Loss Of P53 Function Research Articles

Wnt/B-catenin activation and TP53 mutations associate with distinct immune profiles in advanced thyroid cancer.

Anaplastic thyroid carcinomas (ATCs) and poorly differentiated thyroid carcinomas (PDTCs) exhibit distinct immune-related gene expression profiles. Most ATCs are characterized by active immune interactions (hot or altered immunosuppressed immunophenotypes), while PDTCs are largely immunologically inert (cold immunophenotypes). This study aimed to elucidate the mechanisms driving these divergent immunological fates, focusing on the Wnt/β-catenin pathway and TP53 mutations. Our data reveal that ATCs frequently harbor TP53 mutations (83.3%), which correlate with a hot immunophenotype, characterized by high expression of β-catenin-regulated cytokine CCL4 and recruitment of CD103+ dendritic cells. Conversely, PDTCs, with a lower incidence of TP53 mutations (12.5%), often exhibit a cold immunophenotype. In cold cancers and PDTCs, β-catenin is overexpressed suggesting that Wnt/β-catenin pathway activation drives immune exclusion through CCL4 downregulation.Further analysis indicated that loss of p53 function is inversely correlated with β-catenin expression. P53-mutated cancers showed significantly higher expression of CCL4 and densities of CD103+ dendritic cells compared to their p53-wild-type counterparts. Additionally, p53-mutated ATCs expressed a higher number of immune-related genes, supporting the role of p53 loss in activating immune responses in cancer. Our study indicates a potential correlation between the activation of the Wnt/β-catenin pathway and the development of cold thyroid cancers, which may be mediated by the suppression of CCL4 expression. Concurrently, mutations in the p53 gene appear to be linked with the occurrence of hot thyroid cancers. While these associations are compelling, they are based on observational data. Experimental research is necessary to determine the causal relationships underlying these findings.

17p13 (TP53) Deletions Are Associated With an Aggressive Phenotype but Unrelated to Patient Prognosis in Urothelial Bladder Carcinomas.

17p13 deletions including TP53 and other genes represent a common cause for reduced/lost p53 function in tumor cells. In this study, we analyzed the impact of 17p13 (TP53) deletions and p53 expression on tumor aggressiveness and patient prognosis in urothelial carcinoma. The 17p13 copy number status was analyzed by fluorescence in situ hybridization (FISH) on more than 2700 urothelial bladder carcinomas in a tissue microarray format. 17p13 deletion data were compared to p53 expression data measured by immunohistochemistry (IHC) in a previous study. Different types of p53 alterations were compared with tumor phenotype and clinical outcome data. Deletions of 17p13 occurred in 23% of 2185 analyzable carcinomas. The fraction of tumors with 17p13 deletions increased from pTa G2 low (9%) to pTa G3 (24%, p < 0.0001). In muscle-invasive carcinomas, 17p13 deletions were associated with advanced pT stage (p = 0.0246), but unrelated to patient prognosis (p > 0.5). 17p13 deletions were significantly related to p53 immunostaining (p = 0.0375). 17p13 deletions were most common in tumors with complete lack of p53 staining (31%), which supports the concept that many of these tumors have a complete loss of p53 function (p53 null phenotype). 17p13 deletions were also increased in tumors with high p53 staining (25%). In conclusion, 17p13 deletions were most commonly seen in p53 negative cancers, supporting their role as a cause for the p53 null phenotype in urothelial cancer. The association of 17p13 deletions with high grade and advanced pT stage may reflect increasing genomic instability going along with stage and grade progression.

Activating transcription factor 3 mediates apoptosis and cell cycle arrest in TP53-mutated anaplastic thyroid cancer cells

BackgroundIt is believed that loss of p53 function plays a crucial role in the progression of well to poorly differentiated thyroid cancers including anaplastic thyroid carcinoma (ATC). Given the poor prognosis of ATC due to its strong therapeutic resistance, there is a need to establish new therapeutic targets to extend the survival of ATC patients. Activating transcription factor 3 (ATF3) can inhibit the oncogenic activity of mutant p53 and, as a result, contribute to tumor suppression in several TP53-mutated cancers. Herein, we demonstrate that the ectopic overexpression of ATF3 leads to the suppression of oncogenic mutant p53 activity in chemo-resistant 8305 C thyroid cancer cells harboring R273C p53 gene mutation.MethodsThe biological behavior of 8305 C cells was assessed pre- and post-transfection with pCMV6-ATF3 plasmid using MTT assay, fluorescent microscopy, cell cycle, and annexin V/PI flow cytometric analysis. The effect of ectopic ATF3 overexpression on the cellular level of p53 was examined by western blotting assay. The mRNA expression levels of TP53, TAp63, ΔNp63, and SHARP1 were evaluated in ectopic ATF3-expressing cells compared to controls.ResultsThe overexpression of ATF3 in 8305 C thyroid cancer cells significantly decreased cell viability and induced apoptosis and cell cycle arrest in vitro. The immunoblotting of p53 protein revealed that ATF3 overexpression significantly increased the level of mutant p53 in 8305C cells compared to mock-transfected control cells. Additionally, elevated mRNA levels of TAp63 and SHARP1 and a decreased mRNA level of ΔNp63 were observed in PCMV6-AC-ATF3-transfected 8305 C cells with significant differences compared to the mock and untreated cells.ConclusionIn light of our findings, it is evident that therapeutic strategies aimed at increasing ATF3 expression or enhancing the interaction between ATF3 and mutant p53 can be a promising approach for the treatment of p53-mutated metastatic thyroid cancer.

