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

MiR-199a-3p Regulates the PTPRF/β-Catenin Axis in Hair Follicle Development: Insights into the Pathogenic Mechanism of Alopecia Areata

Alopecia areata is an autoimmune disease characterized by the immune system attacking self hair follicles, mainly in the scalp. There is no complete cure, and the pathogenesis is still not fully understood. Here, sequencing of skin tissues collected from 1-month-old coarse- and fine-wool lambs identified miR-199a-3p as the only small RNA significantly overexpressed in the fine-wool group, suggesting a role in hair follicle development. MiR-199a-3p expression was concentrated in the dermal papillae cells of sheep hair follicles, along with enhanced β-catenin expression and the inhibition of PTPRF protein expression. We also successfully constructed a mouse model of alopecia areata by intracutaneous injection with an miR-199a-3p antagomir. Injection of the miR-199a-3p agomir resulted in hair growth and earlier anagen entry. Conversely, local injection with the miR-199a-3p antagomir resulted in suppressed hair growth at the injection site, upregulation of immune system-related genes, and downregulation of hair follicle development-related genes. In vivo and in vitro analyses demonstrated that miR-199a-3p regulates hair follicle development through the PTPRF/β-catenin axis. In conclusion, a mouse model of alopecia areata was successfully established by downregulation of a small RNA, suggesting the potential value of miR-199a-3p in the study of alopecia diseases. The regulatory role of miR-199a-3p in the PTPRF/β-catenin axis was confirmed, further demonstrating the link between alopecia areata and the Wnt-signaling pathway.

Inheritance-Specific Dysregulation of Th1- and Th17-Associated Cytokines in Alopecia Areata

Autoimmune diseases tend to cluster in families, suggesting genetic predisposition to autoimmunity associated with familial background. We have previously reported similarities in gene expression patterns and PTPN22 polymorphisms between alopecia areata (AA) patients and their healthy relatives, but not unrelated healthy controls. However, the spectrum of disease promoting (or preventing) pathways that may be activated in blood relatives of AA patients remains to be defined. Here, we investigated the extent to which cytokines associated with the Th1 and Th17 pathway are differentially expressed in the blood of patients with AA and its clinical subtypes in comparison to both healthy relatives as well as unrelated healthy controls. A comprehensive set of Th1- and Th17-related cytokines were evaluated by ELISA. We found a significant elevation of the Th17 inducer IL-23, the Th17 product IL-17A, the Th1 hallmark cytokine IFNγ, and TNFα, a Th1 cytokine with relevance to the Th17 pathway in AA patients, regardless of disease subtype, compared to healthy individuals. On further examination, we found that healthy family members grouped together with patients in terms of elevated Th1- and Th17-pathway cytokines in an inheritance-specific manner, distinct from unrelated controls. The elevation of Th17-associated cytokines in healthy controls related to AA patients indicates that Th1 and Th17 dysregulation in AA may be genetically based. Of note, one unrelated control displayed elevated levels of IL-17A and IL-23 similar to those detected in patients. One year after initial blood draw, areas of beard hair loss consistent with the diagnosis of AA were reported by this individual, indicating that the elevation in Th17-related cytokines may have predictive value.

Side effect prediction based on drug-induced gene expression profiles and random forest with iterative feature selection

One in every ten drug candidates fail in clinical trials mainly due to efficacy and safety related issues, despite in-depth preclinical testing. Even some of the approved drugs such as chemotherapeutics are notorious for their side effects that are burdensome on patients. In order to pave the way for new therapeutics with more tolerable side effects, the mechanisms underlying side effects need to be fully elucidated. In this work, we addressed the common side effects of chemotherapeutics, namely alopecia, diarrhea and edema. A strategy based on Random Forest algorithm unveiled an expression signature involving 40 genes that predicted these side effects with an accuracy of 89%. We further characterized the resulting signature and its association with the side effects using functional enrichment analysis and protein-protein interaction networks. This work contributes to the ongoing efforts in drug development for early identification of side effects to use the resources more effectively.

