Concordance of somatic mutation profiles (BRAF,NRAS, and TERT) and tumoral PD-L1 in matched primary cutaneous and metastatic melanoma samples

Genetic Concordance in Primary Cutaneous Melanoma and Matched Metastasis: A Systematic Review and Meta-Analysis

Studying primary melanoma and its corresponding metastasis has twofold benefits. Firstly, to better understand tumor biology, and secondly, to determine which sample should be examined in assessing drug targets. This study systematically analyzed all the literature on primary melanoma and its matched metastasis. Following PRISMA guidelines, we searched multiple medical databases for relevant publications from January 2000 to December 2022, assessed the quality of the primary-level studies using the QUIPS tool, and summarized the concordance rate of the most reported genes using the random-effects model. Finally, we evaluated the inter-study heterogeneity using the subgroup analysis. Thirty-one studies investigated the concordance of BRAF and NRAS in 1220 and 629 patients, respectively. The pooled concordance rate was 89.4% [95% CI: 84.5; 93.5] for BRAF and 97.8% [95% CI: 95.8; 99.4] for NRAS. When high-quality studies were considered, only BRAF mutation status consistency increased. Five studies reported the concordance status of c-KIT (93%, 44 patients) and TERT promoter (64%, 53 patients). Lastly, three studies analyzed the concordance of cancer genes involved in the signaling pathways, apoptosis, and proliferation, such as CDKN2A (25%, four patients), TP53 (44%, nine patients), and PIK3CA (20%, five patients). Our study found that the concordance of known drug targets (mainly BRAF) during melanoma progression is higher than in previous meta-analyses, likely due to advances in molecular techniques. Furthermore, significant heterogeneity exists in the genes involved in the melanoma genetic makeup; although our results are based on small patient samples, more research is necessary for validation.

pTERT C250T mutation: A potential biomarker of poor prognosis in metastatic melanoma

Melanoma is the most aggressive form of skin cancer and the leading cause of death from cutaneous tumors. Several studies have associated alterations in the TERT promoter region (pTERT) with gene overexpression, aggressiveness and poor prognosis of the disease. The aim of this study was to clarify the role of pTERT molecular status in paired samples of primary melanoma and metastasis using tissue and plasma to establish a correlation with disease progression and survival. A total of 88 FFPE tissue samples from 53 patients with advanced melanoma were analyzed. Of these, 35 had paired samples. We also examined cfDNA samples from plasma of 25 patients. We detected a good correlation between primary tumors and metastases in pTERT mutation and methylation status. We were also able to identify pTERT mutations in plasma samples that correlated with mutational status in tissue samples. Interestingly, the C250T mutation was associated with worse survival and higher TERT mRNA expression, compared to the other most common mutation: C228T. In addition, hyper-methylation of the promoter region seems to be related to the progression of pTERT wild type (WT) patients. These results suggest that TERT gene alterations plays an important role during tumor progression, with the detection of the C250T mutation in tissue and plasma as a potential biomarker of poor prognosis in patients with advanced melanoma.

Identification of Three Genes Associated with Metastasis in Melanoma and Construction of a Predictive Model: A Multiracial Identification

The aim of this study was to identify hub genes associated with metastasis and prognosis in melanoma. Weighted gene coexpression network analysis (WGCNA) was performed to screen and identify hub genes. ROC and K-M analyses were used to verify the hub genes in the internal and external data sets. The risk score model and nomogram model were constructed based on the IHC result. Through WGCNA, the three hub genes, SNRPD2, SNRPD3, and EIF4A3, were identified. In the external data set, the hub genes identified were associated with the worse prognosis (TCGA, SNRPD2, $P\le 0.02$ ; SNRPD3, $P=0.12$ ; EIF4A3, $P=0.11$ ; GSE65904, SNRPD2, $P=0.04$ ; SNRPD3, $P=0.10$ ; EIF4A3, $P<0.01$ ; GSE19234, SNRPD2, $P<0.01$ ; SNRPD3, $P<0.01$ ; EIF4A3, $P<0.01$ ). In the GSE8401, we found that the hub genes were highly expressed in the metastasis compared with the nonmetastasis group (SNRPD2, $988.5\pm 47.83$ vs. $738.4\pm 35.35$ , $P<0.01$ ; SNRPD3, $502.7\pm 25.7$ vs. $416.4\pm 23.88$ , $P=0.02$ ; EIF4A3, $567.6\pm 19.56$ vs. $495.2\pm 21.1$ , $P=0.01$ ). Moreover, the hub genes were identified by the IHC in our data set. The result was similar with the external data set. The hub genes could predict the metastasis and prognosis in the Chinese MM patients. Finally, the GSEA and Pearson analysis demonstrated that the SNRPD2 was associated with the immunotherapy. The three hub genes were identified and validated in MM patients in external and internal data sets. The risk factor model was constructed and verified as a powerful model to predict metastasis and prognosis in MM patients.

