Identification of Genes Expressed in Hyperpigmented Skin Using Meta-Analysis of Microarray Data Sets

Prediction of Skin Color Using Forensic DNA Phenotyping in Asian Populations: A Focus on Thailand

Forensic DNA phenotyping (FDP) has emerged as an essential tool in criminal investigations, enabling the prediction of physical traits based on genetic information. This review explores the genetic factors influencing skin pigmentation, particularly within Asian populations, with a focus on Thailand. Key genes such as Oculocutaneous Albinism II (OCA2), Dopachrome Tautomerase (DCT), KIT Ligand (KITLG), and Solute Carrier Family 24 Member 2 (SLC24A2) are examined for their roles in melanin production and variations that lead to different skin tones. The OCA2 gene is highlighted for its role in transporting ions that help stabilize melanosomes, while specific variants in the DCT gene, including single nucleotide polymorphisms (SNPs) rs2031526 and rs3782974, are discussed for their potential effects on pigmentation in Asian groups. The KITLG gene, crucial for developing melanocytes, includes the SNP rs642742, which is linked to lighter skin in East Asians. Additionally, recent findings on the SLC24A2 gene are presented, emphasizing its connection to pigmentation through calcium regulation in melanin production. Finally, the review addresses the ethical considerations of using FDP in Thailand, where advances in genetic profiling raise concerns about privacy, consent, and discrimination. Establishing clear guidelines is vital to balancing the benefits of forensic DNA applications with the protection of individual rights.

Role of interleukin-6 and endothelin-1 receptors in enhanced melanocyte dendricity of facial spots and suppression of their ligands by niacinamide and tranexamic acid

BACKGROUND

Hyperpigmented spots are common issues in all ethnicities with a hallmark characteristic of increased melanocyte dendricity.

OBJECTIVES

To determine (1) potential receptors and/or cytokines that are involved in increased melanocyte dendricity in multiple facial spot types; (2) treatment effects of skin-lightening compounds on identified cytokine release from keratinocytes and on dendricity in melanocytes.

METHODS

Facial spots (melasma, solar lentigo, acne-induced post-inflammatory hyperpigmentation) and adjacent non-spot skin biopsies were collected from Chinese women (age 20-70). The epidermal supra and basal layers were laser dissected to enrich keratinocyte or melanocyte biology respectively for transcriptome analysis. Melanocyte dendricity was assessed histologically by immunofluorescent staining. Effect of interleukin-6 (IL-6) and endothelin-1 (ET-1) on melanocyte dendricity and melanosome transfer were assessed in human melanocytes or melanocyte-keratinocyte co-culture models. Treatment effects of skin-lightening compounds (niacinamide, tranexamic acid [TxA], sucrose laurate/dilaurate mixture [SDL]) were assessed on IL-6 or ET-1 release from keratinocytes and on dendricity in melanocytes.

RESULTS

Transcriptome analysis revealed IL-6 receptor and ET-1 receptor were significantly upregulated compared to the adjacent normal skin, visually confirmed at the protein level through immunostaining. Melanocytes in spot areas are more dendritic than melanocytes in adjacent non-spot skin. The addition of IL-6 and ET-1 to cell culture models increased melanocyte dendricity and melanosome transfer. IL-6 release was significantly suppressed by niacinamide and its combination, while ET-1 release was significantly reduced by both niacinamide and TxA. In contrast, SDL acted directly upon melanocytes to reduce dendricity.

CONCLUSION

Interleukin-6 and ET-1 receptors are significantly upregulated in multiple facial spot types. The in vitro testing demonstrated their respective ligands increased melanocyte dendricity. Tested skin-lightening compounds showed reduction in release of IL-6/ET-1 from epidermal keratinocytes and/or inhibition of melanocyte dendricity. This work sheds light on pathophysiological mechanism of facial spots and potential new mechanisms of these skin-lightening compounds which warrant further human clinical validation.

TRIM63 is a sensitive and specific biomarker for MiT family aberration-associated renal cell carcinoma