Abstract SY12-01: Targeting validated but un-drugged oncogenes with small molecule protein degraders

Abstract SY12-01: Targeting validated but un-drugged oncogenes with small molecule protein degraders

Amyloid aggregates induced by the p53-R280T mutation lead to loss of p53 function in nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is a malignant tumor that is highly prevalent in Southeast Asia, especially in South China. The pathogenesis of NPC is complex, and genetic alterations of tumor suppressors and proto-oncogenes play important roles in NPC carcinogenesis. p53 is unexpectedly highly expressed in NPC and possesses an uncommon mutation of R280T, which is different from a high frequency of hotspot mutations or low expression in other tumors. However, the mechanism of p53 loss of function and its correlation with R280T in NPC are still unclear. In this study, p53 amyloid aggregates were found to be widespread in NPC and can be mainly induced by the R280T mutation. Aggregated p53-R280T impeded its entry into the nucleus and was unable to initiate the transcription of downstream target genes, resulting in decreased NPC cell cycle arrest and apoptosis. In addition, NPC cells with p53-R280T amyloid aggregates also contributed aggressively to tumor growth in vivo. Transcriptome analysis suggested that p53 amyloid aggregation dysregulated major signaling pathways associated with the cell cycle, proliferation, apoptosis, and unfolded protein response (UPR). Further studies revealed that Hsp90, as a key molecular chaperone in p53 folding, was upregulated in NPC cells with p53-R280T aggregation, and the upregulated Hsp90 facilitated p53 aggregation in turn, forming positive feedback. Therefore, Hsp90 inhibitors could dissociate p53-R280T aggregation and restore the suppressor function of p53 in vitro and in vivo. In conclusion, our study demonstrated that p53-R280T may misfold to form aggregates with the help of Hsp90, resulting in the inability of sequestered p53 to initiate the transcription of downstream target genes. These results revealed a new mechanism for the loss of p53 function in NPC and provided novel mechanistic insight into NPC pathogenesis.

Histone deacetylase inhibition sensitizes p53-deficient B-cell precursor acute lymphoblastic leukemia to chemotherapy.

In pediatric acute lymphoblastic leukemia (ALL), mutations/deletions affecting the TP53 gene are rare at diagnosis. However, at relapse about 12% of patients show TP53 aberrations, which are predictive of a very poor outcome. Since p53-mediated apoptosis is an endpoint for many cytotoxic drugs, loss of p53 function frequently leads to therapy failure. In this study we show that CRISPR/Cas9-induced loss of TP53 drives resistance to a large majority of drugs used to treat relapsed ALL, including novel agents such as inotuzumab ozogamicin. Using a high-throughput drug screen, we identified the histone deacetylase inhibitor romidepsin as a potent sensitizer of drug responsiveness, improving sensitivity to all chemotherapies tested. In addition, romidepsin improved the response to cytarabine in TP53-deleted ALL cells in vivo. Together, these results indicate that the histone deacetylase inhibitor romidepsin can improve the efficacy of salvage therapies for relapsed TP53-mutated leukemia. Since romidepsin has been approved for clinical use in some adult malignancies, these findings may be rapidly translated to clinical practice.

Loss of p53 function promotes DNA damage-induced formation of nuclear actin filaments

Tumor suppressor p53 plays a central role in response to DNA damage. DNA-damaging agents modulate nuclear actin dynamics, influencing cell behaviors; however, whether p53 affects the formation of nuclear actin filaments remains unclear. In this study, we found that p53 depletion promoted the formation of nuclear actin filaments in response to DNA-damaging agents, such as doxorubicin (DOXO) and etoposide (VP16). Even though the genetic probes used for the detection of nuclear actin filaments exerted a promotive effect on actin polymerization, the detected formation of nuclear actin filaments was highly dependent on both p53 depletion and DNA damage. Whilst active p53 is known to promote caspase-1 expression, the overexpression of caspase-1 reduced DNA damage-induced formation of nuclear actin filaments in p53-depleted cells. In contrast, co-treatment with DOXO and the pan-caspase inhibitor Q-VD-OPh or the caspase-1 inhibitor Z-YVAD-FMK induced the formation of nuclear actin filament formation even in cells bearing wild-type p53. These results suggest that the p53-caspase-1 axis suppresses DNA damage-induced formation of nuclear actin filaments. In addition, we found that the expression of nLifeact-GFP, the filamentous-actin-binding peptide Lifeact fused with the nuclear localization signal (NLS) and GFP, modulated the structure of nuclear actin filaments to be phalloidin-stainable in p53-depleted cells treated with the DNA-damaging agent, altering the chromatin structure and reducing the transcriptional activity. The level of phosphorylated H2AX (γH2AX), a marker of DNA damage, in these cells also reduced upon nLifeact-GFP expression, whilst details of the functional relationship between the formation of nLifeact-GFP-decorated nuclear actin filaments and DNA repair remained to be elucidated. Considering that the loss of p53 is associated with cancer progression, the results of this study raise a possibility that the artificial reinforcement of nuclear actin filaments by nLifeact-GFP may enhance the cytotoxic effect of DNA-damaging agents in aggressive cancer cells through a reduction in gene transcription.

Targeting TP53 disruption in chronic lymphocytic leukemia: Current strategies and future directions.

