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Mitra A, Somaiah N, Conley AP, Amini B, Lin H, Sanchez BE, Garcia-Prieto C, Mathew G, Bernatchez C, Ravi V, Araujo D, Zarzour MA, Livingston JA, Roland CL, Daw N, Baguley J, Wang WL, Beird H, Tate T, Haymaker C, Little LD, Gumbs C, Song X, Keung EZ, Zhang S, Gite S, Zhang J, Solis L, Tawbi H, Wang L, Patel S, Benjamin RS, Lazar AJ, Wistuba II, Futreal A. Abstract 518: Immunogenomic correlates of response to combination immune checkpoint blockade in advanced sarcoma. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-518] [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
Sarcomas encompass a rare but highly diverse set of tumor malignancies, contributing disproportionately to years of life lost. Immune checkpoint blockade (ICB) has been successful across various tumor types; however, their efficacy and predictability in sarcomas remain unknown. We conducted a translational study using pre- and on-treatment tumor biopsies collected prospectively on a Phase II clinical trial (NCT02815995) evaluating the role of combination anti-PD-L1 and anti-CTLA-4 in 57 patients, enrolled across multiple histologies of metastatic sarcoma. We obtained tumor biopsies at baseline and after 6 weeks of treatment and performed whole-exome, T-cell repertoire (TCR) and RNA-sequencing, along with multiplexed-immunofluorescence (mIF).We deconvoluted substantial variability present in the tumor microenvironment (TME) within sarcomas and found instances of relatively inflamed tumors which failed to respond to ICB. However, amongst those potential molecular correlates of response analyzed, elevated levels of B-cells both at the transcriptome and through validation staining (p = 0.047 and p = 0.022) were most significantly correlated with response. In order to gain more insight into the phenotype and function of B-cells in contributing to response, we inferred BCR-templates and found higher levels of both IGH and IGL diversity (p = 0.0276 and p = 0. 0889 respectively) in responders to ICB. Additionally, we detected increased levels of hyperexpanded IGH clones at the on-treatment time point in patients that responded to therapy (p = 0.048). This B-cell enrichment was validated and found to be predictive of response (p = 0.043) in an independent sarcoma anti-PD-1 treated cohort with matched molecular data. Responsive tumors were also associated with higher levels of TCR richness indicating a strong association of diversity in the TCR of responders (p = 0.047). This work demonstrates the potential for multi-lineage immune cell enrichment and frames the potential molecular features of the TME that may influence response in ICB treated sarcomas.
Citation Format: Akash Mitra, Neeta Somaiah, Anthony P. Conley, Behrang Amini, Heather Lin, Beatriz E. Sanchez, Celia Garcia-Prieto, Grace Mathew, Chantale Bernatchez, Vinod Ravi, Dejka Araujo, Maria A. Zarzour, John A. Livingston, Christina L. Roland, Najat Daw, Joshua Baguley, Wei-Lien Wang, Hannah Beird, Taylor Tate, Cara Haymaker, Latasha D. Little, Curtis Gumbs, Xingshi Song, Emily Z. Keung, Shaojun Zhang, Swati Gite, Jianhua Zhang, Luisa Solis, Hussein Tawbi, Linghua Wang, Shreyaskumar Patel, Robert S. Benjamin, Alexander J. Lazar, Ignacio I. Wistuba, Andrew Futreal. Immunogenomic correlates of response to combination immune checkpoint blockade in advanced sarcoma [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 518.
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Affiliation(s)
- Akash Mitra
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Neeta Somaiah
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Behrang Amini
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Heather Lin
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Grace Mathew
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Vinod Ravi
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Dejka Araujo
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Najat Daw
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Joshua Baguley
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wei-Lien Wang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hannah Beird
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Taylor Tate
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Cara Haymaker
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Curtis Gumbs
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xingshi Song
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Emily Z. Keung
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shaojun Zhang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Swati Gite
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianhua Zhang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Luisa Solis
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hussein Tawbi
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Linghua Wang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Andrew Futreal
- University of Texas MD Anderson Cancer Center, Houston, TX
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Lee OW, Mitra A, Lee WC, Fukumura K, Beird H, Andrews M, Fischer G, Weinstein JN, Davies MA, Huse J, Futreal PA. Abstract 5704: Pan-cancer genomic characterization of patient-matched primary, extracranial, and brain metastases. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5704] [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
Brain metastases (BM) occur in 10-30% of patients with cancer. Approximately 200,000 new cases of brain metastases are diagnosed in the United States annually, with median survival after diagnosis ranging from 3 to 27 months. Recently, studies have identified significant genetic differences between BM and their corresponding primary tumors. It has been shown that BM harbor clinically actionable mutations that are distinct from those in the primary tumor samples. Additional genomic profiling of BM will provide deeper understanding of the pathogenesis of BM and suggest new therapeutic approaches.
