Aberrant TP53 Research Articles

Clinicopathologic and genomic characteristics of patients with advanced ovarian, breast, and prostate cancer treated with poly (ADP-ribose) polymerase inhibitors (PARPi) in a real-world setting.

3159 Background: PARPis induce synthetic lethality in tumors that have homologous repair deficiencies (HRD). Due to relative rarity of HRD-related genomic and germline alterations across solid malignancies, it remains unclear which patients (pts) may derive most benefit from PARPis across different tumor types. Methods: We analyzed clinicopathologic and genomic characteristics of pts with advanced ovarian (OC, n=33), prostate (PC, n=28) and breast cancer (BC, n=13) treated with PARPi monotherapy at our institution. Only pts with HRD-related pathogenic alterations detected via next-generation sequencing of tumor tissue, with or without genetic susceptibility testing, were included. Results: Forty-one (55%) pts had a confirmed germline HRD-related gene alteration, of which 33 had BRCA1/2 and 8 had non-BRCA1/2 gene alterations. Average age of pts with BC was 54 years, OC 62 years, and PC 68 years. Median number of prior lines of therapy in the advanced setting was 1 (1-4) for OC and BC (0-7) and 3 (1-6) for PC. Median time to progression (TTP) in pts with OC was 8.3 months, BC 4.9 months and PC 3.6 months, likely due to i) majority of pts with OC received maintenance PARPi following favorable response to first-line chemotherapy, ii) pts with PC were older, and iii) more pts with PC had somatic rather than germline HRD-related mutations. Pts with germline vs somatic HRD mutation had longer median TTP in PC (5.0 vs 3.3 months) and BC (6.1 vs 4.0 months), but the opposite was true for OC (7.9 vs 10.8 months). Pathogenic TP53 mutations were identified in all but one pt with OC (32/33), 10/13 pts with BC, and 6/28 PCs. [table] Average TP53gene variant allele fraction (VAF) was similar in OC and BC (49.8% and 51.1%, respectively) but significantly lower in PC (26.4%), suggesting that TP53 mutations in PC were subclonal. No specific TP53 VAF or HRD-to- TP53 VAF ratio cut-off was associated with TTP or overall survival in any of the 3 cancer types. In addition, 7/28 (25%) of pts with PC had PTEN loss associated with modified response to PARPis, whereas none of the pts with BC had PTEN loss and only 3/13 had alterations of the PTEN/PI3K/AKTpathway. Conclusions: Double-strand DNA breaks caused by synergistic effects of aberrant TP53 and HRD-related genes can possibly explain the more favorable response of pts with OC and BC to PARPi, compared to those with PC. Co-alterations in other signaling pathways, epigenetic factors and/or tumor microenvironment likely play a role in the degree of response to PARPis, rather than TP53 clonality alone. In the era of expansion of genomic testing and new indications for PARPi larger genomic studies are needed to identify biomarkers of response to PARPi beyond HRD. [Table: see text]

Abstract 1124: Prevention of radiation-induced malignancies in Li-Fraumeni syndrome

Abstract PURPOSE: Li-Fraumeni Syndrome (LFS) is a genetic disorder associated with a significant risk of early-onset cancer. This condition is driven by germline mutations in the TP53 gene which plays a primary role in the regulation of the radiation response. Aberrant TP53 function contributes to radiation vulnerability and a greater risk of secondary, radiation-induced malignancies (RIMs). As a result, therapeutic options for LFS patients are often limited to exclude radiotherapy (RT), which may otherwise be beneficial for the treatment of certain primary tumors. Data from our lab demonstrate an aberrant transcriptomic response to irradiation (IR) in mutant p53 patient skin fibroblasts compared to wildtype; however, it is unknown whether reprogramming this radiation response can decrease the risk of RIM in LFS. Metformin, a commonly prescribed anti-diabetic drug, is associated with lower cancer incidence and may decrease cancer-related mortality in murine LFS models. In addition to its potential anti-tumorigenicity, studies have shed light on the ability of metformin to prevent IR-induced damage in normal tissue; hence, we hypothesize that metformin can reprogram the radiation response to protect against radiation injury and delay the onset of RIM in LFS. METHODS: To establish a murine model of RIM in LFS, and to investigate whether metformin can delay tumor onset in this model, whole-body or localized IR were administered to mice harboring a hotspot Trp53R172H/+ mutation in the presence and absence of metformin. Serial MRI was conducted to monitor for tumor development. To understand the effect of metformin on the mutant p53 radiation response in vivo, a similar murine workflow was established and irradiated skin was collected longitudinally from untreated and metformin-treated cohorts for whole transcriptome sequencing. Sequencing data were functionally validated in a separate cohort of mice using flow cytometry. In parallel, we performed RNA sequencing on LFS patient fibroblasts to characterize the effect of metformin on the human radiation response. RESULTS: We demonstrate that IR decreases tumor latency in TP53R172H/+ mice, and that metformin significantly delays tumor onset within the radiation field. Moreover, transcriptomic data revealed that metformin upregulates apoptosis following IR in TP53R172H/+ mice. Flow cytometry analysis of the radiation response validated these findings, demonstrating that metformin promotes the apoptosis-driven clearance of damaged, potentially tumorigenic cells following IR. Transcriptomic data from patient cell lines will be presented. CONCLUSIONS: Overall, we show that metformin may delay RIM in LFS mice, and have begun to characterize the biology underpinning this reprogrammed response to IR. This study is the first to highlight metformin as a radioprotective agent in the context of germline mutant p53, with the potential to broaden RT treatment options for LFS patients. Citation Format: Pamela Psarianos, Nicholas Fischer, David Malkin. Prevention of radiation-induced malignancies in Li-Fraumeni syndrome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1124.

Implementation of endometrial cancer molecular subtyping into a hybrid community-academic practice.

We sought to confirm utility of our institution's modified Proactive Molecular Risk Classifier for Endometrial Cancer protocol in our daily practice, which includes mismatch repair (MMR), p53, and L1 cell adhesion molecule (L1CAM) immunohistochemistry with in-house next-generation sequencing for POLE, TP53, and CTNNB1. We conducted a retrospective review of all patients in our institution who underwent primary endometrial carcinoma resection from the year prior to protocol implementation (PRE; October 1, 2020, to September 30, 2021) through first year of implementation (POST; October 1, 2021, to September 30, 2022) to compare the distribution of molecular and traditional staging factors using GOG-249 criteria to assign clinical risk. In total, 136 of 260 PRE patients were classified as clinically low risk (LR), of whom 31 were MMR deficient. Of the 157 LR POST patients with endometrioid-type carcinoma, 45 were MMR deficient, 5 were POLE mutant, 5 were TP53 mutant, 56 were of no specific molecular profile (NSMP), and 46 did not receive full protocol testing. Of all 79 POST NSMP endometrioid-type cases, 18 were CTNNB1 mutated and 8 showed L1CAM expression. Our protocol identified 22 (14%) of 157 LR tumors that harbored incipient intermediate- to high-risk molecular aberrations in TP53, CTNNB1, or L1CAM. Moving forward, results of ongoing trials assessing adjuvant therapy decisions based on molecular classification are necessary to confirm protocol utility and identify appropriate modifications.

