Plasma thymidine kinase activity (TKa) as a novel prognostic biomarker in metastatic melanoma

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Background: In the recent decade, new effective immunotherapies and targeted therapies have emerged for the treatment of disseminated melanoma. However, a considerable fraction of patients does not respond or get lasting effects and the treatments also have significant side effects. Biomarkers can contribute with more knowledge on prognosis and the efficacy of these therapies in different patients. In other cancer types, the plasma activity of the enzyme thymidine kinase (TKa), has been demonstrated as a marker of tumor stage and prognosis. The TK enzyme is part of a reaction chain to introduce thymidine into the DNA strand. TK thereby has a key function in DNA-synthesis, -repair and cell division. Dividing cells release TK during mitotic exit and TK can thus be detected in the blood. This study is the first to investigate plasma TKa as a potential biomarker in melanoma patients. Methods: Plasma samples were collected within five days prior to treatment start in patients with unresectable metastatic cutaneous melanoma, treated with immunotherapy (anti-CTLA-4 and/or anti-PD-1) or targeted therapy (BRAF±MEK inhibitors). Plasma TKa levels were determined using the DiviTum TKa ELISA assay (Biovica, Sweden). TKa levels were correlated with the patients’ baseline criteria, response rate (RR), progression free survival (PFS) and overall survival (OS). Results: Among the 124 study patients, the median TKa was 50 Du/L (range < 20-3491 Du/L). Significantly higher plasma TKa levels were found in patients with ECOG performance status ≥1 vs. 0-1 ( P< 0.001), M1c-d vs. M1a-b disease ( P< 0.001), ≥3 vs. 1-2 affected organs ( P= 0.002) or elevated vs. non-elevated LDH ( P< 0.001). In the patients treated with immunotherapy (n = 86) the RR was 63.2% vs. 37.9% in those with low ( < 60 Du/L) vs. high TKa ( P= 0.024). The median PFS and OS was 19.9 and > 60 months in those with low TKa vs. 12.6 and 18.5 months in those with high TKa (HR for PFS: 1.73 (95% CI, 1.01-2.97), P= 0.044 and HR for OS: 2.16 (95% CI, 1.17-3.98), P= 0.011). In the patients treated with BRAF±MEK inhibitor (n = 38) a similar trend was observed, with shorter PFS and OS in those with high TKa, but the differences were not statistically significant. Conclusions: In this first study on plasma TKa in melanoma patients, high pretreatment TKa was significantly associated with poor baseline factors and poor response and survival in immunotherapy treated patients. Currently, plasma LDH is the only non-clinical factor that is routinely used as a prognostic marker in melanoma. Several other candidate markers have been described, such as PD-L1 tumor immunohistochemistry, tumor mutational burden, gut microbiome and circulating tumor DNA. Compared to these assays, TKa measured with DiviTum is a simpler, ELISA based test for a single plasma marker. TKa is hence a novel and interesting marker in melanoma and should be further studied to define its role as a prognostic and predictive marker in this disease.

MC1R variants and cutaneous melanoma risk according to histological type, body site, and Breslow thickness: a pooled analysis from the M-SKIP project

Little is known on whether melanocortin 1 receptor (MC1R) associated cutaneous melanoma (CM) risk varies depending on histological subtype and body site, and whether tumour thickness at diagnosis (the most important prognostic factor for CM patients) differs between MC1R variant carriers and wild-type individuals. We studied the association between MC1R variants and CM risk by histological subtype, body site, and Breslow thickness, using the database of the M-SKIP project. We pooled individual data from 15 case-control studies conducted during 2005-2015 in Europe and the USA. Study-specific, multi-adjusted odds ratios were pooled into summary odds ratios (SOR) and 95% confidence intervals (CI) using random-effects models. Six thousand eight hundred ninety-one CM cases and 5555 controls were included. CM risk was increased among MC1R variant carriers vs. wild-type individuals. The increase in risk was comparable across histological subtypes (SOR for any variant vs. wild-type ranged between 1.57 and 1.70, always statistical significant) except acral lentiginous melanoma (ALM), for which no association emerged; and slightly greater on chronically (1.74, 95% CI 1.47-2.07) than intermittently (1.55, 95% CI 1.34-1.78) sun-exposed skin. CM risk was greater for those carrying 'R' vs. 'r' variants; correlated with the number of variants; and was more evident among individuals not showing the red hair colour phenotype. Breslow thickness was not associated with MC1R status. MC1R variants were associated with an increased risk of CM of any histological subtype (except ALM) and occurring on both chronically and intermittently sun-exposed skin.

