Anatomic position determines oncogenic specificity in melanoma.

Oncogenic alterations to DNA are not transforming in all cellular contexts1,2. This may be due to pre-existing transcriptional programmes in the cell of origin. Here we define anatomic position as a major determinant of why cells respond to specific oncogenes. Cutaneous melanoma arises throughout the body, whereas the acral subtype arises on the palms of the hands, soles of the feet or under the nails3. We sequenced the DNA of cutaneous and acral melanomas from a large cohort of human patients and found a specific enrichment for BRAF mutations in cutaneous melanoma and enrichment for CRKL amplifications in acral melanoma. We modelled these changes in transgenic zebrafish models and found that CRKL-driven tumours formed predominantly in the fins of the fish. The fins are the evolutionary precursors to tetrapod limbs, indicating that melanocytes in these acral locations may be uniquely susceptible to CRKL. RNA profiling of these fin and limb melanocytes, when compared with body melanocytes, revealed a positional identity gene programme typified by posterior HOX13 genes. This positional gene programme synergized with CRKL to amplify insulin-like growth factor (IGF) signalling and drive tumours at acral sites. Abrogation of this CRKL-driven programme eliminated the anatomic specificity of acral melanoma. These data suggest that the anatomic position of the cell of origin endows it with a unique transcriptional state that makes it susceptible to only certain oncogenic insults.

Wet and dry extremes reduce arthropod biomass independently of leaf phenology in the wet tropics.

Warming temperatures are increasing rainfall extremes, yet arthropod responses to climatic fluctuations remain poorly understood. Here, we used spatiotemporal variation in tropical montane climate as a natural experiment to compare the importance of biotic versus abiotic drivers in regulating arthropod biomass. We combined intensive field data on arthropods, leaf phenology and in situ weather across a 1700-3100 m elevation and rainfall gradient, along with desiccation-resistance experiments and multi-decadal modelling. We found limited support for biotic drivers with weak increases in some herbivorous taxa on shrubs with new leaves, but no landscape-scale effects of leaf phenology, which tracked light and cloud cover. Instead, rainfall explained extensive interannual variability with maximum biomass at intermediate rainfall (130 mm month-1 ) as both 3 months of high and low rainfall reduced arthropods by half. Based on 50 years of regional rainfall, our dynamic arthropod model predicted shifts in the timing of biomass maxima within cloud forests before plant communities transition to seasonally deciduous dry forests (mean annual rainfall 1000-2500 mm vs. <800 mm). Rainfall magnitude was the primary driver, but during high solar insolation, the 'drying power of air' (VPDmax ) reduced biomass within days contributing to drought related to the El Niño-Southern Oscillation (ENSO). Highlighting risks from drought, experiments demonstrated community-wide susceptibility to desiccation except for some caterpillars in which melanin-based coloration appeared to reduce the effects of evaporative drying. Overall, we provide multiple lines of evidence that several months of heavy rain or drought reduce arthropod biomass independently of deep-rooted plants with the potential to destabilize insectivore food webs.

