Germline ATM variants predispose to melanoma: a joint analysis across the GenoMEL and MelaNostrum consortia.

PURPOSE: Ataxia-Telangiectasia Mutated (ATM) has been implicated in the risk of several cancers, but establishing a causal relationship is often challenging. Although ATM single-nucleotide polymorphisms have been linked to melanoma, few functional alleles have been identified. Therefore, ATM impact on melanoma predisposition is unclear. METHODS: From 22 American, Australian, and European sites, we collected 2,104 familial, multiple primary (MPM), and sporadic melanoma cases who underwent ATM genotyping via panel, exome, or genome sequencing, and compared the allele frequency (AF) of selected ATM variants classified as loss-of-function (LOF) and variants of uncertain significance (VUS) between this cohort and the gnomAD non-Finnish European (NFE) data set. RESULTS: LOF variants were more represented in our study cohort than in gnomAD NFE, both in all (AF = 0.005 and 0.002, OR = 2.6, 95% CI = 1.56-4.11, p < 0.01), and familial + MPM cases (AF = 0.0054 and 0.002, OR = 2.97, p < 0.01). Similarly, VUS were enriched in all (AF = 0.046 and 0.033, OR = 1.41, 95% CI = 1.6-5.09, p < 0.01) and familial + MPM cases (AF = 0.053 and 0.033, OR = 1.63, p < 0.01). In a case-control comparison of two centers that provided 1,446 controls, LOF and VUS were enriched in familial + MPM cases (p = 0.027, p = 0.018). CONCLUSION: This study, describing the largest multicenter melanoma cohort investigated for ATM germline variants, supports the role of ATM as a melanoma predisposition gene, with LOF variants suggesting a moderate-risk.

External validation of a prognostic model to predict survival of patients with sentinel node-negative melanoma.

BACKGROUND: Identifying patients with sentinel node-negative melanoma at high risk of recurrence or death is important. The European Organisation for Research and Treatment of Cancer (EORTC) recently developed a prognostic model including Breslow thickness, ulceration and site of the primary tumour. The aims of the present study were to validate this prognostic model externally and to assess whether it could be improved by adding other prognostic factors. METHODS: Patients with sentinel node-negative cutaneous melanoma were included in this retrospective single-institution study. The ß values of the EORTC prognostic model were used to predict recurrence-free survival and melanoma-specific survival. The predictive performance was assessed by discrimination (c-index) and calibration. Seeking to improve the performance of the model, additional variables were added to a Cox proportional hazards model. RESULTS: Some 4235 patients with sentinel node-negative cutaneous melanoma were included. The median follow-up time was 50 (i.q.r. 18·5-81·5) months. Recurrences and deaths from melanoma numbered 793 (18·7 per cent) and 456 (10·8 per cent) respectively. Validation of the EORTC model showed good calibration for both outcomes, and a c-index of 0·69. The c-index was only marginally improved to 0·71 when other significant prognostic factors (sex, age, tumour type, mitotic rate) were added. CONCLUSION: This study validated the EORTC prognostic model for recurrence-free and melanoma-specific survival of patients with negative sentinel nodes. The addition of other prognostic factors only improved the model marginally. The validated EORTC model could be used for personalizing follow-up and selecting high-risk patients for trials of adjuvant systemic therapy.

ANTECEDENTES: Es importante identificar a los pacientes con melanoma y ganglio centinela negativo con alto riesgo de recidiva o muerte. Con este fin, la European Organisation for Research and Treatment of Cancer (EORTC) ha desarrollado recientemente un modelo pronóstico que incluye el índice de Breslow, la presencia de úlcera y la localización del tumor primario. Los objetivos del presente estudio fueron efectuar la validación externa de este modelo pronóstico y evaluar si pudiera mejorarse agregando otros factores pronósticos. MÉTODOS: Estudio retrospectivo de una sola institución, en el que se incluyeron 4.235 pacientes con melanoma cutáneo y ganglio centinela negativo. La mediana de seguimiento fue de 50 meses (rango intercuartílico 18,5-81,5). Para predecir la supervivencia sin recidiva y la supervivencia específica para el melanoma se utilizaron los valores beta del modelo de pronóstico de la EORTC. La capacidad predictiva se evaluó mediante los índices de discriminación (índice c) y de calibración. Para mejorar el rendimiento de este modelo, se agregaron más variables utilizando un modelo de riesgos proporcionales de Cox. RESULTADOS: Las recidivas y muertes por melanoma fueron 793 (19%) y 456 (11%), respectivamente. La validación del modelo EORTC mostró una buena calibración para ambos resultados y un índice c de 0,69. El índice c sólo mejoró marginalmente a 0,71 cuando se agregaron otros factores pronósticos significativos (género, edad, tipo de tumor, índice mitótico). CONCLUSIÓN: La validación externa del modelo de pronóstico EORTC para la supervivencia sin recidiva y específica en pacientes con melanoma y ganglio centinela negativo fue satisfactoria. La adición de otros factores pronósticos solo mejoró marginalmente el modelo. El modelo validado de la EORTC podría utilizarse para personalizar las estrategias de seguimiento y seleccionar a pacientes de alto riesgo para ensayos con terapia sistémica adyuvante.

