Genomic progression for local invasion of cutaneous squamous cell carcinoma from the superficial to the deep portion.

Cutaneous squamous cell carcinoma (cSCC) is the second most common skin cancer. While many treatments exist, our understanding of its genomic progression, especially from the epidermis to the deep dermis, remains limited. This study aims to identify genetic mutations associated with the progression of cSCC into the deep dermis, providing insights into its aggressive behavior and high-risk features. We performed high-depth whole-exome sequencing on 12 cSCC tissues, along with paired normal tissues from six patients, using microdissection techniques. The mutational analysis focused on identifying alterations enriched during cSCC progression. Gene Ontology enrichment analysis, immunohistochemical assays, and external single-cell RNA data were utilized for validation. A total of 8863 non-synonymous somatic mutations were identified in 4092 genes across the superficial and deep portions of cSCCs. Analysis of deep portion mutations revealed a significant correlation with gene ontology biological processes, particularly cell junction organization, and cell-cell adhesion. Clonal mutations in these processes were more prevalent in the deep portions, indicating their impact on the cSCC mutation landscape. Genetic evolution analysis identified 29 causal genes associated with dermal invasion in cSCC. We highlight somatic mutations in cSCC, revealing heterogeneity between superficial and deep regions. Altered genes in cell junction organization and cell-cell adhesion emerged as pivotal in dermal invasion. We identified 29 causal genes primarily in deep tumor regions. Our findings emphasize analyzing multiple tumor regions to capture varied mutational landscapes. These insights advance our understanding of cSCC progression, emphasizing genetic and cellular changes during tumor evolution.

The Quality of Life and Psychosocial Impact on Female Pattern Hair Loss.

BACKGROUND: Alopecia, a benign dermatologic condition affecting both genders, particularly harms female patients due to psychosocial effects. Female pattern hair loss (FPHL), the primary cause of hair loss in women, lacks sufficient Korean epidemiological studies examining its psychosocial aspects. OBJECTIVE: This study aimed to explore FPHL's psychosocial impacts, including quality of life (QoL), depression, anxiety, medical consumption, and hair loss factors in Korean women. METHODS: A total of 202 patients with FPHL were interviewed using a validated questionnaire to assess the QoL, psychological impact, and pattern of medical consumption. The severity of hair loss was evaluated using the "basic and specific (BASP) classification" by dermatologists. The Hair-Specific Skindex-29 (HSS29) was used to assess the QoL and Beck depression inventory (BDI), Beck anxiety inventory (BAI) to evaluate psychological aspects, and medical expenses and the number of clinic visits to determine medical consumption. RESULTS: The global HSS29 score of FPHL was 40.97±18.92, indicating a notable impact on QoL. The mean BDI and BAI scores were 14.47 and 10.06, respectively. In multivariable regression analysis, HSS29, BDI, and BAI scores were most affected by the severity of hair loss (p<0.001). CONCLUSION: FPHL damages the psychosocial aspects of patients, such as QoL, depression, and medical consumption, according to the severity of hair loss.

Guidelines for the Management of Patients with Alopecia Areata in Korea: Part I Topical and Device-based Treatment.

BACKGROUND: Alopecia areata (AA) is a chronic disease with an unpredictable disease course and severe psychological impact. OBJECTIVE: To provide evidence- and consensus-based insights regarding the treatment of patients with AA in Korea. METHODS: We searched for relevant studies on the topical and device-based treatment of AA in the literature from inception until May 2021. Evidence-based recommendations were also prepared. The evidence for each statement was graded and classified according to the strength of the recommendations. Hair experts from the Korean Hair Research Society (KHRS) voted on the statements, and an agreement of 75% or greater was considered as consensus. RESULTS: Currently, there remains a scarcity of topical treatments, which is supported by robust evidence from a number of high-quality randomized controlled trials. Current evidence supports the efficacy of topical corticosteroids, corticosteroid intralesional injection, and contact immunotherapy in AA patients. Topical corticosteroids and contact immunotherapy are recommended for pediatric AA. A consensus was achieved in 6 out of 14 (42.8%), and 1 out of 5 (20.0%) statements pertaining to topical and device-based treatments in AA, respectively. The expert consensus was from a single country, and the study may not cover all the treatments used. CONCLUSION: The present study provides up-to-date, evidence-based treatment guidelines for AA based on the consensus reached among experts after considering regional healthcare circumstances, adding diversity to the previous guidelines.

