Genome-wide gene expression dataset used to identify potential therapeutic targets in androgenetic alopecia.

The microarray dataset attached to this report is related to the research article with the title: "A genomic approach to susceptibility and pathogenesis leads to identifying potential novel therapeutic targets in androgenetic alopecia" (Dey-Rao and Sinha, 2017) [1]. Male-pattern hair loss that is induced by androgens (testosterone) in genetically predisposed individuals is known as androgenetic alopecia (AGA). The raw dataset is being made publicly available to enable critical and/or extended analyses. Our related research paper utilizes the attached raw dataset, for genome-wide gene-expression associated investigations. Combined with several in silico bioinformatics-based analyses we were able to delineate five strategic molecular elements as potential novel targets towards future AGA-therapy.

A genomic approach to susceptibility and pathogenesis leads to identifying potential novel therapeutic targets in androgenetic alopecia.

We studied genome-wide gene expression from bald and haired scalp of individuals to evaluate pathogenic mechanisms underlying the development and progression of androgenetic alopecia (AGA). Unbiased analyses revealed a "bald pathology" based signature. Ontology enrichment analyses of the differentially expressed genes (DEGs) underscored apoptosis, cell proliferation, perturbed neurological pathways, and WNT signaling as central drivers of the hair loss process. Interactome analysis uncovered several known and novel key transcriptional regulators potentially affecting disease pathogenesis both within and "hidden" from the dataset. One DEG mapped within one of the fourteen identified transcriptionally active "hot spots" across the genome and coincided with a previous AGA-associated gene. The remaining DEGs within the "hot spots" offer an additional set of potential disease linked loci that may help to guide future studies aimed at identifying disease risk genes. Finally, we used in silico analyses to identify five molecular targets for exploration in future AGA therapies.

Accuracy and evaluation of a new regression equation in predicting the width of unerupted permanent canines and premolar teeth.

AIM: To assess the applicability of two regression equations based on mixed dentition analysis and to propose and evaluate a new regression equation using the mandibular incisors and first permanent molars as predictors in calculating the size of unerupted permanent canines and premolar teeth in school children. METHODS: Dental study casts of 100 children (50 males and 50 females) aged 11-14 years from schools situated in Moradabad, Uttar Pradesh, India were used. The analysis of Tanaka Johnston, Bernabe Flores-Mir and the proposed equation were tested on the casts. RESULTS: The analysis of Tanaka Johnston and Bernabe Flores-Mir tended to overestimate the mesio-distal width of the canines and premolars. The proposed equation also overestimated but the mean difference showed a closer approximation with the actual measured values compared to the other two equations. CONCLUSION: Validating studies with a similar population must be conducted to confirm the applicability and precision of the proposed equation.

Nuclear magnetic resonance titration of the interaction between pemphigus vulgaris autoantibodies and REWVKFAKPCRE, a therapeutic desmoglein 3 peptide.

BACKGROUND: Pemphigus vulgaris (PV) is an autoimmune skin disease, the primary autoantigen of which is the desmosomal cadherin desmoglein (Dsg)3. The exact defin-ition of Dsg3 epitopes and their relationship(s) to the pathophysiology of blister formation are important for the advancement of efforts to develop more effective and specific therapies for PV. AIM: To characterize the binding of autoantibodies from patients with PV to a Dsg3 peptide, REWVKFAKPCRE, which shows therapeutic effectiveness but does not induce pathogenic antibodies. METHODS: We carried out a titration experiment of the reaction between PV autoantibodies and the peptide Dsg349-60REWVKFAKPCRE using nuclear magnetic resonance (NMR) spectroscopy. RESULTS: The interaction between Dsg349-60REWVKFAKPCRE and PV autoantibodies at concentrations of 20, 40 and 60 mg was found to involve R49 and A55 residues. CONCLUSIONS: Our data seem to suggest that the REWVKFAKPCRE peptide may mimic epitopic Dsg3 extracellular sequences related to pathogenic autoantibodies.

