Ixekizumab (IXE), an IL-17A antagonist, and guselkumab (GUS), an IL-23p19 antagonist, are common psoriasis treatments. This longitudinal analysis assessed gene expression profiles in IXE- and GUS-treated patients with plaque psoriasis through week 4. In IXORA-R (NCT03573323), a head-to-head phase 4 study, adults with moderate-to-severe plaque psoriasis were assigned 1:1 to receive IXE or GUS. RNA expression was assessed in lesional tissue (n=72) from IXE-treated patients, GUS-treated patients, and healthy control groups (199 samples in total). Empirical Bayes was used to model RNA-sequencing data; differential expression was analyzed by tissue type, treatment, and time point, correcting for random effects. At week 1, lesions from IXE-treated patients had greater numbers of differentially expressed genes (392 upregulated, 696 downregulated) than those from GUS-treated patients (0 upregulated 0 downregulated). By week 4, the numbers of differentially expressed genes increased in both groups (IXE: 1882 upregulated, 1649 downregulated; GUS: 318 upregulated, 131 downregulated). Molecular shifts from baseline to week 4 occurred earlier with greater magnitude in IXE- than in GUS-treated patients. Rapid normalization of transcriptomic changes in patients receiving an IL-17A antagonist reflected downregulation of key inflammatory genes in psoriatic epidermis. Differentially expressed genes involved in epidermal IL-17A and IL-36 responses correlated with PASI 100 response.

Objectives/Goals: We aim to develop an intuitive interface to understand the possible relationships between data from different RNA-Seq technologies. It can help novice users and educators to understand, analyze, explain, and visualize such datasets from diverse platforms, all without the need for additional software installations or strong programming expertise. Methods/Study Population: An online interactive interface is developed, integrating robust algorithms for three distinct types of analyses: DESeq2 for bulk RNA-seq, CIBERSORTx for deconvolution, and Seurat for single-cell analysis, with plans to include more algorithms. It allows a demo mode for training using the sample datasets and option for tailored analysis using user’s partially processed data. The interface provides capability to process bulk RNA-seq data from raw counts or a differential gene list. Further, deconvolution analysis for bulk RNA-seq data can be done using raw counts and single-cell data analysis can be performed using processed sequence reads, organized into three key files: barcodes, matrix, and features. Users also have an option to download the results as a zipped file, for samples from human and mouse studies. Results/Anticipated Results: Users with an active internet connection can access the interface from any major web browser. They can adjust parameters – such as genome type, cutoff thresholds, and batch effect correction – according to their specific needs. Bulk RNA-seq results are presented in the form of volcano plots, heat-maps, clusters, gene expression across samples, DEGs, and enrichment plots from KEGG and GO analyses. Deconvolution analysis can be performed using either the “LM22” signature matrix (for human leukocyte cell types) or Derm22 (for skin-specific cell types). The single-cell workflow provides results including quality control metrics, UMAP clustering, gene expression plots/tables, and cluster annotation using CellTypist. Comprehensive details on methods and tutorials are available in the GitHub repository. Discussion/Significance of Impact: Although multiple workflows are available to process bulk and single cell RNA-Seq data along with deconvolution methods to bridge the gap between the two, this is the first online interface to provide the capability to explore and analyze data from all three approaches in one place, without requiring strong computational expertise or resources.

Hidradenitis suppurativa (HS) is a chronic inflammatory disease that is difficult to control, and its mechanism remains unclear. Hepatocyte growth factor (HGF) has been reported to be significantly upregulated in the serum and skin of HS patients, especially in the lesions with tunnels. In this study, we examined the transcriptome of HGF-treated keratinocytes (KCs) and compared it with genetic profiling of HS lesions. HGF was highly expressed in HS skin, especially in the deep dermis, compared to healthy controls, and its source was mainly fibroblasts. HGF upregulated more genes in KCs than interleukin-17A or tumor necrosis factor-α, and these genes included multiple epithelial-mesenchymal transition (EMT)-related genes. Differentially expressed genes in HGF-stimulated KCs were involved in activation of EMT-related pathways. These HGF-induced genes were significantly upregulated in HS lesions compared to healthy skin and non-lesions and were more strongly associated with HS tunnels.In summary, HGF was highly expressed in HS and induced EMT-related genes in KCs; HGF-induced genes were highly associated with gene profiling of HS with tunnels, suggesting that HGF may be involved in HS tunnel formation via EMT.

