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Staudt, L.

Publications and source records attributed to Staudt, L..

2 recordsLinked to original sources

Clathrin recruitment and assembly of phosphorylated B cell receptor is impaired in human diffuse large B cell lymphoma

The B cell receptor (BCR) drives the differentiation of naive B cells into activated plasma cells that produce antibodies. The BCR consists of a plasma membrane-bound surface immunoglobulin (sIg) that binds antigens, and two coreceptor subunits CD79A and CD79B. The intracellular domains of CD79A and CD79B initiate immune signaling and endocytosis of the receptor in healthy B cells. In diffuse large B cell lymphoma (DLBCL), an aggressive form of human blood cancer, the activated B cell like (ABC) subtype exhibits constitutive signaling that drives survival and proliferation. Here, in a model of human ABC DLBCL, we determine the localization of BCR components relative to plasma membrane structures using correlative super-resolution light and platinum replica transmission electron microscopy. We find that spontaneous clusters of the surface Immunoglobulin common to ABC lymphoma localize to smooth raised membrane domains. These structures are involved in the endocytosis of large receptor clusters. Surprisingly, activated phosphorylated CD79A (pCD79A) shows little colocalization with clathrin on or off smooth raised membranes. Furthermore, pCD79A spatially segregates away from both the slg and CD79B subunits of the BCR complex. A similar distribution was found for downstream phosphorylated Src family kinases. We propose that a disengagement of pCD79A away from sIg and CD79B allows the receptor to evade down-regulation through endocytosis and maintains signaling at the plasma membrane. This mechanism could drive aberrant signaling and the proliferation of lymphomas leading to disease.

cell biology↗

Uniform Genomic Data Analysis in the NCI Genomic Data Commons

The goal of the National Cancer Institute (NCI) Genomic Data Commons (GDC) is to provide the cancer research community with a data repository of uniformly processed genomic and associated clinical data that enables data sharing and collaborative analysis in the support of precision medicine. The initial GDC dataset include genomic, epigenomic, proteomic, clinical and other data from the NCI TCGA and TARGET programs. Data production for the GDC started in June, 2015 using an OpenStack-based private cloud. By June of 2016, the GDC had analyzed more than 50,000 raw sequencing data inputs, as well as multiple other data types. Using the latest human genome reference build GRCh38, the GDC generated a variety of data types from aligned reads to somatic mutations, gene expression, miRNA expression, DNA methylation status, and copy number variation. In this paper, we describe the pipelines and workflows used to process and harmonize the data in the GDC. The generated data, as well as the original input files from TCGA and TARGET, are available for download and exploratory analysis at the GDC Data Portal and Legacy Archive (https://gdc.cancer.gov/).

bioinformatics↗