Elisabeth Bloemena

Differential Immunogenicity of Epstein-Barr Virus Latent-Cycle Proteins for Human CD4+ T-Helper 1 Responses

ABSTRACT Human CD4+ T-helper 1 cell responses to Epstein-Barr virus (EBV) infection are likely to be important in the maintenance of virus-specific CD8+ memory and/or as antiviral effectors in their own right. The present work has used overlapping peptides as stimulators of gamma interferon release (i) to identify CD4+ epitopes within four EBV latent-cycle proteins, i.e., the nuclear antigens EBNA1 and EBNA3C and the latent membrane proteins LMP1 and LMP2, and (ii) to determine the frequency and magnitude of memory responses to these proteins in healthy virus carriers. Responses to EBNA1 and EBNA3C epitopes were detected in the majority of donors, and in the case of EBNA1, their antigen specificity was confirmed by in vitro reactivation and cloning of CD4+ T cells using protein-loaded dendritic cell stimulators. By contrast, responses to LMP1 and LMP2 epitopes were seen much less frequently. EBV latent-cycle proteins therefore display a marked hierarchy of immunodominance for CD4+ T-helper 1 cells (EBNA1, EBNA3C ≫ LMP1, LMP2) which is different from that identified for the same proteins with respect to CD8+-T-cell responses (EBNA3C > EBNA1 > LMP2 ≫ LMP1). Furthermore, the range of CD4+ memory T-cell frequencies in peripheral blood of healthy virus carriers was noticeably lower and narrower than the corresponding range of latent antigen-specific CD8+-T-cell frequencies.

The mutational landscape of adenoid cystic carcinoma

Adenoid cystic carcinomas (ACCs) are among the most enigmatic of human malignancies. These aggressive salivary gland cancers frequently recur and metastasize despite definitive treatment, with no known effective chemotherapy regimen. Here we determined the ACC mutational landscape and report the exome or whole-genome sequences of 60 ACC tumor-normal pairs. These analyses identified a low exonic somatic mutation rate (0.31 non-silent events per megabase) and wide mutational diversity. Notably, we found mutations in genes encoding chromatin-state regulators, such as SMARCA2, CREBBP and KDM6A, suggesting that there is aberrant epigenetic regulation in ACC oncogenesis. Mutations in genes central to the DNA damage response and protein kinase A signaling also implicate these processes. We observed MYB-NFIB translocations and somatic mutations in MYB-associated genes, solidifying the role of these aberrations as critical events in ACC. Lastly, we identified recurrent mutations in the FGF-IGF-PI3K pathway (30% of tumors) that might represent new avenues for therapy. Collectively, our observations establish a molecular foundation for understanding and exploring new treatments for ACC.

