Hotspot Mutants Research Articles

Gb3-cSrc complex in glycosphingolipid-enriched microdomains contributes to the expression of p53 mutant protein and cancer drug resistance via β-catenin-activated RNA methylation.

Glucosylceramide synthase (GCS) is a key enzyme catalyzing ceramide glycosylation to generate glucosylceramide (GlcCer), which in turn serves as the precursor for cells to produce glycosphingolipids (GSLs). In cell membranes, GSLs serve as essential components of GSL‐enriched microdomains (GEMs) and mediate membrane functions and cell behaviors. Previous studies showed that ceramide glycosylation correlates with upregulated expression of p53 hotspot mutant R273H and cancer drug resistance. Yet, the underlying mechanisms remain elusive. We report herewith that globotriaosylceramide (Gb3) is associated with cSrc kinase in GEMs and plays a crucial role in modulating expression of p53 R273H mutant and drug resistance. Colon cancer cell lines, either WiDr homozygous for missense‐mutated TP53 (R273H+/+) or SW48/TP53‐Dox bearing heterozygous TP53 mutant (R273H/+), display drug resistance with increased ceramide glycosylation. Inhibition of GCS with Genz‐161 (GENZ 667161) resensitized cells to apoptosis in these p53 mutant‐carrying cancer cells. Genz‐161 effectively inhibited GCS activity, and substantially suppressed the elevated Gb3 levels seen in GEMs of p53‐mutant cells exposed to doxorubicin. Complex formation between Gb3 and cSrc in GEMs to activate β‐catenin was detected in both cultured cells and xenograft tumors. Suppression of ceramide glycosylation significantly decreased Gb3‐cSrc in GEMs, β‐catenin, and methyltransferase‐like 3 for m6A RNA methylation, thus altering pre‐mRNA splicing, resulting in upregulated expression of wild‐type p53 protein, but not mutants, in cells carrying p53 R273H. Altogether, increased Gb3‐cSrc complex in GEMs of membranes in response to anticancer drug induced cell stress promotes expression of p53 mutant proteins and accordant cancer drug resistance.

Abstract 724: Application of oncoMonitor™ ctDNA tracking technology for monitoring of therapy and early detection of recurrence in metastatic colorectal cancer

Abstract Introduction: Liquid biopsy based on detection of circulating tumor DNA (circulating-tumor DNA, ctDNA) is finding new applications in clinical management of solid cancers. From the initial use as an alternative to classical tissue biopsy for investigation of molecuar profiles in prediction or resistance detection of targeted therapies the approach is now applied to monitoring of minimal residual disease (MRD). Patients with metastatic colorectal cancer undergoing liver resection are subject to standard post-operative surveillance based mainly on periodic CT or PET/CT imaging (complemented eventually by MR imaging). Some reports have previously demonstrated benefit from performing a ctDNA detection complimentary to standard imaging to improve follow-up efficiency. Methods: In this report we demonstrate use of our oncoMonitor™ ctDNA technology, based on detection of somatic mutations derived from tumor in patient plasma. Unlike various approaches targeting oncogenic hotspot mutants, this technology can trace virtually any somatic mutation found in any gene (e.g. a tumor supressor). The relatively simple approach is based on rapid scanning of 100 to 140bp target amplicons for presence of mutations revealed based on differential melting by high-resolution denaturing capillary electrophoresis (DCE). The detection sensitivity is 0.1% MAF. Patients: In our concordance study during which a total of 41 patients with metatatic colorectal cancer were followed for 3 years from metastasectomy. oncoMonitor™ tast was applied to evaluate ctDNA along with standard CT or PET/CT imaging and tumor markers (CEA/CA19-9). Results: A total of 23 recurrences were clinically confirmed during surveillance. All recurrences were detected by oncoMonitor™ (23/23, 100%), while at the same time only 17 instances were detected by CT or PET/CT imaging (17/23, 73.9%) and 16 by tumor markers CEA/CA19-9 (16/23, 69.6%). There were 2 patients after R0 resection with persistent ctDNA positivity who had recurrence within 6 months from surgery. Conclusions: oncoMonitor™ technology is suitable for quick and sensitive detection of ctDNA in plasma of patients with metatatic colorectal cancer after liver resection. Evaluation of ctDNA presence improves efficiency of post-operative surveillance. Supported by Czech Ministry of Health project no. 17-31909A. Citation Format: Marek Minarik, Barbora Belsanova, Renata Ptackova, Tereza Halkova, Filip Pazdirek, Jiri Pudil, Miroslav Levy, Jaromir Simsa, Jiri Hoch, Miroslav Ryska, Lubos Petruzelka, Lucie Benesova. Application of oncoMonitor™ ctDNA tracking technology for monitoring of therapy and early detection of recurrence in metastatic 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 724.

