B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstruction) that accurately reconstructs the paired heavy and light chain immunoglobulin gene sequences from Illumina single-cell RNA-seq data. BALDR was accurate for clonotype identification in human and rhesus macaque influenza vaccine and simian immunodeficiency virus vaccine induced vaccine-induced plasmablasts and naïve and antigen-specific memory B cells. BALDR enables matching of clonotype identity with single-cell transcriptional information in B cell lineages and will have broad application in the fields of vaccines, human immunodeficiency virus broadly neutralizing antibody development, and cancer.BALDR is available at https://github.com/BosingerLab/BALDR .

Psoriasis is a debilitating chronic inflammatory disease. In addition to the characteristic effects on the skin, chronic inflammation associated with the disease is recognized to contribute to cardiovascular, hepatic and renal comorbidities. Immature myeloid regulatory cells, known as myeloid‑derived suppressor cells (MDSCs), have been demonstrated to accumulate in various diseases and chronic inflammatory states, including inflammatory bowel disease and various types of cancer. The results of the present study, obtained using flow cytometry and cell culture analysis of peripheral blood mononuclear cells from psoriasis and healthy patients, revealed that MDSC levels are significantly increased in the blood of patients with psoriasis compared with healthy controls. Furthermore, these cells are capable of producing various molecules, including matrix metalloproteinase‑9 and‑1, interleukin‑8, growth‑related oncogene, and monocyte chemoattractant protein 1. These molecules may recruit additional immune cells involved in the pathogenesis of the disease, and contribute to the chronic inflammatory state in these patients. Therefore, MDSCs, which have various immune regulatory functions, may contribute to the pathogenesis of psoriasis as a systemic inflammatory disease.

Flow cytometry is a valuable tool for the detection and characterization of proteins expressed by individual cells. Flow cytometry can be used to measure cell expression of 2 intracellular proteins that are involved in the regulation of immune homeostasis, SLAM-associated protein (SAP) and X-linked inhibitor of apoptosis (XIAP). These proteins are defective in patients with the immune deficiency X-linked lymphoproliferative disease (XLP), due to mutations in the SH2D1A and XIAP/BIRC4 genes, respectively (Coffey et al. Nat Genet 20:129-135 1998; Nichols et al. Proc Natl Acad Sci U S A 95:13765-13770, 1998; Sayos et al. Nature 395:462-469, 1998; Rigaud et al. Nature 444:110-114, 2006). This procedure describes a technique that can be efficiently used to detect SAP and XIAP by flow cytometry.