Background A major impediment in the treatment of ovarian cancer is the relapse of chemotherapy-resistant tumors, which occurs in approximately 25% of patients. A better understanding of the biological mechanisms underlying chemotherapy resistance will improve treatment efficacy through genetic testing and novel therapies. Methods Using data from high-grade serous ovarian carcinoma (HGSOC) patients in the Cancer Genome Atlas (TCGA), we classified those who remained progression-free for 12 months following platinum-taxane combination chemotherapy as “chemo-sensitive” (N = 160) and those who had recurrence within 6 months as “chemo-resistant” (N = 110). Univariate and multivariate analysis of expression microarray data were used to identify differentially expressed genes and co-expression gene networks associated with chemotherapy response. Moreover, we integrated genomics data to determine expression quantitative trait loci (eQTL). Results Differential expression of the Valosin-containing protein (VCP) gene and five co-expression gene networks were significantly associated with chemotherapy response in HGSOC. VCP and the most significant co-expression network module contribute to protein processing in the endoplasmic reticulum, which has been implicated in chemotherapy response. Both univariate and multivariate analysis findings were successfully replicated in an independent ovarian cancer cohort. Furthermore, we identified 192 cis-eQTLs associated with the expression of network genes and 4 cis-eQTLs associated with BRCA2 expression. Conclusion This study implicates both known and novel genes as well as biological processes underlying response to platinum-taxane-based chemotherapy among HGSOC patients.

Cell-derived influenza vaccines provide better protection and a host of other advantages compared to the egg-derived vaccines that currently dominate the market, but their widespread use is hampered by a lack of high yield, low cost production platforms. Identification and knockout of innate immune and metabolic restriction factors within relevant host cell lines used to grow the virus could offer a means to substantially increase vaccine yield. In this paper, we describe and validate a novel genomewide pooled CRISPR/Cas9 screening strategy that incorporates a reporter virus and a FACS selection step to identify and rank restriction factors in a given vaccine production cell line. Using the HEK-293SF cell line and A/PuertoRico/8/1934 H1N1 influenza as a model, we identify 64 putative influenza restriction factors to direct the creation of high yield knockout cell lines. In addition, gene ontology and protein complex enrichment analysis of this list of putative restriction factors offers broader insights into the primary host cell determinants of viral yield in cell-based vaccine production systems. Overall, this work will advance efforts to address the public health burden posed by influenza. Cell-based influenza vaccine production. Mitigating the disease burden of influenza virus is an ongoing public health challenge, with 290,000-650,000 deaths annually and tenfold as many hospitalizations worldwide 1,2. The efficacy of influenza vaccines, which must be reformulated annually to adjust for antigenic drift and changes in dominantly circulating strains, has fluctuated between 10 and 60% since 2005 3. The vast majority (85-90%) of these vaccines are currently produced using embryonated chicken eggs, but a growing body of evidence suggests significant improvements in vaccine efficacy could be made by switching to cell-based manufacturing platforms 4. Passaging influenza through eggs induces antigenic drift as the virus adapts to an avian host 4-6. As a result, egg-based vaccines exhibit a 15-20% decrease in protection rate compared to similarly formulated cell-based vaccines 6-8. Cell-based platforms can also drastically reduce production lead time by accelerating seed stock reassortment via reverse genetics 9. This, in turn, reduces the chance of major changes in circulating strains occurring between initial strain selection and vaccine release, an issue that rendered the 2014-2015 seasonal vaccine largely ineffective 10,11. Additionally, the manufacturing capacity of cell-based vaccines is not constrained by the availability of billions of pathogen-free, synchronously fertilized chicken eggs, which would facilitate rapid response to influenza pandemics if they arise. Other advantages of cell-based vaccines include a lack of allergen contamination and better growth of certain strains 8. For all the benefits of cell-based influenza vaccines, current production platforms generally exhibit 4 to 10 fold lower volumetric yield than egg-based counterparts and are 40-100% more expensive 8,12. Given that influenza vaccine ...

