1
|
Johnson BE, Creason AL, Stommel JM, Keck JM, Parmar S, Betts CB, Blucher A, Boniface C, Bucher E, Burlingame E, Camp T, Chin K, Eng J, Estabrook J, Feiler HS, Heskett MB, Hu Z, Kolodzie A, Kong BL, Labrie M, Lee J, Leyshock P, Mitri S, Patterson J, Riesterer JL, Sivagnanam S, Somers J, Sudar D, Thibault G, Weeder BR, Zheng C, Nan X, Thompson RF, Heiser LM, Spellman PT, Thomas G, Demir E, Chang YH, Coussens LM, Guimaraes AR, Corless C, Goecks J, Bergan R, Mitri Z, Mills GB, Gray JW. An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer. Cell Rep Med 2022; 3:100525. [PMID: 35243422 PMCID: PMC8861971 DOI: 10.1016/j.xcrm.2022.100525] [Citation(s) in RCA: 16] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/15/2021] [Accepted: 01/19/2022] [Indexed: 12/15/2022]
Abstract
Mechanisms of therapeutic resistance and vulnerability evolve in metastatic cancers as tumor cells and extrinsic microenvironmental influences change during treatment. To support the development of methods for identifying these mechanisms in individual people, here we present an omic and multidimensional spatial (OMS) atlas generated from four serial biopsies of an individual with metastatic breast cancer during 3.5 years of therapy. This resource links detailed, longitudinal clinical metadata that includes treatment times and doses, anatomic imaging, and blood-based response measurements to clinical and exploratory analyses, which includes comprehensive DNA, RNA, and protein profiles; images of multiplexed immunostaining; and 2- and 3-dimensional scanning electron micrographs. These data report aspects of heterogeneity and evolution of the cancer genome, signaling pathways, immune microenvironment, cellular composition and organization, and ultrastructure. We present illustrative examples of how integrative analyses of these data reveal potential mechanisms of response and resistance and suggest novel therapeutic vulnerabilities.
Collapse
Affiliation(s)
- Brett E. Johnson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Allison L. Creason
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jayne M. Stommel
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jamie M. Keck
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Swapnil Parmar
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Courtney B. Betts
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Aurora Blucher
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christopher Boniface
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Elmar Bucher
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Erik Burlingame
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Todd Camp
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Koei Chin
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jennifer Eng
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joseph Estabrook
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Heidi S. Feiler
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Michael B. Heskett
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Zhi Hu
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Annette Kolodzie
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ben L. Kong
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Pharmacy Services, Oregon Health & Science University, Portland, OR 97239, USA
| | - Marilyne Labrie
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jinho Lee
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Patrick Leyshock
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Souraya Mitri
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Janice Patterson
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jessica L. Riesterer
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Multiscale Microscopy Core, Oregon Health & Science University, Portland, OR 97239, USA
| | - Shamilene Sivagnanam
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Julia Somers
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, OR 97239, USA
| | - Guillaume Thibault
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Benjamin R. Weeder
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christina Zheng
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Cancer Early Detection Advanced Research Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Reid F. Thompson
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Division of Hospital and Specialty Medicine, VA Portland Healthcare System, Portland, OR 97239, USA
| | - Laura M. Heiser
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Paul T. Spellman
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - George Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Pathology & Laboratory Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Emek Demir
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Lisa M. Coussens
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Alexander R. Guimaraes
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Diagnostic Radiology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Christopher Corless
- Department of Pharmacy Services, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Pathology & Laboratory Medicine, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jeremy Goecks
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| | - Raymond Bergan
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Zahi Mitri
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Medicine, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Gordon B. Mills
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Joe W. Gray
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97239, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA
| |
Collapse
|
2
|
Labrie M, Li A, Creason A, Betts C, Keck J, Johnson B, Sivagnanam S, Boniface C, Ma H, Blucher A, Chang YH, Chin K, Vuky J, Guimaraes AR, Downey M, Lim JY, Gao L, Siex K, Parmar S, Kolodzie A, Spellman PT, Goecks J, Coussens LM, Corless CL, Bergan R, Gray JW, Mills GB, Mitri ZI. Multiomics analysis of serial PARP inhibitor treated metastatic TNBC inform on rational combination therapies. NPJ Precis Oncol 2021; 5:92. [PMID: 34667258 PMCID: PMC8526613 DOI: 10.1038/s41698-021-00232-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 10/08/2020] [Accepted: 09/22/2021] [Indexed: 12/26/2022] Open
Abstract
In a pilot study, we evaluated the feasibility of real-time deep analysis of serial tumor samples from triple negative breast cancer patients to identify mechanisms of resistance and treatment opportunities as they emerge under therapeutic stress engendered by poly-ADP-ribose polymerase (PARP) inhibitors (PARPi). In a BRCA-mutant basal breast cancer exceptional long-term survivor, a striking tumor destruction was accompanied by a marked infiltration of immune cells containing CD8 effector cells, consistent with pre-clinical evidence for association between STING mediated immune activation and benefit from PARPi and immunotherapy. Tumor cells in the exceptional responder underwent extensive protein network rewiring in response to PARP inhibition. In contrast, there were minimal changes in the ecosystem of a luminal androgen receptor rapid progressor, likely due to indifference to the effects of PARP inhibition. Together, identification of PARPi-induced emergent changes could be used to select patient specific combination therapies, based on tumor and immune state changes.