Comorbidities and inpatient mortality for pemphigus in the U.S.A.

BACKGROUND: The morbidity and mortality associated with pemphigus and its treatments have not been fully described. Previous studies have found conflicting results about certain comorbidities and were limited by small sample sizes. OBJECTIVES: To determine the morbidity and mortality from pemphigus and its treatments in the U.S.A. METHODS: We examined a cross-sectional cohort of 87 039 711 hospitalized patients in the U.S.A. to determine the inpatient comorbidities and mortality of pemphigus. RESULTS: In multivariate survey logistic regression models adjusting for age, sex and race/ethnicity, pemphigus and its treatments were associated with 39 of 122 comorbidities examined. The disorders most strongly associated with pemphigus were Cushing syndrome [adjusted odds ratio (OR) 17·23, 95% confidence interval (CI) 2·41-122·90], adrenal insufficiency (4·08, 1·71-9·73), myasthenia gravis (6·92, 2·55-18·79), mucositis (17·19, 7·73-38·22), herpes infection (7·98, 3·62-17·62), fungal infections (4·03, 3·60-4·52), insomnia (18·02, 2·46-131·88) and hidradenitis (5·34, 1·33-21·43). Among malignancies, only leukaemia (OR 1·56, 95% CI 1·08-2·24) and non-Hodgkin lymphoma (1·52, 1·15-2·03) were associated with pemphigus, but not any solid organ malignancies. Patients with a secondary diagnosis of pemphigus had higher inpatient mortality (3·20%, 95% CI 2·71-3·69) than those with a primary (1·60%, 1·29-1·91) or no (1·78%, 1·78-1·78) diagnosis of pemphigus (P < 0·001). CONCLUSIONS: Pemphigus is associated with increased inpatient mortality, likely through its association with numerous comorbid health conditions. Patients with pemphigus require improved access to dermatological care and increased screening for the myriad of comorbidities.

Interactome analysis of gene expression profile reveals potential novel key transcriptional regulators of skin pathology in vitiligo.

Selective destruction of epidermal melanocytes is central to vitiligo (VL), a common acquired, autoimmune depigmentory disorder of the skin. Like other autoimmune diseases, the pathogenesis of VL is obscure and both multifactorial and polygenic. The prevailing theory is that VL may be part of an autoimmune diathesis. To evaluate mechanisms underlying disease development and progression, we studied genome-wide gene expression from lesional and non-lesional skin of patients with non-segmental VL. Unbiased clustering and principal components analyses reveals a 'lesional pathology'-based signature. Pathway-based analyses of the differentially expressed genes underscore processes such as melanocyte development and cell cycle as central drivers of the disease state. Interactome analysis identifies several key transcriptional regulators potentially affecting disease pathogenesis both within and 'hidden' from the data set. Finally, two genes within six identified transcriptional 'hot spots' coincide with previous VL-associated genetic elements. The remaining genes in the 'hot spots' offer an additional set of potential disease-linked loci that may help to guide future studies aimed at identifying disease risk genes.

Evaluation of Different Root Canal Obturation Methods in Primary Teeth Using Cone Beam Computerized Tomography.

OBJECTIVE: To evaluate the efficiency of 3 different obturation techniques; motor driven lentulospiral, hand held lentulospiral and reamer in primary anterior teeth and presence of voids by analyzing with CBCT. STUDY DESIGN: 60 single rooted extracted primary teeth were prepared and obturated with ZOE paste. Obturation methods were divided into three groups. GROUP I- motor driven lentulo spiral, II- hand held lentulo spiral and III- reamer. Obturated samples were scanned in CBCT machine and images were analysed for the evaluation of their quality of fill comprising presence, location and size of voids. RESULTS: At all the locations, Group II had maximum number of sites with voids when compared to other two groups. However, statistically significant intergroup differences were observed only at coronal third location (p=0.001) and overall assessment (p=0.003). Number of affected sites revealed the difference between Groups I and II be significant statistically (p=0.002) while the difference between Groups I and III and between Groups II and III was not significant statistically (p>0.05). At all the locations as well as for combined assessment, Group I had minimum mean size of the void. CONCLUSION: Motor driven lentulo spiral technique demonstrated more number of optimal fills with fewer voids when compared to hand held lentulo spiral technique and reamer.

