Marker Of Melanoma Progression Research Articles

MCAM/MUC18/CD146 as a Multifaceted Warning Marker of Melanoma Progression in Liquid Biopsy.

Human malignant melanoma shows a high rate of mortality after metastasization, and its incidence is continuously rising worldwide. Several studies have suggested that MCAM/MUC18/CD146 plays an important role in the progression of this malignant disease. MCAM/MUC18/CD146 is a typical single-spanning transmembrane glycoprotein, existing as two membrane isoforms, long and short, and an additional soluble form, sCD146. We previously documented that molecular MCAM/MUC18/CD146 expression is strongly associated with disease progression. Recently, we showed that MCAM/MUC18/CD146 and ABCB5 can serve as melanoma-specific-targets in the selection of highly primitive circulating melanoma cells, and constitute putative proteins associated with disease spreading progression. Here, we analyzed CD146 molecular expression at onset or at disease recurrence in an enlarged melanoma case series. For some patients, we also performed the time courses of molecular monitoring. Moreover, we explored the role of soluble CD146 in different cohorts of melanoma patients at onset or disease progression, rather than in clinical remission, undergoing immune therapy or free from any clinical treatment. We showed that MCAM/MUC18/CD146 can be considered as: (1) a membrane antigen suitable for identification and enrichment in melanoma liquid biopsy; (2) a highly effective molecular “warning” marker for minimal residual disease monitoring; and (3) a soluble protein index of inflammation and putative response to therapeutic treatments.

The discovery of a new marker of melanoma progression

British Journal of DermatologyVolume 185, Issue 2 p. e48-e48 Plain Language SummaryFree Access The discovery of a new marker of melanoma progression First published: 16 August 2021 https://doi.org/10.1111/bjd.20540AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinked InRedditWechat Abstract Linked Article: Perez et al. Br J Dermatol 2021; 185:294–301. Melanoma is a type of skin cancer, which arises from the pigment cells (melanocytes) in the skin. Melanoma is considered to be the most serious type of skin cancer because it is more likely to spread (metastasize) from the skin to other parts of the body than other types of skin cancer. If melanoma has spread to other parts of the body, those deposits are known as secondary melanoma (secondaries/metastases). Metastatic melanoma has a poor 5-year survival rate of 22·5% as it can be resistant to treatment and prone to recurrence. Identifying biomarkers (indicators of a biological process) that better predict likely treatment response and disease severity is therefore important. We believe that understanding the cancer glycome (composed of complex carbohydrates termed glycans), can provide new molecular targets for monitoring disease progression and for developing treatments. Novel findings suggest that glycans play a major role in influencing melanoma progression and could be used to help predict metastatic activity and/or as therapeutic targets. In this review, we discuss the role of aberrant glycosylation (i.e. where the process differs from the normal one), particularly the specialized function of GCNT2 (β1,6 N-acetylglucosaminyltransferase 2), in melanoma pathogenesis. We summarize mechanisms of GCNT2 regulation to shed light on its potential as a predictive marker and as a target for treatment. Volume185, Issue2August 2021Pages e48-e48 RelatedInformation

Genome-wide association study to reveal novel germline markers of melanoma survival.