Guidelines for the Management of Patients with Alopecia Areata in Korea: Part II Systemic Treatment.

BACKGROUND: Alopecia areata (AA) is a chronic disease with an unpredictable course and can have a severe psychological impact on an individual. OBJECTIVE: To provide evidence and consensus-based statements regarding the treatment of patients with AA in Korea. METHODS: We searched for relevant studies from inception to May 2021 regarding the systemic treatment of AA. Evidence-based recommendations were also prepared. The evidence for each statement was graded and classified according to the strength of the recommendations. Hair experts from the Korean Hair Research Society (KHRS) voted on the statement, and an agreement of 75% or greater was considered as having reached consensus. RESULTS: Current evidence supports the efficacy of systemic corticosteroids, oral cyclosporine monotherapy or combination with systemic corticosteroids, and oral Janus kinase inhibitors in severe AA patients. Systemic steroids may be considered for pediatric patients with severe AA. A consensus was achieved in three out of nine (33.3%), and one out of three (33.3%) statements pertaining to systemic treatment in adult and pediatric AA, respectively. CONCLUSION: The present study produced up-to-date, evidence-based treatment guidelines for AA associated with the consensus obtained by experts based on the Korean healthcare system.

Comparison of Risk Allele Frequencies of Psoriasis-Associated Single-Nucleotide Polymorphisms in Different Population Groups.

BACKGROUND: The prevalence of psoriasis differs by population, and it appears to be more common among Europeans than in East Asians. Recent genome-wide association studies (GWAS) have identified alleles that increase the risk of psoriasis, and these alleles may present different frequencies in different geographic regions. OBJECTIVE: We aimed to gain insights into the causes of differences in disease frequencies according to populations and the factors affecting prevalence and pattern differences. METHODS: We collected a total of 147 psoriasis-associated single-nucleotide polymorphisms (SNPs) from the GWAS catalog and compared the allele frequency differences in 27 populations using public population frequency in the 1000 Genomes Project phase 3 (n=2,504) and the Korean Reference Genome Database (n=1,722). Additionally, we calculated the composited genetic risk scores across the population groups. RESULTS: There were distinct patterns of allele frequencies in different population groups. In many cases, East Asians exhibited allele frequencies opposite to that of Europeans. The genetic risk score was higher in Europeans (average: 0.487) and Americans (average: 0.492) than in East Asians (average: 0.471). The prevalence of psoriasis correlated with the average genetic risk score of the population. CONCLUSION: We observed a difference in the allele frequencies of psoriasis-associated SNPs between the studied populations. This result suggests that the difference in the prevalence of psoriasis between population groups can be interpreted to some extent by the genotype.

Risk Allele Frequency Analysis and Risk Prediction of Single-Nucleotide Polymorphisms for Prostate Cancer.

The incidence of prostate cancer (PCa) varies by ethnicity. This study aimed to provide insights into the genetic cause of PCa, which can result in differences in incidence among individuals of diverse ancestry. We collected data on PCa-associated single-nucleotide polymorphisms (SNPs) from a genome-wide association study catalog. Fisher's exact tests were used to analyze the significance of enrichment or depletion of the effect on the allele at a given SNP. A network analysis was performed based on PCa-related SNPs that showed significant differences among ethnicities. The SNP-based polygenic risk score (PRS) was calculated, and its correlation with PCa incidence was evaluated. European, African, and East Asian populations had different heatmap patterns. Calculated PRS from the allele frequencies of PCa was the highest among Africans, followed by Europeans, and was the lowest among East Asians. PRS was positively correlated with the incidence and mortality of PCa. Network analysis revealed that AR, CDKN1B, and MAD1L1 are genes related to ethnic differences in PCa. The incidence and mortality of PCa showed a strong correlation with PRS according to ethnicity, which may suggest the effect of genetic factors, such as the AR gene, on PCa pathogenesis.

