EBV-associated primary CNS lymphoma occurring after immunosuppression is a distinct immunobiological entity.

Primary central nervous system lymphoma (PCNSL) is confined to the brain, eyes, and cerebrospinal fluid without evidence of systemic spread. Rarely, PCNSL occurs in the context of immunosuppression (eg, posttransplant lymphoproliferative disorders or HIV [AIDS-related PCNSL]). These cases are poorly characterized, have dismal outcome, and are typically Epstein-Barr virus (EBV)-associated (ie, tissue-positive). We used targeted sequencing and digital multiplex gene expression to compare the genetic landscape and tumor microenvironment (TME) of 91 PCNSL tissues all with diffuse large B-cell lymphoma histology. Forty-seven were EBV tissue-negative: 45 EBV- HIV- PCNSL and 2 EBV- HIV+ PCNSL; and 44 were EBV tissue-positive: 23 EBV+ HIV+ PCNSL and 21 EBV+ HIV- PCNSL. As with prior studies, EBV- HIV- PCNSL had frequent MYD88, CD79B, and PIM1 mutations, and enrichment for the activated B-cell (ABC) cell-of-origin subtype. In contrast, these mutations were absent in all EBV tissue-positive cases and ABC frequency was low. Furthermore, copy number loss in HLA class I/II and antigen-presenting/processing genes were rarely observed, indicating retained antigen presentation. To counter this, EBV+ HIV- PCNSL had a tolerogenic TME with elevated macrophage and immune-checkpoint gene expression, whereas AIDS-related PCNSL had low CD4 gene counts. EBV-associated PCNSL in the immunosuppressed is immunobiologically distinct from EBV- HIV- PCNSL, and, despite expressing an immunogenic virus, retains the ability to present EBV antigens. Results provide a framework for targeted treatment.

On the meaning of the word 'epimutation'.

The word 'epimutation' is often used in a manner that can be misinterpreted. The strict definition of epimutation is a heritable change in gene activity that is not associated with a DNA mutation but rather with gain or loss of DNA methylation or other heritable modifications of chromatin. Unfortunately, there is a growing tendency in the cancer field to use the word in situations in which underlying DNA sequence changes have occurred.

Pseudogenes and the electron transport chain.

With the advent of easy access to the human genome sequence, molecular biology techniques to target respirome-specific genes have begun to be exploited in the study of human disorders and in particular human cancers. In some recent publications it would appear that some investigators have inappropriately targeted pseudogenes rather than functional genes. The high transcription level and generally small size of many of the genes in the respirome make them prone to duplications in the form of processed pseudogenes within the human genome. Such genes can be challenging to analyse using standard molecular genetics approaches. In this presentation, we offer an analysis of pseudogenes that have been identified to have significant homology with some elements of the respirome. Other sequence elements such as Alu repeats, which present similar research obstacles, are also discussed.

Reliability of biopsy-based diagnostic tests for Helicobacter pylori after treatment aimed at its eradication.

OBJECTIVE: Recurrence of Heliobacter pylori after apparently successful treatment mostly represents resurgence of the infection, rather than a new one. Therefore, the reliability of biopsy-based tests after treatment was investigated. METHODS: Four weeks or more after treatment, antral biopsy samples were taken for culture, histology, urease test and polymerase chain reaction (PCR), and a corpus specimen for culture. Treatment failure was defined as > or = 2 tests positive. If one test was positive, a 13C-urea breath test was performed and considered conclusive. RESULTS: One hundred and ninety-seven patients were evaluated. Endoscopy was performed 53 days (27-92 days) after treatment. Twenty-one patients with missing test results and 19 patients on acid-suppressive drugs were excluded. In 140 of 156 patients (89.7%), H. pylori was eradicated. Sensitivity and specificity of culture of antrum were, respectively, 100% and 100%; culture of corpus, 100% and 100%; rapid urease test, 87% and 99%; haematoxylin/eosin stain, 94% and 95%; Giemsa stain, 81% and 99%; and PCR, 88% and 100%. CONCLUSION: Although all biopsy-based tests are reliable after treatment, culture is the biopsy-based test of first choice as it is the most accurate and gives additional information on antibiotic resistance.

Diagnostic tests for Helicobacter pylori: a prospective evaluation of their accuracy, without selecting a single test as the gold standard.

OBJECTIVE: To assess the accuracy of six commonly used diagnostic tests for Helicobacter pylori in a prospective study without using any specific test as the gold standard (the patient was regarded as H. pylori-infected if two or more tests, whatever their nature, were positive). METHODS: In 105 outpatients undergoing upper GI endoscopy, 62 without significant abnormalities, 28 with gastroesophageal reflux disease, 19 with peptic ulcer, one with erosive gastritis, and one with atrophic gastritis (some patients had more than one diagnosis), antral biopsy specimens were taken for culture, polymerase chain reaction, histological examination (hematoxylineosin and Giemsa stains), and rapid urease test. Corpus biopsy specimens were taken for histological examination. Serology (ELISA) and a 13C-urea breath test were also performed. Consistency of diagnosis between two pathologists was assessed by kappa statistics. RESULTS: Sensitivity and specificity, respectively, were as follows: culture, 98.4 and 100%; polymerase chain reaction, 96.7 and 100%; histological examination (antrum), 96 and 98.8%; histological examination (antrum + corpus), 98.4 and 98.8%; rapid urease test, 90.2 and 100%; 13C-urea breath test, 100 and 100%; and serological examination, 98.4 and 88.4% (95% in those who had not been previously treated for H. pylori). All H. pylori-positive cases were detected by culture and rapid urease test. In 86.4% of these cases all antral biopsy-based tests were positive. Agreement between pathologists was good, with a kappa coefficient around 0.90 for antral biopsy specimens. CONCLUSIONS: All antral biopsy-based tests, as well as the 13C-urea breath test, are accurate for the diagnosis of H. pylori infection. Sampling error is a problem of minor importance. The lower specificity of serological tests may be largely explained by previous treatment of H. pylori.