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George B, Kudryashova O, Kravets A, Thalji S, Malarkannan S, Kurzrock R, Chernyavskaya E, Gusakova M, Kravchenko D, Tychinin D, Savin E, Alekseeva L, Butusova A, Bagaev A, Shin N, Brown JH, Sethi I, Wang D, Taylor B, McFall T, Kamgar M, Hall WA, Erickson B, Christians KK, Evans DB, Tsai S. Transcriptomic-Based Microenvironment Classification Reveals Precision Medicine Strategies for Pancreatic Ductal Adenocarcinoma. Gastroenterology 2024; 166:859-871.e3. [PMID: 38280684 DOI: 10.1053/j.gastro.2024.01.028] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 12/11/2023] [Accepted: 01/18/2024] [Indexed: 01/29/2024]
Abstract
BACKGROUND & AIMS The complex tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) has hindered the development of reliable predictive biomarkers for targeted therapy and immunomodulatory strategies. A comprehensive characterization of the TME is necessary to advance precision therapeutics in PDAC. METHODS A transcriptomic profiling platform for TME classification based on functional gene signatures was applied to 14 publicly available PDAC datasets (n = 1657) and validated in a clinically annotated independent cohort of patients with PDAC (n = 79). Four distinct subtypes were identified using unsupervised clustering and assessed to evaluate predictive and prognostic utility. RESULTS TME classification using transcriptomic profiling identified 4 biologically distinct subtypes based on their TME immune composition: immune enriched (IE); immune enriched, fibrotic (IE/F); fibrotic (F); and immune depleted (D). The IE and IE/F subtypes demonstrated a more favorable prognosis and potential for response to immunotherapy compared with the F and D subtypes. Most lung metastases and liver metastases were subtypes IE and D, respectively, indicating the role of clonal phenotype and immune milieu in developing personalized therapeutic strategies. In addition, distinct TMEs with potential therapeutic implications were identified in treatment-naive primary tumors compared with tumors that underwent neoadjuvant therapy. CONCLUSIONS This novel approach defines a distinct subgroup of PADC patients that may benefit from immunotherapeutic strategies based on their TME subtype and provides a framework to select patients for prospective clinical trials investigating precision immunotherapy in PDAC. Further, the predictive utility and real-world clinical applicability espoused by this transcriptomic-based TME classification approach will accelerate the advancement of precision medicine in PDAC.
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Affiliation(s)
- Ben George
- LaBahn Pancreatic Cancer Program, Division of Hematology and Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin.
| | | | | | - Samih Thalji
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Subramaniam Malarkannan
- Versiti Blood Research Institute, Department of Medicine, Microbiology & Molecular Genetics, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Razelle Kurzrock
- Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Division of Hematology and Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | | | | | | | | | - Egor Savin
- BostonGene Corporation, Waltham, Massachusetts
| | | | | | | | - Nara Shin
- BostonGene Corporation, Waltham, Massachusetts
| | | | - Isha Sethi
- BostonGene Corporation, Waltham, Massachusetts
| | - Dandan Wang
- Versiti Blood Research Institute, Department of Medicine, Microbiology & Molecular Genetics, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Bradley Taylor
- Clinical and Translational Science Institute, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Thomas McFall
- LaBahn Pancreatic Cancer Program, Department of Biochemistry, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Mandana Kamgar
- LaBahn Pancreatic Cancer Program, Division of Hematology and Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - William A Hall
- LaBahn Pancreatic Cancer Program, Department of Radiation Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Beth Erickson
- LaBahn Pancreatic Cancer Program, Department of Radiation Oncology, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Kathleen K Christians
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Douglas B Evans
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
| | - Susan Tsai
- LaBahn Pancreatic Cancer Program, Department of Surgery, Medical College of Wisconsin (MCW), Milwaukee, Wisconsin
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Tumuluru S, Godfrey JK, Cooper A, Yu J, Chen X, MacNabb BW, Venkataraman G, Zha Y, Pelzer B, Song J, Duns G, Sworder BJ, Bolen C, Penuel E, Postovalova E, Kotlov N, Bagaev A, Fowler N, Smith SM, Alizadeh AA, Steidl C, Kline J. Integrative genomic analysis identifies unique immune environments associated with immunotherapy response in diffuse large B cell lymphoma. bioRxiv 2024:2024.01.17.576100. [PMID: 38328071 PMCID: PMC10849512 DOI: 10.1101/2024.01.17.576100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Most diffuse large B-cell lymphoma (DLBCL) patients treated with bispecific antibodies (BsAb) or chimeric antigen receptor (CAR) T cells fail to achieve durable treatment responses, underscoring the need for a deeper understanding of mechanisms that regulate the immune environment and response to treatment. Here, an integrative, multi-omic approach was employed to characterize DLBCL immune environments, which effectively segregated DLBCLs into four quadrants - termed DLBCL-immune quadrants (IQ) - defined by cell-of-origin and immune-related gene set expression scores. Recurrent genomic alterations were enriched in each IQ, suggesting that lymphoma cell-intrinsic alterations contribute to orchestrating unique DLBCL immune environments. In relapsed/refractory DLBCL patients, DLBCL-IQ assignment correlated significantly with clinical benefit with the CD20 x CD3 BsAb, mosunetuzumab, but not with CD19-directed CAR T cells. DLBCL-IQ provides a new framework to conceptualize the DLBCL immune landscape and uncovers the differential impact of the endogenous immune environment on outcomes to BsAb and CAR T cell treatment.