Collapse
Affiliation(s)
- Marilyne Labrie
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA. .,Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR, USA.
| | - Allen Li
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Allison Creason
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA
| | - Courtney Betts
- Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Jamie Keck
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.,Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR, USA
| | - Brett Johnson
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.,Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR, USA.,Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Shamilene Sivagnanam
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.,Computational Biology Program, Oregon Health and Science University, Portland, OR, USA
| | - Christopher Boniface
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Hongli Ma
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.,Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Aurora Blucher
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.,Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Young Hwan Chang
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA.,Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR, USA.,Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Koei Chin
- Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR, USA.,Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Jacqueline Vuky
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Alexander R Guimaraes
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.,Department of Diagnostic Radiology, Oregon Health and Science University, Portland, OR, USA
| | - Molly Downey
- Department of Diagnostic Radiology, Oregon Health and Science University, Portland, OR, USA
| | - Jeong Youn Lim
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Lina Gao
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Kiara Siex
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Swapnil Parmar
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Annette Kolodzie
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.,Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR, USA
| | - Paul T Spellman
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.,Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR, USA.,Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | - Jeremy Goecks
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA
| | - Lisa M Coussens
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.,Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR, USA
| | - Christopher L Corless
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.,Department of Pathology, Oregon Health and Science University, Portland, OR, USA
| | - Raymond Bergan
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Joe W Gray
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.,Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR, USA.,Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.,Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR, USA.,Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zahi I Mitri
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA.
| |
Collapse
|
3
|
Kong BL, Johnson BE, Keck JM, Mitri S, Leyshock P, Stommel JM, Siex K, Klinger M, Zheng CL, Williams-Belizaire R, McWeeney S, Goecks J, Kolodzie A, Guimaraes AR, Thomas GV, Corless CL, Mitri ZI, Gray JW, Mills GB, Bergan RC. Abstract LB010: SMMART Program: A multi-omics tumor board with a focus on breast cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-lb010] [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
Many of the current approaches to personalized medicine rely on sequencing DNA to identify actionable mutations. However, growing evidence suggests that a multi-omic approach to more broadly assess biology is needed to improve patient outcomes. We have implemented a workflow for tissue acquisition, multi-omic clinical testing, and correlated computational biology analysis, within the Serial Measurements of Molecular and Architectural Responses to Therapy (SMMART) Program (Mitri et al, J Transl Med 2018). We report biopsy metrics, CLIA analytics utilized, the operation of a multi-omics tumor board, and clinical outcomes in metastatic breast cancer patients. A detailed clinical history of each patient was obtained, including demographics, tumor type, treatment and response to prior therapies, imaging, and blood tumor biomarkers. A comprehensive set of clinical assays was performed on newly obtained tumor biopsies, including immunohistochemistry (ER, PR, HER2, AR, BCL-2, and PD-L1), a targeted next-generation sequencing panel covering 225 genes (GeneTrails® Comprehensive Solid Tumor Panel), whole exome sequencing (Tempus xE), whole transcriptomic sequencing (Illumina TruSeq RNA exome), and a multiplex protein analysis of 22 key cancer proteins and phosphoproteins on the Nanostring platform (NanoString Vantage 3D™ Solid Tumor Panel). The integrated clinical and analytical information was made available to the multidisciplinary SMMART Clinical Tumor Board that provided treatment recommendations; the final treatment plan was at the discretion of the treating physician. Between 1/1/2017-1/1/2020, 53 breast cancer patients were consented. Seven screen-failed due to a lack of sites amenable to biopsy and 8 were actively co-consented to other clinical trials. The remaining 38 patients are included in this preliminary report. A total of 63 biopsies were collected from lymph node, liver, bone, soft tissue, lung, skin, breast, and brain. Serial biopsies (≥2) were obtained for 15 patients. Analytics were generated in 93.7% of biopsies. Tumor boards were held for 15 patients (17 total sessions). The experience and information gathered thus far have yielded the following unique cases: (1) single patient analysis of omics, imaging, and response over 42 months, (2) identification of an ERBB3 mutation with downstream pathway activation that responded to HER2-targeted therapy, and (3) clinically significant variation in hormonal and HER2 receptor status over time. We will provide an analysis across the 38 patients of treatment outcomes, analytics information content, biological changes observed through serial biopsies, and tumor board interventions. We demonstrate the feasibility of implementing a deep, real-time analytics platform for metastatic breast cancer patients that can provide new insight into therapeutic opportunities. The observed clinical responses support further use and investigation of this approach.