9581 Background: Cutaneous melanoma (CM) is the most invasive form of skin cancer accounting for ̃80% of all skin cancer related deaths. While tumor staging (based on recent AJCC classification) is routinely used in prognostic assessment, a large fraction of the outcomes is not explained by AJCC staging system. This urges for the discovery of a more personalized prognostic surrogates. Growing evidence highlights the role of germline genetics in CM progression; yet, to date no systematic prognostic germline study has been conducted in melanoma. We performed the first genome-wide association analysis (GWAS) to identify germline variants associated with melanoma survival. Methods: A cases/case GWAS was performed using the Infinium global screening array (GSA v3.0) to genotype 1,117 stage 0-III melanoma patients with no history of immunotherapy treatments ascertained at New York University Langone Health (NYULH). We randomly divided the study cohort into a discovery (N=630) and a validation (N=487) sets and tested the association of > 5 million imputed germline variants with melanoma overall survival (OS) by fitting Cox-proportional hazard ratio (HR) regression in an additive genetic model adjusting for sex, age at diagnosis, AJCC 8th staging, tumor anatomic sites, and top 3 principal components. Results: We found 151 independent variants associated with melanoma OS (p< 5×10−5) in the discovery cohort. Two of these associations validated in the independent replication set ( Bonferroni threshold for 151 tests: p < 0.003) with enhanced clinical and statistical significance in the pooled meta-analysis: rs4128212 [HR =2.47(1.75-3.48); p=2.2× 10−7], and rs13212644 [HR =2.59 (1.72-3.88); p=4.2× 10−6]. We further tested the combined effect of these two variants and found the presence of at least one risk allele of the variants associated with a substantially increased risk of death, surpassing GWAS level of significance (HR=3.74 (2.43-5.74); p=1.5×10−9). Conclusions: We present the results of first GWAS testing an association of germline variation with melanoma OS. Stemming from a unique patient population with extensive clinical follow-up data, we identified two prognostic germline loci with large HR effect size >2.5 that were independently validated. The observed association is independent of established histopathologic markers. While rs4128212 was mapped to a putative cancer prognostic gene locus (PLPP4: phospholipid phosphatase 4), rs13212644 was an eQTL (expression quantitative trait loci) for GCLC (Glutamate-Cysteine Ligase Catalytic Subunit), a key regulator in glutathione synthesis previously linked with favorable melanoma survival. The significantly enhanced combined effect of these two loci (HR >3.5; p<5×10−9) indicates a great promise for their clinical utility as independent personalized predictive markers of melanoma progression.

Microphthalmia-Associated Transcription Factor-Dependent Melanoma Cell Adhesion Molecule Activation Promotes Peritoneal Metastasis of Ovarian Cancer.

Ovarian cancer (OvCa) is one of the leading causes of death due to its high metastasis rate to the peritoneum. Recurrent peritoneal tumors also develop despite the use of conventional platinum-based chemotherapies. Therefore, it is still important to explore the factors associated with peritoneal metastasis, as these predict the prognosis of patients with OvCa. In this study, we investigated the function of microphthalmia-associated transcription factor (MITF), which contributes to the development of melanoma, in epithelial ovarian cancer (OvCa). High MITF expression was significantly associated with a poor prognosis in OvCa. Notably, MITF contributed to the motility and invasion of OvCa cells, and specifically with their peri-mesothelial migration. In addition, MITF-positive cells expressed the melanoma cell adhesion molecule (MCAM/CD146), which was initially identified as a marker of melanoma progression and metastasis, and MCAM expression was regulated by MITF. MCAM was also identified as a significant prognostic factor for poor progression-free survival in patients with OvCa. Collectively, our results suggest that MITF is a novel therapeutic target that potentially promotes peritoneal metastasis of OvCa.

