Unraveling inflammatory responses using systems genetics and gene-environment interactions in macrophages.

Many common diseases have an important inflammatory component mediated in part by macrophages. Here we used a systems genetics strategy to examine the role of common genetic variation in macrophage responses to inflammatory stimuli. We examined genome-wide transcript levels in macrophages from 92 strains of the Hybrid Mouse Diversity Panel. We exposed macrophages to control media, bacterial lipopolysaccharide (LPS), or oxidized phospholipids. We performed association mapping under each condition and identified several thousand expression quantitative trait loci (eQTL), gene-by-environment interactions, and eQTL "hot spots" that specifically control LPS responses. We used siRNA knockdown of candidate genes to validate an eQTL hot spot in chromosome 8 and identified the gene 2310061C15Rik as a regulator of inflammatory responses in macrophages. We have created a public database where the data presented here can be used as a resource for understanding many common inflammatory traits that are modeled in the mouse and for the dissection of regulatory relationships between genes.

Early-life inflammation primes a T helper 2 cell-fibroblast niche in skin.

Inflammation early in life can prime the local immune milieu of peripheral tissues, which can cause lasting changes in immunological tone that confer disease protection or susceptibility1. The cellular and molecular mechanisms that prompt changes in immune tone in many nonlymphoid tissues remain largely unknown. Here we find that time-limited neonatal inflammation induced by a transient reduction in neonatal regulatory T cells causes a dysregulation of subcutaneous tissue in mouse skin. This is accompanied by the selective accumulation of type 2 helper T (TH2) cells within a distinct microanatomical niche. TH2 cells are maintained into adulthood through interactions with a fibroblast population in skin fascia that we refer to as TH2-interacting fascial fibroblasts (TIFFs), which expand in response to TH2 cytokines to form subcutaneous fibrous bands. Activation of the TH2-TIFF niche due to neonatal inflammation primes the skin for altered reparative responses to wounding. Furthermore, we identify fibroblasts in healthy human skin that express the TIFF transcriptional signature and detect these cells at high levels in eosinophilic fasciitis, an orphan disease characterized by inflammation and fibrosis of the skin fascia. Taken together, these data define a previously unidentified TH2 cell niche in skin and functionally characterize a disease-associated fibroblast population. The results also suggest a mechanism of immunological priming whereby inflammation early in life creates networks between adaptive immune cells and stromal cells to establish an immunological set-point in tissues that is maintained throughout life.

Layilin Anchors Regulatory T Cells in Skin.

Regulatory T cells (Tregs) reside in nonlymphoid tissues where they carry out unique functions. The molecular mechanisms responsible for Treg accumulation and maintenance in these tissues are relatively unknown. Using an unbiased discovery approach, we identified LAYN (layilin), a C-type lectin-like receptor, to be preferentially and highly expressed on a subset of activated Tregs in healthy and diseased human skin. Expression of layilin on Tregs was induced by TCR-mediated activation in the presence of IL-2 or TGF-ß. Mice with a conditional deletion of layilin in Tregs had reduced accumulation of these cells in tumors. However, these animals somewhat paradoxically had enhanced immune regulation in the tumor microenvironment, resulting in increased tumor growth. Mechanistically, layilin expression on Tregs had a minimal effect on their activation and suppressive capacity in vitro. However, expression of this molecule resulted in a cumulative anchoring effect on Treg dynamic motility in vivo. Taken together, our results suggest a model whereby layilin facilitates Treg adhesion in skin and, in doing so, limits their suppressive capacity. These findings uncover a unique mechanism whereby reduced Treg motility acts to limit immune regulation in nonlymphoid organs and may help guide strategies to exploit this phenomenon for therapeutic benefit.

Rapid single cell evaluation of human disease and disorder targets using REVEAL: SingleCell™.