Incidence and relative survival of melanoma in children and adolescents in the Netherlands, 1989-2013.

BACKGROUND: Melanoma is rare in the first two decades of life. Trends in incidence differ across countries. OBJECTIVE: To describe incidence and relative survival of children and adolescents with melanoma in the Netherlands for children (0 through 11 years) and adolescents (12 through 19 years) separately. We hypothesized that adolescent melanoma increased in contrast to childhood melanoma, possibly due to a difference in cancer biology and sun exposure patterns. METHODS: Data on all patients of 0-19 years diagnosed between 1989 and 2013 with histologically confirmed cutaneous invasive melanoma were retrieved from the Netherlands Cancer Registry (NCR). Incidence trends were analysed with Joinpoint regression. Relative survival analysis was performed. RESULTS: Between 1989 and 2013, 80 children and 544 adolescents with melanoma were registered in the NCR. Median age at diagnosis was 17 years (IQR 15-18); the female-to-male ratio was 1.7 : 1 Statistically significant incidence trends were found in the older age group (12-19 years): an increasing incidence since 1991 [annual percentage change (APC) 3.2%, 95%CI 1.3-5.1] followed by a decrease from 2005 to 2013 (APC -4.9%, 95%CI -9.6-0.0). No incidence trends for childhood melanoma were observed (APC 0.3%, 95% CI -3.0-3.8). Relative survival at 1, 5 and 10 years was 98% (95% CI 97-99), 94% (95% CI 92-96) and 90% (95% CI 87-92), respectively. Survival was worse in males and higher Breslow thickness. CONCLUSIONS: Melanoma is very rare under the age of 12 with stable incidence rates. In comparison with childhood melanoma, melanomas in adolescents are more common with a decreasing trend in the past decade. Male sex and increasing Breslow thickness are associated with worse survival in paediatric melanoma patients.

Complete remission of skin lesions in a patient with subcorneal pustular dermatosis (Sneddon-Wilkinson disease) treated with antimyeloma therapy: association with disappearance of M-protein.

Subcorneal pustular dermatosis (SPD), or Sneddon-Wilkinson disease, is a rare pustular skin disease that follows a chronic relapsing course. A well-known association exists between SPD and IgA monoclonal gammopathy of undetermined significance (MGUS), which exists in up to 40% of cases. SPD has also been observed in patients with IgA myeloma. In SPD, direct and indirect immunofluorescence studies do not reveal in vivo bound IgA to the epithelial cell surface, in contrast to IgA pemphigus, which has similar clinicopathological features. Here we describe the case of a male patient with SPD and a concurrent IgA MGUS who had been treated with dapsone for 20 years with frequent relapses. Following development of multiple myeloma, the patient was treated with intensive antimyeloma treatment consisting of high-dose melphalan with autologous stem cell transplantation. This resulted in a complete remission of the myeloma with disappearance of the M-protein. In addition, a sustained remission of SPD was achieved without further treatment. Twenty-eight months after melphalan therapy the M-protein reappeared in the serum, and 2 months later SPD reappeared with histopathologically proven skin lesions at predilection sites. Presence and absence of skin lesions was found to correlate with the presence and absence of the M-protein in the serum. This is the first report of antimyeloma therapy inducing a long-lasting remission in SPD. The findings in this patient strongly suggest a causal role for circulating IgA antibodies in the pathogenesis of SPD. Antimyeloma treatment should be considered in patients with IgA MGUS-associated SPD refractory to other therapies.

Recommendations for treatment in folliculotropic mycosis fungoides: report of the Dutch Cutaneous Lymphoma Group.

