Evolution of late-stage metastatic melanoma is dominated by aneuploidy and whole genome doubling

Although melanoma is initiated by acquisition of point mutations and limited focal copy number alterations in melanocytes-of-origin, the nature of genetic changes that characterise lethal metastatic disease is poorly understood. Here, we analyze the evolution of human melanoma progressing from early to late disease in 13 patients by sampling their tumours at multiple sites and times. Whole exome and genome sequencing data from 88 tumour samples reveals only limited gain of point mutations generally, with net mutational loss in some metastases. In contrast, melanoma evolution is dominated by whole genome doubling and large-scale aneuploidy, in which widespread loss of heterozygosity sculpts the burden of point mutations, neoantigens and structural variants even in treatment-naïve and primary cutaneous melanomas in some patients. These results imply that dysregulation of genomic integrity is a key driver of selective clonal advantage during melanoma progression

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Estudi d'una metal·lotioneïna d'alzina surera (QsMT)

En aquest treball es caracteriza per primera vegada la capacitat de coordinació metàl·lica d'una metal·lotineïna (MT) de planta i es proposa un model de plegament per a les MTs de planta en general. Els resultat mostren que aquestes proteïnes poden tenir un paper molt important en la regulació de l'estat redox de les cèl·lules, probablement a través de la coordinació a Cu.Les MTs de planta són proteïnes molt desconegudes. Es postula que participen en l'homeòstasi del Cu i en la protecció contra l'estrès oxidatiu, però es desconeix la capacitat de coordinació metàl·lica i el plegament. En aquest treball s'han estudiat una metal·lotioneïna d'alzina surera, QsMT, aïllada d'una llibreria de cDNA de fel·lema. Els objectius concrets han estat: (1) estudiar l'expressió de QsMT i la resposta a l'estrès oxidatiu; (2) determinar la capacitat de coordinació metàl·lica i la funcionalitat in vivo; (3) fer una aproximació al plegament de les MTs de planta. L'expressió del gen s'ha estudiat mitjançant hibridació in situ en plàntules i en embrions d'alzina surera. QsMT s'expressa majoritàriament en cèl·lules amb fort estrès oxidatiu, associat a la síntesi de polifenols (suberització i lignificació) i a la senescència. També s'expressa en cèl·lules meristemàtiques, cèl·lules en divisió molt activa on la funció de les MTs podria estar relacionada amb el manteniment de l'estat redox. L'aplicació d'estrès oxidatiu exogen (H2O2 i paraquat) incrementa fortament l'expressió de QsMT en teixits amb expressió constitutiva, confirmant la regulació de l'expressió del gen per estrès oxidatiu.Per l'estudi de les propietats de coordinació metàl·lica es va expressar QsMT en cèl·lules d'E. coli en medi de cultiu suplementat amb Cu, Zn o Cd. Es van aïllar els agregats metàl·lics corresponents i es van analitzar mitjançant tècniques espectroscòpiques i espectromètriques (ICP-OES, ESI-MS i CD). Els resultats mostren que QsMT coordina de forma estable Cu (8 ions metàl·lics/molècula), Zn (4 ions de Zn/molècula) i Cd (6 ions de Cd/molècula), i adopta una estructura especialment quiral en coordinació a Cu. L'elevada capacitat quelant de la proteïna i la quiralitat de l'estructura indiquen que QsMT possiblement té preferència metàl·lica pel Cu i per tant una funció relacionada amb aquest metall in vivo. Estudis de complementació en llevat demostren que QsMT coordina Cu de forma funcional in vivo. En coordinació a Cd QsMT presenta una peculiaritat no observada fins ara en altres MTs: la participació d'ions sulfur en la formació de l'agregat metàl·lic incrementant la capacitat de coordinació metàl·lica (6 ions metàl·lics divalents de Cd enlloc de 4 ions de Zn). A més QsMT coordina Cd de forma funcional en llevat, i per tant la seva funció també podria estar relacionada amb la destoxicació de Cd en la planta.QsMT s'ha utilitzat com a model per fer una aproximació al plegament de les MTs de planta. Amb aquest objectiu vam dissenyar tres pèptids mutants derivats de QsMT: N25 corresponent a la zona rica en cisteïna en posició amino-terminal, C18 corresponent a la zona rica en cisteïna en posició carboxil-terminal, i N25-C18 corresponent a les dues zones riques en cisteïna enllaçades per 4 glicines substituint