Placental Heterogeneity in Stillbirth and Its Relations to Maternal Exogenous Characteristics

Introduction: Heterogeneous patterns of placental lesions in stillbirth signal important variations in placental histopathology that may be diagnostic in stillbirth. We explore placental heterogeneity and its associations with maternal characteristics (including HIV) using latent class analysis. Methods: Placental and maternal data and slides were assessed retrospectively for 122 confirmed stillbirths (gestational age ≥ 28 weeks) delivered at a major South African academic hospital between January 2016–July 2018. The slides were reviewed by 2 pathologists and classified using the Amsterdam Consensus Classification System. Latent class analyses were conducted on raw data. Results: We identify 5 latent placental classes in stillbirth based on similarity in patterns of observed diagnostic criteria and their associations with maternal characteristics. Three classes bear similarity to generalized patterns of placental injury identified previously. Our study shows that intrauterine infection was the commonest histopathological condition associated with stillbirth in our setting. Novel findings include 2 classes, distinguished by high placental RPH and maternal HIV, respectively, and the non-emergence of a class distinguished by VUE. Conclusion: The size and content of the latent classes and their similarity/dissimilarity to the more generalized patterns identified previously suggest potential new avenues for investigation and theory development concerning the role of the placenta in stillbirth and the impact of HIV.

International initiative for a curated SDHB variant database improving the diagnosis of hereditary paraganglioma and pheochromocytoma

BackgroundSDHB is one of the major genes predisposing to paraganglioma/pheochromocytoma (PPGL). Identifying pathogenic SDHB variants in patients with PPGL is essential to the management of patients and relatives due to the increased risk of recurrences, metastases and the emergence of non-PPGL tumours. In this context, the ‘NGS and PPGL (NGSnPPGL) Study Group’ initiated an international effort to collect, annotate and classify SDHB variants and to provide an accurate, expert-curated and freely available SDHB variant database.MethodsA total of 223 distinct SDHB variants from 737 patients were collected worldwide. Using multiple criteria, each variant was first classified according to a 5-tier grouping based on American College of Medical Genetics and NGSnPPGL standardised recommendations and was then manually reviewed by a panel of experts in the field.ResultsThis multistep process resulted in 23 benign/likely benign, 149 pathogenic/likely pathogenic variants and 51 variants of unknown significance (VUS). Expert curation reduced by half the number of variants initially classified as VUS. Variant classifications are publicly accessible via the Leiden Open Variation Database system (https://databases.lovd.nl/shared/genes/SDHB).ConclusionThis international initiative by a panel of experts allowed us to establish a consensus classification for 223 SDHB variants that should be used as a routine tool by geneticists in charge of PPGL laboratory diagnosis. This accurate classification of SDHB genetic variants will help to clarify the diagnosis of hereditary PPGL and to improve the clinical care of patients and relatives with PPGL.

American Foulbrood in the Czech Republic: ERIC II Genotype of Paenibacillus Larvae Is Prevalent

American foulbrood (AFB) is a dangerous disease of honeybees (Apis mellifera) caused by the spore-forming bacterium Paenibacillus larvae. According to the ERIC (enterobacterial repetitive intergenic consensus) classification, five genotypes are distinguished, i.e., I, II, III, IV, and V, which differ in their virulence and prevalence in colonies. In the Czech Republic, AFB prevalence is monitored by the State Veterinary Administration; however, the occurrence of specific P. larvae genotypes within the country remains unknown. In this study, our aim was to genotype field P. larvae strains collected in the Czech Republic according to the ERIC classification. In total, 102 field isolates from colonies with AFB clinical symptoms were collected from various locations in the Czech Republic, and the PCR genotypization was performed using ERIC primers. We confirmed the presence of both ERIC I and II genotypes, while ERIC III, IV, and V were not detected. The majority of samples (n = 82, 80.4%) were identified as ERIC II, while the ERIC I genotype was confirmed only in 20 samples (19.6%). In contrast to other European countries, the ERIC II genotype is predominant in Czech honeybee colonies. The ERIC I genotype was mostly detected in border regions close to Poland, Slovakia, and Austria.

Molecular Update and Evolving Classification of Large B-Cell Lymphoma

Diffuse large B-cell lymphomas (DLBCLs) are aggressive B-cell neoplasms with considerable clinical, biologic, and pathologic diversity. The application of high throughput technologies to the study of lymphomas has yielded abundant molecular data leading to the identification of distinct molecular identities and novel pathogenetic pathways. In light of this new information, newly refined diagnostic criteria have been established in the fourth edition of the World Health Organization (WHO) consensus classification of lymphomas, which was revised in 2016. This article reviews the histopathological and molecular features of the various aggressive B-cell lymphoma subtypes included in the updated classification.

All genera of the world: an introduction to the inventory

The ’All genera of the world’ series was announced by Zhang (2020) when Megataxa was launched. It aims to publish a full list of all genera (living and fossil) in a current consensus classification, including species richness, type species, and synonyms/homonyms (if any) for each genus. Original references for the generic names, type species, and nomenclatural changes should be checked and listed. This series, when completed, will provide a basis for a full inventory of life on Earth. It is an extension of a previous series of papers to the family level for animal diversity (Zhang 2011, 2013). The series invites individual taxonomists or a large team to submit small articles or large monographs for their taxa.

