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Schuster SJ, Huw LY, Bolen CR, Maximov V, Polson AG, Hatzi K, Lasater EA, Assouline SE, Bartlett NL, Budde LE, Matasar MJ, Koeppen H, Piccione EC, Wilson D, Wei MC, Yin S, Penuel E. Loss of CD20 expression as a mechanism of resistance to mosunetuzumab in relapsed/refractory B-cell lymphomas. Blood 2024; 143:822-832. [PMID: 38048694 PMCID: PMC10934296 DOI: 10.1182/blood.2023022348] [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: 08/28/2023] [Revised: 10/24/2023] [Accepted: 11/15/2023] [Indexed: 12/06/2023] Open
Abstract
ABSTRACT CD20 is an established therapeutic target in B-cell malignancies. The CD20 × CD3 bispecific antibody mosunetuzumab has significant efficacy in B-cell non-Hodgkin lymphomas (NHLs). Because target antigen loss is a recognized mechanism of resistance, we evaluated CD20 expression relative to clinical response in patients with relapsed and/or refractory NHL in the phase 1/2 GO29781 trial investigating mosunetuzumab monotherapy. CD20 was studied using immunohistochemistry (IHC), RNA sequencing, and whole-exome sequencing performed centrally in biopsy specimens collected before treatment at predose, during treatment, or upon progression. Before treatment, most patients exhibited a high proportion of tumor cells expressing CD20; however, in 16 of 293 patients (5.5%) the proportion was <10%. Analyses of paired biopsy specimens from patients on treatment revealed that CD20 levels were maintained in 29 of 30 patients (97%) vs at progression, where CD20 loss was observed in 11 of 32 patients (34%). Reduced transcription or acquisition of truncating mutations explained most but not all cases of CD20 loss. In vitro modeling confirmed the effects of CD20 variants identified in clinical samples on reduction of CD20 expression and missense mutations in the extracellular domain that could block mosunetuzumab binding. This study expands the knowledge about the occurrence of target antigen loss after anti-CD20 therapeutics to include CD20-targeting bispecific antibodies and elucidates mechanisms of reduced CD20 expression at disease progression that may be generalizable to other anti-CD20 targeting agents. These results also confirm the utility of readily available IHC staining for CD20 as a tool to inform clinical decisions. This trial was registered at www.ClinicalTrials.gov as #NCT02500407.
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Affiliation(s)
- Stephen J. Schuster
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | | | | | | | | | | | | | | | - Nancy L. Bartlett
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | | | | | | | | | | | | | - Shen Yin
- Genentech, Inc., South San Francisco, CA
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2
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Tabari E, Lovejoy AF, Lin H, Bolen CR, Lor Saelee S, Lefkowitz JP, Kurtz DM, Bottos A, Nielsen TG, Parreira JM, Luong KT. NGS-determined molecular markers and disease burden metrics from ctDNA correlate with PFS in previously untreated DLBCL. Leuk Lymphoma 2024:1-11. [PMID: 38337191 DOI: 10.1080/10428194.2024.2301924] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/02/2024] [Indexed: 02/12/2024]
Abstract
Personalized risk stratification and treatment may help improve outcomes among patients with diffuse large B-cell lymphoma (DLBCL). We developed a next-generation sequencing (NGS)-based method to assess a range of potential prognostic indicators, and evaluated it using pretreatment plasma samples from 310 patients with previously untreated DLBCL from the GOYA trial (NCT01287741). Variant calls and DLBCL subtyping with the plasma-based method were concordant with corresponding tissue-based methods. Patients with a tumor burden greater than the median (p = .003) and non-germinal center B-cell-like (non-GCB) DLBCL (p = .049) had worse progression-free survival than patients with a tumor burden less than the median or GCB DLBCL. Multi-factor assessment combining orthogonal features from a single pretreatment plasma sample has promise as a prognostic indicator in this setting (p = .085). This minimally invasive plasma-based NGS assay could enable comprehensive prognostic assessment of patients in a clinical setting, with greater accessibility than current methods.
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Affiliation(s)
| | | | - Hai Lin
- Roche Sequencing Solutions, Pleasanton, CA, USA
| | | | | | | | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
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3
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Laurent C, Flores M, Chartier L, Huet S, Bolen CR, Venstrom JM, Chassagne-Clément C, Dartigues-Cuilléres P, Charlotte F, Tesson B, Salles G, Morschhauser F, Xerri L. Long-term follow-up confirms the favourable prognostic impact of high numbers of tumour infiltrating CD3 T-cells in follicular lymphoma patients treated by rituximab-maintenance regimen. Br J Haematol 2023; 202:686-689. [PMID: 37218065 PMCID: PMC10755216 DOI: 10.1111/bjh.18881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/09/2023] [Accepted: 05/13/2023] [Indexed: 05/24/2023]
Affiliation(s)
- Camille Laurent
- Institut Universitaire Cancer-Oncopole, CHU Toulouse, INSERM U1037, Toulouse, France
| | | | | | - Sarah Huet
- Hospices Civils De Lyon, Pierre Bénite, France
| | | | | | | | | | | | | | - Gilles Salles
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Luc Xerri
- Institut Paoli-Calmettes, CRCM and Aix-Marseille University, Marseille, France
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4
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Schuster SJ, Huw LY, Bolen CR, Assouline SE, Bartlett NL, Budde LE, Matasar MJ, Koeppen H, Piccione EC, Wilson D, Wei MC, Yin S, Penuel EM. Characterization of CD20 expression loss as a mechanism of resistance to mosunetuzumab in patients with relapsed/refractory B-cell non-Hodgkin lymphomas. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.7526] [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
7526 Background: Mosunetuzumab (M) is a bispecific antibody targeting CD20 and CD3 that redirects T cells to engage and eliminate malignant B cells being developed for relapsed or refractory (R/R) B-cell non-Hodgkin lymphomas (B-NHL). CD20 is an optimal target, with uniform expression across B-NHL histologies and minimal receptor turnover. We characterized CD20 loss as a potential mechanism of resistance to M in patients (pts) on a Phase I/II trial (NCT02500407) receiving M monotherapy for the treatment (tx) of R/R B-NHL. Methods: Pts with R/R B-NHL received M intravenously in 3-week cycles, for eight to 17 cycles depending on tumor response. At baseline (BL), biomarker-evaluable (archival or fresh) biopsies were collected from 293 pts. Biopsies from 62 pts were collected at additional time points during tx with M and/or at disease progression (PD). The proportion of CD20+ and PAX5+ tumor cells was determined by immunohistochemistry (IHC) using dual-staining with anti-CD20 (clone L26, VENTANA) and anti-PAX5 (clone DAK-PAX5, DAKO) antibodies. Expression of MS4A1, the gene encoding CD20 , was measured by RNA-sequencing (RNA-seq); MS4A1 mutation profiling was performed by whole exome sequencing (WES). Levels of CD20 expression were assessed relative to response rates. Correlative analyses were performed and assessed centrally (IHC, RNA-seq, and WES) and locally (IHC). Results: CD20 levels were consistently high ( > 75% CD20+PAX5+ cells) in the majority of BL biopsies and generally comparable across histologies (FL, DLBCL, tFL, MCL, and RT). BL CD20 loss (≤5% CD20+PAX5+ cells) was seen in 16/293 pts (5.5%), more commonly in aggressive NHL, and responses to M were not seen in these pts. Among 62 pts with BL and on-tx/at-PD biopsies, BL CD20 levels were ≤5% in 7/62 pts (11%) (6/7 pts [86%] progressed before completing Cycle 2). CD20 levels were maintained in on-tx biopsies from 23/24 pts (96%). At PD, biopsies showed CD20 loss in 7/26 pts (27%). For five pts with BL, on-tx and at-PD biopsies, all pts maintained CD20 while on-tx and 1/5 pts (20%) had CD20 loss at PD. There was no clear association between CD20 reduction and histology. Data from 185 BL biopsies showed generally concordant levels of CD20 gene and protein expression (r = 0.72). In 10/185 pts (5%), MS4A1 was expressed without detectable CD20 protein expression; DNA sequencing revealed novel mutations in MS4A1, including mutations leading to truncation of the protein. CD20 transmembrane and extra-cellular domain mutations were also observed but do not block CD20 expression. Conclusions: In pts with R/R B-NHL treated with M, low BL CD20 expression is associated with lack of response to M. During M tx, loss of tumor cell expression of CD20 is one mechanism of acquired resistance; however, CD20 expression is maintained in most pts with PD, implying alternative mechanisms for acquired M resistance. Clinical trial information: NCT02500407.
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Affiliation(s)
- Stephen J. Schuster
- Lymphoma Program, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
| | | | | | | | - Nancy L. Bartlett
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | | | | | | | | | | | | | - Shen Yin
- Genentech, Inc., South San Francisco, CA
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Kostakoglu L, Dalmasso F, Berchialla P, Pierce LA, Vitolo U, Martelli M, Sehn LH, Trněný M, Nielsen TG, Bolen CR, Sahin D, Lee C, El‐Galaly TC, Mattiello F, Kinahan PE, Chauvie S. A prognostic model integrating PET‐derived metrics and image texture analyses with clinical risk factors from GOYA. eJHaem 2022; 3:406-414. [PMID: 35846039 PMCID: PMC9175666 DOI: 10.1002/jha2.421] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 11/05/2022]
Abstract
Image texture analysis (radiomics) uses radiographic images to quantify characteristics that may identify tumour heterogeneity and associated patient outcomes. Using fluoro‐deoxy‐glucose positron emission tomography/computed tomography (FDG‐PET/CT)‐derived data, including quantitative metrics, image texture analysis and other clinical risk factors, we aimed to develop a prognostic model that predicts survival in patients with previously untreated diffuse large B‐cell lymphoma (DLBCL) from GOYA (NCT01287741). Image texture features and clinical risk factors were combined into a random forest model and compared with the international prognostic index (IPI) for DLBCL based on progression‐free survival (PFS) and overall survival (OS) predictions. Baseline FDG‐PET scans were available for 1263 patients, 832 patients of these were cell‐of‐origin (COO)‐evaluable. Patients were stratified by IPI or radiomics features plus clinical risk factors into low‐, intermediate‐ and high‐risk groups. The random forest model with COO subgroups identified a clearer high‐risk population (45% 2‐year PFS [95% confidence interval (CI) 40%–52%]; 65% 2‐year OS [95% CI 59%–71%]) than the IPI (58% 2‐year PFS [95% CI 50%–67%]; 69% 2‐year OS [95% CI 62%–77%]). This study confirms that standard clinical risk factors can be combined with PET‐derived image texture features to provide an improved prognostic model predicting survival in untreated DLBCL.
