scholarly journals HHV-6 in the Lymphoma Microenvironment: Both Chicken and Egg?

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1377-1377
Author(s):  
Genevieve M Crane ◽  
Dmitry Tychinin ◽  
Anton Karelin ◽  
Aleksandr Cherdintsev ◽  
Olga Kudryashova ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Stock Options ◽  
Research Funding ◽  
Cell Lymphoma ◽  
Viral Gene Expression ◽  
T Cell Subsets ◽  
Viral Gene ◽  
Provision Of Services ◽  
Privately Held

Abstract While Epstein-Barr virus (EBV) and the Kaposi sarcoma herpesvirus (KSHV)/human herpesvirus (HHV) 8 have shown a definite association with lymphoproliferative disease, a role for the HHV-6 has been less clear. Similar to other herpesviruses, HHV-6 predominantly remains latent following initial infection, but can be reactivated during stress or immune suppression, and is the cause of roseola in young children. Existing as two distinct species, HHV-6B is more common, infecting ~90% of adults. HHV-6B, a T-lymphotropic virus, enters cells via CD134, a TNF receptor superfamily member, expressed on both naïve and CD4 +CD25 + T cells, leading to CD4 + lymphocyte depletion and impaired T cell activation. HHV-6 has been variably detected in classic Hodgkin (CHL) and T-cell lymphomas (TCL) by immunohistochemistry (IHC) and PCR with more recent data suggesting infection may be confined to tumor-associated lymphocytes. The specificity of these IHC antibodies is not well documented. The question remains whether HHV-6 in the tumor microenvironment of advanced disease is a consequence of immune dysfunction, or may play a more direct role in tumor initiation and progression by altering the tumor microenvironment. To address these questions, we evaluated HHV-6B viral gene expression patterns in lymphoma patient samples by RNA sequencing techniques. Following IRB approval, CHL, TCL, B-cell, and post-transplant lymphoproliferative disease (PTLD) cases were screened for potential HHV-6-association by IHC with an antibody against HHV-6 gp60/110 envelope glycoprotein (Millipore Sigma, MAB8537). Positive cases with available frozen tissue and adequate RNA (5) or sorted T-cell subsets from Hodgkin lymphoma (11) underwent bulk RNA-seq (rRNA depletion (Illumina), 50M reads/sample). Viral transcripts were identified by performing the Burrows-Wheeler Alignment by reference host alignment (to filter host and bad quality reads) followed by viral reference host alignment. Previous TCL databases with available RNAseq data were similarly evaluated. IHC analysis revealed 5/25 CHL, 34/52 TCL, 5/13 PTLD, 4/81 diffuse large B-cell lymphoma (DLBCL) and 2/28 follicular lymphoma (FL) with rare gp60/110-positive cells. This included 11 CHL cases with sorted T-cell subsets, of which one showed membranous and Golgi gp60/110 staining in background T-cells (25-year-old female, nodular sclerosis subtype, EBV-negative). Of these 11 CHL cases, RNAseq of T-cell subsets revealed a pattern of HHV-6B transcripts in only this case. Frozen tumor blocks were available from 5 additional cases with positive gp60/110 staining (2 CHL, 1 DLBCL, 1 FL and 1 PTLD), but RNAseq analysis did not identify any HHV-6B transcripts. Notably, these cases had dim cytoplasmic but not Golgi gp60/110 staining. RNA sequencing data derived from two independent TCL cohorts were analyzed for HHV-6B transcripts. Although no HHV-6B transcripts were detected via RNAseq in 20 angioimmunoblastic T-cell lymphoma samples from one TCL cohort, many had EBV-gene expression. HHV-6B transcripts were detected in two cases of anaplastic large cell lymphoma (ALCL) in a second TCL cohort (2/79 cases). High expression of the U67, U68, U79 and U90 genes was found, revealing overlap of the HHV-6B transcript expression between ALCL and CHL samples (Fig 1). Additionally, detection of two genes that could be driving tumor growth (U51, which encodes a G-protein receptor and U24, which inhibits proper T cell activation, reducing secretion of cytokines at infection site) demonstrates a specific viral gene expression pattern within the intratumor T-cell population. The potential presence of HHV-6B infection in the lymphoma microenvironment is controversial. To our knowledge, this is the first report conclusively demonstrating HHV-6B expression in CHL using RNAseq. Notably, the viral gene expression pattern seen in CHL overlaps with that found in two cases of ALCL, highlighting viral proteins of potential particular significance. These data may aid in development of a more reliable means of HHV-6B detection. For example, the immediate early gene U90, a transcriptional activator that may induce expression of both viral and cellular genes that affect the tumor microenvironment, was consistently expressed and may be a reliable marker of HHV-6B infection. Funding: HHV-6 Foundation Figure 1 Figure 1. Disclosures Tychinin: BostonGene Inc.: Current Employment, Current holder of stock options in a privately-held company, Patents & Royalties. Karelin: BostonGene Inc.: Current Employment, Current holder of stock options in a privately-held company, Patents & Royalties. Cherdintsev: BostonGene Inc.: Current Employment, Current holder of stock options in a privately-held company, Patents & Royalties. Kudryashova: BostonGene: Current Employment, Current holder of stock options in a privately-held company, Patents & Royalties: BostonGene. Egorov: BostonGene: Current Employment, Current holder of stock options in a privately-held company, Patents & Royalties. Degryse: BostonGene Inc.: Current Employment, Current holder of stock options in a privately-held company. Kotlov: BostonGene Corp: Current Employment, Current holder of stock options in a privately-held company, Patents & Royalties. Bagaev: BostonGene Corp.: Current Employment, Current holder of stock options in a privately-held company, Patents & Royalties: BostonGene. Roth: Merck: Consultancy; Janssen: Consultancy. Roshal: Celgene: Other: Provision of services; Physicians' Education Resource: Other: Provision of services; Auron Therapeutics: Other: Ownership / Equity interests; Provision of services. Rabadan: Genotwin: Other: Raul Rabadan is founder of Genotwin; AimedBio: Membership on an entity's Board of Directors or advisory committees. Elemento: Owkin: Consultancy, Other: Current equity holder; Freenome: Consultancy, Other: Current equity holder in a privately-held company; Volastra Therapeutics: Consultancy, Other: Current equity holder, Research Funding; One Three Biotech: Consultancy, Other: Current equity holder; Janssen: Research Funding; Eli Lilly: Research Funding; Champions Oncology: Consultancy; AstraZeneca: Research Funding; Johnson and Johnson: Research Funding.