BACKGROUND: Folliculotropic mycosis fungoides (FMF) is an aggressive variant of mycosis fungoides (MF) and generally less responsive to standard skin-directed therapies (SDTs). Recent studies distinguished indolent (early-stage FMF) and more aggressive (advanced-stage FMF) subgroups. The optimal treatment for both subgroups remains to be defined. OBJECTIVES: To evaluate initial treatment results in patients with early- and advanced-stage FMF. METHODS: A study was undertaken of 203 patients (84 early-stage, 102 advanced-stage, 17 extracutaneous FMF) included in the Dutch Cutaneous Lymphoma Registry between 1985 and 2014. Type and results of initial treatment were retrieved from the Dutch Registry. Main outcomes were complete remission (CR); sustained complete remission; partial remission (PR), > 50% improvement; and overall response (OR; CR + PR). RESULTS: Patients with early-stage FMF were treated with nonaggressive SDTs in 67 of 84 cases resulting, respectively, in CR and OR of 28% and 83% for monotherapy topical steroids, 0% and 83% for ultraviolet B (UVB), and 30% and 88% for psoralen plus ultraviolet A (PUVA). In patients with advanced-stage FMF these SDTs were less effective (combined CR and OR 10% and 52%, respectively). In patients with advanced-stage FMF local radiotherapy (CR 63%; OR 100%), total skin electron beam irradiation (CR 59%; OR 100%) and PUVA combined with local radiotherapy (CR 5%, OR 75%) were most effective. CONCLUSIONS: The results of the present study demonstrate that not all patients with FMF should be treated aggressively. Patients with early-stage FMF may benefit very well from standard SDTs also used in early-stage classic MF and have an excellent prognosis.

Rothmund-Thomson syndrome and osteoma cutis in a patient previously diagnosed as COPS syndrome.

We present a patient with poikiloderma, severe osteoporosis and a mild intellectual disability. At the age of 9 years, this patient was proposed to suffer from a novel disease entity designated as calcinosis cutis, osteoma cutis, poikiloderma and skeletal abnormalities (COPS) syndrome. At the age of 35, he was diagnosed with Hodgkin's lymphoma. Recently, biallelic pathogenic variants in the RECQL4 gene were detected (c.1048_1049delAG and c.1391-1G>A), confirming a diagnosis of Rothmund-Thomson syndrome (RTS). In the brother of this patient, who had a milder phenotype, a similar diagnosis was made. CONCLUSION: We conclude that COPS syndrome never existed as a separate syndrome entity. Instead, osteoma cutis may be regarded as a novel feature of RTS, whereas mild intellectual disability and lymphoma may be underreported parts of the phenotype. What is new: • Osteoma cutis was not a known feature in Rothmund-Thomson patients. • Intellectual disability may be considered a rare feature in RTS; more study is needed. What is known: • RTS is a well-described syndrome caused by mutations in the RECQL4 gene. • Patients with RTS frequently show chromosomal abnormalities like, e.g. mosaic trisomy 8.

Attitudes toward genetic testing, family planning and preimplantation genetic testing in families with a germline CDKN2A pathogenic variant.

Individuals with a germline CDKN2A pathogenic variant (PV) have a highly increased life time risk of melanoma and pancreatic cancer. This cross-sectional study assessed the attitudes among toward genetic testing, family planning, and preimplantation genetic testing (PGT) in confirmed CDKN2A PV carriers and individuals with a 50% risk of the PV (at-risk carriers) using of a one-time questionnaire.A total of 537 individuals were screened for eligibility, of whom 208 of 366 (57%) confirmed carriers (56% female, median age 54 years [IQR 46-63]) and 39 of 171 (23%) at-risk carriers (59% female, median age of 26 years [IQR 22-32]) participated in the study. Primary motivations for genetic testing were to gain control over their personal and children's cancer risk, as well as increasing cancer surveillance practices. In contrast, concerns about obtaining a mortgage and life insurance were frequently cited as reasons for postponing genetic testing. Family planning decisions remained largely unaffected in both confirmed and at-risk carriers; however, the majority of confirmed carriers were still unaware of their familial or personal cancer risk when starting a family. More than 60% of the participants were unfamiliar with PGT and only a minority (19% of confirmed carriers and 10% of at-risk carriers) would be open to considering PGT as a reproductive option. This study found different attitudes toward genetic testing, family planning, and PGT among individuals affected by the CDKN2A PV. Understanding these different attitudes can help clinicians to address the complexities surrounding these issues, especially for younger individuals facing difficult decisions about the timing of genetic testing, family planning, and the potential use of assisted reproductive options.

Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia.