Accuracy of Serologic Tests and HLA-DQ Typing for Diagnosing Celiac Disease

Context The value of adding HLA genetic typing to serologic testing for celiac disease is not well defined. Contribution In this prospective study of patients referred for evaluation of celiac disease, the test performance of combinations of genetic typing and serologic testing was similar to that of either strategy alone. Caution The small number of cases of celiac disease precluded meaningful comparisons of testing strategies. Implications The combination of genetic typing and serologic testing is about as accurate as either strategy alone. Neither is a substitute for small-bowel biopsy in the diagnosis of celiac disease. The Editors The high prevalence and clinical heterogeneity of celiac disease necessitate noninvasive tests for diagnosis. Specifically, tests are needed to select which patients should undergo small-bowel biopsy. Although celiac disease serologic tests, especially IgA tissue antitransglutaminase antibodies (TGA) and IgA antiendomysium antibodies (EMA), are often used for this purpose because of their reported high sensitivity (1), they may perform less well in the clinical setting (2). Most studies have not defined the usefulness of serologic tests prospectively (37), and in addition, some authors doubt the high sensitivity of these tests (8, 9). Susceptibility to celiac disease is related to the presence of distinct HLA-DQ heterodimersthe DQ2 heterodimer encoded by the alleles HLA-DQA1*05 and HLA-DQB1*02, and the DQ8 heterodimer encoded by the alleles HLA-DQA1*03 and HLA-DQB1*0302 (1014). One way to improve the selection of patients to undergo small-bowel biopsy may be to combine serologic tests with HLA-DQ typing (15, 16). We designed a prospective study to define the value of specific serologic tests, HLA-DQ typing, or both in diagnosing celiac disease. Methods The institutional review board of the VU University Medical Center, Amsterdam, the Netherlands, approved the study protocol. All participants received oral and written information according to the usual recommendations for medical research and the Declaration of Helsinki (17) and gave written informed consent. Patients The study was performed in an academic, mixed secondary and tertiary referral center that serves a population of about 200000 people. In the design phase of the study (19992000), the staff of departments of internal medicine and gastroenterology reviewed the literature and agreed that serologic tests could not substitute for small-bowel biopsy in the diagnostic work-up of celiac disease. Therefore, the policy was to perform small-bowel biopsy when celiac disease was suspected. Adults suspected of having celiac disease who were attending the endoscopy department for small-bowel biopsy were requested to give blood samples for serum antibody testing and HLA-DQ typing. We excluded patients younger than 18 years of age, those with known celiac disease, and patients who declined to undergo endoscopy. Endoscopy We performed upper gastrointestinal endoscopy with Olympus video endoscopes (GIF-NT140/160, Olympus Nederland, Zoeterwoude, the Netherlands) and obtained 4 oriented biopsy specimens from the distal duodenum (18). Serum Antibody Tests We performed serologic tests after obtaining small-bowel biopsy specimens in all patients to avoid referral bias. All serologic tests were determined anonymously without knowledge of the clinical status or histologic result. We determined IgA and IgG antigliadin antibodies (AGA-IgA and AGA-IgG, respectively) by using enzyme-linked immunosorbent assay (ELISA). We tested for EMA according to the method of Lerner and colleagues (19) by indirect immunofluorescence assay using monkey esophagus (16). Finally, TGA was determined by ELISA, essentially as described by Dieterich and colleagues (20), with guinea pig TGA (gp-TGA) (Sigma-Aldrich, Poole, United Kingdom; coating 10 g/mL in Tris hydrochloride [pH, 7.5] with 5-mmol/L of CaCl2) as the substrate (20). Sera were diluted and preincubated (30 minutes at room temperature) with 1% bovine serum albumin to avoid nonspecific binding (16, 21). The cutoff values for the titers of AGA and gp-TGA tests are based on measurements in control groups (blood donors, patients without celiac disease, and the general population age 2 to 4 years), and optimization was done by a receiver-operating characteristic curve analysis in well-defined patient groups. Because the recombinant human TGA (rh-TGA) assay became available when the study was already ongoing, we retrospectively reevaluated all samples from patients with an abnormal result on serologic testing or histologic examination by using rh-TGA as substrate (Roboscreen, Leipzig, Germany; coating 5 g/mL and same conditions as those for gp-TGA). When serologic test results did not match histologic findings, we measured total serum IgA and repeated the serologic tests. In cases of IgA deficiency, we evaluated TGA-IgG antibodies. We defined seropositivity as 1 or more