Hidradenitis Suppurativa (HS) is a chronic autoinflammatory skin disease with activated keratinocytes, tunnel formation and a complex immune infiltrate in tissue. The HS microbiome is polymicrobial with an abundance of commensal gram-positive facultative (GPs) Staphylococcus species and gram-negative anaerobic (GNA) bacteria like Prevotella, Fusobacterium and Porphyromonas with increasing predominance of GNAs with disease severity. We sought to define the keratinocyte response to bacteria commonly isolated from HS lesions to probe pathogenic relationships between HS and the microbiome. Type strains of Prevotella nigrescens, Prevotella melaninogenica, Prevotella intermedia, Prevotella asaccharolytica, Fusobacterium nucleatum, as well as Staphylococcus aureus and the normal skin commensal Staphylococcus epidermidis were heat-killed and co-incubated with normal human keratinocytes. RNA was collected and analysed using RNAseq and RT-qPCR. The supernatant was collected from cell culture for protein quantification. Transcriptomic profiles between HS clinical samples and stimulated keratinocytes were compared. Co-staining of patient HS frozen sections was used to localize bacteria in lesions. A mouse intradermal injection model was used to investigate early immune recruitment. TLR4 and JAK inhibitors were used to investigate mechanistic avenues of bacterial response inhibition. GNAs, especially F. nucleatum, stimulated vastly higher CXCL8, IL17C, CCL20, IL6, TNF and IL36 gamma transcription in normal skin keratinocytes than the GPs S. epidermidis and S. aureus. Using RNAseq, we found that F. nucleatum (and Prevotella) strongly induced the IL-17 pathway in keratinocytes and overlapped with transcriptome profiles of HS patient clinical samples. Bacteria were juxtaposed to activated keratinocytes in vivo, and F. nucleatum strongly recruited murine neutrophil and macrophage migration. Both the TLR4 and pan-JAK inhibitors reduced cytokine production. Detailed transcriptomic profiling of healthy skin keratinocytes exposed to GNAs prevalent in HS revealed a potent, extensive inflammatory response vastly stronger than GPs. GNAs stimulated HS-relevant genes, including many genes in the IL-17 response pathway, and were significantly associated with HS tissue transcriptomes. The close association of activated keratinocytes with bacteria in HS lesions and innate infiltration in murine skin cemented GNA pathogenic potential. These novel mechanistic insights could drive future targeted therapies.

