money, increase reproducibility, accelerate discovery and support the construction of a Human Reference Atlas.
Collapse
Affiliation(s)
- Ellen M Quardokus
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Diane C Saunders
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Diabetes Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - John W Hickey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Presha Rajbhandari
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Anna Martinez Casals
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Hua Tian
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | | | - Elizabeth K Neumann
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, University of California Davis, Davis, CA, USA
| | - Frida Björklund
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Josh Croteau
- Department of Business Development, BioLegend Inc., San Diego, CA, USA
| | - Anne E Wiblin
- Department of Research and Development, Abcam PLC, Discovery Drive, Cambridge Biomedical Campus, Cambridge, UK
| | - Jeremy Fisher
- Department of Research and Development, Cell Signaling Technology, Inc., Danvers, MA, USA
| | - April J Livengood
- Department of Protein and Cell Analysis, Thermo Fisher Scientific, Carlsbad, CA, USA
| | | | - Jonathan C Silverstein
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jeffrey M Spraggins
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Gloria S Pryhuber
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Gail Deutsch
- Department of Pathology, University of Washington Medical Center, Seattle, WA, USA
| | | | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Simon Melov
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Danny Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, Germany
- German Center for Lung Research (DZL), Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
- Institute of Pathology, RWTH University of Aachen, Aachen, Germany
| | - Michael A Caldwell
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Ioannis S Vlachos
- Spatial Technologies Unit, Harvard Medical School Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Werner Muller
- Miltenyi Biotec B.V. and Co. KG, Bergisch Gladbach, Germany
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Nils Gehlenborg
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Brent R Stockwell
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Emma Lundberg
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ronald N Germain
- Laboratory of Immune System Biology, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, NIAID, NIH, Bethesda, MD, USA
| | - Jeannie M Camarillo
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Inotiv, Nashville, TN, USA
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Katy Börner
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Andrea J Radtke
- Laboratory of Immune System Biology, Lymphocyte Biology Section and Center for Advanced Tissue Imaging, NIAID, NIH, Bethesda, MD, USA.
| |
Collapse
|
10
|
Ghose S, Ju Y, McDonough E, Ho J, Karunamurthy A, Chadwick C, Cho S, Rose R, Corwin A, Surrette C, Martinez J, Williams E, Sood A, Al-Kofahi Y, Falo LD, Börner K, Ginty F. 3D reconstruction of skin and spatial mapping of immune cell density, vascular distance and effects of sun exposure and aging. Commun Biol 2023; 6:718. [PMID: 37468758 PMCID: PMC10356782 DOI: 10.1038/s42003-023-04991-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/11/2023] [Indexed: 07/21/2023] Open
Abstract
Mapping the human body at single cell resolution in three dimensions (3D) is important for understanding cellular interactions in context of tissue and organ organization. 2D spatial cell analysis in a single tissue section may be limited by cell numbers and histology. Here we show a workflow for 3D reconstruction of multiplexed sequential tissue sections: MATRICS-A (Multiplexed Image Three-D Reconstruction and Integrated Cell Spatial - Analysis). We demonstrate MATRICS-A in 26 serial sections of fixed skin (stained with 18 biomarkers) from 12 donors aged between 32-72 years. Comparing the 3D reconstructed cellular data with the 2D data, we show significantly shorter distances between immune cells and vascular endothelial cells (56 µm in 3D vs 108 µm in 2D). We also show 10-70% more T cells (total) within 30 µm of a neighboring T helper cell in 3D vs 2D. Distances of p53, DDB2 and Ki67 positive cells to the skin surface were consistent across all ages/sun exposure and largely localized to the lower stratum basale layer of the epidermis. MATRICS-A provides a framework for analysis of 3D spatial cell relationships in healthy and aging organs and could be further extended to diseased organs.
Collapse
Affiliation(s)
- Soumya Ghose
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | - Yingnan Ju
- Indiana University, 107 South Indiana Ave, Bloomington, IN, 47405, USA
| | | | - Jonhan Ho
- University of Pittsburgh School of Medicine, 3550 Terrace St, Pittsburgh, PA, 15213, USA
| | | | | | - Sanghee Cho
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | - Rachel Rose
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | - Alex Corwin
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | | | - Jessica Martinez
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | - Eric Williams
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | - Anup Sood
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | - Yousef Al-Kofahi
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | - Louis D Falo
- University of Pittsburgh School of Medicine, 3550 Terrace St, Pittsburgh, PA, 15213, USA
| | - Katy Börner
- Indiana University, 107 South Indiana Ave, Bloomington, IN, 47405, USA.
| | - Fiona Ginty
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA.
| |
Collapse
|
11
|
Duggan WP, Kisakol B, O'Connell E, Matveeva A, O'Grady T, McDonough E, Lindner AU, McNamara D, Longley D, Ginty F, Burke JP, Prehn JHM. Multiplexed Immunofluorescence Imaging Reveals an Immune-Rich Tumor Microenvironment in Mucinous Rectal Cancer Characterized by Increased Lymphocyte Infiltration and Enhanced Programmed Cell Death Protein 1 Expression. Dis Colon Rectum 2023; 66:914-922. [PMID: 36525395 PMCID: PMC10591203 DOI: 10.1097/dcr.0000000000002624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Mucinous rectal cancer is associated with a higher incidence of microsatellite instability and a poorer response to neoadjuvant chemoradiotherapy compared to other subtypes of rectal adenocarcinoma. Immune checkpoint inhibitors are an emerging family of anticancer therapeutics associated with highly variable outcomes in colorectal cancer. Although the immune landscape of mucinous rectal cancer has not been fully explored, the presence of mucin is thought to act as a barrier preventing immune-cell infiltration. OBJECTIVE The aim of this study was to determine the immune properties of mucinous rectal cancer and investigate the degree of lymphocyte infiltration in this cohort. DESIGN This is a retrospective cohort study that involved multiplexed immunofluorescence staining of tumor microarrays. SETTINGS Samples originated from a single university teaching hospital. PATIENTS Our cohort included 15 cases of mucinous and 43 cases of nonmucinous rectal cancer. MAIN OUTCOME MEASURES Immune cells were classified and quantified. Immune-cell counts were compared between mucinous and nonmucinous cohorts. Immune marker expression within tumor epithelial tissue was evaluated to determine the degree of lymphocyte infiltration. RESULTS Cytotoxic ( p = 0.022) and regulatory T cells ( p = 0.010) were found to be overrepresented in the mucinous cohort compared to the nonmucinous group. Programmed cell death protein 1 expression was also found to be significantly greater in the mucinous group ( p = 0.001). CD3 ( p = 0.001) and CD8 ( p = 0.054) expressions within the tumor epithelium were also higher in the mucinous group, suggesting adequate immune infiltration despite the presence of mucin. In our analysis, microsatellite instability status was not a predictor of immune marker expression. LIMITATIONS The relatively small size of the cohort. CONCLUSIONS Mucinous rectal cancer is associated with an immune-rich tumor microenvironment, which was not associated with microsatellite instability status. See Video Abstract at http://links.lww.com/DCR/C65 . IMGENES DE INMUNOFLUORESCENCIA MULTIPLEXADAS REVELAN UN MICROAMBIENTE TUMORAL RICO EN INMUNIDAD EN EL CNCER RECTAL MUCINOSO CARACTERIZADO POR UNA MAYOR INFILTRACIN DE LINFOCITOS Y UNA EXPRESIN MEJORADA DE PD ANTECEDENTES:El cáncer rectal mucinoso se asocia con una mayor incidencia de inestabilidad de microsatélites y una peor respuesta a la quimiorradioterapia neoadyuvante en comparación con otros subtipos de adenocarcinoma rectal. Los inhibidores de puntos de control inmunitarios son una familia emergente de tratamientos contra el cáncer asociados con resultados muy variables en el cáncer colorrectal. Aunque el panorama inmunitario del cáncer rectal mucinoso no se ha explorado completamente, se cree que la presencia de mucina actúa como una barrera que previene la infiltración de células inmunitarias.OBJETIVO:El objetivo de este estudio fue determinar las propiedades inmunes del cáncer de recto mucinoso e investigar el grado de infiltración de linfocitos en esta cohorte.DISEÑO:Este es un estudio de cohorte retrospectivo que involucró la tinción de inmunofluorescencia multiplexada de micromatrices tumorales.AJUSTES:Las muestras se originaron en un solo hospital docente universitario.PACIENTES:Nuestra cohorte incluyó 15 casos de cáncer de recto mucinoso y 43 casos de cáncer de recto no mucinosoPRINCIPALES MEDIDAS DE RESULTADO:Las células inmunitarias se clasificaron y cuantificaron. Se compararon los recuentos de células inmunitarias entre cohortes mucinosas y no mucinosas. Se evaluó la expresión del marcador inmunitario dentro del tejido epitelial tumoral para determinar el grado de infiltración de linfocitos.RESULTADOS:Se encontró que las células T citotóxicas ( p = 0,022) y reguladoras ( p = 0,010) estaban sobrerrepresentadas en la cohorte mucinosa en comparación con el grupo no mucinoso. También se encontró que la expresión de PD-1 era significativamente mayor en el grupo mucinoso ( p = 0,001). La expresión de CD3 ( p = 0,001) y CD8 ( p = 0,054) dentro del epitelio tumoral también fue mayor en el grupo mucinoso, lo que sugiere una infiltración inmunitaria adecuada a pesar de la presencia de mucina. En nuestro análisis, no se encontró que el estado de inestabilidad de los microsatélites sea un predictor de la expresión del marcador inmunitario.LIMITACIONES:El tamaño relativamente pequeño de la cohorte.CONCLUSIONES:El cáncer rectal mucinoso se asocia con un microambiente tumoral rico en inmunidad, que no se asoció con el estado de inestabilidad de microsatélites. Consulte el Video del Resumen en http://links.lww.com/DCR/C65 . (Traducción- Dr. Yesenia Rojas-Khalil ).
Collapse
Affiliation(s)
- William P Duggan
- Department of Colorectal Surgery, Beaumont Hospital, Dublin, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Batuhan Kisakol
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Emer O'Connell
- Department of Colorectal Surgery, Beaumont Hospital, Dublin, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Anna Matveeva
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Tony O'Grady
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | | | - Andreas U Lindner
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Deborah McNamara
- Department of Colorectal Surgery, Beaumont Hospital, Dublin, Ireland
- Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Daniel Longley
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
| | | | - John P Burke
- Department of Colorectal Surgery, Beaumont Hospital, Dublin, Ireland
- Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| |
Collapse
|
12
|
Duggan WP, Salvucci M, Kisakol B, Lindner AU, Reynolds IS, Dussmann H, Fay J, O'Grady T, Longley DB, Ginty F, Mc Donough E, Slade DJ, Burke JP, Prehn JHM. Increased Fusobacterium tumoural abundance affects immunogenicity in mucinous colorectal cancer and may be associated with improved clinical outcome. J Mol Med (Berl) 2023; 101:829-841. [PMID: 37171483 PMCID: PMC10300184 DOI: 10.1007/s00109-023-02324-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/04/2023] [Accepted: 04/19/2023] [Indexed: 05/13/2023]
Abstract
There is currently an urgent need to identify factors predictive of immunogenicity in colorectal cancer (CRC). Mucinous CRC is a distinct histological subtype of CRC, associated with a poor response to chemotherapy. Recent evidence suggests the commensal facultative anaerobe Fusobacterium may be especially prevalent in mucinous CRC. The objectives of this study were to assess the association of Fusobacterium abundance with immune cell composition and prognosis in mucinous CRC. Our study included two independent colorectal cancer patient cohorts, The Cancer Genome Atlas (TCGA) cohort, and a cohort of rectal cancers from the Beaumont RCSI Cancer Centre (BRCC). Multiplexed immunofluorescence staining of a tumour microarray (TMA) from the BRCC cohort was undertaken using Cell DIVE technology. Our cohorts included 87 cases (13.3%) of mucinous and 565 cases (86.7%) of non-mucinous CRC. Mucinous CRC in the TCGA dataset was associated with an increased proportion of CD8 + lymphocytes (p = 0.018), regulatory T-cells (p = 0.001) and M2 macrophages (p = 0.001). In the BRCC cohort, mucinous RC was associated with enhanced CD8 + lymphocyte (p = 0.022), regulatory T-cell (p = 0.047), and B-cell (p = 0.025) counts. High Fusobacterium abundance was associated with an increased proportion of CD4 + lymphocytes (p = 0.031) and M1 macrophages (p = 0.006), whilst M2 macrophages (p = 0.043) were under-represented in this cohort. Patients with increased Fusobacterium relative abundance in our mucinous CRC TCGA cohort tended to have better clinical outcomes (DSS: likelihood ratio p = 0.04, logrank p = 0.052). Fusobacterium abundance may be associated with improved outcomes in mucinous CRC, possibly due to a modulatory effect on the host immune response. KEY MESSAGES: • Increased Fusobacterium relative abundance was not found to be associated with microsatellite instability in mucinous CRC. • Increased Fusobacterium relative abundance was associated with an M2/M1 macrophage switch, which is especially significant in mucinous CRC, where M2 macrophages are overexpressed. • Increased Fusobacterium relative abundance was associated with a significant improvement in disease specific survival in mucinous CRC. • Our findings were validated at a protein level within our own in house mucinous and non-mucinous rectal cancer cohorts.
Collapse
Affiliation(s)
- William P Duggan
- Department of Colorectal Surgery, Beaumont Hospital, Dublin 9, Ireland
- Department of Physiology and Medical Physicsand, RCSI Centre for Systems Medicine , Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physicsand, RCSI Centre for Systems Medicine , Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Batuhan Kisakol
- Department of Physiology and Medical Physicsand, RCSI Centre for Systems Medicine , Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Andreas U Lindner
- Department of Physiology and Medical Physicsand, RCSI Centre for Systems Medicine , Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Ian S Reynolds
- Department of Colorectal Surgery, Beaumont Hospital, Dublin 9, Ireland
- Department of Physiology and Medical Physicsand, RCSI Centre for Systems Medicine , Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Heiko Dussmann
- Department of Physiology and Medical Physicsand, RCSI Centre for Systems Medicine , Royal College of Surgeons in Ireland, Dublin 2, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Joanna Fay
- RCSI Biobank, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Tony O'Grady
- RCSI Biobank, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Daniel B Longley
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | | | | | - Daniel J Slade
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - John P Burke
- Department of Colorectal Surgery, Beaumont Hospital, Dublin 9, Ireland
| | - Jochen H M Prehn
- Department of Physiology and Medical Physicsand, RCSI Centre for Systems Medicine , Royal College of Surgeons in Ireland, Dublin 2, Ireland.
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin 2, Ireland.
| |
Collapse
|
13
|
Ghose S, Cho S, Ginty F, McDonough E, Davis C, Zhang Z, Mitra J, Harris AL, Thike AA, Tan PH, Gökmen-Polar Y, Badve SS. Predicting Breast Cancer Events in Ductal Carcinoma In Situ (DCIS) Using Generative Adversarial Network Augmented Deep Learning Model. Cancers (Basel) 2023; 15:1922. [PMID: 37046583 PMCID: PMC10093091 DOI: 10.3390/cancers15071922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/21/2023] [Accepted: 03/14/2023] [Indexed: 04/14/2023] Open
Abstract
Standard clinicopathological parameters (age, growth pattern, tumor size, margin status, and grade) have been shown to have limited value in predicting recurrence in ductal carcinoma in situ (DCIS) patients. Early and accurate recurrence prediction would facilitate a more aggressive treatment policy for high-risk patients (mastectomy or adjuvant radiation therapy), and simultaneously reduce over-treatment of low-risk patients. Generative adversarial networks (GAN) are a class of DL models in which two adversarial neural networks, generator and discriminator, compete with each other to generate high quality images. In this work, we have developed a deep learning (DL) classification network that predicts breast cancer events (BCEs) in DCIS patients using hematoxylin and eosin (H & E) images. The DL classification model was trained on 67 patients using image patches from the actual DCIS cores and GAN generated image patches to predict breast cancer events (BCEs). The hold-out validation dataset (n = 66) had an AUC of 0.82. Bayesian analysis further confirmed the independence of the model from classical clinicopathological parameters. DL models of H & E images may be used as a risk stratification strategy for DCIS patients to personalize therapy.