El aumento de las temperaturas está incrementando los extremos de precipitación, pero las respuestas de los artrópodos a las fluctuaciones climáticas siguen siendo poco conocidas. Aquí, utilizamos la variación espaciotemporal en el clima montano tropical como un experimento natural para comparar la importancia de los factores bióticos versus abióticos en la regulación de la biomasa de artrópodos. Combinamos datos de campo intensivos de artrópodos, fenología de las hojas y clima in situ a lo largo de un gradiente altitudinal de 1700 a 3100 m y un gradiente de precipitación, junto con experimentos de resistencia a la desecación y modelos multi-decenales. Encontramos evidencia limitada para los factores bióticos con aumentos débiles en algunos taxones de herbívoros en arbustos con hojas nuevas, pero no hubo efectos a escala de paisaje en la fenología de la hoja, que rastreaba la luz y la cubierta de nubes. En cambio, las precipitaciones explicaron la amplia variabilidad interanual con una biomasa máxima en precipitaciones intermedias (130 mm mes−1 ), ya que los tres meses de precipitaciones altas y bajas redujeron los artrópodos a la mitad. Basándose en 50 años de precipitación regional, nuestro modelo dinámico de artrópodos predijo cambios en el momento de los máximos de biomasa dentro del bosque nuboso antes de que las comunidades de plantas hicieran la transición al bosque seco estacional caducifolio (precipitación media anual 1000-2500 mm vs. <800 mm). La magnitud de las lluvias fue el principal factor, pero durante la alta insolación solar, el "poder de secado del aire" (VPDmax ) redujo la biomasa en cuestión de días, lo que contribuyó a la sequía relacionada con El Niño-Southern Oscillation (ENSO). Destacando los riesgos de la sequía, los experimentos demostraron la susceptibilidad de toda la comunidad a la desecación, excepto en el caso de algunas orugas en las que la coloración a base de melanina parece reducir los efectos de la desecación por evaporación. En resumen, proporcionamos múltiples líneas de evidencia de que varios meses de fuertes lluvias o sequías reducen la biomasa de artrópodos independientemente de las plantas de raíces profundas con el potencial de desestabilizar las redes alimentarias de los insectívoros.

Sensitivity of tropical montane birds to anthropogenic disturbance and management strategies for their conservation in agricultural landscapes.

Tropical montane bird communities are hypothesized to be highly sensitive to anthropogenic disturbance because species are adapted to a narrow range of environmental conditions and display high rates of endemism. We assessed avian sensitivity at regional and continental scales for a global epicenter of montane bird biodiversity, the tropical Andes. Using data from an intensive field study of cloud forest bird communities across 7 landscapes undergoing agricultural conversion in northern Peru (1800-3100 m, 2016-2017) and a pan-Andean synthesis of forest bird sensitivity, we developed management strategies for maintaining avian biodiversity in tropical countrysides and examined how environmental specialization predicts species-specific sensitivity to disturbance. In Peru, bird communities occupying countryside habitats contained 29-93% fewer species compared with those in forests and were compositionally distinct due to high levels of species turnover. Fragments of mature forest acted as reservoirs for forest bird diversity, especially when large or surrounded by mixed successional vegetation. In high-intensity agricultural plots, an addition of 10 silvopasture trees or 10% more fencerows per hectare increased species richness by 18-20%. Insectivores and frugivores were most sensitive to disturbance: abundance of 40-70% of species declined in early successional vegetation and silvopasture. These results were supported by our synthesis of 816 montane bird species studied across the Andes. At least 25% of the species declined due to all forms of disturbance, and the percentage rose to 60% in agricultural landscapes. The most sensitive species were those with narrow elevational ranges and small global range sizes, insectivores and carnivores, and species with specialized trophic niches. We recommend protecting forest fragments, especially large ones, and increasing connectivity through the maintenance of early successional vegetation and silvopastoral trees that increase avian diversity in pastures. We provide lists of species-specific sensitivities to anthropogenic disturbance to inform conservation status assessments of Andean birds.