Abstract NG16: Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors

Abstract NG16: Double <i>PIK3CA</i> mutations in <i>cis</i> increase oncogenicity and sensitivity to PI3Kα inhibitors

Real-time monitoring of distinct binding kinetics of hot-spot mutant p53 protein in human cancer cells using an individual nanorod-based plasmonic biosensor

Hot-spot mutant p53 proteins are highly associated with cancer malignancy and chemotherapy resistance of various cancers. Precise detection of the hot-spot mutant protein is therefore important in predicting therapeutic effects in cancer. However, conventional analytical methods such as liquid chromatography couple with tandem mass spectrometry (LC–MS/MS) and immunohistochemistry (IHC) have limited sensitivity as well as accuracy and require labor-intensive pretreatment steps. Here, an efficient individual nanorod-based plasmonic biosensor has been developed to detect hot-spot mutant p53 protein with the growth arrest and DNA damage 45 (GADD45) promoter. DNA-protein interactions of wild-type/mutant p53 proteins are kinetically analyzed on the biosensor surface through real-time monitoring of the localized surface plasmon resonance shift, and their dissociation constants and relative transcriptional activities are estimated. Hot-spot mutant proteins exhibited 14.29-fold higher in the dissociation constants and 19.91-fold lower in the relative transcriptional activities as compared to the wild-type proteins. These distinct kinetic values of hot-spot mutants allowed precise detection of hot-spot mutant protein and identification of mutated site of the protein using very small volume of clinical samples. We also demonstrated the clinical validation of the sensor by evaluating its performance in human breast tumor surgical specimens. The sensor’s ability to identify the mutant protein with high specificity and extremely low detection limit (11.47 fM) in comparison with the LC–MS/MS and IHC. The results confirmed that our sensor could be characterized as an efficient biosensor for application in clinical assays in terms of analytical performance.

Hotspot mutant p53-R273H inhibits KLF6 expression to promote cell migration and tumor metastasis

Hotspot p53 mutant proteins often gain novel functions in promoting tumor metastases. However, the molecular mechanisms by which mutant p53 exerts gain-of-function in cancer are not totally understood. In this study, we demonstrate that hotspot mutant p53, p53-R273H, promotes cell scattering growth and migration via inhibiting the expression of Krupple-like factor 6 (KLF6), a Zinc finger transcription factor and a documented tumor suppressor. Restoration of KLF6 increases the expression of E-cadherin downregulated by p53-R273H and inhibits p53-R273H-induced cell migration and tumor metastasis. Further, p53-R273H reduces KLF6 transcription by upregulating EGFR expression which in turn activates AKT–FOXO1 axis. Pharmacological inhibitor of AKT, MK2206, rescues KLF6 expression and suppresses p53-R273H-induced cell migration. Clinical analyses reveal that KLF6 expression is decreased in human breast cancer specimens harboring p53 mutations, and negatively correlated with EGFR expression in human breast cancer. In addition, low expression of KLF6 is associated with poor overall survival (OS) and relapse-free survival (RFS) in p53 mutated human breast cancer patients. Together, these results reveal an important role for EGFR–AKT–FOXO1–KLF6–E-cadherin axis in mutant p53-induced cell migration and tumor metastasis.

MiR129-1 regulates protein phosphatase 1D protein expression under hypoxic conditions in non-small cell lung cancer cells harboring a TP53 mutation.

Protein phosphatase 1D (PPM1D), which functions as an oncogene, is a known target of the tumor suppressor p53 and is involved in p53-regulated genomic surveillance mechanisms. PPM1D dephosphorylates both p53 and its ubiquitin ligase mouse double minute 2 homolog, as well as the RNA-binding protein (RBM)38, which turns RBM38 from an inducer to inhibitor of TP53 translation. In addition, RBM38 induces PPM1D translation. Hence, the PPM1D-RBM38-p53 axis is important in maintaining genomic integrity and is often altered during tumorigenesis. TP53, which encodes p53, is deleted or mutated in >50% of cancer types, including lung cancer. Mutant p53 has been revealed to complex with hypoxia-inducible factor 1α (HIF1α) and upregulate transcription of pro-metastatic genes. However, the mechanism underlying the action of the PPM1D-RBM38-p53 axis in the context of mutant p53 under normoxic and hypoxic conditions is yet to be elucidated. In the present study, using non-small cell lung cancer (NSCLC) cell lines harboring wild-type (A549 cells) or hot-spot mutant (NCI-H1770 and R249WΔ-TP53-A549 cells) TP53, it was demonstrated that in cells harboring mutant p53, RBM38 was not the primary regulator of PPM1D translation under hypoxic conditions. Knockdown of RBM38 in TP53 mutant cells did not affect the PPM1D protein expression under hypoxic conditions. Instead, in NCI-H1770 cells maintained under normoxic conditions, PPM1D was revealed as a target of micro RNA (miR)-129-1-3p, a known tumor suppressor in lung cancer. Hypoxia resulted in the downregulation of miR-129-1-3p expression, and thus, in the downregulation of PPM1D messenger RNA (mRNA) translation. In NCI-H1770 cells grown under hypoxic conditions, the transient transfection of miR-129-1-3p mimic, and not control mimic, repressed the expression of a reporter containing wild-type, but not miR-129-1-3p binding mutant, of the PPM1D 3′-untranslated region (UTR). Analysis of NSCLC cell lines from the Broad Institute Cancer Cell Encyclopedia and patients with NSCLC from The Cancer Genome Atlas dataset revealed significant co-occurrence of PPM1D/RBM38 and PPM1D/HIF1A mutations. However, there was no significant difference in the overall survival of patients with NSCLC with or without genomic alterations in TP53, RBM38, PPM1D and HIF1A. In summary, the current study demonstrated hypoxia-dependent miR-129-1-3p-mediated regulation of PPM1D protein expression in NSCLC cell line harboring mutant TP53.