Acalabrutinib with Rituximab As First-Line Therapy for Older Patients with Mantle Cell Lymphoma - a Phase II Clinical Trial

Introduction - Previously, our group reported results from ibrutinib with rituximab in older mantle cell lymphoma (MCL) patients (pts) with an atrial fibrillation rate of 22%. To develop a chemotherapy-free combination for elderly MCL pts, we designed this phase II clinical trial to investigate the efficacy and safety of acalabrutinib with rituximab (AR) as a first line approach in MCL pts (≥ 65 yrs). Methods - We enrolled 50 previously untreated pts in this single institution, single arm, phase II clinical trial - NCT05214183. Pts received acalabrutinib 100 mg orally twice a day and intravenous rituximab, weekly for first 4 weeks, followed by once a month for 12 months and subsequently once every 2 months totaling 24 months. Acalabrutinib was continued. The primary objective was to assess best overall response rate (ORR) rate after AR. Responses were assessed as per Lugano response criteria. Clonoseq based minimal residual disease (MRD) assessment was performed. Adverse events were coded as per CTCAE version 5. Genomic studies are ongoing. Results - Among 50 pts, the median age was 69 years (range: 65-81). Male/female were 36 and 14 respectively. Bone marrow was positive for MCL in 45/50 (90%) and GI tract in 35/47 (74%) pts. Forty-six pts had classic morphology while three were blastoid and one was pleomorphic. Ki-67% was available in 42 pts - 13/42 (31%) had high Ki-67% and 29/42 (69%) had a low Ki-67% (< 30%). Simplified MIPI risk stratification included: low (n=4), intermediate (n=35) and high risk (n=11). TP53 aberration status (mutations or deletion) was available in 43/50 pts and 12 pts had aberrant TP53 while 31/43 did not have aberrant TP53. Thirty-nine pts had baseline next generation sequencing (NGS) on tumor tissue biopsy and 25/39 (64%) had ≥ 3 mutations. Median number of AR cycles was 12 (range: 3-24). One pt was not evaluable for response at 12 weeks. Overall, the best response was 94% ORR and 90% CR, 4% PR; 6% were non-responders. Median number of cycles to get complete metabolic response was 3 (range 2-7). Fourteen pts were MRD negative at last follow-up of the 28 evaluable pts. With a median follow up of 17 months, the median PFS and OS were not reached (2 year 92% and 96% respectively). The median PFS and OS was not reached and not significantly different in pts with high and low Ki-67% or with/without TP53 aberrations or among pts with low, medium or high-risk categories. Nine pts (18%) came off study - 3 for adverse events (syncope, atrial fibrillation, intolerance), 3 for disease progression, one melanoma recurrence, one pt choice and one with an unusual monocytosis. Overall, 2 pts died (1 on trial with primary progression). The most common all-grade toxicities were fatigue (82%), myalgia (64%), headache (38%), bruising (28%) and <1% were grade 3 or higher. Among 50 pts, 1 pt had recurrence of grade 2 atrial fibrillation (2%) and one pt had recurrence of grade 3 unstable angina. Conclusions -Chemotherapy-free frontline therapy with AR is highly effective and safe and induced early CR in older pts with MCL.

The Battle within: AML´s p53 Strategies to Evade T-Cell Attack

Bispecific T-cell recruiting antibody constructs (BsAb) have shown clinical efficacy with Blinatumomab, a CD3xCD19 BiTE ® construct used for the treatment of relapsed or refractory B-cell precursor ALL. Despite the success of BsAbs in B-cell malignancies, the translation to a myeloid setting has been unsuccessful, independently of the chosen target antigen. For example, targeting CD33 has failed to provide long-term benefits. Several reports have demonstrated that the diverse genetic makeup of AML confers resistance to T-cell based immunotherapy. Mutations of TP53 occur in 5-10% of patients with de novo AML and up to 50% in older patients with therapy related AML, thus highlighting its role as a potential resistance mechanism. We hypothesize, that genetic aberrations of TP53 in AML contribute to cell intrinsic and cell extrinsic resistance against T-cell based immunotherapy approaches. To study the impact of TP53 aberrations on T-cell based immunotherapy, MV4-11 p53 WT or MV4-11 p53 KD were cocultured with healthy donor T cells at an effector to target ratio of 1:6 with or without BsAbs. BsAb-mediated cytotoxicity was analyzed by specific lysis of the CD33 + target cells and T-cell proliferation was assessed by FarRed ® staining or CD2 + T-cell fold change calculated to day 0. Cytokine secretion was monitored in the coculture supernatants by cytometric beads arrays. To differentiate between secretome vs surfacome mediated differences, transwell assays were performed. To identify the T-cell immunosuppressive factor, secretome analysis were performed using the Olink® proteomics platform. To further dissect the effect of the p53 KD MV-411 on T cells, we performed RNA-Seq analysis of T cells after coculture with MV4-11 p53 KD vs p53 WT. As expected, BsAb-mediated cytotoxicity was reduced against p53 KD vs p53 WT MV4-11 (% specific lysis: p53 KD=47.86±7.37 vs p53 WT=76.42±3.82; p=0,0001). However, BsAb-mediated T-cell proliferation was also significantly decreased in cocultures with p53 KD vs p53 WT (% proliferated: 30.26±2.92 vs 44.25±4.08; p=0.002). In line with these findings, we observed a significant decrease in secretion of the proinflammatory cytokines IFNγ (p53 KD=2985,01±896,69 vs p53 WT=4009.15±764.97 pg/ml; p=0.068), TNF (29,38±8.16 vs 110.21±37.61 pg/ml; p=0.044) and IL-2 (1391.64±375.93 vs 2253.88±604.76 pg/ml; p=0.018). RNA-Seq analysis of T cells after coculture with MV4-11 p53 KD vs p53 WT revealed a decrease in the expression of genes associated with mitosis (such as E2F targets and mitotic spindle related genes). A lower mitotic rate provides a potential explanation for the reduction in T-cell proliferation after coculture with p53 KD. To dissect if the observed effects were due to the AML surfacome or the secretome, we performed transwell assays. Indeed, the negative impact of p53 KD AML cells on T-cell function was also observed without direct cell-cell contact. To gain further insights in the secretome of the AML cells, coculture supernatant was analysed using the Olink ® platform and demonstrated significantly higher secretion of IL-18 and LAP TGF-β1 (TGF-β1 latency associated protein) in the coculture with MV4-11 p53 KD vs MV4-11 p53 WT (normalized protein expression for IL-18: p53 KD=1.86±0.22 vs p53 WT=0.96±0.052; p=0.0153; for LAP TGF-β1: 6.52±0.18 vs 5.84±0.14; p=0.0394). The relevance of TGF-β on T-cell fitness was confirmed by the analysis of BsAb-mediated cytotoxicity with or without the addition of TGF-β. Addition of 3 ng/µl TGF-β to the coculture with p53 WT decreased the specific lysis significantly and was now comparable to the lysis of p53 KD. Confirmatory studies in primary AML samples with or without p53 aberrations further validated our findings with a clear reduction of BsAb-mediated cytotoxicity (% specific lysis: p53 KD=35.82±5.51 vs p53 WT=61.32±8.27; p=0.015), T-cell proliferation (CD2 + fold change: 3.17±0,61 vs 7.1±2.8; p=0.111) and secretion of proinflammatory cytokines. Taken together, we demonstrated that AML cells carrying a p53 aberration are less susceptible to BsAb-mediated cytotoxicity. Surprisingly, immune evasion was mediated by the AML secretome leading to a decrease in T-cell proliferation and cytokine secretion. Secretome analyses indicated TGF-β as a prominent cytokine leading to an impairment of T-cell function. Further studies are needed to understand the influence of p53 on the TGF-β pathway in AML cells.

