Molecular signatures of basal cell carcinoma susceptibility and pathogenesis: a genomic approach

Molecular Profiling and the Interaction of Somatic Mutations with Transcriptomic Profiles in Non-Melanoma Skin Cancer (NMSC) in a Population Exposed to Arsenic

Exposure to inorganic arsenic (As) is recognized as a risk factor for non-melanoma skin cancer (NMSC). We followed up with 7000 adults for 6 years who were exposed to As. During follow-up, 2.2% of the males and 1.3% of the females developed basal cell carcinoma (BCC), while 0.4% of the male and 0.2% of the female participants developed squamous cell carcinoma (SCC). Using a panel of more than 400 cancer-related genes, we detected somatic mutations (SMs) in the first 32 NMSC samples (BCC = 26 and SCC = 6) by comparing paired (tissue-blood) samples from the same individual and then comparing them to the SM in healthy skin tissue from 16 participants. We identified (a) a list of NMSC-associated SMs, (b) SMs present in both NMSC and healthy skin, and (c) SMs found only in healthy skin. We also demonstrate that the presence of non-synonymous SMs in the top mutated genes (like PTCH1, NOTCH1, SYNE1, PKHD1 in BCC and TP53 in SCC) significantly affects the magnitude of differential expressions of major genes and gene pathways (basal cell carcinoma pathways, NOTCH signaling, IL-17 signaling, p53 signaling, Wnt signaling pathway). These findings may help select groups of patients for targeted therapy, like hedgehog signaling inhibitors, IL17 inhibitors, etc., in the future.

Exploring multisite heterogeneity of human basal cell carcinoma proteome and transcriptome

Basal cell carcinoma (BCC) is the most common type of skin cancer. Due to multiple, potential underlying molecular tumor aberrations, clinical treatment protocols are not well-defined. This study presents multisite molecular heterogeneity profiles of human BCC based on RNA and proteome profiling. Three areas from lesions excised from 9 patients were analyzed. The focus was gene expression profiles based on proteome and RNA measurements of intra-tumor heterogeneity from the same patient and inter-tumor heterogeneity in nodular, infiltrative, and superficial BCC tumor subtypes from different patients. We observed significant overlap in intra- and inter-tumor variability of proteome and RNA expression profiles, showing significant multisite heterogeneity of protein expression in the BCC tumors. Inter-subtype analysis has also identified unique proteins for each BCC subtype. This profiling leads to a deeper understanding of BCC molecular heterogeneity and potentially contributes to developing new sampling tools for personalized diagnostics therapeutic approaches to BCC.

Skin Cancer Microenvironment: What We Can Learn from Skin Aging?

Aging is a natural intrinsic process associated with the loss of fibrous tissue, a slower cell turnover, and a reduction in immune system competence. In the skin, the continuous exposition of environmental factors superimposes extrinsic damage, mainly due to ultraviolet radiation causing photoaging. Although not usually considered a pathogenic event, photoaging affects cutaneous biology, increasing the risk of skin carcinogenesis. At the cellular level, aging is typified by the rise of senescence cells a condition characterized by reduced or absent capacity to proliferate and aberrant hyper-secretory activity. Senescence has a double-edged sword in cancer biology given that senescence prevents the uncontrolled proliferation of damaged cells and favors their clearance by paracrine secretion. Nevertheless, the cumulative insults and the poor clearance of injured cells in the elderly increase cancer incidence. However, there are not conclusive data proving that aged skin represents a permissive milieu for tumor onset. On the other hand, tumor cells are capable of activating resident fibroblasts onto a pro-tumorigenic phenotype resembling those of senescent fibroblasts suggesting that aged fibroblasts might facilitate cancer progression. This review discusses changes that occur during aging that can prime neoplasm or increase the aggressiveness of melanoma and non-melanoma skin cancer.

Molecular Classifiers in Skin Cancers: Challenges and Promises

Skin cancers are common and heterogenous malignancies affecting up to two in three Australians before age 70. Despite recent developments in diagnosis and therapeutic strategies, the mortality rate and costs associated with managing patients with skin cancers remain high. The lack of well-defined clinical and histopathological features makes their diagnosis and classification difficult in some cases and the prognostication difficult in most skin cancers. Recent advancements in large-scale "omics" studies, including genomics, transcriptomics, proteomics, metabolomics and imaging-omics, have provided invaluable information about the molecular and visual landscape of skin cancers. On many occasions, it has refined tumor classification and has improved prognostication and therapeutic stratification, leading to improved patient outcomes. Therefore, this paper reviews the recent advancements in omics approaches and appraises their limitations and potential for better classification and stratification of skin cancers.