la zona central de 39 aminoàcids. Es van expressar i estudiar aquests pèptids per les mateixes tècniques utilitzades en l'estudi de QsMT. Els resultats indiquen que QsMT es plega formant un sol agregat metàl·lic per la interacció de les dues zones riques en cisteïna. En aquest model la zona central d'enllaç, típica de les MTs de planta, no participa en la coordinació metàl·lica però és imprescindible per a la funció de la proteïna. El paper de la zona central podria variar en funció del metall que coordina, participant en el plegament i estructura de la proteïna quan coordina Zn i Cd i en la seva regulació i estabilització quan coordina Cu.In this work we characterize for the first time the metal coordination capacity of a plant metallothionein (MT), and propose a model for the protein folding of plant MTs in general. Results show that these proteins can play a very important role in the regulation of the cellular redox, probably through its copper-coordination ability.Plant MTs are largely unknown proteins. It is postulated that they play a role in copper homeostasis and protection against oxidative stress, but precise function of these proteins, as well as its metal coordination capacity remain unknown.In this work we have studied a cork oak metallothionein, QsMT, isolated from phellem cDNA library. Our main objectives were: (1) to study the QsMT gene expression and its response to oxidative stress; (2) to determine the protein metal coordination properties and the functionality in vivo; (3) to estimate a type of folding for plant MTs.The sudy of the gene expression has been carried out by in situ hybridization in cork oak plants and embryos. QsMT is mainly expressed in cells with high oxidative stress associated to both polyphenol synthesis (suberization and lignification) and senescence. QsMT is also expressed in meristematic cells, where its function could be related to the redox regulation. The oxidative treatment (H202 and paraquat) highly increases gene expression in tissues with constitutive expression, confirming its regulation by oxidative stress.To characterize the protein metal coordination properties we expressed QsMT in E. coli cells in culture medium supplemented with Cu, Zn or Cd. We isolated the corresponding metal aggregates and analyzed them using spectroscopic and spectrometric techniques (ICP-OES, ESI-MS, CD). Results show that QsMT effectively binds Cu (8 ions/molecule), Zn (4 ions/molecule) and Cd (6 ions/molecule), and presents highest chirality when folds with copper. The high binding capacity and chirality of the protein in the presence of copper suggest that QsMT may play a function related to this metal in vivo. Functional complementation studies confirm that QsMT functionally binds copper in vivo. When coordinating Cd QsMT presents a peculiarity not seen in other MTs: the participation of sulfur ions in the formation of the metal aggregate, this increasing the coordination capacity (6 Cd/molecule in contrast to 4 Zn/molecule). Moreover, QsMT functionaly binds Cd in yeast, suggesting that the protein function could also be realted to a Cd detoxification role in plant.We have also used QsMT as a model for the study of the folding of plant MTs. With this aim we designed three mutant peptides derived from QsMT: N25 corresponding to the amino Cys-rich domain; C18 corresponding to the carboxy Cys-rich domain; and N25-C18 corresponding to the two Cys-rich domains linked by 4 glycines in substitution to the central 39 amino acid region. Peptides were expressed and studied using same techniques used for the study of QsMT. Results point to a protein folding in one metal cluster formed by the interaction of the two Cys-rich domains. In this model the central region, typical from plant MTs, does not participate in metal coordination but is indispensable for the protein function. The role of the central region could depend on the metal it coordinates, playing a role in the protein folding and structure when it binds Zn or Cd and a role in protein regulation and stability when it binds Cu

Whole exome sequencing reveals activating JAK1 and STAT3 mutations in breast implant-associated anaplastic large cell lymphoma anaplastic large cell lymphoma

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Characterization of the immune profile of oral tongue squamous cell carcinomas with advancing disease