Monitoring Circulating Tumor DNA in Untreated Non-Small-Cell Lung Cancer Patients.

Circulating tumor DNA (ctDNA) has been utilized to monitor the clinical course of patients of non-small-cell lung cancer (NSCLC) who receive therapies targeting druggable mutations. However, despite providing valuable information on how NSCLC would naturally progress, the clinical utility of ctDNA for clinical-course monitoring and prediction of treatment-naïve NSCLC patients without druggable mutations remain unknown. We longitudinally followed a total of 12 treatment-naïve NSCLC patients, who did not harbor EGFR and ALK mutations, by collecting clinical information, radiological data, and plasma samples. Changes in ctDNA levels and tumor burden (TB) were compared with each other. New metastasis development, volume doubling time (VDT), and overall survival (OS) were analyzed regarding ctDNA detection at diagnosis. ctDNA was detected in the plasma of seven (58.3%) patients. Changes in ctDNA levels correlated with those in TB in a substantial fraction (57.1%) of patients and was also associated with brain metastasis, tumor necrosis, or pneumonia in other patients. All patients with ctDNA detection developed new metastasis during follow-ups in the organs that had been devoid of metastasis at diagnosis. The patients without ctDNA detection did not develop new metastasis (median duration of follow-ups: 9.8 months). In addition, patients with ctDNA detection had shorter VDT (p = 0.039) and worse OS (p = 0.019) than those without ctDNA detection. The natural course of NSCLC progression can be monitored by measuring ctDNA levels. Detection of ctDNA at diagnosis can predict development of new metastasis, rapid tumor growth and poor survival of NSCLC patients.

Clinical efficacy of adipocyte-derived stem cells conditioned media combined with micro-injury in refractory patch of alopecia areata.

Management of alopecia areata (AA) is often challenging especially when patients have AA lesion refractory to conventional treatments such as corticosteroids, contact immunotherapy, and systemic therapy. Reports indicate adipocyte-derived stem cell conditioned media (ASC-CM) can activate hair growth and micro-injury using fractional laser or microneedling can also induce wound healing and hair regeneration, which suggests ASC-CM combined with fractional laser or microneedling might provide alternative therapeutic option for a refractory patch of AA. This study aimed to evaluate the clinical efficacy and safety of ASC-CM combined with 10,600 nm carbon dioxide fractional laser or microneedling for the treatment of refractory patch of AA. This retrospective study was based on evaluations of 14 patients with a refractory patch of AA treated with ASC-CM, combined with a 10,600 nm carbon dioxide fractional laser, or microneedling from March 2017 to August 2020. The efficacy of treatment was assessed by extents of hair regrowth percentages of involved areas. Of the 14 enrolled patients, 9 (64.3%) showed > 50% hair regrowth and 6 patients (42.9%) showed complete recovery. In the responder group (n = 9), mean period to achieve > 50% hair regrowth was 11.3 weeks (range 8-16 weeks). In the non-responder group (n = 5), 4 patients (28.6%) showed < 25% of hair regrowth and 1 patient show slight hair regrowth (7.1%) after 3 months of treatment. This study showed ASC-CM combined with 10,600 nm carbon dioxide fractional laser or microneedling may offer effective and safe treatment options for a refractory patch of AA.

Risk Allele Frequency Analysis of Single-Nucleotide Polymorphisms for Vitamin D Concentrations in Different Ethnic Group.

The prevalence of vitamin D deficiency varies from 20.8% to 61.6% among populations of different ethnicities, suggesting the existence of a genetic component. The purpose of this study was to provide insights into the genetic causes of vitamin D concentration differences among individuals of diverse ancestry. We collected 320 single-nucleotide polymorphisms (SNPs) associated with vitamin D concentrations from a genome-wide association studies catalog. Their population-level allele frequencies were derived based on the 1000 Genomes Project and Korean Reference Genome Database. We used Fisher's exact tests to assess the significance of the enrichment or depletion of the effect allele at a given SNP in the database. In addition, we calculated the SNP-based genetic risk score (GRS) and performed correlation analysis with vitamin D concentration that included latitude. European, American, and South Asian populations showed similar heatmap patterns, whereas African, East Asian, and Korean populations had distinct ones. The GRS calculated from allele frequencies of vitamin D concentration was highest among Europeans, followed by East Asians and Africans. In addition, the difference in vitamin D concentration was highly correlated with genetic factors rather than latitude effects.