The Mutant p53-Driven Secretome Has Oncogenic Functions in Pancreatic Ductal Adenocarcinoma Cells

The cancer secretome is a rich repository of useful information for both cancer biology and clinical oncology. A better understanding of cancer secretome is particularly relevant for pancreatic ductal adenocarcinoma (PDAC), whose extremely high mortality rate is mainly due to early metastasis, resistance to conventional treatments, lack of recognizable symptoms, and assays for early detection. TP53 gene is a master transcriptional regulator controlling several key cellular pathways and it is mutated in ~75% of PDACs. We report the functional effect of the hot-spot p53 mutant isoforms R175H and R273H on cancer cell secretome, showing their influence on proliferation, chemoresistance, apoptosis, and autophagy, as well as cell migration and epithelial-mesenchymal transition. We compared the secretome of p53-null AsPC-1 PDAC cells after ectopic over-expression of R175H-mutp53 or R273H-mutp53 to identify the differentially secreted proteins by mutant p53. By using high-resolution SWATH-MS technology, we found a great number of differentially secreted proteins by the two p53 mutants, 15 of which are common to both mutants. Most of these secreted proteins are reported to promote cancer progression and epithelial-mesenchymal transition and might constitute a biomarker secreted signature that is driven by the hot-spot p53 mutants in PDAC.

Ovarian mucinous tumors with mural nodules: immunohistochemical and molecular analysis of 3 cases

BackgroundPrimary ovarian mucinous tumors with mural nodules are very rare. The histogenesis of the mural nodules remains unclear.MethodsWe investigated the clincopathological and molecular features in 3 cases with mural nodules.ResultsPatient 1 was diagnosed as mucinous carcinoma with mural nodules of anaplastic carcinoma that was composed of CK+ and CK7+ spindled cells and polygonal cells with marked pleomorphism. Aberrant p53 staining was found in the mural nodules rather than in the mucinous components. A concordant KRAS mutation (c.35G > A p.G12A) was identified in both mucinous tumors and mural nodules. She died of disease at 44 months. The mural nodule in patient 2 was interpreted as a sarcoma, no other specified. The uniform short spindle cells were separated by abundant myxoid matrix. They were CD10 + , CCND1-, SMA-, and negative for break-apart BCOR, PHF1, and JAZF1 FISH assay. The adenocarcinomatous component harbored LOH at D18S51 and FGA loci while the sarcomatous component had LOH at D19S433. She had lung metastasis at 18 months and was alive without evidence of disease for 40 months. Patient 3 harbored multiple mural nodules that were composed of vimentin+, focal CK+, atypical spindle cells. A diagnosis of sarcoma-like mural nodules was rendered. She was alive with no evidence of disease for 13 months. No hotspot mutant AKT1, KRAS, HRAS, and PI3KCA alleles were found in patients 2 and 3.ConclusionsMural nodules with anaplastic carcinoma or with true sarcomas may represent the dedifferentiation form of mucinous tumors or collision tumors, respectively. The worrisome histology in sarcoma-like mural nodules necessitates meticulous treatment for these patients.

Circulating tumor DNA correlates with microvascular invasion and predicts tumor recurrence of hepatocellular carcinoma.