High-grade serous ovarian cancer (HGSOC) is a highly lethal gynecologic cancer, in part due to resistance to platinum-based chemotherapy reported among 20% of patients. This study aims to generate novel hypotheses of the biological mechanisms underlying chemotherapy resistance, which remain poorly understood. Differential expression analyses of mRNA- and microRNA-sequencing data from HGSOC patients of The Cancer Genome Atlas identified 21 microRNAs associated with angiogenesis and 196 mRNAs enriched for adaptive immunity and translation. Coexpression network analysis identified three microRNA networks associated with chemotherapy response enriched for lipoprotein transport and oncogenic pathways, as well as two mRNA networks enriched for ubiquitination and lipid metabolism. These network modules were replicated in two independent ovarian cancer cohorts. Moreover, integrative analyses of the mRNA/microRNA sequencing and single-nucleotide polymorphisms (SNPs) revealed potential regulation of significant mRNA transcripts by microRNAs and SNPs (expression quantitative trait loci). Thus, we report novel transcriptional networks and biological pathways associated with resistance to platinum-based chemotherapy in HGSOC patients. These results expand our understanding of the effector networks and regulators of chemotherapy response, which will help to improve the management of ovarian cancer.

Background A major impediment in the treatment of ovarian cancer is the relapse of platinum-resistant tumors, which occurs in approximately 25% of patients. A better understanding of the biological mechanisms underlying platinum-based response will improve treatment efficacy through genetic testing and novel therapies.Methods Using data from high-grade serous ovarian carcinoma (HGSOC) patients in the Cancer Genome Atlas (TCGA), we classified those who remained progression-free for 12 months following platinum-based chemotherapy as “chemo-sensitive” (N=160) and those who had recurrence within six months as “chemo-resistant” (N=110). Univariate and multivariate analysis of expression microarrays identified differentially expressed genes and co-expression gene networks associated with chemotherapy response. Moreover, we integrated genomics data to determine expression quantitative trait loci (eQTL).Results Differential expression of the Valosin-containing protein (VCP) gene and five co-expression gene networks were associated with chemotherapy response in HGSOC. VCP and the gene networks contribute to protein processing in the endoplasmic reticulum, which has been implicated in chemotherapy response. These findings were successfully replicated using independent replication cohort. Furthermore, 192 QTLs were associated with these gene networks and BRCA2 expression.Conclusion This study implicates both known and novel genes as well as biological networks underlying response to platinum-based chemotherapy among HGSOC patients.

Ovarian cancer is a highly lethal gynecologic cancer, partly due to resistance to platinum-based chemotherapy reported among 20-30% of patients. This study aims to elucidate the biological mechanisms underlying chemotherapy resistance, which remain poorly understood. Using mRNA and microRNA sequencing data from high-grade serous ovarian cancer (HGSOC) patients from The Cancer Genome Atlas, we identified transcripts and networks associated with chemotherapy response. In total, 196 differentially expressed mRNAs were enriched for adaptive immunity and translation, and 21 differentially expressed microRNAs were associated with angiogenesis. Moreover, co-expression network analysis identified two mRNA networks associated with chemotherapy response, which were enriched for ubiquitination and lipid metabolism, as well as three associated microRNA networks enriched for lipoprotein transport and oncogenic pathways. In addition, integrative analyses of these sequence datasets revealed potential regulation of the mRNA networks by the associated microRNAs and single nucleotide polymorphisms. Thus, we report novel transcriptional networks and pathways associated with resistance to platinum-based chemotherapy among HGSOC patients. These results aid our understanding of the effector networks and regulators of chemotherapy response, which will improve drug efficacy and identify novel therapeutic targets for ovarian cancer.HighlightsmRNA and miRNA transcript networks associated with adjuvant chemotherapy responseIntegrative omics data analysis identified regulatory miRNAs and eQTLsProtein ubiquitination and immune activation associated with chemosensitivityIncreased translation and lipid metabolism may promote chemoresistance