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3
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Cooper A, Tumuluru S, Kissick K, Venkataraman G, Song JY, Lytle A, Duns G, Yu J, Kotlov N, Bagaev A, Hodkinson B, Srinivasan S, Smith SM, Scott DW, Steidl C, Godfrey JK, Kline J. CD5 Gene Signature Identifies Diffuse Large B-Cell Lymphomas Sensitive to Bruton's Tyrosine Kinase Inhibition. J Clin Oncol 2024; 42:467-480. [PMID: 38079587 DOI: 10.1200/jco.23.01574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/29/2023] [Accepted: 09/13/2023] [Indexed: 01/31/2024] Open
Abstract
PURPOSE A genetic classifier termed LymphGen accurately identifies diffuse large B-cell lymphoma (DLBCL) subtypes vulnerable to Bruton's tyrosine kinase inhibitors (BTKis), but is challenging to implement in the clinic and fails to capture all DLBCLs that benefit from BTKi-based therapy. Here, we developed a novel CD5 gene expression signature as a biomarker of response to BTKi-based therapy in DLBCL. METHODS CD5 immunohistochemistry (IHC) was performed on 404 DLBCLs to identify CD5 IHC+ and CD5 IHC- cases, which were subsequently characterized at the molecular level through mutational and transcriptional analyses. A 60-gene CD5 gene expression signature (CD5sig) was constructed using genes differentially expressed between CD5 IHC+ and CD5 IHC- non-germinal center B-cell-like (non-GCB DLBCL) DLBCLs. This CD5sig was applied to external DLBCL data sets, including pretreatment biopsies from patients enrolled in the PHOENIX study (n = 584) to define the extent to which the CD5sig could identify non-GCB DLBCLs that benefited from the addition of ibrutinib to rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). RESULTS CD5 expression was observed in 12% of non-GCB DLBCLs. CD5+ DLBCLs displayed transcriptional features of B-cell receptor (BCR) activation and were enriched for BCR-activating mutations known to correlate with BTKi sensitivity. However, most CD5+ DLBCLs lacked canonical BCR-activating mutations or were LymphGen-unclassifiable (LymphGen-Other). The CD5sig recapitulated these findings in multiple independent data sets, indicating its utility in identifying DLBCLs with genetic and nongenetic bases for BCR dependence. Supporting this notion, CD5sig+ DLBCLs derived a selective survival advantage from the addition of ibrutinib to R-CHOP in the PHOENIX study, independent of LymphGen classification. CONCLUSION CD5sig is a useful biomarker to identify DLBCLs vulnerable to BTKi-based therapies and complements current biomarker approaches by identifying DLBCLs with genetic and nongenetic bases for BTKi sensitivity.
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Affiliation(s)
- Alan Cooper
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL
| | - Sravya Tumuluru
- Committee on Cancer Biology, University of Chicago, Chicago, IL
| | - Kyle Kissick
- Department of Pathology, University of Chicago, Chicago, IL
| | | | - Joo Y Song
- Department of Pathology, City of Hope, Duarte, CA
| | - Andrew Lytle
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC
| | - Gerben Duns
- Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Jovian Yu
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL
| | | | | | - Brendan Hodkinson
- Oncology Translational Research, Janssen Research & Development, Spring House, PA
| | - Srimathi Srinivasan
- Oncology Translational Research, Janssen Research & Development, Lower Gwynedd Township, PA
| | - Sonali M Smith
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL
| | - David W Scott
- Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Christian Steidl
- Lymphoid Cancer Research, BC Cancer Agency, Vancouver, BC, Canada
| | - James K Godfrey
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope, Duarte, CA
| | - Justin Kline
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL
- Committee on Cancer Biology, University of Chicago, Chicago, IL
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4
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Godfrey J, Chen X, Sunseri N, Cooper A, Yu J, Varlamova A, Zarubin D, Popov Y, Jacobson C, Postovalova E, Xiang Z, Nomie K, Bagaev A, Venkataraman G, Zha Y, Tumuluru S, Smith SM, Kline JP. TIGIT is a key inhibitory checkpoint receptor in lymphoma. J Immunother Cancer 2023; 11:e006582. [PMID: 37364933 PMCID: PMC10410806 DOI: 10.1136/jitc-2022-006582] [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] [Accepted: 06/04/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND PD-1 checkpoint blockade therapy (CBT) has greatly benefited patients with select solid tumors and lymphomas but has limited efficacy against diffuse large B-cell lymphoma (DLBCL). Because numerous inhibitory checkpoint receptors have been implicated in driving tumor-specific T cell dysfunction, we hypothesized that combinatorial CBT would enhance the activity of anti-PD-1-based therapy in DLBCL. T cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT) is a coinhibitory receptor expressed on dysfunctional tumor-infiltrating T cells, and TIGIT blockade has demonstrated encouraging activity in combination with PD-1 blockade in murine tumor models and in clinical studies. However, the degree to which TIGIT mediates T cell dysfunction in DLBCL has not been fully explored. RESULTS Here, we demonstrate that TIGIT is broadly expressed on lymphoma-infiltrating T cells (LITs) across a variety of human lymphomas and is frequently coexpressed with PD-1. TIGIT expression is particularly common on LITs in DLBCL, where TIGIT+ LITs often form distinct cellular communities and exhibit significant contact with malignant B cells. TIGIT+/PD-1+ LITs from human DLBCL and murine lymphomas exhibit hypofunctional cytokine production on ex vivo restimulation. In mice with established, syngeneic A20 B-cell lymphomas, TIGIT or PD-1 mono-blockade leads to modest delays in tumor outgrowth, whereas PD-1 and TIGIT co-blockade results in complete rejection of A20 lymphomas in most mice and significantly prolongs survival compared with mice treated with monoblockade therapy. CONCLUSIONS These results provide rationale for clinical investigation of TIGIT and PD-1 blockade in lymphomas, including DLBCL.