scholarly journals Single-Cell and Spatial Analyses Characterize Distinct Subsets of Malignant T Cells in Angioimmunoblastic T Cell Lymphoma

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 2393-2393
Author(s):  
Francois Lemonnier ◽  
Chuang Dong ◽  
Bruno Tesson ◽  
Laurine Gil ◽  
Noudjoud Attaf ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
T Cell ◽  
B Cells ◽  
Research Funding ◽  
Cell Lymphoma ◽  
T Cell Subsets ◽  
Patient Specific ◽  
Malignant T Cells

Abstract Introduction Angioimmunoblastic T-cell lymphoma (AITL) is the most frequent of nodal peripheral T-cell lymphomas. AITL results from the transformation of T follicular helper (T FH) cells and is characterized by chemo-resistance and poor survival (5-year OS around 30%). Recent data from prospective clinical trials suggest that disease outcome may be impacted by factors other than genomic features, such as the tumor microenvironment (TME) and overall intra-tumoral heterogeneity. Our understanding of AITL intra-tumoral genetic, transcriptional and functional heterogeneity is limited because most molecular data generated so far have come from bulk analyses. Single-cell RNA sequencing (scRNA-seq) enables fine characterization of cell types and functional cell states. When focused on T or B cells, 5'-end scRNA-seq also yields the TCR or BCR sequences that allow tracking clonally related cells. Here we studied the intra-tumor heterogeneity of AITL tumors using integrative scRNA-seq. Methods We analyzed lymph node live cell suspensions from AITL patients (n=10) using droplet-based 10x Genomics 5'-end scRNA-seq. Malignant T cells from 4 AITL samples were also analyzed by FACS index sorting and plate-based 5'-end scRNA-seq to link cell surface phenotype and gene expression profile. We identified malignant T cell clones by intersecting the gene expression and TCR sequencing data, and performed separate focused analyses of TME subsets and malignant T cells. We compared subsets of malignant T cells from all patients using marker gene-based metaclustering to identify AITL T cell states conserved across patients. We explored the genetic heterogeneity of malignant T cells by mapping RHOA G17V mutations and inferring copy number variation (CNV) subclones from scRNA-seq data. In select cases, we performed in situ analysis by immunohistochemistry (IHC) or spatial transcriptomics to characterize the spatial distribution of malignant T cell subsets identified by scRNA-seq. Results Based on gene expression, malignant T cells grouped in patient-specific clusters, while non-malignant T, B and myeloid TME cells from all patients clustered by cell type or cell state. Among TME cells, we identified 7 subsets of B cells (including activated B cells, plasma cells, and one patient-specific monoclonal B cell proliferation), 6 subsets of myeloid cells (including macrophages, conventional and plasmacytoid dendritic cells), and 8 subsets of non-malignant T cells (including activated cytotoxic T lymphocytes (CTL) with clonal expansions). Patient-specific malignant T cells were heterogeneous and divided into several gene-expression based clusters. Metaclustering of malignant T cell subsets identified T central memory (T CM)-like and T FH-like states in 10/10 samples. We also identified in 3/10 samples clusters of CTL-like malignant T cells expressing characteristic marker genes (including NKG7, GNLY, GZMK, PRF1). We observed an intra-sample continuum of gene expression states from quiescent T CM-like to proliferating T FH-like states. T FH-like cells were larger in size and expressed higher levels of surface PD1 and ICOS than T CM-like and CTL-like subsets. We detected the RHOA G17V mutation in malignant T cells of 4/4 mutated cases, with no evidence of subclonal heterogeneity for that mutation. We detected clonal and subclonal CNV in most AITL malignant T cells. CTL-like states were enriched in specific CNV subclones, but the T CM-like to T FH-like continuum was observed in all CNV subclones, suggesting that functional plasticity and subclonal genetic evolution may occur independently. In situ staining of markers for T FH-like (PD1, ICOS, CD200) and CTL-like (GZMK, GZMA) cells showed that T FH-like and CTL-like cells occupied distinct tissue niches within the tumor. In spatial transcriptomics analysis, T FH-like cells mapped to follicular dendritic cell (FDC)-rich areas, while T CM-like cells were associated with T-zone reticular cells. Conclusions Our analyses recapitulate known characteristics of AITL TME, and uncover previously unrecognized heterogeneity among malignant T cells across multiple patients. The distinct gene expression programs, phenotypes, genetics, and locations of T FH-like, T CM-like and CTL-like states suggest that AITL malignant T cells undergo significant functional plasticity and genetic divergence, which could influence response to therapy and overall clinical course. Figure 1 Figure 1. Disclosures Lemonnier: Institut Roche: Research Funding; Gilead: Other: travel grant. Gaulard: Gilead: Consultancy; Innate Pharma: Research Funding; Sanofi: Research Funding; Alderaan: Research Funding; Takeda: Consultancy, Honoraria. Milpied: Institut Roche: Research Funding; Innate Pharma: Research Funding; Bristol Myers Squibb: Research Funding.