Collapse
Affiliation(s)
| | - Sanghee Cho
- GE Research Center, Niskayuna, NY 12309, USA
| | - Fiona Ginty
- GE Research Center, Niskayuna, NY 12309, USA
| | | | | | | | | | - Adrian L. Harris
- Department of Oncology, Cancer and Haematology Centre, Oxford University, Oxford OX3 9DU, UK
| | - Aye Aye Thike
- Anatomical Pathology, Singapore General Hospital, Singapore 169608, Singapore
| | - Puay Hoon Tan
- Anatomical Pathology, Singapore General Hospital, Singapore 169608, Singapore
| | - Yesim Gökmen-Polar
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Winship Cancer Institute, Atlanta, GA 30322, USA
| | - Sunil S. Badve
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Winship Cancer Institute, Atlanta, GA 30322, USA
| |
Collapse
|
14
|
Soumya G, Gokmen-Polar Y, Cho S, McDonough E, Davis C, Mitra J, Zhang Z, Ginty F, Badve S. Abstract P6-04-10: Recurrence Prediction in Ductal Carcinoma In Situ (DCIS) Patients from Tissue Microarrays (TMAs). Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p6-04-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Recurrence Prediction in Ductal Carcinoma In Situ (DCIS) Patients Using Generative Adversarial Network (GAN) Augmented Deep Learning Model Background: DCIS patients have an excellent overall survival rate and over-treatment is always a cause for concern due to potential side-effects. Standard clinicopathological factors (age, growth pattern, tumor size, margin status and grade) have been shown to have limited value in predicting recurrence and segregation of high and low risk patients. Early and accurate recurrence prediction would facilitate a more aggressive treatment policy for high-risk patients (mastectomy or adjuvant radiation therapy), and simultaneously reduce over-treatment of low-risk patients. In this work, we have developed a deep learning (DL) classification framework that predicts recurrence in DCIS patients from Tissue microarrays (TMAs) hematoxylin and eosin (H&E) images using a generative adversarial network (GAN) augmented deep learning (DL) classification model. A GAN is a class of DL models, in which two adversarial neural networks, generator and discriminator contest among each other to generate high quality images. During the adversarial training process, the generator learns to synthesize realistic images similar to those in the training set while the discriminator learns to distinguish between real and generated images. In recent years, high quality medical images have been generated by GAN models. To the best of our knowledge, this is the first time a GAN model has been used to generate H&E images to train a DL classification model to predict recurrence in DCIS patients. Materials and methods: The cohort was comprised of 68 DCIS patients, aged between 35-89 years, lesion size of 5-90 mm, with a mix of low (15%), intermediate (35%) and 50% high grade cases. Patients were treated with mastectomy and/or a combination of lumpectomy, radiation and hormone therapy. TMAs were constructed from 2mm cores (1-3 cores per patient) in consultation with a breast pathologist to create hematoxylin and eosin (H&E) images for further analysis. The cohort was split into independent training (n=50 patients, 10 with recurrences at 5years) and validation groups (n=18 patients, 6 with recurrences at 5years). TMA (H&E) images were divided into smaller image patches of size 256x256 to train a GAN to generate image patches. A DL classification network (Resnet-Inception v2) was trained using TMA image patches and aggressive image patches generated by GAN to predict recurrence. The ability to generate synthetic image patches of aggressive lesions permitted training of a large DL classification network and predict recurrence in DCIS patients. Importantly, manual annotation was not necessary for the process. Results: The DL classification model trained with both TMA and GAN generated image patches predicted recurrence with an AUC of 0.87, sensitivity of 0.83 and specificity of 0.91 in the validation dataset. The DL classification model trained with image patches from TMAs only predicted recurrence with an AUC of 0.81. Conclusions: The use of a GAN model to generate H&E images circumvents the needs for a large cohort and accurate labor-intensive manual annotation of histopathological images, which is often required for training a large DL classification model. The use of GAN generated aggressive image patches during training significantly improves recurrence prediction accuracy of the DL classification model. Validation in independent larger cohorts is ongoing, and if successful, could provide a novel assay for risk prediction that does not waste precious tissue samples.
Citation Format: Ghose Soumya, Yesim Gokmen-Polar, Sanghee Cho, Elizabeth McDonough, Cynthia Davis, Jhimli Mitra, Zhanpan Zhang, Fiona Ginty, Sunil Badve. Recurrence Prediction in Ductal Carcinoma In Situ (DCIS) Patients from Tissue Microarrays (TMAs) [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-04-10.
Collapse
|
15
|
Flanagan DJ, Amirkhah R, Vincent DF, Gunduz N, Gentaz P, Cammareri P, McCooey AJ, McCorry AMB, Fisher NC, Davis HL, Ridgway RA, Lohuis J, Leach JDG, Jackstadt R, Gilroy K, Mariella E, Nixon C, Clark W, Hedley A, Markert EK, Strathdee D, Bartholin L, Redmond KL, Kerr EM, Longley DB, Ginty F, Cho S, Coleman HG, Loughrey MB, Bardelli A, Maughan TS, Campbell AD, Lawler M, Leedham SJ, Barry ST, Inman GJ, van Rheenen J, Dunne PD, Sansom OJ. Author Correction: Epithelial TGFβ engages growth-factor signalling to circumvent apoptosis and drive intestinal tumourigenesis with aggressive features. Nat Commun 2023; 14:522. [PMID: 36720858 PMCID: PMC9889781 DOI: 10.1038/s41467-023-36266-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Dustin J Flanagan
- Cancer Research UK Beatson Institute, Glasgow, UK.
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
| | - Raheleh Amirkhah
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | - Nuray Gunduz
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | | | - Aoife J McCooey
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Amy M B McCorry
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Natalie C Fisher
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Hayley L Davis
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Jeroen Lohuis
- Department of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joshua D G Leach
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Rene Jackstadt
- Cancer Research UK Beatson Institute, Glasgow, UK
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH) and Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | | | - Elisa Mariella
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Colin Nixon
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | - Ann Hedley
- Cancer Research UK Beatson Institute, Glasgow, UK
- University of Newcastle upon Tyne, Newcastle, UK
| | - Elke K Markert
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Keara L Redmond
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Emma M Kerr
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Daniel B Longley
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Fiona Ginty
- GE Global Research Center, Niskayuna, NY, USA
| | - Sanghee Cho
- GE Global Research Center, Niskayuna, NY, USA
| | - Helen G Coleman
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Maurice B Loughrey
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Centre for Public Health, Queen's University Belfast, Belfast, UK
- Department of Cellular Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | - Alberto Bardelli
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Timothy S Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | | | - Mark Lawler
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Simon J Leedham
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Simon T Barry
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Gareth J Inman
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Jacco van Rheenen
- Department of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Philip D Dunne
- Cancer Research UK Beatson Institute, Glasgow, UK
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
16
|
Flanagan DJ, Amirkhah R, Vincent DF, Gunduz N, Gentaz P, Cammareri P, McCooey AJ, McCorry AMB, Fisher NC, Davis HL, Ridgway RA, Lohuis J, Leach JDG, Jackstadt R, Gilroy K, Mariella E, Nixon C, Clark W, Hedley A, Markert EK, Strathdee D, Bartholin L, Redmond KL, Kerr EM, Longley DB, Ginty F, Cho S, Coleman HG, Loughrey MB, Bardelli A, Maughan TS, Campbell AD, Lawler M, Leedham SJ, Barry ST, Inman GJ, van Rheenen J, Dunne PD, Sansom OJ. Epithelial TGFβ engages growth-factor signalling to circumvent apoptosis and drive intestinal tumourigenesis with aggressive features. Nat Commun 2022; 13:7551. [PMID: 36477656 PMCID: PMC9729215 DOI: 10.1038/s41467-022-35134-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
The pro-tumourigenic role of epithelial TGFβ signalling in colorectal cancer (CRC) is controversial. Here, we identify a cohort of born to be bad early-stage (T1) colorectal tumours, with aggressive features and a propensity to disseminate early, that are characterised by high epithelial cell-intrinsic TGFβ signalling. In the presence of concurrent Apc and Kras mutations, activation of epithelial TGFβ signalling rampantly accelerates tumourigenesis and share transcriptional signatures with those of the born to be bad T1 human tumours and predicts recurrence in stage II CRC. Mechanistically, epithelial TGFβ signalling induces a growth-promoting EGFR-signalling module that synergises with mutant APC and KRAS to drive MAPK signalling that re-sensitise tumour cells to MEK and/or EGFR inhibitors. Together, we identify epithelial TGFβ signalling both as a determinant of early dissemination and a potential therapeutic vulnerability of CRC's with born to be bad traits.
Collapse
Affiliation(s)
- Dustin J Flanagan
- Cancer Research UK Beatson Institute, Glasgow, UK.
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.
- Cancer Program, Biomedicine Discovery Institute, Monash University, Melbourne, Australia.
| | - Raheleh Amirkhah
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | | | - Nuray Gunduz
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | | | - Aoife J McCooey
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Amy M B McCorry
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Natalie C Fisher
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Hayley L Davis
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Jeroen Lohuis
- Department of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joshua D G Leach
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Rene Jackstadt
- Cancer Research UK Beatson Institute, Glasgow, UK
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH) and Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | | | - Elisa Mariella
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Colin Nixon
- Cancer Research UK Beatson Institute, Glasgow, UK
| | | | - Ann Hedley
- Cancer Research UK Beatson Institute, Glasgow, UK
- University of Newcastle upon Tyne, Newcastle, UK
| | - Elke K Markert
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Keara L Redmond
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Emma M Kerr
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Daniel B Longley
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Fiona Ginty
- GE Global Research Center, Niskayuna, NY, USA
| | - Sanghee Cho
- GE Global Research Center, Niskayuna, NY, USA
| | - Helen G Coleman
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Maurice B Loughrey
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
- Centre for Public Health, Queen's University Belfast, Belfast, UK
- Department of Cellular Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | - Alberto Bardelli
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Timothy S Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | | | - Mark Lawler
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Simon J Leedham
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Simon T Barry
- Bioscience, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Gareth J Inman
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Jacco van Rheenen
- Department of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Philip D Dunne
- Cancer Research UK Beatson Institute, Glasgow, UK
- The Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
17
|
Morton C, Cotero V, Ashe J, Ginty F, Puleo C. Accelerating cutaneous healing in a rodent model of type II diabetes utilizing non-invasive focused ultrasound targeted at the spleen. Front Neurosci 2022; 16:1039960. [PMID: 36478877 PMCID: PMC9721138 DOI: 10.3389/fnins.2022.1039960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/25/2022] [Indexed: 11/18/2022] Open
Abstract
Healing of wounds is delayed in Type 2 Diabetes Mellitus (T2DM), and new treatment approaches are urgently needed. Our earlier work showed that splenic pulsed focused ultrasound (pFUS) alters inflammatory cytokines in models of acute endotoxemia and pneumonia via modulation of the cholinergic anti-inflammatory pathway (CAP) (ref below). Based on these earlier results, we hypothesized that daily splenic exposure to pFUS during wound healing would accelerate closure rate via altered systemic cytokine titers. In this study, we applied non-invasive ultrasound directed to the spleen of a rodent model [Zucker Diabetic Sprague Dawley (ZDSD) rats] of T2DM with full thickness cutaneous excisional wounds in an attempt to accelerate wound healing via normalization of T2DM-driven aberrant cytokine expression. Daily (1x/day, Monday-Friday) pFUS pulses were targeted externally to the spleen area for 3 min over the course of 15 days. Wound diameter was measured daily, and levels of cytokines were evaluated in spleen and wound bed lysates. Non-invasive splenic pFUS accelerated wound closure by up to 4.5 days vs. sham controls. The time to heal in all treated groups was comparable to that of healthy rats from previously published studies (ref below), suggesting that the pFUS treatment restored a normal wound healing phenotype to the ZDSD rats. IL-6 was lower in stimulated spleen (-2.24 ± 0.81 Log2FC, p = 0.02) while L-selectin was higher in the wound bed of stimulated rodents (2.53 ± 0.72 Log2FC, p = 0.003). In summary, splenic pFUS accelerates healing in a T2DM rat model, demonstrating the potential of the method to provide a novel, non-invasive approach for wound care in diabetes.
Collapse
Affiliation(s)
| | | | | | - Fiona Ginty
- Biology and Applied Physics, GE Research, Niskayuna, NY, United States
| | - Christopher Puleo
- GE Research, Niskayuna, NY, United States
- *Correspondence: Christopher Puleo,
| |
Collapse
|
18
|
Badve SS, Cho S, Lu X, Cao S, Ghose S, Thike AA, Tan PH, Ocal IT, Generali D, Zanconati F, Harris AL, Ginty F, Gökmen-Polar Y. Tumor Infiltrating Lymphocytes in Multi-National Cohorts of Ductal Carcinoma In Situ (DCIS) of Breast. Cancers (Basel) 2022; 14:3916. [PMID: 36010908 PMCID: PMC9406008 DOI: 10.3390/cancers14163916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 01/25/2023] Open
Abstract
Tumor-infiltrating lymphocytes (TILs) are prognostic in invasive breast cancer. However, their prognostic significance in ductal carcinoma in situ (DCIS) has been controversial. To investigate the prognostic role of TILs in DCIS outcome, we used different scoring methods for TILs in multi-national cohorts from Asian and European women. Self-described race was genetically confirmed using QC Infinium array combined with radmixture software. Stromal TILs, touching TILs, circumferential TILs, and hotspots were quantified on H&E-stained slides and correlated with the development of second breast cancer events (BCE) and other clinico-pathological variables. In univariate survival analysis, age older than 50 years, hormone receptor positivity and the presence of circumferential TILs were weakly associated with the absence of BCE at the 5-year follow-up in all cohorts (p < 0.03; p < 0.02; and p < 0.02, respectively, adjusted p = 0.11). In the multivariable analysis, circumferential TILs were an independent predictor of a better outcome (Wald test p = 0.01), whereas younger age was associated with BCE. Asian patients were younger with larger, higher grade, HR negative DCIS lesions, and higher TIL variables. The spatial arrangement of TILs may serve as a better prognostic indicator in DCIS cases than stromal TILs alone and may be added in guidelines for TILs evaluation in DCIS.
Collapse
Affiliation(s)
- Sunil S. Badve
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute, Atlanta, GA 30322, USA
| | - Sanghee Cho
- GE Global Research Center, Niskayuna, NY 12309, USA
| | - Xiaoyu Lu
- Center for Computational Biology and Bioinformatics, Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Sha Cao
- Center for Computational Biology and Bioinformatics, Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
| | - Soumya Ghose
- GE Global Research Center, Niskayuna, NY 12309, USA
| | - Aye Aye Thike
- Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
| | - Puay Hoon Tan
- Division of Pathology, Singapore General Hospital, Singapore 169856, Singapore
| | - Idris Tolgay Ocal
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Phoenix, AZ 85054, USA
| | - Daniele Generali
- Department of Medical, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy
| | - Fabrizio Zanconati
- Department of Medical, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy
| | - Adrian L. Harris
- Cancer and Haematology Centre, Department of Oncology, Oxford University, Oxford OX3 7LE, UK
| | - Fiona Ginty
- GE Global Research Center, Niskayuna, NY 12309, USA
| | - Yesim Gökmen-Polar
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute, Atlanta, GA 30322, USA
| |
Collapse
|
19
|
Martinez JS, Peterson S, Hoel CA, Erno DJ, Murray T, Boyd L, Her JH, Mclean N, Davis R, Ginty F, Duclos SJ, Davis BM, Parthasarathy G. High resolution DLP stereolithography to fabricate biocompatible hydroxyapatite structures that support osteogenesis. PLoS One 2022; 17:e0272283. [PMID: 35939440 PMCID: PMC9359536 DOI: 10.1371/journal.pone.0272283] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 07/16/2022] [Indexed: 11/29/2022] Open
Abstract
Lithography based additive manufacturing techniques, specifically digital light processing (DLP), are considered innovative manufacturing techniques for orthopaedic implants because of their potential for construction of complex geometries using polymers, metals, and ceramics. Hydroxyapatite (HA) coupons, printed using DLP, were evaluated for biological performance in supporting viability, proliferation, and osteogenic differentiation of the human cell line U2OS and human mesenchymal stem cells (MSCs) up to 35 days in culture to determine feasibility for future use in development of complex scaffold geometries. Contact angle, profilometry, and scanning electron microscopy (SEM) measurements showed the HA coupons to be hydrophilic, porous, and having micro size surface roughness, all within favourable cell culture ranges. The study found no impact of leachable and extractables form the DLP printing process. Cells seeded on coupons exhibited morphologies comparable to conventional tissue culture polystyrene plates. Cell proliferation rates, as determined by direct cell count and the RealTime-GloTM MT Cell Viability Assay, were similar on HA coupons and standard tissue culture polystyrene plates). Osteogenic differentiation of human MSCs on HA coupons was confirmed using alkaline phosphatase, Alizarin Red S and von Kossa staining. The morphology of MSCs cultured in osteogenic medium for 14 to 35 days was similar on HA coupons and tissue culture polystyrene plates, with osteogenic (geometric, cuboidal morphology with dark nodules) and adipogenic (lipid vesicles and deposits) features. We conclude that the DLP process and LithaBone HA400 slurry are biocompatible and are suitable for osteogenic applications. Coupons served as an effective evaluation design in the characterization and visualization of cell responses on DLP printed HA material. Results support the feasibility of future technical development for 3D printing of sophisticated scaffold designs, which can be constructed to meet the mechanical, chemical, and porosity requirements of an artificial bone scaffold.