positive measured antibody test results and seronegativity as negative results on all 4 tests. HLA-DQ Typing Whole blood was obtained for HLA-DQA1 and HLA-DQB1 genotyping. Polymerase chain reactionamplified exon 2 amplicons were generated for low- to medium-resolution typing in a combined, single-stranded conformation polymorphismheteroduplex assay by a semiautomated electrophoresis and gel-staining method on the PhastSystem (Amersham Pharmacia Biotech, Uppsala, Sweden). Alleles DQA1*05 and DQB1*02 (encoding the HLA-DQ2 heterodimer) and alleles DQA1*03 and DQB1*0302 (encoding the HLA-DQ8 heterodimer) could be reliably characterized in homozygous and heterozygous states. This method has been validated by using a panel of reference DNA against the Dynall Allset sequence-specific primers high-resolution typing kits (Dynal A.S., Oslo, Norway) (16, 22). Histologic Studies A gastrointestinal pathologist who was masked to clinical data evaluated the biopsy material, and an independent pathologist reviewed the samples when histologic examination was abnormal. Consensus was reached on the final diagnosis. Villous (crypt) anatomy and density of intraepithelial lymphocytes were assessed uniformly by using hematoxylineosin and immunohistologic anti-CD3 staining, respectively. Appendix Figures 1 and 2 show the histologic grading of abnormalities, based on the most severe change found according to the modified Marsh classification (23, 24). Appendix Figure 1. Small-bowel histologic findings (Marsh 0 to II). A. B. C. Appendix Figure 2. Small-bowel histologic findings (Marsh IIIa to IIIc). A. B. C. Diagnosis and Follow-up of Celiac Disease The diagnosis of celiac disease was based on the European Society for Paediatric Gastroenterology, Hepatology and Nutrition criteria, revised in 1989 and published in 1990, by identifying characteristic histologic findings (Marsh III) on small-bowel biopsy and unequivocal clinical resolution after a gluten-free diet was initiated (25). Thus, by this definition and for this study, the diagnosis of celiac disease did not require follow-up biopsy. However, we assessed histologic response in most patients and serologic response in all patients who were found to have celiac disease. We defined a serologic response as the disappearance of initially positive celiac disease antibody test results and histologic response as the regression of villi to Marsh 0 to II on a repeated biopsy at least 12 months after a gluten-free diet was initiated (24). Statistical Analysis We compared results of serologic tests and HLA-DQ typing with the diagnosis of celiac disease as previously defined. We performed statistical analysis by using SPSS software, version 11.0 (SPSS, Chicago, Illinois). To calculate exact binomial CIs, we used StatXact software, version 7.0.0 (Cytel Software, Cambridge, Massachusetts). We used 2 2 tables (Bayes theorem) to calculate sensitivities and specificities, predictive values, and likelihood ratios. We used the t test and Fisher exact test to compare continuous data and categorical data, respectively. We calculated posttest probabilities (and CIs) of celiac disease for different diagnostic tests or a combination thereof by using the method recommended by Altman (26). Role of the Funding Source The study received no funding. Results Patients Between January 2001 and January 2004, 502 consecutive patients (originally from community practices in the Amsterdam area) were referred from outpatient internal medicine and gastroenterology clinics for endoscopy and small-bowel biopsy for the diagnosis of celiac disease. Another 16 inpatients were referred from the internal medicine and gastroenterology inpatient wards. No referred patient was under the care of the investigators. We excluded 55 (10.6%) patients because they declined to participate in the study after the small-bowel biopsy. Age, sex, body mass index, ethnicity, and indications for referral did not statistically significantly differ between those included in and those excluded from the study (data not shown). The available serologic data (n = 20), HLA-DQ data (n = 4), and histologic examinations (n = 55) suggested the absence of celiac disease in excluded patients. Therefore, 463 patients were included in the study: 346 (75%) were unrelated Dutch Caucasian persons and 117 (25%) were not Caucasian (Indian, Chinese, North African [Arab], and Central African [black], in descending order of frequency). All patients were on a normal diet at the time of inclusion. Table 1 summarizes the general characteristics and indications for small-bowel biopsy of patients without and with celiac disease. Table 1. Characteristics of and Indications for Referral in Patients without and with Celiac Disease Patients with Celiac Disease Of the 463 patients enrolled, 16 (3.46% [95% CI, 1.99% to 5.55%]) fulfilled the diagnostic criteria for celiac disease (Figure) (25) within a median follow-up interval of 22 months (range, 11 to 44 months). Biopsy readings of the 2 pathologists were concor