scholarly journals High-Throughput Sequence Analysis of Peripheral T-Cell Lymphomas Indicates Subtype-Specific Viral Gene Expression Patterns and Immune Cell Microenvironments

mSphere ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Hani Nakhoul ◽  
Zhen Lin ◽  
Xia Wang ◽  
Claire Roberts ◽  
Yan Dong ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
B Cell ◽  
Immune Cell ◽  
Cell Lymphoma ◽  
Viral Gene Expression ◽  
Cell Receptor ◽  
T Cell Lymphoma ◽  
Viral Gene ◽  
T Cell Lymphomas

ABSTRACTCertain peripheral T-cell lymphomas (PTCLs) have been associated with viral infection, particularly infection with Epstein-Barr virus (EBV). However, a comprehensive virome analysis across PTCLs has not previously been reported. Here we utilized published whole-transcriptome RNA sequencing (RNA-seq) data sets from seven different PTCL studies and new RNA-seq data from our laboratory to screen for virus association, to analyze viral gene expression, and to assess B- and T-cell receptor diversity paradigms across PTCL subtypes. In addition to identifying EBV in angioimmunoblastic T-cell lymphoma (AITL) and extranodal NK/T-cell lymphoma (ENKTL), two PTCL subtypes with well-established EBV associations, we also detected EBV in several cases of anaplastic large-cell lymphoma (ALCL), and we found evidence of infection by the oncogenic viruses Kaposi’s sarcoma-associated herpesvirus and human T-cell leukemia virus type 1 in isolated PTCL cases. In AITLs, EBV gene expression analysis showed expression of immediate early, early, and late lytic genes, suggesting either low-level lytic gene expression or productive infection in a subset of EBV-infected B-lymphocyte stromal cells. Deconvolution of immune cell subpopulations demonstrated a greater B-cell signal in AITLs than in other PTCL subtypes, consistent with a larger role for B-cell support in the pathogenesis of AITL. Reconstructed T-cell receptor (TCR) and B-cell receptor (BCR) repertoires demonstrated increased BCR diversity in AITLs, consistent with a possible EBV-driven polyclonal response. These findings indicate potential alternative roles for EBV in PTCLs, in addition to the canonical oncogenic mechanisms associated with EBV latent infection. Our findings also suggest the involvement of other viruses in PTCL pathogenesis and demonstrate immunological alterations associated with these cancers.IMPORTANCEIn this study, we utilized next-generation sequencing data from 7 different studies of peripheral T-cell lymphoma (PTCL) patient samples to globally assess viral associations, provide insights into the contributions of EBV gene expression to the tumor phenotype, and assess the unique roles of EBV in modulating the immune cell tumor microenvironment. These studies revealed potential roles for EBV replication genes in some PTCL subtypes, the possible role of additional human tumor viruses in rare cases of PTCLs, and a role for EBV in providing a unique immune microenvironmental niche in one subtype of PTCLs. Together, these studies provide new insights into the understudied role of tumor viruses in PTCLs.

scholarly journals Latency Reversing Agents: Kick and Kill of HTLV-1?

2021 ◽  
Vol 22 (11) ◽  
pp. 5545
Author(s):  
Annika P. Schnell ◽  
Stephan Kohrt ◽  
Andrea K. Thoma-Kress
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Viral Gene Expression ◽  
Cytotoxic T Cell ◽  
Viral Gene ◽  
T Cell Leukemia ◽  
Cell Leukemia ◽  
Cell Leukemia Virus Type ◽  
Reversing Agents ◽  
Ctl Responses

Human T-cell leukemia virus type 1 (HTLV-1), the cause of adult T-cell leukemia/lymphoma (ATLL), is a retrovirus, which integrates into the host genome and persistently infects CD4+ T-cells. Virus propagation is stimulated by (1) clonal expansion of infected cells and (2) de novo infection. Viral gene expression is induced by the transactivator protein Tax, which recruits host factors like positive transcription elongation factor b (P-TEFb) to the viral promoter. Since HTLV-1 gene expression is repressed in vivo by viral, cellular, and epigenetic mechanisms in late phases of infection, HTLV-1 avoids an efficient CD8+ cytotoxic T-cell (CTL) response directed against the immunodominant viral Tax antigen. Hence, therapeutic strategies using latency reversing agents (LRAs) sought to transiently activate viral gene expression and antigen presentation of Tax to enhance CTL responses towards HTLV-1, and thus, to expose the latent HTLV-1 reservoir to immune destruction. Here, we review strategies that aimed at enhancing Tax expression and Tax-specific CTL responses to interfere with HTLV-1 latency. Further, we provide an overview of LRAs including (1) histone deacetylase inhibitors (HDACi) and (2) activators of P-TEFb, that have mainly been studied in context of human immunodeficiency virus (HIV), but which may also be powerful in the context of HTLV-1.

scholarly journals The Immune Evasion Paradox: Immunoevasins of Murine Cytomegalovirus Enhance Priming of CD8 T Cells by Preventing Negative Feedback Regulation