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Affiliation(s)
- James Godfrey
- Hematology, City of Hope Comprehensive Cancer Center, Duarte, California, USA
| | - Xiufen Chen
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Nicole Sunseri
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Alan Cooper
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Jovian Yu
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | | | | | | | | | | | | | | | | | | | - Yuanyuan Zha
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Sravya Tumuluru
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Sonali M Smith
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Justin P Kline
- Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
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Valiev I, Kotlov N, Belozerova A, Lopareva A, Butusova A, Samarina N, Boiko A, Degryse S, Sequist L, Mino-Kenudson M, Fowler N, Bagaev A, Lanuti M, Dagogo-Jack I. Abstract 5172: B cell content in the tumor microenvironment is associated with improved survival in stage II lung adenocarcinoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5172] [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
In non-small cell lung cancer (NSCLC), likelihood of cure is heavily influenced by stage at diagnosis. In contrast to stage I where surgery achieves cure for >70% of patients, the majority of patients with stage II NSCLC will develop recurrent disease after surgery. The addition of chemotherapy is associated with modest improvement in survival. Biomarkers that help identify patients at higher risk of relapse following curative intent therapy remain elusive.
In this study, we performed comprehensive profiling of resected stage II lung adenocarcinomas (LUAD) (n=29) to identify features associated with favorable prognostic outcomes. Whole exome (WES) and bulk RNA sequencing (RNAseq) were performed on frozen lung tumor specimens and corresponding normal lung tissue. Novel algorithms were used to digitally reconstruct the tumor microenvironment (TME). H&E slides were reviewed to characterize the immune infiltrate and identify tertiary lymphoid structures (TLS). Patient outcomes were collected and matched to pathological samples. To further validate initial findings, we then created and tested a functional B-cell signature on cohorts as described below.
In the retrospective cohort, 13 (45%) patients developed recurrent disease and 10 (34%) died during the 3+ year follow-up period. Neither the overall density of immune infiltrate nor detection of TLS predicted for improved relapse-free survival (RFS) or overall survival (OS). Similarly, tumor mutational burden (assessed by WES), histological grade (assessed by RNAseq), and expression of immune checkpoints (PD-L1, PD-1, CTLA-4) were not associated with RFS or OS (log-rank test P > 0.05 for both OS and RFS in all comparisons). Interestingly, higher B-cell content in the TME (stratified as high vs low based on 10% threshold value), as deconvolved using validated algorithms (and confirmed via H&E review), was associated with improved OS (log-rank test P = 0.05) with a trend towards improved RFS (P = 0.2). We conducted the same analysis using a TCGA RNAseq cohort of stage II LUAD patients (n = 76) and confirmed that high B-cell levels in the TME were significantly associated with longer OS in stage II LUAD patients (P = 0.03). Finally, to validate our findings with a larger dataset, we developed a functional B-cell gene expression signature which significantly correlated with levels of B cells in both the TCGA (Spearman’s rho = 0.83, P < 0.001) and 29-patient cohort (Spearman’s rho = 0.91, P < 0.001). When this signature was applied to publicly available expression array data, B-cell enrichment status was significantly associated with OS in the external meta-cohort of stage II LUAD patients (log rank test P = 0.004, n=564).
Abundant B-cell infiltrate in the TME is associated with improved survival in patients with surgically resected stage II LUAD. Quantification of B-cell content using RNAseq warrants further investigation for use in routine clinical practice.
Citation Format: Ivan Valiev, Nikita Kotlov, Anna Belozerova, Aleksandra Lopareva, Anna Butusova, Naira Samarina, Alexandra Boiko, Sandrine Degryse, Lecia Sequist, Mari Mino-Kenudson, Nathan Fowler, Aleksander Bagaev, Michael Lanuti, Ibiayi Dagogo-Jack. B cell content in the tumor microenvironment is associated with improved survival in stage II lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5172.