Direct Immunosuppressive Effects of EBV-Encoded Latent Membrane Protein 1

In neoplastic cells of EBV-positive lymphoid malignancies latent membrane protein (LMP1) is expressed. Because no adequate cellular immune response can be detected against LMP1, we investigated whether LMP1 had a direct effect on T lymphocyte activation. In this study we show that nanogram amounts of purified recombinant LMP1 (rLMP1) strongly suppresses activation of T cells. By sequence alignment two sequences (LALLFWL and LLLLAL) in the first transmembrane domain of LMP1 were identified showing strong homology to the immunosuppressive domain (LDLLFL) of the retrovirus-encoded transmembrane protein p15E. The effects of rLMP1 and LMP1-derived peptides were tested in T cell proliferation and NK cytotoxicity assays and an Ag-induced IFN-γ release enzyme-linked immunospot assay. LMP1 derived LALLFWL peptides showed strong inhibition of T cell proliferation and NK cytotoxicity, while acetylated LALLFWL peptides had an even stronger effect. In addition, Ag-specific IFN-γ release was severely inhibited. To exert immunosuppressive effects in vivo, LMP1 has to be excreted from the cells. Indeed, LMP1 was detected in supernatant of EBV-positive B cell lines (LCL), and differential centrifugation in combination with Western blot analysis of the pellets indicated that LMP1 is probably secreted by LCL in the form of exosomes. The amount of secreted LMP1 in B cell cultures is well below the immunosuppressive level observed with rLMP1. Our results demonstrate direct immunosuppressive properties of LMP1 (fragments) and suggest that EBV-positive tumor cells may actively secrete LMP1 and thus mediate immunosuppressive effects on tumor-infiltrating lymphocytes. Moreover, we demonstrate, for the first time, that transmembrane protein-mediated immunosuppression is not solely restricted to RNA tumor viruses, but can also be found in DNA tumor viruses.

EBV-Positive Gastric Adenocarcinomas: A Distinct Clinicopathologic Entity With a Low Frequency of Lymph Node Involvement

PURPOSE Epstein-Barr virus (EBV) is detected in a substantial subgroup of gastric adenocarcinomas worldwide. We have previously reported that these EBV-positive gastric carcinomas carry distinct genomic aberrations. In the present study, we analyzed a large cohort of EBV-positive and EBV-negative gastric adenocarcinomas for their clinicopathologic features to determine whether they constitute a different clinical entity. PATIENTS AND METHODS Using a validated polymerase chain reaction/enzyme immunoassay-based prescreening method in combination with EBER1/2-RNA in situ hybridization, EBV was detected in the tumor cells of 7.2% (n = 41) of the gastric carcinomas from the Dutch D1D2 trial (N = 566; mean follow-up, 9 years). EBV status was correlated with clinicopathologic features collected for the Dutch D1D2 trial. RESULTS EBV-positive gastric carcinomas occurred significantly more frequently in males (P <.0001) and in younger patients (P =.012). Most were of the intestinal type according to the Laurén classification (P =.047) or tubular according to the WHO classification (P =.006) and located in the proximal part of the stomach (P <.0001). A significantly lower tumor-node-metastasis system-stage (P =.026) was observed in the patients with EBV-carrying carcinomas, which was solely explained by less lymph node (LN) involvement (P =.034) in these cases. In addition, a better prognosis, as reflected by a longer disease-free period (P =.04) and a significant better cancer-related survival (P =.02), was observed for these patients, which could be explained by less LN involvement, less residual disease, and younger patient age. CONCLUSION EBV-carrying gastric adenocarcinomas are a distinct entity of carcinomas, characterized not only by unique genomic aberrations, but also by distinct clinicopathologic features associated with significantly better prognosis.

