TP53 Deletion Research Articles

Preferential Genetic Pathways Lead to Relapses in Adult B-Cell Acute Lymphoblastic Leukemia

Adult B-cell acute lymphoblastic leukemia (B-ALL) is characterized by genetic heterogeneity and a high relapse rate, affecting over 40% of adults. However, the mechanisms leading to relapse in adults are poorly understood. Forty-four adult B-ALL patients were studied at both diagnosis and relapse by next-generation sequencing (NGS). Four main genetic pathways leading to relapse in adults were identified: IKZF1plus genetic profile, RAS mutations and TP53 alterations in Ph-negative B-ALL and acquisition of ABL1 mutations in Ph-positive patients. The most frequently deleted gene at diagnosis was IKZF1 (52%), and 70% of these patients had IKZF1plus profile. Notably, 88% of patients with IKZF1plus at diagnosis retained this genetic profile at relapse. Conversely, the acquisition of RAS mutations or the expansion of subclones (normalized variant allele frequency < 25%) present from diagnosis were observed in 24% of Ph-negative patients at relapse. In addition, 24% of relapses in the Ph-negative cohort could potentially be driven by TP53 alterations. Of these cases, five presented from diagnosis, and four emerged at relapse, mostly as “double-hit” events involving both TP53 deletion and mutation. In Ph-positive B-ALL, the main genetic finding at relapse was the acquisition of ABL1 mutations (86%). Three clonal evolution patterns were identified: the persistent clone trajectory (25%), the expanding clone trajectory (11%) and the therapy-boosted trajectory (48%). Our results reveal the presence of preferential biological pathways leading to relapse in adult B-ALL. These findings underscore the need for personalized therapeutic strategies to improve clinical outcomes in adult patients with B-ALL.

Diagnostic and prognostic genomic aberrations in upper tract urothelial carcinoma can be identified in focal barbotage samples.

To investigate whether genetic analysis of focal barbotage samples obtained at ureterorenoscopy (URS) is possible, and to identify genetic aberrations that might add prognostic information. This prospective study included barbotage samples from 42 patients with upper urinary tract urothelial carcinoma (UTUC) confirmed at URS. At URS, focal barbotage specimens were collected for cytology and for gene sequencing. Tumour grades were determined from cytology and/or biopsy, or from radical nephroureterectomy samples. Next-generation sequencing using a 385-gene panel was performed and single nucleotide variants (SNVs), deletions/insertions (indels) and copy number aberrations (CNAs) were identified. Manual filtering of the SNVs/indels was performed to identify possible pathogenic mutations. Of the 42 samples, two failed quality control, therefore, 40 focal barbotage samples were sequenced. We identified known and suspected pathogenic mutations and other genomic aberrations in 36 samples. The most common variants were in TERT (78%), FGFR3 (50%), KMT2D (42%), KDM6A (42%), ARID1A (39%), TP53 (19%) and deletion of 9q (50%). Known pathogenic mutations in FGFR3 were common in grade 1 and 2 tumours, but not present in any grade 3 tumour. No patients with an FGFR3 mutation died during follow-up. TP53 variants or deletions, as well as amplifications of MDM2, were only present in high-grade (HG) tumours or low-grade (LG) tumours in patients who had metastasis/died from urinary tract carcinoma. CNAs were detected in 36/40 barbotage samples, 91% of the HG samples and 69% of the LG samples, including those from all five patients with LG tumours with metastasis or who died from urinary tract cancer. Focal barbotage samples enable identification of gene mutations and other genetic aberrations that may add important prognostic information to histopathology and cytology. Refined prognostication of UTUC patients already at diagnosis can guide treatment decisions and follow-up programmes.

Molecular Insights Into Actinic Cheilitis and Lower Lip Squamous Cell Carcinoma: AURKA and AURKB Amplifications and Their Association With Tumor Microenvironment.

Lip exposure to carcinogens lead to several disorders, such as actinic cheilitis (AC) and lower lip squamous cell carcinoma (LLSCC). Although several studies have described important pathways in lip carcinogenesis, the comprehension of association of target genes in this process and their association with tumor microenvironment still need to be better understood. Tissue samples of 30 AC and 17 LLSCC cases were included for histopathological analysis, immunohistochemical expression of CD4, CD8, and PD-L1, and fluorescence insitu hybridization for AURKA, AURKB, TP53, PTEN, CCND1, and MYC. Non-parametrical tests were done and p < 0.05 was considered significant. LLSCC patients presented higher amplifications of AURKA and AURKB, deletion of TP53, and PTEN and rearrangements of MYC than AC. AURKA, AURKB, TP53, PTEN, and CCND1 changes were correlated with PD-L1 expression. AURKA and AURKB amplifications and other gene changes are pointed by their association of lip disorders.