In the modern era of Chronic Lymphocytic Leukemia (CLL) targeted therapy, the loss of p53 function due to genetic abnormalities remains a significant challenge. This is because even targeted agents, which are currently the mainstay of treatment for CLL, do not directly target p53 or restore its disrupted pathway. Consequently, resistance to therapy and unfavorable clinical outcomes often accompany these p53-related abnormalities. An essential goal of future clinical research should be to address the ostensibly "undruggable" p53 pathway. Currently, multiple therapeutic approaches are being explored to tackle TP53 dysfunction and improve outcomes in high-risk CLL. These approaches include the use of oncoprotein murine double minute 2 inhibitors, small-molecule p53 reactivators, exportin 1 (XPO1) inhibitors, and ataxia-telangiectasia mutated and Rad3-related (ATR) inhibitors. Combinations of these p53-targeting strategies, along with established novel therapies such as B-cell receptor or B-cell lymphoma-2 (BCL-2) inhibitors, may shape the future of therapeutic trials in this challenging-to-treat disease.

TP53 Aberrant B-Cell Precursor Acute Lymphoblastic Leukemia (BCP-ALL) Are Uniquely Sensitive to a Combination of Pyrimidine De Novo Synthesis Blockade and Replication Checkpoint Inhibition

Background Unlike most solid tumors, the incidence of TP53 aberrations in ALL is only 3% at diagnosis. However, in relapsed ALL this number increases to 12%. More importantly, at relapse, loss of p53 function is associated with therapy failure, with an overall survival of only 20%. Hence, there is a clear clinical need for more effective strategies to treat TP53 aberrant relapsed ALL. Owing to their high proliferative state, leukemic blasts show a high dependency on pyrimidines for DNA synthesis. A lack of pyrimidines leads to replication stress, causing activation of p53 and the DNA damage response pathway. Results We used CRISPR/Cas9 to generate TP53 deficient variants of the TP53 proficient BCP-ALL cell lines Nalm6 and RCH-ACV. We used these cell lines in a CRISPR screens and high throughput drug screen, and identified a strong synergy between the targeting of pyrimidine synthesis and DNA checkpoint kinase ATR and its downstream effectors Chk1 and Wee1 in TP53 deficient ALL. To validate these results, we tested the efficacy of a checkpoint inhibition together with Orludodstat (BAY-2402234), an inhibitor of Dihydroorotate Dehydrogenase (DHODH), a key enzyme in de novo pyrimidine biosynthesis. This clinical grade inhibitor was evaluated in either wild type or TP53 deficient BCP-ALL and T-ALL cell line models and patient derived xenografts (PDX). A strong apoptotic response was observed when Orludodstat was combined with the ATR inhibitor Berzosertib, most notably in TP53 deficient ALL. This p53 dependency was confirmed using ex vivo cultures of patient derived xenografts (PDX) of diagnosis and relapse pairs, where each diagnostic sample was wild type for TP53, and the relapse carried a TP53 aberration. While little or no synergy was observed in the diagnostic samples, a strong efficacy of the combination was observed in the matched TP53 deficient relapsed samples (Figure 1 A). Preliminary results from i n vivo experiments using p53 deficient patient derived xenografts indicate that the combination of Orludodstat and Berzosertib is well tolerated, while significantly delaying leukemic growth (Figure 1 B). Conclusion Together, our findings suggest that the combined targeting of de novo pyrimidine synthesis and ATR signaling may present a specific and non-genotoxic vulnerability for TP53 aberrant ALL.

Loss of p53 Impairs Death Receptor Expression and Confers Resistance to CD19-Directed CAR T-Cell Therapy in B-Cell Precursor Acute Lymphoblastic Leukemia

Background In recent years, new therapy strategies such as the antibody-drug conjugate inotuzumab ozogamicin, the bi-specific T-cell engager blinatumomab, and chimeric antigen receptor (CAR) T-cells have been introduced to salvage relapsed precursor B acute lymphoblastic leukemia (ALL). However, recent evidence indicates that these new therapies are ineffective in TP53-aberrant ALL, although the mechanism remains unclear. TP53 is the most frequently mutated gene in cancer, but in ALL, mutations or deletions affecting TP53 are rare, with an incidence of only 3% at diagnosis. However, at relapse, TP53 aberrations are found in approximately 12% of the patients and predict a very poor outcome. Consequently, relapsed TP53 deleted ALL is now classified as ‘very high risk’. Since p53-mediated apoptosis is an endpoint for many (cytotoxic) drugs, loss of p53 function induces therapy resistance to classical chemotherapeutics. Hence, there is a clear clinical need for more effective strategies to treat TP53 aberrant relapsed ALL. Methods Using CRISPR/Cas9, we introduced frameshift mutations in the TP53 gene to generate isogenic wild type and knockout models in TP53 WT ALL cell lines Nalm6 and RCH-ACV. Additionally, we prepared CD19-directed CAR T-cells with a 4-1BB co-stimulatory domain from three healthy donors by isolating, transducing, and expanding CD4+ and CD8+ T-cells separately. With flow cytometry, we assessed survival of p53 WT and p53 KO leukemic cells in the presence of CD4+ and CD8+ CAR T-cells at a 1:1 CD4:CD8 ratio. Moreover, we performed mRNA profiling by qRT-PCR and cell membrane profiling by flow cytometry to determine how loss of p53 affects CAR T mediated killing. Initial findings in cell lines were then validated in patient-derived xenografts. Results We observed that loss of p53 led to up to a 35% decrease in killing by overnight CAR T treatment in both cell line models (Figure 1A). Although loss of p53 has been linked to reduced cell surface expression of CD19 (Pan et al., 2020, Leukemia), no changes in CD19 expression were observed in response to p53 loss. In search for an explanation for the diminished killing, we performed mRNA profiling and found a reduced expression of death receptors CD95/Fas and DR5/TRAILR2 in p53-deficient cells, which was confirmed at the protein level with flow cytometry (Figure 1B). Indeed, CRISPR/Cas9 mediated loss of CD95/Fas expression in p53 wild type cells reduced CAR T mediated cell killing, consistent with a key role for CD95/Fas in T-cell mediated killing. Conversely, treatment of p53 proficient cells with MDM2 inhibitors induced expression of CD95/Fas and DR5/TRAILR2 (Figure 1B), which translated into enhanced killing of target cells. Most of these observations have already been recapitulated in a diagnosis-relapse pair of patient-derived cells in which the diagnosis was p53wild typeand the relapse was p53 deficient (Figure 1A-B). We observed lower baseline mRNA expression of CD95/Fas and DR5/TRAILR2 in p53-deficient cells, accompanied by a 50% reduction in killing relative to the p53 wild type controls. Conversely, MDM2 inhibition increased death receptor expression only in p53-proficient cells. The ongoing experiments validating enhanced killing after MDM2 inhibition in patient-derived cells will be presented during the meeting. Conclusions Loss of p53 impairs expression of CD95/Fas and DR5/TRAILR2, thereby protecting ALL cells from CAR T induced cell death. In addition, our results indicate that the p53-controlled expression of these receptors may be exploited to increase the efficacy of CAR T-cell therapy in p53-proficient patients.