Collapse
Affiliation(s)
| | - Sara Peterson
- GE Research, Niskayuna, New York, United States of America
| | | | - Daniel J. Erno
- GE Research, Niskayuna, New York, United States of America
| | - Tony Murray
- GE Research, Niskayuna, New York, United States of America
| | - Linda Boyd
- GE Research, Niskayuna, New York, United States of America
| | - Jae-Hyuk Her
- GE Research, Niskayuna, New York, United States of America
| | - Nathan Mclean
- GE Research, Niskayuna, New York, United States of America
| | - Robert Davis
- GE Research, Niskayuna, New York, United States of America
| | - Fiona Ginty
- GE Research, Niskayuna, New York, United States of America
| | | | - Brian M. Davis
- GE Research, Niskayuna, New York, United States of America
| | | |
Collapse
|
20
|
Stachtea X, Loughrey MB, Salvucci M, Lindner AU, Cho S, McDonough E, Sood A, Graf J, Santamaria-Pang A, Corwin A, Laurent-Puig P, Dasgupta S, Shia J, Owens JR, Abate S, Van Schaeybroeck S, Lawler M, Prehn JHM, Ginty F, Longley DB. Stratification of chemotherapy-treated stage III colorectal cancer patients using multiplexed imaging and single-cell analysis of T-cell populations. Mod Pathol 2022; 35:564-576. [PMID: 34732839 PMCID: PMC8964416 DOI: 10.1038/s41379-021-00953-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 11/08/2022]
Abstract
Colorectal cancer (CRC) has one of the highest cancer incidences and mortality rates. In stage III, postoperative chemotherapy benefits <20% of patients, while more than 50% will develop distant metastases. Biomarkers for identification of patients at increased risk of disease recurrence following adjuvant chemotherapy are currently lacking. In this study, we assessed immune signatures in the tumor and tumor microenvironment (TME) using an in situ multiplexed immunofluorescence imaging and single-cell analysis technology (Cell DIVETM) and evaluated their correlations with patient outcomes. Tissue microarrays (TMAs) with up to three 1 mm diameter cores per patient were prepared from 117 stage III CRC patients treated with adjuvant fluoropyrimidine/oxaliplatin (FOLFOX) chemotherapy. Single sections underwent multiplexed immunofluorescence staining for immune cell markers (CD45, CD3, CD4, CD8, FOXP3, PD1) and tumor/cell segmentation markers (DAPI, pan-cytokeratin, AE1, NaKATPase, and S6). We used annotations and a probabilistic classification algorithm to build statistical models of immune cell types. Images were also qualitatively assessed independently by a Pathologist as 'high', 'moderate' or 'low', for stromal and total immune cell content. Excellent agreement was found between manual assessment and total automated scores (p < 0.0001). Moreover, compared to single markers, a multi-marker classification of regulatory T cells (Tregs: CD3+/CD4+FOXP3+/PD1-) was significantly associated with disease-free survival (DFS) and overall survival (OS) (p = 0.049 and 0.032) of FOLFOX-treated patients. Our results also showed that PD1- Tregs rather than PD1+ Tregs were associated with improved survival. These findings were supported by results from an independent FOLFOX-treated cohort of 191 stage III CRC patients, where higher PD1- Tregs were associated with an increase overall survival (p = 0.015) for CD3+/CD4+/FOXP3+/PD1-. Overall, compared to single markers, multi-marker classification provided more accurate quantitation of immune cell types with stronger correlations with outcomes.
Collapse
Affiliation(s)
- Xanthi Stachtea
- Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Northern Ireland, UK
| | - Maurice B Loughrey
- Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Northern Ireland, UK
- Department of Cellular Pathology, Royal Victoria Hospital, Belfast Health and Social Care trust, Belfast, UK
| | - Manuela Salvucci
- Department of Physiology and Medical Physics and Centre for Systems Medicine, Royal College of Surgeons in Ireland (RCSI) University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | - Andreas U Lindner
- Department of Physiology and Medical Physics and Centre for Systems Medicine, Royal College of Surgeons in Ireland (RCSI) University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | - Sanghee Cho
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | | | - Anup Sood
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | - John Graf
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | | | - Alex Corwin
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | | | | | - Jinru Shia
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan R Owens
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | - Samantha Abate
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | - Sandra Van Schaeybroeck
- Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Northern Ireland, UK
| | - Mark Lawler
- Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Northern Ireland, UK
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics and Centre for Systems Medicine, Royal College of Surgeons in Ireland (RCSI) University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | - Fiona Ginty
- GE Research Center, 1 Research Circle, Niskayuna, NY, 12309, USA
| | - Daniel B Longley
- Patrick G. Johnston Centre for Cancer Research, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Northern Ireland, UK.
| |
Collapse
|
21
|
Pourmaleki M, Jones CJ, Ariyan CE, Zeng Z, Pirun M, Navarrete DA, Li Y, Zhang M, Nandakumar S, Campos C, Nadeem S, Klimstra DS, Temple-Oberle CF, Brenn T, Lipson EJ, Schenk KM, Stein JE, Taube JM, White MG, Traweek R, Wargo JA, Kirkwood JM, Gasmi B, Goff SL, Corwin AD, McDonough E, Ginty F, Callahan MK, Schietinger A, Socci ND, Mellinghoff IK, Hollmann TJ. Tumor MHC Class I Expression Associates with Intralesional Interleukin-2 Response in Melanoma. Cancer Immunol Res 2022; 10:303-313. [PMID: 35013003 DOI: 10.1158/2326-6066.cir-21-1083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 11/16/2022]
Abstract
Cancer immunotherapy can result in lasting tumor regression, but predictive biomarkers of treatment response remain ill-defined. Here, we performed single-cell proteomics, transcriptomics, and genomics on matched untreated and interleukin-2 (IL-2) injected metastases from patients with melanoma. Lesions that completely regressed following intralesional IL-2 harbored increased fractions and densities of non-proliferating CD8+ T cells lacking expression of PD-1, LAG-3 and TIM-3 (PD-1-LAG-3-TIM-3-). Untreated lesions from patients who subsequently responded with complete eradication of all tumor cells in all injected lesions (individuals referred to herein as "extreme responders") were characterized by proliferating CD8+ T cells with an exhausted phenotype (PD-1+LAG-3+TIM-3+), stromal B-cell aggregates, and expression of IFNgamma and IL-2 response genes. Loss of membranous MHC class I expression in tumor cells of untreated lesions was associated with resistance to IL-2 therapy. We validated this finding in an independent cohort of metastatic melanoma patients treated with intralesional or systemic IL-2. Our study suggests that intact tumor cell antigen presentation is required for melanoma response to IL-2 and describes a multi-dimensional and spatial approach to develop immuno-oncology biomarker hypotheses using routinely collected clinical biospecimens.
Collapse
Affiliation(s)
| | | | | | - Zheng Zeng
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center
| | - Mono Pirun
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center
| | | | - Yanyun Li
- Pathology, Memorial Sloan Kettering Cancer Center
| | | | | | - Carl Campos
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center
| | | | | | | | - Thomas Brenn
- Pathology and Laboratory Medicine, University of Calgary
| | - Evan J Lipson
- Oncology, Johns Hopkins University School of Medicine
| | - Kara M Schenk
- Oncology, Johns Hopkins University School of Medicine
| | | | | | - Michael G White
- Surgical Oncology, The University of Texas MD Anderson Cancer Center
| | - Raymond Traweek
- Surgical Oncology, The University of Texas MD Anderson Cancer Center
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center
| | - John M Kirkwood
- Medicine; Division of Hematology/Oncology, University of Pittsburgh
| | - Billel Gasmi
- Laboratory of Pathology, National Cancer Institute
| | | | | | | | | | - Margaret K Callahan
- Melanoma and Immunotherapeutics Service, Dept. of Medicine, Memorial Sloan Kettering Cancer Center
| | | | | | | | | |
Collapse
|
22
|
Graf J, Cho S, McDonough E, Corwin A, Sood A, Lindner A, Salvucci M, Stachtea X, Van Schaeybroeck S, Dunne PD, Laurent-Puig P, Longley D, Prehn JHM, Ginty F. FLINO: a new method for immunofluorescence bioimage normalization. Bioinformatics 2022; 38:520-526. [PMID: 34601553 PMCID: PMC8723144 DOI: 10.1093/bioinformatics/btab686] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/09/2021] [Accepted: 09/25/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Multiplexed immunofluorescence bioimaging of single-cells and their spatial organization in tissue holds great promise to the development of future precision diagnostics and therapeutics. Current multiplexing pipelines typically involve multiple rounds of immunofluorescence staining across multiple tissue slides. This introduces experimental batch effects that can hide underlying biological signal. It is important to have robust algorithms that can correct for the batch effects while not introducing biases into the data. Performance of data normalization methods can vary among different assay pipelines. To evaluate differences, it is critical to have a ground truth dataset that is representative of the assay. RESULTS A new immunoFLuorescence Image NOrmalization method is presented and evaluated against alternative methods and workflows. Multiround immunofluorescence staining of the same tissue with the nuclear dye DAPI was used to represent virtual slides and a ground truth. DAPI was restained on a given tissue slide producing multiple images of the same underlying structure but undergoing multiple representative tissue handling steps. This ground truth dataset was used to evaluate and compare multiple normalization methods including median, quantile, smooth quantile, median ratio normalization and trimmed mean of the M-values. These methods were applied in both an unbiased grid object and segmented cell object workflow to 24 multiplexed biomarkers. An upper quartile normalization of grid objects in log space was found to obtain almost equivalent performance to directly normalizing segmented cell objects by the middle quantile. The developed grid-based technique was then applied with on-slide controls for evaluation. Using five or fewer controls per slide can introduce biases into the data. Ten or more on-slide controls were able to robustly correct for batch effects. AVAILABILITY AND IMPLEMENTATION The data underlying this article along with the FLINO R-scripts used to perform the evaluation of image normalizations methods and workflows can be downloaded from https://github.com/GE-Bio/FLINO. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- John Graf
- To whom correspondence should be addressed. or
| | - Sanghee Cho
- Department of Biology & Applied Physics, GE Research, Niskayuna, NY 12309, USA
| | - Elizabeth McDonough
- Department of Biology & Applied Physics, GE Research, Niskayuna, NY 12309, USA
| | - Alex Corwin
- Department of Biology & Applied Physics, GE Research, Niskayuna, NY 12309, USA
| | - Anup Sood
- Department of Biology & Applied Physics, GE Research, Niskayuna, NY 12309, USA
| | - Andreas Lindner
- Department of Physiology and Medical Physics, Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen’s Green, Dublin 2, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen’s Green, Dublin 2, Ireland
| | - Xanthi Stachtea
- Department of Oncology, Centre for Cancer Research & Cell Biology, Queen’s University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Sandra Van Schaeybroeck
- Department of Oncology, Centre for Cancer Research & Cell Biology, Queen’s University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Philip D Dunne
- Department of Oncology, Centre for Cancer Research & Cell Biology, Queen’s University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Pierre Laurent-Puig
- Department of Biology, Hôpital Européen Georges-Pompidou, Assistance Publique - Hôpitaux de Paris, 3 Av. Victoria, 75004 Paris, France
| | - Daniel Longley
- Department of Oncology, Centre for Cancer Research & Cell Biology, Queen’s University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen’s Green, Dublin 2, Ireland
| | - Fiona Ginty
- To whom correspondence should be addressed. or
| |
Collapse
|
23
|
O’Connell E, Reynolds IS, Lindner AU, Salvucci M, O’Grady T, Bacon O, Cho S, McDonough E, Longley D, Ginty F, McNamara DA, Burke JP, Prehn JHM. Apoptotic and Necroptotic Mediators are Differentially Expressed in Mucinous and Non-Mucinous Colorectal Cancer. Front Oncol 2022; 12:815001. [PMID: 35912268 PMCID: PMC9334008 DOI: 10.3389/fonc.2022.815001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 06/21/2022] [Indexed: 01/25/2023] Open
Abstract
Background Mucinous colorectal cancer (CRC) represents 10% of all CRC and is associated with chemotherapy resistance. This study aimed to determine expression of apoptosis and necroptosis mediators in mucinous CRC. Methods RNA gene expression data were extracted from TCGA. Protein levels in 14 mucinous and 39 non-mucinous tumors were measured by multiplexed immunofluorescence. Levels of apoptosis and necroptosis signalling proteins were analysed in SW1463 (mucinous rectal), SW837 (non-mucinous rectal), LS174T (mucinous colon) and HCT116 (non-mucinous colon) cell lines by western blot. Cell death was investigated by flow cytometry measurement of propidium iodide stained cells. Results High cleaved-Caspase 3 expression was noted in resected mucinous tumors. Western blot identified alterations in apoptosis proteins in mucinous CRC, most prominently downregulation of Bcl-xL protein levels (p=0.029) which was also observed at the mRNA level in patients by analysis of TCGA gene expression data (p<0.001). Treatment with 5-FU did not significantly elevate cell death in mucinous cells, while non-mucinous cells showed robust cell death responses. However, 5-FU-induced phosphorylation of MLKL in mucinous cancer cells, suggestive of a switch to necroptotic cell death signaling. Conclusion Apoptotic and necroptotic mediators are differentially expressed in mucinous and non-mucinous colorectal cancers and represent targets for investigation of cell death mechanisms in the mucinous subtype.
Collapse
Affiliation(s)
- Emer O’Connell
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Colorectal Surgery, Beaumont Hospital, Dublin, Ireland
| | - Ian S. Reynolds
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Colorectal Surgery, Beaumont Hospital, Dublin, Ireland
| | - Andreas U. Lindner
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Tony O’Grady
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | - Orna Bacon
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Colorectal Surgery, Beaumont Hospital, Dublin, Ireland
| | - Sanghee Cho
- GE Global Research, Niskayuna, NY, United States
| | | | - Daniel Longley
- Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Belfast, United Kingdom
| | - Fiona Ginty
- GE Global Research, Niskayuna, NY, United States
| | - Deborah A. McNamara
- Department of Colorectal Surgery, Beaumont Hospital, Dublin, Ireland
- Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - John P. Burke
- Department of Colorectal Surgery, Beaumont Hospital, Dublin, Ireland
- Department of Surgery, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jochen H. M. Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
- *Correspondence: Jochen H. M. Prehn, ; orcid.org/0000-0003-3479-7794
| |
Collapse
|
24
|
Cheung AMY, Wang D, Liu K, Hope T, Murray M, Ginty F, Nofech-Mozes S, Martel AL, Yaffe MJ. Quantitative single-cell analysis of immunofluorescence protein multiplex images illustrates biomarker spatial heterogeneity within breast cancer subtypes. Breast Cancer Res 2021; 23:114. [PMID: 34922607 PMCID: PMC8684264 DOI: 10.1186/s13058-021-01475-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/11/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The extent of cellular heterogeneity in breast cancer could have potential impact on diagnosis and long-term outcome. However, pathology evaluation is limited to biomarker immunohistochemical staining and morphology of the bulk cancer. Inter-cellular heterogeneity of biomarkers is not usually assessed. As an initial evaluation of the extent of breast cancer cellular heterogeneity, we conducted quantitative and spatial imaging of Estrogen Receptor (ER), Progesterone Receptor (PR), Epidermal Growth Factor Receptor-2 (HER2), Ki67, TP53, CDKN1A (P21/WAF1), CDKN2A (P16INK4A), CD8 and CD20 of a tissue microarray (TMA) representing subtypes defined by St. Gallen surrogate classification. METHODS Quantitative, single cell-based imaging was conducted using an Immunofluorescence protein multiplexing platform (MxIF) to study protein co-expression signatures and their spatial localization patterns. The range of MxIF intensity values of each protein marker was compared to the respective IHC score for the TMA core. Extent of heterogeneity in spatial neighborhoods was analyzed using co-occurrence matrix and Diversity Index measures. RESULTS On the 101 cores from 59 cases studied, diverse expression levels and distributions were observed in MxIF measures of ER and PR among the hormonal receptor-positive tumor cores. As expected, Luminal A-like cancers exhibit higher proportions of cell groups that co-express ER and PR, while Luminal B-like (HER2-negative) cancers were composed of ER+, PR- groups. Proliferating cells defined by Ki67 positivity were mainly found in groups with PR-negative cells. Triple-Negative Breast Cancer (TNBC) exhibited the highest proliferative fraction and incidence of abnormal P53 and P16 expression. Among the tumors exhibiting P53 overexpression by immunohistochemistry, a group of TNBC was found with much higher MxIF-measured P53 signal intensity compared to HER2+, Luminal B-like and other TNBC cases. Densities of CD8 and CD20 cells were highest in HER2+ cancers. Spatial analysis demonstrated variability in heterogeneity in cellular neighborhoods in the cancer and the tumor microenvironment. CONCLUSIONS Protein marker multiplexing and quantitative image analysis demonstrated marked heterogeneity in protein co-expression signatures and cellular arrangement within each breast cancer subtype. These refined descriptors of biomarker expressions and spatial patterns could be valuable in the development of more informative tools to guide diagnosis and treatment.
