Evidence of dynamically dysregulated gene expression pathways in hyperresponsive B cells from African American lupus patients

Binned multinomial logistic regression for integrative cell-type annotation

Categorizing individual cells into one of many known cell type categories, also known as cell type annotation, is a critical step in the analysis of single-cell genomics data. The current process of annotation is time-intensive and subjective, which has led to different studies describing cell types with labels of varying degrees of resolution. While supervised learning approaches have provided automated solutions to annotation, there remains a significant challenge in fitting a unified model for multiple datasets with inconsistent labels. In this article, we propose a new multinomial logistic regression estimator which can be used to model cell type probabilities by integrating multiple datasets with labels of varying resolution. To compute our estimator, we solve a nonconvex optimization problem using a blockwise proximal gradient descent algorithm. We show through simulation studies that our approach estimates cell type probabilities more accurately than competitors in a wide variety of scenarios. We apply our method to ten single-cell RNA-seq datasets and demonstrate its utility in predicting fine resolution cell type labels on unlabeled data as well as refining cell type labels on data with existing coarse resolution annotations. Finally, we demonstrate that our method can lead to novel scientific insights in the context of a differential expression analysis comparing peripheral blood gene expression before and after treatment with interferon- β . An R package implementing the method is available at https://github.com/keshav-motwani/IBMR and the collection of datasets we analyze is available at https://github.com/keshav-motwani/AnnotatedPBMC.

Systemic lupus erythematosus diagnosis and management

SLE presents many challenges for clinicians. The onset of disease may be insidious, with many different symptoms and signs, making early and accurate diagnosis challenging. Tests for SLE in the early stages lack specificity; those that are useful later often appear only after organ damage is manifest. Disease patterns are highly variable; flares are not predictable and not always associated with biomarkers. Children with SLE may have severe disease and present special management issues. Older SLE patients have complicating co-morbid conditions. Therapeutic interventions have improved over recent decades, but available drugs do not adequately control disease in many patients, and successful outcomes are limited by off-target effects; some of these become manifest with longer duration of treatment, now in part revealed by improved rates of survival. Despite all of these challenges, advances in understanding the biological basis of SLE have translated into more effective approaches to patient care. This review considers the current state of SLE diagnosis and management, with a focus on new approaches and anticipated advances.

Transcriptional profiling of leukocytes from rheumatoid arthritis patients before and after anti-tumor necrosis factor therapy: A comparison of anti-nuclear antibody positive and negative subsets

Anti-nuclear antibodies (ANAs) may be induced in patients with rheumatoid arthritis (RA) receiving anti-tumor necrosis factor (TNF) therapy with TNF inhibitors (TNFi), etanercept, infliximab or adalimumab. In the present study, 11 patients who were TNFi drug naive were started on TNFi at a time of high disease activity. Of these, all cases were positive for rheumatoid factor and 9 cases tested were positive for anti-citrullinated peptide (anti-CCP) antibodies prior to TNFi treatment. Peripheral blood mononuclear cells (PBMCs) and serum were collected from all patients before and after TNFi therapy. Serum was assayed for ANAs over time. Total cellular RNA was extracted from PBMCs and assessed using Illumina arrays. Gene expression profiles were examined for alterations in key effector pathways. After 3 or more months on TNFi, 6 patients converted to ANA-positivity. Analysis of transcripts from patients with RA who converted to ANA-positivity after 3 months on TNFi identified complex gene expression profiles that reflected a reduction in cell adhesion, cell stress and lipid metabolism transcripts. In summary, unique transcriptional profiles in PBMCs from patients with RA were observed after TNFi therapy. This pilot study suggests that transcriptional profiling is a precise method of measuring the impact of TNFi therapies and reveals novel pathways that likely influence the immune response.

I too, am America: a review of research on systemic lupus erythematosus in African-Americans

Systemic lupus erythematosus (SLE) is a multi-organ autoimmune disorder that can cause significant morbidity and mortality. A large body of evidence has shown that African-Americans experience the disease more severely than other racial-ethnic groups. Relevant literature for the years 2000 to August 2015 were obtained from systematic searches of PubMed, Scopus, and the EBSCOHost platform that includes MEDLINE, CINAHL, etc. to evaluate research focused on SLE in African-Americans. Thirty-six of the 1502 articles were classified according to their level of evidence. The systematic review of the literature reported a wide range of adverse outcomes in African-American SLE patients and risk factors observed in other mono and multi-ethnic investigations. Studies limited to African-Americans with SLE identified novel methods for more precise ascertainment of risk and observed novel findings that hadn't been previously reported in African-Americans with SLE. Both environmental and genetic studies included in this review have highlighted unique African-American populations in an attempt to isolate risk attributable to African ancestry and observed increased genetic influence on overall disease in this cohort. The review also revealed emerging research in areas of quality of life, race-tailored interventions, and self-management. This review reemphasizes the importance of additional studies to better elucidate the natural history of SLE in African-Americans and optimize therapeutic strategies for those who are identified as being at high risk.