Human SEC14L1 shows partial sequence homology to the budding yeast SEC14 protein and the Japanese flying squid retinal-binding protein and was previously generally localized to 17q25. We more precisely mapped SEC14L1 within a discrete region of 17q25 that likely harbors at least one putative breast and ovarian tumor suppressor gene. We determined that this gene consists of 18 exons ranging in size from 70 bp (exon 11) to 3088 bp (exon 17) and spanning at least 58 kb of DNA. Exon 17 contained a highly polymorphic variable number of tandem repeats (VNTR) and was present only in the larger ubiquitously expressed 5.5-kb transcript. The 3.0-kb ubiquitously expressed transcript included sequences at the beginning of exon 17 (designated exon 17a) and the end of exon 17 (designated exon 18), but lacked the internal 2439 bp of exon 17, including the VNTR. This alternative splicing resulted in a predicted protein of 719 residues from the smaller transcript with four more terminal amino acids than the 715 residue protein predicted from the larger transcript. EST H49244 spanned exon 11 of SEC14L1 and was specifically expressed in human peripheral blood leukocytes. One intragenic single nucleotide polymorphism (SNP) was confirmed. SEC14L1 contained the CRAL/TRIO domain also found in alpha-tocopherol transfer protein (TTPA) and cellular retinaldehyde-binding protein (CRALBP). As retinoids have been shown to inhibit the growth of breast cancer cells, loss of the proposed SEC14L1 retinal-binding function may contribute to breast tumorigenesis. As TTPA and CRALBP have been implicated in retinitis pigmentosa (RP), altered SEC14L1 expression may contribute to RP in previously unlinked families. Coding exon-specific PCR primers were designed to aid in future expression and mutational analyses.
88 Background: Men with metastatic, castration resistant prostate cancer (mCRPC) harboring DNA repair defects (̃20%) achieve a radiographic progression free survival of 7.4 months with PARP inhibitors (PARPi). Preclinical studies combining a PARPi (olaparib) and DNA damage checkpoint inhibitor (ATR inhibitor, ceralasertib) show synergy, providing the rationale to test this combination in men with mCRPC, including where single agent olaparib has been shown to be active. Methods: Two cohorts were accrued to a trial combining ceralasertib with olaparib in men a) with or b) without DNA repair defects. All patients progressed on ≥1 prior mCRPC therapy with no prior PARPi or platinum chemotherapy. The primary endpoint was disease response (confirmed PSA decline ≥50% and/or RECIST response), while disease progression was defined per Prostate Cancer Working Group 3 definition. Each cohort is analyzed independently for disease endpoints, while both groups were combined for toxicity assessments. Results: The 12 person DNA repair-deficient (DRDef) cohort allowed patients with germline BRCA2 loss (n = 4), somatic BRCA2 loss (n = 1) and ATM loss (n = 1 germline, n = 5 somatic and n = 1 somatic with unknown germline). 35 men without BRCA2/BRCA1 or ATM genomic loss were accrued to the DNA repair-proficient (DRPro) cohort. These men had next-generation sequencing (NGS) on contemporary biopsies (prior to enrolment without intervening therapy, 12), prior NGS on metastatic tissue (10), prior NGS on primary prostatic tissue (n = 3), or cell-free analyses (5). Five patients have incomplete cell-free analyses. At data cutoff (October 2021), in the DRDef cohort, the response rate by confirmed ≥50% PSA decline was 4/10 (40%) including 3 of 4 BRCA2 patients, and another is awaiting sufficient follow up; 1 of 6 ATM-deficient patients responded and another is awaiting sufficient follow up. All 4 DRDef responders remain on therapy (median of 8 months). For patients in the DRPro cohort who have completed therapy and response assessment (n = 21), 3 responded, one with a duration of 12 months, two with 6 months. An updated analysis will be presented. Conclusions: This analysis suggests potential activity of the doublet for DRDef (BRCA2 mainly) and DRPro mCRPC. Ongoing biomarker analysis (e.g. ATM IHC, contemporaneous cell-free DNA analysis rather than archived tissue) may help guide selection of patients most likely to benefit. Clinical trial information: NCT03787680.