Collapse
Affiliation(s)
- Alison Min-Yan Cheung
- Biomarker Imaging Research Lab (BIRL), Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - Dan Wang
- Biomarker Imaging Research Lab (BIRL), Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - Kela Liu
- Biomarker Imaging Research Lab (BIRL), Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - Tyna Hope
- Biomarker Imaging Research Lab (BIRL), Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - Mayan Murray
- Biomarker Imaging Research Lab (BIRL), Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - Fiona Ginty
- Biosciences, GE Research (GER), Niskayuna, NY, USA
| | - Sharon Nofech-Mozes
- Department of Anatomic Pathology, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Anne Louise Martel
- Biomarker Imaging Research Lab (BIRL), Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Martin Joel Yaffe
- Biomarker Imaging Research Lab (BIRL), Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
25
|
Lindner AU, Salvucci M, McDonough E, Cho S, Stachtea X, O'Connell EP, Corwin AD, Santamaria-Pang A, Carberry S, Fichtner M, Van Schaeybroeck S, Laurent-Puig P, Burke JP, McNamara DA, Lawler M, Sood A, Graf JF, Rehm M, Dunne PD, Longley DB, Ginty F, Prehn JHM. An atlas of inter- and intra-tumor heterogeneity of apoptosis competency in colorectal cancer tissue at single-cell resolution. Cell Death Differ 2021; 29:806-817. [PMID: 34754079 PMCID: PMC8990071 DOI: 10.1038/s41418-021-00895-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/13/2021] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
Cancer cells’ ability to inhibit apoptosis is key to malignant transformation and limits response to therapy. Here, we performed multiplexed immunofluorescence analysis on tissue microarrays with 373 cores from 168 patients, segmentation of 2.4 million individual cells, and quantification of 18 cell lineage and apoptosis proteins. We identified an enrichment for BCL2 in immune, and BAK, SMAC, and XIAP in cancer cells. Ordinary differential equation-based modeling of apoptosis sensitivity at single-cell resolution was conducted and an atlas of inter- and intra-tumor heterogeneity in apoptosis susceptibility generated. Systems modeling at single-cell resolution identified an enhanced sensitivity of cancer cells to mitochondrial permeabilization and executioner caspase activation compared to immune and stromal cells, but showed significant inter- and intra-tumor heterogeneity.
Collapse
Affiliation(s)
- Andreas Ulrich Lindner
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.,Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.,Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
| | | | | | - Xanthi Stachtea
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Emer P O'Connell
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.,Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.,Department of Surgery, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
| | | | | | - Steven Carberry
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.,Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
| | - Michael Fichtner
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.,Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
| | - Sandra Van Schaeybroeck
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Pierre Laurent-Puig
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université de Paris, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale Contre le Cancer, Paris, France
| | - John P Burke
- Department of Surgery, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland
| | - Deborah A McNamara
- Department of Surgery, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.,Beaumont Hospital, Beaumont Road, Dublin 9, Ireland
| | - Mark Lawler
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Anup Sood
- GE Research, Niskayuna, NY, 12309, USA
| | | | - Markus Rehm
- Institute of Cell Biology and Immunology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Philip D Dunne
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | - Daniel B Longley
- Centre for Cancer Research & Cell Biology, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK
| | | | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland. .,Centre of Systems Medicine, Royal College of Surgeons in Ireland University of Medicine and Health Sciences, 123 St. Stephen's Green, Dublin 2, Ireland.
| |
Collapse
|
26
|
Börner K, Teichmann SA, Quardokus EM, Gee JC, Browne K, Osumi-Sutherland D, Herr BW, Bueckle A, Paul H, Haniffa M, Jardine L, Bernard A, Ding SL, Miller JA, Lin S, Halushka MK, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius MT, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Weber G. Anatomical structures, cell types and biomarkers of the Human Reference Atlas. Nat Cell Biol 2021; 23:1117-1128. [PMID: 34750582 PMCID: PMC10079270 DOI: 10.1038/s41556-021-00788-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 09/29/2021] [Indexed: 02/05/2023]
Abstract
The Human Reference Atlas (HRA) aims to map all of the cells of the human body to advance biomedical research and clinical practice. This Perspective presents collaborative work by members of 16 international consortia on two essential and interlinked parts of the HRA: (1) three-dimensional representations of anatomy that are linked to (2) tables that name and interlink major anatomical structures, cell types, plus biomarkers (ASCT+B). We discuss four examples that demonstrate the practical utility of the HRA.
Collapse
Affiliation(s)
- Katy Börner
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ellen M Quardokus
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - James C Gee
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristen Browne
- Department of Health and Human Services, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - David Osumi-Sutherland
- European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Bruce W Herr
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Andreas Bueckle
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Hrishikesh Paul
- Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | | | | | - Shin Lin
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Avinash Boppana
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Teri A Longacre
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - John Hickey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yiing Lin
- Department of Surgery, Washington University in St Louis, St Louis, MO, USA
| | - M Todd Valerius
- Harvard Institute of Medicine, Harvard Medical School, Boston, MA, USA
| | - Yongqun He
- Department of Microbiology and Immunology, and Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gloria Pryhuber
- Department of Pediatrics, University of Rochester, Rochester, NY, USA
| | - Xin Sun
- Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Marda Jorgensen
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Andrea J Radtke
- Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Clive Wasserfall
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Fiona Ginty
- Biology and Applied Physics, General Electric Research, Niskayuna, NY, USA
| | - Jonhan Ho
- Department of Dermatology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joel Sunshine
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rebecca T Beuschel
- Center for Advanced Tissue Imaging, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Maigan Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Sujin Lee
- Division of Vascular Surgery and Endovascular Therapy, Massachusetts General Hospital, Boston, MA, USA
| | - Rajeev Malhotra
- Harvard Institute of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Vascular Surgery and Endovascular Therapy, Massachusetts General Hospital, Boston, MA, USA
| | - Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Griffin Weber
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
27
|
Badve SS, Cho S, Gökmen-Polar Y, Sui Y, Chadwick C, McDonough E, Sood A, Taylor M, Zavodszky M, Tan PH, Gerdes M, Harris AL, Ginty F. Multi-protein spatial signatures in ductal carcinoma in situ (DCIS) of breast. Br J Cancer 2021; 124:1150-1159. [PMID: 33414541 PMCID: PMC7961015 DOI: 10.1038/s41416-020-01216-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 09/10/2020] [Accepted: 11/25/2020] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND There is limited knowledge about DCIS cellular composition and relationship with breast cancer events (BCE). METHODS Immunofluorescence multiplexing (MxIF) was used to image and quantify 32 cellular biomarkers in FFPE DCIS tissue microarrays. Over 75,000 DCIS cells from 51 patients (median 9 years follow-up for non-BCE cases) were analysed for profiles predictive of BCE. K-means clustering was used to evaluate cellular co-expression of epithelial markers with ER and HER2. RESULTS Only ER, PR and HER2 significantly correlated with BCE. Cluster analysis identified 6 distinct cell groups with different levels of ER, Her2, cMET and SLC7A5. Clusters 1 and 3 were not significant. Clusters 2 and 4 (high ER/low HER2 and SLC7A5/mixed cMET) significantly correlated with low BCE risk (P = 0.001 and P = 0.034), while cluster 6 (high HER2/low ER, cMET and SLC7A5) correlated with increased risk (P = 0.018). Cluster 5 (similar to cluster 6, except high SLC7A5) trended towards significance (P = 0.072). A continuous expression score (Escore) based on these 4 clusters predicted likelihood of BCE (AUC = 0.79, log-rank test P = 5E-05; LOOCV AUC = 0.74, log-rank test P = 0.006). CONCLUSION Multiplexed spatial analysis of limited tissue is a novel method for biomarker analysis and predicting BCEs. Further validation of Escore is needed in a larger cohort.
Collapse
MESH Headings
- Aged
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Breast Neoplasms/therapy
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Ductal, Breast/therapy
- Carcinoma, Intraductal, Noninfiltrating/metabolism
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Carcinoma, Intraductal, Noninfiltrating/therapy
- Combined Modality Therapy
- Female
- Follow-Up Studies
- Humans
- Mastectomy/methods
- Middle Aged
- Prognosis
- Retrospective Studies
- Survival Rate
Collapse
Affiliation(s)
- Sunil S Badve
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | | | - Yesim Gökmen-Polar
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | | | | | - Anup Sood
- GE Research, Niskayuna, NY, 12309, USA
| | - Marian Taylor
- Department of Oncology, Cancer and Haematology Centre, Oxford University, Oxford, OX37LJ, UK
| | | | - Puay Hoon Tan
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | | | - Adrian L Harris
- Department of Oncology, Cancer and Haematology Centre, Oxford University, Oxford, OX37LJ, UK
| | | |
Collapse
|
28
|
Cheung AM, Wang D, Liu K, Ginty F, Nofech-Mozes S, Bayani J, Bartlett JM, Martel A, Yaffe MJ. Abstract PO-084: Protein marker heterogeneity in breast cancer subtypes measured using immunofluorescence protein multiplexing and quantitative, single cell image analysis. Cancer Res 2020. [DOI: 10.1158/1538-7445.tumhet2020-po-084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The extent of intra-tumoral heterogeneity - the variation in the composition of cells in a given tumor and those in the local tumor microenvironment - could have potential impact on diagnosis, treatment planning and subsequent response to treatment. To evaluate the extent of cancer cellular heterogeneity, we conducted quantitative protein marker multiplex imaging to study the variations in protein marker expression patterns on individual cells and spatial localizations. A multiplexed immunofluorescence imaging platform (MxIF, Cell DIVE) was used to measure the cellular expression of Estrogen Receptor (ER), Progesterone Receptor (PR), Epidermal Growth Factor Receptor 2 (HER2), Ki67, p53, p21WAF1 and p16INK4A in cancer epithelium. Analysis was conducted on a tissue microarray (TMA) representing subtypes classified as Luminal A-like, Luminal B-like (HER2-negative), Luminal B-like (HER2-positive), HER2-positive (non-luminal) or Triple-negative based on tumor grade and immune activity according to the St. Gallen surrogate classification. Of the 101 cores from 59 cases studied, high levels of heterogeneity were observed in ER and PR expression among the hormonal receptor-positive tumors. As expected Luminal A-like cancers exhibited higher proportions of individual cells co-expressing ER and PR, while cells in Luminal B-like, HER2-negative cancers showed ER expression only. Luminal B-like, HER2-positive cores were composed of cells with strong HER2 staining, and some cells co-expressing PR and HER2. Single cells with strong ER and HER2 labelling were rarely observed. Spatial visualizations illustrated that cells with similar expression signatures tend to be clustered together. Among cases which showed p53 overexpression with immunohistochemistry, the overall MxIF-measured p53 level was highest in TNBC compared to HER2+ and Luminal B-like cases. TNBC exhibited the highest proliferative fraction and most incidence of abnormal p53 and p16. We did not observe an association of p21 expression to P53 or P16 patterns, yet a slightly higher proportion of Luminal B-like cancers showed increased P21 levels compared to the other subtypes. Our study demonstrated the application of protein marker multiplexing and quantitative image analysis in measuring heterogeneity of protein co-expression signatures within breast cancer subtypes. Our next step is to apply the methods developed here to study a cohort where molecular profiling and radiomics were conducted (Bayani et al.) to reveal the extent of heterogeneity of breast cancer with a multi-omics approach.
Citation Format: Alison M. Cheung, Dan Wang, Kela Liu, Fiona Ginty, Sharon Nofech-Mozes, Jane Bayani, John M.S. Bartlett, Anne Martel, Martin J. Yaffe. Protein marker heterogeneity in breast cancer subtypes measured using immunofluorescence protein multiplexing and quantitative, single cell image analysis [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-084.
Collapse
Affiliation(s)
| | - Dan Wang
- 1Sunnybrook Research Institute, Toronto, ON, Canada,
| | - Kela Liu
- 1Sunnybrook Research Institute, Toronto, ON, Canada,
| | | | | | - Jane Bayani
- 4Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Anne Martel
- 1Sunnybrook Research Institute, Toronto, ON, Canada,
| | | |
Collapse
|
29
|
Stachtea X, Lindner A, Salvucci M, Cho S, Sood A, McDonough E, Santamaria-Pang A, Graf J, Dunne P, Lawler M, Prehn J, Ginty F, Longley D. Abstract 2676: Hyperplexed immunofluorescence analysis (Cell DIVETM) of immune-related tumor heterogeneity in stage III colorectal cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-2676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Colorectal cancer (CRC) has one of the highest Worldwide incidences and mortality rates. Genotoxic chemotherapy following surgery in stage III patients confers treatment benefit to less than 20% of the patients, with more than 50% of stage III patients going on to develop distant metastases. Currently, there are no predictive biomarkers that can identify which stage III patients will recur, which patients will benefit from chemotherapy and which should be redirected towards alternative therapeutic interventions. A major challenge in identifying such a universal biomarker is that CRC is a heterogeneous disease with multiple subtypes. In the current study, we assessed clinically-relevant immune cell populations in the tumour microenvironment (TME) of stage III tumours using a novel hyperplex in situ immunofluorescence imaging technology (Cell DIVETM, GE Healthcare, Issaquah, WA).
Tissue microarrays (TMAs) with up to three 1mm diameter cores per patient were prepared from 139 stage III CRC patients treated with adjuvant FOLFOX chemotherapy. Single sections (5 µm) were iteratively stained with Cy3- and Cy5-conjugated antibodies for immune cell markers as well as markers of cell death and metabolism. The images underwent illumination correction, DAPI-based registration and autofluorescence removal. After image quality control corrections, single cell segmentation was performed using a combination of DAPI [nuclear], pan-cytokeratin [epithelial], NaKATPase [membrane] and S6 [cytoplasmic] segmentation markers and an average of ~3,000 stromal cells and ~ 4,000 epithelial were segmented per tumour core.
A machine learning-based algorithm for immune cell classification and quantification was used to analyse the immune markers CD45, CD3, CD4, CD8, FOXP3 and PD1 to identify: cytotoxic T cells, T helper cells, regulatory T cells and potential relevance of immune checkpoint therapy. In the tumour tissues, the median proportion of CD3+ segmented cells was ~8%. Classified immune cells were counted within epithelial and stromal regions, with patients categorised as Low, Intermediate and High (based on <25th, 25th - 75th and >75th percentile, respectively) for each cell type. Preliminary survival analyses show that patients with ‘CD8 High' intratumoural cytotoxic T cells have better Disease-Free Survival compared to ‘CD8 Low' patients in this FOLFOX-treated cohort. By combining single-cell data with clinicopathological patient data, we aim to identify immune-, cell death- and metabolism-related signatures that can predict benefit from adjuvant FOLFOX chemotherapy for Stage III CRC patients.
Citation Format: Xanthi Stachtea, Andreas Lindner, Manuela Salvucci, Sanghee Cho, Anup Sood, Elizabeth McDonough, Alberto Santamaria-Pang, John Graf, Philip Dunne, Mark Lawler, Jochen Prehn, Fiona Ginty, Daniel Longley. Hyperplexed immunofluorescence analysis (Cell DIVETM) of immune-related tumor heterogeneity in stage III colorectal cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2676.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Philip Dunne
- 1Queen's University Belfast, Belfast, United Kingdom
| | - Mark Lawler
- 1Queen's University Belfast, Belfast, United Kingdom
| | - Jochen Prehn
- 2Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | | |
Collapse
|
30
|
Sood A, Sui Y, McDonough E, Santamaría-Pang A, Al-Kofahi Y, Pang Z, Jahrling PB, Kuhn JH, Ginty F. Comparison of Multiplexed Immunofluorescence Imaging to Chromogenic Immunohistochemistry of Skin Biomarkers in Response to Monkeypox Virus Infection. Viruses 2020; 12:E787. [PMID: 32717786 PMCID: PMC7472296 DOI: 10.3390/v12080787] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/15/2020] [Accepted: 07/19/2020] [Indexed: 12/17/2022] Open
Abstract
Over the last 15 years, advances in immunofluorescence-imaging based cycling methods, antibody conjugation methods, and automated image processing have facilitated the development of a high-resolution, multiplexed tissue immunofluorescence (MxIF) method with single cell-level quantitation termed Cell DIVETM. Originally developed for fixed oncology samples, here it was evaluated in highly fixed (up to 30 days), archived monkeypox virus-induced inflammatory skin lesions from a retrospective study in 11 rhesus monkeys to determine whether MxIF was comparable to manual H-scoring of chromogenic stains. Six protein markers related to immune and cellular response (CD68, CD3, Hsp70, Hsp90, ERK1/2, ERK1/2 pT202_pY204) were manually quantified (H-scores) by a pathologist from chromogenic IHC double stains on serial sections and compared to MxIF automated single cell quantification of the same markers that were multiplexed on a single tissue section. Overall, there was directional consistency between the H-score and the MxIF results for all markers except phosphorylated ERK1/2 (ERK1/2 pT202_pY204), which showed a decrease in the lesion compared to the adjacent non-lesioned skin by MxIF vs an increase via H-score. Improvements to automated segmentation using machine learning and adding additional cell markers for cell viability are future options for improvement. This method could be useful in infectious disease research as it conserves tissue, provides marker colocalization data on thousands of cells, allowing further cell level data mining as well as a reduction in user bias.
