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Study Finds Novel Pathogenic Variants, Inflammatory Cytokines, and Activated JAK-STAT Signaling in Patients With Congenital Ichthyosis


The international study represents the most comprehensive analysis of Southeast Asian patients with CI to date and provides a detailed look into specific CI subtypes.

Ichthyosis | Image credit: DermNet

Ichthyosis | Image credit: DermNet

A one-of-a-kind study recently published in Human Genomics assessed 36 Southeast Asian patients with congenital ichthyosis (CI) subtypes to better understand the relationship between the skin microbiome, immune profile, and disease pathogenesis in CI. Based on 7 different analyzed CI subtypes, Ho et al found 20 novel pathogenic variants; notable differences in the prevalence of Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes in dry, moist, and sebaceous skin sites; increased S. aureus in wounded CI skin; an increased Th17 inflammatory response; and elevated JAK-STAT signaling.

“It was a very rewarding experience collaborating with colleagues in Vietnam to investigate ichthyosis in the Southeast Asian population. International teamwork is exciting and pushes the boundaries of what dermatologic investigation can accomplish,” said Christopher Bunick, MD, PhD, study author, associate professor of dermatology and translational biomedicine at Yale University School of Medicine in New Haven, Connecticut, and Dermatology Times’ 2024 Winter Editor in Chief, in a statement to Dermatology Times.

This CI research was a collaboration between the Bunick Lab at Yale University and the Bui Lab in Vietnam. Bunick has a long-standing interest in ichthyosis research and has served as principal investigator of clinical trials of TMB-001 (Timber Pharmaceuticals and LEO Pharma), a topical isotretinoin formulation in development for congenital ichthyosis.


For the basis of their study, Ho et al addressed the importance of the skin’s microbiome in protecting against body temperature dysregulation, infection, and water loss. Specifically, a healthy human skin microbiome consists mostly of 4 phyla: Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes, which in turn work with stratum corneum biproducts. However, once this balance is disrupted, there is an increased chance of infections or skin diseases such as atopic dermatitis or CI. According to Ho et al, there are case studies detailing the connection between atopic dermatitis and a disrupted skin microbiome, however, the epidermal microbiome in various types of CI is less documented.

Congenital ichthyoses can be categorized into at least 20 different types, which are then divided into non-syndromic and syndromic forms. These forms are characterized by malfunction of barrier physiology, abnormal keratinocyte proteins, lipid biosynthesis, cell adhesion, and/or DNA repair.

“It is logical to hypothesize that CI patients, given the genetic, biochemical, and physiologic diversity underlying their skin barrier defects, may harbor distinct, abnormal microbiome signatures,” wrote Ho et al.

Congenital Ichthyosis Subtype Key

  • Arthrogryposis renal dysfunction cholestasis = ARC
  • Congenital ichthyosiform erythroderma = CIE
  • Epidermolytic ichthyosis = EI
  • Harlequin ichthyosis = HI
  • Ichthyosis vulgaris = IV
  • Lamellar ichthyosis = LI
  • Sjögren-Larsson Syndrome = SLS
  • Trichothiodystrophy = TTD

The study authors referenced previous studies that found Th-17 signaling is elevated, especially with IL-17 involvement in congenital ichthyosiform erythroderma (CIE), lamellar ichthyosis (LI), and epidermolytic ichthyosis (EI).2-4 Another previous study demonstrated that the immune profile and lipid metabolism of CIE, LI, and EI are more similar to psoriasis than atopic dermatitis, suggesting the “potential for psoriasis drugs as viable therapies for ichthyosis patients.”2

Ho et al wrote that to their knowledge, no other similar studies have been conducted among Southeast Asian patients with CI.


Clinical and Genetic Variants

Ho et al categorized 36 patients with CI in one of 7 CI disorders: ichthyosis vulgaris (IV; n=15), Harlequin ichthyosis (HI; n=8), LI (n=3), EI (n=4), Trichothiodystrophy (TTD; n=3), Arthrogryposis renal dysfunction cholestasis (ARC; n=1), and Sjögren-Larsson Syndrome (SLS; n=2). The categorized CI patients were compared to 15 healthy age-matched participants. Patient ages ranged from neonatal to 40 years old.

