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Glioblastoma is an aggressive cancer of the brain and spine. While analysis of glioblastoma ‘omics data has somewhat improved our understanding of the disease, it has not led to direct improvement in patient survival. Cancer survival is often characterized by differences in gene expression, but the mechanisms that drive these differences are generally unknown. We therefore set out to model the regulatory mechanisms associated with glioblastoma survival. We inferred individual patient gene regulatory networks using data from two different expression platforms from The Cancer Genome Atlas. We performed comparative network analysis between patients with long- and short-term survival. Seven pathways were identified as associated with survival, all of them involved in immune signaling; differential regulation of PD1 signaling was validated to correspond with outcome in an independent dataset from the German Glioma Network. In this pathway, transcriptional repression of genes for which treatment options are available was lost in short-term survivors; this was independent of mutational burden and only weakly associated with T-cell infiltration. Collectively, these results provide a new way to stratify patients with glioblastoma that uses network features as biomarkers to predict survival. They also identify new potential therapeutic interventions, underscoring the value of analyzing gene regulatory networks in individual patients with cancer. Significance: Genome-wide network modeling of individual glioblastomas identifies dysregulation of PD1 signaling in patients with poor prognosis, indicating this approach can be used to understand how gene regulation influences cancer progression.

Despite pronounced sex differences in cancer incidence, severity, and response to treatment, most current approaches to clinical management, as well as therapeutics development and selection, are sex-independent. For most cancer types, including liver cancer, males have a higher risk of developing the disease and a lower survival rate than women. However, the molecular features that drive these sex differences are poorly understood. We inferred patient-specific regulatory networks of liver hepatocellular carcinoma using data from TCGA. By comparing the female and male networks, we found marked sex differences in transcriptional regulatory processes relevant to disease development, progression, and response to therapy. We found that oncogenes have significantly higher regulatory targeting in males, while tumor suppressor genes have significantly higher targeting in females. Many “hallmark” cancer pathways, including the HEDGEHOG, WNT, and TGF-β signaling pathways, were significantly more highly targeted in males, while drug metabolism and immune related pathways were enriched for genes highly targeted in females. We also evaluated sex-biased somatic mutation patterns using mutation and copy number alteration data in TCGA. By summarizing mutations found in genes into pathway mutation scores, we found sex-biased mutation profiles for many pathways, providing additional support for biological sex differences associated with WNT, NOTCH, TGF-β, and HEDGEHOG signaling pathways. Our analysis uncovered patterns of gene regulation that differentiate male and female liver cancer and may be associated with sex differences in prognosis and treatment response. These findings provide insight into the mechanisms that drive clinically observed sex differences and underscore the importance of considering sex as a factor influencing disease etiology and in developing and prescribing therapies. Our network approach can provide insights into why some therapies have differential effect in males and females, and suggest new ways to optimize drug response in each sex. Citation Format: Camila M. Lopes-Ramos, Marieke Kuijjer, Kimberly Glass, Dawn DeMeo, John Quackenbush. Regulatory networks of liver carcinoma reveal sex specific patterns of gene regulation [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6569.

Understanding sex differences in colon cancer is essential to advance disease prevention, diagnosis, and treatment. Males have a higher risk of developing colon cancer and a lower survival rate than women. However, the molecular features that drive these sex differences are poorly understood. In this study, we use both transcript-based and gene regulatory network methods to analyze RNA-seq data from The Cancer Genome Atlas for 445 patients with colon cancer. We compared gene expression between tumors in men and women and observed significant sex differences in sex chromosome genes only. We then inferred patient-specific gene regulatory networks and found significant regulatory differences between males and females, with drug and xenobiotics metabolism via cytochrome P450 pathways more strongly targeted in females. This finding was validated in a dataset of 1,193 patients from five independent studies. While targeting, the drug metabolism pathway did not change overall survival for males treated with adjuvant chemotherapy, females with greater targeting showed an increase in 10-year overall survival probability, 89% [95% confidence interval (CI), 78–100] survival compared with 61% (95% CI, 45–82) for women with lower targeting, respectively (P = 0.034). Our network analysis uncovers patterns of transcriptional regulation that differentiate male and female colon cancer and identifies differences in regulatory processes involving the drug metabolism pathway associated with survival in women who receive adjuvant chemotherapy. This approach can be used to investigate the molecular features that drive sex differences in other cancers and complex diseases. Significance: A network-based approach reveals that sex-specific patterns of gene targeting by transcriptional regulators are associated with survival outcome in colon cancer. This approach can be used to understand how sex influences progression and response to therapies in other cancers. Cancer Res; 78(19); 5538–47. ©2018 AACR.

In the original version of [this article][1] ([1][2]), in the Disclosure of Potential Conflicts of Interest section, Dr. Charles S. Fuchs did not report consulting work with the biotechnology and pharmaceutical industry focused on cancer drug development. With respect to an analysis of molecular

Resistance to therapy is a major obstacle to a favorable outcome in cancer treatment. For rectal cancer, neoadjuvant chemoradiotherapy (nCRT) can lead to complete tumor regression in a significant proportion of patients (up to 40%) but approximately 60% of patients have only partial or no tumor remission after nCRT. A number of works searching for a differential gene expression signature has failed. As those gene signatures relies on the sample set, there is an increasing agreement that biological understanding is necessary to produce a signature in terms of pathways and biological processes. In this regard we applied pathway enrichment analysis to RNA-Seq data in order to identify biological pathways involved in tumor resistance and discriminate rectal cancer patients that is refractory to neoadjuvant treatment. Mitochondrial oxidative phosphorylation and phosphatidylinositol signaling were identified as the main pathways involved in resistance to nCRT in patients with rectal cancer. Both pathways have been reported as involved in resistance to radiotherapy and chemotherapy in solid tumors but according to the status of gene regulation observed and the literature, there is evidence that Akt pathway could be central in promoting resistance.Therefore, we evaluated the status of Akt activation by immunohistochemistry of pre-treatment biopsies of rectal tumors as well as by immunoblot of colorectal cancer cell lines utilizing antibodies against phosphorylated Akt (pS473). As a result, we observed an increased proportion of Akt phosphorylation in the resistant cell line, SW480, and in patients with TRG 0-2 in comparison to those with TRG 3-4 and in the sensitive cell line, SW48. To evaluate the implication of Akt in promoting nCRT resistance, we performed colony formation assays using Akt inhibitors as radiosensitizers. We observed an additive effect using MK2206 at sub-doses in combination to radiotherapy (2 Gy) in the resistant cell line. In fact, Akt inhibition improved in approximately 40% the tumoricidal effects of radiotherapy. Moreover, at IC50 dose this effect is even higher, reaching 60% the improvement of radiotherapy. Furthermore, the treatment of MK2206 with radiotherapy alone or in combination with 5-FU have similar effectiveness. In this setting, as Akt is involved in a range of cellular functions that promote tumor progression and metastasis, we propose that combination of Akt inhibitor and radiotherapy as neoadjuvant treatment would maximize tumor remission and improve the rectal cancer treatment. Citation Format: Fernanda C. Koyama, Camila Ramos, Angelita Habr-Gama, Venâncio Avancini Ferreira Alves, Rodrigo O. Perez, Anamaria Aranha Camargo. Implications of Akt inhibition for neoadjuvant radiotherapy: improving the rectal cancer treatment. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 391.