To the Editor: Many effective biologic treatments have been established for moderate-to-severe psoriasis, defined in most clinical trials as psoriasis with ≥10% body surface area and psoriasis area-and-severity index (PASI) ≥12. Although patients with mild-to-moderate psoriasis constitute 82% of the total psoriasis population, mild-to-moderate psoriasis patients are not permitted entry to clinical trials of newer biologic agents.1Strober B. Ryan C. van de Kerkhof P. et al.Recategorization of psoriasis severity: Delphi consensus from the International Psoriasis Council.J Am Acad Dermatol. 2020; 82: 117-122Abstract Full Text Full Text PDF PubMed Scopus (81) Google Scholar In our previous studies comparing gene expression profiles of mild and severe psoriasis, the spectrum of mild-to-severe psoriasis was defined by the common activation of IL-17 pathway genes but with key differences in the immune regulatory gene expression.2Kim J. Bissonnette R. Lee J. et al.The spectrum of mild to severe psoriasis vulgaris is defined by a common activation of IL-17 pathway genes, but with key differences in immune regulatory genes.J Invest Dermatol. 2016; 136: 2173-2182Abstract Full Text Full Text PDF PubMed Scopus (39) Google Scholar Since the expression of immune regulatory genes is high in mild psoriasis, we hypothesized that treatment response and disease remission after IL-17A inhibition differs in mild psoriasis compared with severe psoriasis. To test the efficacy of an IL-17A antagonist in mild-to-moderate psoriasis, we conducted a randomized, double-blinded, placebo-controlled exploratory phase II clinical trial for the use of secukinumab, an IL-17A antagonist, for treatment of mild-to-moderate psoriasis (PASI >6 and <12 and a body surface area <10%; (Supplementary Fig 1 and clinical trial protocol, available via Mendeley at https://data.mendeley.com/datasets/nyhfxz8tt9/1). We also reported the gene expression modifications observed in psoriasis skin (Supplementary experiment protocol, available via Mendeley at https://data.mendeley.com/datasets/nyhfxz8tt9/1). At week 12, secukinumab treatment was more effective than placebo; secukinumab treatment (group 1) of mild-to-moderate psoriasis led to greater rates of PASI75 (72.7% in secukinumab vs 0% in placebo; P < .005), PASI90 (63.6% in secukinumab vs 0% in placebo; P < .005) and Physician Global Assessment 0/1 (81.8% in secukinumab vs 0% in placebo; P < .0005) when compared to placebo (group 2) (Fig 1 and Supplementary Fig 2, available via Mendeley at https://data.mendeley.com/datasets/nyhfxz8tt9/1). Secukinumab treatment of mild-to-moderate psoriasis resulted in more disease improvement than placebo as early as 2 weeks after initiation of treatment (decrease in PASI and Physician Global Assessment at week 2; P < .05). All of the mild-to-moderate psoriasis patients (100%) achieved a PASI75 16 weeks after initiating injections. A gene expression study of skin biopsies revealed that the impact of systemic IL-17A inhibition on psoriasis patients' skin immunity was not confined to only blocking the major cytokine of pathogenic T cells (IL17A) (Fig 2). It extended to blocking the entire feed-forward amplification loop of psoriasis inflammation. In addition, the gene expression of a keratinocyte stem cell marker (KRT15) and cytokines that may promote skin homeostasis (IL343Lelios I. Cansever D. Utz S.G. Mildenberger W. Stifter S.A. Greter M. Emerging roles of IL-34 in health and disease.J Exp Med. 2020; 217e20190290Crossref PubMed Scopus (49) Google Scholar and IL374Rønholt K. Nielsen A.L.-L. Johansen C. et al.IL-37 Expression is downregulated in lesional psoriasis skin.Immunohorizons. 2020; 4: 754-761Crossref PubMed Scopus (15) Google Scholar) was increased in psoriasis skin after systemic IL-17A inhibition. Our study supports the increasing trend to explore systemic treatments for mild-to-moderate psoriasis. The Delphi consensus from the International Psoriasis Council recommends that psoriasis patients be classified as candidates for systemic therapy if topical therapy fails, regardless of their severity category.1Strober B. Ryan C. van de Kerkhof P. et al.Recategorization of psoriasis severity: Delphi consensus from the International Psoriasis Council.J Am Acad Dermatol. 2020; 82: 117-122Abstract Full Text Full Text PDF PubMed Scopus (81) Google Scholar Recent studies showed that an oral phosphodiesterase-4 inhibitor (apremilast), which induces IL-17 reduction in psoriasis skin, effectively treats mild-to-moderate psoriasis.5Gold L.S. Papp K. Pariser D. et al.Efficacy and safety of apremilast in patients with mild-to-moderate plaque psoriasis: results of a phase 3, multicenter, randomized, double-blind, placebo-controlled trial.J Am Acad Dermatol. 2022; 86: 77-85Abstract Full Text Full Text PDF PubMed Scopus (13) Google Scholar Although our conclusions are limited by sample size, drugs that block IL-17A may be more effective for treating mild-to-moderate psoriasis than moderate-to-severe psoriasis. Dr Krueger has received research support (grants paid to the institution) from AbbVie, Amgen, BMS, Boehringer, EMD Serono, Innovaderm, Kineta, LEO Pharma, Novan, Novartis, Paraxel, Pfizer, Regeneron, and Vitae and personal fees from AbbVie, Acros, Allergan, Aurigne, BiogenIdec, Boehringer, Escalier, Janssen, Lilly, Novartis, Pfizer, Roche, and Valeant. The other authors have no conflicts of interest to declare. We thank the Rockefeller University Research Facilitation Office for the regulatory and administrative assistance. Letter from the editor: New paradigms for the treatment of psoriasisJournal of the American Academy of DermatologyVol. 88Issue 2PreviewIn this issue of the Journal of the American Academy of Dermatology, Kim et al report on the efficacy of an interleukin 17A antagonist in mild-to-moderate psoriasis. Most published trials of biologic therapy for psoriasis have focused on moderate to severe disease. This study examined outcomes in patients with milder disease, raising important questions about the future of psoriasis treatment and the role of systemic agents in the treatment of patients with limited disease. Full-Text PDF

