SUMMARY 3q26.2 amplification in high-grade serous ovarian cancer leads to increased expression of mature microRNA miR551b-3p, which is associated with poor clinical outcome. Importantly, miR551b-3p contributes to resistance to apoptosis and increased survival and proliferation of cancer cells in vitro and in vivo. miR551b-3p up-regulates STAT3 protein levels with STAT3 being required for the effects of miR551b-3p on cell proliferation. Rather than decreasing levels of target mRNA as expected, we demonstrate that miR551b-3p binds a complementary sequence on the STAT3 promoter recruiting RNA Polymerase II and the TWIST1 transcription factor to activate STAT3 transcription and thus directly upregulates STAT3 expression. Furthermore, anti-miR551b reduced STAT3 expression in ovarian cancer cells in vitro and in vivo and reduced ovarian cancer growth in vivo. Together our data demonstrates a role for miR551b-3p in transcriptional activation. Thus miR551b-3p represents a promising candidate biomarker and therapeutic target in ovarian cancer.

The goal of this pilot study was to determine in patients with operable breast cancer the incidence of breast cancer cells present in the blood, the clearance rate after surgical resection of the primary tumor, and the incidence of patients with persistent cancer cells in the blood after the primary tumor was removed. Twenty-one patients with operable breast cancer had 15 ml venous blood obtained twice prior to surgery and after surgery at 2, 4, 8, 12, 24, and 48 hours and also on days 7 and 14. Immunomagnetic selection of malignant cells was performed on each sample. Cells were then fixed on slides and immunocytochemistry performed on the collected cells. Cells that had a rosette of magnetic beads, cytoplasmic staining for keratin, and malignant morphology were counted as breast cancer cells. Eighteen of 19 of patients had cancer cells detected in at least one of the two blood samples preceding surgical removal of the primary tumor. The incidence of cancer cells in the blood of patients rapidly declined during the 48 hours postsurgery. The incidence of cancer cells in the blood remained stable in approximately 30% of patients to 14 days. The majority of breast cancer patients in this pilot study (even with small tumors and negative nodes) had detectable cancer cells in the blood prior to resection of the primary tumor. These findings justify further investigation. Successful application of this methodology may serve as a powerful indicator of which patients need systemic adjuvant therapy, the effectiveness of systemic adjuvant therapy, tumor recurrence, and early detection of breast cancer.

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BRAF-activating mutations are the most frequent driver mutations in papillary thyroid cancer (PTC). Targeted inhibitors such as dabrafenib have been used in advanced BRAF-mutated PTC; however, acquired resistance to the drug is common and little is known about other effectors that may play integral roles in this resistance. In addition, the induction of PTC dedifferentiation into highly aggressive KRAS-driven anaplastic thyroid cancer (ATC) has been reported. We detected a novel RAC1 (P34R) mutation acquired during dabrafenib treatment in a progressive metastatic lesion with ATC phenotype. To identify a potential functional link between this novel mutation and tumor dedifferentiation, we developed a cell line derived from the metastatic lesion and compared its behavior to isogenic cell lines and primary tumor samples. Our data demonstrated that RAC1 mutations induce changes in cell morphology, reorganization of F-actin almost exclusively at the cell cortex, and changes in cell adhesion properties. We also established that RAC1 amplification, with or without mutation, is sufficient to drive cell proliferation and resistance to BRAF inhibition. Further, we identified polyploidy of chromosome 7, which harbors RAC1, in both the metastatic lesion and its derived cell line. Copy number amplification and overexpression of other genes located on this chromosome, such as TWIST1, EGFR, and MET were also detected, which might also lead to dabrafenib resistance. Our study suggests that polyploidy leading to increased expression of specific genes, particularly those located on chromosome 7, should be considered when analyzing aggressive thyroid tumor samples and in further treatments.