BackgroundTo evaluate the feasibility of predicting tumor recurrence of hepatocellular carcinoma (HCC) patients after curative hepatectomy by detection of circulating tumor DNA (ctDNA) through droplet digital PCR (ddPCR).MethodsHCC patients receiving surgical treatment were enrolled and peripheral blood samples before and after hepatectomy were collected. Four hotspot mutants, TP53-rs28934571 (c.747G>T), TRET-rs1242535815 (c.1-124C>T), CTNNB1-rs121913412 (c.121A>G) and CTNNB1-rs121913407 (c.133T>C) were selected to detect ctDNA and the mutant allele frequency (MAF) was calculated accordingly. The matched peripheral blood mononuclear cells (PBMCs) were used for Sanger sequencing. The clinicopathologic information of the patients was retrospectively analyzed and the predictive abilities for postoperative recurrence of different clinicopathologic parameters and ctDNA were compared.ResultsEighty-one patients were enrolled and 70.4% (57/81) of them had detectable ctDNA before hepatectomy. Positive preoperative ctDNA status was related to larger tumor size (P=0.001), multiple tumor lesions (P=0.001), microvascular invasion (MVI) (P<0.001), advanced BCLC stages (P<0.001) and shorter disease free survival (DFS) (P<<0.001) and overall survival (OS) (P<<0.001). Multivariate analysis showed that detectable ctDNA was the independent risk factor for postoperative recurrence. Moreover, receiver operating characteristic (ROC) curves proved that ctDNA possessed the second largest area under the curve (AUC) in foretelling postoperative recurrence right after BCLC stage. For patients after surgery, the alterations of MAF were also correlated to postsurgical recurrence. Patients with increased MAF had more incidences of MVI (P=0.016) and recurrence (P<0.001). At the same time, Kaplan-Meier curves revealed a significant shorter DFS and OS in the patients with increased MAF compared to the patients with decreased MAF (P<0.001 and P=0.0045, respectively) and ROC curves showed MAF to possess the greatest AUC among all the indices for postoperative recurrence.ConclusionsDigital droplets PCR assessment of specific gene combination through ctDNA possesses potential prognostic value in HCC patients undergoing surgical treatment.

The novel BET‐CBP/p300 dual inhibitor NEO2734 is active in SPOP mutant and wild‐type prostate cancer

CULLIN3‐based E3 ubiquitin ligase substrate‐binding adaptor gene SPOP is frequently mutated in prostate cancer (PCa). PCa harboring SPOP hotspot mutants (e.g., F133V) are resistant to BET inhibitors because of aberrant elevation of BET proteins. Here, we identified a previously unrecognized mutation Q165P at the edge of SPOP MATH domain in primary and metastatic PCa of a patient. The Q165P mutation causes structural changes in the MATH domain and impairs SPOP dimerization and substrate degradation. Different from F133V hotspot mutant tumors, Q165P mutant patient‐derived xenografts (PDXs) and organoids were modestly sensitive to the BET inhibitor JQ1. Accordingly, protein levels of AR, BRD4 and downstream effectors such as RAC1 and phosphorylated AKT were not robustly elevated in Q165P mutant cells as in F133V mutant cells. However, NEO2734, a novel dual inhibitor of BET and CBP/p300, is active in both hotspot mutant (F133V) and non‐hotspot mutant (Q165P) PCa cells in vitro and in vivo. These data provide a strong rationale to clinically investigate the anti‐cancer efficacy of NEO2734 in SPOP‐mutated PCa patients.

Abstract 4627: Mutant p53 regulation in a Li-Fraumeni mouse model

Abstract The p53 tumor suppressor is maintained mainly at low physiological levels in normal cells by its two major inhibitors, Mdm2 and Mdm4. Mdm2 is a E3 ubiquitin ligase while Mdm4 binds to p53 and inhibits its transactivation activity. Deletion of either inhibitor results in p53-dependent embryonic lethality in mice. p53 is one of the most commonly mutated genes in human cancer. While we have gained considerable knowledge about wild-type p53 regulation and mode of action, our understanding of the oncogenic activity of mutant p53 lags behind. We know that mutant p53 is regulated in the same manner as wild-type p53. In a mouse model of Li-Fraumeni syndrome, Mdm2 binds and inhibits the hot spot mutant p53R172H (p53R175H in humans). Here we show that Mdm4, like Mdm2, regulates p53R172H stability in vivo, and that endogenous Mdm2 cannot compensate for this stabilization. Thus, mutant p53 mice that lack Mdm4 have stable high levels of p53R172H and display accelerated tumor development and an increased range of tumor types, compared to mutant p53 mice. Furthermore, when we compared mutant mice with the loss of two different alleles of both negative regulators, Mdm2 and Mdm4, we observed an even higher level of p53. This finding reveals that several tissues can tolerate high expression of oncogenic p53 and indicates a collaborative activity of these inhibitors in regulating mutant p53. The analysis of these mice uncovered new and unexpected functions of mutant p53 that we will discuss for the first time at the AACR 2019 meeting. Citation Format: Tamara Terzian, Molly Plehaty, Nema Sobhani, Wanida Stevens, Stefan Marasligiller, Tara Srinivas, Rohan Mylavarapu, Yvonne Clarke, Farinaz Arbab, Brendon Podell, Roderick Bronson. Mutant p53 regulation in a Li-Fraumeni mouse model [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 4627.