Epigenetic modification and BRAF gene mutation in thyroid carcinoma

Thyroid cancer remains the most prevailing endocrine malignancy, and a progressively increasing incidence rate has been observed in recent years, with 95% of thyroid cancer represented by differentiated thyroid carcinomas. The genetics and epigenetics of thyroid cancer are gradually increasing, and gene mutations and methylation changes play an important roles in its occurrence and development. Although the role of RAS and BRAF mutations in thyroid cancer have been partially clarified,but the pathogenesis and molecular mechanisms of thyroid cancer remain to be elucidated. Epigenetic modification refer to genetic modification that does not change the DNA sequence of a gene but causes heritable phenotypic changes in its expression. Epigenetic modification mainly includes four aspects: DNA methylation, chromatin remodelling, noncoding RNA regulation, and histone modification. This article reviews the importance of thyroid cancer epigenetic modification and BRAF gene mutation in the treatment of thyroid cancer.

RTP4 is a novel prognosis-related hub gene in cutaneous melanoma

OBJECTIVE

Melanoma accounts for 80% of skin cancer deaths. The pathogenesis of melanoma is regulated by gene networks. Thus, we aimed here to identify gene networks and hub genes associated with melanoma and to further identify their underlying mechanisms.

METHODS

GTEx (normal skin) and TCGA (melanoma tumor) RNA-seq datasets were employed for this purpose. We conducted weighted gene co-expression network analysis (WGCNA) to identify key modules and hub genes associated with melanoma. Log-rank analysis and multivariate Cox model analysis were performed to identify prognosis genes, which were validated using two independent melanoma datasets. We also evaluated the correlation between prognostic gene and immune cell infiltration.

RESULTS

The blue module was the most relevant for melanoma and was thus considered the key module. Intersecting genes were identified between this module and differentially expressed genes (DEGs). Finally, 72 genes were identified and verified as hub genes using the Oncomine database. Log-rank analysis and multivariate Cox model analysis identified 13 genes that were associated with the prognosis of the metastatic melanoma group, and RTP4 was validated as a prognostic gene using two independent melanoma datasets. RTP4 was not previously associated with melanoma. When we evaluated the correlation between prognostic gene and immune cell infiltration, we discovered that RTP4 was associated with immune cell infiltration. Further, RTP4 was significantly associated with genes encoding components of immune checkpoints (PDCD1, TIM-3, and LAG3).

CONCLUSIONS

RTP4 is a novel prognosis-related hub gene in cutaneous melanoma. The novel gene RTP4 identified here will facilitate the exploration of the molecular mechanism of the pathogenesis and progression of melanoma and the discovery of potential new target for drug therapy.

Discordance of immunotherapy response predictive biomarkers between primary lesions and paired metastases in tumours: A systematic review and meta-analysis

Background

Several biomarkers predict the efficacy of immunotherapy, which is essential for selecting patients who would potentially benefit. Discordant status of these biomarkers between primary tumours and paired metastases has been increasingly revealed. We aimed to comprehensively summarize the incidence of this phenomenon.

Methods

Databases were searched to identify studies reporting primary-to-metastatic conversion of biomarkers, including programmed death ligand-1 (PD-L1), programmed cell death protein-1 (PD-1), PD-L2, tumour-infiltrating lymphocyte (TIL), tumour mutational burden (TMB), and microsatellite instability (MSI).

Findings

56 studies with 2739 patients were included. The pooled discordance rate of PD-L1 was 22%. The percentage of PD-L1 changed from positive to negative was 41%, whereas that from negative to positive was 16%. The discordance rate for PD-1 and PD-L2 was 26% and 22%, respectively. TIL level was found with a discordance rate of 39%, and changes from high to low (50%) occurred more than that from low to high (16%). No significant difference in TMB was observed between two sites in most studies. MSI status discordance was found in 6% patients, with a percentage of 9% from MSI-high to microsatellite instable (MSS) and 0% from MSS to MSI-high.

Interpretation

Our study demonstrates that PD-L1, PD-1, PD-L2, and TIL level had high frequency of discordance, while TMB and MSI status were less likely to change between primary tumours and paired metastases. Therefore, evaluating those frequently altered biomarkers of both primary and metastatic tumours is strongly recommended for precise clinical decision of immune checkpoint treatment.