Increasing prevalence rates of HPV attributable oropharyngeal squamous cell carcinomas in the Netherlands as assessed by a validated test algorithm

Human papillomavirus (HPV) infection has been etiologically linked to oropharyngeal squamous cell carcinoma (OPSCC). The prevalence of HPV‐positive OPSCC varies between studies, ranging from 20 to 90%. This may be related to the lack of a standardized HPV detection assay as well as to the time period in which HPV prevalence is investigated, as rising incidence rates are reported over the last decades. Here, we validated our previously defined test algorithm for HPV detection in formalin‐fixed paraffin‐embedded (FFPE) tumor specimen consisting of p16INK4A immunostaining followed by high‐risk HPV DNA detection by GP5+/6+ PCR on the positive cases (Smeets et al., Int J Cancer 2007;121:2465–72). In addition, we analyzed HPV prevalence rates in OPSCCs in the years 1990–2010. The test algorithm was validated on a consecutive series of 86 OPSCCs collected during 2008–2011, of which both fresh frozen and FFPE samples were available. We performed HPV‐E6 RT‐PCR on the frozen samples as gold standard and applied the algorithm to the corresponding FFPE samples. The test algorithm showed an accuracy of 98%. Using the validated algorithm, we determined the presence of an oncogenic HPV infection in 240 OPSCCs of patients diagnosed in the years 1990–2010 at our center. A significant increase in the proportion of HPV‐positive samples was observed, from 5.1% in 1990 to 29.0% in 2010 (p = 0.001). In conclusion, we confirmed the accuracy of the test algorithm for HPV detection in FFPE tumor specimen and we found a significant increase in the prevalence of HPV in OPSCC over the last two decades at our center.

Genome-Wide Association Study Identifies Variants Associated With Autoimmune Hepatitis Type 1

BACKGROUND & AIMS Autoimmune hepatitis (AIH) is an uncommon autoimmune liver disease of unknown etiology. We used a genome-wide approach to identify genetic variants that predispose individuals to AIH. METHODS We performed a genome-wide association study of 649 adults in The Netherlands with AIH type 1 and 13,436 controls. Initial associations were further analyzed in an independent replication panel comprising 451 patients with AIH type 1 in Germany and 4103 controls. We also performed an association analysis in the discovery cohort using imputed genotypes of the major histocompatibility complex region. RESULTS We associated AIH with a variant in the major histocompatibility complex region at rs2187668 (P = 1.5 × 10(-78)). Analysis of this variant in the discovery cohort identified HLA-DRB1*0301 (P = 5.3 × 10(-49)) as a primary susceptibility genotype and HLA-DRB1*0401 (P = 2.8 × 10(-18)) as a secondary susceptibility genotype. We also associated AIH with variants of SH2B3 (rs3184504, 12q24; P = 7.7 × 10(-8)) and CARD10 (rs6000782, 22q13.1; P = 3.0 × 10(-6)). In addition, strong inflation of association signal was found with single-nucleotide polymorphisms associated with other immune-mediated diseases, including primary sclerosing cholangitis and primary biliary cirrhosis, but not with single-nucleotide polymorphisms associated with other genetic traits. CONCLUSIONS In a genome-wide association study, we associated AIH type 1 with variants in the major histocompatibility complex region, and identified variants of SH2B3and CARD10 as likely risk factors. These findings support a complex genetic basis for AIH pathogenesis and indicate that part of the genetic susceptibility overlaps with that for other immune-mediated liver diseases.

Identification and prevalence of CD8(+) T-cell responses directed against Epstein-Barr virus-encoded latent membrane protein 1 and latent membrane protein 2.