530 Background: Localized muscle-invasive bladder cancer (MIBC) exhibits heterogeneous molecular features and outcomes, with a 5-year mortality rate of approximately 30%. Immune checkpoint blockade (ICB) has the potential to improve oncological outcomes but molecular tools are needed to identify those most likely to benefit. Here, we integrate transcriptomically derived tumor immune microenvironment (TIME) data with molecular subtypes to create a novel integrative classifier with prognostic and therapeutic implications. Methods: RNAseq data from patients with localized muscle-invasive bladder cancer (MIBC) from the Cancer Genome Atlas BLCA (TCGA-BLCA) project was utilized (n = 187). CIBERSORT was used for immune cell deconvolution, and unsupervised hierarchical clustering divided the cohort based on similar immune profiles. Consensus molecular clustering information for the cohort was obtained from Kamoun et al. Overall survival (OS) of each cluster were analyzed. The tumor immune dysfunction and exclusion (TIDE) tool, which uses a genomic signature validated on immunotherapy treated melanoma patients to model tumor immune evasion, was then used to predict response to ICB. Results: In the TCGA-BLCA cohort, there were two distinct clusters enriched with macrophages, CL1-M0Hi (n = 18) and CL5-M2Hi (n = 35). Compared to the rest of the cohort, these two macrophage enriched clusters combined exhibited a decreased OS (33.1 mo vs. NR, p = 0.01). TIDE tool predicted ICB response was lowest in CL1 (6/18, 33%; p = 0.09), CL5 (12/35, 34%; p = 0.02), and the Ba/Sq molecular cluster (16/57, 28%; p = 1.3x10-5). Patients designated as CL1 or CL5 by immune clustering and Ba/Sq by molecular consensus were combined into a subgroup (n = 20). Compared to the rest of the cohort, this Ba/Sq_MacrophageHi subgroup had a higher body mass index (31.0 vs. 25.8 BMI, p = 0.0004), more whites (95% vs. 64%, p = 0.03), and had a higher stage (80% Stage III/IV vs. 20% Stage I/II, p = 0.05). The Ba/Sq_MacrophageHi cluster demonstrated higher PD-L1 expression (mean Z score 0.15 vs. -0.09; p = 0.008), there was a higher degree of T cell exclusion (mean Z score 0.16 vs. -0.06; p = 0.003) and cancer-associated fibroblasts (mean Z score 0.03 vs. -0.02; p = 3.4x10-5). Overall, the predicted response to ICB by TIDE in the Ba/Sq_MacrophageHi was lower (OR 0.15, 0.03-0.55 p = 0.002) and OS was significantly shorter (median 16.7 mos vs. 54.9 mo, p = 0.04). Conclusions: We demonstrated the prognostic significance of the Basal/Squamous subtype with macrophage enrichment in patients with localized MIBC. Pending further prospective validation, this sub-population may be less amenable to ICB treatment.
Current cancer therapies typically give rise to dose-limiting normal tissue toxicity. We have developed KLIPP, a precision cancer approach that specifically kills cancer cells using CRISPR/Cas9 technology. The approach consists of guide RNAs that target cancer-specific structural variant junctions to nucleate two parts of a dCas9-conjugated endonuclease, Fok1, leading to its activation. We show that KLIPP causes induction of DNA double strand breaks (DSBs) at the targeted junctions and cell death. When cancer cells were grown orthotopically in mice, activation of Fok1 at only two junctions led to the disappearance of tumor cells in 7/11 mice. This therapeutic approach has high specificity for tumor cells and is independent of tumor-specific drivers. Individualized translation of KLIPP to patients would be transformative and lead to consistent and simplified cancer treatment decisions.
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