Collapse
Affiliation(s)
- Anup Sood
- GE Research, 1 Research Circle, Niskayuna, NY 12309, USA; (A.S.); (Y.S.); (E.M.); (A.S.-P.); (Y.A.-K.); (Z.P.)
| | - Yunxia Sui
- GE Research, 1 Research Circle, Niskayuna, NY 12309, USA; (A.S.); (Y.S.); (E.M.); (A.S.-P.); (Y.A.-K.); (Z.P.)
| | - Elizabeth McDonough
- GE Research, 1 Research Circle, Niskayuna, NY 12309, USA; (A.S.); (Y.S.); (E.M.); (A.S.-P.); (Y.A.-K.); (Z.P.)
| | - Alberto Santamaría-Pang
- GE Research, 1 Research Circle, Niskayuna, NY 12309, USA; (A.S.); (Y.S.); (E.M.); (A.S.-P.); (Y.A.-K.); (Z.P.)
| | - Yousef Al-Kofahi
- GE Research, 1 Research Circle, Niskayuna, NY 12309, USA; (A.S.); (Y.S.); (E.M.); (A.S.-P.); (Y.A.-K.); (Z.P.)
| | - Zhengyu Pang
- GE Research, 1 Research Circle, Niskayuna, NY 12309, USA; (A.S.); (Y.S.); (E.M.); (A.S.-P.); (Y.A.-K.); (Z.P.)
| | - Peter B. Jahrling
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Frederick, MD 21702, USA;
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Frederick, MD 21702, USA;
| | - Fiona Ginty
- GE Research, 1 Research Circle, Niskayuna, NY 12309, USA; (A.S.); (Y.S.); (E.M.); (A.S.-P.); (Y.A.-K.); (Z.P.)
| |
Collapse
|
31
|
Kagan J, Moritz RL, Mazurchuk R, Lee JH, Kharchenko PV, Rozenblatt-Rosen O, Ruppin E, Edfors F, Ginty F, Goltsev Y, Wells JA, LaCava J, Riesterer JL, Germain RN, Shi T, Chee MS, Budnik BA, Yates JR, Chait BT, Moffitt JR, Smith RD, Srivastava S. National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions. J Proteome Res 2020; 19:1900-1912. [PMID: 32163288 DOI: 10.1021/acs.jproteome.0c00021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A Think-Tank Meeting was convened by the National Cancer Institute (NCI) to solicit experts' opinion on the development and application of multiomic single-cell analyses, and especially single-cell proteomics, to improve the development of a new generation of biomarkers for cancer risk, early detection, diagnosis, and prognosis as well as to discuss the discovery of new targets for prevention and therapy. It is anticipated that such markers and targets will be based on cellular, subcellular, molecular, and functional aberrations within the lesion and within individual cells. Single-cell proteomic data will be essential for the establishment of new tools with searchable and scalable features that include spatial and temporal cartographies of premalignant and malignant lesions. Challenges and potential solutions that were discussed included (i) The best way/s to analyze single-cells from fresh and preserved tissue; (ii) Detection and analysis of secreted molecules and from single cells, especially from a tissue slice; (iii) Detection of new, previously undocumented cell type/s in the premalignant and early stage cancer tissue microenvironment; (iv) Multiomic integration of data to support and inform proteomic measurements; (v) Subcellular organelles-identifying abnormal structure, function, distribution, and location within individual premalignant and malignant cells; (vi) How to improve the dynamic range of single-cell proteomic measurements for discovery of differentially expressed proteins and their post-translational modifications (PTM); (vii) The depth of coverage measured concurrently using single-cell techniques; (viii) Quantitation - absolute or semiquantitative? (ix) Single methodology or multiplexed combinations? (x) Application of analytical methods for identification of biologically significant subsets; (xi) Data visualization of N-dimensional data sets; (xii) How to construct intercellular signaling networks in individual cells within premalignant tumor microenvironments (TME); (xiii) Associations between intrinsic cellular processes and extrinsic stimuli; (xiv) How to predict cellular responses to stress-inducing stimuli; (xv) Identification of new markers for prediction of progression from precursor, benign, and localized lesions to invasive cancer, based on spatial and temporal changes within individual cells; (xvi) Identification of new targets for immunoprevention or immunotherapy-identification of neoantigens and surfactome of individual cells within a lesion.
Collapse
Affiliation(s)
- Jacob Kagan
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington, United States
| | - Richard Mazurchuk
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| | - Je Hyuk Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States
| | - Peter Vasili Kharchenko
- Blavatnik Institute for Biomedical Information, Harvard Medical School, Boston, Massachusetts, United States
| | | | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States
| | - Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Fiona Ginty
- Life Sciences and Molecular Diagnostics Laboratory, GE Global Research Center, Niskayuna, New York, United States
| | - Yury Goltsev
- Department of Microbiology and Immunology, Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford Medical School, Stanford, California, United States
| | - James A Wells
- Department of Pharmaceutical Sciences, University of California, San Francisco, California, United States
| | - John LaCava
- Laboratory of Cellular and Structural Biology, Rockefeller University, New York, New York, United States
| | - Jessica L Riesterer
- Center for Spatial Systems Biomedicine, Oregon Health and Science University, Portland, Oregon, United States
| | - Ronald N Germain
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Mark S Chee
- Encodia, Inc., San Diego, California, United States
| | - Bogdan A Budnik
- Faculty of Arts & Sciences, Division of Science. Harvard University, Boston, Massachusetts, United States
| | - John R Yates
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, California, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, United States
| | - Jeffery R Moffitt
- Boston Children's Hospital and Harvard University Medical School, Boston, Massachusetts, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Sudhir Srivastava
- Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States
| |
Collapse
|
32
|
Tanaka A, Zhou Y, Shia J, Ginty F, Ogawa M, Klimstra DS, Hendrickson RC, Wang JY, Roehrl MH. Prolyl 4-hydroxylase alpha 1 protein expression risk-stratifies early stage colorectal cancer. Oncotarget 2020; 11:813-824. [PMID: 32166002 PMCID: PMC7055541 DOI: 10.18632/oncotarget.27491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent and lethal malignancies. Especially for early stage CRC, prognostic molecular markers are needed to guide therapy. In this study, we first extracted total proteomes from matched pairs of fresh cancer and benign mucosal tissues from 22 CRC patients. Global proteomic profiling with Fourier transform liquid chromatography-mass spectrometry sequencing and label free quantitation uncovered that P4HA1 (prolyl 4-hydroxylase alpha 1) was overexpressed in CRC relative to benign colonic mucosa. We then investigated expression by immunohistochemical staining with P4HA1-specific antibodies using CRC tissue microarrays. Independent validation cohorts of 599 cases of early stage CRC and 91 cases of late stage CRC were examined. Multivariate and univariate survival analyses revealed that high expression of P4HA1 protein was an independent poor prognostic marker for patients with early stage CRC, especially of the microsatellite stable subtype. Our study provides strong support for P4HA1 as a predictive protein marker for precision diagnostics, therapeutic decision-making, and drug development for early stage colorectal cancer and demonstrates the utility of proteomic profiling to identify novel protein biomarkers.
Collapse
Affiliation(s)
- Atsushi Tanaka
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yihua Zhou
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- ICU Department, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fiona Ginty
- GE Global Research Center, Niskayuna, NY, USA
| | - Makiko Ogawa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David S. Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronald C. Hendrickson
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Michael H. Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
33
|
Xavier JB, Young VB, Skufca J, Ginty F, Testerman T, Pearson AT, Macklin P, Mitchell A, Shmulevich I, Xie L, Caporaso JG, Crandall KA, Simone NL, Godoy-Vitorino F, Griffin TJ, Whiteson KL, Gustafson HH, Slade DJ, Schmidt TM, Walther-Antonio MRS, Korem T, Webb-Robertson BJM, Styczynski MP, Johnson WE, Jobin C, Ridlon JM, Koh AY, Yu M, Kelly L, Wargo JA. The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View. Trends Cancer 2020; 6:192-204. [PMID: 32101723 PMCID: PMC7098063 DOI: 10.1016/j.trecan.2020.01.004] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/29/2019] [Accepted: 01/06/2020] [Indexed: 02/06/2023]
Abstract
The collection of microbes that live in and on the human body - the human microbiome - can impact on cancer initiation, progression, and response to therapy, including cancer immunotherapy. The mechanisms by which microbiomes impact on cancers can yield new diagnostics and treatments, but much remains unknown. The interactions between microbes, diet, host factors, drugs, and cell-cell interactions within the cancer itself likely involve intricate feedbacks, and no single component can explain all the behavior of the system. Understanding the role of host-associated microbial communities in cancer systems will require a multidisciplinary approach combining microbial ecology, immunology, cancer cell biology, and computational biology - a systems biology approach.
Collapse
Affiliation(s)
- Joao B Xavier
- Program for Computational and Systems Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, The University of Michigan Medical School, Ann Arbor, MI, USA
| | - Joseph Skufca
- Department of Mathematics, Clarkson University, Potsdam, NY, USA
| | | | - Traci Testerman
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA
| | - Alexander T Pearson
- Section of Hematology/Oncology, Department of Medicine, Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, IL, USA
| | - Paul Macklin
- Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA
| | - Amir Mitchell
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | | | - Lei Xie
- Hunter College, Department of Computer Science, New York, NY, USA
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Keith A Crandall
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA
| | - Nicole L Simone
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Katrine L Whiteson
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Heather H Gustafson
- Seattle Children's Research Institute, Ben Towne Center for Childhood Cancer Research, Seattle, WA, USA
| | - Daniel J Slade
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | | | - Marina R S Walther-Antonio
- Department of Surgery, Department of Obstetrics and Gynecology, and Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Tal Korem
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Mark P Styczynski
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - W Evan Johnson
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Christian Jobin
- Departments of Medicine, Anatomy, and Cell Biology, and of Infectious Diseases and Immunology, University of Florida, Gainesville, FL, USA
| | - Jason M Ridlon
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andrew Y Koh
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael Yu
- Toyota Technological Institute at Chicago, Chicago, IL, USA
| | | | - Jennifer A Wargo
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| |
Collapse
|
34
|
Berens ME, Sood A, Barnholtz-Sloan JS, Graf JF, Cho S, Kim S, Kiefer J, Byron SA, Halperin RF, Nasser S, Adkins J, Cuyugan L, Devine K, Ostrom Q, Couce M, Wolansky L, McDonough E, Schyberg S, Dinn S, Sloan AE, Prados M, Phillips JJ, Nelson SJ, Liang WS, Al-Kofahi Y, Rusu M, Zavodszky MI, Ginty F. Multiscale, multimodal analysis of tumor heterogeneity in IDH1 mutant vs wild-type diffuse gliomas. PLoS One 2019; 14:e0219724. [PMID: 31881020 PMCID: PMC6934292 DOI: 10.1371/journal.pone.0219724] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022] Open
Abstract
Glioma is recognized to be a highly heterogeneous CNS malignancy, whose diverse cellular composition and cellular interactions have not been well characterized. To gain new clinical- and biological-insights into the genetically-bifurcated IDH1 mutant (mt) vs wildtype (wt) forms of glioma, we integrated data from protein, genomic and MR imaging from 20 treatment-naïve glioma cases and 16 recurrent GBM cases. Multiplexed immunofluorescence (MxIF) was used to generate single cell data for 43 protein markers representing all cancer hallmarks, Genomic sequencing (exome and RNA (normal and tumor) and magnetic resonance imaging (MRI) quantitative features (protocols were T1-post, FLAIR and ADC) from whole tumor, peritumoral edema and enhancing core vs equivalent normal region were also collected from patients. Based on MxIF analysis, 85,767 cells (glioma cases) and 56,304 cells (GBM cases) were used to generate cell-level data for 24 biomarkers. K-means clustering was used to generate 7 distinct groups of cells with divergent biomarker profiles and deconvolution was used to assign RNA data into three classes. Spatial and molecular heterogeneity metrics were generated for the cell data. All features were compared between IDH mt and IDHwt patients and were finally combined to provide a holistic/integrated comparison. Protein expression by hallmark was generally lower in the IDHmt vs wt patients. Molecular and spatial heterogeneity scores for angiogenesis and cell invasion also differed between IDHmt and wt gliomas irrespective of prior treatment and tumor grade; these differences also persisted in the MR imaging features of peritumoral edema and contrast enhancement volumes. A coherent picture of enhanced angiogenesis in IDHwt tumors was derived from multiple platforms (genomic, proteomic and imaging) and scales from individual proteins to cell clusters and heterogeneity, as well as bulk tumor RNA and imaging features. Longer overall survival for IDH1mt glioma patients may reflect mutation-driven alterations in cellular, molecular, and spatial heterogeneity which manifest in discernable radiological manifestations.
Collapse
Affiliation(s)
- Michael E. Berens
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
- * E-mail: (MEB); (AS); (FG)
| | - Anup Sood
- GE Research Center, Niskayuna, NY, United States of America
- * E-mail: (MEB); (AS); (FG)
| | - Jill S. Barnholtz-Sloan
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - John F. Graf
- GE Research Center, Niskayuna, NY, United States of America
| | - Sanghee Cho
- GE Research Center, Niskayuna, NY, United States of America
| | - Seungchan Kim
- Department of Electrical and Computer Engineering, Roy G. Perry College of Engineering, Prairie View A&M University, Prairie View, TX, United States of America
| | - Jeffrey Kiefer
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Sara A. Byron
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Rebecca F. Halperin
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Sara Nasser
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Jonathan Adkins
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Lori Cuyugan
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Karen Devine
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Quinn Ostrom
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Marta Couce
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | - Leo Wolansky
- Department of Population and Quantitative Health Sciences and Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, United States of America
| | | | | | - Sean Dinn
- GE Research Center, Niskayuna, NY, United States of America
| | - Andrew E. Sloan
- Department of Neurosurgery, University Hospitals-Seidman Cancer Center, Cleveland, OH, United States of America
| | - Michael Prados
- Department of Neurological Surgery, Helen Diller Cancer Center, University of California San Francisco, San Francisco, CA, United States of America
| | - Joanna J. Phillips
- Department of Neurological Surgery, Helen Diller Cancer Center, University of California San Francisco, San Francisco, CA, United States of America
| | - Sarah J. Nelson
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, United States of America
| | - Winnie S. Liang
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | | | - Mirabela Rusu
- GE Research Center, Niskayuna, NY, United States of America
| | | | - Fiona Ginty
- GE Research Center, Niskayuna, NY, United States of America
- * E-mail: (MEB); (AS); (FG)
| |
Collapse
|
35
|
McDonough E, Sood A, Ginty F, Cho S, Graf J, Prehn J, Dunne P, Lindner A, Salvucci M, Longley D, Lawler M, Hollmann T, Shia J. Abstract A039: Lower cellular activation of cMET signaling network is associated with reduced recurrence risk in stage II colorectal cancer. Mol Cancer Ther 2019. [DOI: 10.1158/1535-7163.targ-19-a039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Colorectal cancer (CRC) has one of the highest worldwide incidences and mortality rates. About 25% of stage II patients develop recurrence within 5 years. However, use of adjuvant chemotherapy yields minimal therapeutic benefit. Clinical decision-making in this population would be informed by prognostic and predictive biomarkers that help indicate more targeted interventions and/or intensified disease monitoring. Higher cMET expression has been shown to be a prognostic marker in CRC and has been evaluated as a drug target in several cancers, including CRC. cMET acts as the receptor for hepatocyte growth factor (HGF), and is associated with increased proliferation, migration and morphogenesis of epithelial cells via activation of multiple downstream pathways including PI3K/AKT, MAPK and the NF-kB pathways. Here, we investigated whether increased cellular expression of multiple markers in the cMET/adjacent pathways was correlated with clinical outcome. The study population consisted of 283 patients with stage II CRC, without neoadjuvant treatment. Using a multiplexed immunofluorescence method (MxIF) with cell-level quantification (Cell DIVETM, GE Healthcare), 41 biomarkers in the cMET, mTOR, MAPK and associated pathways, and lymphocyte markers were analyzed in an iterative sequence of staining, imaging and dye inactivation, followed by image registration, cell segmentation and biomarker intensity-quantitation. Poor quality images and cells were filtered based on poor segmentation and tissue quality following manual review. Images that did not perfectly register were also excluded. For epithelial cell analysis, all stromal cells were filtered, resulting in a total of 559,952 epithelial cells. K-means clustering was conducted on cMET and related pathways (cMET, pGSK3β, 4EBP1, p4EBP1, S6, pS6, pStat3, pp38MAPK, pNFkBp65, pNFkBp105, EGFR, pERK1/2, HER2, IGF1R, CA-IX, Glut1, SLC7A5 and Ki67). Cluster analysis identified 6 cell clusters with varying expression levels of cMET and other pathway markers. A cluster corresponding to low cMET network activation (cMETLow) was correlated with reduced risk of recurrence (cox pH model Likelihood ratio test p-value = 0.056). Furthermore, MMR proficient patients (who had a higher recurrence rate) had a significantly greater proportion of cells with elevated cMET and related pathway marker (cMETHigh) s(p= 0.007). They also had a significantly lower fraction of infiltrating helper T cells (CD3+CD4+, pvalue 0.076) and CD68+ cells in the epithelial region, compared to MMR deficient patients (p=0.005). Further research will include continuing in-depth analysis of MMR status, cMET pathway and lymphocyte response as well as the role of cellular heterogeneity. In summary, comprehensive cMET pathway analysis using a multiplexed single cell approach indicates for the first time an association between low cMET network activation and superior clinical outcomes.