After performing whole exome sequencing (WES) and genetic linkage analysis in the 36 patients with CI, the study authors identified 31 pathogenic/likely pathogenic mutations and 20 novel variants. Additionally, 4 novel variants were found in more than one patient with CI. Ho et al identified compound heterozygous and homozygous segregated mutations linked to autosomal recessive loss-of-function of ABCA12, TGM1, ALDH3A2, and ERCC2.

According to the study authors, there were statistically significant associations of intensive care unit admissions with ABCA12 mutation, death examination with ABCA12 and TGM1 mutations, sepsis with ABCA12 mutation, respiratory problems with FLG mutation, collodion membrane at birth with ABCA12 and TGM1 mutation, blistering with ABCA12 and FLG mutation, dry and thick skin with FLG mutation, impaired wound healing with FLG mutation, itch with ABCA12 and FLG mutations, and bacterial infection with FLG mutation.

Infection Risks

To better understand the risk of infections in patients with CI, Ho et al took superficial swabs of sebaceous skin (facial region), dry skin (olecranal or patella regions), and moist skin (antecubital or popliteal region), and compared the results to 15 healthy participants. Focusing on the 4 dominant phyla—Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes, the study authors wrote, “Actinobacteria and Firmicutes both showed decreased average relative abundance of colony forming units (cfu) in CI dry, moist, and sebaceous skin compared to the respective locations in healthy controls.”

Proteobacteria showed decreased relative abundance of cfu in dry CI skin compared to healthy controls, but increased abundance in moist and sebaceous skin. Bacteroidetes was stable to slightly increased in relative abundance of cfu across dry and sebaceous CI skin locations compared to healthy controls, but slightly decreased in abundance in moist skin.

Reduced operational taxonomic unit (OTU) counts of Actinobacteria, Firmicutes, Proteobacteria, and Gram-positive microbes were observed in moist and sebaceous skin, but there was no significant difference in Bacteroidetes OTU counts. After Ho et al analyzed OTU sequences at the species level, they identified a significant reduction in species within the Actinobacteria, Firmicutes, and Bacteroidetes phyla, including C. acnes, S. capitis, S. hominis, S. epidermidis, and B. vulgatus. In contrast, S. aureus of the Firmicutes phylum had statistically significant elevations in patients with IV and EI compared to healthy controls, and statistically non-significant elevations in dry skin of LI patients.

Regarding the impact of CI genotype on the presence of various bacteria, “The difference in the amount of C. acnes between Healthy (WT) skin and skin with CI variants suggests that genotypes may influence the abundance of C. acnes. This may impact biological properties of the skin such as moisture level, pH, lipid barrier, or the skin’s immune capabilities determined by the genotypes,” wrote Ho et al.

Microbiome Subgroups and Impaired Wound Healing

Cluster Group Key

  • Cluster P1 = Healthy control subjects
  • Cluster P2 = Ichthyosis vulgaris
  • Cluster P3 = Epidermolytic ichthyosis and Trichothiodystrophy
  • Cluster P4 = Lamellar ichthyosis and Harlequin ichthyosis
  • Cluster P5 = Arthrogryposis renal dysfunction cholestasis and Sjögren-Larsson Syndrome

Through principal co-ordinate analysis (PCoA) of the superficial swab OTU sequence data, Ho et al identified dysbiosis clusters by collecting high-ratio non-pathogenic (principal component 1, PC1, x-axis) and high ratio pathogenic (principal component 2, PC2, y-axis) microbiomes found in patients with CI. Patients were separated into 5 cluster groups. The study authors found that healthy control subjects (P1) were high in PC1 and low in PC2. Cluster P2–IV patients were high in PC2 and low in PC1 (FLG variants). Cluster P3–EI and TTD patients were low in PC1 and variably elevated in PC2 in moist and sebaceous skin (KRT1 and ERCC2 variants, respectively). Cluster P4–LI and HI patients were consistently lowest in both PC1 and PC2 across all skin sites (TGM1 and ABCA12 variants, respectively). Cluster P5–ARC and SLS patients were low in PC1 and variably elevated in PC2 in sebaceous skin only (VPS33B and ALDH3A2 variants, respectively).