Microphthalmia-associated transcription factor (MiT) family aberration-associated renal cell carcinoma (MiTF-RCC) is a subtype of renal cell carcinoma harboring recurrent chromosomal rearrangements involving TFE3 or TFEB genes. MiTF-RCC is morphologically diverse, can histologically resemble common RCC subtypes like clear cell RCC and papillary RCC, and often poses a diagnostic challenge in genitourinary clinical and pathology practice. To characterize the MiTF-RCC at the molecular level and identify biomarker signatures associated with MiTF-RCC, we analyzed RNAseq data from MiTF-RCC, other RCC subtypes and benign kidney. Upon identifying TRIM63 as a cancer-specific biomarker in MiTF-RCC, we evaluated its expression independently by RNA in situ hybridization (RNA-ISH) in whole tissue sections from 177 RCC cases. We specifically included 31 cytogenetically confirmed MiTF-RCC cases and 70 RCC cases suspicious for MiTF-RCC in terms of clinical and morphological features, to evaluate and compare TRIM63 RNA-ISH results with the results from TFE3/TFEB fluorescence in situ hybridization (FISH), which is the current clinical standard. We confirmed that TRIM63 mRNA was highly expressed in all classes of MiTF-RCC compared to other renal tumor categories, where it was mostly absent to low. While the TRIM63 RNA-ISH and TFE3/TFEB FISH results were largely concordant, importantly, TRIM63 RNA-ISH was strongly positive in TFE3 FISH false-negative cases with RBM10-TFE3 inversion. In conclusion, TRIM63 can serve as a diagnostic marker to distinguish MiTF-RCC from other renal tumor subtypes with overlapping morphology. We suggest a combination of TFE3/TFEB FISH and TRIM63 RNA-ISH assays to improve the accuracy and efficiency of MiTF-RCC diagnosis. Accurate diagnosis of MiTF-RCC and other RCC subtypes would enable effective targeted therapy and avoid poor therapeutic response due to tumor misclassification.

Tigers of the World: Genomics and Conservation

Of all the big cats, or perhaps of all the endangered wildlife, the tiger may be both the most charismatic and most well-recognized flagship species in the world. The rapidly changing field of molecular genetics, particularly advances in genome sequencing technologies, has provided new tools to reconstruct what characterizes a tiger. Here we review how applications of molecular genomic tools have been used to depict the tiger's ancestral roots, phylogenetic hierarchy, demographic history, morphological diversity, and genetic patterns of diversification on both temporal and geographical scales. Tiger conservation, stabilization, and management are important areas that benefit from use of these genome resources for developing survival strategies for this charismatic megafauna both in situ and ex situ.

Effects of the selective TrkA agonist gambogic amide on pigmentation and growth of human hair follicles in vitro

The human hair follicle is a neuroendocrine mini-organ that can be used to study aging processes in vitro. Neurotrophins maintain homeostasis in hair biology via the Trk-family of receptors. TrkA, the high affinity receptor for nerve growth factor (NGF), is expressed in hair follicle melanocytes and keratinocytes, where it regulates proliferation, differentiation and apoptosis and may thereby play a role in hair pigmentation and growth. We investigated TrkA expression during the human hair cycle and the effects of a selective high affinity TrkA agonist, Gambogic Amide, on hair pigmentation and hair growth in human hair follicles in vitro. In human scalp skin, TrkA expression was strongest in proliferating melanocytes re-establishing the pigmentary unit in the hair bulb during the early hair growth phase, anagen. During high anagen and in the de-composing pigmentary-unit of the regression phase, catagen, bulb-melanocytes lost TrkA expression and only undifferentiated outer root sheath melanocytes maintained it. In cultured human anagen hair follicles, Gambogic Amide was able to prevent gradual pigment loss, while it stimulated hair shaft elongation. This was achieved by increased melanocyte activation, migration and dendricity, highlighted by distinct c-KIT-expression in melanocyte sub-populations. Our results suggest that Gambogic Amide can maintain hair follicle pigmentation by acting on undifferentiated melanocytes residing in the outer root sheath and making them migrate to establish the pigmentary-unit. This suggests that the selective TrkA agonist Gambogic Amide acts as an anti-hair greying and hair growth promoting molecule in vitro.

An actionable axis linking NFATc2 to EZH2 controls the EMT-like program of melanoma cells

Discovery of new actionable targets and functional networks in melanoma is an urgent need as only a fraction of metastatic patients achieves durable clinical benefit by targeted therapy or immunotherapy approaches. Here we show that NFATc2 expression is associated with an EMT-like transcriptional program and with an invasive melanoma phenotype, as shown by analysis of melanoma cell lines at the mRNA and protein levels, interrogation of the TCGA melanoma dataset and characterization of melanoma lesions by immunohistochemistry. Gene silencing or pharmacological inhibition of NFATc2 downregulated EMT-related genes and AXL, and suppressed c-Myc, FOXM1, and EZH2. Targeting of c-Myc suppressed FOXM1 and EZH2, while targeting of FOXM1 suppressed EZH2. Inhibition of c-Myc, or FOXM1, or EZH2 downregulated EMT-related gene expression, upregulated MITF and suppressed migratory and invasive activity of neoplastic cells. Stable silencing of NFATc2 impaired melanoma cell proliferation in vitro and tumor growth in vivo in SCID mice. In NFATc2⁺ EZH2⁺ melanoma cell lines pharmacological co-targeting of NFATc2 and EZH2 exerted strong anti-proliferative and pro-apoptotic activity, irrespective of BRAF or NRAS mutations and of BRAF inhibitor resistance. These results provide preclinical evidence for a role of NFATc2 in shaping the EMT-like melanoma phenotype and reveal a targetable vulnerability associated with NFATc2 and EZH2 expression in melanoma cells belonging to different mutational subsets.