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Zarubin D, Belotskiy V, Xiang Z, Varlamova A, Ovcharov P, Galkin I, Polyakova M, Svekolkin V, Perelman G, Bruttan M, Brown JH, Postovalova E, Bagaev A, Fowler N. A clinical AI-driven multiplex immunofluorescence imaging pipeline to characterize tumor microenvironment heterogeneity. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.3020] [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: 11/20/2022] Open
Abstract
3020 Background: Understanding the underlying heterogeneity of the tumor microenvironment (TME) on a single-cell level is becoming increasingly important to predict a patient’s response to immunotherapy. Conventional imaging methods can help reveal tissue heterogeneity, but are not optimal for identifying multiple cellular subpopulations or cellular interactions from a single slide image, limiting their use in clinical settings. Here, we present a clinical artificial intelligence (AI)-driven multiplex immunofluorescence (MxIF) imaging pipeline based on novel cell segmentation and cell typing methods to evaluate tumor cellular heterogeneity, immune cell composition, and cell-to-cell interactions. Methods: A machine learning (ML)-based cell segmentation algorithm was trained on a manually annotated dataset created from 219 different regions of interest (ROIs) that contained 85,991 cells from various tissues (colon, kidney, lung, lymph node, tonsil, and ureter). A dataset containing 58,676 cells from 146 ROIs was used for validation and accuracy was determined between automated and manually annotated images; accuracy was further evaluated by calculating the f1-score using available methods (DeepCell and Stardist). Marker stains with a low signal-to-noise ratio were automatically enhanced, allowing for adequate cell-to-cell interaction analysis. Results: An automated MxIF image processing workflow was developed. Validation of the trained cell segmentation model showed high accuracy (0.80 f1-score), demonstrating superior performance compared to other methods (DeepCell and Stardist - 0.55 and 0.78 f1-score, respectively). The pathologist-determined accuracy (0.84 mean f1-score) indicated a near-human performance of the developed method. Normalized expression values obtained from the cell typing model allowed automated cell recognition. We analyzed cellular heterogeneity across 3 regions of colorectal cancer (CRC), gastric cancer (GC), and non-small cell lung cancer (NSCLC) samples. While proportions of immune cells varied, proportions of malignant epithelial cells were stable across all regions of each sample, as concordant percentages of Ki67+ cells were identified (CRC-19%; GC-21%; NSCLC-5%). Analysis of cell-to-cell interactions and immune communities identified tumor-, immune-, and stromal-enriched communities in all tumor samples that were stable across regions. Conclusions: By analyzing complex tumor tissue at single-cell resolution with high accuracy, this AI-driven MxIF imaging technology is able to characterize tumor and microenvironment heterogeneity across cancer types. This novel AI-based tool is currently being integrated into several ongoing prospective clinical studies to aid in the development of predictive and prognostic biomarkers.
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7
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George B, Thalji S, Malarkannan S, Kudryashova O, Kravets A, Gusakova M, Kravchenko D, Tychinin D, Frenkel F, Bagaev A, Shin N, Mehdi M, Kamgar M, Hall WA, Erickson B, Christians KK, Evans DB, Tsai S. Reconstructing the tumor microenvironment to unlock therapeutic options in pancreatic cancer. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.4_suppl.589] [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: 11/20/2022] Open
Abstract
589 Background: Spatiotemporal heterogeneity, paucity of actionable targets, and complexity of the tumor microenvironment (TME) are major barriers to therapeutic advances in pancreatic ductal adenocarcinoma (PDAC). We reconstructed the transcriptomic data from a heterogeneous cohort of PDAC patients (pts) to examine the TME and identify putative therapeutic strategies. Methods: Transcriptomic profiling and targeted gene sequencing data (Tempus) on primary or metastatic specimens from PDAC pts treated at the Medical College of Wisconsin (MCW) between 2015-2020 were analyzed. Mutation calling, expression analysis, cell type deconvolution from the transcriptome, and TME reconstruction were performed using BostonGene’s automated pipelines. Mann-Whitney U test and Fisher's exact test were used to assess statistical significance. Results: The cohort (N = 79) comprised of resectable (19%), borderline resectable (37%), locally advanced (24%) and metastatic (20%) PDAC pts. The most frequently used tumor sites for transcriptomic profiling were pancreas primary (59%), liver (16%), lung (10%) and peritoneum (10%). Four distinct subtypes were identified based on the BostonGene classification of the transcriptomic TME– Immune Enriched (IE; 14%), Fibrotic (F; 28%), Immune Enriched & Fibrotic (IEF; 36%), and Immune Depleted (ID; 22%). Analyses of the cellular composition of the TME subtypes with RNA-seq-based deconvolution showed that T-cell fractions (CD4, CD8) were higher in the IE/IEF subtypes compared to the F/ID subtypes (CD8 means: 6.4% vs 2.9%, p < 0.001; CD4 means: 15.1% vs. 7.6%, p < 0.001), while fibroblast content was higher in the F/IEF subtypes compared to the IE/ID subtypes (37.4% vs 18.4%; p < 0.001). KRAS wild-type (WT) tumors were enriched in the IEF subtype (58%), while KRAS mutated tumors comprised all four transcriptomic subtypes. Primary PDACs that underwent radiotherapy were significantly more enriched in fibroblasts compared to samples from the TCGA cohort that did not undergo radiotherapy (means: 30%(MCW) vs. 20% (TCGA), p < 0.001). Primary PDACs were enriched in the IEF subtype (46%), while liver and lung metastases were enriched in the ID (74%) and IE subtypes (70%), respectively. When pts were dichotomized to short (< 400 days) versus long (> 800 days) survivors, tumors from pts with longer survival demonstrated a trend towards enrichment in CD4/CD8 T cells and IE subtype that did not meet statistical significance. Conclusions: Lung metastases and KRAS WT PDACs harbor an immunogenic TME while liver metastases harbor an immune-cold TME, highlighting the biologic heterogeneity of PDAC. The efficacy of immunotherapeutic strategies in PDAC pts who demonstrate an IE/IEF transcriptomic subtype merits prospective evaluation. The four distinct subtypes identified by TME transcriptomic classification highlight the possibility of personalized immunotherapeutic strategies in PDAC.