A Sampling of Highlights from the Literature

Prostaglandin E2 (from WikiMedia Commons)Neutrophils can be immunosuppressive when located in the microenvironment of tumors. GM-CSF in the tumor microenvironment stimulates STAT5-upregulation of fatty-acid transporter protein FATP2 primarily on tumor neutrophils. This increases arachidonic acid uptake and the generation of PGE2, with subsequent suppression of tumor-specific T-cell responses. By combining inhibition of FATP2 with blockade of CTLA-4, tumor growth can be effectively inhibited in two mouse tumor models.Veglia F, …, Gabrilovich DI. Nature 2019 Apr 17;569:73–8.Neo open reading frame peptides (from Koster et al., Fig. 2)Cancer cell genomes can contain frameshift mutations, from which long neopeptides can be translated. Examination of over 10,000 TGCA tumor samples finds 143,444 frame-shift mutations, and 70,000 unique peptides ≥ 10 amino acids. Tumor-drivers are commonly frame-shifted genes. The neo-open-reading-frame peptides (NOPs) converge on common peptide sequences, in that by including only 6 driver genes, 1244 new peptides could be found in 30% of the patients. NOPs offer a new source of commonly shared potential neoantigens that could inform production of an “off-the-shelf” library of vaccine reagents.Koster J and Plasterk RHA. Sci Rep 2019 Apr 29;9:6577.Antibody binding sites on PD-1 (from Fenwick et al., Fig. 2F)Clinically useful mAbs to PD-1 block the PD-L1 binding site and thereby block the inhibition signal. Fenwick and colleagues find two new mAbs that bind to PD-1, but structural analysis indicates that binding is on locations away from the PD-1 binding site. The nonblocking mAbs act through the CD28 coreceptor, restoring signaling through the AKT–NF-κB pathway, and helping further rescue exhausted T cells. Combining both types of antibodies in tumor models enhances tumor clearance over monotherapy.Fenwick C, …, Pantaleo G. J Exp Med 2019 May 23. DOI: 10.1084/jem.20182359.Effects of DDR and PD-L1 inhibition (from Sen et al., Fig. 7E)Immune checkpoint blockade is successful only in some cases of small cell lung cancer (SCLC). Sen et al. find that FDA-approved small molecule inhibitors of CHK1 and PARP, which participate in the DNA damage response, can enhance PD-L1 blockade of the CD8+ T cell antitumor response. This is mediated in part through activation of the STING pathway that leads to increased production of T cell chemoattractants like CXCL10 and CCL5. The results suggest dual therapy could improve immunotherapy in SCLC.Sen T, …, Byers LA. Cancer Discov 2019 May 1;9:646–61.Melanoma-associated lymph node (from Broggi et al., Fig. 6A)Two papers show the promise of using tumor-draining lymph node exudate as the substrate for tumor biomarkers and evaluation of antitumor immune responses. Garcia-Silva et al. make use of extracellular vesicles (EVs) to detect markers of melanoma progression and the status of BRAF mutations. Broggi et al. compare plasma to draining lymph node exudate and find the exudate and EVs to be enriched in metastatic tumor–derived factors with protein signatures that can differentiate early from advanced metastasis and provide insights into tumor interactions with the immune system.García-Silva S, …, Peinado H. J Exp Med 2019 MAY 6;216: 1061–70.Broggi MAS, …, Swartz MA. J Exp Med 2019 May 6;216:1091–107.Moderately differentiated gastric tumor (by Nephron via Wikimedia Commons)The ramifications of PD-1 blockade on regulatory T cells (Tregs) are not clear. Almost 10% of patients with gastric cancer treated with anti–PD-1 respond with rapid progression of their tumors. In these patients, treatment increases the proliferative rate and immune suppressive activity of their Tregs. Tregs from PD-1–deficient mice lack PD-1 and both proliferate strongly and have enhanced immunosuppressive activity of antitumor responses. This association of hyperprogressive disease with PD-1 treatment suggests that Tregs be routinely monitored during checkpoint blockade therapy to identify this patient subset.Kamada T, …, Nishikawa H. Proc Natl Acad Sci U S A 2019 May 14;116:9999–10008.

Correction: Use of extracellular vesicles from lymphatic drainage as surrogate markers of melanoma progression and BRAF V600E mutation.

Correction: Use of extracellular vesicles from lymphatic drainage as surrogate markers of melanoma progression and BRAF V600E mutation.

Use of extracellular vesicles from lymphatic drainage as surrogate markers of melanoma progression and BRAF V600E mutation.

Liquid biopsies from cancer patients have the potential to improve diagnosis and prognosis. The assessment of surrogate markers of tumor progression in circulating extracellular vesicles could be a powerful non-invasive approach in this setting. We have characterized extracellular vesicles purified from the lymphatic drainage also known as exudative seroma (ES) of stage III melanoma patients obtained after lymphadenectomy. Proteomic analysis showed that seroma-derived exosomes are enriched in proteins resembling melanoma progression. In addition, we found that the BRAFV600E mutation can be detected in ES-derived extracellular vesicles and its detection correlated with patients at risk of relapse.