THU496 A Positive Relationship Exists Between CARF And AR In Prostate Cancer

Abstract Disclosure: K.M. Hasan: None. H. Khambati: None. R.R. Huerta: None. J. Vadgama: None. A.P. Sinha-Hikim: None. T.C. Friedman: None. Prostate cancer (PCa) is the second most prevalent cancer among men worldwide. Since PCa onset is androgen dependent, androgen deprivation therapy (ADT) is the first treatment choice for a primary tumor or metastatic PCa. However, ADT eventually leads to the development of castration resistant PCa (CRPC), which is the leading cause of higher mortality in PCa. Thus, there is a need to identify the underlying mechanisms of CRPC to manage this aggressive disease. Increased androgen receptor (AR) expression is one of the most important factors contributing to the development of CRPC. It has been shown that tumor suppressor p53 negatively regulates the expression of AR. So, loss of p53 functions has been associated with increased expression of AR in advanced PCa. However, the mechanism of p53-mediated inhibition of AR is not well understood. In this study, we demonstrated that CARF (CDKN2AIP), a p53 pathway regulatory protein, is highly expressed in PCa, but its significance in PCa development is unknown. Since, like AR, CARF is negatively regulated by p53, we hypothesize that a reciprocal relationship between CARF and p53 could regulate AR expression in PCa cells. Indeed, we found that activation of p53 by DNA damage stress inhibited both CARF and AR in LnCap and 22RV1, AR-positive, and wtp53 cell lines. Our result indicated that CARF and AR were decreased dose-dependent manner, and presumably, that could trigger cell death. Consistent with this speculation, we found that silencing CARF by ShRNA in LnCap triggered apoptosis and inhibition of cell proliferation. With great interest, we further demonstrated that silencing of CARF downregulated the AR level in LnCap and 22RV1 cells suggesting that CARF regulates the expression of AR in PCa. RT-PCR results showed that AR transcripts remained unchanged in CARF-depleted LnCap cells. This result indicated that CARF could regulate the AR stability but not the transcription. Intriguingly, we found that the expression of NEDD4, one of the AR-targeting E3 ligases, was increased in CARF-depleted cells. Therefore, by enhancing the stability, CARF could positively regulate the expression of AR in PCa cells. Further studies are in progress to know more details about the CARF-mediated AR regulation and its impact on androgen-independent PCa development and progression. Presentation: Thursday, June 15, 2023

Comprehensive Analysis of the Prognostic Significance of the TRIM Family in the Context of TP53 Mutations in Cancers.

The p53 protein is an important tumor suppressor, and TP53 mutations are frequently associated with poor prognosis in various cancers. Mutations in TP53 result in a loss of p53 function and enhanced expression of cell cycle genes, contributing to the development and progression of cancer. Meanwhile, several tripartite motif (TRIM) proteins are known to regulate cell growth and cell cycle transition. However, the prognostic values between TP53 and TRIM family genes in cancer are unknown. In this study, we analyzed the relationship between the TP53 mutations and TRIM family proteins and evaluated the prognostic significance of TRIM family proteins in cancer patients with P53 mutations. Our findings identified specific TRIM family members that are upregulated in TP53 mutant tumors and are associated with the activation of genes related to a cell-cycle progression in the context of TP53 mutations.