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Affiliation(s)
- Ben George
- Froedtert & The Medical College of Wisconsin, Milwaukee, WI
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Susan Tsai
- Medical College of Wisconsin, Milwaukee, WI
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8
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Li F, Deng L, Jackson KR, Talukder AH, Katailiha AS, Bradley SD, Zou Q, Chen C, Huo C, Chiu Y, Stair M, Feng W, Bagaev A, Kotlov N, Svekolkin V, Ataullakhanov R, Miheecheva N, Frenkel F, Wang Y, Zhang M, Hawke D, Han L, Zhou S, Zhang Y, Wang Z, Decker WK, Sonnemann HM, Roszik J, Forget MA, Davies MA, Bernatchez C, Yee C, Bassett R, Hwu P, Du X, Lizee G. Neoantigen vaccination induces clinical and immunologic responses in non-small cell lung cancer patients harboring EGFR mutations. J Immunother Cancer 2021; 9:jitc-2021-002531. [PMID: 34244308 PMCID: PMC8268925 DOI: 10.1136/jitc-2021-002531] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Accepted: 06/07/2021] [Indexed: 12/22/2022] Open
Abstract
Background Neoantigen (NeoAg) peptides displayed at the tumor cell surface by human leukocyte antigen molecules show exquisite tumor specificity and can elicit T cell mediated tumor rejection. However, few NeoAgs are predicted to be shared between patients, and none to date have demonstrated therapeutic value in the context of vaccination. Methods We report here a phase I trial of personalized NeoAg peptide vaccination (PPV) of 24 stage III/IV non-small cell lung cancer (NSCLC) patients who had previously progressed following multiple conventional therapies, including surgery, radiation, chemotherapy, and tyrosine kinase inhibitors (TKIs). Primary endpoints of the trial evaluated feasibility, tolerability, and safety of the personalized vaccination approach, and secondary trial endpoints assessed tumor-specific immune reactivity and clinical responses. Of the 16 patients with epidermal growth factor receptor (EGFR) mutations, nine continued TKI therapy concurrent with PPV and seven patients received PPV alone. Results Out of 29 patients enrolled in the trial, 24 were immunized with personalized NeoAg peptides. Aside from transient rash, fatigue and/or fever observed in three patients, no other treatment-related adverse events were observed. Median progression-free survival and overall survival of the 24 vaccinated patients were 6.0 and 8.9 months, respectively. Within 3–4 months following initiation of PPV, seven RECIST-based objective clinical responses including one complete response were observed. Notably, all seven clinical responders had EGFR-mutated tumors, including four patients that had continued TKI therapy concurrently with PPV. Immune monitoring showed that five of the seven responding patients demonstrated vaccine-induced T cell responses against EGFR NeoAg peptides. Furthermore, two highly shared EGFR mutations (L858R and T790M) were shown to be immunogenic in four of the responding patients, all of whom demonstrated increases in peripheral blood neoantigen-specific CD8+ T cell frequencies during the course of PPV. Conclusions These results show that personalized NeoAg vaccination is feasible and safe for advanced-stage NSCLC patients. The clinical and immune responses observed following PPV suggest that EGFR mutations constitute shared, immunogenic neoantigens with promising immunotherapeutic potential for large subsets of NSCLC patients. Furthermore, PPV with concurrent EGFR inhibitor therapy was well tolerated and may have contributed to the induction of PPV-induced T cell responses.