2008 ◽  
Vol 82 (23) ◽  
pp. 11637-11650 ◽  
Author(s):  
Verena Böhm ◽  
Christian O. Simon ◽  
Jürgen Podlech ◽  
Christof K. Seckert ◽  
Dorothea Gendig ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cells ◽  
T Cell ◽  
Negative Feedback ◽  
Cd8 T Cells ◽  
Viral Gene Expression ◽  
Cd8 T Cell ◽  
Murine Cytomegalovirus ◽  
Viral Gene ◽  
Infected Cells

ABSTRACT Cytomegaloviruses express glycoproteins that interfere with antigen presentation to CD8 T cells. Although the molecular modes of action of these “immunoevasins” differ between cytomegalovirus species, the convergent biological outcome is an inhibition of the recognition of infected cells. In murine cytomegalovirus, m152/gp40 retains peptide-loaded major histocompatibility complex class I molecules in a cis-Golgi compartment, m06/gp48 mediates their vesicular sorting for lysosomal degradation, and m04/gp34, although not an immunoevasin in its own right, appears to assist in the concerted action of all three molecules. Using the Ld-restricted IE1 epitope YPHFMPTNL in the BALB/c mouse model as a paradigm, we provide here an explanation for the paradox that immunoevasins enhance CD8 T-cell priming although they inhibit peptide presentation in infected cells. Adaptive immune responses are initiated in the regional lymph node (RLN) draining the site of pathogen exposure. In particular for antigens that are not virion components, the magnitude of viral gene expression providing the antigens is likely a critical parameter in priming efficacy. We have therefore focused on the events in the RLN and have related priming to intranodal viral gene expression. We show that immunoevasins enhance priming by downmodulating an early CD8 T-cell-mediated “negative feedback” control of the infection in the cortical region of the RLN, thus supporting the model that immunoevasins improve antigen supply for indirect priming by uninfected antigen-presenting cells. As an important consequence, these findings predict that deletion of immunoevasin genes in a replicative vaccine virus is not a favorable option but may, rather, be counterproductive.

scholarly journals A Phase II Trial of Anakinra for the Prevention of CAR-T Cell Mediated Neurotoxicity

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 2814-2814
Author(s):  
Matthew J. Frigault ◽  
Kathleen M.E. Gallagher ◽  
Marc Wehrli ◽  
Betsy Valles ◽  
Keagan Casey ◽  
...  
Keyword(s):  
T Cell ◽  
Stock Options ◽  
Research Funding ◽  
Leadership Role ◽  
Publicly Traded ◽  
Car T Cell ◽  
Car T ◽  
Post Infusion ◽  
Grade 3 ◽  
Privately Held

Abstract Introduction: Chimeric antigen receptor (CAR)-T cell therapy is limited in most cases to inpatient use due to risk of severe treatment-related toxicities. The two primary toxicities observed with CAR-T therapy, cytokine release syndrome (CRS) and neurotoxicity, are associated with increased circulating inflammatory cytokines such as IL-6 and IL-1. Targeting IL-6 with tocilizumab is effective for treating CRS but not neurotoxicity. Anakinra is an FDA-approved recombinant IL-1 receptor antagonist that competitively inhibits IL-1 receptor signaling and therefore blocks downstream production of inflammatory cytokines including IL-6. Leveraging support from Kite Pharma, we opened an investigator-initiated clinical trial (NCT04150913) with the hypothesis that anakinra could be administered prophylactically to prevent severe CRS and neurologic events (NE) in patients receiving axicabtagene ciloleucel (axi-cel). Here we report preliminary outcomes of this study. Study Design and Methods: This is a phase II single center, open-label study for patients ≥18 years old with relapsed or refractory large cell lymphoma. Patients must have progressed after ≥2 lines of systemic therapy but could not have CNS disease or have been previously treated with CAR-T therapy. Following leukapheresis and manufacturing, patients received 3 days of lymphodepleting chemotherapy (LDC, cyclophosphamide 500mg/m 2 and fludarabine 30 mg/m 2) and 200 mg of subcutaneously administered anakinra starting 4 hours prior to axi-cel infusion and daily thereafter for a total of 7 days. CRS and NE were graded based on the Lee 2013 criteria and the CTCAE 4.03 criteria, respectively, to enable direct comparison to the pivotal Zuma-1 cohorts. The primary endpoint is the rate and severity of NE within the first 30 days of infusion; secondary endpoints include the incidence and severity of CRS and disease response. CAR-T cell expansion, serum cytokines, and circulating biomarkers of toxicity were measured at baseline, day 3, 7, 14, 21, and 28 post CAR-T cell infusion. Results: Interim analysis of the first 6 patients demonstrated a median age of 68 (range 59-72). Patients included a diverse group of histologies including double-hit lymphoma (n=2), transformed indolent NHL (n=3), and DLBCL NOS (n=1). Two patients were considered primary refractory at time of enrollment. Pre-LDC baseline characteristics included a median SPD of 2819 mm 2 (range 1063-5802), median LDH of 415 (range 147-497) which were comparable to the pivotal ZUMA-1 cohorts. Baseline ferritin, CRP, SAA and IL-15 were similar to the pivotal ZUMA-1 cohorts. While low-grade CRS was observed in 5/6 patients, no patients experienced severe CRS and median onset occurred on day +8 (range 1-8). Four patients did not experience any NE, while two patients experienced grade 3 NE on days +6 till +9 (somnolence) and +12 (global aphasia only, for one day) respectively. With a median follow-up of 4 months, the day +28 overall response rate was 100% (4 CRs, 2 PRs), with 4/6 patients having an ongoing complete response at last disease assessment. One patient was re-infused at progression and remains in a CR 3 months from re-infusion. Responses were seen despite varying CAR-T peak level with most patients demonstrating expansion in the lower quartile of the historic ZUMA-1 cohort. Median post-infusion peak of CRP, ferritin, IL-2, GM-CSF, IFNγ, IL-10, IL-6 and SAA were lower than that observed in the pivotal ZUMA-1 cohorts. All patients remain alive at time of data analysis. Conclusions: With a limited number of patients analyzed thus far, anakinra appears to provide benefit to the toxicity profile of axi-cel, presenting reduced and/or delayed CRS and NE and a decrease in post-infusion inflammatory analytes, when compared to ZUMA-1 pivotal cohorts. No severe CRS was observed in this initial analysis and 2/6 patients experienced grade 3 NE (somnolence and global aphasia) after day 6. Despite CAR-T expansion in the lower quartile of that of ZUMA-1, we observed a 100% ORR with 4 patients remaining in CR at a median follow-up of 4 months. Additional subjects will be assessed to investigate the role of prophylactic anakinra in the management of CRS and NE, which has potential for making axi-cel treatment an outpatient therapy. Disclosures Frigault: BMS: Consultancy; Editas: Consultancy; Iovance: Consultancy; Arcellx: Consultancy; Takeda: Consultancy; Kite: Consultancy, Research Funding; Novartis: Consultancy, Research Funding. Wehrli: CSL Behring: Patents & Royalties; Nestle: Current equity holder in publicly-traded company; Novartis: Current equity holder in publicly-traded company. Chou: Kite Pharma: Current Employment. Shen: Atara: Current Employment, Current equity holder in publicly-traded company, Other: Leadership role, Patents & Royalties; Gilead Sciences: Current equity holder in publicly-traded company; Kite, a Gilead Company: Current Employment, Other: Leadership role, Patents & Royalties. Filosto: Kite, a Gilead Company: Current Employment; Gilead Sciences: Other: stock or other ownership ; Tusk Therapeutics: Patents & Royalties: or other intellecular property. Bot: Kite, a Gilead Company: Current Employment; Gilead Sciences: Consultancy, Current equity holder in publicly-traded company, Other: Travel support. Maus: Agenus: Consultancy; Arcellx: Consultancy; Astellas: Consultancy; AstraZeneca: Consultancy; Atara: Consultancy; Bayer: Consultancy; BMS: Consultancy; Cabaletta Bio (SAB): Consultancy; CRISPR therapeutics: Consultancy; In8bio (SAB): Consultancy; Intellia: Consultancy; GSK: Consultancy; Kite Pharma: Consultancy, Research Funding; Micromedicine: Consultancy, Current holder of stock options in a privately-held company; Novartis: Consultancy; Tmunity: Consultancy; Torque: Consultancy, Current holder of stock options in a privately-held company; WindMIL: Consultancy; Adaptimmune: Consultancy; tcr2: Consultancy, Divested equity in a private or publicly-traded company in the past 24 months; century: Current equity holder in publicly-traded company; ichnos biosciences: Consultancy, Current holder of stock options in a privately-held company.