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Purpose: Genomic aberrations in fibroblast growth factor receptor (FGFR) are oncogenic drivers in several cancers. FGFR inhibitors (FGFRi) have demonstrated antitumor activity in cholangiocarcinoma (CCA) with FGFR2 fusions/rearrangements, though acquired resistance remains a therapeutic challenge and has been linked to FGFR2 mutations other than fusions/rearrangements. We sought to investigate mechanisms of acquired resistance to FGFRi and approaches to overcome resistance. Methods: Longitudinal plasma samples were collected from patients with FGFR pathway alterations enrolled in the futibatinib phase I trial (NCT02052778) and sequenced using a targeted, 73-gene panel. A separate retrospective analysis was conducted to evaluate possible evolution of genomic aberrations in CCA patients with FGFR2 fusion/rearrangement who had additional tumor and/or plasma next-generation sequencing (NGS) following FGFRi therapy. To assess the efficacy of futibatinib in cells with FGFR2 fusions in vitro, a FGFR2-BICC1 fusion H69 cholangiocyte cell line was developed. MAPK pathway alterations (BRAF_V600E or KRAS_G12D) were introduced to determine the impact of these co-alterations on FGFRi sensitivity, and combinations were tested to determine if efficacy could be enhanced. Cell viability assays, colony formation assays, and western blots were utilized to determine the effects of these agents in engineered cells. Results: A total of 58 plasma samples were collected from 17 patients with FGFR pathway alterations who were enrolled in the futibatinib phase I trial, including 13 (76.5%) of which had CCA. One patient with a FGFR2-CTNNA3 fusion who had NRAS G12D and BRAF A694T at baseline which were undetected during treatment had a dramatic increase in their variant allele frequency (VAF) upon progression (4.2%-0.0%-100% and 2.8%-0.0%-50.9%, respectively). Further, additional MAPK alterations were detected at time of progression, including BRAF V600E, NRAS Q61K, NRAS G12C, NRAS G13D and KRAS G12K mutations. In our separate retrospective series, of 17 patients who underwent repeat tumor and/or plasma NGS following treatment with one or more FGFRi, 10 (58.8%) had newly detectable alterations in MAPK pathway genes, 10 (58.8%) had new FGFR2 alterations, and 7 (41.2%) developed new alterations in both FGFR2 and MAPK pathway genes. In vitro studies demonstrated that in isogenic H69 biliary cell lines, introduction of FGFR2-BICC1 robustly sensitized to FGFRi when compared to a parental cell line, which was blunted by the introduction of secondary KRAS_G12D or BRAF_V600E mutations. Conclusions: Convergent genomic evolution in the MAPK pathway may be a potential mechanism of acquired resistance to FGFRi therapy. Work is ongoing to determine if targeting co-alterations may enhance the efficacy of FGFRi in FGFR2-fusion driven malignancies. Citation Format: TImothy P. DiPeri, Ming Zhao, Tyler Moss, Michael Kahle, Payal Rauli, Sunyoung S. Lee, Abdel Halim, Hiroshi Hirai, Volker Wacheck, Karim Benhadji, Jordi Rodon, Milind Javle, Funda Meric-Bernstam. Convergent MAPK pathway alterations mediate acquired resistance to FGFR inhibitors in cholangiocarcinoma with FGFR fusions/rearrangements [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2618.

Objective: Metabolic changes occur initially at a molecular level, while genetic alterations further contribute to this shift and promote cancer cell survival and proliferation. We sought to identify genomic correlates of metabolic dysregulation in high grade serous ovarian cancer (HGSOC). Methods: We profiled 101 HGSOC samples and 15 normal ovarian tissues samples by LC/MS and GC/MS metabolic profiling; 172 significantly altered metabolites were identified. We classified these metabolites into altered pathways and carried out full-scale gene expression analyses. Results: We compared expression of measured metabolites for normal ovarian tissues and HGSOC and classified them into super pathways. We created a random forest classifier to generate a prediction model using metabolic profiles from normal tissue versus tumor within 3% error. From the random forest classification, the top 10% of significantly altered metabolites included gluconate, ADMA, and NAA. Carbohydrate, amino acid, and lipid super pathways were identified as the most important, with carbohydrate enrichment as significant (p = 0.03). Metabolites from the pentose phosphate pathway (PPP) and glycolysis were identified with this prediction model and found to be globally downregulated. Gene expression for enzymes in the PPP and glycolysis were compared between HGSOC and normal ovary and not found to be different. Gene expression ratios from the rate limiting steps in these pathways were evaluated. No significant difference was identified between gene ratios from normal and tumor tissues (p = 0.22) within our data set, but relative expression was significantly different within The Cancer Genome Atlas (TCGA) data set (p = 0.009). We subsequently generated a network that merged metabolic and gene level changes for enzymes coding for the synthesis and degradation of these metabolites, while accounting for time to recurrence in ovarian cancer patients for each gene within glycolysis and PPP. We then merged the genes identified by our network analysis with data from a whole-genome siRNA synthetic lethality screen (3 HGSOC chemoresistant cell lines). When GPI, the gene that encodes glucose-6-phosphate isomerase (PGI), was silenced, cellular lethality was observed across all cell lines tested. In our network analysis, GPI was among the most upregulated within the carbohydrate pathway within our cohort of ovarian cancer samples. In the TCGA data, ovarian cancer patients with tumoral GPI levels higher than the median had worse overall survival (p = 0.0002). Conclusions: Here, we present a novel systems-based approach using altered metabolites and genes to predict a malignant phenotype specific to HGSOC patients. Altered metabolism, coupled with genomic analyses, identified the most interconnected gene-biochemical networks that will lead to novel biomarkers and therapeutic targets. Citation Format: Rebecca A. Previs, Tyler J. Moss, Behrouz Zand, Rajesha Rupaimoole, Heather J. Dalton, Jean M. Hansen, Guillermo Armaiz-Pena, Susan Lutgendorf, Robert L. Coleman, Pratip Bhattacharya, Prahlad Ram, Anil K. Sood. Systems-based approach identifies altered carbohydrate metabolism as a predictor of a malignant phenotype in ovarian cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1199. doi:10.1158/1538-7445.AM2015-1199

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