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Affiliation(s)
- Lale Kostakoglu
- Department of Radiology and Medical Imaging University of Virginia Charlottesville Virginia USA
| | | | - Paola Berchialla
- Department of Clinical and Biological Sciences University of Turin Turin Italy
| | - Larry A. Pierce
- Department of Radiology University of Washington Seattle Washington USA
| | - Umberto Vitolo
- Multidisciplinary Oncology Outpatient Clinic Candiolo Cancer Institute Candiolo Italy
| | - Maurizio Martelli
- Hematology Department of Translational and Precision Medicine Sapienza University Rome Italy
| | - Laurie H. Sehn
- BC Cancer Center for Lymphoid Cancer and the University of British Columbia Vancouver British Columbia Canada
| | - Marek Trněný
- 1st Faculty of Medicine Charles University General Hospital Prague Czech Republic
| | | | | | | | - Calvin Lee
- Genentech, Inc. South San Francisco California USA
| | - Tarec Christoffer El‐Galaly
- F. Hoffmann‐La Roche Ltd Basel Switzerland
- Department of Hematology Aalborg University Hospital Aalborg Denmark
| | | | - Paul E. Kinahan
- Department of Radiology University of Washington Seattle Washington USA
| | - Stephane Chauvie
- Department of Clinical and Biological Sciences University of Turin Turin Italy
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6
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Kim E, Jiang Y, Xu T, Bazeos A, Knapp A, Bolen CR, Humphrey K, Nielsen TG, Penuel E, Paulson JN. Prognostic mutational subtyping in de novo diffuse large B-cell lymphoma. BMC Cancer 2022; 22:231. [PMID: 35236331 PMCID: PMC8892802 DOI: 10.1186/s12885-022-09237-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/13/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease defined using a number of well-established molecular subsets. Application of non-negative matrix factorization (NMF) to whole exome sequence data has previously been used to identify six distinct molecular clusters in DLBCL with potential clinical relevance. In this study, we applied NMF-clustering to targeted sequencing data utilizing the FoundationOne Heme® panel from the Phase III GOYA (NCT01287741) and Phase Ib/II CAVALLI studies (NCT02055820) in de novo DLBCL. Biopsy samples, survival outcomes, RNA-Seq and targeted exome-sequencing data were available for 423 patients in GOYA (obinutuzumab [G]-cyclophosphamide, doxorubicin, vincristine, and prednisone [CHOP] vs rituximab [R]-CHOP) and 86 patients in CAVALLI (venetoclax+[G/R]-CHOP). RESULTS When the NMF algorithm was applied to samples from the GOYA study analyzed using a comprehensive genomic profiling platform, four of the six groups previously reported were observed: MYD88/CD79B, BCL2/EZH2, NOTCH2/TNFAIP3, and no mutations. Mutation profiles, cell-of-origin subset distributions and clinical associations of MYD88/CD79B and BCL2/EZH2 groups were similar to those described in previous NMF studies. In contrast, application of NMF to the CAVALLI study yielded only three; MYD88/CD79B-, BCL2/EZH2-like clusters, and a no mutations group, and there was a trend towards improved outcomes for BCL2/EZH2 over MYD88/CD79B. CONCLUSIONS This analysis supports the utility of NMF used in conjunction with targeted sequencing platforms for identifying patients with different prognostic subsets. The observed trend for improved overall survival in the BCL2/EZH2 group is consistent with the mechanism of action of venetoclax, suggesting that targeting sequencing and NMF has potential for identifying patients who are more likely to gain benefit from venetoclax therapy.
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Affiliation(s)
- Eugene Kim
- Department of Biostatistics, Product Development, Genentech, Inc, 1 DNA Way, MS 444A, South San Francisco, CA, 94080, USA
| | - Yanwen Jiang
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA, USA
| | - Tao Xu
- PHC Analytics, Product Development, F. Hoffmann La-Roche Ltd, Basel, Switzerland
| | | | - Andrea Knapp
- Pharma Development Clinical Oncology, F. Hoffmann La-Roche Ltd, Basel, Switzerland
| | - Christopher R Bolen
- Bioinformatics & Computational Biology, Genentech, Inc, South San Francisco, CA, USA
| | | | - Tina G Nielsen
- Pharma Development Clinical Oncology, F. Hoffmann La-Roche Ltd, Basel, Switzerland
| | - Elicia Penuel
- Oncology Biomarker Development, Genentech, Inc, South San Francisco, CA, USA
| | - Joseph N Paulson
- Department of Biostatistics, Product Development, Genentech, Inc, 1 DNA Way, MS 444A, South San Francisco, CA, 94080, USA.
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7
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Abbas HA, Mohanty V, Wang R, Huang Y, Liang S, Wang F, Zhang J, Qiu Y, Hu CW, Qutub AA, Dail M, Bolen CR, Daver N, Konopleva M, Futreal A, Chen K, Wang L, Kornblau SM. Decoupling Lineage-Associated Genes in Acute Myeloid Leukemia Reveals Inflammatory and Metabolic Signatures Associated With Outcomes. Front Oncol 2021; 11:705627. [PMID: 34422660 PMCID: PMC8372368 DOI: 10.3389/fonc.2021.705627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Received: 05/05/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease with variable responses to therapy. Cytogenetic and genomic features are used to classify AML patients into prognostic and treatment groups. However, these molecular characteristics harbor significant patient-to-patient variability and do not fully account for AML heterogeneity. RNA-based classifications have also been applied in AML as an alternative approach, but transcriptomic grouping is strongly associated with AML morphologic lineages. We used a training cohort of newly diagnosed AML patients and conducted unsupervised RNA-based classification after excluding lineage-associated genes. We identified three AML patient groups that have distinct biological pathways associated with outcomes. Enrichment of inflammatory pathways and downregulation of HOX pathways were associated with improved outcomes, and this was validated in 2 independent cohorts. We also identified a group of AML patients who harbored high metabolic and mTOR pathway activity, and this was associated with worse clinical outcomes. Using a comprehensive reverse phase protein array, we identified higher mTOR protein expression in the highly metabolic group. We also identified a positive correlation between degree of resistance to venetoclax and mTOR activation in myeloid and lymphoid cell lines. Our approach of integrating RNA, protein, and genomic data uncovered lineage-independent AML patient groups that share biologic mechanisms and can inform outcomes independent of commonly used clinical and demographic variables; these groups could be used to guide therapeutic strategies.
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Affiliation(s)
- Hussein A Abbas
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Vakul Mohanty
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yuefan Huang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Biostatistics & Data Science, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Shaoheng Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Computer Science, Rice University, Houston, TX, United States
| | - Feng Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yihua Qiu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Chenyue W Hu
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Amina A Qutub
- Department of Bioengineering, Rice University, Houston, TX, United States
| | - Monique Dail
- Oncology Biomarker Development, Genentech Inc, South San Francisco, CA, United States
| | - Christopher R Bolen
- Oncology Bioinformatics, Genentech Inc, South San Francisco, CA, United States
| | - Naval Daver
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Marina Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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8
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Nowicka M, Hilton LK, Ashton-Key M, Hargreaves CE, Lee C, Foxall R, Carter MJ, Beers SA, Potter KN, Bolen CR, Klein C, Knapp A, Mir F, Rose-Zerilli M, Burton C, Klapper W, Scott DW, Sehn LH, Vitolo U, Martelli M, Trneny M, Rushton CK, Slack GW, Farinha P, Strefford JC, Oestergaard MZ, Morin RD, Cragg MS. Prognostic significance of FCGR2B expression for the response of DLBCL patients to rituximab or obinutuzumab treatment. Blood Adv 2021; 5:2945-2957. [PMID: 34323958 PMCID: PMC8361458 DOI: 10.1182/bloodadvances.2021004770] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/08/2021] [Indexed: 01/16/2023] Open
Abstract
Fc γ receptor IIB (FcγRIIB) is an inhibitory molecule capable of reducing antibody immunotherapy efficacy. We hypothesized its expression could confer resistance in patients with diffuse large B-cell lymphoma (DLBCL) treated with anti-CD20 monoclonal antibody (mAb) chemoimmunotherapy, with outcomes varying depending on mAb (rituximab [R]/obinutuzumab [G]) because of different mechanisms of action. We evaluated correlates between FCGR2B messenger RNA and/or FcγRIIB protein expression and outcomes in 3 de novo DLBCL discovery cohorts treated with R plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) reported by Arthur, Schmitz, and Reddy, and R-CHOP/G-CHOP-treated patients in the GOYA trial (NCT01287741). In the discovery cohorts, higher FCGR2B expression was associated with significantly shorter progression-free survival (PFS; Arthur: hazard ratio [HR], 1.09; 95% confidence interval [CI], 1.01-1.19; P = .0360; Schmitz: HR, 1.13; 95% CI, 1.02-1.26; P = .0243). Similar results were observed in GOYA with R-CHOP (HR, 1.26; 95% CI, 1.00-1.58; P = .0455), but not G-CHOP (HR, 0.91; 95% CI, 0.69-1.20; P = .50). A nonsignificant trend that high FCGR2B expression favored G-CHOP over R-CHOP was observed (HR, 0.67; 95% CI, 0.44-1.02; P = .0622); however, low FCGR2B expression favored R-CHOP (HR, 1.58; 95% CI, 1.00-2.50; P = .0503). In Arthur and GOYA, FCGR2B expression was associated with tumor FcγRIIB expression; correlating with shorter PFS for R-CHOP (HR, 2.17; 95% CI, 1.04-4.50; P = .0378), but not G-CHOP (HR, 1.37; 95% CI, 0.66-2.87; P = .3997). This effect was independent of established prognostic biomarkers. High FcγRIIB/FCGR2B expression has prognostic value in R-treated patients with DLBCL and may confer differential responsiveness to R-CHOP/G-CHOP.
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Affiliation(s)
| | - Laura K Hilton
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Margaret Ashton-Key
- School of Cancer Sciences, University of Southampton, Southampton, United Kingdom
- Southampton University Hospitals NHS Foundation Trust, Southampton, United Kingdom
| | - Chantal E Hargreaves
- School of Cancer Sciences, University of Southampton, Southampton, United Kingdom
| | - Chern Lee
- Southampton University Hospitals NHS Foundation Trust, Southampton, United Kingdom
| | - Russell Foxall
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton, Faculty of Medicine, Southampton, United Kingdom
| | - Matthew J Carter
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton, Faculty of Medicine, Southampton, United Kingdom
| | - Stephen A Beers
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton, Faculty of Medicine, Southampton, United Kingdom
| | - Kathleen N Potter
- School of Cancer Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | | | - Farheen Mir
- Royal Marsden Hospital, Sutton, United Kingdom
| | - Matthew Rose-Zerilli
- School of Cancer Sciences, University of Southampton, Southampton, United Kingdom
| | - Cathy Burton
- St James's Institute of Oncology, Leeds, United Kingdom
| | - Wolfram Klapper
- Department of Hematopathology, University of Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - David W Scott
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Laurie H Sehn
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Umberto Vitolo
- Multidisciplinary Oncology Outpatient Clinic, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Maurizio Martelli
- Department of Translational and Precision Medicine, Hematology, Sapienza University, Rome, Italy
| | - Marek Trneny
- 1st Medical Faculty, Charles University, Prague, Czech Republic; and
| | - Christopher K Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; and
| | - Graham W Slack
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
| | - Pedro Farinha
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
| | - Jonathan C Strefford
- School of Cancer Sciences, University of Southampton, Southampton, United Kingdom
| | | | - Ryan D Morin
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; and
| | - Mark S Cragg
- School of Cancer Sciences, University of Southampton, Southampton, United Kingdom
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton, Faculty of Medicine, Southampton, United Kingdom
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9
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Strefford JC, Nowicka M, Hargreaves CE, Burton C, Davies A, Ganderton R, Hiddemann W, Iriyama C, Klapper W, Latham KV, Martelli M, Mir F, Parker H, Potter KN, Rose-Zerilli MJJ, Sehn LH, Trněný M, Vitolo U, Bolen CR, Klein C, Knapp A, Oestergaard MZ, Cragg MS. Single-nucleotide Fcγ receptor polymorphisms do not impact obinutuzumab/rituximab outcome in patients with lymphoma. Blood Adv 2021; 5:2935-2944. [PMID: 34323957 PMCID: PMC8361457 DOI: 10.1182/bloodadvances.2020003985] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/03/2021] [Indexed: 01/16/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) have been shown to influence Fcγ receptor (FcγR) affinity and activity, but their effect on treatment response is unclear. We assessed their importance in the efficacy of obinutuzumab or rituximab combined with chemotherapy in untreated advanced follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) in the GALLIUM (www.clinicaltrials.gov #NCT01332968) and GOYA (#NCT01287741) trials, respectively. Genomic DNA was extracted from patients enrolled in GALLIUM (n = 1202) and GOYA (n = 1418). Key germline SNPs, FCGR2A R131H (rs1801274), FCGR3A F158V (rs396991), and FCGR2B I232T (rs1050501), were genotyped and assessed for their impact on investigator-assessed progression-free survival (PFS). In both cohorts there was no prognostic effect of FCGR2A or FCGR3A. In FL, FCGR2B was associated with favorable PFS in univariate and multivariate analyses comparing I232T with I232I, with a more modest association for rituximab-treated (univariate: hazard ratio [HR], 0.78; 95% confidence interval [CI], 0.54-1.14; P = .21) vs obinutuzumab-treated patients (HR, 0.56; 95% CI, 0.34-0.91; P = .02). Comparing T232T with I232I, an association was found for obinutuzumab (univariate: HR, 2.76; 95% CI, 1.02-7.5; P = .0459). Neither observation retained significance after multiple-test adjustment. FCGR2B was associated with poorer PFS in multivariate analyses comparing T232T with I232I in rituximab- but not obinutuzumab-treated patients with DLBCL (HR, 4.40; 95% CI, 1.71-11.32; P = .002; multiple-test-adjusted P = .03); however, this genotype was rare (n = 13). This study shows that FcγR genotype is not associated with response to rituximab/obinutuzumab plus chemotherapy in treatment-naive patients with advanced FL or DLBCL.