Fund

The National Natural Science Foundation of China (81872152).

TERT amplification but not activation of canonical Wnt/β-catenin pathway is involved in acral lentiginous melanoma progression to metastasis

Acral lentiginous melanoma (ALM) is a rare tumor that occurs on non-sun exposed skin areas of the hands and feet. Reports suggest that ALM exhibits poor prognosis, although mechanisms driving this remain poorly understood. Alterations in TERT and the Wnt/β-catenin (Wnt) pathway have been suggested to correlate with prognosis of ALM. Thus, immunohistochemical expression of β-catenin and LEF1 along with TERT amplification by FISH was investigated in 34 primary ALMs, 20 metastatic ALMs, 10 primary non-ALMs, and 15 acral nevi. Foot/toe was the most common primary tumor location (85%) for ALM. TERT amplification was detected in 6 of 28 (21.4%) primary ALM, 2 of 8 (25%) primary non-ALM, and 8 of 18 (44.4%) metastatic ALM, the latter showing significantly higher frequency compared with primary melanomas (P = 0.043). Most metastatic ALMs positive for TERT amplification lacked BRAF V600E (87.5%). Cytoplasmic and nonnuclear expression of β-catenin was variably detected in all cases. Metastatic ALM revealed lower expression of β-catenin compared with primary ALM (P = 0.017). No differences in LEF1 expression were detected among the groups; however, acral nevi showed decreased labeling with dermal descent, in contrast to melanoma. No molecular-genetic alteration correlated with prognosis. TERT amplification by FISH is a frequent finding in primary ALM and appears to increase in metastatic tumors, suggesting a role in tumor progression to metastasis. Although TERT amplification has been reported to be infrequent in primary non-ALM, it showed comparable frequency with ALM in our series. Our immunohistochemical findings are not fully supportive of activation of either canonical or noncanonical Wnt cascades in ALM. TERT amplification by FISH and LEF1 immunohistochemistry may help in the differential diagnosis between primary ALM and acral nevus. TERT amplification appears to be a promising target for therapy in patients with metastatic ALM.

TERT and TERT promoter in melanocytic neoplasms: Current concepts in pathogenesis, diagnosis, and prognosis

BACKGROUND AND OBJECTIVE

Located on chromosome locus 5p15.33, telomerase reverse transcriptase (TERT or hTERT) encodes the catalytic subunit of telomerase which permits lengthening and preservation of telomeres following mitosis. Mutations in TERT promoter (TERT-p) upregulate expression of TERT, allowing survival of malignant cells and tumor progression in wide variety of malignancies including melanoma. The objective of this review is to examine the roles of TERT and TERT-p in the pathogenesis, diagnosis, and prognostication of cutaneous melanoma.

METHODS

All studies of TERT or TERT-p in cutaneous melanocytic neoplasms with the following inclusion criteria were reviewed: publication date between 2010 and 2019, English language, and series of ≥3 cases were reviewed for evidence supporting the role of TERT in pathogenesis, diagnosis, and prognosis. Studies with <3 cases or focused primarily on mucosal or uveal melanocytic tumors were excluded.

RESULTS AND CONCLUSION

TERT-p mutations are frequent in chronic and non-chronic sun damage melanoma and correlate with adverse prognosis, inform pathogenesis, and may provide diagnostic support. While TERT-p mutations are uncommon in acral melanoma, TERT copy number gains and gene amplification predict reduced survival. Among atypical spitzoid neoplasms, TERT-p mutations identify biologically aggressive tumors and support the diagnosis of spitzoid melanoma. TERT-p methylation may have prognostic value in pediatric conventional melanoma and drive tumorigenesis in melanoma arising within congenital nevi. Finally, TERT-p mutations may aid in the differentiation of recurrent nevi from recurrent melanoma.

PD-L1 Detection-Pearls and Pitfalls Associated With Current Methodologies Focusing on Entities Relevant to Dermatopathology

PD-L1 is a transmembrane glycoprotein with an extracellular as well as an intracellular cytoplasmic domain. Physiologically, it plays a pivotal role in regulating T-cell activation and tolerance. Many tumor cells have exploited this regulatory mechanism by overexpressing PD-L1 in an effort to escape immunologic surveillance. In this review, we parse the literature regarding the prognostic value of tumoral PD-L1 expression before discussing the various methodologies as well as the pearls and pitfalls associated with each for predicting response to anti-PD-1/PD-L1 therapies. Special attention is given to cutaneous entities in which PD-L1 expression has been documented with an emphasis on cutaneous malignancies that have seen the broadest applications of anti-PD-L1/PD-1 therapies. Currently, immunohistochemistry is the method that is most commonly used for detection of PD-L1. However, with the wide array of immunohistochemistry protocols and staining platforms available in the market, there seems to be different cutoffs not just for different entities but also for the same entity. This review is an attempt to address the need for standardization and validation of existing protocols for PD-L1 detection.