We performed whole-exome sequencing of BM and matched tumors from 41 patients collected from renal cell carcinoma (RCC), breast cancer, lung cancer, and melanoma, which are known to be more likely to develop BM. We profiled total 126 fresh-frozen tumor samples and performed subsequent analyses of BM in comparison to paired primary tumor and extracranial metastases (ECM). We found that lung cancer shared the largest number of mutations between BM and matched tumors (83%), followed by melanoma (74%), RCC (51%), and Breast (26%), indicating that cancer type with high tumor mutational burden share more mutations with BM. Mutational signatures displayed limited differences, suggesting a lack of mutagenic processes specific to BM. However, point-mutation heterogeneity revealed that BM evolve separately into different subclones from their paired tumors regardless of cancer type, and some cancer driver genes were found in BM-specific subclones. These models and findings suggest that these driver genes may drive prometastatic subclones that lead to BM. 32 curated cancer gene mutations were detected and 71% of them were shared between BM and primary tumors or ECM. 29% of mutations were specific to BM, implying that BM often accumulate additional cancer gene mutations that are not present in primary tumors or ECM. Co-mutation analysis revealed a high frequency of TP53 nonsense mutation in BM, mostly in the DNA binding domain, suggesting TP53 nonsense mutation as a possible prerequisite for the development of BM. Copy number alteration analysis showed statistically significant differences between BM and their paired tumor samples in each cancer type (Wilcoxon test, p < 0.0385 for all). Both copy number gains and losses were consistently higher in BM for breast cancer (Wilcoxon test, p =1.307e-5) and lung cancer (Wilcoxon test, p =1.942e-5), implying greater genomic instability during the evolution of BM.
Our findings highlight that there are more unique mutations in BM, with significantly higher copy number alterations and tumor mutational burden. These genomic analyses could provide an opportunity for more reliable diagnostic decision-making, and these findings will be further tested with additional transcriptomic and epigenetic profiling for better characterization of BM-specific tumor microenvironments.
Citation Format: Olivia W. Lee, Akash Mitra, Won-Chul Lee, Kazutaka Fukumura, Hannah Beird, Miles Andrews, Grant Fischer, John N. Weinstein, Michael A. Davies, Jason Huse, P. Andrew Futreal. Pan-cancer genomic characterization of patient-matched primary, extracranial, and brain metastases [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 5704.