Enhanced Expression of DNp73 Promotes Drug Resistance and Immune Evasion in Multiple Myeloma By Targeting the MYC and MYCN Pathways

Background Multiple myeloma (MM) is an incurable haematological malignancy with high chromosome instability and is highly dependent on the immunosuppressive bone marrow microenvironment. TP53 mutations and deletions are uncommon in MM patients, with other types of mechanisms involved in the abrogation of TP53 pathway activity. DNp73, an inhibitor of the p53 tumour suppressor family, drives drug resistance and cancer progression in several solid malignancies. However, the biological functions of DNp73, the molecular mechanisms underlying these actions and their correlations with aberrant TP53 expression in myelomagenesis remain unclear. In this study, we investigated the role of DNp73 in the drug resistance of MM, and disclosed the corresponding mechanism of how DNp73 promotes the immune escape of MM cells. Aims To disclose the role of DNp73 in promoting drug resistance and immune evasion in MM, and explore the therapeutic strategy based on the mechanism research. Methods We constructed DNp73 overexpression and sh-RNA interference plasmids to obtain stable cell lines. The effects of DNp73 on proliferation and drug sensitivity were determined by CCK8, flow cytometry and xenotransplantation model. To identify mechanisms of drug resistance, we here perform RNA-seq and CHIP-seq analyses in MM cell lines, while Western blot and RT-PCR were used to confirm the results. The DNA damage repair and invasion ability of MM cells were detected by immunofluorescence and transwell assay. To validate the role of DNp73 in immune escape, we also performed phagocytosis assays in vitro. Results Our previous study revealed that the miRNA-15a is a tumour suppressor involved in aggressive MM cell proliferation and drug resistance. Here, we found that miRNA-15a downregulation in MM cells activated NF-κB-p65, which upregulated the expression of DNp73 at the transcriptional level. In addition, the level of miR-15a was negatively correlated with the expression of DNp73 in MM cells of patients (r=-0.672, p<0.05). Enforced expression of DNp73 promoted aggressive proliferation and multidrug resistance in MM cells (p<0.001). Bulk RNA sequencing data showed that the levels of MYCN, MYC and CDK7 were increased in cells with enforced DNp73 expression. Furthermore, a ChIP-qPCR assay revealed that DNp73 bound to the MYCN gene promoter and upregulated MYCN expression. The MM cell immune evasion rate was notable when DNp73 expression was high because of CD47 and PD-L1 upregulation. Blockade of the CD47/SIRPα and PD-1/PD-L1 signalling pathways by the SIRPα-Fc fusion protein IMM01 and monoclonal antibody atezolizumab significantly re-established the anti-MM function of macrophages and T cells in the MM microenvironment, respectively (p<0.01). Notably, DNp73 dysregulation and its pathogenetic function in MM cells were found to be independent of TP53 expression. Conclusion Altogether, our study demonstrates that DNp73 is a potential oncogene involved in MM pathogenesis and promotes MM cell proliferation and immune evasion by targeting the MYC and MYCN pathways.

TP53 mutations and Their Impact on Survival in Patients with Myeloproliferative Neoplasms

Introduction: TP53 mutations in patients with myeloproliferative neoplasms (MPN) are associated with poor prognosis, including progression to blast phase MPN. However, low variant allele fraction (VAF) TP53 mutations have been reported to remain stable over years in chronic phase MPN. A major unmet clinical need in MPN is the ability to discriminate patients with TP53-mutant MPN who are at high-risk of secondary AML (sAML) and warrant immediate intervention from those who are at lower risk of sAML in whom active surveillance can be employed. Therefore, we sought to identify parameters associated with leukemic transformation and overall survival in the context of MPN with genetic aberrations in TP53. Materials and Methods: We retrospectively analyzed a cohort of 947 MPN patients from the Dana-Farber Cancer Institute Hematologic Malignancies Data Repository (HMDR) with at least one clinical next-generation sequencing (NGS) panel performed. Patient characteristics such as age at MPN diagnosis, gender, MPN subtype and driver mutations were recorded. Furthermore, information about the course of disease was extracted including occurrence of sAML and overall survival (Figure 1). We also analyzed type and number of additional mutations as well as cytogenetics. With respect to TP53-specific parameters, we evaluated the number of TP53 mutations, TP53 VAF, loss of heterozygosity (LOH) at the TP53 locus, phenotypic annotations of TP53 (i.e. PHANTM score) and 17p deletion. We defined “multi-hit” TP53 as the presence of two or more TP53 mutations, TP53 VAF higher than 50%, TP53 mutation plus 17p deletionor TP53 mutation and documented LOH. Results: A total of 947 patients were analyzed, of which 40 harbored at least one detectable TP53 mutation. A total of 13 patients were found to have a multi-hit TP53 mutations defined by > 50% VAF in 6 patients, two or more TP53 mutations in 5 patients and TP53 mutation + 17p deletion in 5 patients. The MPN diagnosis at time of TP53 mutation detection was post ET/PV myelofibrosis (secondary MF) (n=23, 58%), primary myelofibrosis (MF) (n=7, 18%), pre-fibrotic MF (n=2, 5%), essential thrombocythemia (ET) (n=6, 15%) and polycythemia vera (PV) (n=2, 5%). Two patients with ET and one patient with PV did not have a concurrent in-house bone marrow biopsy performed at the time the TP53 mutation was detected. Two patients with ET developed sAML within 12 months of TP53 mutation detection, without prior mention of fibrosis. Age at first MPN diagnosis was not significantly different between patients with or without TP53 mutation. The average time from initial MPN diagnosis to detection of the first TP53 mutation was 9 years (range: 0-33 years). The most common MPN driver mutation among patients with TP53 mutations was JAK2 (75%), followed by CALR (13%)and MPL (5%). Out of all TP53-mutated patients, 8% showed a triple negative status. The most frequent additional mutations among patients with TP53 mutations were TET2 (25%), U2AF1 (15%), ASXL1 (13%), and DNMT3A (10%). There was no significant difference between single-hit and multi-hit TP53 status regarding MPN subtype, driver mutations and co-mutations (Table 1). Seven patients (single-hit: 15%, multi-hit: 23%) with a TP53 mutation developed sAML during the course of their disease, compared with only 3% of all patients without a TP53 mutation and 50% (single-hit: 41%, multi-hit: 69%) were deceased at the time of the last follow-up compared to 18% of all patients without a TP53 mutation. We focused on overall survival from the initial MPN diagnosis and considered whether patients developed bone marrow fibrosis during their disease course (Figure 1). Survival did not differ significantly between single-hit TP53 and patients with multi-hit TP53 (p=0.2), but survival did differ significantly between multi-hit TP53 patients and TP53 wildtype patients with MF/prefibrotic MF/Secondary MF (p=0.02) as well as compared to all MPN patients without a TP53 mutation (p<0.001). Survival was not significantly different between single-hit TP53 and TP53 wildtype MF/prefibrotic MF/Secondary MF patients (p=0.4). Conclusions: In a large cohort of 947 molecularly characterized MPN patients, 4% of the cohort developed a TP53 mutation during their course of disease. 18% of all TP53-mutant patients developed sAML with an adverse effect on overall survival for patients with multi-hit but not single-hit TP53 mutations.