BACKGROUND: Single-cell (sc) sequencing performs unbiased profiling of individual cells and enables evaluation of less prevalent cellular populations, often missed using bulk sequencing. However, the scale and the complexity of the sc datasets poses a great challenge in its utility and this problem is further exacerbated when working with larger datasets typically generated by consortium efforts. As the scale of single cell datasets continues to increase exponentially, there is an unmet technological need to develop database platforms that can evaluate key biological hypotheses by querying extensive single-cell datasets. Large single-cell datasets like Human Cell Atlas and COVID-19 cell atlas (collection of annotated sc datasets from various human organs) are excellent resources for profiling target genes involved in human diseases and disorders ranging from oncology, auto-immunity, as well as infectious diseases like COVID-19 caused by SARS-CoV-2 virus. SARS-CoV-2 infections have led to a worldwide pandemic with massive loss of lives, infections exceeding 7 million cases. The virus uses ACE2 and TMPRSS2 as key viral entry associated proteins expressed in human cells for infections. Evaluating the expression profile of key genes in large single-cell datasets can facilitate testing for diagnostics, therapeutics, and vaccine targets, as the world struggles to cope with the on-going spread of COVID-19 infections. MAIN BODY: In this manuscript we describe REVEAL: SingleCell, which enables storage, retrieval, and rapid query of single-cell datasets inclusive of millions of cells. The array native database described here enables selecting and analyzing cells across multiple studies. Cells can be selected using individual metadata tags, more complex hierarchical ontology filtering, and gene expression threshold ranges, including co-expression of multiple genes. The tags on selected cells can be further evaluated for testing biological hypotheses. One such example includes identifying the most prevalent cell type annotation tag on returned cells. We used REVEAL: SingleCell to evaluate the expression of key SARS-CoV-2 entry associated genes, and queried the current database (2.2 Million cells, 32 projects) to obtain the results in < 60 s. We highlighted cells expressing COVID-19 associated genes are expressed on multiple tissue types, thus in part explains the multi-organ involvement in infected patients observed worldwide during the on-going COVID-19 pandemic. CONCLUSION: In this paper, we introduce the REVEAL: SingleCell database that addresses immediate needs for SARS-CoV-2 research and has the potential to be used more broadly for many precision medicine applications. We used the REVEAL: SingleCell database as a reference to ask questions relevant to drug development and precision medicine regarding cell type and co-expression for genes that encode proteins necessary for SARS-CoV-2 to enter and reproduce in cells.

Impact of second-opinion dermatopathology reviews on surgical management of malignant neoplasms.

BACKGROUND: Second-opinion review is linked to error reduction and treatment changes in anatomic pathology. OBJECTIVE: We sought to establish the rate of diagnostic discrepancy identified by second-opinion dermatopathologic review and the effect on surgical treatment. METHODS: Cases referred for treatment of a malignant neoplasm diagnosed by an outside pathologist were reviewed. The external and internal second-opinion dermatopathologic reports were compared. Discordance in diagnosis, subtype, and treatment change owing to second-opinion review was recorded. The referring pathologist's level of dermatopathologic training was also documented. RESULTS: A total of 358 cases were included. Dermatopathologic second-opinion diagnosis was discordant with the outside diagnosis in 37 of 358 cases (10.3%). In 32 of 358 cases (8.9%), second-opinion review resulted in a change in treatment, with 28 of 32 (87.5%) of these changes resulting in cancelled surgery. Dermatologists without dermatopathologic fellowship training had the highest rate of discordant diagnoses compared with pathologists and dermatopathologists. LIMITATIONS: This was a retrospective study at a tertiary care facility. CONCLUSION: Second-opinion dermatopathologic review is associated with identification of discordant diagnoses and a substantial influence on treatment, with both cancellation of surgery and augmented management. Secondary pathologic review should be considered in high-volume surgical practices.

Validation of the English Basal and Squamous Cell Carcinoma Quality of Life (BaSQoL) Questionnaire.