Abstract 3080: Activity of pan-FGFR inhibitor rogaratinib and PI3K inhibitor copanlisib in preclinical urothelial bladder cancer models

Abstract Rogaratinib is a potent small molecule pan-FGFR inhibitor that leads to downregulation of MAPK and PI3K signaling (1). In a recent Phase I study rogaratinib demonstrated higher ORR in locally advanced or metastatic urothelial bladder cancer (UBC) with FGFR mRNA overexpression in patients with PIK3CA and RASwildtype than in those harboring PIK3CA or RAS mutations (2). In UBC, about 25% of tumors contain mutated PIK3CA of which 75% represent hot spot mutations E545K or E542K (3). Copanlisib is a potent pan class I PI3K inhibitor with predominant activity against the α and δ isoforms being approved for treatment of relapsed follicular lymphoma (4). We evaluated the activity of rogaratinib in cellular and in vivo efficacy studies in bladder cancer models in monotherapy and in combination with copanlisib. Cell proliferation and viability in response to rogaratinib, copanlisib or the combination of both was studied in rogaratinib-sensitive UBC cell lines like RT112 as well as in a recombinant RT112-PIK3CAE545K cell line. Rogaratinib potently inhibited cell proliferation with IC50 values in the double nM range. Copanlisib’s potency varied between 20 and 900 nM. In combination, rogaratinib and copanlisib increased cell death and were synergistic as shown by their proliferation combination indices for the absolute IC50 and IC80. Expression of the PIK3CAE545K hot spot mutant in RT112 cells decreased the anti-proliferative efficacy of rogaratinib but did not change the sensitivity to copanlisib. In vivo, rogaratinib led to tumor regression in the FGFR1-expressing JMSU1 xenograft and strongly inhibited tumor growth in the FGFR3-driven RT112 model. Copanlisib did not show significant inhibition of tumor growth in monotherapy in either model. In the JMSU1 model the combination was not superior to rogaratinib alone at maximal tolerated doses. In the RT112 as well as in the RT112-PIK3CAE545K model, the combination significantly improved anti-tumor activity. In a PDX model with FGFR3 overexpression and a PIK3CAH1047R hot spot mutation rogaratinib did not inhibit tumor growth significantly while copanlisib displayed significant anti-tumor effects. The combination of both drugs reduced tumor growth compared to either monotherapy group. In conclusion, in UBC tumor models overexpressing FGFR with differing sensitivities to rogaratinib, its anti-tumor activity could be further enhanced when combined with copanlisib and suggests that PIK3CA mutations may play a role in reduced sensitivity of UBC to FGFR inhibition. These promising results warrant further development of rogaratinib in monotherapy and in combination. Clinical trials with rogaratinib are currently recruiting (NCT03517956, NCT03410693, NCT03473756).

Abstract 1026: Oncogenic alterations in FGFR3 and ERBB2 lead to ligand-independent activation of PPARG in bladder cancer

Abstract PPARG is genomically activated in muscle-invasive bladder cancer through focal PPARG gene amplification and hotspot mutations in its heterodimer partner, RXRA. However, more than half of the PPARG-activated bladder tumors and cell lines do not have identifiable somatic alterations in either PPARG or RXRA. Using a PPARG-driven reporter assay in RT112 bladder cancer cell line, we screened probe compounds to identify candidate drivers of ligand-independent PPARG activation. We found that pan-FGFR inhibitors and MEK1/2 inhibitors antagonized the PPARG-driven reporter assay with potency similar to reported values for their cognate targets (1-20 nM) and interestingly, RT112 cells carry an FGFR3-TACC3 oncogenic fusion. In addition to the expected effects of these inhibitors on phospho-MEK1/2 and phospho-ERK1/2, they also inhibited production of canonical PPARG targets, including FABP4. In a second subset of cell lines, a parallel story was also observed for the effects of ERBB2 inhibitors in ERBB2 hotspot mutant bladder cancer. Taken together, these data uncover additional mechanisms for functional activation of PPARG in bladder cancer, suggest potential resistance mechanisms for FGFR and ERBB2 inhibitors, and provide a rationale for therapeutic combinations of PPARG modulators. Citation Format: Jonathan T. Goldstein, Ashton C. Berger, Craig A. Strathdee, Matthew Meyerson. Oncogenic alterations in FGFR3 and ERBB2 lead to ligand-independent activation of PPARG in bladder cancer [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 1026.