Interleukin 8 mediates bcl-xL-induced enhancement of human melanoma cell dissemination and angiogenesis in a zebrafish xenograft model.

The protein bcl-xL is able to enhance the secretion of the proinflammatory chemokine interleukin 8 (CXCL8) in human melanoma lines. In this study, we investigate whether the bcl-xL/CXCL8 axis is important for promoting melanoma angiogenesis and aggressiveness in vivo, using angiogenesis and xenotransplantation assays in zebrafish embryos. When injected into wild-type embryos, bcl-xL-overexpressing melanoma cells showed enhanced dissemination and angiogenic activity compared with control cells. Human CXCL8 protein elicited a strong proangiogenic activity in zebrafish embryos and zebrafish Cxcr2 receptor was identified as the mediator of CXCL8 proangiogenic activity using a morpholino-mediated gene knockdown. However, human CXCL8 failed to induce neutrophil recruitment in contrast to its zebrafish homolog. Interestingly, the greater aggressiveness of bcl-xL-overexpressing melanoma cells was mediated by an autocrine effect of CXCL8 on its CXCR2 receptor, as confirmed by an shRNA approach. Finally, correlation studies of gene expression and survival analyses using microarray and RNA-seq public databases of human melanoma biopsies revealed that bcl-xL expression significantly correlated with the expression of CXCL8 and other markers of melanoma progression. More importantly, a high level of co-expression of bcl-xL and CXCL8 was associated with poor prognosis in melanoma patients. In conclusion, these data demonstrate the existence of an autocrine CXCL8/CXCR2 signaling pathway in the bcl-xL-induced melanoma aggressiveness, encouraging the development of novel therapeutic approaches for high bcl-xL-expressing melanoma.

Prognostic value of CD146 in solid tumor: A Systematic Review and Meta-analysis

CD146, also known as melanoma cell adhesion molecule, was initially identified as a marker of melanoma progression and metastasis. Recently many clinical studies investigated overexpression of CD146 predict poor prognosis of solid tumor, however, the results was inconclusive, partly due to small numbers of patients included. This present meta-analysis was therefore performed utilizing the results of all clinical studies concerned to determine the prognostic value of CD146 expression in solid tumors. Relevant articles were identified through searching the PubMed, Web of Science and Embase database. In this meta-analysis, 12 studies involving 2,694 participants were included, and we drew the conclusion that strong significant associations between CD146 expression and all endpoints: overall survival (OS) [hazard ratio (HR) = 2.496, 95% confidence interval (95% CI) 2.115–2.946], time to progression (TTP) (HR = 2.445, 95% CI 1.975–3.027). Furthermore, the subgroup analysis revealed that the associations between CD146 overexpression and the outcome endpoints (OS or TTP) were significant in Mongoloid patients and Caucasian patients, as well in patients with lung cancer and digestive system cancer. In conclusion, these results showed that high CD146 was associated with poor survival in human solid tumors. CD146 may be a valuable prognosis predictive biomarker; nevertheless, whether CD146 could be a potential therapeutic target in human solid tumors needs to be further studied.

Mutation burden as a potential prognostic marker of melanoma progression and survival.

