The ITM2B (BRI2) gene is a target of BCL6 repression: Implications for lymphomas and neurodegenerative diseases

Exosomal miR-196a-5p contributes to esophageal squamous cell carcinoma malignant progression by inhibiting ITM2B

Exosomes from cancer cells function as carriers to spread or transport specific microRNAs (miRNAs) to distant sites to exert their effects, but the mechanism of exosomal miRNA action in esophageal squamous cell carcinoma (ESCC) has not been fully explained. Therefore, in this study, we were interested in the impact of exosomal miR-196a-5p in ESCC progression. We found that miR-196a-5p was expressed enriched in clinical tissues, ESCC cells, and exosomes. Functionally, depletion of miR-196a-5p impeded ESCC cell growth, migration, and invasion, whereas overexpression of miR-196a-5p produced the opposite results. Moreover, enhancement of exosomal miR-196a-5p in recipient ESCC cells triggered more intense proliferation and migration. Mechanistically, we identified integral membrane protein 2B (ITM2B) as a direct target of miR-196a-5p. Silencing of ITM2B partially counteracted the inhibitory effect of miR-196a-5p inhibitors on the malignant phenotype of ESCC. Furthermore, in vivo, lower miR-196a-5p levels triggered by the introduction of antagomiR-196a-5p resulted in the generation of smaller volume and weight xenograft tumors. Thus, our results demonstrated novel mechanisms of exosomal and intracellular miR-196a-5p-mediated ESCC growth and migration and identify the interaction of miR-196a-5p with ITM2B. These works might provide new targets and basis for the development of clinical treatment options for ESCC.

Single-cell analysis of MYD88L265P and MYD88WT Waldenström macroglobulinemia patients

Waldenström macroglobulinemia (WM) is characterized by the expansion of clonal lymphoplasmacytic cells; the MYD88L265P somatic mutation is found in >90% of patients, but malignant B cells may still display intra-clonal heterogeneity. To assess clonal heterogeneity in WM, we generated and performed single-cell RNA sequencing of CD19+ sorted cells from five patients with MYD88 L265P and two patients with MYD88 WT genotype as well as two healthy donors. We identified distinct transcriptional patterns in the clonal subpopulations not only between the two genetically distinct WM subgroups but also among MYD88 L265P patients, which affected the B cell composition in the different subgroups. Comparison of clonal and normal/polyclonal B cells within each patient sample enabled the identification of patient-specific transcriptional changes. We identified gene signatures active in a subset of MYD88L265P patients, while other signatures were active in MYD88 WT patients. Finally, gene expression analysis showed common transcriptional features between patients compared to the healthy control but also differentially expressed genes between MYD88 L265P and MYD88 WT patients involved in distinct pathways, including NFκΒ, BCL2, and BTK. Overall, our data highlight the intra-tumor clonal heterogeneity in WM with potential prognostic and therapeutic implications.

Measuring cell-to-cell expression variability in single-cell RNA-sequencing data: a comparative analysis and applications to B cell aging

BACKGROUND

Single-cell RNA-sequencing (scRNA-seq) technologies enable the capture of gene expression heterogeneity and consequently facilitate the study of cell-to-cell variability at the cell type level. Although different methods have been proposed to quantify cell-to-cell variability, it is unclear what the optimal statistical approach is, especially in light of challenging data structures that are unique to scRNA-seq data like zero inflation.

RESULTS

We systematically evaluate the performance of 14 different variability metrics that are commonly applied to transcriptomic data for measuring cell-to-cell variability. Leveraging simulations and real datasets, we benchmark the metric performance based on data-specific features, sparsity and sequencing platform, biological properties, and the ability to recapitulate true levels of biological variability based on known gene sets. Next, we use scran, the metric with the strongest all-round performance, to investigate changes in cell-to-cell variability that occur during B cell differentiation and the aging processes. The analysis of primary cell types from hematopoietic stem cells (HSCs) and B lymphopoiesis reveals unique gene signatures with consistent patterns of variable and stable expression profiles during B cell differentiation which highlights the significance of these methods. Identifying differentially variable genes between young and old cells elucidates the regulatory changes that may be overlooked by solely focusing on mean expression changes and we investigate this in the context of regulatory networks.

CONCLUSIONS

We highlight the importance of capturing cell-to-cell gene expression variability in a complex biological process like differentiation and aging and emphasize the value of these findings at the level of individual cell types.

The role of the integral type II transmembrane protein BRI2 in health and disease

BRI2 is a type II transmembrane protein ubiquitously expressed whose physiological function remains poorly understood. Although several recent important advances have substantially impacted on our understanding of BRI2 biology and function, providing valuable information for further studies on BRI2. These findings have contributed to a better understanding of BRI2 biology and the underlying signaling pathways involved. In turn, these might provide novel insights with respect to neurodegeneration processes inherent to BRI2-related pathologies, namely Familial British and Danish dementias, Alzheimer's disease, ITM2B-related retinal dystrophy, and multiple sclerosis. In this review, we provided a state-of-the-art outline of BRI2 biology, both in physiological and pathological conditions, and discuss the proposed molecular underlying mechanisms. Overall, the BRI2 knowledge here reviewed is of extreme importance and may contribute to propose BRI2 and/or BRI2 proteolytic fragments as novel therapeutic targets for neurodegenerative diseases, such as Alzheimer's disease.