MC1R variants in childhood and adolescent melanoma: a retrospective pooled analysis of a multicentre cohort

BACKGROUND

Germline variants in the melanocortin 1 receptor gene (MC1R) might increase the risk of childhood and adolescent melanoma, but a clear conclusion is challenging because of the low number of studies and cases. We assessed the association of MC1R variants with childhood and adolescent melanoma in a large study comparing the prevalence of MC1R variants in child or adolescent patients with melanoma to that in adult patients with melanoma and in healthy adult controls.

METHODS

In this retrospective pooled analysis, we used the M-SKIP Project, the Italian Melanoma Intergroup, and other European groups (with participants from Australia, Canada, France, Greece, Italy, the Netherlands, Serbia, Spain, Sweden, Turkey, and the USA) to assemble an international multicentre cohort. We gathered phenotypic and genetic data from children or adolescents diagnosed with sporadic single-primary cutaneous melanoma at age 20 years or younger, adult patients with sporadic single-primary cutaneous melanoma diagnosed at age 35 years or older, and healthy adult individuals as controls. We calculated odds ratios (ORs) for childhood and adolescent melanoma associated with MC1R variants by multivariable logistic regression. Subgroup analysis was done for children aged 18 or younger and 14 years or younger.

FINDINGS

We analysed data from 233 young patients, 932 adult patients, and 932 healthy adult controls. Children and adolescents had higher odds of carrying MC1R r variants than did adult patients (OR 1·54, 95% CI 1·02-2·33), including when analysis was restricted to patients aged 18 years or younger (1·80, 1·06-3·07). All investigated variants, except Arg160Trp, tended, to varying degrees, to have higher frequencies in young patients than in adult patients, with significantly higher frequencies found for Val60Leu (OR 1·60, 95% CI 1·05-2·44; p=0·04) and Asp294His (2·15, 1·05-4·40; p=0·04). Compared with those of healthy controls, young patients with melanoma had significantly higher frequencies of any MC1R variants.

INTERPRETATION

Our pooled analysis of MC1R genetic data of young patients with melanoma showed that MC1R r variants were more prevalent in childhood and adolescent melanoma than in adult melanoma, especially in patients aged 18 years or younger. Our findings support the role of MC1R in childhood and adolescent melanoma susceptibility, with a potential clinical relevance for developing early melanoma detection and preventive strategies.

FUNDING

SPD-Pilot/Project-Award-2015; AIRC-MFAG-11831.

Abstract A38: Role of MC1R variants in childhood and adolescent melanoma

Cutaneous melanoma (CM) is rare in children, representing 1-3% of all paediatric malignancies and occurring at a frequency of 0.3-0.4% before puberty. MC1R is a key gene for skin pigmentation and is highly polymorphic in Caucasians. MC1R gene variants are associated with CM in different populations, and with congenital melanocytic naevi in children. The aim of this study is to evaluate whether the prevalence of MC1R variants differed among sporadic childhood and adolescent CM cases compared to adult patients.

Data were gathered through the M-SKIP project, an international pooled-analysis on MC1R variants, skin cancer and phenotypic characteristics. CM cases with information on age at diagnosis were selected from the M-SKIP dataset and divided into three groups: childhood (age ≤14 years, N=13), adolescent (age 15 to 18 years, N=52) and adult (age &gt; 18 years, N=7,696). The frequency of carrying specific MC1R variants as well as at least one MC1R variant were compared between childhood/adolescent and adult CM cases with Chi Square test.

The prevalence of any MC1R variant was lower in children (≤14 years, 63%) than in adolescents (15-18 years, 71%) or adults (&gt;18 years, 75%), although overall the difference was not statistically significant. A higher prevalence of the MC1R V92M variant was found in childhood and adolescent compared to adult CM cases (23% vs 5%, p=0.06). In contrast, the MC1R R151C variant was found less frequently in childhood and adolescent than in adult cases (9% vs 18%, p=0.06). Looking at rare variants in 5,983 cases with MC1R sequenced, 3 (9%) carriers of MC1R ins86A were found among 32 childhood and adolescent patients, while only 44 (1%) carriers of the same variant were found among 5,951 adult cases (p&lt;0.0001).

MC1R variants ins86A and V92M, but not R151C, may be specifically associated with childhood and adolescent melanoma. Further studies using a larger sample size is needed to validate the present findings.

Citation Format: Sara Raimondi, Sara Gandini, Peter A. Kanetsky, Veronica Hoiom, Rajiv Kumar, Paola Ghiorzo, Tadeusz Debniak, Ricardo Fernandez de Misa, Giuseppe Palmieri, Jiali Han, Maria Teresa Landi, Terry Dwyer, Maria Concetta Fargnoli, Wojciech Branicki, Nelleke A. Gruis, Alexander Stratigos, Gloria Ribas, M. Laurin Council, Manfred Kayser, Philippe Autier, Jose Carlos García-Borrón, Julian Little, Julia Newton-Bishop, Francesco Sera, Eduardo Nagore. Role of MC1R variants in childhood and adolescent melanoma. [abstract]. In: Proceedings of the Thirteenth Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2014 Sep 27-Oct 1; New Orleans, LA. Philadelphia (PA): AACR; Can Prev Res 2015;8(10 Suppl): Abstract nr A38.