Citation Format: Elizabeth McDonough, Anup Sood, Fiona Ginty, Sanghee Cho, John Graf, Jochen Prehn, Philip Dunne, Andreas Lindner, Manuela Salvucci, Daniel Longley, Mark Lawler, Travis Hollmann, Jinru Shia. Lower cellular activation of cMET signaling network is associated with reduced recurrence risk in stage II colorectal cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A039. doi:10.1158/1535-7163.TARG-19-A039
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Jinru Shia
- 4Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
36
|
Rajan A, Heery CR, Thomas A, Mammen AL, Perry S, O'Sullivan Coyne G, Guha U, Berman A, Szabo E, Madan RA, Ballester LY, Pittaluga S, Donahue RN, Tsai YT, Lepone LM, Chin K, Ginty F, Sood A, Hewitt SM, Schlom J, Hassan R, Gulley JL. Efficacy and tolerability of anti-programmed death-ligand 1 (PD-L1) antibody (Avelumab) treatment in advanced thymoma. J Immunother Cancer 2019; 7:269. [PMID: 31639039 PMCID: PMC6805423 DOI: 10.1186/s40425-019-0723-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/28/2019] [Indexed: 12/11/2022] Open
Abstract
Background Thymic epithelial tumors are PD-L1–expressing tumors of thymic epithelial origin characterized by varying degrees of lymphocytic infiltration and a predisposition towards development of paraneoplastic autoimmunity. PD-1–targeting antibodies have been evaluated, largely in patients with thymic carcinoma. We sought to evaluate the efficacy and safety of the anti-PD-L1 antibody, avelumab (MSB0010718C), in patients with relapsed, advanced thymic epithelial tumors and conduct correlative immunological studies. Methods Seven patients with thymoma and one patient with thymic carcinoma were enrolled in a phase I, dose-escalation trial of avelumab (MSB0010718C), and treated with avelumab at doses of 10 mg/kg to 20 mg/kg every 2 weeks until disease progression or development of intolerable side effects. Tissue and blood immunological analyses were conducted. Results Two of seven (29%) patients with thymoma had a confirmed Response Evaluation Criteria in Solid Tumors–defined partial response, two (29%) had an unconfirmed partial response and three patients (two thymoma; one thymic carcinoma) had stable disease (43%). Three of four responses were observed after a single dose of avelumab. All responders developed immune-related adverse events that resolved with immunosuppressive therapy. Only one of four patients without a clinical response developed immune-related adverse events. Responders had a higher absolute lymphocyte count, lower frequencies of B cells, regulatory T cells, conventional dendritic cells, and natural killer cells prior to therapy. Conclusion These results demonstrate anti-tumor activity of PD-L1 inhibition in patients with relapsed thymoma accompanied by a high frequency of immune-related adverse events. Pre-treatment immune cell subset populations differ between responders and non-responders. Trial registration ClinicalTrials.gov - NCT01772004. Date of registration – January 21, 2013. Electronic supplementary material The online version of this article (10.1186/s40425-019-0723-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Arun Rajan
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10-CRC, Room 4-5330, 10 Center Drive, Bethesda, MD, 20892, USA.
| | - Christopher R Heery
- Laboratory of Tumor Immunology and Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Anish Thomas
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10-CRC, Room 4-5330, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Andrew L Mammen
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Susan Perry
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10-CRC, Room 4-5330, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Geraldine O'Sullivan Coyne
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., 13N240, Bethesda, MD, 20892, USA
| | - Udayan Guha
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10-CRC, Room 4-5330, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Arlene Berman
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10-CRC, Room 4-5330, 10 Center Drive, Bethesda, MD, 20892, USA
| | - Eva Szabo
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10-CRC, Room 4-5330, 10 Center Drive, Bethesda, MD, 20892, USA.,Lung and Upper Aerodigestive Cancer Research Group, Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ravi A Madan
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., 13N240, Bethesda, MD, 20892, USA
| | - Leomar Y Ballester
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Renee N Donahue
- Laboratory of Tumor Immunology and Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yo-Ting Tsai
- Laboratory of Tumor Immunology and Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lauren M Lepone
- Laboratory of Tumor Immunology and Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Fiona Ginty
- GE Global Research Center, Niskayuna, NY, USA
| | - Anup Sood
- GE Global Research Center, Niskayuna, NY, USA
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey Schlom
- Laboratory of Tumor Immunology and Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raffit Hassan
- Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10-CRC, Room 4-5330, 10 Center Drive, Bethesda, MD, 20892, USA
| | - James L Gulley
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., 13N240, Bethesda, MD, 20892, USA.
| |
Collapse
|
37
|
Uttam S, Stern AM, Furman SA, Pullara F, Ginty F, Taylor DL, Chennubhotla SC. Abstract 1642: Spatial proteomics with hyperplexed fluorescence imaging predicts risk of colorectal cancer recurrence and infers recurrence-specific protein-protein networks. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Colorectal cancer (CRC) is the third leading cause of cancer related deaths in United States with recurrence after resection-with-a-curative-intent being frequently implicated in these deaths. The basis for CRC recurrence is not completely understood, is multifactorial, and involves dysregulation of heterocellular signaling among tumor cells and their microenvironment. Based on hyperplexed immunofluorescence imaging and novel computational analyses, we have developed a recurrence-risk prediction method that samples these signaling networks within the epithelial and stromal domains of the tumor microenvironment and provides improved performance over current state-of-the-art recurrence-risk prediction assays.
Data: In the retrospective study presented here, we used 52 hyperplexed immunofluorescence biomarkers associated with either canonical oncogenic pathways, immune response, or colon cancer per se to spatially profile tissue microarrays obtained from resected tissue samples from 432 chemo-naïve CRC patients.
Results: Using epithelial- and stromal-domain expression and co-expression diversity of the biomarkers, our preliminary results predicted the risk of CRC recurrence with a concordance index of 0.91. We also generated training and validation sets from the CRC patient cohort and demonstrated that the area under the curve (AUC) of the prediction receiver operating characteristic (ROC) was 0.90. We utilized stratified bootstrapping to show that the AUC was stable with a standard deviation of 0.02. Significantly, the penalized model selection used within our method allowed us to infer epithelial and stromal-domain protein networks specific to the risk-of-recurrence from the underlying signaling networks. Despite the limited sampling intrinsic to tissue microarrays we were able to capture immune cell infiltration and the differential modulation of these outcome specific protein-protein networks.
Conclusions: Our CRC recurrence-risk prediction method exploits our spatial proteomics computational pathology platform involving hyperplexed immunofluorescence imaging. This study demonstrates the potential of this paradigm to not only accurately predict risk of CRC recurrence but also to reveal the underlying systems pathophysiology. Inferring outcome- and domain-specific CRC protein networks will enable biomarkers mechanistically linked to disease progression to be determined and their causality corroborated. In turn, this knowledge can be used to inform optimal therapeutic strategies for individual patients.
Citation Format: Shikhar Uttam, Andrew M. Stern, Samantha A. Furman, Filippo Pullara, Fiona Ginty, D. Lansing Taylor, S. Chakra Chennubhotla. Spatial proteomics with hyperplexed fluorescence imaging predicts risk of colorectal cancer recurrence and infers recurrence-specific protein-protein networks [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1642.
Collapse
Affiliation(s)
| | | | | | | | - Fiona Ginty
- 2General Electric Global Research, Niskayuna, NY
| | | | | |
Collapse
|
38
|
Yan Y, Leontovich AA, Gerdes MJ, Desai K, Dong J, Sood A, Santamaria-Pang A, Mansfield AS, Chadwick C, Zhang R, Nevala WK, Flotte TJ, Ginty F, Markovic SN. Understanding heterogeneous tumor microenvironment in metastatic melanoma. PLoS One 2019; 14:e0216485. [PMID: 31166985 PMCID: PMC6550385 DOI: 10.1371/journal.pone.0216485] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/22/2019] [Indexed: 01/05/2023] Open
Abstract
A systemic analysis of the tumor-immune interactions within the heterogeneous tumor microenvironment is of particular importance for understanding the antitumor immune response. We used multiplexed immunofluorescence to elucidate cellular spatial interactions and T-cell infiltrations in metastatic melanoma tumor microenvironment. We developed two novel computational approaches that enable infiltration clustering and single cell analysis-cell aggregate algorithm and cell neighborhood analysis algorithm-to reveal and to compare the spatial distribution of various immune cells relative to tumor cell in sub-anatomic tumor microenvironment areas. We showed that the heterogeneous tumor human leukocyte antigen-1 expressions differently affect the magnitude of cytotoxic T-cell infiltration and the distributions of CD20+ B cells and CD4+FOXP3+ regulatory T cells within and outside of T-cell infiltrated tumor areas. In a cohort of 166 stage III melanoma samples, high tumor human leukocyte antigen-1 expression is required but not sufficient for high T-cell infiltration, with significantly improved overall survival. Our results demonstrate that tumor cells with heterogeneous properties are associated with differential but predictable distributions of immune cells within heterogeneous tumor microenvironment with various biological features and impacts on clinical outcomes. It establishes tools necessary for systematic analysis of the tumor microenvironment, allowing the elucidation of the "homogeneous patterns" within the heterogeneous tumor microenvironment.
Collapse
Affiliation(s)
- Yiyi Yan
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Alexey A. Leontovich
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Michael J. Gerdes
- Diagnostics, Imaging and Biomedical Technologies, GE Global Research Center, Niskayuna, New York, United States of America
| | - Keyur Desai
- Diagnostics, Imaging and Biomedical Technologies, GE Global Research Center, Niskayuna, New York, United States of America
| | - Jinhong Dong
- Clinical Immunology and Immunotherapeutics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Anup Sood
- Diagnostics, Imaging and Biomedical Technologies, GE Global Research Center, Niskayuna, New York, United States of America
| | - Alberto Santamaria-Pang
- Diagnostics, Imaging and Biomedical Technologies, GE Global Research Center, Niskayuna, New York, United States of America
| | - Aaron S. Mansfield
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Chrystal Chadwick
- Diagnostics, Imaging and Biomedical Technologies, GE Global Research Center, Niskayuna, New York, United States of America
| | - Rong Zhang
- Diagnostics, Imaging and Biomedical Technologies, GE Global Research Center, Niskayuna, New York, United States of America
| | - Wendy K. Nevala
- Division of Hematology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Thomas J. Flotte
- Division of Anatomic Pathology and Division of Dermatopathology and Cutaneous Immunopathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Fiona Ginty
- Diagnostics, Imaging and Biomedical Technologies, GE Global Research Center, Niskayuna, New York, United States of America
| | - Svetomir N. Markovic
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota, United States of America
- * E-mail:
| |
Collapse
|
39
|
Badve SS, Cho S, Gokmen-Polar Y, Zavodszky M, Sui Y, Chadwick C, Tan PH, Gerdes M, Harris AL, Ginty F. Abstract P4-08-17: Expression score (Escore) for the prediction of likelihood of recurrence of DCIS. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p4-08-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Ductal carcinoma in situ (DCIS) accounts for at least 20% of breast cancers. Factors associated with recurrence of DCIS or progression to invasive carcinoma are not well delineated. The goals of the current study were to profile the epithelial cells using the GE Cell DIVE™ immuno-fluorescent based analyses. This was coupled with semi-automated algorithms to characterize the inter-relationships between cell populations and likelihood of recurrence.
Patients and Methods: A TMA-based (total 8 TMAs) cohort of cases of DCIS with and without recurrence was obtained from Oxford University. Recurrence in this cohort was defined as ipsilateral DCIS, ipsilateral invasive, contralateral invasive and metastatic. Analysis for 31 epithelial markers (HER4, CK56, ABCG2, PTEN, S6, CKAE1, PR, ER, NaKATPase, CK19, ALDH1, CK PCK26, cMET, CD44v6, HER2, CDCP1, p53, CK15, COX2, VEGFR2, ABCb1, HTF9C, CD10, MRP4, CEACAM5, EGFR, p21, MRP5, SLC7A5, Ki67, DAPI) was performed on a single FFPE TMA section containing cases of DCIS. Briefly, FFPE sections from TMAs containing DCIS were sequentially (cyclically) stained for the markers. Each cycle entailed staining with 2-3 markers followed by imaging, dye inactivation, and re-staining. DAPI was used for nuclear demarcation and for registration of the images, while S6, pan-cadherin, Na+K+ATPase and pan-cytokeratin were used for epithelial segmentation. K-means clustering followed regression analysis was performed to identify inter-relationships between markers and association with likelihood of recurrence. Log-rank analysis was performed and the relapse-free survival data depicted using Kaplan Meier plots. Escore was developed by logistic regression model, classification model on recurrence
Results: Filtering of the expression analysis by the quality, specificity, compartment localization and fields entirely composed of DCIS, in addition to availability of clinical data resulted final analysis of 31 markers in 67 cases. Correlation analyses were performed on each of the markers to identify markers that were significantly correlated in univariate analysis. K-means cluster analysis was performed using a set of 4 markers (ER, HER2, SLC7A5 and cMET) to identify 6 clusters. High cMET (cluster 1; low HER2 and SLC7A5) and High ER (low cMET, HER2, SLC7A5; Cluster 5) were associated with low risk of recurrence (p values 0.014 and <0.0001). In contrast, Cluster 2 (High HER2, high SLC7A5, low ER) and Cluster 3 (High HER2, low ER, SLC7A5and cMET) were associated with increased risk of recurrence (P values 0.038 and 0.076). A regression analysis based algorithm was developed using these markers to calculate a numerical score which could predict likelihood of recurrence. As depicted in the KM plots, the HR for recurrence increases significantly (P-value 2.4E-05; p=0.02 with LOOCV) with increase in expression score (Escore).
Conclusions: We describe the development of an Escore using expression 4 markers to predict likelihood of recurrence. Additional ongoing studies will seek to validate the utility of the Escore in predicting likelihood of recurrence of DCIS and development of invasive carcinomas and comparison with other scoring systems.
Citation Format: Badve SS, Cho S, Gokmen-Polar Y, Zavodszky M, Sui Y, Chadwick C, Tan PH, Gerdes M, Harris AL, Ginty F. Expression score (Escore) for the prediction of likelihood of recurrence of DCIS [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-08-17.