9567 Background: Recently, tumor mutation burden (TMB) has been shown to increase the presentation of neoantigens that stimulate immune tumor recognition, resulting in improved immunotherapy (IT) outcomes in melanoma and other cancers. As melanoma is highly immunogenic, here we tested whether TMB associates with immune recognition during tumor progression, hence impacting melanoma overall survival (OS), independently of IT treatment. Methods: We have generated somatic mutation data from 314 IT-naive metastatic melanomas from The Cancer Genome Atlas (TCGA). In the TCGA cohort, TMB has been calculated for 210 genes (200GS) previously established from TMB studies of anti-CTLA4 and anti-PD1/PD-L1 IT. For validation, we have sequenced exonic regions of 20 genes (20GS) with the highest TMB among 200GS in 89 IT-naive metastatic melanomas ascertained at New York University Langone Medical Center. The TMB was defined using total number of somatic, non-synonymous mutations in either 200GS (TCGA discovery) or 20GS (validation), respectively. For discovery and validation cohorts, OS from primary diagnosis of samples with high TMB was compared against low TMB, using thresholds established in previous studies. Results: We found that total TMB predicts better OS (p = 0.03, HR = 2.64) in TCGA melanomas. Restricting the analysis only to the established 200GS, this association became more significant in all patients (p = 0.01, HR = 2.67) as well as in patients without IT (p = 0.01, HR = 2.67). In the validation stage of 89 melanomas without prior IT treatment, a high TMB in a subset of 20GS accurately determined favorable OS (p = 0.02, HR = 2.69) and confirmed TCGA observations from the 200GS. Conclusions: Here we show, for the first time, that in addition to IT, high TMB predicts more favorable OS in patients that never received IT, potentially serving as a novel marker of prognosis of melanoma and likely other immunogenic tumors at early stages. In addition, our study suggests that TMB test can be robust when applied to only a small subset of genes that trigger significantly higher immunogenicity. This may also eventually assist with accurate sub-selection of early stage patients likely to respond to IT regimens.

Enhanced expression of melanoma progression markers in mouse model of sleep apnea

IntroductionObstructive sleep apnea has been associated with higher cancer incidence and mortality. Increased melanoma aggressivity was reported in obstructive sleep apnea patients. Mice exposed to intermittent hypoxia (IH) mimicking sleep apnea show enhanced melanoma growth. Markers of melanoma progression have not been investigated in this model. ObjectiveThe present study examined whether IH affects markers of melanoma tumor progression. MethodsMice were exposed to isocapnic IH to a nadir of 8% oxygen fraction for 14 days. One million B16F10 melanoma cells were injected subcutaneously. Immunohistochemistry staining for Ki-67, PCNA, S100-beta, HMB-45, Melan-A, TGF-beta, Caspase-1, and HIF-1alpha were quantified using Photoshop. ResultsPercentage of positive area stained was higher in IH than sham IH group for Caspase-1, Ki-67, PCNA, and Melan-A. The greater expression of several markers of tumor aggressiveness, including markers of ribosomal RNA transcription (Ki-67) and of DNA synthesis (PCNA), in mice exposed to isocapnic IH than in controls provide molecular evidence for a apnea–cancer relationship. ConclusionsThese findings have potential repercussions in the understanding of differences in clinical course of tumors in obstructive sleep apnea patients. Further investigation is necessary to confirm mechanisms of these descriptive results.

AC-93253 triggers the downregulation of melanoma progression markers and the inhibition of melanoma cell proliferation

A major challenge in anti-melanoma therapy is to develop treatments that are effective for advanced melanoma patients. Unfortunately, the currently used regimens are not efficient and have unsatisfactory effects on disease progression, thus increasing the pressure to develop new, profitable drugs and to identify new molecular targets. Here, we show for the first time that AC-93253, a SIRT2 inhibitor, exerts a negative effect on the expression of a set of genes involved in the progression and chemoresistance (e.g., oncogenes, apoptosis-related genes, ABC transporter genes, and cell cycle control genes) of melanoma cells. Furthermore, melanoma cells exposed to AC-93253 and doxorubicin displayed altered biological responses, including apoptosis and proliferation, compared to cells exposed to single treatments. Taken together, we conclude that the usage of AC-93253 in combined therapy could be a promising strategy for melanoma patients.