We investigated whether a unique immune response was instigated with the development of oral tongue squamous cell carcinomas (OTSCC), with/without nodal involvement, with/without recurrent metastatic disease, or within tumor involved nodes. One hundred and ten formalin-fixed paraffin-embedded samples were collected from a retrospective cohort of 67 OTSCC patients and 10 non-cancerous tongue samples. Targets including CD4, CD8, FOXP3, PD-L1, and PD-1 were analyzed by immunohistochemistry. The Nanostring PanCancer Immune Profiling Panel was used for gene expression profiling. Data were externally validated in the The Cancer Genome Atlas (TCGA) head and neck (HNSCC), melanoma and lung squamous cell carcinoma (LSCC) cohorts. A 24-immune gene signature was identified that discriminated more aggressive OTSCC cases, and although not prognostic in HNSCC was associated with survival in other TCGA cohorts (improved survival for melanoma, P \u3c .001 and worse survival for LSCC, P = .038). OTSCC exhibited concordant gene and immunohistochemical (IHC) features characterized by a TH-2 biased, proinflammatory profile with upregulated B cell and neutrophil gene activity and increased CD4, FOXP3, and PD-L1 expression (P \u3c .001 for all by IHC). Compared to less advanced disease, nodal involvement and recurrent OTSCC did not induce a different immune response although recurrent disease was characterized by significantly higher PD-L1 expression (P = .004 by SP263, P = .013 by 22C3, P = .004 for gene expression). Identification of a gene signature associated with different prognostic effects in other cancers highlights common pathways of immune dysregulation that are impacted by the tumor origin. The significant immunosuppressive signaling in OTSCC indicates primary failure of immune system to control carcinogenesis emphasizing the need for early, combi- nation therapeutic approaches

Additional file 1: of Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue

Figure S1. Profile of chromosome 7 for LPS1; Figure S2. Profile of chromosome 4 for LPS1; Figure S3.Comparison of measurement variability (MAPD); Figure S4. Alignment of reads from a WGA sample; Figure S5. Clustering of MCT-4 and MCT-6 5 ng, 20 ng, 100 ng (UA) and WGA; Figure S6. Correlation of FFPE block age with QC score. (PDF 823 kb

Embryonic Lethality in Homozygous Human Her-2 Transgenic Mice Due to Disruption of the <i>Pds5b</i> Gene

<div><p>The development of antigen-targeted therapeutics is dependent on the preferential expression of tumor-associated antigens (TAA) at targetable levels on the tumor. Tumor-associated antigens can be generated <i>de novo</i> or can arise from altered expression of normal basal proteins, such as the up-regulation of human epidermal growth factor receptor 2 (Her2/ErbB2). To properly assess the development of Her2 therapeutics in an immune tolerant model, we previously generated a transgenic mouse model in which expression of the human Her2 protein was present in both the brain and mammary tissue. This mouse model has facilitated the development of Her2 targeted therapies in a clinically relevant and suitable model. While heterozygous Her2^+/- mice appear to develop in a similar manner to wild type mice (Her2^-/-), it has proven difficult to generate homozygous Her2^+/+ mice, potentially due to embryonic lethality. In this study, we performed whole genome sequencing to determine if the integration site of the Her2 transgene was responsible for this lethality. Indeed, we report that the Her2 transgene had integrated into the <i>Pds5b</i> (precocious dissociation of sisters) gene on chromosome 5, as a 162 copy concatemer. Furthermore, our findings demonstrate that Her2^+/+ mice, similar to Pds5b^-/- mice, are embryonic lethal and confirm the necessity for Pds5b in embryonic development. This study confirms the value of whole genome sequencing in determining the integration site of transgenes to gain insight into associated phenotypes.</p></div

Her2^+/- mice harbour 162 copies of the Her 2 transgene in their genome.

<p>Genomic DNA from Her2^+/- mice was extracted and analysed using whole genome sequencing. The WAP-Her2 transgene had integrated at positions 150719804 (entry) and 150719794 (exit) on chromosome 5, resulting in a 10 nucleotide repeat (from position 150719804–794). A unidirectional concatemer with 162 copies of the WAP-Her2 transgene was found in Her2^+/- mice.</p