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

Abstract

Certain 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.

Comprehensive Epstein-Barr Virus Transcriptome by RNA-Sequencing in Angioimmunoblastic T Cell Lymphoma (AITL) and Other Lymphomas

“…It has been proposed that AITL generates an immunodeficiency at the origin of EBV reactivation promoting the expansion of Tfh and B cells, thus playing a role in the development of the tumor microenvironment. Or EBV itself could induce AITL development by activating Tfh cells [28] unless the interaction between B lymphocytes and neoplastic cells provides support for tumor development [29]. Depending on the hypotheses considered, the mechanisms are different.…”

Genetics and genomics of extranodal natural killer/T cell lymphoma: from etiology to treatment

“…There are two infection routes of EBV-infected cells: latent infection and lytic infection [101] . Similar to latent genes, lytic genes also play a crucial role in the promotion of EBV infection and tumorigenesis of NKTCL.…”

The Roles of the Virome in Cancer

“…Possible involvement of EBV in gastric cancer and precursor lesions [35]; patients with EBV-positive gastric cancer had a better response to chemotherapy and better survival [36] EBV (HHV4) Hepatic EBV infections detected in HCC tissues [37] EBV (HHV4) Lymphoma (DLBCL) EBV RNA detected in B-cell lymphoma samples [38] EBV (HHV4) Lymphoma (PTCL) EBV expression associated with some subtypes of peripheral T-cell lymphomas [39] EBV (HHV4) Oral Higher proportion of EBV-positive oral squamous cell carcinoma in industrialized countries [40] EBV (HHV4) Skin and mucosal EBV DNA frequently detected in skin and mucosal cancers [26] HHV6 Lymphoma (DLBCL) HHV6 RNA detected in B-cell lymphoma samples [38] HHV6 Malignant melanoma HHV6 DNA frequently detected in malignant melanoma [26] HHV7 Bladder HHV7 DNA frequently detected in bladder cancer [26] HHV7 Lymphoma (CTCL) HHV7 DNA frequently detected in cutaneous T-cell lymphoma (Mycosis fungoides) [26] HHV7 Oral HHV7 DNA frequently detected in oral cavity cancer [26] HSV (HHV1/2) Oral Higher proportion of HSV-positive oral squamous cell carcinoma in industrialized countries [40] KSHV (HHV8) Kaposi sarcoma In HIV-infected individuals, KSHV infection is associated with Kaposi sarcoma [41] Polyomaviridae BKV Bladder Possible association of BKV with bladder cancer [26] BKV Colorectal Possible association of BKV with colorectal cancer [42,43], however, other studies found no association [16,44] JCV Colorectal JCV is associated with colorectal cancer [44,45] and may be involved in carcinogenesis [46], specifically in chromosomal instability [47]; JCV Tantigen is expressed in early stage colorectal cancer [48], however, another study found no association [16] MCV Merkel cell carcinoma MCV is the major causative factor for Merkel cell carcinoma [49,50] Retroviridae HIV Anal HIV-positive people have increased risk for anal cancer [51,52] and worse overall colostomy-free survival rates [53] HIV Cervical Cervical cancer...…”

“…Various members have been implicated in cancer formation, including cytomegalovirus (CMV, also known as human herpesvirus 5, HHV5), Epstein-Barr virus (EBV or HHV4), herpes simplex virus (HSV or HHV1/2) and HHV6 and HHV7 (Table 1). The strongest association with cancer has been reported for EBV, which has been linked to colorectal carcinoma (CRC) [33] (although a later study found no association [16]), esophageal [34] and gastric cancer [35] (interestingly, however, patients with EBV-positive gastric cancer had a better response to chemotherapy and better survival [36]), hepatocellular carcinoma [37], lymphoma [38,39], oral [40], as well as skin and mucosa associated cancers [26]. Therefore, it has been proposed that vaccination against EBV might be a viable means to prevent EBV-associated cancers [75].…”