IMP-3 Promotes Migration and Invasion of Melanoma Cells by Modulating the Expression of HMGA2 and Predicts Poor Prognosis in Melanoma

IGF II mRNA-binding protein 3 (IMP-3) has been reported to be a marker of melanoma progression. However, the mechanisms by which it impacts melanoma are incompletely understood. In this study, we investigate the clinical significance of IMP-3 in melanoma progression and also its underlying mechanisms. We found that IMP-3 expression was much higher in advanced-stage/metastatic melanomas and that it was associated with a poor prognosis (P=0.001). Univariate analysis showed that IMP-3 expression was associated with stage III/IV melanomas (odds ratio=5.40, P=0.031) and the acral lentiginous subtype (odds ratio=3.93, P=0.0034). MeWo cells with overexpression of IMP-3 showed enhanced proliferation and migration and significantly increased tumorigenesis and metastatic ability in nude mice. We further demonstrated that IMP-3 could bind and enhance the stability of the mRNA of high mobility group AT-hook 2 (HMGA2). It was also confirmed that IMP-3 had an important role in melanoma invasion and metastasis through regulating HMGA2 mRNA expression. IMP-3 expression was positively correlated with HMGA2 expression in melanoma cells and also in melanoma tissues. Our results show that IMP-3 expression is a strong prognostic factor for melanoma, especially acral lentiginous melanoma.

C-reactive protein as a marker of melanoma progression.

To investigate the association between blood levels of C-reactive protein (CRP) in patients with melanoma and overall survival (OS), melanoma-specific survival (MSS), and disease-free survival. Two independent sets of plasma samples from a total of 1,144 patients with melanoma (587 initial and 557 confirmatory) were available for CRP determination. Kaplan-Meier method and Cox regression were used to evaluate the relationship between CRP and clinical outcome. Among 115 patients who underwent sequential blood draws, we evaluated the relationship between change in disease status and change in CRP using nonparametric tests. Elevated CRP level was associated with poorer OS and MSS in the initial, confirmatory, and combined data sets (combined data set: OS hazard ratio, 1.44 per unit increase of logarithmic CRP; 95% CI, 1.30 to 1.59; P < .001; MSS hazard ratio, 1.51 per unit increase of logarithmic CRP; 95% CI, 1.36 to 1.68; P < .001). These findings persisted after multivariable adjustment. As compared with CRP < 10 mg/L, CRP ≥ 10 mg/L conferred poorer OS in patients with any-stage, stage I/II, or stage III/IV disease and poorer disease-free survival in those with stage I/II disease. In patients who underwent sequential evaluation of CRP, an association was identified between an increase in CRP and melanoma disease progression. CRP is an independent prognostic marker in patients with melanoma. CRP measurement should be considered for incorporation into prospective studies of outcome in patients with melanoma and clinical trials of systemic therapies for those with melanoma.

CD271 is expressed in melanomas with more aggressive behaviour, with correlation of characteristic morphology by in vivo reflectance confocal microscopy.

Melanoma is the most highly aggressive type of skin cancer. Its resistance to existing treatments and the rapid rise in incidence underscore the importance of acquiring a better understanding of melanomagenesis. To assess the impact of reflectance confocal microscopy (RCM) on the description of cell morphology, which may influence the growth pattern and changes with increasing tumour severity, correlating with biological aspects. A retrospective analysis of 30 primary melanomas in vivo, evaluated by RCM, to correlate cell morphology and cellular arrangement with a marker of melanoma progression (CD271) using immunohistochemical evaluations. Typical cells organized in dermal nests with peculiar in vivo confocal morphology result in melanoma with high malignancy and positivity to CD271. This architecture might be due to the presence of a type of cells, intrinsically predisposed to invasion, as a result of dedifferentiation programming, revealed by expression of the neural crest marker CD271. With the hypothesis that dedifferentiated cells would be strongly responsible for initiation of tumour development and progression, we propose that CD271 detection could be associated with RCM evaluation in order to detect more aggressive melanoma subtypes.