CREATION OF ISOGENIC CELL LINE MODELS OF 17P DELETION TO STUDY CLONAL EVOLUTION AND MECHANISMS OF THERAPY RESISTANCE IN CLL AND DLBCL

Introduction: A deletion of chromosome 17p (del17p), on which the tumour suppressor gene TP53 is located, is a prevalent genetic aberration in many cancer types. In chronic lymphocytic leukaemia (CLL), diffuse large B-cell lymphoma (DLBCL), and other B cell malignancies this chromosomal mutation is associated with high fitness advantage in the setting of therapy, and the most adverse clinical outcome. Whilst resistance to the chemoimmunotherapies often used in the treatment of CLL and DLBCL can be explained by the functional loss of p53, such deactivation does not explain the increase in aggressive behaviour of the malignant cells. To study this, we aimed to develop in-vitro models of 17p deletion in CLL and DLBCL by creating TP53 (15.6 kbp) and 17p (20.5 Mbp) deletions by means of CRISPR-Cas9 genome editing. Methods: The efficiency of the gene editing machineries were firstly assessed in the adherent human colorectal cancer cell line HCT116 prior to their application on the B-cell lines, which are less amenable to genetic manipulation. TP53 gene removal (15.6 kbp) was performed by transient transfection of a vector encoding Cas9 as well as single guide (sg) RNAs targeting upstream and downstream of the TP53 coding region. For deletion of 17p (20.5 Mbp) sgRNAs targeting exon 2 of GEMIN4 (telomeric) and intron 5 of MAP2K3 (centromeric) were designed. PCR was used to confirm deletions. Results: Isogenic HCT116 cell lines with hemizygous and homozygous TP53 deletion, as well as hemizygous 17p deletion were obtained (Figure 1). HG-3 cells, a CLL cell line, were successfully transduced with inducible-Cas9, and subsequently with the sgRNAs for removal of TP53 and 17p. Keyword: Tumor Biology and Heterogeneity No conflicts of interests pertinent to the abstract.

Longitudinal mutational analysis of TP53 in plasma circulating tumor DNA (ctDNA) in patients (pts) with solid tumors in a phase I study of BI 907828, an MDM2–p53 antagonist.

3036 Background: Inactivation of p53 can occur due to TP53 mutations or downregulation of wild-type p53 by its primary negative regulator, MDM2. Targeting the MDM2–p53 interaction may therefore restore p53 function. BI 907828, a highly potent MDM2–p53 antagonist, is being evaluated in a phase Ia/b study in pts with advanced solid tumors (NCT03449381). During dose escalation (phase Ia), BI 907828 demonstrated a manageable safety profile and early signs of efficacy. Here we present data from a longitudinal mutational analysis of TP53 using ctDNA. The objective of the analysis was to identify if mutations in TP53 can be associated with possible acquired resistance to BI 907828. Methods: Collection of blood samples for ctDNA analyses was optional and sampled longitudinally from pts at baseline and every cycle until end of treatment (EoT). ctDNA was purified from plasma and analyzed using tumor-specific next generation sequencing (NGS; custom-made 8-gene panel using KAPA HyperCap technology, including TP53) to identify tumor-derived somatic mutations that may be relevant to understanding resistance mechanisms to BI 907828. The limit of detection was determined to be 0.5% mutant allele frequency; common polymorphisms were filtered out. Results: Plasma samples for ctDNA analysis were available from 44/54 (81%) pts enrolled to phase Ia. Baseline plasma samples from 26/54 (48%) pts and EoT samples from 41/54 (76%) pts were analyzed. Mutations were found in 6/26 (23%) samples at baseline. In 2 pt samples, mutations were found in both tumor and ctDNA, but concordant results were limited to 1 pt. At EoT, no (0) mutations were found in 16/41 (39%) samples, 1 mutation in 11/41 (27%), 2 mutations in 6/41 (15%), 3 mutations in 2/41 (5%) and 4 mutations in 6/41 (15%). No sample had more than 4 mutations. The most frequent mutation at EoT (in 9/41 [22%] samples) was R175H, a known p53 loss of function (LOF) mutation, followed by R248Q/W LOF (in 6/41 [15%) samples). Mutations in non- TP53 genes were detectable independent of TP53 mutation status, suggesting ctDNA was present in all samples. No clear association of induction of mutations could be identified for any BI 907828 dose or dosing schedule, treatment duration, or tumor type. 9/20 (45%) pts with no detectable mutations at baseline maintained wild-type TP53 status at EoT. Signs of efficacy were observed in pts with acquired TP53 LOF mutations, suggesting that these mutations have no effect on efficacy. Analysis of TP53 mutational status at EoT in conjunction with correlative clinical efficacy will be presented. Conclusions: This mutation analysis represents one of the most comprehensive assessments of longitudinal ctDNA by NGS for TP53 from a clinical trial of an MDM2–p53 antagonist. Preliminary data suggest that BI 907828 does not systematically lead to broad acquisition of resistance by inducing alterations in TP53. Clinical trial information: NCT03449381 .

Squalene epoxidase/SQLE is a candidate target for treatment of colorectal cancers with p53 mutation and elevated c-MYC expression.

Elevated expression of c-MYC and inactivation of p53 represent two of the most common alterations in colorectal cancer (CRC). However, c-MYC and defective p53 are difficult to target therapeutically. Therefore, effectors downstream of both c-MYC and p53 may represent attractive, alternative targets for cancer treatment. In a bioinformatics screen we identified Squalene epoxidase/SQLE as a candidate therapeutic target that appeared to be especially relevant for cell survival in CRCs, which display elevated c-MYC expression and loss of p53 function. SQLE is a rate-limiting enzyme in the cholesterol synthesis. Here, we show that p53 supresses SQLE expression, cholesterol levels, and cell viability via the induction of miR-205, which directly targets SQLE. Furthermore, c-MYC induced SQLE expression directly and via its target gene AP4. The transcription factor AP4/TFAP4 directly induced SQLE expression and cholesterol levels, whereas inactivation of AP4 resulted in decreased SQLE expression and caused resistance to Terbinafine, an inhibitor of SQLE. Inhibition of SQLE decreased viability of CRC cells. This effect was enhanced in CRCs cells with p53 inactivation and/or enhanced c-MYC/AP4 expression. Altogether, our results demonstrate that SQLE represents a vulnerability for CRCs with p53 inactivation and elevated c-MYC activity.