Citation Format: Ben L. Kong, Brett E. Johnson, Jamie M. Keck, Souraya Mitri, Patrick Leyshock, Jayne M. Stommel, Kiara Siex, Marlana Klinger, Christina L. Zheng, Rochelle Williams-Belizaire, Shannon McWeeney, Jeremy Goecks, Annette Kolodzie, Alexander R. Guimaraes, George V. Thomas, Christopher L. Corless, Zahi I. Mitri, Joe W. Gray, Gordon B. Mills, Raymond C. Bergan. SMMART Program: A multi-omics tumor board with a focus on breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB010.
Collapse
Affiliation(s)
- Ben L. Kong
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | - Brett E. Johnson
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | - Jamie M. Keck
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | - Souraya Mitri
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | - Patrick Leyshock
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | - Jayne M. Stommel
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | - Kiara Siex
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | - Marlana Klinger
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | - Christina L. Zheng
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | | | - Shannon McWeeney
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | - Jeremy Goecks
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | - Annette Kolodzie
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | | | - George V. Thomas
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | | | - Zahi I. Mitri
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | - Joe W. Gray
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | - Gordon B. Mills
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| | - Raymond C. Bergan
- Oregon Health & Science University Knight Cancer Institute, Portland, OR
| |
Collapse
|
4
|
Parmar S, Keck JM, Kong B, Look R, Johnson B, Patterson J, Labrie M, Guimaraes AR, Corless CL, Beadling C, Kolodzie A, Bergan R, Gray JW, Mills GB, Mitri ZI. Exceptional Response to Trastuzumab in a Heavily Pretreated Patient With ERBB3-Mutated Metastatic Breast Cancer. JCO Precis Oncol 2021; 5:PO.20.00183. [PMID: 34250408 DOI: 10.1200/po.20.00183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/16/2020] [Accepted: 10/28/2020] [Indexed: 12/13/2022] Open
Affiliation(s)
- Swapnil Parmar
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - Jamie M Keck
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR.,Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR
| | - Ben Kong
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | | | - Brett Johnson
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR.,Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR.,Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR
| | - Janice Patterson
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - Marilyne Labrie
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR.,Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR
| | - Alexander R Guimaraes
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR.,Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR.,Department of Diagnostic Radiology, Oregon Health and Science University, Portland, OR
| | - Christopher L Corless
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR.,Department of Pathology, Oregon Health and Science University, Portland, OR
| | - Carol Beadling
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - Annette Kolodzie
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR.,Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR
| | - Raymond Bergan
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| | - Joe W Gray
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR.,Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, OR.,Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR.,Department of Cell, Developmental & Cancer Biology, Oregon Health and Science University, Portland, OR.,Department of Systems Biology, the University of Texas MD Anderson Cancer Center, Houston, TX
| | - Zahi I Mitri
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR
| |
Collapse
|
5
|
Keck JM, Parmar S, Kong B, Mitri Z, Corless C, Kolodzie A, Creason A, Goecks J, Leyshock P, Siex K, Johnson BE, Patterson J, Heiser L, Olson A, Viehdorfer M, Mayfield G, Laverdure J, Gray JW, Mills GB, Bergan RC. Abstract 4929: Leveraging multi-omics tumor boards for precision medicine in the OHSU SMMART Treatments Program. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4929] [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
Comprehensive characterization of an individual’s cancer using multi-omic analyses and an expanding list of targeted therapies is providing an opportunity to uncover therapeutic vulnerabilities and rationally target multiple driving alterations in the tumor. To leverage this opportunity, a multi-disciplinary team is required to unravel the complexity of tumor behavior and genomic variant information, integrate data from multi-omic assays, and exploit potential synergies from combination therapy while avoiding toxicity, all of which occurs within the context of the patient’s clinical history and comorbidities. We report the preliminary experience of OHSU Knight Cancer Institute’s SMMART (Serial Measurements of Molecular and Architectural Responses to Therapy) Treatments Program Multi-omics Tumor Board (MTB). The role of the SMMART MTB, to date, has been to develop and optimize procedures in a feasibility protocol for future application in the clinical setting where we will provide personalized combinatorial treatment suggestions. Here we report our preliminary experience over the last 15 months with multi-disciplinary tumor boards for metastatic breast cancer. A deep analysis of data, in many cases from serial biopsies, enabled identification of personalized, multi-targeted therapy. Clinical and laboratory data are explored individually and collectively by oncologists, oncology pharmacists, molecular pathologists, cancer biologists, and computational biologists. Data from CLIA-certified analytics include, but are not limited to, a 124 gene targeted panel, whole exome sequencing, MSI, gene-fusion, RNAseq, and clinical IHC assays that provide status information about receptors (ER/PR/AR/HER2), proliferation rate, and tumor immunogenicity along with reflexive assays for expression of relevant proteins such as p16, RB, and PTEN. A customized LabKey® system allows for visual display of a patient’s clinical timeline with information about diagnoses, treatments, biopsies events, radiographic changes, and blood biomarkers; thereby providing MTB participants with a holistic view of the patient’s case summary. Our experience with several example breast cancer case scenarios identified therapeutic vulnerabilities that would not have been considered by a standard clinical tumor board with genomic data alone. Recent cases have included observations such as HER2 status switching, a rare pathogenic germline mutation, high PD-L1 expression, and gained expression of the androgen receptor. These cases further emphasize the value and importance of MTB discussions to oncologists for interpreting and analyzing complex multi-omic data and uncovering therapeutic options for patients. This experience will be utilized in the future for employing SMMART MTBs in a clinical setting as a platform to triage patients into different multi-targeted combinatorial treatment options.