Novel Insight Into the Association Between Obesity and Hepatocellular Carcinoma Occurrence and Recurrence: High-Throughput Microarray Data Set Analysis of Differentially Expressed Genes

PURPOSE

This study aims to identify potential biomarkers of hepatocellular carcinoma (HCC) occurrence/recurrence and obesity, along with the molecular mechanisms that involve these biomarkers.

METHODS

Three microarray data sets, namely GSE18897, GSE25097, and GSE36376 (genetic suppressor elements associated with obesity, tumor, and recurrence, respectively), were downloaded from Gene Expression Omnibus database to be investigated for their expression as differentially expressed genes (DEGs) in HCC and obesity. The functional and pathway enrichment analysis of these DEGs were identified by the Database for Annotation Visualization and Integrated Discovery. The protein-protein interaction network analysis was performed with STRING online tool and Cytoscape software.

RESULTS

One hundred sixty common DEGs were screened. We found that these genes were associated with certain pathways such as metabolic pathways, terpenoid backbone biosynthesis, and adipocytokine signaling pathway. The involvements of 10 genes, including RPS16, RPS7, CCT3, HNRNPA2B1, EIF4G1, PSMC4, NHP2, EGR1, FDPS, and MCM4, were identified in the subnetwork. HNRNPA2B1 and RPS7 in the GSE18897 data set, RPS16, RPS7, CCT3, HNRNPA2B1, PSMC4, NHP2, FDPS, and MCM4 in the GSE25097 data set, and RPS16, RPS7, CCT3, HNRNPA2B1, EIF4G1, PSMC4, NHP2, FDPS, and MCM4 in the GSE36376 data set exhibited positive fold changes.

CONCLUSION

These DEGs and pathways could be of diagnostic value as potential biomarkers involved in the pathogenesis of HCC, pertaining to both obesity and HCC occurrence/recurrence.

Molecular Profile of Skin Cancer

Neoplasia occurs as a result of genetic mutations. Research evaluating the association between gene mutations and skin cancer is limited and has produced inconsistent results. There are no established guidelines for screening skin cancer at molecular level. It should also be noted that the combinations of some mutations may play a role in skin tumors’ biology and immune response. There are three major types of skin cancer, and the originality of this study comes from its approach of each of them.

Recent Advances in Signaling Pathways Comprehension as Carcinogenesis Triggers in Basal Cell Carcinoma

Basal cell carcinoma (BCC) is the most common malignant skin tumor. BCC displays a different behavior compared with other neoplasms, has a slow evolution, and metastasizes very rarely, but sometimes it causes an important local destruction. Chronic ultraviolet exposure along with genetic factors are the most important risk factors involved in BCC development. Mutations in the PTCH1 gene are associated with Gorlin syndrome, an autosomal dominant disorder characterized by the occurrence of multiple BCCs, but are also the most frequent mutations observed in sporadic BCCs. PTCH1 encodes for PTCH1 protein, the most important negative regulator of the Hedgehog (Hh) pathway. There are numerous studies confirming Hh pathway involvement in BCC pathogenesis. Although Hh pathway has been intensively investigated, it remains incompletely elucidated. Recent studies on BCC tumorigenesis have shown that in addition to Hh pathway, there are other signaling pathways involved in BCC development. In this review, we present recent advances in BCC carcinogenesis.

Identification of Potential Biomarkers Associated with Basal Cell Carcinoma

Purpose

This work is aimed at identifying several molecular markers correlated with the diagnosis and development of basal cell carcinoma (BCC).

Methods

The available microarray datasets for BCC were obtained from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEGs) were identified between BCC and healthy controls. Afterward, the functional enrichment analysis and protein-protein interaction (PPI) network analysis of these screened DEGs were performed. An external validation for the DEG expression level was also carried out, and receiver operating characteristic curve analysis was used to evaluate the diagnostic values of DEGs.

