J. Mol. Pathol., Volume 6, Issue 1 (March 2025) – 3 articles

The occurrence of cervical cancer is often linked to a previous infection with a human papillomavirus (HPV). In order to detect HPV infections in cervical smears, a broad range of tests can be used. This study compares the two hybridisation-based DNA-microarray systems “HPV 3.5 LCD-Array” (Chipron GmbH) and “PapilloCheck^®” (Greiner Bio-One GmbH), based on their ability to detect and differentiate HPV infections in 42 different cervical smears. PapilloCheck^® can detect and individually identify 24 HPV types, whereas the 3.5 LCD-Array can differentiate among 32 HPV genotypes. However, both systems include all 13 high-risk (HR)-classified types. With Chipron having already stopped the production of the 3.5 LCD-Array test, quite a few laboratories are confronted with the need to establish a new HPV testing method. The two methods were found to have a high agreement regarding the clinical significance of the detected HR HPV types. Discrepant cases were additionally validated with the help of a third test (VisionArray^® HPV, ZytoVision GmbH). The results of the VisionArray^® test corresponded rather well with the results of the 3.5 LCD-Array. Full article

Background: T cell clonality is commonly assessed in the diagnostic work-up of mature T cell lymphoid neoplasms. Although fragment-length polymerase chain reaction (FL-PCR) assays are most widely used, next-generation sequencing (NGS) of the TRG and TRB genes is increasingly being used to assess T cell clonality. Objective: The present work is a scoping review of studies that assessed T cell clonality by NGS for diagnostic purposes, including only studies that provided integrated clinicopathologic diagnoses in comparing FL-PCR and NGS assays to evaluate if it is preferable to use NGS-based assays for T cell clonality evaluation in diagnostic pathology. Methods: Papers published from 1992 to 3 August 2024 were searched in PubMed. Twenty-nine cohort studies and five instructive case reports, published from 2013–2024 from the USA, UK, Europe, and Australia that provided integrated clinicopathologic diagnoses and used NGS to evaluate T cell clonality in clinical specimens from patients with mature T cell neoplasms and related non-neoplastic and neoplastic diseases were included, with additional relevant studies. Results: Ten (34.4%) of the 29 cohorts included clinical samples from patients having various cutaneous and non-cutaneous T cell malignancies, related neoplasms, and reactive conditions; 2 (6.8%) studies focused on T cell prolymphocytic leukemia, 16 (55%) on cutaneous T cell lymphoma, and one on pediatric pityriasis lichenoides. Eleven (38%) of the 29 cohort studies compared NGS with FL-PCR assays in 908 clinical samples. Eight (72.7%) of the 11 studies compared TRG FL-PCR with TRG NGS (n = 5), TRB NGS (n = 2), and TRG NGS and TRB NGS (n = 1); the remaining three compared EuroClonality/BIOMED-2 FL-PCR (TRG and TRB) with TRG NGS (n = 1), TRB NGS (n = 1), and the EuroClonality-NGS DNA capture assay (n = 1). TRB NGS was used in 16 (55%) of 29, TRG NGS in 6 (20.6%) of 29, and both TRG and TRB NGS in 7 (24%) of 29. Two (6.8%) of the 29 studies compared TRB NGS with flow cytometric immunophenotyping assays for Vβ and T cell receptor β constant region 1. One additional study compared long-read sequencing with NGS for TRG and TRB rearrangements. Conclusions: NGS is highly specific and sensitive for assessing T cell clonality. NGS precisely tracks unique rearranged sequences, which FL-PCR cannot. NGS findings for clonality must be interpreted in the context of all clinicopathologic and immunophenotypic findings, like FL-PCR. With such interpretations, NGS is much preferable to FL-PCR for evaluating T cell clonality for diagnostic purposes. It is necessary to reduce costs, increase accessibility, and educate providers about NGS for clonality evaluation. TRB NGS has been primarily assessed in the peripheral blood and skin, whereas TRG NGS has also been evaluated in formalin-fixed and non-cutaneous fresh lymphoid tissues. TRG NGS performed better than TRB NGS in comparative studies. Full article

Background/Objectives: The highly polymorphic Major Histocompatibility Complex (MHC) genomic region, located on the short arm of chromosome 6, is implicated genetically in Parkinson’s disease (PD), a progressive neurodegenerative disorder with motor and non-motor symptoms. Previously, we reported significant associations between SINE-VNTR-Alu (SVA) expression quantitative trait loci (eQTLs) and Human Leucocyte Antigen (HLA) class I genotypes in PD. In this study, we aimed to evaluate SVA associations and their regulatory effects on transposable element (TE) transcription in the MHC class I region. Methods: Transcriptome data from the peripheral blood cells of 1530 individuals in the Parkinson’s Progression Markers Initiative (PPMI) cohort were reanalyzed for TE and gene expression using publicly available bioinformatics tools, including Salmon and Matrix-eQTL. Results: Four structurally polymorphic SVAs regulated the transcription of 18 distinct clusters of 235 TE loci, comprising LINEs (33%), SINEs (19%), LTRs (35%), and ancient transposon DNA elements (12%) located near HLA genes. The transcribed TEs were predominantly short, with an average length of 445 nucleotides. The regulatory effects of these SVAs varied significantly in terms of TE types, numbers, and transcriptional activation or repression. The SVA-regulated TE RNAs in blood cells appear to function as enhancer-like elements, differentially influencing the expression of HLA class I genes, non-HLA genes, and noncoding RNAs. Conclusions: These findings highlight the roles of SVAs and their associated TEs in the complex regulatory networks governing coding and noncoding gene expression in the MHC class I region, with potential implications for immune function and disease susceptibility. Full article