Abstract A73: In vivo evidence of TIMPv as a potential target of CD146-signaling inhibiting breast tumor invasion

Abstract CD146, also known as melanoma cell adhesion molecule (Mel-CAM, MCAM) or MUC18, was initially identified as a marker of melanoma progression and a promoter of melanoma and prostate cancer (PC) metastasis. In contrast, CD146 appears to play a tumor suppression role in breast cancer (BC). Here, we applied microarray gene expression profiling analysis, using a tetracycline (tet On)-inducible system of CD146 in the MDA-MB-231 BC cell line, and we identified TIMPv (a variant of Tissue Inhibitor of Metalloproteinases), showing a 7 fold increase, as a potential CD146-downstream signaling transcriptional target; this was confirmed in vitro by both time-course western blotting and RT-PCR. Furthermore, breast tumor tissues from both Omani patients and patients from New Orleans area in Louisiana, were examined by immunohistochemistry for the expression of CD146 and TIMPv. Strikingly, the results revealed that the expression levels of both CD146 and its downstream target TIMPv showed parallel inhibition patterns in BC progression, with high expression in normal and benign but low or no expression in malignant and metastatic breast tumor tissue. These findings support the hypothesis that the expression of both, CD146 and its downstream target TIMPv, is lost during BC progression and metastasis. Ongoing studies in our laboratory aim to shed light on the molecular components linking CD146 to the activation of TIMPv transcription. Citation Format: Allal Ouhtit, Zakariya Y. Abd Elmageed, Sunil Bhat, Pravrutha Raman, Suad H. Al-Jardani, Ishita Gupta, Somya Shanmuganathan, Hamad Al-Riyami. In vivo evidence of TIMPv as a potential target of CD146-signaling inhibiting breast tumor invasion. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Invasion and Metastasis; Jan 20-23, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;73(3 Suppl):Abstract nr A73.

Multilevel omic data integration in cancer cell lines: advanced annotation and emergent properties

BackgroundHigh-throughput (omic) data have become more widespread in both quantity and frequency of use, thanks to technological advances, lower costs and higher precision. Consequently, computational scientists are confronted by two parallel challenges: on one side, the design of efficient methods to interpret each of these data in their own right (gene expression signatures, protein markers, etc.) and, on the other side, realization of a novel, pressing request from the biological field to design methodologies that allow for these data to be interpreted as a whole, i.e. not only as the union of relevant molecules in each of these layers, but as a complex molecular signature containing proteins, mRNAs and miRNAs, all of which must be directly associated in the results of analyses that are able to capture inter-layers connections and complexity.ResultsWe address the latter of these two challenges by testing an integrated approach on a known cancer benchmark: the NCI-60 cell panel. Here, high-throughput screens for mRNA, miRNA and proteins are jointly analyzed using factor analysis, combined with linear discriminant analysis, to identify the molecular characteristics of cancer. Comparisons with separate (non-joint) analyses show that the proposed integrated approach can uncover deeper and more precise biological information. In particular, the integrated approach gives a more complete picture of the set of miRNAs identified and the Wnt pathway, which represents an important surrogate marker of melanoma progression. We further test the approach on a more challenging patient-dataset, for which we are able to identify clinically relevant markers.ConclusionsThe integration of multiple layers of omics can bring more information than analysis of single layers alone. Using and expanding the proposed integrated framework to integrate omic data from other molecular levels will allow researchers to uncover further systemic information. The application of this approach to a clinically challenging dataset shows its promising potential.

SKINOMICS: Transcriptional Profiling in Dermatology and Skin Biology.

Recent years witnessed the birth of bioinformatics technologies, which greatly advanced biological research. These ‘omics’ technologies address comprehensively the entire genome, transcriptome, proteome, microbiome etc. A large impetus in development of bioinformatics was the introduction of DNA microarrays for transcriptional profiling. Because of its accessibility, skin was among the first organs analyzed using DNA microarrays, and dermatology among the first medical disciplines to embrace the approach. Here, DNA microarray methodologies and their application in dermatology and skin biology are reviewed. The most studied disease has been, unsurprisingly, melanoma; markers of melanoma progression, metastatic potential and even melanoma markers in blood have been detected. The basal and squamous cell carcinomas have also been intensely studied. Psoriasis has been comprehensively explored using DNA microarrays, transcriptional changes correlated with genomic markers and several signaling pathways important in psoriasis have been identified. Atopic dermatitis, wound healing, keloids etc. have been analyzed using microarrays. Noninvasive skin sampling for microarray studies has been developed. Simultaneously, epidermal keratinocytes have been the subject of many skin biology studies because they respond to a rich variety of inflammatory and immunomodulating cytokines, hormones, vitamins, UV light, toxins and physical injury. The transcriptional changes occurring during epidermal differentiation and cornification have been identified and characterized. Recent studies identified the genes specifically expressed in human epidermal stem cells. As dermatology advances toward personalized medicine, microarrays and related ‘omics’ techniques will be directly applicable to the personalized dermatology practice of the future.