Genome-wide transcriptional profiling data from chronic cutaneous lupus erythematosus (CCLE) peripheral blood.

The disease Lupus erythematosus (LE), exhibits a variety of clinical manifestations with potentially wide-ranging multi-organ damage to joints, tendons, kidney, lung, heart, blood vessels, central nervous system and skin [1,2] Systemic changes are likely to trigger organ specific manifestation of the disease. Here, we provide the data examined to address the gap in knowledge regarding causes and mechanisms contributing to the autoimmune attack on skin in chronic cutaneous lupus erythematosus (CCLE). The raw gene expression data files (CEL files) are provided with this article [3].

Genome-wide transcriptional profiling data from skin of chronic cutaneous lupus erythematosus (CCLE) patients.

Cutaneous features manifest as a wide range of clinically significant, and in many cases disfiguring and debilitating components of lupus erythematosus (LE). While the definitive etiology is in question, multifactorial and polygenic causes are likely to be involved in the production of the characteristic anti-nuclear autoantibody titers and immune cell infiltrates observed in chronic cutaneous LE (CCLE) [1-3]. There is significant overlap of patients with systemic and cutaneous manifestations of LE, which suggests shared pathways and genetic background between the two. We have employed genome-wide microarray technology along with pathway-based analyses to investigate transcriptional differences between lesional and non-lesional skin from CCLE patients to address existing gaps in knowledge regarding disease mechanisms in lupus [4].

Genome-wide transcriptional profiling of chronic cutaneous lupus erythematosus (CCLE) peripheral blood identifies systemic alterations relevant to the skin manifestation.

Major gaps remain regarding pathogenetic mechanisms underlying clinical heterogeneity in lupus erythematosus (LE). As systemic changes are likely to underlie skin specific manifestation, we analyzed global gene expression in peripheral blood of a small cohort of chronic cutaneous LE (CCLE) patients and healthy individuals. Unbiased hierarchical clustering distinguished patients from controls revealing a "disease" based signature. Functional annotation of the differentially expressed genes (DEGs) highlight enrichment of interferon related immune response and apoptosis signatures, along with other key pathways. There is a 26% overlap of the blood and lesional skin transcriptional profile from a previous analysis by our group. We identified four transcriptional "hot spots" at chromosomal regions harboring statistically increased numbers of DEGs which offer prioritized potential loci for downstream fine mapping studies in the search for CCLE specific susceptibility loci. Additionally, we uncover evidence to support both shared and distinct mechanisms for cutaneous and systemic manifestations of lupus.

Detailed profiling of anti-desmoglein autoantibodies identifies anti-Dsg1 reactivity as a key driver of disease activity and clinical expression in pemphigus vulgaris.