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Affiliation(s)
- Jonathan C Strefford
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | | | - Chantal E Hargreaves
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Cathy Burton
- Haematological Malignancy Diagnostic Service, Leeds Cancer Centre, Leeds, United Kingdom
| | - Andrew Davies
- Southampton Cancer Research United Kingdom (CRUK)/National Institute of Health Research (NIHR) Experimental Cancer Medicines Centre, University of Southampton, Southampton, United Kingdom
| | - Rosalind Ganderton
- Southampton University Hospitals National Health Service (NHS) Foundation Trust, Southampton, United Kingdom
| | - Wolfgang Hiddemann
- Department of Medicine III, Ludwig-Maximilians University Hospital Munich, Munich, Germany
| | - Chisako Iriyama
- Department of Pathology and Tumor Biology, Nagoya Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Wolfram Klapper
- Department of Hematopathology, University of Kiel, Kiel, Germany
| | - Kate V Latham
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Maurizio Martelli
- Department of Translational and Precision Medicine, Section of Hematology, Sapienza University, Rome, Italy
| | - Farheen Mir
- Royal Marsden Hospital, London, United Kingdom
| | - Helen Parker
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Kathleen N Potter
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Matthew J J Rose-Zerilli
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Laurie H Sehn
- BC Cancer Centre for Lymphoid Cancer
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marek Trněný
- 1st Department of Medicine, 1st Faculty of Medicine, Charles University General Hospital, Prague, Czech Republic
| | - Umberto Vitolo
- Multidisciplinary Oncology Outpatient Clinic, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | | | - Christian Klein
- Roche Innovation Center Zurich, Roche Glycart AG, Schlieren, Switzerland; and
| | | | | | - Mark S Cragg
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton Faculty of Medicine, University of Southampton, Southampton, United Kingdom
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10
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Trabucco SE, Sokol ES, Maund SL, Moore JA, Frampton GM, Albacker LA, Oestergaard MZ, Venstrom J, Sehn LH, Bolen CR. Prediction and characterization of diffuse large B-cell lymphoma cell-of-origin subtypes using targeted sequencing. Future Oncol 2021; 17:4171-4183. [PMID: 34313135 DOI: 10.2217/fon-2021-0370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The aim of the present study was to determine cell of origin (COO) from a platform using a DNA-based method, COO DNA classifier (COODC). A targeted exome-sequencing platform that applies the mutational profile of a sample was used to classify COO subtype. Two major mutational signatures associated with COO were identified: Catalogue of Somatic Mutations in Cancer (COSMIC) signature 23 enriched in activated B-cell (ABC) and COSMIC signature 3, which suggested increased frequency in germinal center B-cell (GCB). Differential mutation signatures linked oncogenesis to mutational processes during B-cell activation, confirming the putative origin of GCB and ABC subtypes. Integrating COO with comprehensive genomic profiling enabled identification of features associated with COO and demonstrated the feasibility of determining COO without RNA.
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Affiliation(s)
| | | | | | - Jay A Moore
- Foundation Medicine, Inc., Cambridge MA 02141, USA
| | | | | | | | | | - Laurie H Sehn
- BC Cancer Centre for Lymphoid Cancer & University of British Columbia, Vancouver, BC, V5Z 1L3, Canada
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11
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Mir F, Mattiello F, Grigg A, Herold M, Hiddemann W, Marcus R, Seymour JF, Bolen CR, Knapp A, Nielsen T, Casulo C. Follicular Lymphoma Evaluation Index (FLEX): A new clinical prognostic model that is superior to existing risk scores for predicting progression-free survival and early treatment failure after frontline immunochemotherapy. Am J Hematol 2020; 95:1503-1510. [PMID: 32815559 PMCID: PMC7756469 DOI: 10.1002/ajh.25973] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 03/09/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 12/28/2022]
Abstract
Patients with advanced‐stage follicular lymphoma (FL) who progress early after receiving first‐line therapy have poor overall survival (OS). Currently applied clinical prognostic models such as FL International Prognostic Index [FLIPI], FLIPI‐2 and PRIMA‐Prognostic Index [PRIMA‐PI] have suboptimal sensitivity and specificity to predict this poor prognosis subgroup. The primary objective was to develop a novel prognostic model, the FL Evaluation Index (FLEX) score, to identify high‐risk patients and compare its performance with FLIPI, FLIPI‐2 and PRIMA‐PI. Progression‐free survival (PFS) after first‐line immunochemotherapy was the key endpoint, while OS and progression of disease within 24 months (POD24) were also assessed. The model, which includes nine clinical variables, was developed using a cohort of patients with previously untreated advanced‐stage FL from the phase 3 GALLIUM trial (NCT01332968). The performance of the model was validated using data from the SABRINA trial (NCT01200758). In GALLIUM (n = 1004; 127 with and 877 without POD24), FLEX increased the intergroup (low‐risk/high‐risk) difference in 2‐year and 3‐year PFS rates and demonstrated superior intergroup differences in 2‐year and 3‐year OS rates compared with FLIPI, FLIPI‐2 and PRIMA‐PI. Sensitivity for a high‐risk score to predict POD24 was 60% using FLEX compared with 53% for FLIPI and FLIPI‐2, and 69% for PRIMA‐PI, while specificity was 68% for FLEX compared with 58% for FLIPI, 59% for FLIPI‐2 and 48% for PRIMA‐PI. The prognostic value of FLEX in SABRINA was similar to FLIPI. Therefore, FLEX appears to perform better than existing prognostic models in previously untreated FL, in particular for the newer treatment regimens.
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Affiliation(s)
- Farheen Mir
- The Royal Marsden NHS Trust Foundation London UK
| | | | | | | | | | | | - John F. Seymour
- Peter MacCallum Cancer Centre Royal Melbourne Hospital and University of Melbourne Melbourne Victoria Australia
| | | | | | | | - Carla Casulo
- Wilmot Cancer Institute University of Rochester New York New York USA
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12
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Kater AP, Wu JQ, Kipps T, Eichhorst B, Hillmen P, D’Rozario J, Assouline S, Owen C, Robak T, de la Serna J, Jaeger U, Cartron G, Montillo M, Dubois J, Eldering E, Mellink C, Van Der Kevie-Kersemaekers AM, Kim SY, Chyla B, Punnoose E, Bolen CR, Assaf ZJ, Jiang Y, Wang J, Lefebure M, Boyer M, Humphrey K, Seymour JF. Venetoclax Plus Rituximab in Relapsed Chronic Lymphocytic Leukemia: 4-Year Results and Evaluation of Impact of Genomic Complexity and Gene Mutations From the MURANO Phase III Study. J Clin Oncol 2020; 38:4042-4054. [PMID: 32986498 PMCID: PMC7768340 DOI: 10.1200/jco.20.00948] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2020] [Indexed: 12/30/2022] Open
Abstract
PURPOSE In previous analyses of the MURANO study, fixed-duration venetoclax plus rituximab (VenR) resulted in improved progression-free survival (PFS) compared with bendamustine plus rituximab (BR) in patients with relapsed or refractory chronic lymphocytic leukemia (CLL). At the 4-year follow-up, we report long-term outcomes, response to subsequent therapies, and the predictive value of molecular and genetic characteristics. PATIENTS AND METHODS Patients with CLL were randomly assigned to 2 years of venetoclax (VenR for the first six cycles) or six cycles of BR. PFS, overall survival (OS), peripheral-blood minimal residual disease (MRD) status, genomic complexity (GC), and gene mutations were assessed. RESULTS Of 389 patients, 194 were assigned to VenR and 195 to BR. Four-year PFS and OS rates were higher with VenR than BR, at 57.3% and 4.6% (hazard ratio [HR], 0.19; 95% CI, 0.14 to 0.25), and 85.3% and 66.8% (HR, 0.41; 95% CI, 0.26 to 0.65), respectively. Undetectable MRD (uMRD) at end of combination therapy (EOCT) was associated with superior PFS compared with low MRD positivity (HR, 0.50) and high MRD positivity (HR, 0.15). Patients in the VenR arm who received ibrutinib as their first therapy after progression (n = 12) had a reported response rate of 100% (10 of 10 evaluable patients); patients subsequently treated with a venetoclax-based regimen (n = 14) had a reported response rate of 55% (six of 11 evaluable patients). With VenR, the uMRD rate at end of treatment (EOT) was lower in patients with GC than in those without GC (P = .042); higher GC was associated with shorter PFS. Higher MRD positivity rates were seen with BIRC3 and BRAF mutations at EOCT and with TP53, NOTCH1, XPO1, and BRAF mutations at EOT. CONCLUSION Efficacy benefits with fixed-duration VenR are sustained and particularly durable in patients who achieve uMRD. Salvage therapy with ibrutinib after VenR achieved high response rates. Genetic mutations and GC affected MRD rates and PFS.
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MESH Headings
- Antineoplastic Combined Chemotherapy Protocols/adverse effects
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biomarkers, Tumor/genetics
- Bridged Bicyclo Compounds, Heterocyclic/administration & dosage
- Bridged Bicyclo Compounds, Heterocyclic/adverse effects
- Follow-Up Studies
- Humans
- Kaplan-Meier Estimate
- Karyopherins/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Mutation
- Progression-Free Survival
- Proto-Oncogene Proteins B-raf/genetics
- Receptor, Notch1/genetics
- Receptors, Cytoplasmic and Nuclear/genetics
- Rituximab/administration & dosage
- Rituximab/adverse effects
- Sulfonamides/administration & dosage
- Sulfonamides/adverse effects
- Treatment Outcome
- Tumor Suppressor Protein p53/genetics
- Exportin 1 Protein
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Affiliation(s)
- Arnon P. Kater
- Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, Academic Medical Center, on behalf of Hovon Chronic Lymphocytic Leukemia Working Group, Amsterdam, the Netherlands
| | | | - Thomas Kipps
- University of California School of Medicine, San Diego, CA
| | | | - Peter Hillmen
- St James’s University Hospital, Leeds, United Kingdom
| | - James D’Rozario
- The John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Sarit Assouline
- Segal Cancer Center, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | | | - Tadeusz Robak
- Medical University of Lodz, Copernicus Memorial Hospital, Lodz, Poland
| | | | - Ulrich Jaeger
- Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria
| | - Guillaume Cartron
- Department of Clinical Hematology, University Hospital Montpellier, Montpellier, France
| | - Marco Montillo
- Department of Hematology, Niguarda Cancer Center, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Julie Dubois
- Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, Academic Medical Center, on behalf of Hovon Chronic Lymphocytic Leukemia Working Group, Amsterdam, the Netherlands
| | - Eric Eldering
- Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, Academic Medical Center, on behalf of Hovon Chronic Lymphocytic Leukemia Working Group, Amsterdam, the Netherlands
| | - Clemens Mellink
- Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, Academic Medical Center, on behalf of Hovon Chronic Lymphocytic Leukemia Working Group, Amsterdam, the Netherlands
| | - Anne-Marie Van Der Kevie-Kersemaekers
- Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Centers, Academic Medical Center, on behalf of Hovon Chronic Lymphocytic Leukemia Working Group, Amsterdam, the Netherlands
| | | | | | | | | | | | | | - Jue Wang
- Genentech, South San Francisco, CA
| | | | - Michelle Boyer
- Roche Products Limited, Welwyn Garden City, United Kingdom
| | | | - John F. Seymour
- Royal Melbourne Hospital, Peter MacCallum Cancer Centre and University of Melbourne, Melbourne, Victoria, Australia
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13
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Hilton LK, Nowicka M, Ashton-Key M, Hargreaves CE, Lee C, Foxall R, Carter MJ, Beers SA, Potter KN, Bolen CR, Klein C, Knapp A, Mir F, Rose-Zerilli M, Burton C, Klapper W, Scott DW, Sehn LH, Vitolo U, Martelli M, Trneny M, Slack GW, Farinha P, Strefford JC, Oestergaard MZ, Morin RD, Cragg MS. Abstract PO-26: Prognostic significance of Fc gamma receptor IIB expression in the response of previously untreated diffuse large B-cell lymphomas to anti-CD20 monoclonal antibodies: Differing impact of rituximab and obinutuzumab. Blood Cancer Discov 2020. [DOI: 10.1158/2643-3249.lymphoma20-po-26] [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] Open
Abstract
Abstract
Background: The anti-CD20 monoclonal antibody (mAb), obinutuzumab (G), has shown improved outcomes versus rituximab (R) in indolent lymphomas; however, no improvement was seen in diffuse large B-cell lymphoma (DLBCL), and the molecular basis is unclear. The inhibitory Fc gamma receptor IIB (Fc γRIIB), expressed on lymphoma cells, can impair the effects of direct targeting mAbs, such as R, by binding and internalizing them, reducing opsonization and limiting FcγR-mediated killing. We hypothesized that FcγRIIB expression on cellular effectors and/or the lymphoma confers treatment resistance in some patients (pts) and evaluated if outcomes differ for therapies involving a non-internalized mAb (G).