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Affiliation(s)
- Fenge Li
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ligang Deng
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Kyle R Jackson
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amjad H Talukder
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Arjun S Katailiha
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sherille D Bradley
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Qingwei Zou
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Caixia Chen
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Chong Huo
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Yulun Chiu
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Matthew Stair
- Mary Bird Perkins Cancer Center, Baton Rouge, Louisiana, USA
| | - Weihong Feng
- Department of Oncology, Tianjin Beichen Hospital, Tianjin, China
| | | | | | | | | | | | | | - Yaling Wang
- Tianjin HengJia Biotechnology Development Co Ltd, Tianjin, China
| | - Minying Zhang
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - David Hawke
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ling Han
- Department of Oncology, Tianjin Beichen Hospital, Tianjin, China
| | - Shuo Zhou
- Provincial Clinical College, Fujian Medical University, Fujian, China
| | - Yan Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China
| | - Zhenglu Wang
- Biological Sample Resource Sharing Center, Tianjin First Central Hospital, Tianjin, China
| | - William K Decker
- Department of Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - Heather M Sonnemann
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jason Roszik
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Marie-Andree Forget
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael A Davies
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chantale Bernatchez
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cassian Yee
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.,Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Roland Bassett
- Department of Immunology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Patrick Hwu
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xueming Du
- Department of Oncology, Tianjin Beichen Hospital, Tianjin, China
| | - Gregory Lizee
- Department of Melanoma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA .,Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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9
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Sarkar S, Thakkar PK, Lenz H, Enzinger P, Ko AH, Ocean AJ, Lu Y, Zhang C, Bhinder B, Plotnikova O, Kotlov N, Frenkel F, Bagaev A, Elemento O, Betel D, Giannakakou P, Pittman ME, Shah MA. Abstract 2011: HER2 expression and M2-like tumor infiltrating macrophages associated with Cabazitaxel activity in gastric cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-2011] [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
Gastric cancer (GC), responsible for ~700,000 deaths worldwide annually, is a dismal disease, with median survival for metastatic disease less than 1 year. We examined the efficacy and safety of cabazitaxel, a novel 3rd generation taxane, in the 2nd line treatment setting in advanced GC. Comprehensive correlative studies were performed to identify genetic aberrations or tumor microenvironment signatures associated with cabazitaxel activity.
Patients with previously treated GC were eligible for this multicenter phase II study of single agent cabazitaxel (NCT01757171). The progression-free survival (PFS) rate at 3-mo using RECIST 1.1 was 28% (95%CI 17-42%) in taxane-naïve and 35% (95%CI 16-57%) in taxane treated cohorts. A fresh tissue biopsy of the tumor and matching adjacent non-tumor tissue was obtained from each of the 66 patients (87% of the study population) and was examined using whole exome sequencing (WES) and bulk RNAseq. We performed CIBERSORT deconvolution of the RNA expression data into its constituent immune cell types. Tumor samples were segregated into those with high or low macrophage M2 levels using the cohort specific median M2 abundance as the threshold. 26 tumor samples were examined for validation of the M2 signature by immunohistochemistry (IHC) using CD68 (pan-macrophage), CD163 (M2), and iNOS (M1) markers.
GC WES showed numerous somatic alterations including missense mutations, chromosomal rearrangements, SNVs, small indels and CNAs with prevalent mutations in TP53 (26/47 cases), RHOA, and RTK/RAS signaling. Clinically actionable alterations included BRAF V600E, EGFR amplifications (10/47) and HER2 amplifications (8/47). One patient had a KRAS Q61H mutation predictive of resistance to a broad spectrum of RTK inhibitors. Other alterations included mutations in RTK signaling components, deletions of MTOR and STK11 suppressor gene and mutations in PI3K/mTOR pathway.
We found that HER2 amplification was significantly more prevalent in responders, 50% HER2 positive among patients with PR/SD vs 10% in patients with PD (p=0.003). Patients with HER2 positive tumors had better PFS (p=0.04) and OS (45% 2-year survival vs 15%, p=0.002). Deconvolution analysis revealed an enrichment of an M2 macrophage signature in a cohort of patients having an improved PFS (45% vs 20% at 12 months, p=0.031). IHC analysis also showed M2 enrichment in 65% tissue samples examined (n=26). The M2-like macrophage signature was associated with improved outcome independent of HER2 amplification/ over-expression. In 8 out of 10 matched on-treatment biopsies, the M2-like signature significantly decreased post treatment.
We have identified two novel biomarkers, HER2 overexpression and M2-high tumor macrophage signature, associated with improved outcomes in patients with GC treated with cabazitaxel. Additional correlative analyses and integration are underway.
Citation Format: Sandipto Sarkar, Prashant K. Thakkar, Heinz Lenz, Peter Enzinger, Andrew H. Ko, Allyson J. Ocean, Yao Lu, Chao Zhang, Bhavneet Bhinder, Olga Plotnikova, Nikita Kotlov, Feliz Frenkel, Aleksander Bagaev, Olivier Elemento, Doron Betel, Paraskevi Giannakakou, Meredith E. Pittman, Manish A. Shah. HER2 expression and M2-like tumor infiltrating macrophages associated with Cabazitaxel activity in gastric 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 2011.