Sensibilidad de aves montanas a perturbaciones antropogénicas y estrategias de manejo para su conservación en paisajes agrícolas Resumen Se ha hipotetizado que las comunidades de aves tropicales montanas son sumamente sensibles a la perturbación antropogénica porque las especies están adaptadas a una reducida gama de condiciones ambientales y tienen altas tasas de endemismo. Evaluamos la sensibilidad aviar a escalas regional y continental para un epicentro global de biodiversidad de aves montanas, los Andes tropicales. Utilizando datos de un estudio intensivo de campo de comunidades de aves de bosques nublados en 7 paisajes bajo conversión agrícola en el norte de Perú (1800 - 3100 m, 2016-2017) y una síntesis pan-Andina de sensibilidad de aves de bosque, desarrollamos estrategias de manejo para el mantenimiento de la biodiversidad de aves en campiñas tropicales y examinamos cómo la especialización ambiental predice la sensibilidad de cada especie a la perturbación. Las comunidades de aves ocupando hábitats campestres tropicales en Perú contenían 29 - 93% menos especies en comparación con las de bosques y tuvieron una composición distinta debido a los altos niveles de recambio de especies. Los fragmentos de bosque maduro fungieron como reservorios para la diversidad de aves de bosque, especialmente cuando eran extensos y estaban rodeados por vegetación secundaria mixta. En las parcelas con actividad agrícola intensiva, la adición de 10 árboles silvopastoriles o 10% más de cercos por hectárea incrementó la riqueza de especies en 18 - 20%. Las insectívoras y frugívoras fueron más sensibles a la perturbación: la abundancia de 40 - 70% de especies declinó en la vegetación secundaria temprana y en la silvopastura. Estos resultados fueron sustentados por nuestra síntesis de 816 especies de aves montanas estudiadas en los Andes. Por lo menos 25% de estas especies declinaron debido a todas las formas de perturbación, y el porcentaje incrementó a 60% en paisajes agrícolas. Las especies más sensibles fueron aquellas con rangos altitudinales estrechos y extensiones de distribución pequeñas, las insectívoras y carnívoras y las especies con nichos tróficos especializados. Recomendamos la protección de fragmentos de bosque, especialmente los extensos, y el incremento de la conectividad mediante el mantenimiento de vegetación secundaria temprana y árboles silvopastoriles que incrementan la diversidad de aves en los pastizales. Proporcionamos listas de la sensibilidad de cada especie a la perturbación antropogénica para contribuir a las evaluaciones del estatus de conservación de aves Andinas.

Whole-genome landscape of pancreatic neuroendocrine tumours.

The diagnosis of pancreatic neuroendocrine tumours (PanNETs) is increasing owing to more sensitive detection methods, and this increase is creating challenges for clinical management. We performed whole-genome sequencing of 102 primary PanNETs and defined the genomic events that characterize their pathogenesis. Here we describe the mutational signatures they harbour, including a deficiency in G:C > T:A base excision repair due to inactivation of MUTYH, which encodes a DNA glycosylase. Clinically sporadic PanNETs contain a larger-than-expected proportion of germline mutations, including previously unreported mutations in the DNA repair genes MUTYH, CHEK2 and BRCA2. Together with mutations in MEN1 and VHL, these mutations occur in 17% of patients. Somatic mutations, including point mutations and gene fusions, were commonly found in genes involved in four main pathways: chromatin remodelling, DNA damage repair, activation of mTOR signalling (including previously undescribed EWSR1 gene fusions), and telomere maintenance. In addition, our gene expression analyses identified a subgroup of tumours associated with hypoxia and HIF signalling.

Corrigendum: Whole-genome landscape of pancreatic neuroendocrine tumours.

This corrects the article DOI: 10.1038/nature21063.

Whole-genome landscapes of major melanoma subtypes.

Melanoma of the skin is a common cancer only in Europeans, whereas it arises in internal body surfaces (mucosal sites) and on the hands and feet (acral sites) in people throughout the world. Here we report analysis of whole-genome sequences from cutaneous, acral and mucosal subtypes of melanoma. The heavily mutated landscape of coding and non-coding mutations in cutaneous melanoma resolved novel signatures of mutagenesis attributable to ultraviolet radiation. However, acral and mucosal melanomas were dominated by structural changes and mutation signatures of unknown aetiology, not previously identified in melanoma. The number of genes affected by recurrent mutations disrupting non-coding sequences was similar to that affected by recurrent mutations to coding sequences. Significantly mutated genes included BRAF, CDKN2A, NRAS and TP53 in cutaneous melanoma, BRAF, NRAS and NF1 in acral melanoma and SF3B1 in mucosal melanoma. Mutations affecting the TERT promoter were the most frequent of all; however, neither they nor ATRX mutations, which correlate with alternative telomere lengthening, were associated with greater telomere length. Most melanomas had potentially actionable mutations, most in components of the mitogen-activated protein kinase and phosphoinositol kinase pathways. The whole-genome mutation landscape of melanoma reveals diverse carcinogenic processes across its subtypes, some unrelated to sun exposure, and extends potential involvement of the non-coding genome in its pathogenesis.