Transcriptomic subtyping of malignant peripheral nerve sheath tumours highlights immune signatures, genomic profiles, patient survival and therapeutic targets

Malignant peripheral nerve sheath tumour (MPNST) is an aggressive orphan disease commonly affecting adolescents or young adults. Current knowledge of molecular tumour biology has been insufficient for development of rational treatment strategies. We aimed to discover molecular subtypes of potential clinical relevance. Fresh frozen samples of MPNSTs (n=94) and benign neurofibromas (n=28) from 115 patients in a European multicentre study were analysed by DNA copy number and/or transcriptomic profiling. Unsupervised transcriptomic subtyping was performed and the subtypes characterized for genomic aberrations, clinicopathological associations and patient survival. MPNSTs were classified into two transcriptomic subtypes defined primarily by immune signatures and proliferative processes. "Immune active" MPNSTs (44%) had sustained immune signals relative to neurofibromas, were more frequently low-grade (P=0.01) and had favourable prognostic associations in a multivariable model of disease-specific survival with clinicopathological factors (hazard ratio 0.25, P=0.003). "Immune deficient" MPNSTs were more aggressive and characterized by proliferative signatures, high genomic complexity, aberrant TP53 and PRC2 loss, as well as high relative expression of several potential actionable targets (EGFR, ERBB2, EZH2, KIF11, PLK1, RRM2). Integrated gene-wise analyses suggested a DNA copy number-basis for proliferative transcriptomic signatures in particular, and the tumour copy number burden further stratified the transcriptomic subtypes according to patient prognosis (P<0.01). Approximately half of MPNSTs belong to an "immune deficient" transcriptomic subtype associated with an aggressive disease course, PRC2 loss and expression of several potential therapeutic targets, providing a rationale for molecularly-guided intervention trials. Research grants from non-profit organizations, as stated in the Acknowledgements.

Mechanisms of impaired expression of p53-responsive microRNA genes in diffuse B-large cell lymphoma

Introduction. A more in-depth description of molecular events that disrupt the functioning of the p53 signaling pathway is important for understanding the mechanisms of formation and progression of diffuse B-large cell lymphoma (DCCL), as well as its sensitivity to treatment. The p53 protein exhibits its oncosuppressive function and mediates the antitumor effects of drugs by regulating transcription and/or maturation of a wide range of target genes, including MIR-34A, MIR34B/C, MIR-129-2 and MIR-203. In the tumor tissue of lymphomas, in comparison with normal lymphoid tissue, a decrease in the level of microRNAs encoded by these genes is shown.Aim. The aim of this study was to conduct a comprehensive analysis of the methylation of the genes of the p53-responsive microRNAs MIR-34A, MIR-34B/C, MIR-203 and MIR-129-2, as well as mutations in the DNA-binding domain and destruction of the polyadenylation signal of the TP53 gene in DLBCL.Materials and methods. 136 DNA samples isolated from tumor tissue of patients with DLBCL and 11 DNA samples obtained from lymph nodes with reactive B-cell follicular hyperplasia were analyzed. The methylation status of MIR-203 and MIR-129-2 genes was determined by the method of methyl-specific polymerase chain reaction, MIR-34A and MIR-34B/C genes by the method of methyl-sensitive analysis of high-resolution melting curves. In tumor samples, rs78378222 genotyping was performed by polymerase chain reaction with restriction fragment length polymorphism, resulting in the destruction of the polyadenylation signal, and the nucleotide sequence of the region of the TP53 gene encoding the DNA-binding domain was determined by capillary direct sequencing by Sanger.Results. The methylation detected in lymphoma tissue was tumor-specific. The frequency of analyzed aberrations in the TP53 gene and methylation of MIR-34A, MIR-34B/C, MIR-129-2 and MIR-203 was 21, 23, 55, 65 and 66 %, respectively. At the same time, methylation of the analyzed genes of p53-responsive microRNAs and aberrations in the TP53 gene in the tumor tissue of patients with DLBCL were independent events with a tendency to mutual exclusion. At the same time, it was shown that in the vast majority of lymphoma samples, the methylation of the MIR-34A, MIR-34B/C, MIR-129-2 and MIR-203 genes was combined.Conclusion. Along with aberrations in TP53, methylation of MIR-34A, MIR-34B/C, MIR-129-2 and MIR-203 genes may be an important cause of decreased expression of miR-34a, miR-34b, miR-34c, miR-129 and miR-203 in DLBCL. The combined methylation of the MIR-203, MIR-129-2 and MIR-34B/C genes, as well as the MIR-34B/C and MIR-34A pairs, potentially has a more pronounced pro-tumor effect due to the presence of common targets in the microRNAs encoded by them.

P53/TP53 Status Assessment in Gastroesophageal Adenocarcinoma.

Chromosomal instability (CIN) is very frequent in gastroesophageal adenocarcinoma (GEA) and it is characterized by TP53 deletions/mutations resulting in p53 nuclear accumulation, as revealed by immunohistochemistry (IHC), which considers the cases with "high" staining levels to be positive. Aiming to improve aberrant TP53 detection, droplet digital PCR (ddPCR) was used to evaluate TP53 deletion in formalin-fixed, paraffin-embedded DNA (FFPE-DNA) and cell-free DNA (cfDNA). To further investigate the mutational TP53 profile, next-generation sequencing (NGS) was performed in a subset of FFPE samples. After combining "low" and "high" IHC staining level groups, the proportion of deletion events was significantly higher compared to the "intermediate" group (72.9% vs. 47.5%, p-value = 0.002). The ddPCR TP53 deletion assay was feasible for cfDNA but only had good agreement (72.7%, Cohen's kappa = 0.48) with the assay performed with FFPE-DNA of the "low-level" group. NGS analysis confirmed that, in the "low-level" group, a high percentage (66.7%) of cases were aberrant, with disruptive mutations that probably led to p53 loss. Data suggested that p53 IHC alone underestimates the CIN phenotype in GEA and that molecular analysis in both solid and liquid biopsies could be integrated with it; in particular, in cases of completely negative staining.