scholarly journals Delineation of Novel Subtypes Based on Microenvironment Immune Signature Provides Prognostic Stratification Strategy in Peripheral T-Cell Lymphoma

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4108-4108
Author(s):  
Takeshi Sugio ◽  
Kohta Miyawaki ◽  
Koji Kato ◽  
Hiroaki Miyoshi ◽  
Koichi Ohshima ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
B Cell ◽  
Research Funding ◽  
Cell Lymphoma ◽  
M2 Macrophage ◽  
Cell Type ◽  
Peripheral T Cell Lymphoma ◽  
Immune Signature ◽  
Prognostic Stratification

Abstract Peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS) is the largest subgroup with dismal prognosis in peripheral T-cell lymphomas (PTCL) that do not fit into any of the specifically defined categories in the World Health Organization classification, and it comprises over 25% of PTCL. PTCL-NOS is sometimes referred to as the gwaste-basketh category because of the lack of specific features, and therefore contains heterogeneous disease entities. Its heterogeneity represents a major obstacle to elucidation of pathogenesis, development of novel therapeutic targets and establishment of standardized therapeutic strategies and results in its poor prognosis. The stratification strategy of PTCL-NOS still remains controversial, although previous studies tried to reclassify PTCL-NOS from the viewpoint of gCell-of-Originh of tumor cells (e.g. T helper 1/2 cells, regulatory T cells) by utilizing histopathologic methods or gene expression profiling. These situations prompted us to investigate microenvironment profile of PTCL-NOS and to develop the novel stratification strategy. For this purpose, we analyzed the expression levels of 800 of tumor microenvironment-related genes including the phenotypic markers, transcription factors and functional molecules of microenvironment cells in formalin fixed paraffin embedded (FFPE) samples derived from 33 PTCL-NOS patients utilizing nCounter system, which is novel RNA counting system based on a digital molecular barcoding technology and enables accurate quantification of genes with low expression levels. Thirty-three patients who were diagnosed as PTCL-NOS between 1993 and 2011 were included in this study. The median follow-up time was 796 days (range, 15-2973). The overall survival rate at 1 year after diagnosis (1yr OS) was 40%, and it was comparable to previous reports. Unsupervised hierarchical clustering analysis revealed three distinct clusters based on the gene expression pattern of the microenvironment-related genes: B-cell type (42.4 %), M2 macrophage type (24.2 %), and others (33.3 %) (Figure 1). On the other hand, the expression patterns of the major T-cell subset-associated genes were complicated and diverse depending on patients, and failed to form any distinct clusters. B-cell-related genes, such as CD19, CD79B and PAX5 were highly expressed in the B-cell type, and the M2 macrophage-related genes, such as CD68, CD163, CD14 and MARCO were highly expressed in the M2 macrophage type. More importantly, these microenvironment-based subgroups, B-cell type and M2 macrophage type, represent prognostically favorable and unfavorable subgroups, respectively (1yr OS: B-cell type, 84.8%; M2 macrophage type, 16.7%; others, 56.2%; log rank test, p = 0.01) (Figure 2). Interestingly, genes associated with immune checkpoint, such as PD-L1, TIM-3 and IDO-1, were highly expressed in the M2 macrophage type than the others (PD-L1, p = 0.02; TIM-3, p = 0.05; IDO-1, p < 0.01), indicating the existence of specific subgroup of PTCL-NOS patients as anticipated good-responder for immunotherapeutic agents including immune checkpoint inhibitors. Collectively, our findings strongly suggest that microenvironment immune signature, not gCell-of-Originh of tumor cells, could provide novel prognostic stratification method and therapeutic strategy of PTCL-NOS. Disclosures Akashi: Asahi Kasei Pharma Corporation: Research Funding; Shionogi & Co., Ltd: Research Funding; Astellas Pharma: Research Funding; Celgene: Research Funding; Kyowa Hakko Kirin: Consultancy, Research Funding; Sunitomo Dainippon Pharma: Consultancy; Bristol Meyers Squibb: Research Funding; Chugai Pharmaceutical Co., Ltd.: Research Funding.