Analysis of hereditary cancer gene variant classifications from ClinVar indicates a need for regular reassessment of clinical assertions.

The clinical classification of variants may change with new information, however, there is limited guidance on how often significant changes in variant classification occur. We used ClinVar to examine how variant classification changes over time. We developed a custom parser and accessed variant data from ClinVar between January 2015 and July 2021. The ClinVar-assigned "aggregate" classification of variants in 121 hereditary cancer genes was harmonized across releases to align to the American College of Medical Genetics and Genomics and the Association for Molecular Pathology terms. Aggregate classification categories were grouped as: benign/likely benign (B/LB); likely pathogenic/pathogenic (LP/P); variant of uncertain significance (VUS); conflicting interpretations of pathogenicity (Conflicting); or Other. We profiled changes in aggregate variant classification between consecutive semi-annual ClinVar releases. The proportion of variants that changed aggregate classification between semi-annual ClinVar releases ranged from 0.6% to 6.4%. The most frequent changes were "VUS to conflicting," "other to LP/P," and "B/LB to Conflicting." A limited number of variants changed aggregate classification from "LP/P to B/LB," or vice versa. Our analysis indicates need for regular reassessment of clinical variant interpretations. The parser developed for this project will facilitate extraction of relevant interpretation data from ClinVar.

Functional response traits and altered ecological niches drive the disassembly of cloud forest bird communities in tropical montane countrysides.

Anthropogenic disturbance contributes to global change by reshaping the ecological niche space available to biological communities. Quantifying the range of functional response traits required for species persistence is central towards understanding the mechanisms underlying community disassembly in disturbed landscapes. We used intensive field surveys of cloud forest bird communities across seven replicate landscapes undergoing agricultural conversion in the Peruvian Andes to examine how a suite of 16 functional response traits related to morphology, diet, foraging behaviour and environmental niche breadth predict (1) species-specific abundance changes in countryside habitats compared to forest and (2) differential changes to the ecological niche space occupied by communities. Our analyses relied on (1) hierarchical distance sampling models to examine the functional predictors of abundance change across the agricultural land use gradient while accounting for imperfect detection and (2) n-dimensional hypervolumes to quantify the expansion and contraction of ecological niche space in countryside habitats. Key traits related to increased abundance in early successional and mixed-intensity agricultural areas included (1) morphological adaptations to dense understorey habitats, (2) plant-based diets (flowers, fruit and seeds) and (3) broad elevational range limits and habitat breadth. Species occupying mixed and high-intensity agricultural land use regimes had mean elevational range limits 20%-60% wider than species found within forests. Collectively, ecological niche space expanded within agricultural habitats for traits related to diet and environmental niche breadth, while contracting for foraging and dispersal traits. Such changes were driven by species with unique functional trait combinations. Our results reveal the dynamic changes to ecological niche space that underly community structure in disturbed landscapes and highlight how increased niche breadth can ameliorate disturbance sensitivity for generalist species. We emphasize that functional traits can be used to predict changes in community structure across disturbance gradients, allowing insights into specific mechanisms underlying community disassembly beyond emergent patterns of functional diversity. By identifying key functional trait groups that align with different countryside habitats, we demonstrate how conservation practitioners can contribute to the retention of avian functional diversity in agricultural landscapes throughout the world.