Collapse
Affiliation(s)
- SS Badve
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - S Cho
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - Y Gokmen-Polar
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - M Zavodszky
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - Y Sui
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - C Chadwick
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - PH Tan
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - M Gerdes
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - AL Harris
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| | - F Ginty
- Indiana University, Indianapolis, IN; GE Global Research Center, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore; Oxford University, Oxford, United Kingdom
| |
Collapse
|
40
|
Sood A, Ginty F, Chadwick C, Janz S, Holman C. In Situ Multiplex Immunofluorescence Analysis of Plasma Cell Myeloma Tissue Sections. Am J Clin Pathol 2018. [DOI: 10.1093/ajcp/aqy112.375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Anup Sood
- General Electric Global Research Center, Niskayuna, NY
| | - Fiona Ginty
- General Electric Global Research Center, Niskayuna, NY
| | | | - Siegfried Janz
- University of Iowa Carver College of Medicine, Iowa City, IA
| | - Carol Holman
- University of Iowa Carver College of Medicine, Iowa City, IA
| |
Collapse
|
41
|
Berens ME, Barnholtz-Sloan JS, Rusu M, Graf J, Sood A, Cho S, Zavodszky M, Byron S, Halperin R, Fritz Y, Kim S, Ginty F. Abstract 3039: Role of IDH mutation status on molecular and spatial heterogeneity in glial tumors across progression and recurrence. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
We developed and deployed a workflow for generating multi-scale, multiparametric imaging data, feature extraction and/or converting to higher scales which equips multiple analysis approaches to differentiate clinically variable phenotypes of glial tumors. The workflow quantifies spatial heterogeneity (concordance of adjoining cells) and molecular heterogeneity (varied cell states determined by protein abundance) of glial tumors at the genomic, tissue, and medical imaging scales including IDH mutation status and progression/recurrence status. A panel of 24 multiplexed immunofluorescence (MxIF) markers (addressing 9 hallmarks of cancer) was used to profile single cells (in the thousands) in tissue sections from each of 31 glial tumors (ranging from primary grade II to IV, and recurrent grade IV). Pre-resection multi-parameter MR images were feature extracted from discreet habitats (necrosis, enhancing, and edema); whole exome and transcriptome sequencing from bulk viable tumor were analyzed. By MxIF, the various states of individual cells from treatment-naive patient specimens resolved unsupervised into 7 clusters, for which Cluster 2 (including cells from 9 patients) and Cluster 6 (including cells from 8 patients) contained the two larger bundles of patient cases. When separated into IDHmt and IDHwt cases, cells from IDHmt cases frequently contained cell populations dominated by a single cluster (low molecular heterogeneity); cells from cases with IDHwt represented multiple different clusters (high molecular heterogeneity). In grade III astrocytomas, and grade IV recurrent glioblastomas, spatial heterogeneity of the hallmark “inducing angiogenesis” was elevated in the IDHmt tumors compared to IDHwt, while between the same groups, molecular heterogeneity was lower in the IDHmt cases than wild type. Edema from T1w post contrast MR imaging was found to be elevated in IDHwt gliomas relative to IDHmt, while enhancement was reduced in IDHwt compared to IDHmt tumors. The findings demonstrate that IDHmt gliomas, irrespective of grade, show less edema, greater enhancement, and greater spatial heterogeneity of the “inducing angiogenesis” hallmark but lower molecular heterogeneity than IDHwt tumors. Molecular heterogeneity of “cancer invasion” also differed between IDHmt and IDHwt cases. Longer survival duration following diagnosis for patients with IDHmt gliomas may reflect generalized altered molecular and spatial heterogeneity, which is a phenotype evident on medical imaging. [Clinically-annotated specimens originated from the Ohio Brain Tumor Study and the Ivy GBM Clinical Trials Consortium]
Citation Format: Michael E. Berens, Jill S. Barnholtz-Sloan, Miribella Rusu, John Graf, Anup Sood, Sanghee Cho, Maria Zavodszky, Sara Byron, Rebecca Halperin, Yi Fritz, Seungchan Kim, Fiona Ginty. Role of IDH mutation status on molecular and spatial heterogeneity in glial tumors across progression and recurrence [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3039.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Sara Byron
- 1TGen (The Translational Genomics Research Institute), Phoenix, AZ
| | - Rebecca Halperin
- 1TGen (The Translational Genomics Research Institute), Phoenix, AZ
| | - Yi Fritz
- 2Case Western Reserve University Comprehensive Cancer Center, Cleveland, OH
| | | | | |
Collapse
|
42
|
Gerdes MJ, Gökmen-Polar Y, Sui Y, Pang AS, LaPlante N, Harris AL, Tan PH, Ginty F, Badve SS. Single-cell heterogeneity in ductal carcinoma in situ of breast. Mod Pathol 2018; 31:406-417. [PMID: 29148540 PMCID: PMC6192037 DOI: 10.1038/modpathol.2017.143] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 09/06/2017] [Accepted: 09/11/2017] [Indexed: 12/24/2022]
Abstract
Heterogeneous patterns of mutations and RNA expression have been well documented in invasive cancers. However, technological challenges have limited the ability to study heterogeneity of protein expression. This is particularly true for pre-invasive lesions such as ductal carcinoma in situ of the breast. Cell-level heterogeneity in ductal carcinoma in situ was analyzed in a single 5 μm tissue section using a multiplexed immunofluorescence analysis of 11 disease-related markers (EGFR, HER2, HER4, S6, pmTOR, CD44v6, SLC7A5 and CD10, CD4, CD8 and CD20, plus pan-cytokeratin, pan-cadherin, DAPI, and Na+K+ATPase for cell segmentation). Expression was quantified at cell level using a single-cell segmentation algorithm. K-means clustering was used to determine co-expression patterns of epithelial cell markers and immune markers. We document for the first time the presence of epithelial cell heterogeneity within ducts, between ducts and between patients with ductal carcinoma in situ. There was moderate heterogeneity in a distribution of eight clusters within each duct (average Shannon index 0.76; range 0-1.61). Furthermore, within each patient, the average Shannon index across all ducts ranged from 0.33 to 1.02 (s.d. 0.09-0.38). As the distribution of clusters within ducts was uneven, the analysis of eight ducts might be sufficient to represent all the clusters ie within- and between-duct heterogeneity. The pattern of epithelial cell clustering was associated with the presence and type of immune infiltrates, indicating a complex interaction between the epithelial tumor and immune system for each patient. This analysis also provides the first evidence that simultaneous analysis of both the epithelial and immune/stromal components might be necessary to understand the complex milieu in ductal carcinoma in situ lesions.
Collapse
Affiliation(s)
- Michael J Gerdes
- GE Global Research, Diagnostics, Imaging and Biotechnology (DIBT), Niskayuna, NY, USA
| | - Yesim Gökmen-Polar
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yunxia Sui
- GE Global Research, Diagnostics, Imaging and Biotechnology (DIBT), Niskayuna, NY, USA
| | | | | | - Adrian L Harris
- Department of Oncology, Cancer and Haematology Centre, Oxford University, Oxford, UK
| | - Puay-Hoon Tan
- Division of Pathology, Singapore General Hospital, Singapore
| | - Fiona Ginty
- GE Global Research, Diagnostics, Imaging and Biotechnology (DIBT), Niskayuna, NY, USA
| | - Sunil S Badve
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| |
Collapse
|
43
|
Spagnolo DM, Al-Kofahi Y, Zhu P, Lezon TR, Gough A, Stern AM, Lee AV, Ginty F, Sarachan B, Taylor DL, Chennubhotla SC. Platform for Quantitative Evaluation of Spatial Intratumoral Heterogeneity in Multiplexed Fluorescence Images. Cancer Res 2017; 77:e71-e74. [PMID: 29092944 DOI: 10.1158/0008-5472.can-17-0676] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/17/2017] [Accepted: 09/12/2017] [Indexed: 11/16/2022]
Abstract
We introduce THRIVE (Tumor Heterogeneity Research Interactive Visualization Environment), an open-source tool developed to assist cancer researchers in interactive hypothesis testing. The focus of this tool is to quantify spatial intratumoral heterogeneity (ITH), and the interactions between different cell phenotypes and noncellular constituents. Specifically, we foresee applications in phenotyping cells within tumor microenvironments, recognizing tumor boundaries, identifying degrees of immune infiltration and epithelial/stromal separation, and identification of heterotypic signaling networks underlying microdomains. The THRIVE platform provides an integrated workflow for analyzing whole-slide immunofluorescence images and tissue microarrays, including algorithms for segmentation, quantification, and heterogeneity analysis. THRIVE promotes flexible deployment, a maintainable code base using open-source libraries, and an extensible framework for customizing algorithms with ease. THRIVE was designed with highly multiplexed immunofluorescence images in mind, and, by providing a platform to efficiently analyze high-dimensional immunofluorescence signals, we hope to advance these data toward mainstream adoption in cancer research. Cancer Res; 77(21); e71-74. ©2017 AACR.
Collapse
Affiliation(s)
- Daniel M Spagnolo
- Program in Computational Biology, Joint Carnegie Mellon University-University of Pittsburgh, Pittsburgh, Pennsylvania.,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yousef Al-Kofahi
- Software Science and Analytics Organization, GE Global Research Center, Niskayuna, New York
| | - Peihong Zhu
- Software Science and Analytics Organization, GE Global Research Center, Niskayuna, New York
| | - Timothy R Lezon
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Albert Gough
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Andrew M Stern
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Adrian V Lee
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Fiona Ginty
- Biosciences Organization, GE Global Research Center, Niskayuna, New York
| | - Brion Sarachan
- Software Science and Analytics Organization, GE Global Research Center, Niskayuna, New York
| | - D Lansing Taylor
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.,Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania.,University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - S Chakra Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania.
| |
Collapse
|
44
|
Uhlik MT, Liu J, Falcon BL, Iyer S, Stewart J, Celikkaya H, O'Mahony M, Sevinsky C, Lowes C, Douglass L, Jeffries C, Bodenmiller D, Chintharlapalli S, Fischl A, Gerald D, Xue Q, Lee JY, Santamaria-Pang A, Al-Kofahi Y, Sui Y, Desai K, Doman T, Aggarwal A, Carter JH, Pytowski B, Jaminet SC, Ginty F, Nasir A, Nagy JA, Dvorak HF, Benjamin LE. Stromal-Based Signatures for the Classification of Gastric Cancer. Cancer Res 2017; 76:2573-86. [PMID: 27197264 DOI: 10.1158/0008-5472.can-16-0022] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/19/2016] [Indexed: 12/27/2022]
Abstract
Treatment of metastatic gastric cancer typically involves chemotherapy and monoclonal antibodies targeting HER2 (ERBB2) and VEGFR2 (KDR). However, reliable methods to identify patients who would benefit most from a combination of treatment modalities targeting the tumor stroma, including new immunotherapy approaches, are still lacking. Therefore, we integrated a mouse model of stromal activation and gastric cancer genomic information to identify gene expression signatures that may inform treatment strategies. We generated a mouse model in which VEGF-A is expressed via adenovirus, enabling a stromal response marked by immune infiltration and angiogenesis at the injection site, and identified distinct stromal gene expression signatures. With these data, we designed multiplexed IHC assays that were applied to human primary gastric tumors and classified each tumor to a dominant stromal phenotype representative of the vascular and immune diversity found in gastric cancer. We also refined the stromal gene signatures and explored their relation to the dominant patient phenotypes identified by recent large-scale studies of gastric cancer genomics (The Cancer Genome Atlas and Asian Cancer Research Group), revealing four distinct stromal phenotypes. Collectively, these findings suggest that a genomics-based systems approach focused on the tumor stroma can be used to discover putative predictive biomarkers of treatment response, especially to antiangiogenesis agents and immunotherapy, thus offering an opportunity to improve patient stratification. Cancer Res; 76(9); 2573-86. ©2016 AACR.
Collapse
Affiliation(s)
- Mark T Uhlik
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Jiangang Liu
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Beverly L Falcon
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Seema Iyer
- Lilly Research Laboratories, Eli Lilly and Company, New York, New York
| | - Julie Stewart
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Hilal Celikkaya
- Lilly Research Laboratories, Eli Lilly and Company, New York, New York
| | | | | | - Christina Lowes
- General Electric Global Research Center, Niskayuna, New York
| | - Larry Douglass
- Department of Pathology, Wood Hudson Medical Center, Covington, Kentucky
| | - Cynthia Jeffries
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Diane Bodenmiller
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | | | - Anthony Fischl
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Damien Gerald
- Lilly Research Laboratories, Eli Lilly and Company, New York, New York
| | - Qi Xue
- Lilly Research Laboratories, Eli Lilly and Company, New York, New York
| | - Jee-Yun Lee
- Department of Hematology-Oncology, Samsung Medical Center, Seoul, Seoul Korea
| | | | | | - Yunxia Sui
- General Electric Global Research Center, Niskayuna, New York
| | - Keyur Desai
- General Electric Global Research Center, Niskayuna, New York
| | - Thompson Doman
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Amit Aggarwal
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Julia H Carter
- Department of Pathology, Wood Hudson Medical Center, Covington, Kentucky
| | | | - Shou-Ching Jaminet
- Department of Pathology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Fiona Ginty
- General Electric Global Research Center, Niskayuna, New York
| | - Aejaz Nasir
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana
| | - Janice A Nagy
- Department of Pathology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Harold F Dvorak
- Department of Pathology and Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Laura E Benjamin
- Lilly Research Laboratories, Eli Lilly and Company, New York, New York.
| |
Collapse
|
45
|
Sui Y, Rusu M, Shanbhag D, Patil U, Kiefer J, Barnholtz-Sloan J, Berens M, Ginty F, John G, Gupta S, Kodira C, Newberg L, Raghunath S, Sood A, Raghunath S. Abstract 883: Elucidating cancer hallmark context from glioma MR imaging and RNA expression data. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Radiogenomics or radiomics is an emerging field where tumor genomic data is correlated with radiology image features, thereby potentially providing more biological information about the tumor phenotype. A central challenge is the potential for model over-fitting due to analysis of many thousands of genomic data-points with hundreds of corresponding patient image features. Biological interpretation of the imaging feature correlations is also challenged by overlapping pathways and common gene effects. Our goals were: i) to explore correlations between gene expression and corresponding Magnetic Resonance (MR) Apparent Diffusion Coefficient (ADC) derived imaging features in low grade glioma (LGG); ii) to classify significant gene and imaging correlates by cancer hallmark1. RNA expression data from 32 LGG patients were extracted from The Cancer Genome Atlas (TCGA) and matched with corresponding MR image data from The Cancer Imaging Archive (TCIA). Among 32 patients, 18 were males (56%), and ages ranged from 21 to 74 years (mean age 44). Tumor and normal regions in the MR images were annotated by an expert radiologist using ITK-Snap. The normal reference region was used normalize image intensities in corresponding tumor regions. Tumor texture features were computed on ADC Maps at each voxel location within the disease region (including first and second order statistics, Run Length and co-occurrence matrix derived measures features. The voxel features were finally aggregated within the tumor region using statistical measures of mean, variance, median, kurtosis, and skewness. ADC imaging features (n=310) were correlated with each single gene expression value (11614 genes after MAD>0.4 filtering). Only image features and genes with pairwise correlations higher than 0.68 (0.68 is the 3-standard deviation above average correlation) and FDR (False Discovery Rate) <0.1 were used for follow-up analyses. Significant genes and MR image features were aggregated into 3 groups based on gene expression and correlated with cancer hallmarks. Seven Haralick image features (reflecting the average level of image intensity heterogeneity) were independently, significantly correlated with the Angiogenesis Hallmark (FDR all < 0.001). Three Haralick image features (reflecting asymmetric distribution of intensity) were significantly correlated with the Activating Invasion and Metastasis Hallmark (FDR all < 0.001). Validation of these findings in additional LGG cases with additional imaging protocols and features is ongoing. Radiogenomics informed by genomic profiling may usher in processes to infer cancer hallmarks to aid treatment planning and prognosis of glioma patients.1 Hanahan D and Weinberg RA (2011). Hallmarks of cancer: the next generation. Cell 144(5):646-74.