The Gene Expression Profile of Nodal T-Cell Lymphomas Identifies a Molecular Link between Angioimmunoblastic T-Cell Lymphoma (AITL) and Follicular Helper T Cells (TFH), and between CD30+ Peripheral T-Cell Lymphoma and ALK-Negative Anaplastic Large Cell Lymphoma (ALCL).

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 289-289 ◽  
Author(s):  
Laurence de Leval ◽  
David Rickman ◽  
Caroline Thielen ◽  
Aurélien de Reynies ◽  
Yen-Lin Huang ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Cell Lymphoma ◽  
T Cell Subsets ◽  
Molecular Signature ◽  
Tissue Samples ◽  
Tfh Cells ◽  
T Cell Lymphomas

Abstract AITL and PTCL-U, the two most common forms of T-cell lymphomas in western countries, usually present as nodal disease and pursue an aggressive clinical course. AITL is commonly associated with a constellation of clinical symptoms and distinct pathological features. Conversely, PTCL-U lacks precise diagnostic criteria, and by default comprises cases not fulfilling criteria for other entities, including tumors with borderline features to ALCL and AITL. The genetic alterations and pathogenic mechanisms underlying AITL and PTCL-U are largely unknown. To determine whether the molecular signature of AITL and PTCL-U could help in distinguishing both entities and in understanding ther ontogeny, we performed gene expression profile (GEP) analysis of 15 PTCL-U tissue samples (6 CD30+ and 9 CD30−) and 19 AITL samples (including 2 sorted tumor cell suspensions) using Affymetrix HG-U133A Plus2.0 pan-genomic oligonucleotide microarrays, with comparison to that of previously published normal T-cell subsets (J Immunol173:68; J Immunol175: 7837; Blood 104: 1952). Principle component analysis (PCA, accumulated variance 95%) of all 33 tissue samples yielded three groups of tumors: one group of 12 AITLs, one group of 10 PTCLs-U and one mixed group comprising 5 AITLs (some with features borderline to PTCL-U) and 6 PTCLs-U (including 5 of 6 CD30+ tumors). The AITL molecular signature consisted of 442 genes with increased levels of expression in AITL compared to PTCL-U (t test, p<0.002), including genes encoding cell adhesion molecules, immune receptors, extracellular matrix components and several chemokines, B-cell-related and follicular dendritic cell-related genes, genes involved in endothelial and vascular biology, and several genes reported to belong to the gene expression signature of normal TFH cells (CXCL13, BCL6, PDCD1, CD40L, CD200). To specifically address the question of a molecular link beween AITL and TFH cells, we performed gene set enrichment analysis (GSEA) of our dataset using published gene sets specific of distinct normal T-cell subsets (TFH, TH1, TH2). Compared to that of PTCL-U, the molecular signature of AITL was significantly enriched in TFH-specific genes, and the enrichment was even higher for sorted AITL cells compared to AITL tissues. GSEA failed to disclose a molecular link between PTCL-U and known T-cell subsets (TH1, TH2, TFH). Compared to CD30− PTCL-U, CD30+ PTCL-U had lower expression of genes involved in TCR signalling (t test, p<0.002), and showed molecular similarities with ALK-negative ALCL. In conclusion, GEP of non-anaplastic nodal PTCL (1) segregates AITL and PTCL-U, supporting the basis for histotyping; (2) shows molecular analogies between AITL and TFH cells, strongly supporting the hypothesis of a histogenetic link; (3) suggests molecular analogies between CD30+ PTCL-U and ALK-negative ALCL.