Identification of plasma RGS18 and PPBP mRNAs as potential biomarkers for gastric cancer using transcriptome arrays

Coding and noncoding RNAs serve a crucial role in tumorigenesis. Circulating RNAs have been recognized as a novel category of biomarkers for a variety of physiological and pathological conditions. To identify plasma RNA biomarkers for gastric cancer (GC), a genome-wide transcriptome analysis using GeneChip^® Human Transcriptome Array, which contains probe sets covering exons of ~67500 coding and noncoding transcripts of annotated genes, was performed to screen for the RNAs that exhibited differential expression in the plasma samples of patients with GC and controls. The expression levels of 6 candidate RNAs, including regulator of G-protein signaling 18 (RGS18), integral membrane protein 2B, pro-platelet basic protein (PPBP), nucleosome assembly protein1-like 1, n324674 and ENST00000442382 were assessed in the plasma samples of 81 patients with GC and 77 healthy participants using reverse transcription-quantitative polymerase chain reaction. Furthermore, the expression levels of RGS18 and PPBP mRNAs were indicated to be significantly differentially expressed (P<0.0001) in an independent panel of plasma samples of 36 patients with GC compared with 34 healthy participants. The potential association of RGS18 and PPBP mRNA expression levels with clinicopathological features was subsequently analyzed. Receiver operating characteristic analysis indicated that the combination of these 2 mRNAs with an area under curve <0.812 was an improved indicator for gastric cancer compared with respective individual levels. The results of the present study indicate that RGS18 and PPBP mRNA expression was significantly downregulated in the plasma of patients with GC, and the combination of these 2 mRNAs may be a useful diagnostic or prognostic marker for GC.

Quantitative Analysis of Seven New Prostate Cancer Biomarkers and the Potential Future of the 'Biomarker Laboratory'

Prostate cancer is the third highest cause of male mortality in the developed world, with the burden of the disease increasing dramatically with demographic change. There are significant limitations to the current diagnostic regimens and no established effective screening modality. To this end, research has discovered hundreds of potential ‘biomarkers’ that may one day be of use in screening, diagnosis or prognostication. However, the barriers to bringing biomarkers to clinical evaluation and eventually into clinical usage have yet to be realised. This is an operational challenge that requires some new thinking and development of paradigms to increase the efficiency of the laboratory process and add ‘value’ to the clinician. Value comes in various forms, whether it be a process that is seamlessly integrated into the hospital laboratory environment or one that can provide additional ‘information’ for the clinical pathologist in terms of risk profiling. We describe, herein, an efficient and tissue-conserving pipeline that uses Tissue Microarrays in a semi-automated process that could, one day, be integrated into the hospital laboratory domain, using seven putative prostate cancer biomarkers for illustration.

Expression Pattern of the BCL6 and ITM2B Proteins in Normal Human Brains and in Alzheimer Disease

We reported that the integral membrane 2B gene (ITM2B, also called BRI2) is a target of BCL6 repression in lymphomas. Molecular alterations in ITM2B are associated with 2 neurodegenerative diseases, Familial British and Danish dementia, and dysregulation of ITM2B function has been implicated in the pathogenesis of Alzheimer disease (AD). Although ITM2B expression has been studied, the distribution of BCL6 in human brain has not been described. Our goal is to analyze BCL6 and ITM2B localization in normal human brains and in AD by immunohistochemistry to understand their relationship. We found that, in general, they have a reciprocal relationship. BCL6 expression is present in isolated cortical neurons, granule cells in the cerebellum, scattered glial cells, and in some cells of the ependyma and choroid plexus. ITM2B is expressed in most cortical neurons, neurons of the hippocampus and dentate nucleus, cerebellar Purkinje and granule cells, and (newly described here) in focal neurons in the basal ganglia, many neurons of the thalamus and brainstem, many cells in the ependyma and choroid plexus, and in the smooth muscle of blood vessels. ITM2B expression is prominent in plaques in AD-containing dystrophic neurites but absent in neurofibrillary tangles; BCL6 expression is absent in neurofibrillary tangles and in the nuclei of cells associated with plaques in AD. It is essential to understand the localization of BCL6 and ITM2B in the brain before considering manipulation of their expression as a potential therapeutic tool.

The Relationship between RUVBL1 (Pontin, TIP49, NMP238) and BCL6 in Benign and Malignant Human Lymphoid Tissues

The human BCL6 gene, which is involved in the pathogenesis of certain human lymphomas, encodes a transcriptional repressor that is needed for germinal center B cell development and T follicular helper cell differentiation. Our goal was to identify BCL6 target genes using a cell system in which BCL6 repressive effects are inhibited followed by subtractive hybridization, and we detected the RUVBL1 (Pontin, TIP49) gene as a potential target of BCL6 repression. Here we show that the BCL6 protein significantly represses RUVBL1 transcription (6.8-fold). Knockdown of endogenous BCL6 in a human B cell lymphoma line leads to significant upregulation of RUVBL1, and there is an inverse expression pattern between the BCL6 and RUVBL1 proteins in certain human lymphomas. RUVBL1 is part of the AAA+ superfamily and participates in multiple processes, including gene transcription regulation, chromatin remodeling, and DNA repair, which, if dysregulated, may promote lymphoma development. A further understanding of the relationship between RUVBL1 and BCL6 should improve our understanding of the pathogenesis of human lymphomas.

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BCL6, a transcriptional repressor, is deregulated in human lymphomas.

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The RUVBL1 (Pontin, TIP49) gene is a target of BCL6 repression.

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Regulation of RUVBL1 by BCL6 may be important in lymphomagenesis.