In silico Analyses of Skin and Peripheral Blood Transcriptional Data in Cutaneous Lupus Reveals CCR2-A Novel Potential Therapeutic Target

Cutaneous lesions feature prominently in lupus erythematosus (LE). Yet lupus and its cutaneous manifestations exhibit extraordinary clinical heterogeneity, making it imperative to stratify patients with varying organ involvement based on molecular criteria that may be of clinical value. We conducted several in silico bioinformatics-based analyses integrating chronic cutaneous lupus erythematosus (CCLE)-skin and blood expression profiles to provide novel insights into disease mechanisms and potential future therapy. In addition to substantiating well-known prominent apoptosis and interferon related response in both tissue environments, the overrepresentation of GO categories in the datasets, in the context of existing literature, led us to model a “disease road-map” demonstrating a coordinated orchestration of the autoimmune response in CCLE reflected in three phases: (1) initiation, (2) amplification, and (3) target damage in skin. Within this framework, we undertook in silico interactome analyses to identify significantly “over-connected” genes that are potential key functional players in the metabolic reprogramming associated with skin pathology in CCLE. Furthermore, overlapping and distinct transcriptional “hot spots” within CCLE skin and blood expression profiles mapping to specified chromosomal locations offer selected targets for identifying disease-risk genes. Lastly, we used a novel in silico approach to prioritize the receptor protein CCR2, whose expression level in CCLE tissues was validated by qPCR analysis, and suggest it as a drug target for use in future potential CCLE therapy.

Genomewide differential expression profiling of long non-coding RNAs in androgenetic alopecia in a Chinese male population

BACKGROUND

Androgenetic alopecia (AGA), or male pattern baldness (MPB), is the most common form of hair loss in males. A combination of genetic and androgen causes have been suggested as factors that contribute to the development of AGA. However, the specific molecular mechanisms that underly AGA remain largely unknown. Long non-coding RNAs (lncRNAs), a new class of regulatory non-coding RNAs that are longer than 200 nucleotides, have been shown to play important roles in a number of cellular processes, including transcription, chromosome remodelling and post-transcriptional processing. The dysregulation of lncRNAs is associated with many forms of diseases, but it remains unknown whether lncRNAs are associated with AGA.

OBJECTIVE

The aim of this study was to identify AGA-associated lncRNAs and predict the potential roles of these lncRNAs in AGA.

METHODS

A genomewide microarray was used to identify lncRNAs that are differentially expressed between AGA and adjacent normal tissues. Real-time qRT-PCR was used to validate the microarray data.

RESULTS

A large number of lncRNAs were differentially expressed (fold change >2.4) between AGA and adjacent normal tissues. Of these, 770 were upregulated and 1373 were downregulated. Moreover, pathway analysis revealed that 53 functional pathways were associated with the upregulated transcripts, while 11 pathways were associated with the downregulated transcripts.

CONCLUSION

To our knowledge, this is the first study to investigate AGA-associated lncRNAs. lncRNA profiles are altered in AGA, and these lncRNAs and their target genes may serve as novel candidates for preventing and treating AGA.

Big Data, Big Opportunities, and Big Challenges

High-throughput assays have begun to revolutionize modern biology and medicine. The advent of cheap next-generation sequencing (NGS) has made it possible to interrogate cells and human populations as never before. Although this has allowed us to investigate the genetics, gene expression, and impacts of the microbiome, there remain both practical and conceptual challenges. These include data handling, storage, and statistical analysis, as well as an inherent problem of the analysis of heterogeneous cell populations.