Single-cell RNA sequencing of human nail unit defines RSPO4 onychofibroblasts and SPINK6 nail epithelium.

Research on human nail tissue has been limited by the restricted access to fresh specimen. Here, we studied transcriptome profiles of human nail units using polydactyly specimens. Single-cell RNAseq with 11,541 cells from 4 extra digits revealed nail-specific mesenchymal and epithelial cell populations, characterized by RSPO4 (major gene in congenital anonychia) and SPINK6, respectively. In situ RNA hybridization demonstrated the localization of RSPO4, MSX1 and WIF1 in onychofibroblasts suggesting the activation of WNT signaling. BMP-5 was also expressed in onychofibroblasts implicating the contribution of BMP signaling. SPINK6 expression distinguished the nail-specific keratinocytes from epidermal keratinocytes. RSPO4+ onychofibroblasts were distributed at close proximity with LGR6+ nail matrix, leading to WNT/ß-catenin activation. In addition, we demonstrated RSPO4 was overexpressed in the fibroblasts of onychomatricoma and LGR6 was highly expressed at the basal layer of the overlying epithelial component, suggesting that onychofibroblasts may play an important role in the pathogenesis of onychomatricoma.

Long-term efficacy and safety of intravenous injection of clonal mesenchymal stem cells derived from bone marrow in five adults with moderate to severe atopic dermatitis.

Atopic dermatitis is a chronic and relapsing inflammatory skin disease that is treated with immunosuppressants. However, long-term use of immunosuppressants may cause toxicity and severe side-effects. To confirm the long-term efficacy and safety of clonal mesenchymal stem cell therapy, we performed investigator-initiated clinical trials and long-term observation in five adult patients with moderate to severe atopic dermatitis that was refractory to conventional treatments. The clinical response assessment values such as Eczema Area and Severity Index (EASI) improved significantly at 16 weeks, and 80% (4/5) of the patients achieved EASI-50 after one or two treatment cycles. Patients were observed for long-term efficacy and safety for an average of 38 weeks (range, 16-86) and showed no serious side-effects. Among the cytokines tested, CCL-17, interleukin (IL)-13, and IL-22 significantly decreased at the end-point of the five participants, two patients who maintained good clinical response over 84 weeks showed increased IL-17 cytokine levels in the blood.

Analysis of risk allele frequencies of single nucleotide polymorphisms related to open-angle glaucoma in different ethnic groups.

BACKGROUND: The prevalence of open-angle glaucoma (OAG) varies from 0.5% to 7.0% among populations of diverse ancestry, suggesting the existence of genetic differences. The purposes of this study were to provide insights into genetic causes of OAG, which can result in prevalence and phenotype differences among populations of diverse ancestry for OAG, and to compare allele frequencies of intraocular pressure (IOP) elevation-related SNPs in OAG among Koreans and other ethnic groups. METHODS: We collected the data on a total of 135 OAG-associated single nucleotide polymorphisms (SNPs) from a genome-wide association studies (GWAS) catalog. The population-level allele frequencies of these SNPs were derived based on the 1000 Genomes Project and Korean Reference Genome Database. We used Fisher's exact test to assess whether the effect allele at a given SNP was significantly enriched or depleted. RESULTS: European, American, and South Asian populations showed similar heatmap patterns, while African, East Asian, and Korean populations had distinct patterns. Korean population presented different profiles compared to other groups; rs1579050 (FMNL2 gene), rs2024211 (CAV2;CAV1), and rs8141433 (GNB1L;TXNRD2 gene), which are known to be associated with IOP variation, were enriched in Americans, Europeans, and Africans, and depleted in Koreans. These can be the candidates for the causative genes of differences in the prevalence of IOP variation in OAG according to ethnic groups. CONCLUSIONS: Differences in allele frequencies associated with IOP related SNPs between Koreans and other ethnicities were observed, which may explain the high prevalence of OAG with normal IOP predominantly in Koreans and East Asians.