Citation Format: Jamie M. Keck, Swapnil Parmar, Ben Kong, Zahi Mitri, Christopher Corless, Annette Kolodzie, Allison Creason, Jeremy Goecks, Patrick Leyshock, Kiara Siex, Brett E. Johnson, Janice Patterson, Laura Heiser, Anastasiya Olson, Matt Viehdorfer, Georgia Mayfield, Jennifer Laverdure, Joe W. Gray, Gordon B. Mills, Raymond C. Bergan. Leveraging multi-omics tumor boards for precision medicine in the OHSU SMMART Treatments Program [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 4929.
Collapse
Affiliation(s)
| | | | - Ben Kong
- OHSU Knight Cancer Inst., PORTLAND, OR
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Johnson B, Keck J, Morris M, Siex K, Kolodzie A, Parmar S, Riesterer J, Chin K, Gibbs S, Heiser L, Spellman P, Ellrott K, Babur O, Demir E, Margolin A, Goecks J, Coussens L, Bergan R, Gray J. Abstract 3296: SMMART: Serial measurements of molecular and architectural responses to therapy. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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
SMMART is a precision medicine research program focused on understanding the evolution of actionable biology and mechanisms of resistance in human tumors during therapy. This is accomplished through in depth functional, ‘omic and multiscale image analysis of longitudinal samples acquired during treatment. Here we present a case report detailing the insights that can be gained from the comparative analysis of pre- and post-treatment biopsy specimens in a late-stage metastatic breast cancer patient. To understand the molecular evolution of cancer, we interrogated genomics with targeted and whole exome sequencing, transcriptomics with RNA and gene-fusion sequencing, and proteomics with reverse phase protein arrays. To understand cellular organization and architectural changes, we employed multi-scale imaging tools, including scanning electron microscopy (SEM), cyclic immunofluorescence, immune cell profiling with cyclic immunohistochemistry, and traditional pathological assessment. During the course of treatment, we monitored patient response to therapy with clinical imaging, circulating tumor DNA sequencing and cancer protein assessment.
Individual assays revealed key aspects of how this individual's cancer evolved under therapeutic pressure. For example, mutational profiling revealed the patterns of clonal evolution and the acquisition of new genetic driver events. 2D and 3D SEM showed changes in ECM organization, macropinocytosis, mitochondrion size, number and density and number and organization of filopodia-like protrusions. We used a 30-color cyclic immunofluorescence analysis to identify differences in cancer cell proliferation and differentiation state, as well as the composition and organization of infiltrating immune cells. In addition, integrative analyses of multiple data types provided insight into the evolution of actionable biology within this patient's disease. This included changes in the suitability of the patient for immune checkpoint inhibitors as well as specific tyrosine kinase inhibitors. The comprehensive molecular and architectural characterization of an individual patient's cancer at multiple time points provides biologically novel and clinically relevant insight into the ways in which cancers become resistant to treatment.
Citation Format: Brett Johnson, Jamie Keck, Max Morris, Kiara Siex, Annette Kolodzie, Swapnil Parmar, Jessica Riesterer, Koei Chin, Summer Gibbs, Laura Heiser, Paul Spellman, Kyle Ellrott, Ozgun Babur, Emek Demir, Adam Margolin, Jeremy Goecks, Lisa Coussens, Raymond Bergan, Joe Gray. SMMART: Serial measurements of molecular and architectural responses to therapy [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 3296.
Collapse
|