Methods: We evaluated correlates between FCGR2B mRNA and/or FcγRIIB protein expression and pt outcomes in two discovery cohorts of de novo DLBCL treated with R-CHOP (Arthur et al. 2018, n=372; Schmitz et al. 2018, n=234), and the phase III GOYA trial (NCT01287741; n=552), which compared R-CHOP with G-CHOP in pts with previously untreated DLBCL. FCGR2B mRNA expression was assessed by RNA-Seq, and protein expression was assessed in evaluable cohorts by immunohistochemistry, using tissue microarrays with macrophages identified by CD68. FCGR2B expression was also measured by a NanoString assay (Arthur cohort). Cox regression analyzed the impact of FcγRIIB/FCGR2B expression on progression-free survival (PFS), with univariate and multivariate models adjusted for International Prognostic Index (IPI), cell of origin (COO), and BCL2 protein expression.
Results: In the discovery cohorts, a higher FCGR2B expression was significantly associated with shorter PFS (Arthur: HR 1.09 [95% CI: 1.01–1.19], P=0.036; Schmitz: HR 1.13 [95% CI: 1.02–1.26], P=0.0243). Expression by NanoString strongly correlated with RNA-Seq, confirming the association with shorter PFS (HR 1.13 [95% CI: 1.04–1.23], P=0.0048). In GOYA, a significant association between PFS and FCGR2B was observed in the R arm (HR 1.26 [95% CI: 1.00–1.58], P=0.0455), with no prognostic effect observed for G (HR 0.91 [95% CI: 0.69–1.20], P=0.5). Pts with high FCGR2B expression appeared to benefit more from G than R (HR 0.67 [95% CI: 0.44–1.02], P=0.0622), in contrast to pts with low FCGR2B expression (HR 1.58 [95% CI: 1.00–2.50], P=0.0503). In both Arthur and GOYA cohorts, FCGR2B expression by RNA-Seq was associated with FcγRIIB on the tumor, which correlated with a shorter PFS for R (HR 2.17 [95% CI: 1.04–4.50], P=0.03), but not G (HR 1.37 [95% CI: 0.66–2.87], P=0.4). This prognostic effect on PFS was independent of established prognostic biomarkers, IPI, COO and BCL2.
Conclusion: High FcγRIIB/FCGR2B expression in pts with DLBCL has prognostic value in those treated with R and may confer differential responsiveness to R or G.
Citation Format: Laura K. Hilton, Malgorzata Nowicka, Margaret Ashton-Key, Chantal E. Hargreaves, Chern Lee, Russell Foxall, Matthew J. Carter, Stephen A. Beers, Kathleen N. Potter, Christopher R. Bolen, Christian Klein, Andrea Knapp, Farheen Mir, Matthew Rose-Zerilli, Cathy Burton, Wolfram Klapper, David W. Scott, Laurie H. Sehn, Umberto Vitolo, Maurizio Martelli, Marek Trneny, Graham W. Slack, Pedro Farinha, Jonathan C. Strefford, Mikkel Z. Oestergaard, Ryan D. Morin, Mark S. Cragg. Prognostic significance of Fc gamma receptor IIB expression in the response of previously untreated diffuse large B-cell lymphomas to anti-CD20 monoclonal antibodies: Differing impact of rituximab and obinutuzumab [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-26.
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Affiliation(s)
- Laura K. Hilton
- 1BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada,
- 2Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
- *Shared first authorship,
| | | | - Margaret Ashton-Key
- 4School of Cancer Sciences, University of Southampton, Southampton, United Kingdom,
- 5Southampton University Hospitals NHS Foundation Trust, Southampton, United Kingdom,
| | - Chantal E. Hargreaves
- 4School of Cancer Sciences, University of Southampton, Southampton, United Kingdom,
- 6Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,
| | - Chern Lee
- 5Southampton University Hospitals NHS Foundation Trust, Southampton, United Kingdom,
| | - Russell Foxall
- 7Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom,
| | - Matthew J. Carter
- 7Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom,
| | - Stephen A. Beers
- 7Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom,
| | - Kathleen N. Potter
- 4School of Cancer Sciences, University of Southampton, Southampton, United Kingdom,
| | | | | | | | - Farheen Mir
- 10Royal Marsden Hospital, Sutton, United Kingdom,
| | - Matthew Rose-Zerilli
- 4School of Cancer Sciences, University of Southampton, Southampton, United Kingdom,
| | - Cathy Burton
- 11St. James's Institute of Oncology, Leeds, United Kingdom,
| | | | - David W. Scott
- 1BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada,
- 13University of British Columbia, Vancouver, BC, Canada,
| | - Laurie H. Sehn
- 1BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada,
- 13University of British Columbia, Vancouver, BC, Canada,
| | - Umberto Vitolo
- 14Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO), Italy,
| | - Maurizio Martelli
- 15Department of Translational and Precision Medicine, Hematology, Sapienza University, Rome, Italy,
| | - Marek Trneny
- 16Charles University General Hospital, Prague, Czech Republic,
| | - Graham W. Slack
- 1BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada,
| | - Pedro Farinha
- 1BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada,
| | - Jonathan C. Strefford
- 4School of Cancer Sciences, University of Southampton, Southampton, United Kingdom,
- #shared senior authorship
| | - Mikkel Z. Oestergaard
- 17F. Hoffmann-La Roche Ltd., Basel, Switzerland (currently, Novo Nordisk, Zurich, Switzerland),
- #shared senior authorship
| | - Ryan D. Morin
- 2Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
- 18Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- #shared senior authorship
| | - Mark S. Cragg
- 4School of Cancer Sciences, University of Southampton, Southampton, United Kingdom,
- 7Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom,
- #shared senior authorship
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14
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Bolen CR, Klanova M, Trneny M, Sehn LH, He J, Tong J, Paulson JN, Kim E, Vitolo U, Di Rocco A, Fingerle-Rowson G, Nielsen T, Lenz G, Oestergaard MZ. Prognostic impact of somatic mutations in diffuse large B-cell lymphoma and relationship to cell-of-origin: data from the phase III GOYA study. Haematologica 2020; 105:2298-2307. [PMID: 33054054 PMCID: PMC7556630 DOI: 10.3324/haematol.2019.227892] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/14/2019] [Indexed: 11/25/2022] Open
Abstract
Diffuse large B-cell lymphoma represents a biologically and clinically heterogeneous diagnostic category with well-defined cell-of-origin subtypes. Using data from the GOYA study (NCT01287741), we characterized the mutational profile of diffuse large B-cell lymphoma and evaluated the prognostic impact of somatic mutations in relation to cell-of-origin. Targeted DNA next-generation sequencing was performed in 499 formalin-fixed paraffin-embedded tissue biopsies from previously untreated patients. Prevalence of genetic alterations/mutations was examined. Multivariate Cox regression was used to evaluate the prognostic effect of individual genomic alterations. Of 465 genes analyzed, 59 were identified with mutations occurring in at least 10 of 499 patients (≥2% prevalence); 334 additional genes had mutations occurring in ≥1 patient. Single nucleotide variants were the most common mutation type. On multivariate analysis, BCL2 alterations were most strongly associated with shorter progression-free survival (multivariate hazard ratio: 2.6; 95% confidence interval: 1.6 to 4.2). BCL2 alterations were detected in 102 of 499 patients; 92 had BCL2 translocations, 90% of whom had germinal center B-cell-like diffuse large B-cell lymphoma. BCL2 alterations were also significantly correlated with BCL2 gene and protein expression levels. Validation of published mutational subsets revealed consistent patterns of co-occurrence, but no consistent prognostic differences between subsets. Our data confirm the molecular heterogeneity of diffuse large B-cell lymphoma, with potential treatment targets occurring in distinct cell-of-origin subtypes. clinicaltrials.gov identifier: NCT01287741.
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Affiliation(s)
- Christopher R Bolen
- Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA, USA
| | - Magdalena Klanova
- Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, CA, USA
| | - Marek Trneny
- 1st Department of Medicine, Charles University General Hospital, Prague, Czech Republic
| | - Laurie H Sehn
- British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, Canada
| | - Jie He
- Foundation Medicine, Inc., Cambridge, MA, USA
| | - Jing Tong
- Foundation Medicine, Inc., Cambridge, MA, USA
| | - Joseph N Paulson
- Department of Biostatistics, Product Development, Genentech Inc., South San Francisco, CA, USA
| | - Eugene Kim
- Department of Biostatistics, Product Development, Genentech Inc., South San Francisco, CA, USA
| | - Umberto Vitolo
- A.O. Universitaria Città della Salute e della Scienza di Torino, Ematologia, Torino, Italy
| | - Alice Di Rocco
- Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | | | - Tina Nielsen
- Pharma Development Clinical Oncology, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Georg Lenz
- Department of Medicine A,Hematology, Oncology and Pneumology, University Hospital Muenster,Muenster
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15
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Sehn LH, Martelli M, Trněný M, Liu W, Bolen CR, Knapp A, Sahin D, Sellam G, Vitolo U. A randomized, open-label, Phase III study of obinutuzumab or rituximab plus CHOP in patients with previously untreated diffuse large B-Cell lymphoma: final analysis of GOYA. J Hematol Oncol 2020; 13:71. [PMID: 32505213 PMCID: PMC7276080 DOI: 10.1186/s13045-020-00900-7] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 05/15/2020] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Rituximab (R) plus cyclophosphamide, doxorubicin, vincristine, and prednisone (CHOP) is the current standard therapy for diffuse large B cell lymphoma (DLBCL). Obinutuzumab (G), a glycoengineered, type II anti-CD20 monoclonal antibody, has shown activity and an acceptable safety profile when combined with CHOP (G-CHOP) in patients with advanced DLBCL. We present the final analysis results of the Phase III GOYA study (NCT01287741), which compared the efficacy and safety of G-CHOP versus R-CHOP in patients with previously untreated DLBCL. METHODS Patients aged ≥ 18 years with previously untreated advanced DLBCL were randomly assigned to receive eight 21-day cycles of R or G, plus six or eight cycles of CHOP. The primary endpoint was investigator-assessed progression-free survival (PFS). Secondary endpoints included overall survival, other time-to-event endpoints, and safety; investigator-assessed PFS by cell of origin subgroup was an exploratory endpoint. RESULTS A total of 1418 patients were randomized, with 1414 included in this final analysis (G-CHOP, N = 704; R-CHOP, N = 710). Five-year PFS rates were 63.8% and 62.6% for G-CHOP and R-CHOP, respectively (stratified hazard ratio 0.94, 95% CI 0.78-1.12; p = 0.48). The results of the secondary efficacy endpoints did not show a benefit of G-CHOP over R-CHOP. In the exploratory analysis, a trend towards benefit with G-CHOP over R-CHOP was apparent in the patients with germinal center B cell DLBCL. The safety profile of G-CHOP was as expected, and no new safety signals were observed. More grade 3-5 (75.1% vs 65.8%), serious (44.4% vs 38.4%), and fatal (6.1% vs 4.4%) adverse events (AEs) were observed in the G-CHOP arm compared with the R-CHOP arm, respectively, with the most common fatal AEs being infections. A higher incidence of late-onset neutropenia occurred in the G-CHOP arm (8.7%) versus the R-CHOP arm (4.9%). CONCLUSIONS The final analysis, similar to the primary analysis, did not show a PFS benefit of G-CHOP over R-CHOP in previously untreated patients with DLBCL. The results of the secondary endpoints were consistent with the primary endpoint. Further exploratory analyses and investigation of biomarkers are ongoing.