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Affiliation(s)
| | | | - Heinz Lenz
- 2University of Southern California, Los Angeles, CA
| | | | | | | | - Yao Lu
- 1Weill Cornell Medicine, New York, NY
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10
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Shah MA, Enzinger P, Ko AH, Ocean AJ, Philip PA, Thakkar PV, Cleveland K, Lu Y, Kortmansky J, Christos PJ, Zhang C, Kaur N, Elmonshed D, Galletti G, Sarkar S, Bhinder B, Pittman ME, Plotnikova OM, Kotlov N, Frenkel F, Bagaev A, Elemento O, Betel D, Giannakakou P, Lenz HJ. Multicenter Phase II Study of Cabazitaxel in Advanced Gastroesophageal Cancer: Association of HER2 Expression and M2-Like Tumor-Associated Macrophages with Patient Outcome. Clin Cancer Res 2020; 26:4756-4766. [PMID: 32641434 DOI: 10.1158/1078-0432.ccr-19-3920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 03/31/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022]
Abstract
PURPOSE We examined cabazitaxel, a novel next-generation taxoid, in patients with metastatic gastric cancer in a multicenter phase II study. PATIENTS AND METHODS Patients who have progressed on one or more prior therapies for locally advanced, unresectable, or metastatic disease were eligible, and prior taxane therapy was allowed. Taxane-naïve and pretreated cohorts were analyzed independently for efficacy. The primary endpoint for both cohorts was progression-free survival (PFS) using RECIST 1.1, using a Simon's two-stage design (10% significance and 80% power) for both cohorts. Comprehensive molecular annotation included whole exome and bulk RNA sequencing. RESULTS Fifty-three patients enrolled in the taxane-naïve cohort (Arm A) and 23 patients in the prior-taxane cohort (Arm B), from January 8, 2013, to April 8, 2015: median age 61.7 years (range, 35.5-91.8 years), 66% male, 66% Caucasian. The most common adverse events included neutropenia (17% Arm A and 39% Arm B), fatigue/muscle weakness (13%), and hematuria (12%). In Arm A, the 3-month PFS rate was 28% [95% confidence interval (CI), 17%-42%] and did not meet the prespecified efficacy target. The 3-month PFS rate in Arm B was 35% (95% CI, 16%-57%) and surpassed its efficacy target. HER2 amplification or overexpression was associated with improved disease control (P = 0.003), PFS (P = 0.04), and overall survival (P = 0.002). An M2 macrophage signature was also associated with improved survival (P = 0.031). CONCLUSIONS Cabazitaxel has modest activity in advanced gastric cancer, including in patients previously treated with taxanes. Her2 amplification/overexpression and M2 high macrophage signature are potential biomarkers for taxane efficacy that warrant further evaluation.
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Affiliation(s)
- Manish A Shah
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York. .,Englander Institute of Precision Medicine, Meyer Cancer Center, New York, New York
| | - Peter Enzinger
- Dana-Farber Cancer Center, Medical Oncology, Boston, Massachusetts
| | - Andrew H Ko
- University of California San Francisco, Medical Oncology, San Francisco, California
| | - Allyson J Ocean
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Philip Agop Philip
- Department of Medical Oncology, Barbara Ann Karmanos Cancer Institute, Detroit, Michigan
| | - Prashant V Thakkar
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Kyle Cleveland
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Yao Lu
- Division of Biostatistics and Epidemiology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Jeremy Kortmansky
- Yale Cancer Center, Division of Medical Oncology and Hematology, New Haven, Connecticut
| | - Paul J Christos
- Division of Biostatistics and Epidemiology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Chao Zhang
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Navjot Kaur
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Dina Elmonshed
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Giuseppe Galletti
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Sandipto Sarkar
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Bhavneet Bhinder
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York.,Englander Institute of Precision Medicine, Meyer Cancer Center, New York, New York.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Meredith E Pittman
- Department of Anatomic and Clinical Pathology, Weill Cornell, New York, New York
| | | | | | | | | | - Olivier Elemento
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Doron Betel
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Paraskevi Giannakakou
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Heinz-Josef Lenz
- University of Southern California, Norris Cancer Center, Medical Oncology, Los Angeles, California
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11
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Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell 2020; 37:551-568.e14. [PMID: 32289277 PMCID: PMC8459709 DOI: 10.1016/j.ccell.2020.03.015] [Citation(s) in RCA: 511] [Impact Index Per Article: 127.8] [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: 10/19/2019] [Revised: 01/03/2020] [Accepted: 03/16/2020] [Indexed: 12/22/2022]
Abstract
The development of precision medicine approaches for diffuse large B cell lymphoma (DLBCL) is confounded by its pronounced genetic, phenotypic, and clinical heterogeneity. Recent multiplatform genomic studies revealed the existence of genetic subtypes of DLBCL using clustering methodologies. Here, we describe an algorithm that determines the probability that a patient's lymphoma belongs to one of seven genetic subtypes based on its genetic features. This classification reveals genetic similarities between these DLBCL subtypes and various indolent and extranodal lymphoma types, suggesting a shared pathogenesis. These genetic subtypes also have distinct gene expression profiles, immune microenvironments, and outcomes following immunochemotherapy. Functional analysis of genetic subtype models highlights distinct vulnerabilities to targeted therapy, supporting the use of this classification in precision medicine trials.