BACKGROUND: Keratinocyte carcinomas (KC) impact patient quality of life (QoL). There is a need for validated QoL instruments specific to KC. The Basal and Squamous Cell Carcinoma QoL (BaSQoL) questionnaire was developed to comprehensively measure issues of importance to patients with KC. OBJECTIVE: To validate and characterize the BaSQoL questionnaire for QoL measurement after diagnosis and treatment of KC. METHODS: This was a prospective, observational study. Patients with basal cell carcinoma (BCC) or squamous cell carcinoma (SCC) were asked to fill out BaSQoL, Skin Cancer Index (SCI), and Hospital Anxiety and Depression Scale (HADS) questionnaires. Descriptive statistics and classical test theory were used to assess validity. RESULTS: One hundred eighty-seven subjects enrolled in this study: 122 with BCC and 65 with SCC. One hundred seventy-one subjects (91.4%) completed questionnaires at all 3 time points; 16 patients (8.6%) were lost to follow-up. Overall performance using classical test theory was good, with good internal consistency (Cronbach's α 0.63-0.80). BaSQoL subscales were strongly correlated with subscales of the SCI, demonstrating convergent validity, and weakly correlated with HADS, showing divergent validity. CONCLUSION: The English language version of BaSQoL has good face, content, and construct validity. This study validates BaSQoL for use in English-speaking patients with BCC and SCC.

Genome-wide transcriptome analysis identifies novel dysregulated genes implicated in Alzheimer's pathology.

INTRODUCTION: Abnormal gene expression patterns may contribute to the onset and progression of late-onset Alzheimer's disease (LOAD). METHODS: We performed transcriptome-wide meta-analysis (N = 1440) of blood-based microarray gene expression profiles as well as neuroimaging and cerebrospinal fluid (CSF) endophenotype analysis. RESULTS: We identified and replicated five genes (CREB5, CD46, TMBIM6, IRAK3, and RPAIN) as significantly dysregulated in LOAD. The most significantly altered gene, CREB5, was also associated with brain atrophy and increased amyloid beta (Aß) accumulation, especially in the entorhinal cortex region. cis-expression quantitative trait loci mapping analysis of CREB5 detected five significant associations (P < 5 × 10-8 ), where rs56388170 (most significant) was also significantly associated with global cortical Aß deposition measured by [18 F]Florbetapir positron emission tomography and CSF Aß1-42 . DISCUSSION: RNA from peripheral blood indicated a differential gene expression pattern in LOAD. Genes identified have been implicated in biological processes relevant to Alzheimer's disease. CREB, in particular, plays a key role in nervous system development, cell survival, plasticity, and learning and memory.

Sebaceous carcinoma: evidence-based clinical practice guidelines.

Sebaceous carcinoma usually occurs in adults older than 60 years, on the eyelid, head and neck, and trunk. In this Review, we present clinical care recommendations for sebaceous carcinoma, which were developed as a result of an expert panel evaluation of the findings of a systematic review. Key conclusions were drawn and recommendations made for diagnosis, first-line treatment, radiotherapy, and post-treatment care. For diagnosis, we concluded that deep biopsy is often required; furthermore, differential diagnoses that mimic the condition can be excluded with special histological stains. For treatment, the recommended first-line therapy is surgical removal, followed by margin assessment of the peripheral and deep tissue edges; conjunctival mapping biopsies can facilitate surgical planning. Radiotherapy can be considered for cases with nerve or lymph node involvement, and as the primary treatment in patients who are ineligible for surgery. Post-treatment clinical examination should occur every 6 months for at least 3 years. No specific systemic therapies for advanced disease can be recommended, but targeted therapies and immunotherapies are being developed.

canvasDesigner: a versatile interactive high-resolution scientific multi-panel visualization toolkit.

Summary: We present a bioinformatics and systems biology visualization toolkit harmonizing real time interactive exploring and analyzing of big data, full-fledged customizing of look-n-feel and producing multi-panel publication-ready figures in PDF format simultaneously. Availability and implementation: Source code and detailed user guides are available at http://canvasxpress.org, https://baohongz.github.io/canvasDesigner and https://baohongz.github.io/canvasDesigner/demo_video.html. Supplementary information: Supplementary data are available at Bioinformatics online.

CRISPR-DAV: CRISPR NGS data analysis and visualization pipeline.

SUMMARY: The simplicity and precision of CRISPR/Cas9 system has brought in a new era of gene editing. Screening for desired clones with CRISPR-mediated genomic edits in a large number of samples is made possible by next generation sequencing (NGS) due to its multiplexing. Here we present CRISPR-DAV (CRISPR Data Analysis and Visualization) pipeline to analyze the CRISPR NGS data in a high throughput manner. In the pipeline, Burrows-Wheeler Aligner and Assembly Based ReAlignment are used for small and large indel detection, and results are presented in a comprehensive set of charts and interactive alignment view. AVAILABILITY AND IMPLEMENTATION: CRISPR-DAV is available at GitHub and Docker Hub repositories: https://github.com/pinetree1/crispr-dav.git and https://hub.docker.com/r/pinetree1/crispr-dav/. CONTACT: xuning.wang@bms.com.