Genome-Wide Evolutionary Analysis of Natural History and Adaptation in the World's Tigers

No other species attracts more international resources, public attention, and protracted controversies over its intraspecific taxonomy than the tiger (Panthera tigris) [1, 2]. Today, fewer than 4,000 free-ranging tigers survive, covering only 7% of their historical range, and debates persist over whether they comprise six, five, or two subspecies [3-6]. The lack of consensus over the number of tiger subspecies has partially hindered the global effort to recover the species from the brink of extinction, as both captive breeding and landscape intervention of wild populations increasingly require an explicit delineation of the conservation management units [7]. The recent coalescence to a late Pleistocene bottleneck (circa 110 kya) [5, 8, 9] poses challenges for detecting tiger subspecific morphological traits, suggesting that elucidating intraspecific evolution in the tiger requires analyses at the genomic scale. Here, we present whole-genome sequencing analyses from 32 voucher specimens that resolve six statistically robust monophyletic clades corresponding to extant subspecies, including the recently recognized Malayan tiger (P. tigris jacksoni). The intersubspecies gene flow is very low, corroborating the recognized phylogeographic units. We identified multiple genomic regions that are candidates for identifying the adaptive divergence of subspecies. The body-size-related gene ADH7 appears to have been strongly selected in the Sumatran tiger, perhaps in association with adaptation to the tropical Sunda Islands. The identified genomic signatures provide a solid basis for recognizing appropriate conservation management units in the tiger and can benefit global conservation strategic planning for this charismatic megafauna icon.

Molecular and histological characterization of age spots

Age spots, also called solar lentigines and lentigo senilis, are light brown to black pigmented lesions of various sizes that typically develop in chronically sun-exposed skin. It is well known that age spots are strongly related to chronic sun exposure and are associated with photodamage and an increased risk for skin cancer; however, the mechanisms underlying their development remain poorly understood. We used immunohistochemical analysis and microarray analysis to investigate the processes involved in their formation, focusing on specific markers associated with the functions and proliferation of melanocytes and keratinocytes. A total of 193 genes were differentially expressed in age spots, but melanocyte pigment genes were not among them. The increased expression of keratins 5 and 10, markers of basal and suprabasal keratinocytes, respectively, in age spots suggests that the increased proliferation of basal keratinocytes combined with the decreased turnover of suprabasal keratinocytes leads to the exaggerated formation of rete ridges in lesional epidermis which in turn disrupts the normal processing of melanin upwards from the basal layer. Based on our results, we propose a model for the development of age spots that explains the accumulation of melanin and the development of extensive rete ridges in those hyperpigmented lesions.

Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways

The prototypical neurotropic virus, rabies, is a member of the Rhabdoviridae family that causes lethal encephalomyelitis. Although there have been a plethora of studies investigating the etiological mechanism of the rabies virus and many precautionary methods have been implemented to avert the disease outbreak over the last century, the disease has surprisingly no definite remedy at its late stages. The psychological symptoms and the underlying etiology, as well as the rare survival rate from rabies encephalitis, has still remained a mystery. We, therefore, undertook a systems biomedicine approach to identify the network of gene products implicated in rabies. This was done by meta-analyzing whole-transcriptome microarray datasets of the CNS infected by strain CVS-11, and integrating them with interactome data using computational and statistical methods. We first determined the differentially expressed genes (DEGs) in each study and horizontally integrated the results at the mRNA and microRNA levels separately. A total of 61 seed genes involved in signal propagation system were obtained by means of unifying mRNA and microRNA detected integrated DEGs. We then reconstructed a refined protein–protein interaction network (PPIN) of infected cells to elucidate the rabies-implicated signal transduction network (RISN). To validate our findings, we confirmed differential expression of randomly selected genes in the network using Real-time PCR. In conclusion, the identification of seed genes and their network neighborhood within the refined PPIN can be useful for demonstrating signaling pathways including interferon circumvent, toward proliferation and survival, and neuropathological clue, explaining the intricate underlying molecular neuropathology of rabies infection and thus rendered a molecular framework for predicting potential drug targets.