HIV pre-exposure prophylaxis (PrEP) is dominated by clinical therapeutic antiretroviral (ARV) drugs. Griffithsin (GRFT) is a non-ARV lectin with potent anti-HIV activity. GRFT's preclinical safety, lack of systemic absorption after vaginal administration in animal studies, and lack of cross-resistance with existing ARV drugs prompted its development for topical HIV PrEP. We investigated safety, pharmacokinetics (PK), pharmacodynamics (PD), and immunogenicity of PC-6500 (0.1% GRFT in a carrageenan (CG) gel) in healthy women after vaginal administration. This randomized, placebo-controlled, parallel group, double-blind first-in-human phase 1 study enrolled healthy, HIV-negative, non-pregnant women aged 24-45 years. In the open label period, all participants (n = 7) received single dose of PC-6500. In the randomized period, participants (n = 13) were instructed to self-administer 14 doses of PC-6500 or its matching CG placebo (PC-535) once daily for 14 days. The primary outcomes were safety and PK after single dose, and then after 14 days of dosing. Exploratory outcomes were GRFT concentrations in cervicovaginal fluids, PD, inflammatory mediators and gene expression in ectocervical biopsies. This trial is registered with ClinicalTrials.gov, number NCT02875119. No significant adverse events were recorded in clinical or laboratory results or histopathological evaluations in cervicovaginal mucosa, and no anti-drug (GRFT) antibodies were detected in serum. No cervicovaginal proinflammatory responses and no changes in the ectocervical transcriptome were evident. Decreased levels of proinflammatory chemokines (CXCL8, CCL5 and CCL20) were observed. GRFT was not detected in plasma. GRFT and GRFT/CG in cervicovaginal lavage samples inhibited HIV and HPV, respectively, in vitro in a dose-dependent fashion. These data suggest GRFT formulated in a CG gel is a safe and promising on-demand multipurpose prevention technology product that warrants further investigation.

BACKGROUND:Hidradenitis suppurativa (HS) is an inflammatory skin disease with dysregulation of the interleukin (IL)-17 axis. Recently, we reported the clinical benefit of brodalumab, a human anti-IL-17 receptor A (IL-17RA) monoclonal antibody, in moderate-to-severe HS. OBJECTIVES:To characterize the molecular response to brodalumab in HS skin and serum, and to identify biomarkers of treatment response. METHODS:Ten participants, who received brodalumab 210 mg /1·5 mL subcutaneously at weeks 0, 1, 2, 4 and every 2 weeks thereafter, were included in this molecular profiling study (NCT03960268). RNA sequencing and immunohistochemistry of nonlesional, perilesional and lesional HS skin biopsies, and Olink high-throughput proteomics of serum at baseline, weeks 4 and 12 were assessed. RESULTS:At week 12, brodalumab led to a decrease of overall inflammation, and improvement of psoriasis-, keratinocyte- and neutrophil-related pathways. Despite perilesional and lesional skin exhibiting no differentially expressed genes at baseline, treatment response was best assessed in perilesional skin. In serum, brodalumab treatment decreased pathways involved in neutrophil inflammation. Patients with higher baseline expression of neutrophil-associated lipocalin-2 (LCN2) in the skin or IL-17A in the serum demonstrated greater decreases of HS-related inflammatory cytokines as measured in skin biopsies at week 12. CONCLUSIONS:IL-17RA inhibition by brodalumab decreases several pathogenic inflammatory axes in HS. Perilesional skin provides a valid and robust assessment of treatment response. Expression of LCN2 in skin or IL-17A in serum may be used as biomarkers to stratify patients that may have a superior molecular response to brodalumab.

BACKGROUND:Hidradenitis suppurativa (HS) is a chronic inflammatory skin disease presenting with diverse manifestations ranging from nodules and abscesses to draining tunnels. Whether the underlying inflammation from lesions extends to relatively healthy-appearing adjacent perilesional and distant nonlesional skin has not been systematically evaluated.OBJECTIVE:We sought to characterize lesional, perilesional, and nonlesional skin in patients with HS.METHODS:Skin biopsy samples were collected under ultrasound guidance from patients with active, untreated moderate-to-severe HS. Site-matched control biopsy samples from healthy volunteers were used for comparison.RESULTS:RNA sequencing demonstrated that HS skin clustered separately from healthy control skin, with perilesional and lesion skin clustering together and away from nonlesional skin. Immunohistochemistry analysis identified psoriasiform hyperplasia with keratin 16 positivity in both perilesional and lesional skin, with comparable levels of CD3+, CD11c+, and neutrophil elastase-positive cellular infiltration. There was a marked upregulation of IL-17 signaling in perilesional and lesional skin. HS samples clustered on the basis of expression of lipocalin-2 (LCN2), with samples characterized by high LCN2 expression in the skin exhibiting a differing transcriptomic profile with significantly higher overall inflammation than that of skin characterized by low LCN2 levels.CONCLUSIONS:Perilesional HS skin has a transcriptomic and molecular profile comparable to that of lesional skin. HS can be grouped into 2 distinct subtypes based on molecular levels of LCN2 in the skin, with the LCN2-high subtype exhibiting an overall higher inflammatory burden and an upregulation of targetable cytokines. To our knowledge, this is the first study to characterize a unique HS subtype (and a potential endotype) that may guide future therapeutic targets.