Citation Format: Yunxia Sui, Mirabela Rusu, Dattesh Shanbhag, Uday Patil, Jeffrey Kiefer, Jill Barnholtz-Sloan, Michael Berens, Fiona Ginty, Graf John, Sandeep Gupta, Chinnappa Kodira, Lee Newberg, Sushravya Raghunath, Anup Sood, Sushravya Raghunath. Elucidating cancer hallmark context from glioma MR imaging and RNA expression data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 883. doi:10.1158/1538-7445.AM2017-883
Collapse
|
46
|
Graf J, Rusu M, Sui Y, Shanbhag D, Patil U, Kiefer J, Barnholtz-Sloan J, Berens M, Ginty F, Gupta S, Kodira C, Newberg L, Raghunath S, Sood A. Abstract 882: Interpreting glioma MR imaging and somatic mutations in a cancer hallmark context. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Extracting biologically relevant data from radiology images can enable better monitoring of disease progression and therapy response. The field of radiogenomics is providing new approaches for such genomic/radiology correlations. However, there are several challenges in validation and clinical translation in that few DNA mutations are shared between tumors from different individuals and the differences in scale between imaging and genomic features can limit interpretation of underlying mechanisms. The goals of this work were to i) analyze correlations between low grade glioma (LGG) DNA somatic mutations, using a novel DNA impact scoring approach, and MRI derived imaging features; and ii) to interpret results in context of cancer hallmarks1. Multi-parametric MRI and corresponding DNA data from 32 LGG patients were extracted from The Cancer Genome Atlas (TCGA) and The Cancer Imaging Archive (TCIA). The cohort included 18 males (56%), with mean age of 44 years (range: 21-74 years). An expert radiologist outlined the normal and tumor regions of interest using ITK-Snap tool. The normal region was used as a reference to normalize image intensities in the tumor region. Tumor mean intensity and mean variance were computed from Apparent Diffusion Coefficient (ADC), T1 enhancement ratio (derived from T1 pre- and post- contract MRI), and Fluid-Attenuated Inversion Recovery (FLAIR) images. A novel algorithm was used to compute DNA impact scores for each somatic mutation. The score represents the probability of a DNA variant being pathogenic vs. nonpathogenic. First, the scoring algorithm computes a score for nucleotide base insertions, deletions, or single base changes and then computes the consequence of such changes on amino acid coding, binding sites, splice sites and protein phosphorylation sites. An impact score was then computed based on the individual DNA impact scores of mutations within the gene. Finally, an average DNA impact score was computed at the Cancer Hallmark level using a gene-cancer hallmark map. At gene level, significant positive correlations were found between the ATRX (p=0.0002), TP53 (p=0.02) and ADC mean intensity. At pathway level, regulation of TP53 expression and degradation, and DNA damage response, signal transduction by p53 class mediator, and DNA translocase activity were found to be enriched with genes that correlated with ADC and FLAIR. These pathways also contained genes that were enriched in the following cancer hallmarks: replicative immortality, evading growth suppression and genome instability. The ATRX gene is a member of all three hallmarks and TP53 a member of two. Since ADC is a measure of water diffusion and hence an indirect measure of cellularity, these findings demonstrate that mutations in replication and repair pathways are contributing to imaging features at the tumor level.1 Hanahan, D. and Weinberg, R.A. (2011). Hallmarks of cancer: the next generation. Cell 144(5):646-74.
Citation Format: John Graf, Mirabela Rusu, Yunxia Sui, Dattesh Shanbhag, Uday Patil, Jeffrey Kiefer, Jill Barnholtz-Sloan, Michael Berens, Fiona Ginty, Sandeep Gupta, Chinnappa Kodira, Lee Newberg, Sushravya Raghunath, Anup Sood. Interpreting glioma MR imaging and somatic mutations in a cancer hallmark context [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 882. doi:10.1158/1538-7445.AM2017-882
Collapse
|
47
|
Yan Y, Leontovich A, Flotte T, Gerdes M, Ginty F, Santamaria-Pang A, Sood A, Desai K, Chadwick C, Zhang R, Markovic SN. Abstract A71: Tumor HLA Class I expression influences immune cells infiltration in metastatic melanoma tumor microenvironment. Cancer Immunol Res 2017. [DOI: 10.1158/2326-6074.tumimm16-a71] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The variable clinical success with immune checkpoint inhibitors in the treatment of solid tumors challenges us to further understand the regulatory mechanisms of immune cells infiltration – a critical step of tumor elimination – in a highly heterogenous tumor microenvironment (TME). Systemic analyses of the tumor-immune cell interface and interactions are of particular significance with direct clinical impact. We employed a multiplexed immunofluorescence (MxIF) method, a novel technology that allows in situ quantitative single cell characterization with high order protein multiplexing on whole tumor sections, to elucidate the key components in TME governing the immune cells' composition and function in metastatic melanoma lymph node metastases. Here, we show that the expression of tumor cell Human Leukocyte Antigen 1 (HLA-1) is highly heterogeneous both within the TME and between patients. The level of tumor HLA-1 expression directly correlates with the magnitude of cytotoxic T lymphocytes (CTLs) infiltration in the TME. In addition, decreased tumor HLA-1 expression is associated with accumulation of CD20+ cells at the edge of the tumor as well as an increased population of CD4+FOXP3+ cells. The association between tumor HLA-1 expression and immune cell distribution is highly consistent yet heterogenous across the entire tumor mass. Moreover, using quantitative single cell data, we developed algorithms for computational and spatial modeling of tumor-immune cell interfaces, allowing statistical comparison of cellular interactions in the context of tumor heterogeneity. Spatial analysis demonstrates that tumor HLA-1 expression favors CTL invasion, while lack of tumor HLA-1 expression results in CTL evasion. Furthermore, in a cohort of 166 Stage III melanoma patients, we confirm that CTLs infiltration is only present in regions with high tumor HLA-1 expressions, and that patients with tumors high in both tumor HLA-1 and CTLs have significantly improved progression free survival (PFS) compared with those with tumors low in HLA-1 and/or CTLs. Our study demonstrates that the heterogeneous tumor HLA-1 expression results in various immune cell distribution patterns in the TME, directly contributing to the varied antitumor immunities and ultimately influencing tumor outcomes. As part of the antigen presentation machinery, HLA-1 expression on tumors is necessary for CTLs infiltration and is indispensable for T cell mediated tumor elimination with direct clinical benefits. We also establish a novel platform for visualization and spatial representation of the cellular heterogeneity within the TME, providing data processing and modeling algorithms necessary for understanding the cellular interplay mediating tumor surveillance, which will ultimately improve therapeutic efficacy and clinical outcomes.
Citation Format: Yiyi Yan, Alexey Leontovich, Thomas Flotte, Michael Gerdes, Fiona Ginty, Alberto Santamaria-Pang, Anup Sood, Keyur Desai, Chrystal Chadwick, Rong Zhang, Svetomir N. Markovic. Tumor HLA Class I expression influences immune cells infiltration in metastatic melanoma tumor microenvironment. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2016 Oct 20-23; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2017;5(3 Suppl):Abstract nr A71.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Anup Sood
- 2GE Global Research Center, Niskayuna, NY
| | | | | | - Rong Zhang
- 2GE Global Research Center, Niskayuna, NY
| | | |
Collapse
|
48
|
Badve S, Gökmen-Polar Y, Harris AL, Sui Y, Sevinsky C, Santamaria-Pang A, Ginty F, Tan PH, Gerdes MJ. Abstract P1-06-02: Impact of heterogeneity of DCIS on immune cell infiltrations. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p1-06-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Ductal carcinoma in situ (DCIS) accounts for at least 20% of breast cancers. Factors associated with recurrence of DCIS or progression to invasive carcinoma are not well delineated. The goals of the current study were to profile the epithelial and immune cells using the MultiOmyx hyperplexed immuno-fluorescent based analyses. This was coupled with semi-automated algorithms to characterize the inter-relationships between cell populations within individual DCIS lesions.
Patients and Methods: Analysis for 15 antibody markers (EGFR, Her2, Her4, S6, pMTOR, PCAD, CD44v6, NaKATPase, SLC7A5, CD4, CD8, CD20, CD68, and CD10) was performed on a single FFPE section containing 10-20 distinct ducts from 13 cases of DCIS. Briefly, approximately 40 fields of view (FOV) from digitized sections containing DCIS or normal tissue were sequentially (cyclically) stained for the 15 markers. Each cycle entailed staining with 2-3 markers followed by imaging, dye inactivation, and re-staining. DAPI was used for nuclear demarcation and for registration of the images, while S6, pan-cadherin, Na+K+ATPase and pan-cytokeratin were used for epithelial segmentation. K-means clustering was used to determine patterns of co-expression of markers at the single cell, duct, and patient levels. These clusters were then correlated with immune marker expression by tumor infiltrating lymphocytes (TILs) by marker type (CD4, CD8, and CD20) and tumor compartment (stromal versus intraepithelial).
Results: Analysis of the epithelial component in each of 13 cases of DCIS (n= 415 ducts) revealed 8 distinct expression patterns (clusters) using a panel of 7 markers (EGFR, Her2, Her4, pmTOR, CD44v6, SLC7A5, and CD10). The frequency and distribution of clusters, annotated at the single cell level, showed that 4 DCIS's were dominated (>80%) by a single cell phenotype represented by cluster groups 3 and 7 (high Her2), cluster 6 (High Her4 and SLC7A5 and low Her2), or cluster 4 (non-descript). In 5 pts, the pattern was more heterogeneous consisting of mixture of cell populations with 50-70% of the cells belonging to cluster 1 (moderate to high levels for all markers except EGFR and CD10). The remaining pts had a strong representation of cluster 4 and 5 (CD44v6 and phospho-mTOR) cells. The distribution of both intra-epithelial and stromal TILs in DCIS cases were either consisted of a mixed B-cell (CD20+) and T-cell response (n=4), or one dominated by T-cells. Cluster 2 (High EGFR and CD10) was associated with a largely T-cell response (rs = 0.83, P value = 0.0004), while Cluster 7 (strong HER2) was associated with a B-cell response (rs = 0.68, P value = is 0.009).
Conclusions: Analysis 15 markers and use of K-means clustering algorithm, shows prominent inter-tumoral (but not intra-tumoral) heterogeneity in DCIS. Furthermore, epithelial cell specific clusters (high HER2 or EGFR) were associated with distinct B or T cell infiltration by TILs. Additional ongoing studies will determine the clinical significance of the clusters with respect to recurrence of DCIS and development of invasive carcinomas.
Citation Format: Badve S, Gökmen-Polar Y, Harris AL, Sui Y, Sevinsky C, Santamaria-Pang A, Ginty F, Tan PH, Gerdes MJ. Impact of heterogeneity of DCIS on immune cell infiltrations [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-06-02.
Collapse
Affiliation(s)
- S Badve
- Indiana University School of Medicine, Indianapolis, IN; University of Oxford, Oxford, United Kingdom; GE Global Research, Diagnostic Imaging and Biomedical Technologies, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore
| | - Y Gökmen-Polar
- Indiana University School of Medicine, Indianapolis, IN; University of Oxford, Oxford, United Kingdom; GE Global Research, Diagnostic Imaging and Biomedical Technologies, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore
| | - AL Harris
- Indiana University School of Medicine, Indianapolis, IN; University of Oxford, Oxford, United Kingdom; GE Global Research, Diagnostic Imaging and Biomedical Technologies, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore
| | - Y Sui
- Indiana University School of Medicine, Indianapolis, IN; University of Oxford, Oxford, United Kingdom; GE Global Research, Diagnostic Imaging and Biomedical Technologies, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore
| | - C Sevinsky
- Indiana University School of Medicine, Indianapolis, IN; University of Oxford, Oxford, United Kingdom; GE Global Research, Diagnostic Imaging and Biomedical Technologies, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore
| | - A Santamaria-Pang
- Indiana University School of Medicine, Indianapolis, IN; University of Oxford, Oxford, United Kingdom; GE Global Research, Diagnostic Imaging and Biomedical Technologies, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore
| | - F Ginty
- Indiana University School of Medicine, Indianapolis, IN; University of Oxford, Oxford, United Kingdom; GE Global Research, Diagnostic Imaging and Biomedical Technologies, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore
| | - PH Tan
- Indiana University School of Medicine, Indianapolis, IN; University of Oxford, Oxford, United Kingdom; GE Global Research, Diagnostic Imaging and Biomedical Technologies, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore
| | - MJ Gerdes
- Indiana University School of Medicine, Indianapolis, IN; University of Oxford, Oxford, United Kingdom; GE Global Research, Diagnostic Imaging and Biomedical Technologies, Niskayuna, NY; Singapore General Hospital, Singapore, Singapore
| |
Collapse
|
49
|
Spagnolo DM, Gyanchandani R, Al-Kofahi Y, Stern AM, Lezon TR, Gough A, Meyer DE, Ginty F, Sarachan B, Fine J, Lee AV, Taylor DL, Chennubhotla SC. Pointwise mutual information quantifies intratumor heterogeneity in tissue sections labeled with multiple fluorescent biomarkers. J Pathol Inform 2016; 7:47. [PMID: 27994939 PMCID: PMC5139455 DOI: 10.4103/2153-3539.194839] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 08/09/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Measures of spatial intratumor heterogeneity are potentially important diagnostic biomarkers for cancer progression, proliferation, and response to therapy. Spatial relationships among cells including cancer and stromal cells in the tumor microenvironment (TME) are key contributors to heterogeneity. METHODS We demonstrate how to quantify spatial heterogeneity from immunofluorescence pathology samples, using a set of 3 basic breast cancer biomarkers as a test case. We learn a set of dominant biomarker intensity patterns and map the spatial distribution of the biomarker patterns with a network. We then describe the pairwise association statistics for each pattern within the network using pointwise mutual information (PMI) and visually represent heterogeneity with a two-dimensional map. RESULTS We found a salient set of 8 biomarker patterns to describe cellular phenotypes from a tissue microarray cohort containing 4 different breast cancer subtypes. After computing PMI for each pair of biomarker patterns in each patient and tumor replicate, we visualize the interactions that contribute to the resulting association statistics. Then, we demonstrate the potential for using PMI as a diagnostic biomarker, by comparing PMI maps and heterogeneity scores from patients across the 4 different cancer subtypes. Estrogen receptor positive invasive lobular carcinoma patient, AL13-6, exhibited the highest heterogeneity score among those tested, while estrogen receptor negative invasive ductal carcinoma patient, AL13-14, exhibited the lowest heterogeneity score. CONCLUSIONS This paper presents an approach for describing intratumor heterogeneity, in a quantitative fashion (via PMI), which departs from the purely qualitative approaches currently used in the clinic. PMI is generalizable to highly multiplexed/hyperplexed immunofluorescence images, as well as spatial data from complementary in situ methods including FISSEQ and CyTOF, sampling many different components within the TME. We hypothesize that PMI will uncover key spatial interactions in the TME that contribute to disease proliferation and progression.
Collapse
Affiliation(s)
- Daniel M Spagnolo
- Program in Computational Biology, Joint Carnegie Mellon University-University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Rekha Gyanchandani
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yousef Al-Kofahi
- GE Global Research Center, Diagnostics, Imaging and Biomedical Technologies, Niskayuna, NY, USA
| | - Andrew M Stern
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Timothy R Lezon
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Albert Gough
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Dan E Meyer
- GE Global Research Center, Diagnostics, Imaging and Biomedical Technologies, Niskayuna, NY, USA
| | - Fiona Ginty
- GE Global Research Center, Diagnostics, Imaging and Biomedical Technologies, Niskayuna, NY, USA
| | - Brion Sarachan
- GE Global Research Center, Software Science and Analytics Organization, Niskayuna, NY, USA
| | - Jeffrey Fine
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Adrian V Lee
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania; University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - D Lansing Taylor
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania; Drug Discovery Institute, University of Pittsburgh, Pittsburgh, Pennsylvania; University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - S Chakra Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| |
Collapse
|
50
|
Lee LH, Sadot E, Ivelja S, Vakiani E, Hechtman JF, Sevinsky CJ, Klimstra DS, Ginty F, Shia J. ARID1A expression in early stage colorectal adenocarcinoma: an exploration of its prognostic significance. Hum Pathol 2016; 53:97-104. [PMID: 26980037 PMCID: PMC4994515 DOI: 10.1016/j.humpath.2016.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/23/2016] [Accepted: 02/04/2016] [Indexed: 02/07/2023]
Abstract
ARID1A is a chromatin remodeling gene that is mutated in a number of cancers including colorectal carcinoma (CRC). Loss of ARID1A has been associated with an adverse outcome in some types of cancer. However, literature data have not been consistent. Major limitations of some outcome studies include small sample size and heterogeneous patient population. In this study, we evaluated the prognostic value of ARID1A in a homogeneous group of early stage CRC patients, a population where prognostic markers are particularly relevant. We collected a retrospective series of 578 stage I or II CRCs. All patients underwent surgery with curative intent and without neoadjuvant or adjuvant therapy. ARID1A expression was analyzed by immunohistochemistry using tissue microarray. We found ARID1A loss in 49 of 552 analyzable tumors (8.9%). Compared with the ARID1A-retained group, cases with ARID1A loss were associated with female sex (P<.001), mismatch-repair protein deficiency (P<.001), poor differentiation (P<.001), lymphovascular invasion (P=.001), and higher pT stage (P=.047). However, at a median follow-up of 49months, ARID1A loss did not correlate with overall, disease-specific, or recurrence-free survival. This is the first systematic analysis to evaluate the prognostic significance of ARID1A in stage I/II CRCs, and our data indicate that ARID1A loss lacks prognostic significance in this population despite its association with other adverse features. Such data are clinically relevant, as efforts are ongoing in identifying markers that can detect the small but significant subset of early stage CRCs that will have a poor outcome.
Collapse
Affiliation(s)
- Lik Hang Lee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065.
| | - Eran Sadot
- Department of Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065.
| | - Sinisa Ivelja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065.
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065.
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065.
| | - Christopher J Sevinsky
- Life Sciences & Molecular Diagnostics, GE Global Research, General Electric Company, 1 Research Circle, Niskayuna, NY, 12309.
| | - David S Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065.
| | - Fiona Ginty
- Life Sciences & Molecular Diagnostics, GE Global Research, General Electric Company, 1 Research Circle, Niskayuna, NY, 12309.
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065.
| |
Collapse
|