Abstract IA012: Reducing disparities in breast cancer mortality through the identification of novel targets in triple-negative breast cancer

Abstract Triple-negative breast cancer (TNBC) remains a challenge to clinicians, laboratory investigators, and patients due to its disproportionate number of breast cancer deaths and its lack of an established therapeutic target. Numerous studies have identified potential novel mutational gene targets in TNBC, but single-agent therapeutics have lacked substantial impact in TNBC. Novel effective therapies are desperately needed. Alongside these therapies, we need accurate biomarkers that can be used to predict which patients will respond. We find that the ARF tumor suppressor expression is lost alongside p53 mutation in 60% of TNBC. ARF is the key player in sensing cellular oncogene-induced stress, such as signals emanating from oncogenic Ras and Myc alleles. ARF suppresses tumor formation in both p53-dependent and -independent mechanisms by interacting with proteins within the cell nucleolus. Our findings have advanced the premise that the p53-indendent functions of ARF are critical to preventing epithelial-based cancers. Our data show that mammary epithelial cells rapidly induce ARF expression in vitro and in vivo upon loss of functional p53. This induced ARF suppresses mammary tumor formation in vivo, wherein loss of both p53 and ARF dramatically accelerates tumorigenesis. This is consistent with our evidence that ARF and p53 function are concomitantly lost in TNBC. Potentially stemming from the dual loss of ARF and p53, we have observed that type I IFN signaling is elevated in TNBC. Our laboratory and others have shown that cancer cell lines, including those derived from TNBC, with elevated IFN signaling are dependent on the RNA deaminase ADAR1. Loss of ADAR1 in these cells leads to hyperactivation of the type I IFN pathway and cell death. We hypothesized that loss of ARF and p53 results in elevated type I IFN signaling and sensitizes cells to ADAR1 depletion. Beyond the potential genetic interaction between ARF-loss and ADAR1-dependency in TNBC, recent work from our lab has revealed that ARF and ADAR1 physically interact in cells lacking functional p53. We find that ARF can fully titrate much of the cellular ADAR1 into ARF complexes. Additionally, TNBC cells, but not non-TNBC cells, are sensitive to ADAR1 knockdown. Sensitivity to ADAR1 depletion appears to require type I IFN signaling and subsequent PKR activation. Analysis of primary human TNBC showed a marked separation of IFN signaling and ADAR1 localization/function between African American and Caucasian TNBC patients, suggesting that this pathway may serve as a functional marker of African American TNBC. Citation Format: Kyle Cottrell, Pat Kung, Sua Ryu, Leonard Maggi, Catherine Kuzmicki, Raleigh Kladney, Ling Yiu, Graham Colditz, Jason D. Weber. Reducing disparities in breast cancer mortality through the identification of novel targets in triple-negative breast cancer [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr IA012.

Histone Deacetylase Inhibition Restores Therapy Response in TP53mutated Acute Lymphoblastic Leukemia to Chemotherapy

Background: Although TP53 is the most frequently mutated gene in cancer, in Acute Lymphoblastic leukemia (ALL), mutations or deletions affecting TP53 are rare, with an incidence of only 3% at diagnosis. However, at relapse TP53 aberrations are found in about 12% of the patients and predict a very poor outcome. As a consequence, relapsed TP53 deleted ALL is now classified as 'very high risk, together with t(1;19) and t(17;19) ALL. Since p53-mediated apoptosis is an endpoint for many (cytotoxic) drugs, loss of p53 function induces therapy resistance not only to classical chemotherapeutics, but also newly introduced immunotherapies such as bi-specific T cell engagers such as Blinatumomab or CAR-T cell therapies. Therefore, there is an urgent clinical need for more effective strategies to treat TP53 aberrant relapsed ALL. Methods: Using CRISPR/Cas9, we introduced frameshift mutations in the TP53 gene to generate isogenic wildtype and knockout models in the TP53WT B-cell precursor ALL (BCP-ALL) cell lines Nalm6 and RCH-ACV. After confirming the presence of TP53 deletions, we treated these isogenic models with a panel of treatment protocol drugs, demonstrating that TP53 loss negatively affects response to therapy to most contemporary drugs used in the treatment of relapsed ALL. To identify drug combinations that may reverse TP53 mediated therapy resistance, we assessed the viability of these isogenic models in a drug screen containing 198 (pre)clinical drugs. The most interesting targets were subsequently combined with the previously tested treatment protocol drugs to determine potential synergies. Effects on cell viability were determined by amine exposure and MTT assay and confirmed by measuring PARP cleavage. Additionally, positive drug interactions were validated in vivo using immunocompromised mice engrafted with RCH-ACV p53KO cells expressing a luciferase reporter gene. Results: We observed that loss of p53 protects BCP-ALL cell lines Nalm6 and RCHACV from drug-induced apoptosis, leading to increased resistance to all drugs used currently in the treatment of relapsed ALL, except for Asparaginase. In a subsequent drug screen, we found that the histone deacetylase (HDAC) 1/2 inhibitor romidepsin shows strong single agent activity at single nanomolar concentrations. Moreover, romidepsin was found to strongly synergize with contemporary ALL treatment drugs in TP53KO and TP53WT cells (Figure 1A). This effect was strongest in TP53KO cells, effectively reversing therapy resistance induced by TP53 loss. Gene expression profiling suggest that romidepsin may lead to reactivation of TP53 target genes in response to cellular stress, even in the absence of functional p53. Finally, preliminary mouse experiments using TP53 deleted RCH-ACV cells showed that romidepsin improves the response to cytarabine in TP53 aberrant leukemia in vivo (Figure 1B) without signs of added toxicity. A mouse trial testing a potential synergy between romidepsin and cytarabine using TP53 deleted patient derived xenografts (PDX) is currently underway. Conclusions: Loss of p53 protects BCP-ALL cells from currently used (chemo)therapy strategies. Romidepsin can restore response to therapy in TP53 deleted ALL, presumably by reactivation of p53 target genes in response to cellular stress. Therefore, romidepsin may be used to improve therapy response in relapsed TP53 deleted ALL. Since romidepsin already has FDA approval for use in other hematological malignancies, our findings may be rapidly translated into clinical practice. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