KIT, NRAS, BRAF, and PTEN alterations in acral lentiginous melanomas

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Background: Acral lentiginous melanoma (ALM) accounts for ~5% of all melanomas. ALMs are often located on palms, soles and under nails. Patients with ALM are significantly older at diagnosis and have a poorer prognosis than patients with other types of cutaneous melanoma. We analyzed a large series of ALMs from Swedish patients to better define the frequency of KIT, BRAF, NRAS, and PTEN mutations in ALM. The effect of mutation status on tumor and patients characteristics was also studied. Methods: A total of 77 primary ALMs and 8 paired metastases were analyzed. Laser capture microdissection was used to dissect tumor cells from formalin-fixed paraffin-embedded tissue. Tumors were screened for mutations in the KIT (exons 11, 13, 17 and 18), NRAS (exons 1 and 2), BRAF (exons 11 and 15) and PTEN (exons 1, 3-6, 10, 11 and 12) genes by direct sequencing. Results: There were 42 females and 35 males with a median age at diagnosis of 71 years. The most common location was the feet (60.5%), followed by subungual sites (34.2%). Overall, mutations in KIT, NRAS and BRAF were detected in 11.8%, 14.5% and 16.0% of the ALMs, respectively. In no case were KIT, NRAS and BRAF mutations detected in the same tumor. For 8 primary ALMs the corresponding metastases were available for analysis. In five metastases the same KIT (n=3) or BRAF (n=2) mutation was detected as in the primary ALMs, suggesting that the KIT and BRAF mutations had occurred before metastasis. BRAF and NRAS mutations were significantly more common in females (P=0.044). ALMs with NRAS and BRAF mutations were more commonly located on the feet compared with KIT mutated ALMs which were more frequent on subungual sites (P=0.041). Other clinicopathological features such as age at diagnosis, thickness, ulceration, histological subtype and Clark’s level showed no significant correlation with the mutation status. A subset of 25 tumors was evaluated for mutations in the PTEN tumor suppressor gene. One tumor was found to carry a nonsense mutation (W111X). To our knowledge, this is the first description of a PTEN mutation in ALM. Conclusions: Our results confirm the presence of KIT, NRAS and BRAF mutations in ALM. KIT, NRAS and BRAF mutation status associated significantly with anatomical site. PTEN mutations seem to be rare in ALMs.

BAP1: The first mutated gene causing familial uveal melanoma

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Background: Uveal melanoma (UM) is a rare malignancy with a poor prognosis. Familial predisposition to UM is rare and accounts for only a few percent of all cases. The genetic background of hereditary UM is unknown and the aim of our project was to identify susceptibility gene(s) for UM. Methods: We identified a family with hereditary predisposition for UM – the proband of which is a young female diagnosed with UM at age 16 who within 6 months developed liver metastases. We also identified two older paternal relatives who were diagnosed with UM at 39 and 44 years of age, respectively. We performed massively parallel sequencing using the Illumina Hiseq2000 technology on germline DNA from the proband, her parents and a healthy sibling. After QC and mapping against the human reference genome the average coverage across the exome was between 35 and 86 for the four sequenced samples. Results: Out of more than 260,000 single nucleotide variants (SNVs) and small insertion / deletion variants (indels), 51 gene variants were filtered out by being novel, shared by the affected proband and her father (considered an obligate mutation carrier), but not by the healthy mother, of predicted functional importance and /or located within strongly conserved regions. The strongest candidate among these was a loss of function-variant in the BAP1 gene, since BAP1 has been suggested as a tumor suppressor in several cancer-related syndromes, including cases of UM. The sequence data indicated an insertion of one base-pair in exon 3 of the BAP1 genecausing a frame-shift and subsequently a truncated protein lacking all its functional domains. The mutation was also present in UM tumor tissue from the two deceased paternal relatives and was found to segregate with the UM phenotype in the family. We also detected loss of heterozygosity in the tumor of the proband, supporting BAP1 as the causative gene in this family. Conclusions: The identification of BAP1 as the gene responsible for this syndrome is the first demonstration of a germline mutation causing UM. This enables us to identify and monitor risk individuals belonging to mutation positive families with predisposition to UM, and possibly other cancer syndromes. We are continuously screening other cases of familial UM for mutations in BAP1.