Comparison of risk allele frequencies of single nucleotide polymorphisms associated with age-related macular degeneration in different ethnic groups.

BACKGROUND: The prevalence of age-related macular degeneration (AMD) varies from 6.8 to 18.3% for all forms of AMD and from 0.6 to 2.6% for late AMD according to race, suggesting the existence of genetic differences among races. The purpose of this study was to determine the genetic causes of differences in the prevalence of AMD among individuals of different races. METHODS: We collected 138 AMD-associated single nucleotide polymorphisms (SNPs) from a genome-wide association studies catalog. Their population-level allele frequencies were derived based on the 1000 Genomes Project and Korean Reference Genome Database. We used Fisher's exact tests to assess whether the effect allele at a given SNP was significantly enriched or depleted in the database. RESULTS: European, American, and South Asian populations showed similar heatmap patterns, whereas East Asian, and Korean populations had distinct patterns. Korean populations exhibited patterns that were different from those of the other groups; rs5754227 (SYN3), rs1626340 (TGFBR1/COL15A1), rs3750846(ARMS2/HTRA1), and rs9564692 (B3GALTL) were enriched, whereas rs2230199 (C3) and rs73036519 (EXOC3L2/MARK4) were depleted in Koreans; these SNPs are associated with late AMD. The genetic risk score calculated from allele frequencies was not less in East Asians than in Europeans. CONCLUSION: The prevalence of AMD is lower in Asians than in Europeans. However, our study showed that genetic risk scores in East Asians were similar to those in Europeans, which may explain why the global projected number of people with AMD by 2040 is in largest for East Asians, including Koreans.

Dysregulation of cancer genes by recurrent intergenic fusions.

BACKGROUND: Gene fusions have been studied extensively, as frequent drivers of tumorigenesis as well as potential therapeutic targets. In many well-known cases, breakpoints occur at two intragenic positions, leading to in-frame gene-gene fusions that generate chimeric mRNAs. However, fusions often occur with intergenic breakpoints, and the role of such fusions has not been carefully examined. RESULTS: We analyze whole-genome sequencing data from 268 patients to catalog gene-intergenic and intergenic-intergenic fusions and characterize their impact. First, we discover that, in contrast to the common assumption, chimeric oncogenic transcripts-such as those involving ETV4, ERG, RSPO3, and PIK3CA-can be generated by gene-intergenic fusions through splicing of the intervening region. Second, we find that over-expression of an upstream or downstream gene by a fusion-mediated repositioning of a regulatory sequence is much more common than previously suspected, with enhancers sometimes located megabases away. We detect a number of recurrent fusions, such as those involving ANO3, RGS9, FUT5, CHI3L1, OR1D4, and LIPG in breast; IGF2 in colon; ETV1 in prostate; and IGF2BP3 and SIX2 in thyroid cancers. CONCLUSION: Our findings elucidate the potential oncogenic function of intergenic fusions and highlight the wide-ranging consequences of structural rearrangements in cancer genomes.

Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer.

Immunotherapy for metastatic colorectal cancer is effective only for mismatch repair-deficient tumors with high microsatellite instability that demonstrate immune infiltration, suggesting that tumor cells can determine their immune microenvironment. To understand this cross-talk, we analyzed the transcriptome of 91,103 unsorted single cells from 23 Korean and 6 Belgian patients. Cancer cells displayed transcriptional features reminiscent of normal differentiation programs, and genetic alterations that apparently fostered immunosuppressive microenvironments directed by regulatory T cells, myofibroblasts and myeloid cells. Intercellular network reconstruction supported the association between cancer cell signatures and specific stromal or immune cell populations. Our collective view of the cellular landscape and intercellular interactions in colorectal cancer provide mechanistic information for the design of efficient immuno-oncology treatment strategies.

Evolutionary processes of melanomas from giant congenital melanocytic nevi.