Abstract 2303: Adverse clinical outcomes and distinct genomic phenotype of BRCA-deficient metastatic castration-resistant prostate cancer (mCRPC)

Abstract Defects in the homologous recombination (HR) pathway, particularly in BRCA2, are of particular therapeutic relevance in mCRPC as they confer sensitivity to PARP inhibitors (PARPi). Nevertheless, durable responses to PARPi remain elusive and primary resistance is an additional major challenge. As a result, dissecting therapeutic vulnerabilities in HR-aberrant patients is crucial and may reveal novel PARPi-based combinations for evaluation in future clinical trials.In this multi-institutional study, we used the CLIA-certified PredicineCARE™ cell-free DNA (cfDNA) assay that assesses 152 genes to profile plasma from 375 mCRPC patients from Australia and the USA. Reportable alterations included pathogenic single-nucleotide (somatic and germline) and copy number variants. Association between alterations and clinical outcomes were assessed using log rank, cox proportional, and chi-squared analyses.Overall, 65 patients (17%) had evidence of a pathogenic BRCA2 aberration, which were commonly hemizygous (78% vs 22% homozygous deletions), monoallelic (70% vs 30% bi-allelic), somatic (87% vs 13% germline), and clonal (83% vs 17% subclonal) in nature. There was no significant difference in plasma tumour fraction in patients with single vs two-copy loss of BRCA2, and BRCA2 zygosity did not have differing effects on outcomes, with both being similarly associated with shorter overall survival (HR 0.48, p&amp;lt;0.002, and HR 0.45, p=0.003, respectively). Pathogenic BRCA1 aberrations were present in 10 patients (3%). PSA response rates to androgen-receptor pathway inhibitors (ARPI) were significantly lower in patients with a BRCA1 and/or a BRCA2 aberration (32% vs 60%, p=0.02), and we observed this BRCA-defective subgroup to be enriched for AR aberrations (71% had &amp;gt;1 AR aberration vs 38% in BRCA-intact patients, p=0.001). BRCA-defective cancers were also significantly enriched for aberrations in key neuroendocrine markers TP53 (62% vs 28%), RB1 (60% vs 17%), and MYC (27% vs 9%), as well as for PI3K pathway aberrations (PTEN 63% vs 25% and PIK3CA 37% vs 14%). In summary, we show that BRCA alterations are associated with worse prognosis in mCRPC and reduced benefit from ARPI, and that the prognostic and predictive utility of cfDNA-detected BRCA2 may be independent of zygosity state, potentially due to constraints with copy number loss identification in samples with low tumour DNA. Additionally, on top of a high proportion of AR alterations, BRCA-defective cancers were also enriched in a number of potentially actionable targets and neuroendocrine markers. Clinical trials that leverage rational co-targeting strategies will provide an opportunity to enhance the efficacy of PARPi in mCRPC. Citation Format: Heidi Fettke, Chao Dai, Edmond M. Kwan, Tiantian Zheng, Winston Tan, P Du, Nicole Ng, Patricia Bukszynska, Maria Docanto, L K. Graham, Kate Mahon, Lisa G. Horvath, Shidong Jia, Manish Kohli, Arun A. Azad. Adverse clinical outcomes and distinct genomic phenotype of BRCA-deficient metastatic castration-resistant prostate cancer (mCRPC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2303.

MS-553, a Selective PKC-ß Inhibitor Inhibits BCR Signaling and Synergizes with Venetoclax for the Treatment of High Risk CLL

Inhibitors of Bruton's tyrosine kinase (BTK) have been transformative in treating patients with chronic lymphocytic leukemia (CLL) due to their ability to inhibit B-Cell Receptor (BCR) signaling. However, despite durable remissions in many patients, complete responses are uncommon and acquired mutations in BTK and its downstream target phospholipase Cγ2 (PLCγ2) lead to relapses and poor survival. In parallel, genomic high-risk features such as aberrations in TP53 represent an independent risk factor that favor progression on BTK inhibitors (BTKi). TP53 aberrations comprise of deletions in chromosome 17 (del17p) which result in the loss of one allele of TP53 and point mutations in the TP53 gene. CLL patients with del17p acquire clonal mutations that affect the other p53 allele in 82% of cases and largely express only mutant TP53 protein. Therefore, there is an urgent need to identify therapies for patients who progress on BTKi. We have observed over-expression of protein kinase C-β (PKC-β) in primary CLL patient samples including in those that have mutations in TP53. PKC-β is a downstream of the BCR and functions downstream of BTK. PKC-β is required for CLL cell survival and proliferation and therefore can be a potential target for patients with mutations in p53 that do not respond to other targeted therapies. We hypothesized that targeting PKC-β will inhibit BCR signaling downstream of BTK and may offer an effective therapeutic strategy for patients who relapse on ibrutinib. Mechanistically, we found that CLL cells (n=6 patients) in contact with stromal support upregulated their levels of PKC-β. Pre-exposure of stromal cells to MS-553, a selective PKC-β inhibitor prevented the stromal cell contact-induced increase in PKC-β within the CLL cells establishing that stromal contact was an important source of PKC-β in CLL cells. We have shown in primary CLL patient samples that exposure to MS-553 decreases activation of PKC-β and its downstream effectors GSK3-β and ERK in a dose-dependent manner regardless of mutations in p53 both in the presence and absence of stromal support. In parallel, MS-553 also decreased the levels of BCL-xL, a key pro-survival BCL2 family protein via downregulation of β-catenin. Using dynamic BH3 profiling we show that CLL samples (both WT and mutant TP53) exposed to MS-553 (5µM, 24h) increase their dependence on BCL-2 and BCL-xL for survival. This finding suggested that MS-553 could synergize with the BCL-2 inhibitor venetoclax to eliminate CLL cells. Correspondingly, cells exposed to a combination of MS-553 and venetoclax released more cytochrome c (Cyt c), used as a measure of mitochondrial dysfunction, compared to each single agent alone and led to a synergistic increase in apoptosis as measured by Annexin V positivity. These data provide strong rationale for an ongoing Phase I/II trial that evaluates MS-553 as a single agent and in combination with targeted agents such as venetoclax. Early interim data indicate that MS-553 is safe, tolerable and effective both as a single agent and in combination with venetoclax.

Prognostic Discrimination within a Heterogeneous Population of TP53-Aberrant Myelodysplastic Syndromes and Acute Myeloid Leukemia