Regarding wound healing and microbiota changes in patients with CI, Ho et al created 5 mm punch biopsy wounds in a CI wound cohort (n=32) and matched healthy controls (n=5), and then evaluated the wounds for microbial infections, wound healing time, and inflammation.

In non-wounded skin, S. epidermidis abundance was high for healthy and CI skin, and patients with IV and EI had the least abundant S. epidermidis. Also in non-wounded skin, S. aureus abundance was significantly lower than S. epidermidis, yet higher among CI types than healthy controls.

“In contrast, wounded skin demonstrated a large shift towards more abundant S. aureus (mean = 48.5% total relative abundance) for healthy and CI patients, with concomitant reduction in S. epidermidis (mean = 43.76% total relative abundance), as supported by two-way ANOVA analysis,” wrote Ho et al.

To better understand wound healing time, the study authors observed 5 mm punch biopsy wounds in CI and healthy control patients and the overall healing time without the use of oral β-lactam antibiotics (carbapenems and cephalosporins). Without antibiotics, wound healing time was significantly delayed in P2, P3, and P4 patients with CI compared to healthy controls. When antibiotics were used, Ho et al observed almost complete wound healing in all 4 CI dysbiosis clusters (P2-P5).

Immune and Cytokine Inflammation

When evaluating inflammatory responses in patients with CI, Ho et al measured immune cell levels and cytokine responses. Levels of granulocytes (neutrophils, eosinophils, and basophils) were measured from blood samples of patients with CI and healthy controls, without wounding. Ho et al observed a statistically significant elevation in neutrophil count for all CI clusters compared to the healthy controls. There was no difference in basophils counts in patients with CI compared to healthy controls.

Regarding levels of T- and B- cells, the percentage of Th2+/CD4+ and Th17+/CD4+ cells were significantly increased in patients with CI compared to healthy controls. Additionally, total Th1+/ CD4+ cells were significantly increased in P3 patients with CI, while Treg+/CD4+ cells were significantly increased in P2, P3, and P5 CI patients compared to healthy controls. B cells were significantly induced in P2, P4, and P5 patients with CI compared to healthy controls.

Using Fisher exact tests and odds ratio calculations for 6 immune cell types, Ho et al “observed statistically significant association of FLG mutation with neutrophil, B cell, Th1, Th2, Th17, and Treg counts; ABCA12 mutation was also associated with neutrophil elevation.” Overall, patients with CI had higher mRNA levels of Th17 cytokines compared to healthy controls, except for “notable insignificance” in IL-22 in P3 and IL-1β, IL-6, IL17A, IL-17F, and CCL20 in the P5 group compared with healthy controls. In P2, P3, and P5,mRNA levels of IL-4, IL-5, IL-13, and CCL18 of Th2 were induced in patients with CI, however, mRNA levels of IL-13 were not significant in P5. Ho et al found an increase in the mRNA level of Th1 cytokines IFN-γ and TNF-α in P3 compared to healthy controls.

Ho et al assessed the levels of phosphorylated STAT3 Tyr705 (pY705) as a marker of Janus kinase (JAK) signaling activity in peripheral blood mononuclear cells (PBMCs) and found significantly elevated levels of STAT3 pY705 in patients with CI, specifically P2, P3, and P4.