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Affiliation(s)
- Olivia W. Lee
- 1The University of Texas MD Anderson Cancer Center, TX
| | - Akash Mitra
- 1The University of Texas MD Anderson Cancer Center, TX
| | - Won-Chul Lee
- 1The University of Texas MD Anderson Cancer Center, TX
| | | | - Hannah Beird
- 1The University of Texas MD Anderson Cancer Center, TX
| | - Miles Andrews
- 2Olivia Newton-John Cancer Research Institute and School of Cancer Medicine, La Trobe University, Australia
| | - Grant Fischer
- 1The University of Texas MD Anderson Cancer Center, TX
| | | | | | - Jason Huse
- 1The University of Texas MD Anderson Cancer Center, TX
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Wang W, Beird H, Kroll CJ, Hu S, Bueso-Ramos CE, Fang H, Tang G, Tang Z, Wang F, Takahashi K, You MJ, Khoury JD, Medeiros LJ, Futreal PA. T(6;14)(q25;q32) involves BCL11B and is highly associated with mixed-phenotype acute leukemia, T/myeloid. Leukemia 2020; 34:2509-2512. [PMID: 32099038 DOI: 10.1038/s41375-020-0761-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/11/2020] [Accepted: 02/11/2020] [Indexed: 11/09/2022]
Affiliation(s)
- Wei Wang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Hannah Beird
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caleb Jonathan Kroll
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shimin Hu
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carlos E Bueso-Ramos
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hong Fang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Feng Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Koichi Takahashi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M James You
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph D Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Kannan S, Livingston JA, Roth M, Benjamin J, Wang Y, Zhang Z, Zhang W, Wu CC, Beird H, Futreal A, Gorlick R. Abstract 1291: Notch2 inhibition as a therapeutic intervention in osteosarcoma. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1291] [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
Notch signaling pathway is a mediator of cell differentiation and is critical for normal bone development. Four functional Notch ligands DLL1 and DLL4, and JAG1 and JAG2 showed various levels of affinity for Notch1-4 receptors. Dose dependent Notch signaling activation or blocking is attributed to anchored or soluble form of Notch ligands binding. Interestingly, Notch pathway is shown to play a dual role, either oncogenic or tumor suppressive, depending on signal dose and tissue-context. To understand Notch signaling activities in osteosarcoma (OS), we first studied the cell surface levels of Notch receptor expression in OS cell lines and patient derived xenograft (pdx) models. Cytometry based screening of NOTCH1-4 receptors showed NOTCH2 as a predominant surface expressed protein in most of the samples. Interestingly, the canonical Notch target genes HES1 and DTX1 were higher (~5-fold) in OS cells compared to mesenchymal cells (MSC). Subsequently, we evaluated selected Notch pathway gene expression in 48 patients with recurrent/metastatic OS by RNAseq analysis. High expression of Notch pathway-related genes was seen in a subset of patients. NOTCH2 expression was comparable between primary and metastatic OS specimens, highest as compared to other Notch receptors and was significantly higher than normal tissue. Thus we aimed to elucidate soluble Notch ligands mediated blocking of Notch signaling using immunoglobulin-G bound DLL-1, -3, and -4 and JAG-1, and -2 in in vitro studies using OS cells. Soluble DLL1-Fc treatment increased OS cell death as compared to the other Notch ligands as well as control-Fc cells. Addition of soluble DLL1 resulted in the decreased expression of Notch downstream genes such as HES1, DTX1 and HEY1. Taken together, these findings identify soluble DLL1 as a potent Notch pathway inhibitor in OS in vitro and support further exploration of NOTCH2 as a potential therapeutic target in OS.
Citation Format: Sankaranarayanan Kannan, John A. Livingston, Michael Roth, Jonathan Benjamin, Yifei Wang, Zhongting Zhang, Wendong Zhang, Chia-Chin Wu, Hannah Beird, Andrew Futreal, Richard Gorlick. Notch2 inhibition as a therapeutic intervention in osteosarcoma [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 1291.
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Affiliation(s)
| | | | - Michael Roth
- The Univeristy of Texas M.D.Anderson Cancer Center, Houston, TX
| | | | - Yifei Wang
- The Univeristy of Texas M.D.Anderson Cancer Center, Houston, TX
| | - Zhongting Zhang
- The Univeristy of Texas M.D.Anderson Cancer Center, Houston, TX
| | - Wendong Zhang
- The Univeristy of Texas M.D.Anderson Cancer Center, Houston, TX
| | - Chia-Chin Wu
- The Univeristy of Texas M.D.Anderson Cancer Center, Houston, TX
| | - Hannah Beird
- The Univeristy of Texas M.D.Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- The Univeristy of Texas M.D.Anderson Cancer Center, Houston, TX
| | - Richard Gorlick
- The Univeristy of Texas M.D.Anderson Cancer Center, Houston, TX
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5
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Wu CC, Beird H, Livingston JA, Cao S, Advani SM, Ingram D, Wang WL, Lazar AJ, Reuben A, Zheng Y, Roszik J, Wang W, Gorlick RG, Benjamin RS, Patel S, Daw NC, Futreal A, Lewis VO. Genome and transcriptome profiling of relapsed and metastatic osteosarcoma. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.11522] [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: 11/20/2022] Open
Affiliation(s)
- Chia Chin Wu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hannah Beird
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - J Andrew Livingston
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shaolong Cao
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Davis Ingram
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wei-Lien Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Jason Roszik