Next-Generation Sequencing Suggests Complex, Heterogeneous Pathogenesis In Peripheral T-Cell Lymphoma Unspecified

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 843-843 ◽  
Author(s):  
Jonathan H. Schatz ◽  
Steven M. Horwitz ◽  
Matthew A. Lunning ◽  
Igor Dolgalev ◽  
Kety Huberman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Next Generation Sequencing ◽  
T Cell ◽  
Candidate Genes ◽  
Research Funding ◽  
Cell Lymphoma ◽  
Next Generation ◽  
Peripheral T Cell Lymphoma ◽  
Tumor Dna ◽  
Generation Sequencing

Abstract Peripheral T-cell lymphoma (PTCL) makes up about 12 percent of non-Hodgkin lymphoma, comprising 18 diseases that are poorly understood and carry a generally worse prognosis than B-lymphomas. PTCL not otherwise specified (PTCL-NOS), a diagnosis of exclusion, is most common, making up 25-30 percent. Gene-expression studies suggest a heterogeneous origin of this diagnosis, with overlap to other PTCL types, but the genetic factors underlying its pathogenesis are undefined. Current therapy for PTCL-NOS is empiric and ultimately ineffective for most patients. Identification of specific therapeutic targets is therefore a high priority. We have sought better understanding of pathogenesis through next-generation sequencing of PTCL-NOS tumor DNA. Whole-exome sequencing revealed candidate genes but low availability of fresh-frozen samples limited our ability to draw conclusions by this method alone. We therefore sequenced the coding regions of 237 candidate genes in a collection formalin-fixed paraffin-embedded samples. We used Nimblegen Sequence Capture for PCR amplification of exons and Illumina hiSeq for raw sequence generation. Results were aligned to hg19 and compared to dbSNP and the 1,000 genomes data to exclude germline variants. Analysis, including comparison to the COSMIC database of cancer-specific mutations, revealed high-confidence mutations affecting more than 60 known cancer-related genes in 25 PTCL-NOS cases. Recurrent mutations pointed to frequent activation of three key signaling pathways: NF-kB (TNFAIP3), WNT/B-Catenin (APC, CHD8, CELSR2), and NOTCH (NOTCH1, FBXW7). Recurrent deregulation of epigenetic processes was indicated by mutations in genes affecting histone acetylation (EP300, CREBBP), histone methylation (MLL2, KDM6A), and DNA methylation (TET2, DNMT3A). In addition, components of core tumor suppressor pathways showed evidence of frequent inactivation (TP53, ATM, RB1, CUL9, PRKDC). In all, 22 of 25 cases had mutations in at least one of these 17 recurrently mutated genes. Multiple additional candidate disease mechanisms also were suggested by lower-confidence mutations but require confirmation studies, which are under way. In sum, analysis of the coding region of PTCL-NOS tumor DNA suggests a complex and heterogeneous pathogenesis, in line with gene-expression profiling. This work provides an opportunity to better sub-classify entities within the diagnosis of PTCL-NOS and identify specific therapeutic targets and their associated biomarkers. Disclosures: Horwitz: Seattle Genetics, Inc.: Consultancy, Research Funding; Millennium: Consultancy, Research Funding.

scholarly journals Oncolytic Reovirus Is an Effective Treatment for Histone Deacetylase Inhibitor Resistant T-Cell Lymphoma

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2941-2941 ◽  
Author(s):  
Shariful Islam ◽  
Claudia M Espitia ◽  
Ning Qu ◽  
Daniel Persky ◽  
Jennifer S. Carew ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Hdac Inhibitor ◽  
Research Funding ◽  
Cell Lymphoma ◽  
Hdac Inhibitors ◽  
T Cell Lymphoma ◽  
Drug Resistant ◽  
Inhibitor Resistance ◽  
Resistant Cells

Abstract Aberrant gene expression plays a pivotal role during tumorigenesis and cancer progression. The acetylation status of histones is an important determinant of gene expression and is controlled by two opposing classes of enzymes: histones acetyl transferases (HATs) and histone deacetylases (HDACs). The deacetylation of histones is associated with repression of key tumor suppressor genes and has been linked to HDAC overexpression in multiple forms of cancer including lymphomas. Several HDAC inhibitors have been FDA approved for T-cell lymphoma (TCL) therapy including belinostat, vorinostat, and romidepsin. Despite the promising anti-lymphoma activity of HDAC inhibitors as a drug class, resistance is a significant clinical issue. Identification of new strategies that are more effective in the drug resistant patient population is a high priority, but the mechanisms underlying HDAC inhibitor-induced cell death and the development of drug resistance are not completely understood. Elucidating the molecular mechanisms driving HDAC inhibitor resistance and/or the specific targets that are altered in drug-resistant cells may facilitate the development of strategies that overcome drug resistance and are effective for refractory patients. To pursue this goal, we generated novel TCL cell line models of acquired HDAC inhibitor resistance through repeated exposure to belinostat. The sensitivity of parental and resistant TCL cells to belinostat and other clinically relevant HDAC inhibitors was initially characterized using cell viability and flow cytometric assays. Notably, belinostat-resistant cells displayed significant cross-resistance to other HDAC inhibitors including vorinostat, romidepsin, panobinostat, and ricolinostat. This indicates that TCL patients that fail one HDAC inhibitor regimen may not benefit significantly from subsequent treatment with other drugs of this class. Consistent with a lack of sensitivity to HDAC inhibitors, the resistant cells failed to induce increased acetylated histones, tubulin acetylation (an HDAC6 target), and exhibited reduced upregulation of the CDK inhibitor p21 following belinostat treatment. In agreement with the absence of these hallmark characteristics of HDAC inhibition, belinostat also failed to cleave caspase-3 in the belinostat-resistant cells. Comprehensive transcriptome analysis was conducted to further characterize these new drug-resistant models and identify potential mechanisms of resistance and targets for second-line treatment. Drug resistant cells featured significantly increased basal levels of the reovirus receptor junctional adhesion molecule-A (JAM-A) as well as decreased JAK/STAT activity, a key antiviral response pathway. Based on these findings, we investigated the efficacy of the proprietary clinical formulation of reovirus (Reolysin) in parental and drug-resistant models. Our investigation revealed that belinostat-resistant cells displayed enhanced sensitivity to oncolytic reovirus-induced cell death compared to their parental counterparts. The increased benefit of Reolysin in resistant models was linked to elevated viral loads and more efficient endoplasmic reticular stress-mediated apoptosis. The heightened sensitivity of HDAC-resistant TCL cells to Reolysin was further validated in parental and belinostat-resistant T-cell lymphoma xenograft models. Collectively, these data demonstrate that oncolytic reovirus may be a novel therapeutic approach to treat T-cell lymphoma patients that are relapsed/refractory to HDAC inhibitors. We are currently planning an early phase clinical trial to further test the safety and benefit of this new approach. Disclosures Persky: Morphosys (IDMC): Consultancy; Merck: Research Funding; Spectrum: Research Funding; Genentech: Honoraria.