Abstract 3917: Double PIK3CA mutations in cis enhance oncogene activation and sensitivity to PI3K alpha inhibitors in breast cancer

Abstract Activating mutations in PIK3CA, the gene coding for the catalytic subunit (p110α) of phosphoinositide 3-kinase (PI3K), are the most frequent oncogenic alterations in all cancers, including estrogen receptor-positive (ER+) breast cancer. There are many distinct oncogenic PIK3CA mutations including major hotspot mutations (e.g. E542K, E545K, H1047R) which are predictive of response to PI3Kα inhibitors. While responses to PI3Kα inhibitors can be variable, some patients with single hotspot mutant tumors derive a deep and prolonged clinical benefit. In a comprehensive analysis of the genomic data available in breast cancer, we observed double PIK3CA mutations and investigated their potential biological relevance and potential correlation with sensitivity to PI3Kα inhibitors. We detected double PIK3CA mutations in 10-15% of all PIK3CA-mutant cancers including breast cancer. Double PIK3CA mutations in breast cancer are defined by a pattern of co-expression of a major hotspot mutation associated with a recurrent second-site PIK3CA mutation (‘minor mutation’). We have found that these double PIK3CA mutations are compound, that is in cis on the same allele, using single molecule real time sequencing (SMRT-seq) of fresh breast tumor samples. Double compound PIK3CA mutations result in increased PI3K activity and downstream signaling compared to single hotspot mutants in nontransformed cells and in ER+ breast cancer cells. Double compound mutations also increase cell proliferation and xenograft growth compared to single hotspot mutants. Biochemical experiments using recombinant PI3K compound mutant protein complexes reveal a combination mechanism of action, with simultaneous PI3K destabilization and increased membrane binding compared to single hotspot mutants, leading to increased kinase activity. Importantly, these compound mutations predict for increased sensitivity to PI3Kα inhibitors compared to single hotspot mutants in both preclinical models and also in patients with breast cancer. Together, our data support that double compound PIK3CA mutations enhance the oncogenicity of single hotspot PIK3CA mutations and this increased dependency results in increased sensitivity to PI3Kα inhibitors compared to single hotspot mutations. We propose that double compound activating mutations are an additional mechanism of oncogenic transformation in addition to other known mechanisms such as gene amplification, point mutation, or gene translocation. We speculate that double compound mutant PIK3CA may function as a clinical biomarker of increased sensitivity to PI3K-directed targeted therapies and may improve the therapeutic window of PI3K inhibitors in ER+ breast cancer and other PIK3CA-mutant tumor histologies. Citation Format: Neil Vasan, Pedram Razavi, Jared Johnson, Hong Shao, Hardik Shah, Alesia Antoine, Erik Ladewig, Alexander Gorelick, Eneda Toska, Guotai Xu, Abiha Kazmi, Matthew T. Chang, Barry S. Taylor, Maura N. Dickler, Komal Jhaveri, Raul Rabadan, Ed Reznik, Melissa L. Smith, Robert Sebra, Lewis C. Cantley, Maurizio Scaltriti, Jose Baselga. Double PIK3CA mutations in cis enhance oncogene activation and sensitivity to PI3K alpha inhibitors in breast cancer [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 3917.

The prognostic role of a novel TP53 mutation classifier in resectable esophageal squamous-cell carcinoma.

e14749 Background: TP53 is the most recurrently mutated gene in esophageal squamous-cell carcinoma (ESCC). However, the effect of TP53 mutation status on the prognosis for patients with ESCC remains controversial. Also, there has been no consensus on the minimal genomic region necessary for clinical TP53 genetic testing. Methods: We retrospectively examined somatic mutations in all coding exons of the TP53 gene in 161 resectable ESCC patients by next-generation sequencing. We then stratified patients by multiple TP53 mutation classifiers based on different mutant features and analyzed its association with clinicopathological features and disease outcome by univariable and multivariable analysis. Results: We detected TP53 mutations in 138 of the 161 patients (85.7%), among which 61 patients harbored a non-disruptive mutation in the DNA-binding domain (DBD). The presence of TP53 mutation, hotspot mutant, and the mutation number alone was not predictive of any disease features and prognosis. We identified a prognostic effect of harboring the non-disruptive and DBD mutation of TP53 with an HR 0.362 (95% CI: 0.212–0.620, P &lt; 0.001) and 0.486 (95% CI: 0.277–0.853, P = 0.012) for 5-year progression-free (PFS) and overall survival (OS), respectively. Multivariable analysis revealed it as an independent prognostic predictor for PFS (HR: 0.414, 95% CI: 0.230–0.746, P = 0.003) and OS (HR: 0.414, 95% CI: 0.207–0.825, P = 0.012). In particular, this TP53 mutation classifier defined a patient subset more beneficial from peri-operative radiotherapy with improved 5-year PFS (P = 0.020) and OS (P = 0.036). Conclusions: It is of clinical importance to examine and identify the non-disruptive somatic mutation in DBD of the TP53 gene for resectable ESCC.

The lung-enriched p53 mutants V157F and R158L/P regulate a gain of function transcriptome in lung cancer.