Background:TP53-aberrant myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) constitute the highest risk molecular subgroup of myeloid neoplasms, and there are currently no FDA-approved targeted therapies for this subset of patients. We have recently explored the reasons for these distinctly adverse outcomes using clonal dynamic modeling. However, prognostic discrimination within this heterogeneous group of patients has not been validated in large-scale efforts. More recently, efforts to gain clarity on this disease subset include the IPSS-M model for MDS, the European LeukemiaNet (ELN) 2022 classification for AML, and the 2022 International Consensus Classification (ICC) for both MDS and AML. For example, the IPSS-M model has shown an adjusted hazard ratio of 3.27 (95% CI 2.38 - 4.48) for multi-hit TP53 aberration; the ELN 2022 classification now includes a new category termed "AML with mutated TP53" for patients with TP53 variant allele frequency (VAF) ≥ 10%; and the 2022 ICC has designated categories for MDS and AML with TP53 mutation. However, these systems do not discern among the subtypes of TP53 genomic aberrations with regard to clinical outcomes. Methods: Identification of patients from the UMass Chan Leukemia Registry was performed via UMass Clarity, a Microsoft SQL Server database comprised of 23,000 tables, in conjunction with the main reporting environment in EPIC. The Registry identified patients harboring one or more aberrations in TP53 and with ICD-10 code of either D46.9 (MDS, including its subentities) or C92.00 (AML, including its subentities) between 2011-2022. A total of 63 patients were identified. Patients with TP53-aberrant MDS or AML were stratified by the presence or absence of multi-hit status and/or TP53 VAF >50%. Multi-hit status was defined as per the 2022 ICC: two or more distinct TP53 mutations with VAF ≥ 10%, or a single TP53 mutation plus one of the following abnormalities: (1) del(17p13.1), (2) TP53 VAF >50%, (3) copy-neutral loss-of-heterozygosity, or (4) any complex karyotype. Monoallelic status was defined as non-multi-hit. Kaplan-Meier survival with log rank p value analysis was performed on subgroups based on the TP53 genomic state. Results: Median age of the UMass cohort (n = 63) was 69.8 ± 11.3 years. There were 35 patients (55.6%) with AML. We identified 58 patients who met the 2022 ICC definition for myeloid neoplasm with mutated TP53 (after exclusion of 5 patients with VAF < 10%) then stratified patients based on hit status and VAF. Median overall survival (OS) was similar among patients with monoallelic TP53-mutant MDS, multi-hit TP53-mutant MDS, and monoallelic TP53-mutant AML (median OS 440 days vs. 437 days vs. 440 days, respectively) (Panel A). In contrast, patients with multi-hit TP53-mutant AML had distinctly shorter survival (median 46 days) (Panel A). For patients with multi-hit status MDS or AML per the 2022 ICC (n = 41), we sub-stratified patients based on TP53 VAF. OS for patients with MDS with VAF ≤ 50% and VAF > 50% was similar (median 376 days vs. 435 days, respectively) (Panel B). Patients with AML with TP53 VAF > 50% had significantly inferior OS (median 43 days) (Panel B). Twelve (19.0%) of 63 patients underwent allogeneic hematopoietic cell transplant (allo-HCT) (2 had VAF >50%). Allo-HCT significantly improved median OS (732 days with allo-HCT vs. 161 days for n = 51 without allo-HCT; p = 0.0033) (data not shown). Only 3 (25%) of the 12 allo-HCT recipients achieved MRD-free remission lasting beyond 1000 days; VAF was ≤ 10% in all of these long-term survivors with TP53-mutant MDS or AML. Conclusion:TP53-aberrant MDS and AML comprise a prognostically heterogeneous group of patients with inferior clinical outcomes, though the highest risk subgroup appears to be AML with multi-hit TP53 status or AML with TP53 VAF > 50%. There is high value in determining the allelic state and hit status at the time of diagnosis to help prognosticate and develop a long-term management plan. Allo-HCT improves median OS, though durable MRD-negative remission is rare. Our data suggest that there may be a limited window of VAF ≤ 10% for the success of allo-HCT for TP53-aberrant myeloid neoplasm. We acknowledge that there is a selection bias for proceeding with allo-HCT. Large-scale systematic studies are needed to comprehensively profile patients classified as myeloid neoplasm with mutated TP53 such that risk-adapted management strategies can implemented. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Erythroid and Megakaryocytic Differentiation Program in JAK2-Mutated Acute Myeloid Leukemia with or without Antecedent Myeloproliferative Neoplasm

JAK2 V617F is the most common driver mutation for Ph-negative MPN and related blast transformation (MPN-BP). In contrast, JAK2 V617F is rare (<5%) in acute myeloid leukemia (AML) lacking an antecedent MPN (nonMPN AML). JAK2 V617F skews the differentiation of hematopoietic stem/progenitor cells (HSPC) towards erythroid and megakaryocytic lineages and in conjunction with TP53 deficiency/mutations results in acute erythroid leukemia in mice (Rampal et al., PNAS 2014). These phenotypes, although also reported in patients with MPN-BP (Mesa et al., Blood 2005), remain incompletely understood. In this study, we set out to study these phenotypes at the protein, epigenomic and transcriptomic levels in JAK2-mutated AML comparing MPN-BP to nonMPN AML. The study cohort included 58 MPN-BP (16 PV, 16 ET, 14 PMF and 12 MPN-U) and 27 nonMPN AML patients (11 de novo AML, 12 AML-MRC, 4 t-AML) with JAK2 V617F mutation (Table 1). In addition, 100 patients with JAK2 WT AML were also included as control group. The median age at diagnosis in MPN-BP and nonMPN AML subgroups as well as in JAK2 WT AML was similar (70 years vs 71 years vs 70 years, respectively) and showed a male preponderance. The median interval between MPN diagnosis and blast transformation was 4.3 years (range, 0-20.5 years). Overall survival was inferior in MPN-BP compared to nonMPN AML (median survival: 7.4 vs 19.3 months). MPN-BP showed a higher rate of MF-2 or 3 myelofibrosis (78% vs 33%, p<0.05), osteosclerosis (50% vs 15%, p<0.05) and marrow necrosis (7% vs 0%) on bone marrow biopsies than nonMPN AML. On immunohistochemistry, 28% (10/32) MPN-BP cases (vs 0% nonMPN AML, p<0.05) were classified as acute leukemia with erythroid/megakaryocytic differentiation (M6b and/or M7) based on expression of E-cadherin, CD71, Glycophorin A, and CD61 on leukemic blasts. ERG, FLI1, and LMO2, transcription factors that are often expressed in HSPCs, were also expressed in leukemic blasts of MPN-BP and nonMPN AML. Aberrant TP53 expression by immunohistochemistry was seen in 31% of MPN-BP (5/9 and 5/21 cases with and without erythroid/megakaryocytic differentiation, respectively) and 17% (3/18) of nonMPN AML. The most common mutations on next-generation sequencing included TP53, RUNX1, ASXL1, TET2, DNMT3A, SRSF2, IDH1, IDH2 and EZH2 in each group. However, of these, TP53 mutations were more frequent in MPN-BP (34% vs 11% in nonMPN AML, p<0.05) and TET2 mutations more frequent in nonMPN AML (48% vs 24% in MPN-BP, p<0.05). Interestingly, NPM1 and FLT3, which are among the most mutated genes in AML were not detected in either MPN-BP or nonMPN AML. Based on the over-representation of erythroid/megakaryocytic phenotype in MPN-BP seen on immunohistochemistry, we hypothesized that MPN-BP blasts might exhibit an upregulated epigenetic and transcriptional program involved in erythroid/megakaryocytic differentiation. RNA-seq and ATAC-seq analysis were performed on flow cytometry sorted CD34+ leukemic blast populations from 11 MPN-BP and 6 nonMPN AML, as well as similar sorted populations from normal controls and JAK2 WT AML. Principal component analysis showed overlapping MPN-BP and nonMPN AML samples, both of which were separated from JAK2 WT AML. Differential expression analysis confirmed nearly identical gene expression between blasts from MPN-BP and nonMPN AML. In addition, consistent with findings by immunohistochemistry, the expression of genes specifically involved in erythroid/megakaryocytic differentiation (TFRC, GYPA, HBB, SPTA1, EPOR, ITGA2B, ITGB3, PF4, ALAS2, GP1BA, ENG and MPL) were upregulated in MPN-BP. Hierarchical clustering using Ward's method on both RNA-seq and ATAC-seq normalized counts revealed that the JAK2 WT AML cluster was distinct from the MPN-BP and nonMPN AML cluster (Figure 1). Lineage deconvolution of ATAC-seq using hematopoietic differentiation stages (Glass et al., Blood 2017, Dilip et al., Blood 2021) to evaluate lineage characteristics of the blasts showed hematopoietic stem cell (HSC) predominance in JAK2 WT AML while MPN-BP and nonMPN AML displayed enrichment of multipotent progenitor (MPP), megakaryocyte-erythrocyte progenitor (MEP) and erythroid signatures. Collectively, our data demonstrates enrichment of erythroid and megakaryocytic programs in both JAK2-mutated MPN-BP and JAK2-mutated nonMPN AML, suggesting that chromatin accessibility and transcription may be driven by mutated JAK2 regardless of antecedent MPN. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Mutation profile of diffuse large B-cell lymphoma with relapses in the central nervous system

