Engineered nanotherapeutics for pulmonary aerosol delivery

Despite centuries of use and widespread application, aerosol delivery of therapeutics remains limited to a small subset of diseases and active pharmaceutical ingredients, mainly restricted to small molecule delivery for asthma management. Respiratory diseases which would benefit from direct and localized treatment span a much larger landscape; chronic obstructive pulmonary disease (COPD), lower respiratory infections, and lung cancers alone globally contribute 7.8 million annual deaths, with a reported 117 million pulmonary cases (~37% of population, 2012) and over $88 billion in health care costs in the US[1, 2]. To expand the application of aerosol delivery, novel approaches are needed. To address this need, we have explored various applications of nanoparticle immune engineering for respiratory therapeutics[3]. Incorrect immune responses lie at the heart of most respiratory diseases and advances in these therapeutic areas requires consideration of the unique environment. Notably, the lung has an abundance of antigen presenting cells (APCs), such as macrophages and dendritic cells (DC), which phagocytose foreign materials at the air-lung interface. There are a number of lung-specific APC populations[4, 5]. Some subsets are well understood, however, other specialized subsets have only recently been identified due to historic challenges in differentiating these populations[6, 7]. Thus, there are many remaining questions as to the division of labor between these cells, their significance in different disease conditions, and their interactions with other adjacent cell populations at the mucosal interface[8]. Advancing this understanding is critical to develop new therapeutics; APCs are poised as the gatekeepers to lung regulation and lung DC-subset specifically are likely cellular targets for therapeutic intervention[9]. In order to better understand how these lung innate immune cells respond to inhaled particle therapeutics, we have developed sets of engineered particles with defined physical properties that originate at the molecular level. We have developed a series of metal organic framework (MOF) nanoparticle carriers with independently tunable particle size and internal porosity, enabling systematic investigation of the effect of particle pore structure on cellular interactions. These UIO-66 MOF derivatives have not only been optimized as pulmonary aerosol carriers but provide critical insight on the role of internal particle porosity following cellular internalization. To further modulate the lung immune environment and evaluate the role of ligand surface density on immune-modulation, we simultaneously developed a series of degradable polymeric nanoparticle carriers with controlled surface densities of two Toll-like receptor (TLR) ligands, lipopolysaccharide (LPS), corresponding to TLR-4, and CpG oligodeoxynucleotide, corresponding to TLR-9[10]. Our in vitro results with murine bone marrow derived macrophages and in vivo studies following a direct instillation to murine airways both support a trade-off between particle dosage and optimal surface density; proinflammatory cytokine production was driven by the distribution of the adjuvant dose to a maximal number of innate cells, whereas the upregulation of costimulatory molecules on individual cells required an optimal density of TLR ligand on the particle surface. Taken together, results from these two sets of particle types demonstrate that both particle porosity and ligand surface density are critical parameters for tight control of immune stimulation and association with lung APCs and provide a foundation to build pathogen mimicking particle (PMP) vaccines and immunostimulatory therapeutics. References: 1. WHO: World Health Organization 2012. 2. NIH: National Heart, Lung, and Blood Institute 2012. 3. Moon, J. J.; Huang, B.; Irvine, D. J., Advanced materials (Deerfield Beach, Fla.) 2012, 24 (28), 3724-46. 4. Guilliams, M.; Lambrecht, B. N.; Hammad, H., Mucosal Immunol 2013, 6 (3), 464-73. 5. Kopf, M.; Schneider, C.; Nobs, S. P., Nat Immunol 2015, 16 (1), 36-44. 6. Blank, F.; Stumbles, P. A.; Seydoux, E.; Holt, P. G.; Fink, A.; Rothen-Rutishauser, B.; Strickland, D. H.; von Garnier, C., Am J Respir Cell Mol Biol 2013, 49 (1), 67-77. 7. Fytianos, K.; Drasler, B.; Blank, F.; von Garnier, C.; Seydoux, E.; Rodriguez-Lorenzo, L.; Petri-Fink, A.; Rothen-Rutishauser, B., Nanomedicine (Lond) 2016, 11 (18), 2457-2469. 8. Hasenberg, M.; Stegemann-Koniszewski, S.; Gunzer, M., Immunol Rev 2013, 25 (1), 189-214. 9. Zhao, L.; Seth, A.; Wibowo, N.; Zhao, C. X.; Mitter, N.; Yu, C.; Middelberg, A. P., Vaccine 2014, 32 (3), 327-37. 10. Noble, J.; Zimmerman, A.; Fromen, C. A., ACS Biomater Sci Eng 2017, 3 (4), 560-571

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothripsis across 2,658 tumors from 38 cancer types using whole-genome sequencing data. We find that chromothripsis events are pervasive across cancers, with a frequency of more than 50% in several cancer types. Whereas canonical chromothripsis profiles display oscillations between two copy-number states, a considerable fraction of events involve multiple chromosomes and additional structural alterations. In addition to non-homologous end joining, we detect signatures of replication-associated processes and templated insertions. Chromothripsis contributes to oncogene amplification and to inactivation of genes such as mismatch-repair-related genes. These findings show that chromothripsis is a major process that drives genome evolution in human cancer

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

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe

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

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

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.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 (VAFPeer reviewe