Animals encounter microorganisms in their habitats, adapting physiology and behavior accordingly. The nematode Caenorhabditis elegans is found in microbe-rich environments; however, its responses to fungi are not extensively studied. Here, we describe interactions of C. elegans and Penicillium brevicompactum, an ecologically relevant mold. Transcriptome studies reveal that co-culture upregulates stress response genes, including xenobiotic-metabolizing enzymes (XMEs), in C. elegans intestine and AMsh glial cells. The nuclear hormone receptors (NHRs) NHR-45 and NHR-156 are induction regulators, and mutants that cannot induce XMEs in the intestine when exposed to P. brevicompactum experience mitochondrial stress and exhibit developmental defects. Different C. elegans wild isolates harbor sequence polymorphisms in nhr156, resulting in phenotypic diversity in AMsh glia responses to microbe exposure. We propose that P. brevicompactum mitochondria-targeting mycotoxins are deactivated by intestinal detoxification, allowing tolerance to moldy environments. Our studies support the idea that C. elegans NHRs may be regulated by environmental cues.

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Despite extensive studies suggesting increased susceptibility to HIV during the secretory phase of the menstrual cycle, the molecular mechanisms involved remain unclear. Our goal was to analyze transcriptomes of the endocervix and ectocervix during the proliferative and secretory phases using RNA sequencing to explore potential molecular signatures of susceptibility to HIV. We identified 202 differentially expressed genes (DEGs) between the proliferative and secretory phases of the cycle in the endocervix (adjusted p < 0.05). The biofunctions and pathways analysis of DEGs revealed that cellular assembly and epithelial barrier function in the proliferative phase and inflammatory response/cellular movement in the secretory phase were among the top biofunctions and pathways. The gene set enrichment analysis of ranked DEGs (score = log fold change/ p value) in the endocervix and ectocervix revealed that (i) unstimulated/not activated immune cells gene sets positively correlated with the proliferative phase and negatively correlated with the secretory phase in both tissues, (ii) IFNγ and IFNα response gene sets positively correlated with the proliferative phase in the ectocervix, (iii) HIV restrictive Wnt/β-catenin signaling pathway negatively correlated with the secretory phase in the endocervix. Our data show menstrual cycle phase-associated changes in both endocervix and ectocervix, which may modulate susceptibility to HIV.

X-linked dominant incontinentia pigmenti (IP) and X-linked recessive anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) are caused by loss-of-function and hypomorphic IKBKG (also known as NEMO) mutations, respectively. We describe a European mother with mild IP and a Japanese mother without IP, whose 3 boys with EDA-ID died from ID. We identify the same private variant in an intron of IKBKG, IVS4+866 C>T, which was inherited from and occurred de novo in the European mother and Japanese mother, respectively. This mutation creates a new splicing donor site, giving rise to a 44-nucleotide pseudoexon (PE) generating a frameshift. Its leakiness accounts for NF-κB activation being impaired but not abolished in the boys' cells. However, aberrant splicing rates differ between cell types, with WT NEMO mRNA and protein levels ranging from barely detectable in leukocytes to residual amounts in induced pluripotent stem cell-derived (iPSC-derived) macrophages, and higher levels in fibroblasts and iPSC-derived neuronal precursor cells. Finally, SRSF6 binds to the PE, facilitating its inclusion. Moreover, SRSF6 knockdown or CLK inhibition restores WT NEMO expression and function in mutant cells. A recurrent deep intronic splicing mutation in IKBKG underlies a purely quantitative NEMO defect in males that is most severe in leukocytes and can be rescued by the inhibition of SRSF6 or CLK.

Social behaviors are crucial to all mammals. Although the prelimbic cortex (PL, part of medial prefrontal cortex) has been implicated in social behavior, it is not clear which neurons are relevant or how they contribute. We found that PL contains anatomically and molecularly distinct subpopulations that target three downstream regions that have been implicated in social behavior: the nucleus accumbens (NAc), amygdala, and ventral tegmental area. Activation of NAc-projecting PL neurons (PL-NAc), but not the other subpopulations, decreased the preference for a social target. To determine what information PL-NAc neurons convey, we selectively recorded from them and found that individual neurons were active during social investigation, but only in specific spatial locations. Spatially specific manipulation of these neurons bidirectionally regulated the formation of a social-spatial association. Thus, the unexpected combination of social and spatial information within the PL-NAc may contribute to social behavior by supporting social-spatial learning.