With their near-universal presence in patients and ease of clinical measurement, anti-desmoglein (Dsg) antibodies serve as primary candidates for creating prognostic tools in Pemphigus vulgaris (PV). Although the desmoglein compensation hypothesis postulates a clear relationship between anti-Dsg autoantibodies and clinical phenotype in PV, recent studies have questioned the fidelity of this hypothesis as a predictor of lesion morphology. Moreover, few studies address the association of anti-Dsg antibodies to other clinical parameters such as disease phase and age at onset. Using the largest patient repository to date in PV, we present a detailed analysis of anti-desmoglein antibody profiles across a comprehensive range of dynamic (disease phase, therapy, lesion morphology) and temporal (disease duration, age at sampling, age at onset) clinical parameters. Our data highlight the non-traditional but key role of anti-Dsg1 levels in tracking disease activity. We show that declining anti-Dsg1 levels may predict progression from active phase to early remission and long-term maintenance of remission, regardless of lesion morphology. In contrast, many remittent patients have elevated levels of anti-Dsg3 without lesional activity. Furthermore, we describe a unique subset of remittent patients that develop chronic transient lesions (lasting <1 week) in the setting of elevated anti-Dsg3 levels but do not meet the consensus criteria for active phase. Re-classification of patients with transient lesions as "active" may shed new light on pathophysiological processes underlying cycles of blister formation and rapid spontaneous healing in PV. Additionally, we provide evidence for the potential attenuation of the immune response with prolonged disease duration. Our data fit into the broader effort of immunoprofiling to promote data-informed decision-making regarding diagnosis, prognosis and treatment of complex diseases.

Identification of a new disease cluster of pemphigus vulgaris with autoimmune thyroid disease, rheumatoid arthritis and type I diabetes.

BACKGROUND: Pemphigus vulgaris (PV) is a potentially fatal autoimmune blistering skin disease. It is known that individuals with autoimmune diseases such as PV, as well as their family members, are at increased risk of developing other autoimmune diseases. However, it is unknown whether there are specific autoimmune diseases that cluster with PV. OBJECTIVES: To investigate the frequency of coexisting autoimmune diseases in patients with PV and their relatives, to determine the prevalence of specific autoimmune diseases in patients with PV vs. the general population and to identify statistically significant clinical clusters linking PV with other autoimmune disorders. METHODS: We performed a cross-sectional study and meta-analysis of patient data from our own patient database (n = 230), an anonymous online survey conducted by our laboratory (n = 171) and the International Pemphigus & Pemphigoid Foundation registry (n = 393). RESULTS: We found that the prevalences of autoimmune thyroid disease (AITD), rheumatoid arthritis and type 1 diabetes were significantly increased in patients with PV compared with the general population. These diseases were also among the most frequent in family members of patients with PV, in addition to systemic lupus erythematosus (SLE). Descriptive cluster analysis using basic principle components methods revealed that PV forms a distinct cluster with AITD, rheumatoid arthritis and type 1 diabetes, and another cluster with SLE, AITD and rheumatoid arthritis. CONCLUSIONS: PV belongs to an established autoimmune disease cluster that includes AITD, rheumatoid arthritis and type 1 diabetes. Our data suggest the possibility of common genetic elements across clinically distinct diseases that might underlie autoimmune susceptibility.

Differential gene expression analysis in CCLE lesions provides new insights regarding the genetics basis of skin vs. systemic disease.

Lupus erythematosus is a heterogeneous autoimmune condition affecting multiple organs including skin, which remains poorly understood. To investigate pathogenetic processes relevant to cutaneous lupus as compared to systemic disease, we generated genome-wide expression data from lesional and non-lesional skin of chronic cutaneous LE (CCLE) patients. We reveal LE skin-associated transcriptional profiles and identify prominent functional pathways. A subset of CCLE differentially expressed genes (DEGs) was found to overlap with systemic lupus, including those linked to interferon and apoptosis. We identified 13 skin associated transcriptional "hot spots" that represent activated chromosomal regions. Seventeen CCLE DEGs (eight within "hot spots") were found to overlap with previously reported SLE-associated susceptibility loci. Additionally, we identify chromosomal regions not previously associated with lupus, potentially harboring distinct susceptibility loci for CCLE. This study suggests that overlapping as well as distinct genetic factors underlie disease pathogenesis in systemic and cutaneous lupus.

Genome-wide expression analysis suggests unique disease-promoting and disease-preventing signatures in Pemphigus vulgaris.