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wenyi Wang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Robert S. Benjamin
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shreyaskumar Patel
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Najat C. Daw
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Valerae O. Lewis
- Department of Orthopedic Oncology, University of Texas MD Anderson Cancer Center, Houston, TX
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6
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Livingston JA, Beird H, Wu CC, Cao S, Advani SM, Ingram D, Wang WL, Lazar AJ, Leung CH, Lin HY, Reuben A, Zheng Y, Roszik J, Wang W, Patel S, Benjamin RS, Gorlick RG, Lewis VO, Futreal A, Daw NC. Parallel genomic and immune profiling of relapsed and metastatic osteosarcoma to reveal bases of low immunogenicity. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.10520] [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: 11/20/2022] Open
Affiliation(s)
- J Andrew Livingston
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hannah Beird
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chia Chin Wu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shaolong Cao
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Davis Ingram
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wei-Lien Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Heather Y. Lin
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Jason Roszik
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wenyi Wang
- University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shreyaskumar Patel
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Robert S. Benjamin
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Valerae O. Lewis
- Department of Orthopedic Oncology, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Najat C. Daw
- The University of Texas MD Anderson Cancer Center, Houston, TX
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7
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Beird H, Goldstein JB, Zhang J, Belmont C, Lari B, Basu P, Pathak D, Fassett R, Jin J, Barbosa G, Kell T, Punugoti V, Suh E, Smith B, Futreal A. A methodological framework for establishing a translational research accelerator (TRA) for cancer research. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e23204] [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: 11/20/2022] Open
Affiliation(s)
- Hannah Beird
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jianjun Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chris Belmont
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bryan Lari
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Jeff Jin
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gregory Barbosa
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Trey Kell
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vamshi Punugoti
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Edward Suh
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Brett Smith
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Narayanan S, Beird H, Goldstein JB, Zhang J, Belmont C, Lari B, Pathak D, Jin J, Barbosa G, Kell T, Punugoti V, Suh E, Smith B, Futreal A. Visualization techniques for identifying patients cohorts for hypothesis-testing in cancer research. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e23203] [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: 11/20/2022] Open
Affiliation(s)
| | - Hannah Beird
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jianjun Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chris Belmont
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bryan Lari
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jeff Jin
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gregory Barbosa
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Trey Kell
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vamshi Punugoti
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Edward Suh
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Brett Smith
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Beird H, Goldstein JB, Zhang J, Narayanan S, Belmont C, Lari B, Fassett R, Pathak D, Akella P, Jin J, Barbosa G, Kell T, Punugoti V, Suh E, Smith B, Futreal A. A case-study using big data to increase scientific productivity in cancer research. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e23202] [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: 11/20/2022] Open
Affiliation(s)
- Hannah Beird
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jianjun Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Chris Belmont
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bryan Lari
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Jeff Jin
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gregory Barbosa
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Trey Kell
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vamshi Punugoti
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Edward Suh
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Brett Smith
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Goldstein JB, Beird H, Zhang J, Belmont C, Lari B, Mynhier M, Pathak D, Basu P, Jin J, Barbosa G, Kell T, Punugoti V, Suh E, Smith B, Chin L, Futreal A. Tackling "big data" for accelerating cancer research. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e23160] [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: 11/20/2022] Open
Affiliation(s)
| | - Hannah Beird
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianjun Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chris Belmont
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bryan Lari
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Jeff Jin
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gregory Barbosa
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Trey Kell