Data-driven Derivation and Validation of Novel Phenotypes for Acute Kidney Transplant Rejection using Semi-supervised Clustering

BackgroundOver the past decades, an international group of experts iteratively developed a consensus classification of kidney transplant rejection phenotypes, known as the Banff classification. Data-driven clustering of kidney transplant histologic data could simplify the complex and discretionary rules of the Banff classification, while improving the association with graft failure.MethodsThe data consisted of a training set of 3510 kidney-transplant biopsies from an observational cohort of 936 recipients. Independent validation of the results was performed on an external set of 3835 biopsies from 1989 patients. On the basis of acute histologic lesion scores and the presence of donor-specific HLA antibodies, stable clustering was achieved on the basis of a consensus of 400 different clustering partitions. Additional information on kidney-transplant failure was introduced with a weighted Euclidean distance.ResultsBased on the proportion of ambiguous clustering, six clinically meaningful cluster phenotypes were identified. There was significant overlap with the existing Banff classification (adjusted rand index, 0.48). However, the data-driven approach eliminated intermediate and mixed phenotypes and created acute rejection clusters that are each significantly associated with graft failure. Finally, a novel visualization tool presents disease phenotypes and severity in a continuous manner, as a complement to the discrete clusters.ConclusionsA semisupervised clustering approach for the identification of clinically meaningful novel phenotypes of kidney transplant rejection has been developed and validated. The approach has the potential to offer a more quantitative evaluation of rejection subtypes and severity, especially in situations in which the current histologic categorization is ambiguous.

Molecular subtype variation within metastasis of urothelial carcinoma.

471 Background: Molecular subtyping of cancer based on gene expression is a new prognostic tool with potential to guide treatment in the future. Urothelial carcinoma is one such cancer for which numerous molecular subtyping systems have been developed, but the diversity of these systems has hindered their clinical application. Recently, a consensus classification system was derived from six independent systems, defining six molecular classes with distinct oncogenic mechanisms and mutations (Kamoun A, et al. 2020). Considering the high heterogeneity in urothelial carcinoma, we hypothesized that molecular subtype variation may occur between primary and metastatic samples. We further evaluated whether variation in subtype was associated with any unique patient characteristics. Methods: As part of the University of Washington Bladder Cancer Rapid Autopsy Program (BCRAP), primary and metastatic tumor tissue samples were acquired from 14 deceased patients with urothelial carcinoma within 6 hours of death. Patient history was collected and deidentified for analysis. RNA exome sequencing was used for assigning molecular subtype for each of the 61 tumor samples, using the consensus and six comprising systems. Results: Molecular subtype variation within metastatic tumors according to any classification system was detected in 8 out of 14 patients, independent of histologic morphologies. Amongst the patients with variation, on average 2.1 out of 7 classification systems identified a major difference in subtype between sites. Patients with variation (mean age 70 years (SD 7 years)) were older than those without variation (mean age 59 years (SD 11 years), P = 0.04). Furthermore, patients with variation tended to have decreased survival from diagnosis and received less chemotherapy, although these were not statistically significant (p > 0.05). Conclusions: Molecular subtype variation within metastasis is relatively common amongst BCRAP patients with urothelial carcinoma. Older patients are more likely to have variation, possibly due to a higher tumor mutation burden. Potential variation must be taken into account when considering prognosis and developing a recommended drug regimen specific to molecular subtypes.

cola: an R/Bioconductor package for consensus partitioning through a general framework

Classification of high-throughput genomic data is a powerful method to assign samples to subgroups with specific molecular profiles. Consensus partitioning is the most widely applied approach to reveal subgroups by summarizing a consensus classification from a list of individual classifications generated by repeatedly executing clustering on random subsets of the data. It is able to evaluate the stability of the classification. We implemented a new R/Bioconductor package, cola, that provides a general framework for consensus partitioning. With cola, various parameters and methods can be user-defined and easily integrated into different steps of an analysis, e.g., feature selection, sample classification or defining signatures. cola provides a new method named ATC (ability to correlate to other rows) to extract features and recommends spherical k-means clustering (skmeans) for subgroup classification. We show that ATC and skmeans have better performance than other commonly used methods by a comprehensive benchmark on public datasets. We also benchmark key parameters in the consensus partitioning procedure, which helps users to select optimal parameter values. Moreover, cola provides rich functionalities to apply multiple partitioning methods in parallel and directly compare their results, as well as rich visualizations. cola can automate the complete analysis and generates a comprehensive HTML report.

Hepatoblastoma: Review of Pathology, Diagnosis and Modern Treatment Strategies

Hepatoblastoma (HB) is the most common primary malignant hepatic tumor of childhood and, occurring predominantly in the first two years of life. Approximately 100 cases are diagnosed every year in the United States of America. The management of HB has changed markedly over the last three decades. Alfa feto protein (AFP) and beta human chorionic gonadotrophin (beta HCG) are the main tumor markers and are markers for diagnosis and follow up. International collaborative efforts have led to the implementation of the Pre - Treatment Extent of the Disease PRETEXT staging system consensus classification to assess upfront resectability. Complete surgical resection plays a key role in successful management. Overall, outcomes have greatly improved over the past decades mainly because of advances in chemotherapy (CTR) agents and administration protocols, newer surgical approaches and liver transplantation (LT). Targeted medications towards the newly discovered β-catenin and Wnt genetic pathways in tumor cells may soon become an option for treatment. The current disease free survival (DFS) rates are approaching 85%. For the 25% of patients with metastasis at presentation, the overall survival (OS) remains poor. A more individualized approach to treating the heterogeneous spectrum of HB may become the basis of successful treatment in complex cases. Newer medications and surgical techniques are being exploited. Here we present a comprehensive review of the recent advances in the management of HB. A wide literature search was made using internet search engines such as PubMed and Google scholar. More than 100 articles were reviewed and the information extrapolated was arranged to produce this review.