Introduction . The recurrence of diffuse large B-cell cell lymphoma in the central nervous system in the vast majority of cases is a fatal manifestation of the disease. The study of the lymphoma mutational profile can improve the accuracy of the prognosis of relapse in the central nervous system and justify the selection of patients for preventive treatment. Aim. To evaluate the mutational profile of cases of diffuse large B-cell cell lymphoma with central nervous system damage in relapse based on the results of our own experiment on high-performance sequencing. Materials and methods . On the Illumina platform, full-exome sequencing of diagnostic samples of diffuse large B-cell cell lymphoma with relapses in the central nervous system was performed. A panel including more than 70 genes was analyzed. Results . Four main groups of genetic events can be distinguished in the group of studied samples, namely: combined mutations in the NF-kB ( MYD88, NOTCH1, CD79B, CARD11 ) and JAK-STAT ( PIM1, STAT6 ) signaling pathways, as well as aberrations in the main oncosuppressor TP53 and chromatin remodeling system genes ( ARID1A, KMT2D, EP300, SMARCA4 ). A recurrent mutation c. 794T&gt;C, p.L265P MYD88 was detected in the study group. Among other findings, mutations in the CIITA and CD58 genes should be noted, which are important in avoiding tumor cells from immune surveillance. Conclusion . Despite the apparent heterogeneity of the mutational profile of diffuse large B-cell cell lymphoma with relapses in the central nervous system, in most cases, tumor cells were characterized by genetic disorders leading to the production of a large number of pro-inflammatory cytokines by malignant lymphocytes, as well as aberrations that reduce immunogenicity and contribute to the avoidance of immune surveillance by the tumor.

Abstract A013: CDK2 and CDK4/6 inhibition in GIST: Mechanisms of response and resistance

Abstract Advanced GIST is characterized by genomic perturbations of key cell cycle regulators. Oncogenic activation of CDK4/6 results in RB1 inactivation and cell cycle progression. Given that single-agent CDK4/6 inhibitor (CDK4/6i) therapy failed to show clinical activity in advanced GIST, we evaluated strategies for maximizing response to therapeutic CDK4/6 inhibition. Targeted next-generation sequencing and multiplexed protein imaging were used to detect cell cycle regulator aberrations in GIST clinical samples (N=18), including 8 metastatic TKI-resistant GISTs. Multiple metastases were analyzed in 3 patients. The impact of CDK2i (CDK2 inhibitor-II), CDK4/6i (palbociclib or abemaciclib), and CDK2/4/6i (PF-06873600) was determined through cell proliferation and protein detection assays in vitro and in vivo. Mechanisms of acquired CDK2i and CDK4/6i resistance were characterized in GIST cell lines after long-term exposure. The results demonstrate recurrent genomic aberrations in cell cycle regulators causing co-activation of the CDK2 and CDK4/6 pathways. Identical aberrations of p16, RB1, and TP53 were present in all metastases from 3 patients. We show that therapeutic co-targeting of CDK2 and CDK4/6 is synergistic in GIST cell lines with intact RB1, through inhibition of RB1 hyperphosphorylation and cell proliferation (P&amp;lt;0.01). Intact RB1 predicted response to treatment, whereas RB1-deficient models were resistant. Moreover, we identify RB1 inactivation and a novel oncogenic cyclin D1 resulting from an intragenic rearrangement (CCND1::chr11.g:70025223) as mechanisms of acquired CDK inhibitor resistance in GIST. The CCND1 rearrangement deleted the cyclin D1 C-terminal Thr286 and Thr288 residues which mediate cyclin D1 proteasomal degradation, resulting in overexpression of an abnormal cyclin D1. CDK inhibitor resistance properties were corroborated by lentiviral transduction of the CCND1 fusion gene into fusion-negative GIST, leiomyosarcoma, and breast cancer cells. These studies establish the biologic rationale for CDK2 and CDK4/6 co-inhibition as therapeutic strategy in patients with advanced GIST, including patients with metastatic GIST progressing on TKIs. In addition, these findings expand the spectrum of potential CDK inhibitor resistance mechanisms with translational potential for improving cell cycle targeted therapies in other cancer types. Citation Format: Inga-Marie Schaefer, Matthew L. Hemming, Meijun Z. Lundberg, Matthew P. Serrata, Isabel Goldaracena, Ninning Liu, Peng Yin, Joao A. Paulo, Steven P. Gygi, Suzanne George, Jeffrey A. Morgan, Monica M. Bertagnolli, Ewa T. Sicinska, Adrian Mariño-Enríquez, Jason L. Hornick, Chandrajit P. Raut, George D. Demetri, Wen-Bin Ou, Sinem K. Saka, Jonathan A. Fletcher. CDK2 and CDK4/6 inhibition in GIST: Mechanisms of response and resistance [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A013.

Structural variants shape driver combinations and outcomes in pediatric high-grade glioma.

We analyzed the contributions of structural variants (SVs) to gliomagenesis across 179 pediatric high-grade gliomas (pHGGs). The most recurrent SVs targeted MYC isoforms and receptor tyrosine kinases (RTKs), including an SV amplifying a MYC enhancer in 12% of diffuse midline gliomas (DMG), indicating an underappreciated role for MYC in pHGG. SV signature analysis revealed that tumors with simple signatures were TP53 wild type (TP53WT) but showed alterations in TP53 pathway members PPM1D and MDM4. Complex signatures were associated with direct aberrations in TP53, CDKN2A and RB1 early in tumor evolution and with later-occurring extrachromosomal amplicons. All pHGGs exhibited at least one simple-SV signature, but complex-SV signatures were primarily restricted to subsets of H3.3K27M DMGs and hemispheric pHGGs. Importantly, DMGs with complex-SV signatures were associated with shorter overall survival independent of histone mutation and TP53 status. These data provide insight into the impact of SVs on gliomagenesis and the mechanisms that shape them.

