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Pancreatic adenocarcinoma presents as a spectrum of a highly aggressive disease in patients. The basis of this disease heterogeneity has proved difficult to resolve due to poor tumor cellularity and extensive genomic instability. To address this, a dataset of whole genomes and transcriptomes was generated from purified epithelium of primary and metastatic tumors. Transcriptome analysis demonstrated that molecular subtypes are a product of a gene expression continuum driven by a mixture of intratumoral subpopulations, which was confirmed by single-cell analysis. Integrated whole-genome analysis uncovered that molecular subtypes are linked to specific copy number aberrations in genes such as mutant KRAS and GATA6 . By mapping tumor genetic histories, tetraploidization emerged as a key mutational process behind these events. Taken together, these data support the premise that the constellation of genomic aberrations in the tumor gives rise to the molecular subtype, and that disease heterogeneity is due to ongoing genomic instability during progression. Whole-genome sequencing, transcriptome sequencing and single-cell analysis of primary and metastatic pancreatic adenocarcinoma identify molecular subtypes and intratumor heterogeneity.

Integrated whole genome and transcriptome sequencing can unveil distinct molecular subgroups in pancreatic cancer (PDAC). The COMPASS trial (NCT02750657) enrolled 268 patients with advanced PDAC; patients were given either modified (m) FOLFIRINOX or Gemcitabine-nab-paclitaxel (GnP) as per physicians choice. Median follow-up is 52 months and median overall survival in those receiving mFOLFIRINOX is 10.6 months and 8.4 months for GnP. KRAS specific mutants and allelic states alone are not prognostic; however basal-like PDAC are more likely to harbour major imbalances in mutant KRAS (KRAS maj ). In the presence of KRAS maj , pre-existing type II DM is more common. Distinct prognostic cohorts include homologous-recombination deficient PDAC, predictive of mFOLFIRINOX response. Basal-like PDAC and patients exhibiting evidence of systemic inflammation as annotated using the Gustave Roussy Immune Score are unique poor prognostic cohorts. The latter associates with low CD8 T cell infiltration while basal-like PDAC documents an inflamed tumour microenvironment. The COMPASS trial is a prospective observational study seeking to establish biomarkers in advanced pancreatic cancer through in-depth profiling prior to commencing chemotherapy. Here, the authors report the final data for the complete cohort of 268 patients enrolled in the COMPASS trial.

Estrogen receptor-positive, human epidermal growth factor receptor negative (ER + /HER2−) breast cancer, poses challenges in adjuvant treatment decisions due to its propensity for late recurrence. We propose a model that leverages our previously identified circulating tumor cell (CTC) genomic signature, linked to metastasis. Furthermore, we investigated the impact of CTC signature intratumour heterogeneity (ITH) on recurrence risk. Using Oncotype DX recurrence score as a surrogate for survival, we trained expression and copy number-based models using 194 early stage ER + /HER2− breast cancer patients and validated them in the METABRIC dataset. Multispectral fluorescence in situ hybridization (Multiplex-FISH) was used to evaluate the ITH of 6 CTC genomic regions in primary tumors. The expression-based model strongly correlated with Oncotype DX, while the copy number-based model achieved a moderate correlation. Both models were able to predict long-term recurrence free survival in METABRIC. Higher CTC signature ITH was associated with increased Oncotype DX risk and higher overall grade. These findings highlight the value of our CTC signature in disease progression and the role of ITH on recurrence risk.

Pancreatic cancer is not caused by a specific series of genetic alterations that occur sequentially but by one, or few, catastrophic events that result in simultaneous oncogenic genetic rearrangements, giving rise to highly aggressive tumours. Pancreatic cancer genome evolution Pancreatic cancer is a highly aggressive tumour type. With a view to examining the evolution of rapid tumour progression in this cancer, this paper presents an analysis of more than a hundred tumour-enriched whole-genome sequences from primary and metastatic pancreas cancers obtained from collaborating hospitals in Canada and the United States of America. Challenging a traditional model of progressive evolution based on ordered mutations in several genes, the authors find support for a role of complex rearrangements and chromothripsis in pancreatic cancer progression, which suggests that the genomic instability that marks this cancer may be explained by a punctuated equilibrium model. Pancreatic cancer, a highly aggressive tumour type with uniformly poor prognosis, exemplifies the classically held view of stepwise cancer development 1 . The current model of tumorigenesis, based on analyses of precursor lesions, termed pancreatic intraepithelial neoplasm (PanINs) lesions, makes two predictions: first, that pancreatic cancer develops through a particular sequence of genetic alterations 2 , 3 , 4 , 5 ( KRAS , followed by CDKN2A , then TP53 and SMAD4 ); and second, that the evolutionary trajectory of pancreatic cancer progression is gradual because each alteration is acquired independently. A shortcoming of this model is that clonally expanded precursor lesions do not always belong to the tumour lineage 2 , 5 , 6 , 7 , 8 , 9 , indicating that the evolutionary trajectory of the tumour lineage and precursor lesions can be divergent. This prevailing model of tumorigenesis has contributed to the clinical notion that pancreatic cancer evolves slowly and presents at a late stage 10 . However, the propensity for this disease to rapidly metastasize and the inability to improve patient outcomes, despite efforts aimed at early detection 11 , suggest that pancreatic cancer progression is not gradual. Here, using newly developed informatics tools, we tracked changes in DNA copy number and their associated rearrangements in tumour-enriched genomes and found that pancreatic cancer tumorigenesis is neither gradual nor follows the accepted mutation order. Two-thirds of tumours harbour complex rearrangement patterns associated with mitotic errors, consistent with punctuated equilibrium as the principal evolutionary trajectory 12 . In a subset of cases, the consequence of such errors is the simultaneous, rather than sequential, knockout of canonical preneoplastic genetic drivers that are likely to set-off invasive cancer growth. These findings challenge the current progression model of pancreatic cancer and provide insights into the mutational processes that give rise to these aggressive tumours.