La perturbación antropogénica contribuye al cambio global al remodelar el espacio de nicho ecológico disponible para las comunidades biológicas. Cuantificar la gama de rasgos de respuesta funcional requeridos para la persistencia de las especies es fundamental para comprender los mecanismos que subyacen al desensamble de la comunidad en los paisajes perturbados. Utilizamos muestreos de campo intensivos de las comunidades de aves del bosque nublado en siete paisajes replicados convertidos a uso agrícola en los Andes peruanos para examinar cómo un conjunto de 16 rasgos de respuesta funcional relacionados con la morfología, dieta, comportamiento de forrajeo, y la amplitud del nicho ambiental predicen (1) cambios en las abundancias de especies específicas en paisajes agrícolas ("countrysides") en comparación con el bosque y (2) cambios diferenciales en el espacio del nicho ecológico ocupado por las comunidades. Nuestros análisis se basaron en (1) modelos jerárquicos de muestreo por la distancia para examinar los predictores funcionales del cambio de abundancia a través del gradiente de uso de suelo para agricultura teniendo en cuenta la detección imperfecta, y (2) "n-dimensional hypervolumes" para cuantificar la expansión y contracción del espacio de nicho ecológico en los hábitats agrícolas. Los rasgos clave relacionados con el aumento de la abundancia en áreas agrícolas de sucesión temprana y de intensidad mixta incluyeron (1) adaptaciones morfológicas a hábitats de sotobosque denso, (2) dietas basadas en plantas (flores, frutas y semillas), y (3) amplios límites de rango de elevación y amplitud de hábitat. Las especies que ocupan regímenes de suelo agrícola mixto y de alta intensidad tenían límites de rango de elevación promedio 20%-60% más amplios que las especies que se encuentran en los bosques. En conjunto, el espacio del nicho ecológico se expandió dentro de los hábitats agrícolas para los rasgos relacionadas con la dieta y la amplitud del nicho ambiental, mientras que se contrajo para los rasgos de forrajeo y dispersión. Dichos cambios fueron impulsados por especies con combinaciones de rasgos funcionales únicos. Nuestros resultados revelan los cambios dinámicos en el espacio del nicho ecológico que subyacen a la estructura de la comunidad en los paisajes perturbados y destacan cómo una mayor amplitud del nicho puede mejorar la sensibilidad a las perturbaciones para las especies generalistas. Enfatizamos que los rasgos funcionales pueden utilizarse para predecir los cambios en la estructura de la comunidad a través de gradientes de perturbación, lo que permite comprender los mecanismos específicos que subyacen al desensamble de la comunidad más allá de los patrones emergentes de diversidad funcional. Al identificar grupos de rasgos funcionales claves que se alinean con diferentes hábitats agrícolas como en "countrysides" demostramos cómo los profesionales de la conservación pueden contribuir a la retención de la diversidad funcional de las aves en los paisajes agrícolas en todo el mundo.

Genomic analyses identify molecular subtypes of pancreatic cancer.

Integrated genomic analysis of 456 pancreatic ductal adenocarcinomas identified 32 recurrently mutated genes that aggregate into 10 pathways: KRAS, TGF-ß, WNT, NOTCH, ROBO/SLIT signalling, G1/S transition, SWI-SNF, chromatin modification, DNA repair and RNA processing. Expression analysis defined 4 subtypes: (1) squamous; (2) pancreatic progenitor; (3) immunogenic; and (4) aberrantly differentiated endocrine exocrine (ADEX) that correlate with histopathological characteristics. Squamous tumours are enriched for TP53 and KDM6A mutations, upregulation of the TP63∆N transcriptional network, hypermethylation of pancreatic endodermal cell-fate determining genes and have a poor prognosis. Pancreatic progenitor tumours preferentially express genes involved in early pancreatic development (FOXA2/3, PDX1 and MNX1). ADEX tumours displayed upregulation of genes that regulate networks involved in KRAS activation, exocrine (NR5A2 and RBPJL), and endocrine differentiation (NEUROD1 and NKX2-2). Immunogenic tumours contained upregulated immune networks including pathways involved in acquired immune suppression. These data infer differences in the molecular evolution of pancreatic cancer subtypes and identify opportunities for therapeutic development.

Considerations for using population frequency data in germline variant interpretation: Cancer syndrome genes as a model.