Case Report of Multiple Keratoacanthomas and Squamous Cell Carcinomas in a Patient Receiving Pembrolizumab.

PD-1 is expressed on antigen-stimulated T cells and induces a downstream signaling pathway that works by negative feedback to inhibit T cell proliferation, cytokine release, and cytotoxicity. PD-1 antibodies increase tumor cell killing peripherally and have a role in advanced melanoma treatment. We describe a case of an 84 year old female with stage 4 metastatic melanoma in a trial of the PD-1 inhibitor pembrolizumab who developed multiple keratoacanthomas after several months of treatment. While keratoacanthomas have been reported in patients taking BRAF inhibitors, no such reports exist for those on pembrolizumab, making this the first case report to point out this association for further investigative studies.

J Drugs Dermatol. 2017;16(5):513-515.

The distribution of cutaneous metastases correlates with local immunologic milieu.

BACKGROUND: Metastases to the skin are found with increased frequency at certain sites, such as the scalp, but the biological factors that influence this distribution are not understood. OBJECTIVE: We aimed to compare the proportional frequency of metastases at various cutaneous locations with the immunologic microenvironments at those sites. METHODS: We retrospectively identified all biopsy specimens of cutaneous metastases diagnosed at our institution from 1991 to 2014 (n = 1984) and mapped their anatomic distribution while controlling for regional surface area. Using a separate, mapped cohort of normal-appearing skin samples (n = 140), we measured the density of regulatory T cells, CD4(+) effector T cells, and CD8(+) T cells by flow cytometry. RESULTS: Per unit surface area, cutaneous metastases arise most commonly on the head and neck, followed by the trunk, upper extremities, and lower extremities, respectively. Sites with more frequent metastases tend to contain a greater density of regulatory T cells and a lower proportion of CD8(+) T cells (P < .05). LIMITATIONS: Immunologic factors were only assessed in control tissue and were not measured from patients with metastatic disease in this correlative single-center study. CONCLUSION: The distribution of cutaneous metastases follows the distribution of regulatory and effector T cells in skin. Further studies are required to prove a mechanistic association between local immunologic factors and the development of cutaneous metastases.

Consensus for sclerotherapy.

BACKGROUND: The American Society for Dermatologic Surgery (ASDS) periodically develops consensus documents for its members concerning various aspects of dermatologic surgery. Unwanted and painful leg veins are a very widespread problem. Many advances in sclerotherapy of varicose and telangiectatic leg veins have occurred since the previous consensus documents. OBJECTIVE: In 2013, the ASDS Board of Directors voted to have a committee of experts in the field to develop consensus documents on sclerotherapy. MATERIALS AND METHODS: An expert panel reviewed the literature on sclerotherapy and discussed the findings. A consensus was reached with evidence-based recommendations on diagnostic evaluation and treatment of varicose and telangiectatic leg veins. RESULTS: The consensus documents include discussion of indications for treatment, patient selection, contraindications, diagnostic testing, treatment approaches, use of compression, and expected outcome. Common sclerosants and their mechanisms of action, advantages and disadvantages of foam sclerotherapy, and minimizing and treating complications are presented. CONCLUSION: The ASDS consensus documents on sclerotherapy will be helpful in educating their members on safe and effective sclerotherapy of varicose and telangiectatic leg veins.

Comparative analysis of proteome and transcriptome variation in mouse.