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Affiliation(s)
- Laurie H Sehn
- BC Cancer Centre for Lymphoid Cancer and the University of British Columbia, Vancouver, BC, Canada.
| | - Maurizio Martelli
- Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Marek Trněný
- Charles University General Hospital, Prague, Czech Republic
| | - Wenxin Liu
- Roche Pharma Development, Shanghai, China
| | | | | | - Deniz Sahin
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Gila Sellam
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Umberto Vitolo
- Candiolo Cancer Institute, FPO-IRCCS, (Turin), Candiolo, Italy
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16
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Haynes WA, Haddon DJ, Diep VK, Khatri A, Bongen E, Yiu G, Balboni I, Bolen CR, Mao R, Utz PJ, Khatri P. Integrated, multicohort analysis reveals unified signature of systemic lupus erythematosus. JCI Insight 2020; 5:122312. [PMID: 31971918 DOI: 10.1172/jci.insight.122312] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 01/17/2020] [Indexed: 12/27/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease that follows an unpredictable disease course and affects multiple organs and tissues. We performed an integrated, multicohort analysis of 7,471 transcriptomic profiles from 40 independent studies to identify robust gene expression changes associated with SLE. We identified a 93-gene signature (SLE MetaSignature) that is differentially expressed in the blood of patients with SLE compared with healthy volunteers; distinguishes SLE from other autoimmune, inflammatory, and infectious diseases; and persists across diverse tissues and cell types. The SLE MetaSignature correlated significantly with disease activity and other clinical measures of inflammation. We prospectively validated the SLE MetaSignature in an independent cohort of pediatric patients with SLE using a microfluidic quantitative PCR (qPCR) array. We found that 14 of the 93 genes in the SLE MetaSignature were independent of IFN-induced and neutrophil-related transcriptional profiles that have previously been associated with SLE. Pathway analysis revealed dysregulation associated with nucleic acid biosynthesis and immunometabolism in SLE. We further refined a neutropoiesis signature and identified underappreciated transcripts related to immune cells and oxidative stress. In our multicohort, transcriptomic analysis has uncovered underappreciated genes and pathways associated with SLE pathogenesis, with the potential to advance clinical diagnosis, biomarker development, and targeted therapeutics for SLE.
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Affiliation(s)
- Winston A Haynes
- Institute for Immunity, Transplantation and Infection.,Division of Biomedical Informatics Research
| | - D James Haddon
- Institute for Immunity, Transplantation and Infection.,Division of Immunology and Rheumatology, Department of Medicine, and
| | - Vivian K Diep
- Institute for Immunity, Transplantation and Infection.,Division of Immunology and Rheumatology, Department of Medicine, and
| | - Avani Khatri
- Institute for Immunity, Transplantation and Infection.,Division of Immunology and Rheumatology, Department of Medicine, and
| | - Erika Bongen
- Institute for Immunity, Transplantation and Infection.,Division of Immunology and Rheumatology, Department of Medicine, and
| | - Gloria Yiu
- Institute for Immunity, Transplantation and Infection.,Division of Immunology and Rheumatology, Department of Medicine, and
| | - Imelda Balboni
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | | | - Rong Mao
- Institute for Immunity, Transplantation and Infection.,Division of Immunology and Rheumatology, Department of Medicine, and
| | - Paul J Utz
- Institute for Immunity, Transplantation and Infection.,Division of Immunology and Rheumatology, Department of Medicine, and
| | - Purvesh Khatri
- Institute for Immunity, Transplantation and Infection.,Division of Biomedical Informatics Research
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17
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Wagar LE, Bolen CR, Sigal N, Lopez Angel CJ, Guan L, Kirkpatrick BD, Haque R, Tibshirani RJ, Parsonnet J, Petri WA, Davis MM. Increased T Cell Differentiation and Cytolytic Function in Bangladeshi Compared to American Children. Front Immunol 2019; 10:2239. [PMID: 31620139 PMCID: PMC6763580 DOI: 10.3389/fimmu.2019.02239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 09/04/2019] [Indexed: 01/03/2023] Open
Abstract
During the first 5 years of life, children are especially vulnerable to infection-related morbidity and mortality. Conversely, the Hygiene Hypothesis suggests that a lack of exposure to infectious agents early in life could explain the increasing incidence of allergies and autoimmunity in high-income countries. Understanding these phenomena, however, is hampered by a lack of comprehensive, direct immune monitoring in children with differing degrees of microbial exposure. Using mass cytometry, we provide an in-depth profile of the peripheral blood mononuclear cells (PBMCs) of children in regions at the extremes of exposure: the San Francisco Bay Area, USA and an economically poor district of Dhaka, Bangladesh. Despite variability in clinical health, functional characteristics of PBMCs were similar in Bangladeshi and American children at 1 year of age. However, by 2–3 years of age, Bangladeshi children's immune cells often demonstrated altered activation and cytokine production profiles upon stimulation with PMA-ionomycin, with an overall immune trajectory more in line with American adults. Conversely, immune responses in children from the US remained steady. Using principal component analysis, donor location, ethnic background, and cytomegalovirus infection status were found to account for some of the variation identified among samples. Within Bangladeshi 1-year-olds, stunting (as measured by height-for-age z-scores) was found to be associated with IL-8 and TGFβ expression in PMA-ionomycin stimulated samples. Combined, these findings provide important insights into the immune systems of children in high vs. low microbial exposure environments and suggest an important role for IL-8 and TGFβ in mitigating the microbial challenges faced by the Bangladeshi children.
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Affiliation(s)
- Lisa E Wagar
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Christopher R Bolen
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Natalia Sigal
- Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, United States
| | - Cesar J Lopez Angel
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States
| | - Leying Guan
- Data Sciences and Statistics, Stanford University, Stanford, CA, United States
| | - Beth D Kirkpatrick
- Department of Microbiology and Molecular Genetics, University of Vermont College of Medicine and Vaccine Testing Center, Burlington, VT, United States
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Robert J Tibshirani
- Data Sciences and Statistics, Stanford University, Stanford, CA, United States
| | - Julie Parsonnet
- Departments of Medicine and of Health Research and Policy, Stanford University, Stanford, CA, United States
| | - William A Petri
- Department of Medicine, Pathology, and Microbiology, Immunology and Cancer Biology, University of Virginia, Charlottesville, VA, United States
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, United States.,Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, CA, United States.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, United States
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18
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Hamid O, Molinero L, Bolen CR, Sosman JA, Muñoz-Couselo E, Kluger HM, McDermott DF, Powderly JD, Sarkar I, Ballinger M, Fassò M, O'Hear C, Chen DS, Hegde PS, Hodi FS. Safety, Clinical Activity, and Biological Correlates of Response in Patients with Metastatic Melanoma: Results from a Phase I Trial of Atezolizumab. Clin Cancer Res 2019; 25:6061-6072. [DOI: 10.1158/1078-0432.ccr-18-3488] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/29/2019] [Accepted: 07/11/2019] [Indexed: 11/16/2022]
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19
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Toghi Eshghi S, Au-Yeung A, Takahashi C, Bolen CR, Nyachienga MN, Lear SP, Green C, Mathews WR, O'Gorman WE. Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses. Front Immunol 2019; 10:1194. [PMID: 31231371 PMCID: PMC6560168 DOI: 10.3389/fimmu.2019.01194] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/10/2019] [Indexed: 11/17/2022] Open
Abstract
Dimensionality reduction using the t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm has emerged as a popular tool for visualizing high-parameter single-cell data. While this approach has obvious potential for data visualization it remains unclear how t-SNE analysis compares to conventional manual hand-gating in stratifying and quantitating the frequency of diverse immune cell populations. We applied a comprehensive 38-parameter mass cytometry panel to human blood and compared the frequencies of 28 immune cell subsets using both conventional bivariate and t-SNE-guided manual gating. t-SNE analysis was capable of stratifying every general cellular lineage and most sub-lineages with high correlation between conventional and t-SNE-guided cell frequency calculations. However, specific immune cell subsets delineated by the manual gating of continuous variables were not fully separated in t-SNE space thus causing discrepancies in subset identification and quantification between these analytical approaches. Overall, these studies highlight the consistency between t-SNE and conventional hand-gating in stratifying general immune cell lineages while demonstrating that particular cell subsets defined by conventional manual gating may be intermingled in t-SNE space.
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Affiliation(s)
- Shadi Toghi Eshghi
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | - Amelia Au-Yeung
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | - Chikara Takahashi
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | | | - Maclean N Nyachienga
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | - Sean P Lear
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | - Cherie Green
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | - W Rodney Mathews
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
| | - William E O'Gorman
- OMNI Biomarker Development, Genentech Inc., South San Francisco, CA, United States
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20
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Klanova M, Oestergaard MZ, Trněný M, Hiddemann W, Marcus R, Sehn LH, Vitolo U, Bazeos A, Goede V, Zeuner H, Knapp A, Sahin D, Spielewoy N, Bolen CR, Cardona A, Klein C, Venstrom JM, Nielsen T, Fingerle-Rowson G. Prognostic Impact of Natural Killer Cell Count in Follicular Lymphoma and Diffuse Large B-cell Lymphoma Patients Treated with Immunochemotherapy. Clin Cancer Res 2019; 25:4634-4643. [PMID: 31053601 DOI: 10.1158/1078-0432.ccr-18-3270] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/06/2019] [Accepted: 04/29/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Natural killer (NK) cells are key effector cells for anti-CD20 monoclonal antibodies (mAb), such as obinutuzumab and rituximab. We assessed whether low pretreatment NK-cell count (NKCC) in peripheral blood or tumor tissue was associated with worse outcome in patients receiving antibody-based therapy. PATIENTS AND METHODS Baseline peripheral blood NKCC was assessed by flow cytometry (CD3-CD56+ and/or CD16+ cells) in 1,064 of 1,202 patients with follicular lymphoma treated with obinutuzumab or rituximab plus chemotherapy in the phase III GALLIUM trial (NCT01332968) and 1,287 of 1,418 patients with diffuse large B-cell lymphoma (DLBCL) treated with obinutuzumab or rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (G-CHOP or R-CHOP) in the phase III GOYA trial (NCT01287741). The prognostic value of tumor NK-cell gene expression, as assessed by whole-transcriptome gene expression using TruSeq RNA sequencing, was also analyzed. The association of baseline variables, such as treatment arm, was evaluated using multivariate Cox regression models using a stepwise approach. RESULTS In this exploratory analysis, low baseline peripheral blood NKCC was associated with shorter progression-free survival (PFS) in both follicular lymphoma [hazard ratio (HR), 1.48; 95% confidence interval (CI), 1.02-2.14; P = 0.04] and DLBCL (HR, 1.36; 95% CI, 1.01-1.83; P = 0.04), and overall survival in follicular lymphoma (HR, 2.20; 95% CI, 1.26-3.86; P = 0.0058). Low tumor NK-cell gene expression was associated with shorter PFS in G-CHOP-treated patients with DLBCL (HR, 1.95; 95% CI, 1.22-3.15; P < 0.01). CONCLUSIONS These findings indicate that the number of NK cells in peripheral blood may affect the outcome of patients with B-cell non-Hodgkin lymphoma receiving anti-CD20-based immunochemotherapy.