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vamshi Punugoti
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Edward Suh
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Brett Smith
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lynda Chin
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Houston, TX
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11
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Garber HR, Beird H, Cao Y, Zhang J, Sargent R, Lin P, Seth S, Song X, Sun H, Mao X, St John L, Clise-Dwyer K, Alatrash G, Futreal PA, Molldrem JJ. Abstract LB-222: Long-term subclonal evolution of CLL from immune selective pressure after allogeneic stem cell transplant and donor lymphocyte infusion. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-lb-222] [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
Next-generation sequencing (NGS) has revealed that the malignant subclones comprising a patient's cancer can possess tremendous genetic heterogeneity at different sites of disease and over time. In leukemia, chemotherapy can hasten subclonal evolution allowing for rare leukemic subclones with aggressive driver mutations to gain a competitive advantage and to predominate at relapse, often portending an inferior treatment response. The impact of immunotherapy on subclonal evolution is less well studied. To determine the effects of allogeneic stem cell transplant (alloSCT) and donor lymphocyte infusion (DLI) on subclonal evolution, we performed whole exome sequencing (WES) on longitudinal peripheral blood and bone marrow from 4 patients with CLL. Specifically, timepoints analyzed included pre-transplant, post-transplant relapse, and post-DLI relapse over a period of up to 8.5 years. B-CLL cells (CD19+CD5+) and normal T cells (CD3+) were sort-purified by fluorescence-activated cell sorting prior to genomic DNA extraction. Libraries for WES were constructed and sequenced to an average depth of 300x on an Illumina HiSeq 2000 using 76 bp paired-end reads. Somatic single nucleotide variants (sSNVs) and indels were called using MuTect and Pindel, respectively, and copy number changes were assessed using an in-house algorithm. In general, these patients had more nonsynonymous mutations per pre-alloSCT sample than reported in other CLL NGS studies (average 30.3; range 8-45), likely related to the significant amount of pre-transplant therapies. Heterogeneous patterns of linear and branched subclonal evolution were seen after alloSCT and DLI in both responders and non-responders. Mutations in several candidate CLL driver genes were seen in this cohort, including SF3B1, SAMHD1, BCOR, EGR2, TP53, and DDX3X. Interestingly, sSNVs in multiple recurrently mutated CLL or cancer census genes (e.g. MAP2K1) rose to levels of detection only after alloSCT or DLI, suggesting they may play a role in immune evasion. In addition, several subclonal genetic variants, including missense mutations in FAM126B and LTBP3, were no longer detected after alloSCT or DLI and may thus represent potential neoantigens. In one treatment-refractory patient, a somatic nonsynonymous clonal CHEK2 mutation was found in 8 longitudinal samples and may represent a novel unique driver mutation. Finally, in one patient who experienced a durable complete remission after DLI, concurrent CLL WES and T-cell receptor beta chain CDR3 NGS was performed, which demonstrated a rapidly evolving T-cell repertoire at the time of complete remission after DLI. For CLL, alloSCT and DLI offer a potentially curative treatment strategy and a better understanding of the genes that confer susceptibility or resistance to these immunotherapies may help unlock the mechanisms that underlie these durable responses.
Citation Format: Haven R. Garber, Hannah Beird, Yu Cao, Jianhua Zhang, Rachel Sargent, Pei Lin, Sahil Seth, Xingzhi Song, Huandong Sun, Xizeng Mao, Lisa St John, Karen Clise-Dwyer, Gheath Alatrash, P. Andrew Futreal, Jeffrey J. Molldrem. Long-term subclonal evolution of CLL from immune selective pressure after allogeneic stem cell transplant and donor lymphocyte infusion. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-222. doi:10.1158/1538-7445.AM2015-LB-222
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Affiliation(s)
| | | | - Yu Cao
- UT MD Anderson Cancer Center, Houston, TX
| | | | | | - Pei Lin
- UT MD Anderson Cancer Center, Houston, TX
| | - Sahil Seth
- UT MD Anderson Cancer Center, Houston, TX
| | | | | | - Xizeng Mao
- UT MD Anderson Cancer Center, Houston, TX
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Somaiah N, Beird H, Shaw KR, Wang WL, Conley AP, Ravi V, Torres KE, Ingram D, Roland CL, Subbiah V, Feig BW, Lazar AJF, Benjamin RS, Patel S, Hwu P, Futreal A, Meric-Bernstam F, Hong DS. Targeted next generation sequencing in well-differentated/dedifferentiated liposarcoma (WD/DD LPS): Multiple gene amplifications but few mutations. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.10550] [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: 11/20/2022] Open
Affiliation(s)
- Neeta Somaiah
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hannah Beird
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kenna Rael Shaw
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wei-Lien Wang
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Anthony Paul Conley
- Department of Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vinod Ravi
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Keila E Torres
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Davis Ingram
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics (Phase 1 Program), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Barry W. Feig
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Patrick Hwu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - David S. Hong
- Department of Investigational Cancer Therapeutics (Phase 1 Program), The University of Texas MD Anderson Cancer Center, Houston, TX
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