The relationships between the levels of transcripts and the levels of the proteins they encode have not been examined comprehensively in mammals, although previous work in plants and yeast suggest a surprisingly modest correlation. We have examined this issue using a genetic approach in which natural variations were used to perturb both transcript levels and protein levels among inbred strains of mice. We quantified over 5,000 peptides and over 22,000 transcripts in livers of 97 inbred and recombinant inbred strains and focused on the 7,185 most heritable transcripts and 486 most reliable proteins. The transcript levels were quantified by microarray analysis in three replicates and the proteins were quantified by Liquid Chromatography-Mass Spectrometry using O(18)-reference-based isotope labeling approach. We show that the levels of transcripts and proteins correlate significantly for only about half of the genes tested, with an average correlation of 0.27, and the correlations of transcripts and proteins varied depending on the cellular location and biological function of the gene. We examined technical and biological factors that could contribute to the modest correlation. For example, differential splicing clearly affects the analyses for certain genes; but, based on deep sequencing, this does not substantially contribute to the overall estimate of the correlation. We also employed genome-wide association analyses to map loci controlling both transcript and protein levels. Surprisingly, little overlap was observed between the protein- and transcript-mapped loci. We have typed numerous clinically relevant traits among the strains, including adiposity, lipoprotein levels, and tissue parameters. Using correlation analysis, we found that a low number of clinical trait relationships are preserved between the protein and mRNA gene products and that the majority of such relationships are specific to either the protein levels or transcript levels. Surprisingly, transcript levels were more strongly correlated with clinical traits than protein levels. In light of the widespread use of high-throughput technologies in both clinical and basic research, the results presented have practical as well as basic implications.

Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma.

Squamous cell carcinomas (SCCs) are one of the most frequent forms of human malignancy, but, other than TP53 mutations, few causative somatic aberrations have been identified. We identified NOTCH1 or NOTCH2 mutations in ~75% of cutaneous SCCs and in a lesser fraction of lung SCCs, defining a spectrum for the most prevalent tumor suppressor specific to these epithelial malignancies. Notch receptors normally transduce signals in response to ligands on neighboring cells, regulating metazoan lineage selection and developmental patterning. Our findings therefore illustrate a central role for disruption of microenvironmental communication in cancer progression. NOTCH aberrations include frameshift and nonsense mutations leading to receptor truncations as well as point substitutions in key functional domains that abrogate signaling in cell-based assays. Oncogenic gain-of-function mutations in NOTCH1 commonly occur in human T-cell lymphoblastic leukemia/lymphoma and B-cell chronic lymphocytic leukemia. The bifunctional role of Notch in human cancer thus emphasizes the context dependency of signaling outcomes and suggests that targeted inhibition of the Notch pathway may induce squamous epithelial malignancies.

Rosacea Core Domain Set for Clinical Trials and Practice: A Consensus Statement.

Importance: Inconsistent reporting of outcomes in clinical trials of rosacea is impeding and likely preventing accurate data pooling and meta-analyses. There is a need for standardization of outcomes assessed during intervention trials of rosacea. Objective: To develop a rosacea core outcome set (COS) based on key domains that are globally relevant and applicable to all demographic groups to be used as a minimum list of outcomes for reporting by rosacea clinical trials, and when appropriate, in clinical practice. Evidence Review: A systematic literature review of rosacea clinical trials was conducted. Discrete outcomes were extracted and augmented through discussions and focus groups with key stakeholders. The initial list of 192 outcomes was refined to identify 50 unique outcomes that were rated through the Delphi process Round 1 by 88 panelists (63 physicians from 17 countries and 25 patients with rosacea in the US) on 9-point Likert scale. Based on feedback, an additional 11 outcomes were added in Round 2. Outcomes deemed to be critical for inclusion (rated 7-9 by ≥70% of both groups) were discussed in consensus meetings. The outcomes deemed to be most important for inclusion by at least 85% of the participants were incorporated into the final core domain set. Findings: The Delphi process and consensus-building meetings identified a final core set of 8 domains for rosacea clinical trials: ocular signs and symptoms; skin signs of disease; skin symptoms; overall severity; patient satisfaction; quality of life; degree of improvement; and presence and severity of treatment-related adverse events. Recommendations were also made for application in the clinical setting. Conclusions and Relevance: This core domain set for rosacea research is now available; its adoption by researchers may improve the usefulness of future trials of rosacea therapies by enabling meta-analyses and other comparisons across studies. This core domain set may also be useful in clinical practice.

A high-resolution association mapping panel for the dissection of complex traits in mice.