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Affiliation(s)
- Magdalena Klanova
- Charles University General Hospital, Prague, Czech Republic. .,Institute of Pathological Physiology, Charles University, Prague, Czech Republic.,F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | | | - Marek Trněný
- Charles University General Hospital, Prague, Czech Republic
| | | | | | - Laurie H Sehn
- Centre for Lymphoid Cancer, British Columbia Cancer Agency and the University of British Columbia, Vancouver, Canada
| | - Umberto Vitolo
- A.O.U. Citta' Della Salute e della Scienza, S.C. Ematologia, Turin, Italy
| | | | - Valentin Goede
- Center of Integrated Oncology Cologne-Bonn, University Hospital Cologne, Cologne, Germany
| | | | | | - Deniz Sahin
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
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21
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Meng H, Yaari G, Bolen CR, Avey S, Kleinstein SH. Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE). PLoS Comput Biol 2019; 15:e1006899. [PMID: 30939133 PMCID: PMC6461294 DOI: 10.1371/journal.pcbi.1006899] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 04/12/2019] [Accepted: 02/24/2019] [Indexed: 01/20/2023] Open
Abstract
Small sample sizes combined with high person-to-person variability can make it difficult to detect significant gene expression changes from transcriptional profiling studies. Subtle, but coordinated, gene expression changes may be detected using gene set analysis approaches. Meta-analysis is another approach to increase the power to detect biologically relevant changes by integrating information from multiple studies. Here, we present a framework that combines both approaches and allows for meta-analysis of gene sets. QuSAGE meta-analysis extends our previously published QuSAGE framework, which offers several advantages for gene set analysis, including fully accounting for gene-gene correlations and quantifying gene set activity as a full probability density function. Application of QuSAGE meta-analysis to influenza vaccination response shows it can detect significant activity that is not apparent in individual studies.
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Affiliation(s)
- Hailong Meng
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan, Israel
| | - Christopher R. Bolen
- Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
| | - Stefan Avey
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Steven H. Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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22
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Xerri L, Huet S, Venstrom JM, Szafer-Glusman E, Fabiani B, Canioni D, Chassagne-Clément C, Dartigues-Cuilléres P, Charlotte F, Laurent C, Gelas-Dore B, Bolen CR, Punnoose E, Bouabdallah R, Brice P, Morschhauser F, Cartron G, Olive D, Salles G. Rituximab treatment circumvents the prognostic impact of tumor-infiltrating T-cells in follicular lymphoma patients. Hum Pathol 2017; 64:128-136. [PMID: 28414090 DOI: 10.1016/j.humpath.2017.03.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 03/13/2017] [Accepted: 03/26/2017] [Indexed: 01/10/2023]
Abstract
Previous immunohistochemical (IHC) studies showed controversial data about the prognostic value of tumor-infiltrating lymphocytes (TILs) in follicular lymphoma (FL). To clarify this issue, a large series of FL samples from rituximab-treated patients enrolled in the randomized PRIMA trial was examined. IHC was quantified using automated image analysis in 417, 287, 418, 406, 379, and 369 patients for CD3, CD4, CD8, PD1, ICOS, and FOXP3, respectively. RNAseq analysis was used to quantify TIL-related mRNA transcripts from 148 patients. When each IHC marker was used as a continuous variable in the whole cohort, high CD3 counts were associated with better progression-free survival (PFS) (P = .025). When an optimal IHC cut point was applied to the whole patient population, high CD3 counts and high PD1 counts were associated with better PFS (P = .011 and P = .044, respectively), whereas none of the other TIL markers had any significant correlation with outcome. When a stringent analysis was performed by dividing the whole cohort into a training set and a validation set, none of the TIL markers showed a prognostic significance in both groups. RNAseq analysis showed a significant correlation between high levels of CD3 and CD8 transcripts and better PFS (P = .001 and P = .037, respectively). No prognostic correlation was found as to the level of other immune gene transcripts. These results suggest that the IHC prognostic value of TILs is circumvented by rituximab treatment, although there is a trend for high numbers of CD3+ TILs to correlate with better PFS.
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Affiliation(s)
- Luc Xerri
- Department of Bio-Pathology, Hematology, and Tumor Immunology, Institut Paoli-Calmettes and Aix-Marseille Univ, Marseille, France; Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, Marseille, F-13009, France; CNRS, UMR7258, Marseille, F-13009, Institut Paoli-Calmettes, Marseille, F-13009, France; Aix-Marseille University, UM, 105, F-13284, Marseille, France.
| | - Sarah Huet
- INSERM1052, CNRS 5286, Centre de Recherche en Cancerologie de Lyon, Faculté de Médecine Lyon-Sud Charles Mérieux, Hospices Civils De Lyon, Laboratoire d'hématologie, F-69495 Pierre Bénite cedex
| | | | | | - Bettina Fabiani
- Department of Pathology, Centre Hospitalier Saint Antoine, F-75571 Paris, France
| | - Danielle Canioni
- Department of Pathology, Centre Hospitalier Necker, F-75743 Paris, France
| | | | | | - Fréderic Charlotte
- Department of Pathology, Centre Hospitalier Pitié-Salpêtriére, F-75651 France
| | - Camille Laurent
- Department of Pathology, INSERM U.1037, Institut Universitaire du Cancer-Oncopole, F-31059 Toulouse
| | - Benedicte Gelas-Dore
- INSERM1052, CNRS 5286, Centre de Recherche en Cancerologie de Lyon, Faculté de Médecine Lyon-Sud Charles Mérieux, Hospices Civils De Lyon, Laboratoire d'hématologie, F-69495 Pierre Bénite cedex
| | | | | | - Reda Bouabdallah
- Department of Bio-Pathology, Hematology, and Tumor Immunology, Institut Paoli-Calmettes and Aix-Marseille Univ, Marseille, France; Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, Marseille, F-13009, France; CNRS, UMR7258, Marseille, F-13009, Institut Paoli-Calmettes, Marseille, F-13009, France; Aix-Marseille University, UM, 105, F-13284, Marseille, France
| | - Pauline Brice
- Department of Hematology, Centre Hospitalier Saint Louis, F-75475 Paris, France
| | - Franck Morschhauser
- Department of Hematology, Hopital Claude Huriez, Unité GRITA, Université de Lille 2, F-59000 Lille, France
| | - Guillaume Cartron
- Departement of Hematology, CHU Montpellier, UMR CNRS-5235, F-34295 Montpellier, France
| | - Daniel Olive
- Department of Bio-Pathology, Hematology, and Tumor Immunology, Institut Paoli-Calmettes and Aix-Marseille Univ, Marseille, France; Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068, Marseille, F-13009, France; CNRS, UMR7258, Marseille, F-13009, Institut Paoli-Calmettes, Marseille, F-13009, France; Aix-Marseille University, UM, 105, F-13284, Marseille, France
| | - Gilles Salles
- INSERM1052, CNRS 5286, Centre de Recherche en Cancerologie de Lyon, Faculté de Médecine Lyon-Sud Charles Mérieux, Hospices Civils De Lyon, Laboratoire d'hématologie, F-69495 Pierre Bénite cedex
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23
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O'Gorman WE, Kong DS, Balboni IM, Rudra P, Bolen CR, Ghosh D, Davis MM, Nolan GP, Hsieh EWY. Mass cytometry identifies a distinct monocyte cytokine signature shared by clinically heterogeneous pediatric SLE patients. J Autoimmun 2017; 81:S0896-8411(16)30412-7. [PMID: 28389038 PMCID: PMC5628110 DOI: 10.1016/j.jaut.2017.03.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/22/2017] [Accepted: 03/22/2017] [Indexed: 12/11/2022]
Abstract
Systemic Lupus Erythematosus (SLE) is a heterogeneous autoimmune disease with heightened disease severity in children. The incomplete understanding of the precise cellular and molecular events that drive disease activity pose a significant hurdle to the development of targeted therapeutic agents. Here, we performed single-cell phenotypic and functional characterization of pediatric SLE patients and healthy controls blood via mass cytometry. We identified a distinct CD14hi monocyte cytokine signature, with increased levels of monocyte chemoattractant protein-1 (MCP1), macrophage inflammatory protein-1β (Mip1β), and interleukin-1 receptor antagonist (IL-1RA). This signature was shared by every clinically heterogeneous patient, and reproduced in healthy donors' blood upon ex-vivo exposure to plasma from clinically active patients only. This SLE-plasma induced signature was abrogated by JAK1/JAK2 selective inhibition. This study demonstrates the utility of mass cytometry to evaluate immune dysregulation in pediatric autoimmunity, by identification of a multi-parametric immune signature that can be further dissected to delineate the events that drive disease pathogenesis.
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Affiliation(s)
- W E O'Gorman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - D S Kong
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - I M Balboni
- Department of Pediatrics, Division of Allergy, Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - P Rudra
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
| | - C R Bolen
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - D Ghosh
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA
| | - M M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; The Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - G P Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - E W Y Hsieh
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Pediatrics, Division of Allergy, Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pediatrics, Division of Allergy and Immunology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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24
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Blazkova J, Gupta S, Liu Y, Gaudilliere B, Ganio EA, Bolen CR, Saar-Dover R, Fragiadakis GK, Angst MS, Hasni S, Aghaeepour N, Stevenson D, Baldwin N, Anguiano E, Chaussabel D, Altman MC, Kaplan MJ, Davis MM, Furman D. Multicenter Systems Analysis of Human Blood Reveals Immature Neutrophils in Males and During Pregnancy. J Immunol 2017; 198:2479-2488. [PMID: 28179497 PMCID: PMC5337813 DOI: 10.4049/jimmunol.1601855] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/11/2017] [Indexed: 12/22/2022]
Abstract
Despite clear differences in immune system responses and in the prevalence of autoimmune diseases between males and females, there is little understanding of the processes involved. In this study, we identified a gene signature of immature-like neutrophils, characterized by the overexpression of genes encoding for several granule-containing proteins, which was found at higher levels (up to 3-fold) in young (20-30 y old) but not older (60 to >89 y old) males compared with females. Functional and phenotypic characterization of peripheral blood neutrophils revealed more mature and responsive neutrophils in young females, which also exhibited an elevated capacity in neutrophil extracellular trap formation at baseline and upon microbial or sterile autoimmune stimuli. The expression levels of the immature-like neutrophil signature increased linearly with pregnancy, an immune state of increased susceptibility to certain infections. Using mass cytometry, we also find increased frequencies of immature forms of neutrophils in the blood of women during late pregnancy. Thus, our findings show novel sex differences in innate immunity and identify a common neutrophil signature in males and in pregnant women.