We previously reported that T-cadherin (CDH13, H-cadherin), a unique cadherin molecule, was expressed on the basal cell layer in normal murine and human epidermis. In the present study, T-cadherin expression in archival human skin specimens comprising a spectrum of human squamous cell neoplasia was investigated. T-cadherin expression was observed in both normal epidermal basal cells and adnexal epithelial cells of formalin-fixed and paraffin-embedded tissue sections. Western immunoblotting also revealed that mature T-cadherin protein was expressed in cultured human skin tissue equivalent. Atypical keratinocytes in 27 of 53 specimens of actinic keratosis and 23 of 30 specimens of Bowen's disease expressed T-cadherin. In contrast, T-cadherin was focally expressed in 6 of 56 invasive cutaneous squamous cell carcinomas. To explore the molecular mechanism of down-regulation of T-cadherin expression in invasive squamous cell carcinoma, loss of heterozygosity, genetic alternations, and methylation status in the 5′ region of the T-cadherin gene were investigated. Loss of heterozygosity at intron 1 of the T-cadherin gene was observed in 8 of 28 informative cases of invasive squamous cell carcinoma. Although no structural genomic alternations were found by sequence analysis, aberrant promoter methylation of the T-cadherin gene was found in 12 of 28 invasive squamous cell carcinomas. T-cadherin expression was restored in cultured A431 cells, in which aberrant methylation was found by treatment with the demethylating agent 5′-aza-2-deoxycytidine. These findings suggest that a combination of deletion and aberrant methylation of the T-cadherin gene may play a role in loss of gene expression in a considerable number of invasive cutaneous squamous cell carcinomas.

T-cadherin is a unique member of the cadherin superfamily that shares the ectodomain organization with classical cadherins, but lacks both transmembrane and cytoplasmic regions and is instead anchored to the plasma membrane through a glycosyl-phosphatidylinositol (GPI) moiety. The function of T-cadherin has not been revealed yet. The special structure of T-cadherin might endow this molecule with specific intracellular targeting properties and functions that are distinct from classical cadherins. T-cadherin was originally cloned from chicken embryo brain and then was also found in mouse and human nervous and cardiovascular systems; however, T-cadherin in the keratinocytes and skin tissue is still an unknown area that remains to be explored. To test whether the unusual truncated T-cadherin is expressed in keratinocytes, we performed the reverse transcriptase-polymerase chain reaction of T-cadherin, as well as several classical cadherins (E-, P-, and N-cadherin), on the mouse keratinocyte cell line Pam212, fibroblast NIH3T3, and melanoma cell B16. The result indicated that mouse keratinocytes expressed the mRNA of truncated T-cadherin apart from classical cadherins, E-, and P-cadherin. To confirm the expression of T-cadherin in mouse keratinocytes, immunocytochemistry staining was carried out on Pam212 cells by using rabbit anti-T-cadherin antibody and rat antimouse E- and P-cadherin antibody. The result of immunofluorescence staining proved that T-cadherin was expressed in mouse keratinocytes. In order to analyze the distribution patterns of T-cadherin and classical cadherins on the keratinocytes, 3D scanning was performed by using a confocal microscope. From the Z-sections and XZ-sections, it was clearly demonstrated that T-cadherin was distributed diffusely on the whole cell surface, while E- and P-cadherin were concentrated on the cell–cell contacts. To examine the expression and the localization of T-cadherin on skin tissue, the frozen sections of the mouse back skin were immunohistochemically labeled by using anti-T-cadherin antibody. It was found that T-cadherin was intensively expressed only on the basal cell layer of the mouse skin. Apart from mouse keratinocytes and mouse skin, we further examined the expression of T-cadherin in human keratinocytes and human skin by western blot, immunocytochemistry, and immunohistochemistry staining. The same results were achieved with human samples. In this study, we found and verified that T-cadherin was expressed on the mouse and human keratinocytes and specifically localized on the basal cell layer of skin. The nature of T-cadherin function and its mechanism of localization at the basal cell layer of skin are important issues to be addressed concerning this unique member of the cadherin family and its physiologic and pathologic roles in the skin.