Aggregate population genomics data from large cohorts are vital for assessing germline variant pathogenicity. However, there are no specifications on how sequencing quality metrics should be considered, and whether exome-derived and genome-derived allele frequencies should be considered in isolation. Germline genome sequence data were simulated for nine read-depths to identify a minimum acceptable read-depth for detecting variants. gnomAD exome-derived and genome-derived datasets were assessed for read-depth, for six key cancer genes selected for variant curation by ClinGen expert panels. Non-Finnish European allele frequency (AF) or filter AF of coding variants in these genes, assigned into frequency bins using modified ACMG-AMP criteria, was compared between exome-derived and genome-derived datasets. A 30X read-depth achieved acceptable precision and recall for detection of substitutions, but poor recall for small insertions/deletions. Exome-derived and genome-derived datasets exhibited low read-depth for different gene exons. Individual variants were mostly assigned to non-divergent AF bins (>95%) or filter AF bins (>97%). Two major bin divergences were resolved by applying the minimal acceptable read-depth threshold. These findings show the importance of assessing read-depth separately for population datasets sourced from different short-read sequencing technologies before assigning a frequency-based ACMG-AMP classification code for variant interpretation.

Whole-genome characterization of chemoresistant ovarian cancer.

Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.

Whole genomes redefine the mutational landscape of pancreatic cancer.

Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole-genome sequencing and copy number variation (CNV) analysis of 100 pancreatic ductal adenocarcinomas (PDACs). Chromosomal rearrangements leading to gene disruption were prevalent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A and ROBO2) and new candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2). Patterns of structural variation (variation in chromosomal structure) classified PDACs into 4 subtypes with potential clinical utility: the subtypes were termed stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3 and PIK3CA), but at low individual patient prevalence. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2 or PALB2) and a mutational signature of DNA damage repair deficiency. Of 8 patients who received platinum therapy, 4 of 5 individuals with these measures of defective DNA maintenance responded.

Correction: Defining the genetic susceptibility to cervical neoplasia-A genome-wide association study.

[This corrects the article DOI: 10.1371/journal.pgen.1006866.].

Defining the genetic susceptibility to cervical neoplasia-A genome-wide association study.

A small percentage of women with cervical HPV infection progress to cervical neoplasia, and the risk factors determining progression are incompletely understood. We sought to define the genetic loci involved in cervical neoplasia and to assess its heritability using unbiased unrelated case/control statistical approaches. We demonstrated strong association of cervical neoplasia with risk and protective HLA haplotypes that are determined by the amino-acids carried at positions 13 and 71 in pocket 4 of HLA-DRB1 and position 156 in HLA-B. Furthermore, 36% (standard error 2.4%) of liability of HPV-associated cervical pre-cancer and cancer is determined by common genetic variants. Women in the highest 10% of genetic risk scores have approximately >7.1% risk, and those in the highest 5% have approximately >21.6% risk, of developing cervical neoplasia. Future studies should examine genetic risk prediction in assessing the risk of cervical neoplasia further, in combination with other screening methods.

Whole genome sequencing of melanomas in adolescent and young adults reveals distinct mutation landscapes and the potential role of germline variants in disease susceptibility.

Cutaneous melanoma accounts for at least >10% of all cancers in adolescents and young adults (AYA, 15-30 years of age) in Western countries. To date, little is known about the correlations between germline variants and somatic mutations and mutation signatures in AYA melanoma patients that might explain why they have developed a cancer predominantly affecting those over 65 years of age. We performed genomic analysis of 50 AYA melanoma patients (onset 10-30 years, median 20); 25 underwent whole genome sequencing (WGS) of both tumor and germline DNA, exome data were retrieved from 12 TCGA AYA cases, and targeted DNA sequencing was conducted on 13 cases. The AYA cases were compared with WGS data from 121 adult cutaneous melanomas. Similar to mature adult cutaneous melanomas, AYA melanomas showed a high mutation burden and mutation signatures of ultraviolet radiation (UVR) damage. The frequencies of somatic mutations in BRAF (96%) and PTEN (36%) in the AYA WGS cohort were double the rates observed in adult melanomas (Q < 6.0 × 10-6 and 0.028, respectively). Furthermore, AYA melanomas contained a higher proportion of non-UVR-related mutation signatures than mature adult melanomas as a proportion of total mutation burden (p = 2.0 × 10-4 ). Interestingly, these non-UVR mutation signatures relate to APOBEC or mismatch repair pathways, and germline variants in related genes were observed in some of these cases. We conclude that AYA melanomas harbor some of the same molecular aberrations and mutagenic insults occurring in older adults, but in different proportions. Germline variants that may have conferred disease susceptibility correlated with somatic mutation signatures in a subset of AYA melanomas.