TP53 CRISPR/Cas9 Reveals Strict BAX Dependence in the Response to BH3 Mimetic Targeting MCL1

Background In multiple myeloma (MM), 1q gain/amplification (1q+) and deletion of the short arm of chromosome 17 (del17p), encompassing MCL1 and TP53, respectively, as well as the t(4;14) translocation are adverse events that reduce both event-free survival and overall survival of patients. The genome gatekeeper p53 is well known for its multiple roles in the regulation of mitochondrial apoptosis: p53 induces early direct transactivation of the BH3-only protein PUMA (BBC3) and the death effector BAX (BAX) and late direct-to-indirect transactivation of NOXA (PMAIP1) and BAK (BAK1). To investigate the direct impact of loss of p53 function in myeloma cells, we generated TP53 CRISPR/Cas9 isogenic cells from cell lines harboring t(4;14) and 1q+. Materials and Methods To knockout the expression of all p53 isoforms in two TP53wt t(4;14)+ 1q+ myeloma cell lines, NCI-H929 and XG7 cells were sequentially transduced with 2 lentiviruses expressing Cas9 and a doxycycline-inducible TP53-specific sgRNA targeting exon 5. TP53-/-clones (n=3) and control clones (n=3) were derived for each cell line by limiting dilution. Results RNAseq analysis was performed in triplicate in the 12 clones of the two MM cell lines: analysis of the 6 TP53-/-clones versus the 6 control clones showed significant changes (log2FC>0.4, p>0.05) in the expression of 92 genes under steady-state conditions (and of more than 3000 upon nutlin3a-induced p53 accumulation) : 27% of the genes were known to be direct p53 target genes, 39% were known to be indirectly regulated, and 35% of the genes were not identified as p53 targets in solid cancer cell lines (Andrysik Z Genome Res 2017). Among the 51 downregulated genes, only 2 belonged to apoptosis pathways, namely BAX and TNFRSF10B, both direct early targets of p53. Of note, the expression of BAK1, PMAIP1 or BBC3 was not significantly modified. To directly assess the impact of BAX decrease in the 6 TP53-/- clones, we used 3 BH3 mimetics specific for BCL2, Venetoclax, MCL1, S63845, and BCLXL, A1155463. The XG7 and NCI-H929 cell lines were predominantly resistant to Venetoclax and to A1155463, and TP53 knockout did not alter responses. In contrast, as compared to control clones, the response to S63845 was decreased 5.7 to 7.4-fold in NCI-H929 TP53-/- (LD50 median values increased from 7 to 40nM, p<0.0001) and XG7 TP53-/- clones (LD50 median values increased from 25 to 186nM, p=0.0007), respectively. This result suggested a major role of BAX in the response to S63845. Indeed, BAX silencing significantly inhibited S63845-induced cell death while BAK silencing had no protective effect, demonstrating the BAX dependence of the S63845 response. Of note, this strong dependence on p53-dependent BAX expression was not limited to XG7 or NCI-H929 : in 21 TP53abnormal myeloma cell lines, BAX expression (GEP) was 1.7-fold lower than in 11 TP53wt cell lines (LD50 median values 34 vs. 59, p=0.0004), and sensitivity to S63845 was also significantly lower in TP53abn MM cell lines compared to MM TP53wt (LD50 median values 75 nM vs. 12 nM, p=0.0296). The resistance of TP53-/- cells to S63845 was overcome by the addition of Venetoclax, although the death remained lower in TP53-/- clones compared to control clones (p=0.001). BAX and BAK activation and MCL1 co-immunoprecipitation assays further demonstrated the central role of MCL1/BAX expression and complexes in the response to S63845. In 63 consecutive independent samples from patients with MM (23 at diagnosis, 40 at relapse), 33 1q+ and 30 1q-, we show that 1q gain/amplification favored response to 25 nM S63845 alone (death median 16% in 29 1q- vs 30% in 34 1q+, p=0.0132) and had a trend in combination with 300 nM Venetoclax (80% vs 89%, p=0.152). Finally, we show that 1q was sufficient to induce responses to S63845 plus Venetoclax regardless of del17p status (death median 30% in 26 1q+ del17p- vs. 40% in 6 1q+ del17p+ samples). To analyze the response to the combination of S63845 and Venetoclax at the single cell level, we performed scRNASeq analysis in t(4;14)+ 1q+ del17p+/- patients and determined the transcriptomic profile of cells surviving the combination: we show that BH3 mimetics combination heterogeneously induced death in and between patient's samples and we identified a resistance signature that is under evaluation. All these results support the S63845 / Venetoclax combination for patients with double (1q+, del17p) to triple (t(4;14), 1q+, del17p) hit. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Improving Reporter Gene Assay Methodology for Evaluating the Ability of Compounds to Restore P53 Activity.