Melanoma can develop in a congenital melanocytic nevus (CMN). In fact, a large CMN is associated with a high risk of developing melanoma. Although melanomas arising from CMNs are thought to have a pathogenesis distinct from conventional melanomas, no studies have been conducted on the evolution or tumor heterogeneity of CMN melanomas. We applied multi-region whole-exome sequencing to investigate the clonal nature of driver events and evolutionary processes in CMNs and melanomas arising from CMNs. In two patients, we observed an independent subclonal evolution in cancerized fields of CMNs and chromosome 8q amplification in both melanomas arising from CMNs. The amplification of MYC, located in chromosome 8q, was correlated with the percentage of tumor cells expressing high levels of MYC protein detected in melanoma cells by immunohistochemistry. Our analysis suggests that each CMN cell may evolve sporadically and that amplification of MYC might be a key event for melanoma development in CMNs.

Junction Location Identifier (JuLI): Accurate Detection of DNA Fusions in Clinical Sequencing for Precision Oncology.

Accurate detection of genomic fusions by high-throughput sequencing in clinical samples with inadequate tumor purity and formalin-fixed, paraffin-embedded tissue is an essential task in precise oncology. We developed the fusion detection algorithm Junction Location Identifier (JuLI) for optimization of high-depth clinical sequencing. Novel filtering steps were implemented to minimize false positives in the clinical setting. The algorithm was comprehensively validated using high-depth sequencing data from cancer cell lines and clinical samples and genome sequencing data from NA12878. JuLI showed improved performance mainly in positive predictive value over state-of-the-art fusion callers in cases with high-depth clinical sequencing and rescued a driver fusion from false negative in plasma cell-free DNA using joint calling.

Assessment of intratumoral heterogeneity with mutations and gene expression profiles.

Intratumoral heterogeneity (ITH) refers to the presence of distinct tumor cell populations. It provides vital information for the clinical prognosis, drug responsiveness, and personalized treatment of cancer patients. As genomic ITH in various cancers affects the expression patterns of genes, the expression profile could be utilized for determining ITH level. Herein, we present a novel approach to directly detect high ITH defined as a larger number of subclones from the gene expression pattern through machine learning approaches. We examined associations between gene expression profile and ITH of 12 cancer types from The Cancer Genome Atlas (TCGA) database. Using stomach adenocarcinoma (STAD) showing high association, we evaluated the performance of our method in predicting ITH by employing three machine learning algorithms using gene expression profile data. We classified tumors into high and low heterogeneity groups using the learning model through the selection of LASSO feature. The result showed that support vector machines (SVMs) outperformed other algorithms (AUC = 0.84 in SVMs and 0.82 in Naïve Bayes) and we were able to improve predictive power by using both combined data from mutation and expression. Furthermore, we evaluated the prediction ability of each model using simulation data generated by mixing cell lines of the Cancer Cell Line Encyclopedia (CCLE), and obtained consistent results with using real dataset. Our approach could be utilized for discriminating tumors with heterogeneous cell populations to characterize ITH.

The concept of nail matrix onychodermis (onychomatricodermis) in the nail unit: Histology and elastin immunohistochemistry.

BACKGROUNDS: We previously demonstrated the presence of onychodermis below nail matrix and nail bed. Because nail matrix is a producer of nail plate, we hypothesized that onychodermis below nail matrix could be the nail counterpart of follicular dermal papilla. In this study, we sought to further characterize histologic, histochemical, and immunohistochemical features of nail matrix onychodermis. METHODS AND RESULTS: Hematoxylin and eosin slides of 10 polydactyly nail units and 10 nail matrix biopsies from children and adults were reviewed. In polydactyly nail units, the onychodermis beneath nail matrix was characterized by onychofibroblasts showing abundant cytoplasm, and this area was slightly separated from the undersurface of the nail matrix. Nail matrix biopsy specimens also showed similar histology in the nail matrix onychodermis. Alcian blue stain demonstrated mucin deposition in onychofibroblasts within the nail matrix onychodermis. Immunohistochemically, elastin was rarely expressed in the nail matrix onychodermis while it was strongly expressed in the dermis of other areas of polydactyly nail units. Elastin was not expressed in follicular dermal papilla of terminal hair follicles of the scalp. CONCLUSION: Our findings demonstrate the presence and localization of nail matrix onychodermis (onychomatricodermis). Our study also demonstrates similar elastin expression patterns in the onychomatricodermis and follicular dermal papilla.