Mixed ductal-lobular carcinomas: evidence for progression from ductal to lobular morphology.

Mixed ductal-lobular carcinomas (MDLs) show both ductal and lobular morphology, and constitute an archetypal example of intratumoural morphological heterogeneity. The mechanisms underlying the coexistence of these different morphological entities are poorly understood, although theories include that these components either represent 'collision' of independent tumours or evolve from a common ancestor. We performed comprehensive clinicopathological analysis of a cohort of 82 MDLs, and found that: (1) MDLs more frequently coexist with ductal carcinoma in situ (DCIS) than with lobular carcinoma in situ (LCIS); (2) the E-cadherin-catenin complex was normal in the ductal component in 77.6% of tumours; and (3) in the lobular component, E-cadherin was almost always aberrantly located in the cytoplasm, in contrast to invasive lobular carcinoma (ILC), where E-cadherin is typically absent. Comparative genomic hybridization and multiregion whole exome sequencing of four representative cases revealed that all morphologically distinct components within an individual case were clonally related. The mutations identified varied between cases; those associated with a common clonal ancestry included BRCA2, TBX3, and TP53, whereas those associated with clonal divergence included CDH1 and ESR1. Together, these data support a model in which separate morphological components of MDLs arise from a common ancestor, and lobular morphology can arise via a ductal pathway of tumour progression. In MDLs that present with LCIS and DCIS, the clonal divergence probably occurs early, and is frequently associated with complete loss of E-cadherin expression, as in ILC, whereas, in the majority of MDLs, which present with DCIS but not LCIS, direct clonal divergence from the ductal to the lobular phenotype occurs late in tumour evolution, and is associated with aberrant expression of E-cadherin. The mechanisms driving the phenotypic change may involve E-cadherin-catenin complex deregulation, but are yet to be fully elucidated, as there is significant intertumoural heterogeneity, and each case may have a unique molecular mechanism. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

HLA and KIR Associations of Cervical Neoplasia.

Background: Cervical cancer is the fourth most common cancer in women, and we recently reported human leukocyte antigen (HLA) alleles showing strong associations with cervical neoplasia risk and protection. HLA ligands are recognized by killer immunoglobulin-like receptors (KIRs) expressed on a range of immune cell subsets, governing their proinflammatory activity. We hypothesized that the inheritance of particular HLA-KIR combinations would increase cervical neoplasia risk. Methods: Here, we used HLA and KIR dosages imputed from single-nucleotide polymorphism genotype data from 2143 cervical neoplasia cases and 13858 healthy controls of European decent. Results: The following 4 novel HLA alleles were identified in association with cervical neoplasia, owing to their linkage disequilibrium with known cervical neoplasia-associated HLA-DRB1 alleles: HLA-DRB3*9901 (odds ratio [OR], 1.24; P = 2.49 × 10-9), HLA-DRB5*0101 (OR, 1.29; P = 2.26 × 10-8), HLA-DRB5*9901 (OR, 0.77; P = 1.90 × 10-9), and HLA-DRB3*0301 (OR, 0.63; P = 4.06 × 10-5). We also found that homozygosity of HLA-C1 group alleles is a protective factor for human papillomavirus type 16 (HPV16)-related cervical neoplasia (C1/C1; OR, 0.79; P = .005). This protective association was restricted to carriers of either KIR2DL2 (OR, 0.67; P = .00045) or KIR2DS2 (OR, 0.69; P = .0006). Conclusions: Our findings suggest that HLA-C1 group alleles play a role in protecting against HPV16-related cervical neoplasia, mainly through a KIR-mediated mechanism.