Tumor suppressor protein P53 induces cycle arrest and apoptosis by mediating the transcriptional expression of its target genes. Mutations causing conformational abnormalities and post-translational modifications that promote degradation are the main reasons for the loss of P53 function in tumor cells. Reporter gene assays that can scientifically reflect the biological function can help discover the mechanism and therapeutic strategies that restore P53 function. In the reporter gene system of this work, tetracycline-inducible expression of wild-type P53 was used to provide a fully activated state as a 100% activity reference for the objective measurement of biological function. It was confirmed by RT-qPCR, cell viability assay, immunofluorescence, and Western blot analysis that the above-mentioned reporter gene system could correctly reflect the differences in biological activity between the wild-type and mutants. After that, the system was tentatively used for related mechanism research and compound activity evaluation. Through the tetracycline-induced co-expression of wild-type P53 and mutant P53 in exact proportion, it was observed that the response modes of typical transcriptional response elements (TREs) to dominant negative P53 mutation effect were not exactly the same. Compared to the relative multiple-to-solvent control, the activity percentage relative to the 100% activity reference of wild-type P53 can better reflect the actual influence of the so-called P53 mutant reactivator. Similarly, relative to the 100% activity reference, it can objectively reflect the biological effects caused by the inhibitor of P53 negative factors, such as MDM2. In conclusion, this study provides a 100% activity reference and a reliable calculation model for relevant basic research and drug development.

Abstract 6217: TP53 loss with whole genome doubling mediates heterogeneous intra-patient therapy response in EGFR-driven lung adenocarcinoma: A TRACERx study

Abstract Introduction: Mutations in the epidermal growth factor receptor (EGFR) are often found in never-smokers who develop lung adenocarcinoma (LUAD) and resistance to receptor-targeted tyrosine kinase inhibitors (TKIs) generally occurs within five years of treatment. Mixed responses, where individual tumor lesions within the same patient respond differently to treatment, contribute to early treatment failure and indicate the involvement of multiple genomic alterations. TP53 loss of function has been associated with both tolerance to chromosomal instability (CIN) and with shortened progression free survival in EGFR-driven tumors. The aim of this study was to investigate the hypothesis that CIN, together with loss of p53 function, may lead to diverse genotypes that underlie the mixed responses observed in EGFR-driven LUAD. Experimental Procedures: We used genetically engineered mouse models (GEMMs), driven by EGFR with or without concomitant Trp53 loss and human isogenic cell lines to investigate cellular evolution and the effect of whole genome doubling on targeted therapy responses and mechanisms of resistance. Next generation sequencing and shallow whole genome single cell analyses, together with longitudinal imaging analysis from the Aura clinical trials (AURA2, AURA3 and the AURA extension cohort, Identifiers: NCT02094261, NCT02151981 and NCT01802632) was used to investigate the effect of p53 loss on tumor evolution. Results: EGFR mutant tumors with clonal Trp53 loss or TP53 pathway disruption displayed increased Weighted Genome Integrity Index (wGII) and higher cell to cell variation in both the mouse and TRACERx data sets. We found that TP53 loss of function increased the incidence of mixed responses and resistance to targeted therapy in both mouse and human tumors leading to early treatment failure and reduced survival. Whole-exome sequencing (median depth of 92x, range: 58-169x) of nine erlotinib-resistant EGFR mouse tumors identified four EGFR bypassing mutations (oncogenic KRAS mutations; Q61H, Q61R, and two G12D mutations) and one likely driver mutation in FGFR2 (C286R). We could only identify one known resistance associated mutation, EGFRT790M, in EGFR mutant tumors with concomitant loss of Trp53. In depth analysis revealed no major copy number differences in treatment naÏve vs resistant EGFR mutant tumors. In contrast, 70% of all tumors with concomitant Trp53 loss had amplified a region of mouse chromosome 7, harboring MET and BRAF. Investigating an isogenic EGFR/TP53 mutant cell model system revealed whole genome doubling as advantageous in overcoming the selection pressure induced by targeted therapy. Conclusion: We find that loss of TP53 in the context of mutated EGFR leads to an altered and plastic genomic landscape, with multiple copy number changes, which in turn facilitates therapy resistance. Citation Format: Sebastijan Hobor, Maise Al Bakir, Marcin Skrzypski, Alexander M. Frankell, Bjorn Bakker, Thomas B. Watkins, Aleksandra Markovets, Jonathan R. Dry, Andrew P. Brown, Jasper van der Aart, Dahmane Oukrif, Marco Novelli, Matthew J. Renshaw, William Hill, Hilda van den Bos, Diana C. Spierings, Juliann Chmielecki, Carl Barrett, Kevin Litchfield, Elza de Bruin, Floris Foijer, Karen H. Vousden, TRACERx consortium, Robert E. Hynds, Crispin T. Hiley, Nnennaya Kanu, Simone Zaccaria, Eva C. Gronroos, Charles Swanton. TP53 loss with whole genome doubling mediates heterogeneous intra-patient therapy response in EGFR-driven lung adenocarcinoma: A TRACERx study [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 6217.