Regarding the immune system’s response to wounding and wound healing, Ho et al found that Gr1+ granulocytes were elevated across P1-P5 16 hours after wounding, yet by 24 hours post-wounding, all Gr1+ granulocytes dropped closer to baseline except P2 and P3. According to the study authors, this finding suggests prolonged inflammation in P2 and P3 patients post-wounding. After assessing neutrophil, Th17/Treg, and dopamine-2 receptor (D2R) neural antibody counts in patients with CI over 24 hours, 28 hours, and 7 days, post-wounding with a 5mm punch biopsy, Ho et al found a statistically significant higher proportion of neutrophils in P2, P3, and P4 at 24-hour post-wounding. The Th17/ Treg count ratio was statistically elevated for all patients with CI compared to healthy controls at 48 hours post-wounding, “indicating skin wounding in CI patients leads to a prolonged Th17 inflammatory response.”

Key Takeaways

“What we are interested in after completing the microbiome research on rare ichthyosis is that we will continue to build a diagnostic model to manage the risk of infection due to skin changes and moreover, to learn whether current climate change will affect the risk of skin irritation for people in tropical Asia,” Chi‑Bao Bui, PhD, senior author and deputy head of the medical science department at Vietnam National University in Ho Chi Minh City, Vietnam, told Dermatology Times.

According to Bui and author Minh Van Hoang, MD, because CI is a rare disease, typical treatments include topicals in combination with antibiotics. However, because the group of bacteria causing CI is unknown, antibiotics may damage the digestive tract.5

Ho et al’s analysis of the skin’s 4 phyla in dry, moist, and sebaceous skin sites demonstrated low diversity of all phyla in patients with CI. According to the study authors, some dermatologic conditions share signatures of microbiome alterations, such as a decreased abundance of S. epidermidis and C. acnes compared to S. aureus within cutaneous inflammation in patients with psoriasis.

Considering unwounded skin, the majority of patients with CI had a decreased abundance of S. epidermidis and C. acnes. “Reduced commensal C. acnes likely diminishes the skin barrier integrity of CI patients, since C. acnes produces short-chain fatty acids (propionic acid) that activate PPARα signaling leading to increased keratinocyte lipid synthesis, which ultimately supports ceramide production for the epidermal barrier,” wrote Ho et al.

During skin wounding, the abundance of S. aureus was significantly higher in patients with CI, and there was a significant delay in wound healing time in clusters P2, P3, and P4. Ho et al attributed the delay in wound healing directly to the microbiome’s alteration. “This data suggests that oral antibiotics, used with appropriate antibiotic stewardship in mind, may be an effective therapy for healing skin wounds in CI patients,” wrote Ho et al.

From their immune profiling analysis of unwounded CI skin, the study authors found many notable differences among Th17 and Treg cell elevations among CI clusters. For example, if Th17 levels were elevated, IL-1β, IL-6, IL-17A, and IL-17F were also elevated based on mRNA expression levels. Ho et al noted that such an intense ongoing inflammatory response may inhibit effective wound healing in patients with CI.

In their analysis, Ho et al also highlighted available therapeutics that may be able to treat patients with CI, including abrocitinib, bimekizumab, dupilumab, lebrikizumab, ruxolitinib, tralokinumab, and upadacitinib.

“Consistent with one study from 2019, our data shows all CI dysbiosis clusters with elevated IL-17A and IL-17F. These two cytokines have synergistic/cooperative effects on one another, and clinical trial data for bimekizumab, a biologic with dual IL-17A and IL-17F inhibition, has achieved high rates of Psoriasis Area and Severity Index (PASI)-100 clearance. Thus, it is plausible that treatment of CI patients with dual IL-17A/F inhibition will prove more effective than IL-17A inhibition alone,” wrote Ho et al.

With the findings of elevated JAK-STAT signaling in patients with CI, it’s also possible that JAK inhibitors such as upadacitinib, ruxolitinib, and abrocitinib may be effective in reducing skin inflammation and barrier defects in patients with CI.