Result

In total, five microarray datasets for BCC were downloaded and 804 DEGs (414 upregulated and 390 downregulated genes) were identified. Functional enrichment analysis showed that these genes including CYFIP2, HOXB5, EGFR, FOXN3, PTPN3, CDC20, MARCKSL1, FAS, and PTCH1 were closely correlated with the cell process and PTCH1 played central roles in the BCC signaling pathway. Moreover, EGFR was a hub gene in the PPI network. The expression changes of six genes (CYFIP2, HOXB5, FOXN3, PTPN3, MARCKSL1, and FAS) were validated by an external GSE74858 dataset analysis. Finally, ROC analysis revealed that CYFIP2, HOXB5, PTPN3, MARCKSL1, PTCH1, and CDC20 could distinguish BCC and healthy individuals.

Conclusion

Nine gene signatures (CYFIP2, HOXB5, EGFR, FOXN3, PTPN3, CDC20, MARCKSL1, FAS, and PTCH1) may serve as promising targets for BCC detection and development.

Scalp basal cell carcinoma: A different entity?

Basal cell carcinoma is the most frequent malignant neoplasm in white-skinned individuals. It develops in different body areas, including in the scalp, which is a unique anatomical region due to the high number of pilosebaceous follicles; the scalp is protected from UV exposure, a main risk factor for basal cell carcinoma development. Moreover, scalp basal cell carcinoma has been described as more aggressive and difficult to treat than other forms of basal cell carcinoma. In this study, we reviewed the clinical and pathological characteristics, risk factors, genetics, and treatment options for scalp basal cell carcinoma to better understand this special type of cancer. Even though it is not yet clear whether scalp basal cell carcinomas represent a different entity, it seems important to give them special attention due to their potential aggressiveness, invasion capacities, tendency to relapse, and treatment difficulties.

Expression profile of the amino acid transporters SLC7A5, SLC7A7, SLC7A8 and the enzyme TDO2 in basal cell carcinoma

Background

The incidence of basal cell carcinoma (BCC) is increasing and the costs for care rising. Therefore, the need for simplified and cost‐effective treatment choices is substantial. Aberrant signalling in several pathways, induced by ultraviolet radiation, is of importance in the development of BCC. Alterations in tumour metabolic activity are part of general carcinogenesis; however, these alterations are only partially recognized in skin cancer.

Objectives

To study expression profiles in BCCs compared with individually matched nontumour skin, with a focus on finding differences associated with tumour metabolism.

Materials and methods

Gene expression in biopsies from BCCs (n = 14) compared with biopsies from nontumour gluteal skin was analysed with microarrays (n = 4 + 4) and/or quantitative real‐time polymerase chain reaction (qPCR, n = 14 + 14). Protein expression and localization was assessed using immunohistochemistry (IHC) in formalin‐fixed and paraffin‐embedded BCC samples.

Results

Microarray analysis revealed increased expression of the amino acid transporters SLC7A5, SLC7A7 and SLC7A8 as well as the cytosolic enzyme tryptophan 2,3‐dioxygenase (TDO) 2 in BCC. Higher expression of SLC7A5 (P < 0·001), SLC7A8 (P < 0·001) and TDO2 (P = 0·002), but not SLC7A7 (P = 0·50), was confirmed by qPCR, and IHC demonstrated correlating tumour cell protein expression of SLC7A5 and SLC7A8. Protein expression of SLC7A7 was observed in the stratum granulosum, and TDO2 in immune cells.

Conclusions

This study highlights the upregulation of SLC7A5, SLC7A8 and TDO2 in BCC compared with nontumour skin. Our findings imply that amino acid transporters may be further explored as potential targets for future medical treatment.

What's already known about this topic?

The incidence of basal cell carcinoma (BCC) is increasing and consequently also the costs of care.

The transport and metabolism of amino acids are often altered in tumours although the knowledge of whether this applies to BCCs is limited.

What does this study add?

Alterations of amino acid transporters SLC7A5 and SLC7A8 and the cytosolic enzyme TDO2 is suggested in BCC and are possible potential targets for treatment.

SLC7A7 (transporter of e.g. lysine) is expressed in the stratum granulosum of normal epidermis and may be involved in the cornification process.

What is the translational message?

We have found tumour‐specific changes in proteins involved in nutrient transport and metabolism.

These changes may be of importance for carcinogenesis and should be explored further for future drug development.

Linked Comment: O’Shaughnessy. Br J Dermatol 2019; 180:16–17.