Hypermutation In Pancreatic Cancer.

Pancreatic cancer is molecularly diverse, with few effective therapies. Increased mutation burden and defective DNA repair are associated with response to immune checkpoint inhibitors in several other cancer types. We interrogated 385 pancreatic cancer genomes to define hypermutation and its causes. Mutational signatures inferring defects in DNA repair were enriched in those with the highest mutation burdens. Mismatch repair deficiency was identified in 1% of tumors harboring different mechanisms of somatic inactivation of MLH1 and MSH2. Defining mutation load in individual pancreatic cancers and the optimal assay for patient selection may inform clinical trial design for immunotherapy in pancreatic cancer.

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes.

Pancreatic cancer is a highly lethal malignancy with few effective therapies. We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma. Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 non-silent mutations and 1,628 copy-number variations. We define 16 significantly mutated genes, reaffirming known mutations (KRAS, TP53, CDKN2A, SMAD4, MLL3, TGFBR2, ARID1A and SF3B1), and uncover novel mutated genes including additional genes involved in chromatin modification (EPC1 and ARID2), DNA damage repair (ATM) and other mechanisms (ZIM2, MAP2K4, NALCN, SLC16A4 and MAGEA6). Integrative analysis with in vitro functional data and animal models provided supportive evidence for potential roles for these genetic aberrations in carcinogenesis. Pathway-based analysis of recurrently mutated genes recapitulated clustering in core signalling pathways in pancreatic ductal adenocarcinoma, and identified new mutated genes in each pathway. We also identified frequent and diverse somatic aberrations in genes described traditionally as embryonic regulators of axon guidance, particularly SLIT/ROBO signalling, which was also evident in murine Sleeping Beauty transposon-mediated somatic mutagenesis models of pancreatic cancer, providing further supportive evidence for the potential involvement of axon guidance genes in pancreatic carcinogenesis.

Integrated genomic and transcriptomic analysis of human brain metastases identifies alterations of potential clinical significance.

Treatment options for patients with brain metastases (BMs) have limited efficacy and the mortality rate is virtually 100%. Targeted therapy is critically under-utilized, and our understanding of mechanisms underpinning metastatic outgrowth in the brain is limited. To address these deficiencies, we investigated the genomic and transcriptomic landscapes of 36 BMs from breast, lung, melanoma and oesophageal cancers, using DNA copy-number analysis and exome- and RNA-sequencing. The key findings were as follows. (a) Identification of novel candidates with possible roles in BM development, including the significantly mutated genes DSC2, ST7, PIK3R1 and SMC5, and the DNA repair, ERBB-HER signalling, axon guidance and protein kinase-A signalling pathways. (b) Mutational signature analysis was applied to successfully identify the primary cancer type for two BMs with unknown origins. (c) Actionable genomic alterations were identified in 31/36 BMs (86%); in one case we retrospectively identified ERBB2 amplification representing apparent HER2 status conversion, then confirmed progressive enrichment for HER2-positivity across four consecutive metastatic deposits by IHC and SISH, resulting in the deployment of HER2-targeted therapy for the patient. (d) In the ERBB/HER pathway, ERBB2 expression correlated with ERBB3 (r(2) = 0.496; p < 0.0001) and HER3 and HER4 were frequently activated in an independent cohort of 167 archival BM from seven primary cancer types: 57.6% and 52.6% of cases were phospho-HER3(Y1222) or phospho-HER4(Y1162) membrane-positive, respectively. The HER3 ligands NRG1/2 were barely detectable by RNAseq, with NRG1 (8p12) genomic loss in 63.6% breast cancer-BMs, suggesting a microenvironmental source of ligand. In summary, this is the first study to characterize the genomic landscapes of BM. The data revealed novel candidates, potential clinical applications for genomic profiling of resectable BMs, and highlighted the possibility of therapeutically targeting HER3, which is broadly over-expressed and activated in BMs, independent of primary site and systemic therapy.