“Another common driver of itch, IL-13, was elevated for IV, EI, and TTD patients (P2 and P3), suggesting that the atopic dermatitis biologics tralokinumab or lebrikizumab, both IL-13 inhibitors, might prove useful in reducing itch and inflammation in some CI patients, or alternatively, the IL-4/IL-13 inhibitor dupilumab,” wrote Ho et al.

“Evidence that FDA-approved dermatology medicines, both biologics and JAK inhibitors, may benefit certain CI subtypes is exciting because dermatologists are familiar with these medicines and comfortable using them. If proven efficacious in CI, these medicines will pave the way for an easier uptake and utilization in CI patients because they are established in dermatology,” said Bunick.

Overall, Ho et al’s study represents the most comprehensive analysis of Southeast Asian patients with CI to date and provides a detailed look into specific CI subtypes.

“Given the link between STAT3 and FOS-JUN regulation of inflammatory memory in stem cells, these findings warrant further research into the role of stem cell inflammatory memory in CI pathogenesis. Ultimately, the microbiome dysbiosis clustering described here suggests that optimized treatment regimens for CI types will have to account for their heterogeneity from a genetic, microbiome, and immunological viewpoint,” concluded the study authors.

Looking ahead to additional treatments, TMB-001, a topical isotretinoin formulation, is currently in phase 3 clinical trials (ASCEND) for the treatment of congenital ichthyosis. TMB-001 was granted FDA breakthrough therapy designation in May 2022.6

“There is great anticipation for the clinical efficacy results of topical isotretinoin in the phase 3 ASCEND trial, run by Timber/LEO Pharma, which should be coming later this year. Based on the phase 2b data, and the early phase 3 maximum use arm trial data I presented at the 2023 American Academy of Dermatology late-breaking session, topical isotretinoin is poised to become the first FDA-approved therapy for CI patients. This will be a game-changer for CI patients, and for our specialty," said Bunick.


Author Spotlight

First author Minh Ho, MS, is a research associate at the Bunick Lab who first worked in the Bui Lab in Vietnam. After coming across keratin structure research from Bunick, Bui encouraged Ho to transfer to the Bunick Lab. There, Ho helped foster the ichthyosis collaboration and facilitated the US and Vietnam teams.

  1. Ho M, Nguyen HN, Van Hoang M, et al. Altered skin microbiome, inflammation, and JAK/STAT signaling in Southeast Asian ichthyosis patients. Hum Genomics. 2024;18(1):38. Published 2024 Apr 16. doi:10.1186/s40246-024-00603-x
  2. Paller AS, Renert‑Yuval Y, Suprun M, Esaki H, Oliva M, Huynh TN, et al. An IL‑17‑dominant immune profile is shared across the major orphan forms of ichthyosis. J Allergy Clin Immunol. 2017;139(1):152–65. 20.
  3. Malik K, He H, Huynh TN, Tran G, Mueller K, Doytcheva K, et al. Ichthyosis molecular fingerprinting shows profound T(H)17 skewing and a unique barrier genomic signature. J Allergy Clin Immunol. 2019;143(2):604–18. 21.
  4. Czarnowicki T, He H, Leonard A, Malik K, Magidi S, Rangel S, et al. The major orphan forms of ichthyosis are characterized by systemic T‑cell activation and Th‑17/Tc‑17/Th‑22/Tc‑22 polarization in blood. J Invest Dermatol. 2018;138(10):2157–67.
  5. An H. Decoding genes to help treat rare fish scales. VN Express. June 28, 2024. Accessed July 9, 2024. https://vnexpress.net/giai-ma-gene-giup-tri-benh-vay-ca-hiem-gap-4763653.html
  6. Timber Pharmaceuticals to present interim analyses from phase 3 ASCEND study of TMB-001 in congenital ichthyosis. Globe Newswire. June 20, 2023. Accessed July 10, 2024. https://www.globenewswire.com/news-release/2023/06/20/2691018/0/en/Timber-Pharmaceuticals-to-Present-Interim-Analyses-From-Phase-3-ASCEND-Study-of-TMB-001-in-Congenital-Ichthyosis.html
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