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MESH Headings
- Animals
- Apoptosis
- Biomarkers, Tumor/genetics
- Cell Proliferation
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Genetic Heterogeneity
- Humans
- Lymphoma, Large B-Cell, Diffuse/classification
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Molecular Targeted Therapy
- Precision Medicine
- Tumor Cells, Cultured
- Tumor Microenvironment
- Xenograft Model Antitumor Assays
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Affiliation(s)
- George W Wright
- Biometric Research Branch, Division of Cancer Diagnosis and Treatment, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Da Wei Huang
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James D Phelan
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zana A Coulibaly
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandrine Roulland
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan M Young
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James Q Wang
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Roland Schmitz
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Jeffrey Tang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Aixiang Jiang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | | | | | | | - Calvin A Johnson
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wyndham H Wilson
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David W Scott
- British Columbia Cancer, Vancouver, BC V5Z 4E6, Canada
| | - Louis M Staudt
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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12
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Li F, Lizee G, Hwu P, Du X, Deng L, Talukder A, Katailiha A, Zou Q, Roszik J, Hawke D, Jackson K, Bradley S, Wang Y, Ataullakhanov R, Bagaev A, Kotlov N, Svekolkin V, Miheecheva N, Frenkel F, Sonnemann H. The role of EGFR inhibitor (EGFRi) in immune cell infiltration and CD8+ T-cell activation in EGFR mutant lung cancer. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz238.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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13
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Bagaev A, Mizyuk A, Khatmullina L, Isachenko I, Chubarenko I. Anthropogenic fibres in the Baltic Sea water column: Field data, laboratory and numerical testing of their motion. Sci Total Environ 2017; 599-600:560-571. [PMID: 28494282 DOI: 10.1016/j.scitotenv.2017.04.185] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/21/2017] [Accepted: 04/24/2017] [Indexed: 05/06/2023]
Abstract
Distribution of microplastics particles (MPs) in the water column is investigated on the base of 95 water samples collected from various depths in the Baltic Sea Proper in 2015-2016. Fibres are the prevalent type of MPs: 7% of the samples contained small films; about 40% had (presumably) paint flakes, while 63% contained coloured fibres in concentrations from 0.07 to 2.6 items per litre. Near-surface and near-bottom layers (defined as one tenth of the local depth) have 3-5 times larger fibre concentrations than intermediate layers. Laboratory tests demonstrated that sinking behaviour of a small and flexible fibre can be complicated, with 4-fold difference in sinking velocity for various random fibres' curvature during its free fall. Numerical tests on transport of fibres in the Baltic Sea Proper were performed using HIROMB reanalysis data (2007) for the horizontal velocity field and laboratory order-of-magnitude estimates for the sinking velocity of fibres. The model takes into account (i) motion of fibres together with currents, (ii) their very slow sinking, and (iii) their low re-suspension threshold. Sensitivity of the final distribution of fibres to variations of those parameters is examined. These experiments are the first step towards modelling of transport of fibres in marine environment and they seem to reproduce the main features of fibres distribution quite well.
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Affiliation(s)
- A Bagaev
- Atlantic Branch of P.P. Shirshov Institute of Oceanology of Russian Academy of Sciences, Prospect Mira, 1, Kaliningrad 236022, Russia.
| | - A Mizyuk
- Marine Hydrophysical Institute of Russian Academy of Sciences, Kapitanskaya str., 31, Sevastopol 299011, Russia
| | - L Khatmullina
- Atlantic Branch of P.P. Shirshov Institute of Oceanology of Russian Academy of Sciences, Prospect Mira, 1, Kaliningrad 236022, Russia
| | - I Isachenko
- Atlantic Branch of P.P. Shirshov Institute of Oceanology of Russian Academy of Sciences, Prospect Mira, 1, Kaliningrad 236022, Russia
| | - I Chubarenko
- Atlantic Branch of P.P. Shirshov Institute of Oceanology of Russian Academy of Sciences, Prospect Mira, 1, Kaliningrad 236022, Russia
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14
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Chubarenko I, Bagaev A, Zobkov M, Esiukova E. On some physical and dynamical properties of microplastic particles in marine environment. Mar Pollut Bull 2016; 108:105-12. [PMID: 27184128 DOI: 10.1016/j.marpolbul.2016.04.048] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 04/22/2016] [Accepted: 04/24/2016] [Indexed: 05/06/2023]
Abstract
Simplified physical models and geometrical considerations reveal general physical and dynamical properties of microplastic particles (0.5-5mm) of different density, shape and size in marine environment. Windage of extremely light foamed particles, surface area and fouling rate of slightly positively buoyant microplastic spheres, films and fibres and settling velocities of negatively buoyant particles are analysed. For the Baltic Sea dimensions and under the considered idealised external conditions, (i) only one day is required for a foamed polystyrene particle to cross the sea (ca. 250km); (ii) polyethylene fibres should spend about 6-8months in the euphotic zone before sinking due to bio-fouling, whilst spherical particles can be retained on the surface up to 10-15years; (iii) for heavy microplastic particles, the time of settling through the water column in the central Gotland basin (ca. 250m) is less than 18h. Proper physical setting of the problem of microplastics transport and developing of physically-based parameterisations are seen as applications.
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Affiliation(s)
- I Chubarenko
- Atlantic Branch of P.P. Shirshov Institute of Oceanology of Russian Academy of Sciences, Prospect Mira, 1, Kaliningrad, 236022, Russia.
| | - A Bagaev
- Atlantic Branch of P.P. Shirshov Institute of Oceanology of Russian Academy of Sciences, Prospect Mira, 1, Kaliningrad, 236022, Russia.
| | - M Zobkov
- Atlantic Branch of P.P. Shirshov Institute of Oceanology of Russian Academy of Sciences, Prospect Mira, 1, Kaliningrad, 236022, Russia.
| | - E Esiukova
- Atlantic Branch of P.P. Shirshov Institute of Oceanology of Russian Academy of Sciences, Prospect Mira, 1, Kaliningrad, 236022, Russia.
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