Lung cancer is the leading cause of cancer-related deaths in the USA, and alterations in the tumor suppressor gene TP53 are the most frequent somatic mutation among all histologic subtypes of lung cancer. Mutations in TP53 frequently result in a protein that exhibits not only loss of tumor suppressor capability but also oncogenic gain-of-function (GOF). The canonical p53 hotspot mutants R175H and R273H, for example, confer upon tumors a metastatic phenotype in murine models of mutant p53. To the best of our knowledge, GOF phenotypes of the less often studied V157, R158 and A159 mutants-which occur with higher frequency in lung cancer compared with other solid tumors-have not been defined. In this study, we aimed to define whether the lung mutants are simply equivalent to full loss of the p53 locus, or whether they additionally acquire the ability to drive new downstream effector pathways. Using a publicly available human lung cancer dataset, we characterized patients with V157, R158 and A159 p53 mutations. In addition, we show here that cell lines with mutant p53-V157F, p53-R158L and p53-R158P exhibit a loss of expression of canonical wild-type p53 target genes. Furthermore, these lung-enriched p53 mutants regulate genes not previously linked to p53 function including PLAU. Paradoxically, mutant p53 represses genes associated with increased cell viability, migration and invasion. These findings collectively represent the first demonstration that lung-enriched p53 mutations at V157 and R158 regulate a novel transcriptome in human lung cancer cells and may confer de novo function.

Cancer therapeutic targeting using mutant\u2013p53-specific siRNAs

Mutations in Tp53 compromise therapeutic response, due either to the dominant-negative effect over the functional wild-type allele; or as a result of the survival advantage conferred by mutant p53 to which cancer cells become addicted. Thus, targeting mutant p53 represents an effective therapeutic strategy to treat over half of all cancers. We have therefore generated a series of small-interfering-RNAs, capable of targeting four p53 hot-spot mutants which represent ~20% of all p53 mutations. These mutant–p53-specific siRNAs (MupSi) are highly specific in silencing the expression of the intended mutants without affecting wild-type p53. Functionally, these MupSis induce cell death by abrogating both the addiction to mutant p53 and the dominant-negative effect; and retard tumor growth in xenografts when administered in a therapeutic setting. These data together demonstrate the possibility of targeting mutant p53 specifically to improve clinical outcome.

Hotspot Mutations in SF3B1 Result in Increased Alternative Splicing in Multiple Myeloma and Activation of Key Cellular Pathways

Introduction: Mutations in the components of the spliceosome have been shown to occur at relatively high frequency in many cancers such as chronic lymphocytic leukemia, myelodysplastic syndromes and breast cancer. One component in particular, encoded by SF3B1, has hotspot missense mutations that result in a significant increase in alternatively spliced transcripts. RNA splicing in Multiple Myeloma (MM) has not been investigated and in particular the extent of mutations in SF3B1 and its effects on the transcriptome.Methods: Using the MMRF CoMMpass dataset (N=1273) of newly diagnosed MM patients, samples with whole exome sequencing (WES) were analyzed for mutations using Strelka and Mutect, and samples with SF3B1 mutations identified. A range of approaches were used to explore the effect of the SF3B1 mutations on the transcriptome and to determine possible downstream effects. Using RNA-seq with matched WES samples (n=615), the splice junction usage of SF3B1 mutants was compared against non-mutated samples which were matched for key MM molecular sub-types. The RNA-seq data was analyzed using a pipeline that included STAR and Salmon, aligning to human reference genome hg38, gene and transcript differential expression analysis tools DESeq2 and StringTie/Ballgown, differential splicing exon usage tools JunctionSeq/QoRTs, DEXSeq, and SUPPA and for Gene Set Enrichment Analysis (GSEA) the R package FGSEA was used.Results: From the WES data 1.7% (22/1273) of samples had mutations in SF3B1 of which 5 had mutations in the hotpot codons of K666 and K700. Differential isoform analysis of the 22 SF3B1 mutant samples compared to non-mutated samples did not identify any transcripts. However, when the analysis was restricted to the 5 samples with hotspot mutations differential gene expression identified 146 genes that were significantly differentially expressed at an adjusted p-value <0.05. Additionally, many genes that did not show an overall gene expression change between the control and the SF3B1 hotspot mutants did at transcriptional level where we observed isoform switching which included the protein coding genes BCL2L1, SNUR, ACKR3 and CRLF2.Results of differential gene analysis between the control and SF3B1 mutants were used in GSEA and significant normalized enrichment scores (NES) identifying increased protein secretion (p-value =0.009, NES= 1.9) and unfolded protein response (UPR) (p-value = 0.02, NES = 1.52) pathways. Conversely GSEA identified decreased apoptosis (p-value = 0.008, NES = -1.76), KRAS signaling (p-value = 0.008, NES = -1.92), TNFA signaling via NF-κB (p-value = 0.008, NES= 2.12) pathways in SF3B1 mutant samples.Investigation of splicing loci revealed that novel splice loci were significantly more abundant in the SF3B1 mutants versus control samples. Differential splicing analysis detected 474 genes to be significantly differentially spliced and of those 311 were not found to be differentially expressed at the gene level, indicating that alternative splicing is as important alternative mechanism to gene expression differences. 59 novel splice sites were identified, as well as 152 known splice sites and 218 exon significant differential usage with a p-value of < 0.05. The genes with most significant levels of alternative splicing and found by more than one approach were DYNLL1, TMEM14C, CRNDE, BRD4 and BCL2L1, several of which are also seen in other cancers with mutated SF3B1.Conclusions: Hotspot mutations in SF3B1 result in alternative splicing of genes as well as the introduction of novel splice sites. The confirmation that SF3B1 hotspot mutations in MM increases alternative splicing as well as the identification of the genes undergoing alternative splicing may present novel therapeutic targets. Gene expression analysis of these samples identifies key deregulated pathways, perhaps in response to alternative splicing, including the UPR and protein secretion pathways. These analyses indicate that disruption of these pathways are potential avenues of therapeutic intervention in patients with SF3B1 mutations. DisclosuresOrtiz:Celgene Corporation: Employment, Equity Ownership. Flynt:Celgene Corporation: Employment, Equity Ownership. Thakurta:Celgene Corporation: Employment, Equity Ownership. Morgan:Celgene: Consultancy, Honoraria, Research Funding; Takeda: Consultancy, Honoraria; Janssen: Research Funding; Bristol-Myers Squibb: Consultancy, Honoraria.