Epstein‐Barr virus (EBV) is associated with several human malignancies that each show different viral gene expression profiles. In malignancies such as Hodgkins disease and nasopharyngeal carcinoma only Epstein‐Barr nuclear antigen 1 (EBNA1) and varying levels of latent membrane proteins 1 and 2 (LMP1 and ‐2) are expressed. Since endogenously expressed EBNA1 is protected from CTL recognition, LMP1 and LMP2 are the most likely target antigens for anti‐tumor immunotherapy. Therefore, we sought to identify in a systematic way CD8+ T‐cell responses directed against eptitopes derived from LMP1 and LMP2. Using IFNγ‐ELISPOT assays of interferon‐γ release, peripheral blood mononuclear cells (PBMC) of healthy donors were screened with peptide panels (15 mer overlapping by 10) spanning the LMP1 and LMP2 sequences of the prototype EBV strain B95.8. When positive responses were found, CD4+ or CD8+ T cells were depleted from donor PBMC to determine the origin of the responder population. We detected CD8+ T‐cell responses to LMP1 in 9/50(18%) donors and to LMP2 in 15/28 (54%) donors. In addition to the already described epitopes, 3 new LMP1‐ and 5 new LMP2‐derived CD8+ epitopes were identified. In most donors LMP1‐ and LMP2‐specific CD8+ precursor frequencies were low compared with precursors against immunodominant EBV epitopes from latent (EBNA3A, ‐3B and ‐3C) and lytic cycle antigens. These results demonstrate that CD8+ memory T cell responses to LMP1 and especially to LMP2 do exist in Caucasians, albeit at low levels and could potentially be exploited for therapeutic use.

Selective gene delivery toward gastric and esophageal adenocarcinoma cells via EpCAM-targeted adenoviral vectors

Application of recombinant adenoviral vectors for cancer gene therapy is currently limited due to lack of specificity for tumor cells. For gastric and esophageal adenocarcinoma, we present here that the relative abundant expression of the primary adenovirus receptor, coxsackie/adenovirus receptor (CAR), on normal epithelium compared to carcinoma favors the transduction of the epithelium. As such, to achieve specific transduction of cancer cells, targeting approaches are required that ablate the binding of the virus to CAR and redirect the virus to tumor-specific receptors. By immunohistochemistry and reverse transcriptase polymerase chain reaction assays, we demonstrate a marked difference in expression of the human epithelial cell adhesion molecule (EpCAM) between normal and (pre)malignant lesions of the stomach and esophagus. Based on this, we explored the feasibility of using EpCAM to achieve gastric and esophageal adenocarcinoma selective gene transfer. Adenoviral vectors redirected to EpCAM using bispecific antibodies against the adenovirus fiber-knob protein and EpCAM specifically infected gastric and esophageal cancer cell lines. Using primary human cells, an improved ratio of tumor transduction over normal epithelium transduction was accomplished by the EpCAM-targeted vectors. This study thus indicates that EpCAM-targeted adenoviral vectors may be useful for gastric and esophageal cancer–specific gene therapy in patients. Cancer Gene Therapy (2001) 8, 342–351

Clinical and Molecular Characteristics of Squamous Cell Carcinomas From Fanconi Anemia Patients

Fanconi anemia is a recessively inherited disease that is characterized by congenital abnormalities, bone marrow failure, and a predisposition to develop cancer, particularly squamous cell carcinomas (SCCs) in the head and neck and anogenital regions. Previous studies of Fanconi anemia SCCs, mainly from US patients, revealed the presence of high-risk human papillomavirus (HPV) DNA in 21 (84%) of 25 tumors analyzed. We examined a panel of 21 SCCs mainly from European Fanconi anemia patients (n = 19 FA patients; 16 head and neck squamous cell carcinomas [HNSCCs], 2 esophageal SCCs, and 3 anogenital SCCs) for their clinical and molecular characteristics, including patterns of allelic loss, TP53 mutations, and the presence of HPV DNA by GP5+/6+ polymerase chain reaction. HPV DNA was detected in only two (10%) of 21 tumors (both anogenital SCCs) but in none of the 16 HNSCCs. Of the 18 tumors analyzed, 10 contained a TP53 mutation. The patterns of allelic loss were comparable to those generally found in sporadic SCCs. Our data show that HPV does not play a major role in squamous cell carcinogenesis in this cohort of Fanconi anemia patients and that the Fanconi anemia SCCs are genetically similar to sporadic SCCs despite having a different etiology.