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Affiliation(s)
- Jana Blazkova
- Division of Translational Medicine, Department of Systems Biology, Sidra Medical and Research Center, 26999 Doha, Qatar
| | - Sarthak Gupta
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Yudong Liu
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Edward A Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Christopher R Bolen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Ron Saar-Dover
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Gabriela K Fragiadakis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Martin S Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - Sarfaraz Hasni
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | - David Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
| | | | | | - Damien Chaussabel
- Division of Translational Medicine, Department of Systems Biology, Sidra Medical and Research Center, 26999 Doha, Qatar
| | - Matthew C Altman
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Mariana J Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
- Institute for Immunity, Transplantation of Infection, Stanford University School of Medicine, Stanford, CA 94305; and
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305
| | - David Furman
- Division of Translational Medicine, Department of Systems Biology, Sidra Medical and Research Center, 26999 Doha, Qatar;
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
- Institute for Immunity, Transplantation of Infection, Stanford University School of Medicine, Stanford, CA 94305; and
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25
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Bolen CR, Rubelt F, Vander Heiden JA, Davis MM. The Repertoire Dissimilarity Index as a method to compare lymphocyte receptor repertoires. BMC Bioinformatics 2017; 18:155. [PMID: 28264647 PMCID: PMC5340033 DOI: 10.1186/s12859-017-1556-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 02/21/2017] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The B and T cells of the human adaptive immune system leverage a highly diverse repertoire of antigen-specific receptors to protect the human body from pathogens. The sequencing and analysis of immune repertoires is emerging as an important tool to understand immune responses, whether beneficial or harmful (in the case of autoimmunity). However, methods for studying these repertoires, and for directly comparing different immune repertoires, are lacking. RESULTS In this paper, we present a non-parametric method for directly comparing sequencing repertoires, with the goal of rigorously quantifying differences in V, D, and J gene segment utilization. This method, referred to as the Repertoire Dissimilarity Index (RDI), uses a bootstrapped subsampling approach to account for variance in sequencing depth, and, coupled with a data simulation approach, allows for direct quantification of the average variation between repertoires. We use the RDI method to recapitulate known differences in the formation of the CD4+ and CD8+ T cell repertoires, and further show that antigen-driven activation of naïve CD8+ T cells is more selective than in the CD4+ repertoire, resulting in a more specialized CD8+ memory repertoire. CONCLUSIONS We prove that the RDI method is an accurate and versatile method for comparisons of immune repertoires. The RDI method has been implemented as an R package, and is available for download through Bitbucket.
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Affiliation(s)
- Christopher R. Bolen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, 94305 CA USA
- Genentech, Inc., 1 DNA Way, MS 93, South San Francisco, 94080 CA USA
| | - Florian Rubelt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, 94305 CA USA
| | - Jason A. Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Department of Computational Biology & Bioinformatics, Yale University, New Haven, 06520 CT USA
| | - Mark M. Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, 94305 CA USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, 94305 CA USA
- Institute of Immunity, Department of Microbiology and Immunology, Transplantation and Infection, Stanford University School of Medicine, Stanford, 94305 CA USA
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26
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Furman D, Chang J, Lartigue L, Bolen CR, Haddad F, Gaudilliere B, Ganio EA, Fragiadakis GK, Spitzer MH, Douchet I, Daburon S, Moreau JF, Nolan GP, Blanco P, Déchanet-Merville J, Dekker CL, Jojic V, Kuo CJ, Davis MM, Faustin B. Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states. Nat Med 2017; 23:174-184. [PMID: 28092664 DOI: 10.1038/nm.4267] [Citation(s) in RCA: 265] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 12/13/2016] [Indexed: 12/13/2022]
Abstract
Low-grade, chronic inflammation has been associated with many diseases of aging, but the mechanisms responsible for producing this inflammation remain unclear. Inflammasomes can drive chronic inflammation in the context of an infectious disease or cellular stress, and they trigger the maturation of interleukin-1β (IL-1β). Here we find that the expression of specific inflammasome gene modules stratifies older individuals into two extremes: those with constitutive expression of IL-1β, nucleotide metabolism dysfunction, elevated oxidative stress, high rates of hypertension and arterial stiffness; and those without constitutive expression of IL-1β, who lack these characteristics. Adenine and N4-acetylcytidine, nucleotide-derived metabolites that are detectable in the blood of the former group, prime and activate the NLRC4 inflammasome, induce the production of IL-1β, activate platelets and neutrophils and elevate blood pressure in mice. In individuals over 85 years of age, the elevated expression of inflammasome gene modules was associated with all-cause mortality. Thus, targeting inflammasome components may ameliorate chronic inflammation and various other age-associated conditions.
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Affiliation(s)
- David Furman
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA.,Department of Systems Biology, Division of Translational Medicine, Sidra Medical and Research Center, Doha, Qatar
| | - Junlei Chang
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - Lydia Lartigue
- INSERM U916 VINCO, Institut Bergonié, Bordeaux Cedex, France
| | - Christopher R Bolen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - François Haddad
- Institute of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Brice Gaudilliere
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Edward A Ganio
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Gabriela K Fragiadakis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew H Spitzer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Isabelle Douchet
- CIRID, UMR CNRS 5164, Université Bordeaux 2, Bordeaux Cedex, France
| | - Sophie Daburon
- CIRID, UMR CNRS 5164, Université Bordeaux 2, Bordeaux Cedex, France
| | | | - Garry P Nolan
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Patrick Blanco
- CIRID, UMR CNRS 5164, Université Bordeaux 2, Bordeaux Cedex, France
| | | | - Cornelia L Dekker
- Department of Pediatrics, Division of Infectious Diseases, Stanford University, Stanford, California, USA
| | - Vladimir Jojic
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Calvin J Kuo
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin Faustin
- CIRID, UMR CNRS 5164, Université Bordeaux 2, Bordeaux Cedex, France
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27
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Vander Heiden JA, Stathopoulos P, Zhou JQ, Chen L, Gilbert TJ, Bolen CR, Barohn RJ, Dimachkie MM, Ciafaloni E, Broering TJ, Vigneault F, Nowak RJ, Kleinstein SH, O'Connor KC. Dysregulation of B Cell Repertoire Formation in Myasthenia Gravis Patients Revealed through Deep Sequencing. J Immunol 2017; 198:1460-1473. [PMID: 28087666 DOI: 10.4049/jimmunol.1601415] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 12/13/2016] [Indexed: 01/14/2023]
Abstract
Myasthenia gravis (MG) is a prototypical B cell-mediated autoimmune disease affecting 20-50 people per 100,000. The majority of patients fall into two clinically distinguishable types based on whether they produce autoantibodies targeting the acetylcholine receptor (AChR-MG) or muscle specific kinase (MuSK-MG). The autoantibodies are pathogenic, but whether their generation is associated with broader defects in the B cell repertoire is unknown. To address this question, we performed deep sequencing of the BCR repertoire of AChR-MG, MuSK-MG, and healthy subjects to generate ∼518,000 unique VH and VL sequences from sorted naive and memory B cell populations. AChR-MG and MuSK-MG subjects displayed distinct gene segment usage biases in both VH and VL sequences within the naive and memory compartments. The memory compartment of AChR-MG was further characterized by reduced positive selection of somatic mutations in the VH CDR and altered VH CDR3 physicochemical properties. The VL repertoire of MuSK-MG was specifically characterized by reduced V-J segment distance in recombined sequences, suggesting diminished VL receptor editing during B cell development. Our results identify large-scale abnormalities in both the naive and memory B cell repertoires. Particular abnormalities were unique to either AChR-MG or MuSK-MG, indicating that the repertoires reflect the distinct properties of the subtypes. These repertoire abnormalities are consistent with previously observed defects in B cell tolerance checkpoints in MG, thereby offering additional insight regarding the impact of tolerance defects on peripheral autoimmune repertoires. These collective findings point toward a deformed B cell repertoire as a fundamental component of MG.
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Affiliation(s)
- Jason A Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511
| | | | - Julian Q Zhou
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511
| | - Luan Chen
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511
| | | | - Christopher R Bolen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305
| | - Richard J Barohn
- Department of Neurology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Mazen M Dimachkie
- Department of Neurology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Emma Ciafaloni
- Department of Neurology, University of Rochester School of Medicine, Rochester, NY 14642
| | | | | | - Richard J Nowak
- Department of Neurology, Yale School of Medicine, New Haven, CT 06511
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511; .,Department of Immunobiology, Yale School of Medicine, New Haven, CT 06511; and.,Department of Pathology, Yale School of Medicine, New Haven, CT 06511
| | - Kevin C O'Connor
- Department of Neurology, Yale School of Medicine, New Haven, CT 06511;
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28
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Rubelt F, Bolen CR, McGuire HM, Vander Heiden JA, Gadala-Maria D, Levin M, Euskirchen GM, Mamedov MR, Swan GE, Dekker CL, Cowell LG, Kleinstein SH, Davis MM. Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells. Nat Commun 2016; 7:11112. [PMID: 27005435 PMCID: PMC5191574 DOI: 10.1038/ncomms11112] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/20/2016] [Indexed: 01/10/2023] Open
Abstract
The adaptive immune system's capability to protect the body requires a highly diverse lymphocyte antigen receptor repertoire. However, the influence of individual genetic and epigenetic differences on these repertoires is not typically measured. By leveraging the unique characteristics of B, CD4+ T and CD8+ T-lymphocyte subsets from monozygotic twins, we quantify the impact of heritable factors on both the V(D)J recombination process and on thymic selection. We show that the resulting biases in both V(D)J usage and N/P addition lengths, which are found in naïve and antigen experienced cells, contribute to significant variation in the CDR3 region. Moreover, we show that the relative usage of V and J gene segments is chromosomally biased, with ∼1.5 times as many rearrangements originating from a single chromosome. These data refine our understanding of the heritable mechanisms affecting the repertoire, and show that biases are evident on a chromosome-wide level. The diversity of antigen receptor specificities is largely generated by random recombination of its segments. Here the authors show, by genetic comparison of monozygotic twin lymphocyte subsets, that individual genetic and epigenetic biases also contribute to the shape of the B and T cell repertoires.
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Affiliation(s)
- Florian Rubelt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Christopher R Bolen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Helen M McGuire
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jason A Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Deaptment of Computational Biology &Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Daniel Gadala-Maria
- Interdepartmental Program in Computational Biology and Bioinformatics, Deaptment of Computational Biology &Bioinformatics, Yale University, New Haven, Connecticut 06520, USA
| | - Mikhail Levin
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Ghia M Euskirchen
- Department of Genetics, Stanford University School of Medicine, Palo Alto, California 94304, USA
| | - Murad R Mamedov
- Program in Immunology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
| | - Gary E Swan
- Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, California 94304, USA
| | - Cornelia L Dekker
- Department of Pediatrics (Infectious Diseases), Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lindsay G Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Deaptment of Computational Biology &Bioinformatics, Yale University, New Haven, Connecticut 06520, USA.,Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, 06520, USA.,Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305, USA.,Institute of Immunity, Department of Microbiology and Immunology, Transplantation and Infection, Stanford University School of Medicine, Stanford, California 94305, USA
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29
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Turner JA, Bolen CR, Blankenship DM. Quantitative gene set analysis generalized for repeated measures, confounder adjustment, and continuous covariates. BMC Bioinformatics 2015; 16:272. [PMID: 26316107 PMCID: PMC4551517 DOI: 10.1186/s12859-015-0707-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 03/20/2015] [Accepted: 08/17/2015] [Indexed: 12/20/2022] Open
Abstract
Background Gene set analysis (GSA) of gene expression data can be highly powerful when the biological signal is weak compared to other sources of variability in the data. However, many gene set analysis approaches utilize permutation tests which are not appropriate for complex study designs. For example, the correlation of subjects is broken when comparing time points within a longitudinal study. Linear mixed models provide a method to analyze longitudinal studies as well as adjust for potential confounding factors and account for sources of variability that are not of primary interest. Currently, there are no known gene set analysis approaches that fully account for these study design and analysis aspects. In order to do so, we generalize the QuSAGE gene set analysis algorithm, denoted Q-Gen, and provide the necessary estimation adjustments to incorporate linear mixed model analyses. Results We assessed the performance of our generalized method in comparison to the original QuSAGE method in settings such as longitudinal repeated measures analysis and accounting for potential confounders. We demonstrate that the original QuSAGE method can not control for type-I error when these complexities exist. In addition to statistical appropriateness, analysis of a longitudinal influenza study suggests Q-Gen can allow for greater sensitivity when exploring a large number of gene sets. Conclusions Q-Gen is an extension to the gene set analysis method of QuSAGE, and allows for linear mixed models to be applied appropriately within a gene set analysis framework. It provides GSA an added layer of flexibility that was not currently available. This flexibility allows for more appropriate statistical modeling of complex data structures that are inherent to many microarray study designs and can provide more sensitivity. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0707-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jacob A Turner
- Baylor Research Institute, 3310 Live Oak, Dallas, 75204, TX, USA.
| | - Christopher R Bolen
- Department of Microbiology and Immunology, Stanford University School, Stanford, 94305, CA, USA.