Sorghum production is seriously threatened by the root parasitic weeds (RPWs) Striga hermonthica and Striga asiatica in sub-Saharan Africa. Research has shown that Striga control depends on eliminating its seed reserves in soil. Several species of the genus Fusarium (Nectriaceae, Hypocreales), which have been isolated from diseased Striga plants have proven to be highly pathogenic to all developmental stages of these RPWs. In the present study 439 isolates of Fusarium spp. were found associated with soils from Sorghum growing fields, Sorghum rhizosphere, or as endophytes with Sorghum roots and seeds, or as endophytes of Striga stems and seeds. Based on multi-locus phylogenies of combinations of CaM, tef1, rpb1 and rpb2 alignments, and morphological characteristics, 42 species were identified, including three species that are newly described, namely F. extenuatum and F. tangerinum from Sorghum soils, and F. pentaseptatum from seed of Striga hermonthica. Using a previously published AFLP-derived marker that is specific to detect isolates of F. oxysporum f.sp. strigae, an effective soil-borne biocontrol agent against Striga, we also detected the gene in several other Fusarium species. As these isolates were all associated with the Striga/Sorghum pathosystem, the possibility of horizontal gene transfer among these fusaria will be of interest to further investigate in future. Citation: Lombard L, van Doorn R, Groenewald JZ, Tessema T, Kuramae EE, Etolo DW, Raaijmakers JM, Crous PW (2022). Fusarium diversity associated with the Sorghum-Striga interaction in Ethiopia. Fungal Systematics and Evolution 10: 177-215. doi: 10.3114/fuse.2022.10.08.

The Genera of Fungi - G6: Arthrographis, Kramasamuha, Melnikomyces, Thysanorea, and Verruconis.

The Genera of Fungi series, of which this is the sixth contribution, links type species of fungal genera to their morphology and DNA sequence data. Five genera of microfungi are treated in this study, with new species introduced in Arthrographis, Melnikomyces, and Verruconis. The genus Thysanorea is emended and two new species and nine combinations are proposed. Kramasamuha sibika, the type species of the genus, is provided with DNA sequence data for first time and shown to be a member of Helminthosphaeriaceae (Sordariomycetes). Aureoconidiella is introduced as a new genus representing a new lineage in the Dothideomycetes.

Robust detection and identification of multiple oomycetes and fungi in environmental samples by using a novel cleavable padlock probe-based ligation detection assay.

Simultaneous detection and identification of multiple pathogenic microorganisms in complex environmental samples are required in numerous diagnostic fields. Here, we describe the development of a novel, background-free ligation detection (LD) system using a single compound detector probe per target. The detector probes used, referred to as padlock probes (PLPs), are long oligonucleotides containing asymmetric target complementary regions at both their 5' and 3' ends which confer extremely specific target detection. Probes also incorporate a desthiobiotin moiety and an internal endonuclease IV cleavage site. DNA samples are PCR amplified, and the resulting products serve as potential targets for PLP ligation. Upon perfect target hybridization, the PLPs are circularized via enzymatic ligation, captured, and cleaved, allowing only the originally ligated PLPs to be visualized on a universal microarray. Unlike previous procedures, the probes themselves are not amplified, thereby allowing a simple PLP cleavage to yield a background-free assay. We designed and tested nine PLPs targeting several oomycetes and fungi. All of the probes specifically detected their corresponding targets and provided perfect discrimination against closely related nontarget organisms, yielding an assay sensitivity of 1 pg genomic DNA and a dynamic detection range of 10(4). A practical demonstration with samples collected from horticultural water circulation systems was performed to test the robustness of the newly developed multiplex assay. This novel LD system enables highly specific detection and identification of multiple pathogens over a wide range of target concentrations and should be easily adaptable to a variety of applications in environmental microbiology.

Accurate quantification of microorganisms in PCR-inhibiting environmental DNA extracts by a novel internal amplification control approach using Biotrove OpenArrays.

PCR-based detection assays are prone to inhibition by substances present in environmental samples, thereby potentially leading to inaccurate target quantification or false-negative results. Internal amplification controls (IACs) have been developed to help alleviate this problem but are generally applied in a single concentration, thereby yielding less-than-optimal results across the wide range of microbial gene target concentrations possible in environmental samples (J. Hoorfar, B. Malorny, A. Abdulmawjood, N. Cook, M. Wagner, and P. Fach, J. Clin. Microbiol. 42:1863-1868, 2004). Increasing the number of IACs for each quantitative PCR (qPCR) sample individually, however, typically reduces sensitivity and, more importantly, the reliability of quantification. Fortunately, current advances in high-throughput qPCR platforms offer the possibility of multiple reactions for a single sample simultaneously, thereby allowing the implementation of more than one IAC concentration per sample. Here, we describe the development of a novel IAC approach that is specifically designed for the state-of-the-art Biotrove OpenArray platform. Different IAC targets were applied at a range of concentrations, yielding a calibration IAC curve for each individual DNA sample. The developed IACs were optimized, tested, and validated by using more than 5,000 unique qPCR amplifications, allowing accurate quantification of microorganisms when applied to soil DNA extracts containing various levels of PCR-inhibiting compounds. To our knowledge, this is the first study using a suite of IACs at different target concentrations to monitor PCR inhibition across a wide target range, thereby allowing reliable and accurate quantification of microorganisms in PCR-inhibiting DNA extracts. The developed IAC is ideally suited for high-throughput screenings of, for example, ecological and agricultural samples on next-generation qPCR platforms.