scholarly journals ALK-Negative Anaplastic Large Cell Lymphomas Encompass Distinct Subgroups Including an ALK-Positive-like Subgroup with Favorable Prognosis

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 2403-2403
Author(s):  
Kwok Him Rex Au Yeung ◽  
Veronica Russell ◽  
William Choi ◽  
Alice Wong ◽  
Lawrence Tsui ◽  
...  
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Research Funding ◽  
Gene Expression Analysis ◽  
Cell Lymphoma ◽  
Large Cell ◽  
Genetic Alterations ◽  
The Other ◽  
Molecular Features ◽  
Alk Positive

Abstract Introduction ALK-negative anaplastic large cell lymphoma (ALK- ALCL) is an uncommon type of T-cell non-Hodgkin lymphoma (T-NHL) with worse prognosis compared to ALK-positive (ALK+) ALCLs. Most published studies on the genomics of T-NHL have focused on peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS), and previous studies of ALCL described rearrangements in DUSP22 and TP63 and mutations in genes comprising the JAK/STAT pathway as common genetic drivers in ALK- ALCL. The degree to which these drivers affect survival or other molecular features of ALK- ALCL remains unknown. Here, we describe novel subgroups of ALK- ALCL that exhibit distinct survival. One subgroup appears molecularly similar to ALK+ALCLs and is associated with favorable survival while the second subgroup is quite distinct from ALK- ALCLs and associated with poor outcomes. Methods and Results Eighty-two ALK- ALCL patients were recruited to the Atlas of Blood Cancer (ABC) genomes project, a worldwide consortium established to define the molecular origins of blood cancers. Tumor biopsies from these patients, as well as 10 ALK+ ALCL samples for comparison were obtained from participating institutions. Each case was subjected to centralized pathology review by an experienced panel of hematopathologists to ensure the accuracy of the diagnosis. All cases, along with paired normal tissues, were subjected to DNA and RNA (whole exome-level) sequencing on the Illumina platform to identify mutations and expression changes for each of these cases using methods well established in our group and described previously. We first examined the genetic alterations in ALK- ALCLs. In addition to frequently described genetic alterations such as TP63 and DUSP22 rearrangements, as well as mutations in JAK1, STAT3 and TP53, we also detected mutations in ERBB4, SETD2 and KMT2D, which may serve as potential novel drivers and have not been described previously to our knowledge. We next performed comparative gene expression analysis of the ALK- and ALK+ ALCLs. Surprisingly, a proportion of ALK- ALCL cases (38%) clustered together with ALK+ ALCLs and had a signature resembling ALK+ cases, which we designated as "ALK-like ALCL" here. Both the ALK-like ALCLs and the other ALK- ALCL cases showed decreased ALK expression compared to the ALK+ ALCLs by gene expression analysis. These results point to downstream pathways that are common among ALK+ALCLs and ALK-like ALCLs, but different from the other ALK- ALCLs. Gene set enrichment analysis revealed that the ALK-like ALCLs overexpressed genes in pathways related to monocyte and fibroblast activation, whereas the remaining ALK- ALCLs overexpressed genes in the T follicular helper cells, memory T cells and adaptive immune response-related pathways (P&lt;0.001 in all cases). Kaplan-Meier survival analysis revealed that patients with ALK-like ALCL had significantly better overall survival compared to the other cases (P=0.01, Wald test). Conclusion Our data indicate that ALK- ALCLs represent a heterogeneous group of diseases and comprise at least two distinct subgroups that can be identified based on their similarity to the ALK+ ALCLs. The ALK-like ALCLs demonstrated distinct molecular features and favorable outcomes. Our results provide a potentially new approach to patient risk-stratification and pathological classification of this disease. Disclosures Kwong: Celgene: Consultancy, Honoraria, Research Funding; Bayer: Consultancy, Honoraria, Research Funding; Astellas: Consultancy, Honoraria, Research Funding; Amgen: Consultancy, Honoraria, Research Funding; Bristol Myers Squibb: Consultancy, Honoraria, Research Funding; BeiGene: Consultancy, Honoraria, Research Funding; Gilead: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria, Research Funding; Merck: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria, Research Funding; Roche: Consultancy, Honoraria, Research Funding; Takeda: Consultancy, Honoraria, Research Funding. Jaye: Stemline Therapeutics: Honoraria. Behdad: Roche/Foundation Medicine: Speakers Bureau; Thermo Fisher: Speakers Bureau; Lilly: Speakers Bureau. Hsi: AbbVie Inc, Eli Lilly: Research Funding. Dave: Data Driven Bioscience: Current equity holder in publicly-traded company.

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