Nature 538, 378–382 (2016); doi:10.1038/nature19823 In this Letter, owing to a typesetter error the ‘received date’ was incorrectly shown as ‘8 August 2015’ instead of ‘27 November 2015’ in both the print and PDF versions; this has been corrected online.

Gene therapy for prostate cancer may be realized through transduction of whole genes, such as PSA or PSMA, into immunotherapeutic dendritic cells (DCs). An oncoretroviral vector encoding human PSMA and a bicistronic oncoretroviral vector encoding human PSA and cell surface CD25 cDNAs were constructed. Remarkably, transfer of PSA/CD25 or PSMA cDNA during murine hematopoietic cell differentiation into DCs occurred with approximately 80% efficiency. In vitro , transduced DCs retained allostimulatory function and primed syngeneic T cells for tumor antigen-specific IFN- γ secretion. In test experiments designed to elucidate mechanisms in vivo , syngeneic recipients of transduced DCs had increased anti-human PSA antibody titers and tumor-specific CD8 + T cell IFN- γ secretion with no detectable immune response to CD25. Gene-modified DC recipients had increased protection from specific tumor challenge for at least 18 weeks post-vaccination. DC vaccination also protected both male and female recipients. Gene-modified DC vaccination mediated regression of established, specific gene-expressing, TRAMP-C1 prostate cancer cell tumors. These findings indicate that antibody and cellular responses generated through PSA and PSMA gene transfer into DC yielded protective immunity, thereby providing further preclinical support for the implementation of immuno-gene therapy approaches for prostate cancer.

Loss of human mismatch repair (hMSH2) gene function has been linked to hereditary non-polyposis colorectal cancer (HNPCC), Muir-Torre syndrome (MTS), and sporadic cancers, excluding skin cancers unrelated to MTS. We immunohistochemically examined 125 squamous cell carcinomas (SCCs) using a monoclonal antibody to the hMSH2 protein and compared the results with those for 106 precursor lesions of SCC, consisting of actinic keratosis (AK), Bowenoid type of actinic keratosis (BAK), and Bowen's disease (BOD). In contrast to the homogeneous immunoreactivity of proliferating cells composed of AK, BAK, and BOD, heterogeneous and diminished immunostaining to hMSH2 was observed in tumor cells of SCCs examined. In addition, two SCCs (2 of 125; 1.6%) at multiple loci exhibited a complete lack of immunoreaction to hMSH2. Immunohistochemical staining of hMSH2 was semiquantitatively scored as 0 (0% of total cells examined), 1 (less than 10%), 2 (10-50%), or 3 (more than 50%). Percentage preservation of and average score for hMSH2 expression in normal, AK, BAK, BOD, and SCC were 56% and 2.06, 100% and 2.80, 94% and 2.88, 83% and 2.78, 63% and 2.36, respectively. The percentage preservation of and average scores for hMSH2 in AK, BAK, and BOD were significantly higher than those in presumably normal skin (P<0.01). There were no significant differences in the percentage preservation of and average scores for hMSH2 between presumably normal skin and SCC. The score for hMSH2 expression was significantly correlated with score for sun exposure in presumably normal skin of each lesion (R=0.70). These findings for hMSH2 expression in precursor lesions and SCC suggest that promotion or activation of hMSH2 expression may be induced by the increased DNA damage caused by sun exposure and that diminished expression of it might occur according to the transformation from precancerous lesions to SCC.

Hematopoietic cell transplantation can impact lysosomal storage disorders (LSDs) and will be enhanced by gene therapy. Transduced cells in LSDs often secrete the therapeutic hydrolase, which can be used by bystander cells. However, toxicity associated with myeloablative transplant preparative regimens limits many applications of this approach in gene therapy. We hypothesized that reduced-intensity (RI) conditioning regimens would allow stable engraftment of therapeutically transduced cells and allow correction of Fabry disease. We transplanted transduced cells into Fabry mice receiving eight different clinically relevant chemotherapy- and/or radiotherapy-based RI conditioning regimens generating modest and transient lymphoid/myeloid cell depletion. Two comprehensive transplantation Protocols were performed. Firstly, transplantation of 0.38 × 106 gene-modified stem/progenitor cells was nominally effective; none of the RI regimens led to stable α-galactosidase A (α-gal A) correction. Secondly, transduced cells were preselected for functional transgene expression and transplanted at a higher dose (0.72 × 106 cells). Each RI regimen yielded engraftment of functional transgene-positive cells through 180 days along with increased plasma α-gal A activity. Importantly, the RI regimens mediated broad organ enzyme correction and were not associated with immune responses against α-gal A. RI conditioning thus has an important role in gene therapy for LSDs; a variety of regimens can be effective in this context.