Abstract 5648: Response and resistance to CDK2 and CDK4/6 inhibition in GIST

Abstract Gastrointestinal stromal tumor (GIST) is the most common GI sarcoma and is generally initiated by KIT or PDGFRA mutations which are compelling therapeutic targets for tyrosine kinase inhibitors (TKI). However, the emergence of secondary mutations results in clinical resistance to available TKIs. GIST progression is driven by genomic events which incrementally target the p16-CDK4/6-RB1 and p14-TP53-RB1 pathways to create CDK4/6 and CDK2 oncogenic co-dependency. Based on limited efficacy of single-agent CDK4/6-inhibitor (CDK4/6i) therapy in GIST, we evaluated strategies of co-targeting CDK2 and CDK4/6. Multiplexed protein imaging (via Immuno-SABER) was validated for the detection of cell cycle regulator aberrations in GIST clinical samples (N=18), 7 of which were TKI-resistant, and including 3 patients in whom multiple metastases were analyzed. The impact of various CDK perturbants using CDK2i (CDK2 inhibitor-II), CDK4/6i (palbociclib or abemaciclib), and CDK2/4/6i (PF-06873600) was determined through cell proliferation and protein detection assays in GIST cell lines and murine xenografts. Mechanisms of acquired CDK2i and CDK4/6i resistance were characterized in GIST cell lines after long-term exposure. Abnormal expression/biallelic inactivation of CDKN2A/p16, RB1, and TP53 were identified in 7 (39%), 2 (11%), and 2 (11%) of 18 GISTs, respectively. Identical aberrations of p16, RB1, and TP53 were present in all metastases from 3 patients. Since 5 of 7 RB1-intact advanced GISTs had co-dysregulation of the CDK2 and CDK4/6 pathways, we evaluated co-inhibition of CDK2 and CDK4/6 in vitro and in vivo which inhibited cell proliferation (P&amp;lt;0.01) and RB1 hyperphosphorylation. Intact RB1 predicted response to treatment, whereas RB1-deficient models were resistant. Two resistant sub-lines emerged after 11 and 14 months of palbociclib exposure: one with biallelic genomic RB1 inactivation and the other with the first known example of a cyclin D1 coding sequence fusion with oncogenic properties (CCND1::chr11.g:70025223). The CCND1 fusion deleted the cyclin D1 C-terminal Thr286 and Thr288 residues which mediate cyclin D1 proteasomal degradation, resulting in overexpression of an abnormal cyclin D1. Palbociclib-resistance properties were corroborated by lentiviral transduction of the CCND1 fusion gene into fusion-negative GIST, leiomyosarcoma, and breast cancer cells. CDK2 and CDK4/6 pathway perturbations with retained RB1 are frequent in advanced GIST and can be conserved across metastases, creating a compelling biologic rationale for therapeutic cell cycle restoration. We show that co-inhibition of CDK2 and CDK4/6 is synergistic in GIST and highlight RB1 inactivation and a novel oncogenic cyclin D1 as mechanisms of acquired CDKi resistance. Hence, combination therapies targeting CDK2 and CDK4/6 with correlative biomarkers predictive of response should be evaluated in patients with metastatic or TKI-resistant GIST. Citation Format: Inga-Marie Schaefer, Meijun Z. Lundberg, Matthew L. Hemming, Sinem K. Saka, Matthew P. Serrata, Isabel Goldaracena, Ninning Liu, Peng Yin, Joao A. Paulo, Steven Gygi, George D. Demetri, Ewa Sicinska, Adrian Mariño-Enríquez, Jason L. Hornick, Chandrajit P. Raut, Wen-Bin Ou, Jonathan A. Fletcher. Response and resistance to CDK2 and CDK4/6 inhibition in GIST [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 5648.

Abstract 849: Characterization and prevention of radiation-induced malignancies in Li-Fraumeni Syndrome

Abstract PURPOSE: Li-Fraumeni Syndrome (LFS) is a genetic disorder associated with a significant risk of early-onset cancer. This condition is largely driven by germline mutations in the TP53 tumor suppressor, which has a broad spectrum of functions including the transcriptional regulation of radiation response. Termed the guardian of the genome, TP53 serves as a critical checkpoint which coordinates DNA repair, cell cycle progression and apoptosis following DNA damage, ultimately controlling the fate of the cell. Aberrant or deficient TP53 function, such as occurs in LFS, contributes to radiation vulnerability. As a result, there is particular caution in the use of radiotherapy to treat primary LFS tumors, in order to prevent the formation of secondary, radiation-induced malignancies. To this end, therapeutic options for LFS are often limited to surgery and chemotherapy, posing substantial constraints for the treatment of patients who may otherwise benefit from primary tumor radiation. Metformin, a commonly prescribed anti-diabetic drug, is associated with lower cancer incidence in populations worldwide. Recent studies have shed light on the potential utility of metformin as a pharmacopreventive agent for primary tumors in LFS; hence, we hypothesize that the utility of metformin can be extended to the prevention of secondary malignancies following radiotherapy in LFS. METHODS/RESULTS: To explore the chemopreventive potential of metformin in LFS, we completed tumor challenges using a p53R172H/+ LFS mouse model. Mice treated prophylactically with metformin showed slower xenograft tumor growth compared to vehicle-treated mice. Ongoing work in our lab aims to characterize the effects of metformin on tumor growth following the administration of localized ionizing radiation (IR) to LFS mice. Briefly, these mice are treated with either vehicle or metformin, and IR is administered to the left hindlimbs to induce tumor formation. The timing and rates of tumor growth are monitored using magnetic resonance imaging. At endpoint, excised tumors are subjected to global profiling via RNA sequencing, proteomic analysis, and single-cell sequencing of discrete cell populations to characterize the effects of metformin on the development of radiation-induced malignancies. Results of these studies will be presented. SIGNIFICANCE: Overall, this work will advance our understanding of the chemopreventive effects of metformin, with the potential to broaden the treatment options available to LFS patients. Citation Format: Pamela Psarianos, Nicholas Fischer, Camilla Giovino, Noel Ong, David Malkin. Characterization and prevention of radiation-induced malignancies in Li-Fraumeni Syndrome [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 849.

HGG-60. Structural variants shape driver combinations and outcomes in pediatric high-grade glioma

Abstract Pediatric high-grade gliomas (pHGGs), encompassing hemispheric and diffuse midline gliomas (DMGs), remain a devastating disease. The last decade has revealed oncogenic drivers including single nucleotide variants (SNVs) in histones. However, the contribution of structural variants (SVs) to gliomagenesis has not been systematically explored due to limitations in early SV analysis approaches. Using SV algorithms, we recently created, we analyzed SVs in whole-genome sequences of 179 pHGGs including a novel cohort of treatment naïve samples–the largest WGS cohort assembled in adult or pediatric glioma. The most recurrent SVs targeted MYC isoforms and receptor tyrosine kinases, including a novel SV amplifying a MYC enhancer in the lncRNA CCDC26 in 12% of DMGs and revealing a more central role for MYC in these cancers than previously known. Applying de novo SV signature discovery, we identified five signatures including three (SVsig1-3) involving primarily simple SVs, and two (SVsig4-5) involving complex, clustered SVs. These SV signatures associated with genetic variants that differed from what was observed for SV signatures in other cancers, suggesting different links to underlying biology. Tumors with simple SV signatures were TP53 wild-type but were enriched with alterations in TP53 pathway members PPM1D and MDM4. Complex signatures were associated with direct aberrations in TP53, CDKN2A, and RB1 early in tumor evolution, and with extrachromosomal amplicons that likely occurred later. All pHGGs exhibited at least one simple SV signature but complex SV signatures were primarily restricted to subsets of H3.3K27M DMGs and hemispheric pHGGs. Importantly, DMGs with the complex SV signatures SVsig4-5 were associated with shorter overall survival independent of histone type and TP53 status. These data inform the role and impact of SVs in gliomagenesis and mechanisms that shape them.