Association of combined PD-L1 expression and tumour-infiltrating lymphocyte features with survival and treatment outcomes in patients with metastatic melanoma

BACKGROUND

Recent advances obtained with immune checkpoint inhibitors (ICIs) targeting the programmed cell death-1 (PD-1) protein have significantly improved the outcome of patients with metastatic melanoma. The PD-L1 expression in tumour cells as detected by immunohistochemistry is a predictive biomarker in some solid tumours, but appears insufficient as prognostic or predictive factor of response to ICIs in metastatic melanomas.

OBJECTIVES

We investigated whether the presence and the features of pretreatment CD8⁺ tumour-infiltrating T lymphocytes (TILs) could be a complementary prognostic or predictive biomarker in patients with metastatic melanoma.

METHODS

In this retrospective study, we evaluated the association of PD-L1 expression ≥5% of tumour cells combined with TIL features (CD8, CD28, Ki67) with the overall survival (OS) among 51 patients treated with ICIs and 54 patients treated with other treatment options (non-ICIs).

RESULTS

PD-L1 positivity was observed in 33% and 39% of primary melanomas and matched metastases, respectively, with, however, poor concordance between the primary and the matched metastatic site (κ = 0.283). No significant association was noted between PD-L1 expression and CD8⁺ TIL profile analysed as single markers and OS or response to immunotherapy. Instead, their combined analysis in primary melanoma samples showed that the PD-L1-/CD8⁺ status was significantly associated with prolonged OS in the whole population (P = 0.04) and in the subgroup treated with non-ICIs (P = 0.009). Conversely, the PD-L1+/CD8⁺ status was a good prognostic factor in patients treated with ICIs (P = 0.022), whereas was significantly associated with poor prognosis in patients treated with non-ICIs (P = 0.014). While the expression of CD28 was not related to outcome, the Ki67 expression was significantly associated with poor OS in the subgroup CD8⁺ TIL+/PD-L1- (P = 0.02).

CONCLUSIONS

The pretreatment combination of PD-L1 expression with the level of CD8⁺ TILs could better assess OS and predict therapeutic response of patients with metastatic melanoma treated by either immunotherapy or other treatment regimens.

Coexpression network analysis identified that plakophilin 1 is associated with the metastasis in human melanoma

BACKGROUND AND AIMS

Malignant melanoma is a fatal cancer with high metastatic characteristics. Approximately 80% of skin cancer deaths are caused by metastatic melanoma. It has been established that the metastatic ability of melanoma is regulated by an intricate gene interconnection network. Thus, the aim of this study was to identify and validate hub genes associated with metastatic melanoma and to further illustrate its potential mechanisms.

METHODS

The method of weighted gene coexpression network analysis (WGCNA) was applied to explore potential regulatory targets and investigate the relationship between the key module and hub genes associated with the metastasis ability of melanoma.

RESULTS

In the turquoise module, 26 hub genes were initially selected, and 6 of them were identified as "real" hub genes with high connectivity in the protein-protein interaction network. In terms of validation, PKP1 had the highest correlation with metastasis among all the "real" hub genes. Data obtained from the GEPIA database and the Gene Expression Omnibus database showed a lower expression of PKP1 in melanoma tissues compared to normal skin tissues. The results also showed that PKP1 was downregulated in metastatic melanomas (n = 367) compared with primary melanomas (n = 103) in The Cancer Genome Atlas (TCGA) database (n = 470). Furthermore, an ROC curve showed that PKP1 expression had good power in the diagnostics of both primary melanoma (p =  5.30e-06, AUC = 0.8) and metastatic melanoma (p =  1.13e-10, AUC = 0.925). We also found that PKP1 could distinguish low- and high-grade of metastatic melanomas and was associated with inflammatory melanoma. Moreover, in a tumor-bearing mouse model, melanoma tissues also showed lower mRNA expression of PKP1 than the adjacent normal skin. Finally, Gene Set Enrichment Analysis indicated that the calcium signaling was significantly enriched in metastatic melanoma with highly expressed PKP1.

CONCLUSIONS

PKP1 was identified as a new potential tumor suppressor in human melanoma, likely through regulating calcium signaling pathways.