Prior facility affects alopecia in adulthood for rhesus macaques

Alopecia has proven to be a persistent problem for captive macaques; many cases continue to elude explanations and effective treatments. Although almost all captive populations exhibit alopecia rates higher than those seen in the wild, there also appear to be wide ranges in rates reported across primate facilities. In this study we looked at alopecia ratings for rhesus macaques (Macaca mulatta) obtained from five primary suppliers and currently housed at the Washington National Primate Research Center (WaNPRC). There were significant differences in alopecia ratings based on prior facility, despite the fact that animals had left their prior facilities at least 10 months previously and 60% had left more than 2 years previously. Possible explanations for the facility effect may include longer than anticipated time lines for alopecia amelioration, early experience effects, and genetic contributions. Our results should provide a cautionary note for those evaluating alopecia, treatments for alopecia, and the current environments of alopecic animals. It is possible that not all alopecia is caused, or can be ameliorated, by changes in the immediate environment. Am. J. Primatol. 79:e22551, 2017. © 2016 Wiley Periodicals, Inc.

Emerging Role and Therapeutic Implication of Wnt Signaling Pathways in Autoimmune Diseases

The Wnt signaling pathway plays a key role in many biological aspects, such as cellular proliferation, tissue regeneration, embryonic development, and other systemic effects. Under a physiological condition, it is tightly controlled at different layers and arrays, and a dysregulated activation of this signaling has been implicated into the pathogenesis of various human disorders, including autoimmune diseases. Despite the fact that therapeutic interventions are available for ameliorating disease manifestations, there is no curative therapy currently available for autoimmune disorders. Increasing lines of evidence have suggested a crucial role of Wnt signaling during the pathogenesis of many autoimmune diseases; in addition, some of microRNAs (miRNAs), a class of small, noncoding RNA molecules capable of transcriptionally regulating gene expression, have also recently been demonstrated to possess both physiological and pathological roles in autoimmune diseases by regulating the Wnt signaling pathway. This review summarizes currently our understanding of the pathogenic roles of Wnt signaling in several major autoimmune disorders and miRNAs, those targeting Wnt signaling in autoimmune diseases, with a focus on the implication of the Wnt signaling as potential biomarkers and therapeutic targets in immune diseases, as well as miRNA-mediated regulation of Wnt signaling activation in the development of autoimmune diseases.

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.

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.

The genetics of pemphigus

Pemphigus vulgaris (PV) is an autoimmune blistering disorder with a complex etiology involving an interplay of genetic as well as environmental factors, most of which remain unknown. Despite the identification of several human leukocyte antigen (HLA) alleles as risk factors for disease, no other non-HLA genes have clearly been implicated in disease susceptibility. Newer candidate gene and whole-genome approaches are needed to illuminate the full palate of genetic risk elements in PV. Based on this information, genetic-based tools can be expected to provide a scientific rationale for future clinical decision-making by physicians and facilitate an era of personalized medicine.

Transcriptional profiling in alopecia areata defines immune and cell cycle control related genes within disease-specific signatures

Alopecia areata (AA) is a non-scarring inflammatory hair loss disease with a complex autoimmune etiopathogenesis that is poorly understood. In order to investigate the pathogenesis of AA at the molecular level, we examined the gene expression profiles in skin samples from lesional (n=10) and non-lesional sites (n=10) of AA patients using Affymetrix Hu95A-v2 arrays. 363 genes were found to be differentially expressed in AA skin compared to non-lesional skin; 97 were up-regulated and 266 were down-regulated. Functional classification of the differentially expressed genes (DEGs) provides evidence for T-cell mediated immune response (CCL5, CXCL10, CD27, ICAM2, ICAM3, IL7R, and CX3CL1), and a possible humoral mechanism (IGHG3, IGHM, and CXCR5) in AA. We also find modulation in gene expression favoring cellular proliferation arrest at various levels (FGF5, FGF18, EREG, and FOXC2) with apoptotic dysregulation (LCK, TNF, TRAF2, and SFN) and decreased expression of hair follicle structural proteins. Further analysis of patients with AAT (<1 year duration, n=4) and AAP (>1 year duration, n=6) of disease revealed 262 DEGs distinctly separating the 2 groups, indicating the existence of gene profiles unique to the initial and later stages of disease.