Abstract 307: KSR1-dependent modulation of the translational landscape in Ras-driven colorectal cancer

KRAS is mutated and activated in an estimated 40% of colon cancers but has proven difficult to target directly due to the lack of drug-binding pockets on the surface of Ras. Thus, identifying effectors that transmit signals from oncogenic Ras is a critical step in targeting vulnerabilities in the tumors of patients with colorectal cancer (CRC). Kinase Suppressor of Ras 1 (KSR1) is a molecular scaffold that coordinates the interaction of effectors in the Raf/MEK/ERK signaling cascade downstream of Ras. KSR1 is necessary for oncogenic transformation of cells expressing mutated Ras but is dispensable for normal cell growth making KSR1 an attractive therapeutic target for Ras-driven colon cancers. In CRC cells, KSR1 and ERK mediate Ras-dependent effects on protein translation, notably driving cap-dependent and cap-independent translation of the Myc oncogene. Depletion of KSR1 or treatment with ERK inhibitor (SCH772984) leads to a decrease in phophorylated 4EBP1 and a decrease in PDCD4, which collectively impair protein translation, notably leading to a decrease in Myc translation. Patient-derived CRC organoids with deletion of APC, p53, and SMAD4, and an activating G12D mutation in KRAS treated with ERK inhibitor show a marked decrease in Myc protein expression, coincident with changes in PDCD4 and 4EBP1 that impair protein translation. These observations indicate that the KSR1-dependent ERK activation observed in CRC cell lines is present in pre-clinical colon tumoroid models. Genome-wide polysome profiling in CRC cell lines HCT116 and HCT15 depleted of KSR1 identified mRNAs that were preferentially translated in a KSR1 and ERK-dependent manner. Several of these mRNAs were previously predicted by our Functional Signature Ontology (FUSION) screen to be critical to CRC viability but dispensable for normal cell growth. GSEA identified functional classes of mRNAs whose translation is KSR1-dependent, including mediators of oncogenic signaling in pathways that regulate mTOR, MAPK, WNT and JAK-STAT. Our data suggest that an essential component of oncogenic Ras-induced and KSR1-dependent signaling is the preferential translation of mRNAs supporting the transformed phenotype of CRC cells.

Citation Format: Heidi Vieira, Chaitra Rao, Adrian R. Black, Siddesh Southekal, Tomohiro Mizutani, Babu Guda, Hans Clevers, Jennifer D. Black, Robert E. Lewis. KSR1-dependent modulation of the translational landscape in Ras-driven colorectal cancer [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 307.

Abstract 743: Fusion gene identification from common cancer cell lines and comparison to primary tumors

Fusion transcripts, frequently observed in cancer, contribute to oncogenicity by either altering the expression of tumor suppressors/proto-oncogenes or modifying the original function of a protein resulting in an abnormal chimeric protein that stimulates tumorigenesis. Cancer cell lines, extensively used as in-vitro molecular models to study biological processes related to cancer, often do not represent the genomic profiles of primary tumors. To examine the true representation of the cancer cell lines, we examined fusions in tumor- derived cancer cell lines from 20 cancer types in the Cancer Cell Line Encyclopedia (CCLE) and compared them to fusions present in the primary tumors from the TCGA (The Cancer Genome Atlas). ChimeRScope, an alignment-free algorithm developed by our group, was used to screen fusion genes using level 1 paired-end RNA sequencing read data from CCLE and TCGA (GDC data portal). A total of 8,883 primary tumor samples, 730 normal samples spanning 33 cancer types from TCGA, and 802 common laboratory cell lines from CCLE were analyzed in this study. The pool of recurrent fusions identified from CCLE was vastly different from those identified in primary tumors with merely 2% of an overlap. Canonical fusions were found to be more common than non-canonical fusions (fusions containing genes in antisense strand) between TCGA and CCLE. Hierarchical clustering analysis of both canonical and non-canonical recurrent fusions in CCLE and TCGA clustered the primary tumors and cell lines into separate clusters, revealing that fusions in cell lines are vastly different from primary tumors. However, canonical and non-canonical fusion profiles of endometrial cancer cell lines were very similar to female primary tumors (ovarian and breast) and thyroid cancer cell lines were similar to bladder cancer in TCGA. The results from this study indicate that the recurrent fusions in common cancer cell lines harbor fusions that are significantly different from primary tumors.

Citation Format: Neetha Nanoth Vellichirammal, Abrar Albahrani, Jasjit K. Banwait, You Li, Babu Guda. Fusion gene identification from common cancer cell lines and comparison to primary tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 743.

Changes in ovarian protein expression during primordial follicle formation in the hamster

Although many proteins have been shown to affect the transition of primordial follicles to the primary stage, factors regulating the formation of primordial follicles remains sketchy at best. Differentiation of somatic cells into early granulosa cells during ovarian morphogenesis is the hallmark of primordial follicle formation; hence, critical changes are expected in protein expression. We wanted to identify proteins, the expression of which would correlate with the formation of primordial follicles as a first step to determine their biological function in folliculogenesis. Proteins were extracted from embryonic (E15) and 8-day-old (P8) hamster ovaries and fractionated by two-dimensional gel electrophoresis. Gels were stained with Proteosilver, and images of protein profiles corresponding to E15 and P8 ovaries were overlayed to identify protein spots showing altered expression. Some of the protein spots were extracted from SyproRuby-stained preparative gels, digested with trypsin, and analyzed by mass spectrometry. Both E15 and P8 ovaries had high molecular weight proteins at acidic, basic, and neutral ranges; however, we focused on small molecular weight proteins at 4-7 pH range. Many of those spots might represent post-translational modification. Mass spectrometric analysis revealed the identity of these proteins. The formation of primordial follicles on P8 correlated with many differentially and newly expressed proteins. Whereas Ebp1 expression was downregulated in ovarian somatic cells, Sfrs3 expression was specifically upregulated in newly formed granulosa cells of primordial follicles on P8. The results show for the first time that the morphogenesis of primordial follicles in the hamster coincides with altered and novel expression of proteins involved in cell proliferation, transcriptional regulation, and metabolism. Therefore, formation of primordial follicles is an active process requiring differentiation of somatic cells into early granulosa cells and their interaction with the oocytes.