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Gene networks in basal cell carcinoma of the eyelid, analyzed using gene expression profiling

Basal cell carcinoma (BCC) is the most frequent malignant tumor of the eyelid; it progresses slowly and rarely metastasizes. However, BCC of the eyelid is partially invasive and can extend to the surrounding ocular adnexa even if appropriate treatment is performed. To understand the molecular mechanism underlying its pathogenesis, global gene expression analysis of surgical tissue samples of BCC of the eyelid (n=2) and normal human epidermal keratinocytes was performed using a GeneChip^® system. The histopathological examination of surgically removed eyelid tissues showed the tumor nest composed with small basaloid. In the samples from patients 1 and 2, 687 and 713 genes were identified, respectively, demonstrating ≥5.0-fold higher expression than that noted in normal human epidermal keratinocytes. For the 640 genes with upregulated expression in both patient samples, Ingenuity^® pathway analysis showed that the gene network in BCC of the eyelid included many BCC-associated genes, such as the following: BCL2 apoptosis regulator; Patched-1; and SRY-box 9. In addition, unique gene networks related to cancer cell growth, tumorigenesis, and cell survival were identified. These results of integrating microarray analyses provide further insights into the molecular mechanisms involved in BCC of the eyelid and may provide a therapeutic approach for this disease.

Identification of Distinct Tumor Subpopulations in Lung Adenocarcinoma via Single-Cell RNA-seq

Single-cell sequencing, which is used to detect clinically important tumor subpopulations, is necessary for understanding tumor heterogeneity. Here, we analyzed transcriptomic data obtained from 34 single cells from human lung adenocarcinoma (LADC) patient-derived xenografts (PDXs). To focus on the intrinsic transcriptomic signatures of these tumors, we filtered out genes that displayed extensive expression changes following xenografting and cell culture. Then, we performed clustering analysis using co-regulated gene modules rather than individual genes to minimize read drop-out errors associated with single-cell sequencing. This combined approach revealed two distinct intra-tumoral subgroups that were primarily distinguished by the gene module G64. The G64 module was predominantly composed of cell-cycle genes. E2F1 was found to be the transcription factor that most likely mediates the expression of the G64 module in single LADC cells. Interestingly, the G64 module also indicated inter-tumoral heterogeneity based on its association with patient survival and other clinical variables such as smoking status and tumor stage. Taken together, these results demonstrate the feasibility of single-cell RNA sequencing and the strength of our analytical pipeline for the identification of tumor subpopulations.

Molecular classification of basal cell carcinoma of skin by gene expression profiling

Non-melanoma skin cancers (NMSC) including basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) are more common kinds of skin cancer. Although these tumors share common pathological and clinical features, their similarity and heterogeneity at molecular levels are not fully elaborated yet. Here, by performing comparative analysis of gene expression profiling of BCC, SCC, and normal skin tissues, we could classify the BCC into three subtypes of classical, SCC-like, and normal-like BCCs. Functional enrichment and pathway analyses revealed the molecular characteristics of each subtype. The classical BCC showed the enriched expression and transcription signature with the activation of Wnt and Hedgehog signaling pathways, which were well known key features of BCC. By contrast, the SCC-like BCC was enriched with immune-response genes and oxidative stress-related genes. Network analysis revealed the PLAU/PLAUR as a key regulator of SCC-like BCC. The normal-like BCC showed prominent activation of metabolic processes particularly the fatty acid metabolism. The existence of these molecular subtypes could be validated in an independent dataset, which demonstrated the three subgroups of BCC with distinct functional enrichment. In conclusion, we suggest a novel molecular classification of BCC providing insights on the heterogeneous progression of BCC.

Advanced Basal Cell Carcinoma: Epidemiology and Therapeutic Innovations

Advanced basal cell carcinomas are a subset of basal cell carcinomas that can be difficult to treat either due to their local invasiveness, proximity to vital structures, or metastasis. The incidence of all basal cell carcinoma is increasing in the United States, although it is not known whether advanced basal cell carcinomas (aBCCs) are also increasing. Recently, highly targeted therapy based on knowledge of the basal cell carcinoma pathogenesis has become available either commercially or through human clinical trials. These orally available drugs inhibit the Hedgehog signaling pathway, and lead to advanced basal cell carcinoma shrinkage that can enable preservation of adjacent vital organs. In this review, we outline the role of Hedgehog pathway inhibitors as well as other treatment modalities such as excision, radiotherapy and more traditional chemotherapy in treating advanced basal cell carcinomas. We also highlight current gaps in knowledge regarding the use and side effects of this targeted therapy.