Abstract 381: Non-invasive histology for early detection of cutaneous melanoma and pigmented lesions in vivo

Abstract Rationale The diagnosis of melanoma is based on clinical identification followed by histopathologic confirmation. Surgical excision remains the mainstay for a suspicious lesion that will be evaluated for the morphological and cytological signatures of melanomas. However, in some patients such as those with atypical mole syndrome, multiple biopsies of each lesion can be burdensome. We have previously reported that imaging the distribution of eumelanin and pheomelanin can be used to detect melanomas from benign lesions (Matthews TE et al. Sci Transl Med Feb 23;3(71)). In this pre-clinical study we extend our investigation in vivo using nonlinear pump-probe microscopy. We assess cellular morphology and detect the expression of eumelanin and pheomelanin, the two forms of melanin found in skin as markers of melanoma progression. Methods Two melanoma cells lines (A2058; SK-MEL-28) were incubated in human skin dermis. Grafts were xenotransplanted onto SCID mice (n=13, A2058; n=6, SK-MEL-28; n=2 control) and imaged every 8-10-days for cancer progression and morphological changes. Pump-probe microscopy was performed concurrently with two other established laser scanning microscopy methods, multiphoton autofluorescence (MPAF) and reflectance confocal scanning laser microscopy (RCSLM). After 4-8 weeks the subjects were euthanized and the tumor excised for histological examination. Hematoxylin and eosin staining was performed to confirm the presence of the tumor and to correlate with the morphological findings after laser image acquisition. Results The in vivo pump-probe images of the cancer subjects showed an irregular distribution of the pigment, lacking the organized structure typical of skin. Pump-probe images of both melanoma cell lines indicated pigmentation that was either primarily eumelanin or a mixture of eumelanin and pheomelanin with marked spatial heterogeneity. Pigmentation was observed in the two control mice but localized on the basal cells with a well-organized cellular architecture. At the end of the cancer subjects’ life the histological examination showed atypical melanocytes mainly present as single cells in the dermal area. Hyperplasia was also present in the dermal compartment and in the dermal-epidermal junction of the skin. Conclusions The present work may open new avenues for the non-invasive detection of cellular and pigment lesions to prevent melanoma development and invasiveness. Such method can play a role in the diagnosis of melanoma in those patients with multiple lesions or in the areas of the body where the lesion is very exposed such as the face or neck and in ocular region. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 381. doi:1538-7445.AM2012-381

Use of Immunohistochemistry in the Diagnosis of Melanocytic Lesions: Applications and Pitfalls

The accurate diagnosis of melanocytic lesions is essential for the adequate clinical management of the patients. Besides the histopathologic examination, immunohistochemical studies are often used as an adjunct in distinguishing melanocytic lesions from tumors with different origin or between benign and malignant melanocytic lesions. In the first part of this article, we analyze data on currently used immunohistochemical markers, with special emphasis on their applicability to clinical practice, and underline their potential pitfalls. The pathogenesis of malignant transformation of melanocytes is not completely understood. Recent studies report that various melanoma progression markers are preferentially expressed in benign or malignant melanocytic lesions or show different expression in subsequent stages of tumor development. Furthermore, in recent years, emerging genetic studies suggest that there are distinctive patterns of chromosomal aberrations in different subtypes of melanoma that can be altered by newly developed targeted therapies. In the second part of our article, we will discuss the most significant progression markers in melanoma that can be detected by immunohistochemistry and their potential usefulness for diagnosis, prognosis, staging or as therapeutic targets.