Systems genetics relies on common genetic variants to elucidate biologic networks contributing to complex disease-related phenotypes. Mice are ideal model organisms for such approaches, but linkage analysis has been only modestly successful due to low mapping resolution. Association analysis in mice has the potential of much better resolution, but it is confounded by population structure and inadequate power to map traits that explain less than 10% of the variance, typical of mouse quantitative trait loci (QTL). We report a novel strategy for association mapping that combines classic inbred strains for mapping resolution and recombinant inbred strains for mapping power. Using a mixed model algorithm to correct for population structure, we validate the approach by mapping over 2500 cis-expression QTL with a resolution an order of magnitude narrower than traditional QTL analysis. We also report the fine mapping of metabolic traits such as plasma lipids. This resource, termed the Hybrid Mouse Diversity Panel, makes possible the integration of multiple data sets and should prove useful for systems-based approaches to complex traits and studies of gene-by-environment interactions.

High-resolution association mapping of atherosclerosis loci in mice.

OBJECTIVE: The purpose of this study was to fine map previously identified quantitative trait loci affecting atherosclerosis in mice using association analysis. METHODS AND RESULTS: We recently showed that high-resolution association analysis using common inbred strains of mice is feasible if corrected for population structure. To use this approach for atherosclerosis, which requires a sensitizing mutation, we bred human apolipoprotein B-100 transgenic mice with 22 different inbred strains to produce F1 heterozygotes. Mice carrying the dominant transgene were tested for association with high-density single nucleotide polymorphism maps. Here, we focus on high-resolution mapping of the previously described atherosclerosis 30 locus on chromosome 1. Compared with the previous linkage analysis, association improved the resolution of the atherosclerosis 30 locus by more than an order of magnitude. Using expression quantitative trait locus analysis, we identified one of the genes in the region, desmin, as a strong candidate. CONCLUSIONS: Our high-resolution mapping approach accurately identifies and fine maps known atherosclerosis quantitative trait loci. These results suggest that high-resolution genome-wide association analysis for atherosclerosis is feasible in mice.

Tobacco smoking and dermatologic surgery.

BACKGROUND: Cigarette smoking is the leading cause of preventable death and a major public health concern. Numerous clinical and experimental studies have examined the effect of nicotine on wound healing and surgical procedures, but there are limited published reports in the dermatologic surgery literature. OBJECTIVE: This article seeks to develop evidence-based recommendations regarding the effect of tobacco use in patients undergoing dermatologic surgery procedures. METHODS: This article reviews the existing published English-language literature pertaining to the effects of tobacco on wound healing and surgical complications. RESULTS: Tobacco use is associated with a higher incidence of postoperative complications including wound dehiscence, flap or graft necrosis, prolonged healing time, and infections. LIMITATIONS: This review article only summarizes past reports and studies. CONCLUSION: Recommendations for smoking cessation before dermatologic surgery are provided based on the available data.

Accuracy and completeness of patient information in organic World-Wide Web search for Mohs surgery: a prospective cross-sectional multirater study using consensus criteria.

BACKGROUND: Many patients obtain medical information from the Internet. Inaccurate information affects patient care and perceptions. OBJECTIVE: To assess the accuracy and completeness of information regarding Mohs micrographic surgery (MMS) on the Internet. METHODS: Prospective cross-sectional Internet-based study reviewing 30 consecutive organic results from three U.S. urban areas on "Mohs surgery" using Google. Text was assessed using a consensus-derived rating scale that quantified necessary and additional or supplementary information about MMS, as well as wrong information. Websites were classified according to type of sponsor. RESULTS: Ninety-one percent of sites conveyed basic information about MMS. There was variation in the mean amount of additional information items (range 0-9) according to website type: 8.4, medical societies; 6.7, academic practices; 5.9, web-based medical information resources; 4.7, private practices; and 4.4, other (p < .001). Cumulatively, academic practices and professional societies (mean 7.42) provided more additional information than private practices and web-based sources (mean 5.11, p < .001). There were no differences based on geographic location. Wrong items included misspelling Mohs (10%), indicating that only plastic surgeons could reconstruct (7%), and noting MMS was never cost-effective (7%). CONCLUSIONS: High-ranking websites provide basic information about MMS. Academic practice and professional society sites provide more-comprehensive information, but private practice sites and web-based medical information sources also provide additional information.