To evaluate pathogenetic mechanisms underlying disease development and progression in the autoimmune skin disease Pemphigus vulgaris (PV), we examined global peripheral blood gene expression in patients and healthy controls. Our goals were to: (1) assign blood gene expression signatures to patients and controls; (2) identify differentially expressed genes (DEGs) and investigate functional pathways associated with these signatures; and (3) evaluate the distribution of DEGs across the genome to identify transcriptional 'hot spots'. Unbiased hierarchical clustering clearly separated patients from human leukocyte antigen (HLA)-matched controls (MCRs; 'disease' signature), and active from remittent patients ('activity' signature). DEGs associated with these signatures are involved in immune response, cytoskeletal reorganization, mitogen-activated protein kinase (MAPK) signaling, oxidation-reduction and apoptosis. We further found that MCRs carrying the PV-associated HLA risk alleles cluster distinctly from unmatched controls (UMCR) revealing an HLA-associated 'control' signature. A subset of DEGs within the 'control' signature overlap with the 'disease' signature, but are inversely regulated in MCR when compared with either PV patients or UMCR, suggesting the existence of a 'protection' signature in healthy individuals carrying the PV HLA genetic risk elements. Finally, we identified 19 transcriptional 'hot spots' across the signatures, which may guide future studies aimed at pinpointing disease risk genes.

Peripheral blood gene expression in alopecia areata reveals molecular pathways distinguishing heritability, disease and severity.

Alopecia areata (AA) is an autoimmune hair loss disorder in which systemic disturbances have been described, but are poorly understood. To evaluate disease mechanisms, we examined gene expression in the blood of defined clinical subgroups (patchy AA persistent type, AAP, n=5; alopecia universalis, AU, n=4) and healthy controls (unaffected relatives, UaR, n=5; unaffected non-relatives, UaNR, n=4) using microarrays. Unsupervised hierarchical clustering separates all four patient and control groups, producing three distinct expression patterns reflective of 'inheritance', 'disease' and 'severity' signatures. Functional classification of differentially expressed genes (DEGs) comparing disease (AAP, AU) vs normal (UaR) groups reveals upregulation in immune response, cytokine signaling, signal transduction, cell cycle, proteolysis and cell adhesion-related genes. Pathway analysis further reveals the activation of several genes related to natural killer-cell cytotoxicity, apoptosis, mitogen activated protein kinase, Wnt signaling and B- and T-cell receptor signaling in AA patients. Finally, 35 genes differentially expressed in AA blood overlap with DEGs previously identified in AA skin lesions. Our results implicate innate and adaptive immune processes while also revealing novel pathways, such as Wnt signaling and apoptosis, relevant to AA pathogenesis. Our data suggest that peripheral blood expression profiles of AA patients likely carry new biomarkers associated with disease susceptibility and expression.

Systematic comparison of nonmelanoma skin cancer microarray datasets reveals lack of consensus genes.

BACKGROUND: DNA microarray technology has revealed vast numbers of gene expression alterations associated with human malignancies. Assigning validity and biological significance to these changes, however, remains a considerable hurdle. Recently, microarray analysis has been applied to the study of nonmelanoma skin cancer. OBJECTIVES: To compare experimental data rigorously in order to strengthen conclusions regarding the pathogenesis of basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), and to evaluate systematically the experimental and statistical parameters that may impact the degree of consensus among differentially expressed genes (DEGs) between studies. METHODS: We performed a systematic comparison of 10 studies that applied DNA microarray technology to study BCC/SCC. RESULTS: A total of 1133 DEGs collectively reported across the studies were compared, and 64 DEG overlaps were found: 18 DEG overlaps in SCC vs. SCC study comparisons, 18 DEG overlaps in BCC vs. BCC study comparisons and 28 DEG overlaps in BCC vs. SCC study comparisons. We documented differences in several experimental methods that may account for the relative lack of consensus between studies, including sample type, tissue procurement/handling, microarray chip and statistical analysis. The two most dysregulated biological pathways across all studies involved genes with enzymatic and structural/adhesion functions. CONCLUSIONS: DEGs that were found to overlap across two or more studies and biological pathways with the largest representation of DEGs across studies may be particularly relevant to disease pathogenesis and serve as targets for future therapy. In future work, more consistent experimental methods across laboratories may improve the validity of reported DEGs and strengthen conclusions drawn from microarray data.