Wild-type p53 oligomerizes more efficiently than p53 hot-spot mutants and overcomes mutant p53 gain-of-function via a “dominant-positive” mechanism

Human p53 protein acts as a transcription factor predominantly in a tetrameric form. Single residue changes, caused by hot-spot mutations of the TP53 gene in human cancer, transform wild-type (wt) p53 tumor suppressor proteins into potent oncoproteins - with gain-of-function, tumor-promoting activity. Oligomerization of p53 allows for a direct interplay between wt and mutant p53 proteins if both are present in the same cells – where a mutant p53's dominant-negative effect known to inactivate wt p53, co-exists with an opposite mechanism – a “dominant-positive” suppression of the mutant p53's gain-of-function activity by wt p53. In this study we determine the oligomerization efficiency of wt and mutant p53 in living cells using FRET-based assays and describe wt p53 to be more efficient than mutant p53 in entering p53 oligomers. The biased p53 oligomerization helps to interpret earlier reports of a low efficiency of the wt p53 inactivation via the dominant-negative effect, while it also implies that the “dominant-positive” effect may be more pronounced. Indeed, we show that at similar wt:mutant p53 concentrations in cells – the mutant p53 gain-of-function stimulation of gene transcription and cell migration is more efficiently inhibited than the wt p53's tumor-suppressive transactivation and suppression of cell migration. These results suggest that the frequent mutant p53 accumulation in human tumor cells does not only directly strengthen its gain-of-function activity, but also protects the oncogenic p53 mutants from the functional dominance of wt p53.

Exome Sequencing of Plasma DNA Portrays the Mutation Landscape of Colorectal Cancer and Discovers Mutated VEGFR2 Receptors as Modulators of Antiangiogenic Therapies.

Purpose: Despite the wide use of antiangiogenic drugs in the clinical setting, predictive biomarkers of response to these drugs are still unknown.Experimental Design: We applied whole-exome sequencing of matched germline and basal plasma cell-free DNA samples (WES-cfDNA) on a RAS/BRAF/PIK3CA wild-type metastatic colorectal cancer patient with primary resistance to standard treatment regimens, including inhibitors to the VEGF:VEGFR2 pathway. We performed extensive functional experiments, including ectopic expression of VEGFR2 mutants in different cell lines, kinase and drug sensitivity assays, and cell- and patient-derived xenografts.Results: WES-cfDNA yielded a 77% concordance rate with tumor exome sequencing and enabled the identification of the KDR/VEGFR2 L840F clonal, somatic mutation as the cause of therapy refractoriness in our patient. In addition, we found that 1% to 3% of samples from cancer sequencing projects harbor KDR somatic mutations located in protein residues frequently mutated in other cancer-relevant kinases, such as EGFR, ABL1, and ALK. Our in vitro and in vivo functional assays confirmed that L840F causes strong resistance to antiangiogenic drugs, whereas the KDR hot-spot mutant R1032Q confers sensitivity to strong VEGFR2 inhibitors. Moreover, we showed that the D717V, G800D, G800R, L840F, G843D, S925F, R1022Q, R1032Q, and S1100F VEGFR2 mutants promote tumor growth in mice.Conclusions: Our study supports WES-cfDNA as a powerful platform for portraying the somatic mutation landscape of cancer and discovery of new resistance mechanisms to cancer therapies. Importantly, we discovered that VEGFR2 is somatically mutated across tumor types and that VEGFR2 mutants can be oncogenic and control sensitivity/resistance to antiangiogenic drugs. Clin Cancer Res; 24(15); 3550-9. ©2018 AACR.