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30
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Bolen CR, Ding S, Robek MD, Kleinstein SH. Dynamic expression profiling of type I and type III interferon-stimulated hepatocytes reveals a stable hierarchy of gene expression. Hepatology 2014; 59:1262-72. [PMID: 23929627 PMCID: PMC3938553 DOI: 10.1002/hep.26657] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [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: 04/01/2013] [Accepted: 07/22/2013] [Indexed: 12/13/2022]
Abstract
Despite activating similar signaling cascades, the type I and type III interferons (IFNs) differ in their ability to antagonize virus replication. However, it is not clear whether these cytokines induce unique antiviral states, particularly in the liver, where the clinically important hepatitis B and C viruses cause persistent infection. Here, clustering and promoter analyses of microarray-based gene expression profiling were combined with mechanistic studies of signaling pathways to dynamically characterize the transcriptional responses induced by these cytokines in Huh7 hepatoma cells and primary human hepatocytes. Type I and III IFNs differed greatly in their level of interferon-stimulated gene (ISG) induction with a clearly detectable hierarchy (IFN-β > IFN-α > IFN-λ3 > IFN-λ1 > IFN-λ2). Notably, although the hierarchy identified varying numbers of differentially expressed genes when quantified using common statistical thresholds, further analysis of gene expression over multiple timepoints indicated that the individual IFNs do not in fact regulate unique sets of genes. The kinetic profiles of IFN-induced gene expression were also qualitatively similar with the important exception of IFN-α. While stimulation with either IFN-β or IFN-λs resulted in a similar long-lasting ISG induction, IFN-α signaling peaked early after stimulation then declined due to a negative feedback mechanism. The quantitative expression hierarchy and unique kinetics of IFN-α reveal potential specific roles for individual IFNs in the immune response, and elucidate the mechanism behind previously observed differences in IFN antiviral activity. While current clinical trials are focused on IFN-λ1 as a potential antiviral therapy, the finding that IFN-λ3 invariably possesses the highest activity among type III IFNs suggests that this cytokine may have superior clinical activity.
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Affiliation(s)
- Christopher R. Bolen
- Interdepartmental program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
| | - Siyuan Ding
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | - Michael D. Robek
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | - Steven H. Kleinstein
- Interdepartmental program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
- Department of Pathology, Yale University School of Medicine, New Haven, CT
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31
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Yaari G, Bolen CR, Thakar J, Kleinstein SH. Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations. Nucleic Acids Res 2013; 41:e170. [PMID: 23921631 PMCID: PMC3794608 DOI: 10.1093/nar/gkt660] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Enrichment analysis of gene sets is a popular approach that provides a functional interpretation of genome-wide expression data. Existing tests are affected by inter-gene correlations, resulting in a high Type I error. The most widely used test, Gene Set Enrichment Analysis, relies on computationally intensive permutations of sample labels to generate a null distribution that preserves gene–gene correlations. A more recent approach, CAMERA, attempts to correct for these correlations by estimating a variance inflation factor directly from the data. Although these methods generate P-values for detecting gene set activity, they are unable to produce confidence intervals or allow for post hoc comparisons. We have developed a new computational framework for Quantitative Set Analysis of Gene Expression (QuSAGE). QuSAGE accounts for inter-gene correlations, improves the estimation of the variance inflation factor and, rather than evaluating the deviation from a null hypothesis with a P-value, it quantifies gene-set activity with a complete probability density function. From this probability density function, P-values and confidence intervals can be extracted and post hoc analysis can be carried out while maintaining statistical traceability. Compared with Gene Set Enrichment Analysis and CAMERA, QuSAGE exhibits better sensitivity and specificity on real data profiling the response to interferon therapy (in chronic Hepatitis C virus patients) and Influenza A virus infection. QuSAGE is available as an R package, which includes the core functions for the method as well as functions to plot and visualize the results.
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Affiliation(s)
- Gur Yaari
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06511, USA, Bioengineering program, Faculty of engineering, Bar Ilan University, 5290002, Ramat Gan, Israel and Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Christopher R. Bolen
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06511, USA, Bioengineering program, Faculty of engineering, Bar Ilan University, 5290002, Ramat Gan, Israel and Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Juilee Thakar
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06511, USA, Bioengineering program, Faculty of engineering, Bar Ilan University, 5290002, Ramat Gan, Israel and Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Steven H. Kleinstein
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06511, USA, Bioengineering program, Faculty of engineering, Bar Ilan University, 5290002, Ramat Gan, Israel and Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
- *To whom correspondence should be addressed. Tel: +1 203 785 6685; Fax: +1 203 785 6486;
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32
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Qian F, Bolen CR, Jing C, Wang X, Zheng W, Zhao H, Fikrig E, Bruce RD, Kleinstein SH, Montgomery RR. Impaired toll-like receptor 3-mediated immune responses from macrophages of patients chronically infected with hepatitis C virus. Clin Vaccine Immunol 2013; 20:146-55. [PMID: 23220997 PMCID: PMC3571267 DOI: 10.1128/cvi.00530-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 11/23/2012] [Indexed: 12/23/2022]
Abstract
Hepatitis C virus (HCV) is the most common chronic blood-borne infection in the United States, with the majority of patients becoming chronically infected and a subset (20%) progressing to cirrhosis and hepatocellular carcinoma. Individual variations in immune responses may help define successful resistance to infection with HCV. We have compared the immune response in primary macrophages from patients who have spontaneously cleared HCV (viral load negative [VL-], n = 37) to that of primary macrophages from HCV genotype 1 chronically infected (VL+) subjects (n = 32) and found that macrophages from VL- subjects have an elevated baseline expression of Toll-like receptor 3 (TLR3). Macrophages from HCV patients were stimulated ex vivo through the TLR3 pathway and assessed using gene expression arrays and pathway analysis. We found elevated TLR3 response genes and pathway activity from VL- subjects. Furthermore, macrophages from VL- subjects showed higher production of beta interferon (IFN-β) and related IFN response genes by quantitative PCR (Q-PCR) and increased phosphorylation of STAT-1 by immunoblotting. Analysis of polymorphisms in TLR3 revealed a significant association of intronic TLR3 polymorphism (rs13126816) with the clearance of HCV and the expression of TLR3. Of note, peripheral blood mononuclear cells (PBMCs) from the same donors showed opposite changes in gene expression, suggesting ongoing inflammatory responses in PBMCs from VL+ HCV patients. Our results suggest that an elevated innate immune response enhances HCV clearance mechanisms and may offer a potential therapeutic approach to increase viral clearance.
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Affiliation(s)
| | | | | | | | - Wei Zheng
- W. M. Keck Biotechnology Resource Laboratory
| | - Hongyu Zhao
- W. M. Keck Biotechnology Resource Laboratory
- Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Erol Fikrig
- Section of Infectious Diseases, Department of Internal Medicine
- The Howard Hughes Medical Institute
| | | | - Steven H. Kleinstein
- Department of Pathology
- Interdepartmental Program in Computational Biology and Bioinformatics
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Bolen CR, Robek MD, Brodsky L, Schulz V, Lim JK, Taylor MW, Kleinstein SH. The blood transcriptional signature of chronic hepatitis C virus is consistent with an ongoing interferon-mediated antiviral response. J Interferon Cytokine Res 2012; 33:15-23. [PMID: 23067362 DOI: 10.1089/jir.2012.0037] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Blood transcriptional profiling is a powerful tool for understanding global changes after infection, and may be useful for prognosis and prediction of drug treatment responses. This study characterizes the effects of chronic hepatitis C virus (HCV) infection on gene expression by analyzing blood samples from 10 treatment-naïve HCV patients and 6 healthy volunteers. Differential expression analysis of microarray data from peripheral blood mononuclear cells (PBMCs) identified a 136-gene signature, including 66 genes elevated in infected individuals. Most of the upregulated genes were associated with interferon (IFN) activity (including members of the OAS and MX families, ISG15, and IRF7), suggesting an ongoing immune response. This HCV signature was also found to be consistently enriched in many other viral infection and vaccination datasets. These genes were validated using a second cohort composed of 5 HCV patients and 5 healthy volunteers, confirming the upregulation of the IFN signature. In summary, this is the first study to directly compare blood transcriptional profiles from HCV patients with healthy controls. The results show that chronic HCV infection has a pronounced effect on gene expression in PBMCs of infected individuals, and significantly elevates the expression of a subset of IFN-stimulated genes.
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Affiliation(s)
- Christopher R Bolen
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA
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Taylor MW, Bolen CR, Kleinstein SH, Brodsky L. PS2-108. Infection with Hepatitis C down-regulates the expression of cytokine genes in peripheral blood. Cytokine 2011. [DOI: 10.1016/j.cyto.2011.07.274] [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: 11/26/2022]
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Abstract
BACKGROUND Genome-wide transcriptional profiling of patient blood samples offers a powerful tool to investigate underlying disease mechanisms and personalized treatment decisions. Most studies are based on analysis of total peripheral blood mononuclear cells (PBMCs), a mixed population. In this case, accuracy is inherently limited since cell subset-specific differential expression of gene signatures will be diluted by RNA from other cells. While using specific PBMC subsets for transcriptional profiling would improve our ability to extract knowledge from these data, it is rarely obvious which cell subset(s) will be the most informative. RESULTS We have developed a computational method (Subset Prediction from Enrichment Correlation, SPEC) to predict the cellular source for a pre-defined list of genes (i.e. a gene signature) using only data from total PBMCs. SPEC does not rely on the occurrence of cell subset-specific genes in the signature, but rather takes advantage of correlations with subset-specific genes across a set of samples. Validation using multiple experimental datasets demonstrates that SPEC can accurately identify the source of a gene signature as myeloid or lymphoid, as well as differentiate between B cells, T cells, NK cells and monocytes. Using SPEC, we predict that myeloid cells are the source of the interferon-therapy response gene signature associated with HCV patients who are non-responsive to standard therapy. CONCLUSIONS SPEC is a powerful technique for blood genomic studies. It can help identify specific cell subsets that are important for understanding disease and therapy response. SPEC is widely applicable since only gene expression profiles from total PBMCs are required, and thus it can easily be used to mine the massive amount of existing microarray or RNA-seq data.
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Affiliation(s)
- Christopher R Bolen
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut 06511, USA
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Pagliaccetti NE, Chu EN, Bolen CR, Kleinstein SH, Robek MD. Lambda and alpha interferons inhibit hepatitis B virus replication through a common molecular mechanism but with different in vivo activities. Virology 2010; 401:197-206. [PMID: 20303135 PMCID: PMC2864496 DOI: 10.1016/j.virol.2010.02.022] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Revised: 12/21/2009] [Accepted: 02/18/2010] [Indexed: 12/15/2022]
Abstract
The type III interferons (IFN-lambda1, 2, and 3) induce an antiviral response similar to IFN-alpha/beta, but mediate their activity through a unique receptor. We found that like IFN-alpha/beta, IFN-lambda prevents the assembly of HBV capsids, demonstrating convergence of the two signaling pathways through a single antiviral mechanism. In contrast to IFN-lambda, the structurally related cytokine interleukin (IL)-22 only minimally reduced HBV replication. The transcriptional program activated by IL-22 displayed little similarity to that induced by IFN-lambda, but instead resembled the response elicited by IL-6. We also found that murine IFN-lambda2 had only weak antiviral activity against HBV in the liver of transgenic mice, and that human IFN-lambda2 activity in serum correlated with the sensitivity of the cytokine to proteases. These results demonstrate that the IFN-alpha/beta and IFN-lambda anti-HBV responses operate through a single molecular mechanism, and support the notion that IFN-lambda plays a local, rather than systemic, role in antiviral immunity.
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Affiliation(s)
| | - Esther N. Chu
- Department of Pathology, Yale University School of Medicine, New Haven, CT
| | | | | | - Michael D. Robek
- Department of Pathology, Yale University School of Medicine, New Haven, CT
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