Profile of 513 patients with alopecia areata: associations of disease subtypes with atopy, autoimmune disease and positive family history.

BACKGROUND: Several lines of evidence support a genetic component to alopecia areata (AA), including differences in patients based on severity of AA, associated diseases and family history. OBJECTIVE: We aimed to examine clinical and genetic features of patients with AA with a focus on associated diseases, especially atopy, and family history of AA in the USA. METHODS: From 1998 to 2001, 513 patients with AA completed interviews consisting of demographic information, patient's medical history, and family history of AA. RESULTS: Forty per cent of respondents had alopecia totalis and/or universalis (AT/AU). These patients were younger at the age of onset than those with patchy AA (P < 0.001), were more likely to have associated autoimmune or atopic disease (P = 0.047), most notably atopic dermatitis (P = 0.021) and thyroid disease (P = 0.012). They also had a greater number of relatives affected by AA (P < 0.05). CONCLUSIONS: Our findings show marked associations between severity of AA, atopic dermatitis, thyroid disease and other autoimmune diseases, and extensive family history of AA, suggesting two clinically distinct subtypes of AA with the severe subtype possibly associated with greater familial autoimmunity. Further research exploring the possibility of a genetic basis to explain these clinical findings will be helpful in clarifying our understanding of AA, leading to improvements in diagnosis and treatment.

Direct characterization of human T cells in pemphigus vulgaris reveals elevated autoantigen-specific Th2 activity in association with active disease.

Pemphigus vulgaris (PV) is a blistering skin disorder mediated by autoantibodies targeting the epidermal adhesion molecule desmoglein 3 (Dsg3). As Th2-associated cytokines are necessary for directing antibody production, it is hypothesized that Dsg3-specific Th2 activity is associated with active disease. We used cell-surface-matrix technology in combination with flow cytometry to characterize the Dsg3-reactive T-cell population using peripheral blood mononucleocytes sampled from PV patients stratified by active (n = 9) or remittent disease (n = 6), and healthy human leucocyte antigen-matched controls (n = 5). We evaluated interferon-gamma-producing CD4+ cells (Th1) and interleukin (IL)-10- or IL-4-producing CD4+ cells (Th2). The mean frequency of Th2 CD4+ T cells was significantly elevated for five of nine PV patients with active disease. No significant Th2 responses were detected for patients with remittent disease or controls. There was a significant association of Th2 activity with active disease compared with remittent and control groups (P = 0.026 and P =0.012, respectively), and Th2 activity was significantly correlated with anti-Dsg3 IgG titre (P = 0.044). One patient with remittent disease converted from a Th2-negative to a Th2-positive response with the initiation of disease activity. An antigen-specific CD4- lymphocyte response was detected in five PV patients (36%), and was shown to correlate closely with the CD8+ population. These results are consistent with the hypothesis that Th2 response directs autoantibody production and is therefore associated with disease activity in PV.

Angiontensin-converting enzyme activity in dunning rat prostate tumor.

A dipeptidyl carboxypeptidase activity in the Dunning rat prostate tumor was characterized. This enzyme demonstrated the most prominent properties of angiotensin converting enzyme (ACE): that is, it was stimulated by NaCl and Co(2+) and was potently inhibited by captopril. The enzyme solubilized by Triton X-100 had a molecular mass of 110 kDa as determined by gel filtration chromatography. The specific activity of ACE did not change with castration, indicating that ACE activities are not controlled by androgen. The role of ACE in the prostate and its tumors is not understood, but the ability of this enzyme to hydrolyze a number of bioactive peptides suggests that it may function in controlling the molecular forms or activity of regulatory peptides.