Predictors of Radiotherapy Utilization and Outcome in Multiple Myeloma: A Single-Center Retrospective Study

Introduction/Background Radiotherapy (RT) is frequently used in the management of multiple myeloma (MM) for local control and symptom palliation. However, racial disparities and predictors of RT utilization in MM remain underexplored. This study aims to evaluate the relationship between patient demographics, disease characteristics, and RT utilization in a diverse MM patient cohort. Methods We conducted a single-center retrospective study of 208 MM patients treated with RT between 2008-2023 at Northwell Health. Patients without a MM diagnosis, initial diagnostic data, or follow up were excluded. We collected data on patient demographics, myeloma risk status based on cytogenetics and Revised International Staging System (R-ISS) criteria, self-identified race, and RT frequency. Statistical analysis was done using Stata v.18. High risk group is categorized as patients who had FGFR3/IGH fusion or t(4;14), MAF/IGH fusion or t(14;16), IGH/MAFB fusion or t (14:20), TP53 (17p) deletion, 1q amplification or stage 2/3 disease. Logistic regression analysis was performed to identify predictors of receiving three or more RT courses, and survival analysis was conducted to assess the impact of repeat RT on patient outcomes. Results The study included 124 patients, with race data available for 121 patients. Median age was 66 years, and 51.6% were male. Racial distribution was as follows: African American/Black 35.54%, White 28.93% Asian 6.61%, American Indian or Alaska Native 1.65%, and Others 27.27%. There was no significant relationship between MM risk status and the number of RT courses. However, White patients were more likely to receive multiple RT treatments to the same site of the body compared to all other racial groups (p=0.04). Logistic regression showed age as the only significant predictor for receiving three or more RT courses [odds ratio=0.92, 95% confidence interval (CI) 0.87-0.98, p=0.006], indicating that younger patients were more likely to undergo multiple RT courses. Age at diagnosis negatively correlated with the number of RT courses. At median follow up of 30 months, 36 deaths (29%) occurred. There was no significant difference in overall survival (OS) between patients who received one RT course compared to those who received more than one RT course (p= 0.27). However, survival analysis revealed that patients receiving repeat RT to the same site had higher risk of death compared to those who did not get repeat RT [hazard ratio 2.37, 95% CI 0.70-8.03, p=0.04], with median OS 52.3 months vs. 87.8 months, respectively. Conclusions This study highlights significant racial disparities in the utilization of RT among MM patients, with White patients more likely to receive multiple RT treatments to the same site. Age is a significant predictor of RT utilization, with younger patients receiving more courses. Additionally, repeat RT to the same site is associated with shorter OS. However, our study is limited by the sample size and exclusion of patients with insufficient data, with to potential bias. Further studies are needed to explore the role of race in access to RT.

Cyclin-D1 rearrangement as a secondary event in the large cell transformation of splenic marginal zone lymphoma with a TP53 deletion.

IGH::CCND1 translocation has been implicated as a preliminary finding in mantle cell lymphoma (MCL) and plasma cell myeloma, with cyclin D1 over-expression by immunohistochemistry stain, without gene rearrangement, reported in other hematologic neoplasms. CCND1 rearrangement has been reported infrequently as a secondary event in high-grade B-cell lymphomas. We present the case of an elderly man who was found to have a splenic marginal zone lymphoma with a heterozygous TP53 deletion. Years later at the time of relapse, the patient acquired a CCND1 rearrangement, in addition to apersistent TP53 deletion. Sequencing of the two lymphomas demonstrated clonal relatedness of the two processes. To our knowledge, this is the first report of a splenic marginal zone lymphoma witha TP53 deletion at diagnosis, evolving into a large B-cell lymphoma with a CCND1 rearrangement.

High-Grade Progression, Sarcomatous Transformation, and/or Metastasis of Pituitary Neuroendocrine Neoplasms (PitNENs): The UCSF Experience.

Pituitary neuroendocrine tumors (PitNET) that metastasize comprise ~ 0.2% of adenohypophyseal tumors are aggressive and are challenging to treat. However, many non-metastatic tumors are also aggressive. Herein, we review 21 specimens from 13 patients at UCSF with metastatic PitNETs (CSF or systemic, N = 7 patients), high-grade pituitary neuroendocrine neoplasms (HG-PitNEN, N = 4 patients), and/or PitNETs with sarcomatous transformation (PitNET-ST, N = 5 patients). We subtyped cases using the World Health Organization (WHO) and International Agency for Research on Cancer (IARC) criteria for neuroendocrine neoplasms (NENs). Lineage subtypes included acidophil stem cell, null cell, thyrotroph, corticotroph, lactotroph, and gonadotroph tumors. The median Ki-67 labeling index was 25% (range 5-70%). Lack of p16 was seen in 3 cases, with overexpression in 2. Strong diffuse p53 immunopositivity was present in 3 specimens from 2 patients. Loss of Rb expression was seen in 2 cases, with ATRX loss in one. Molecular analysis in 4 tumors variably revealed TERT alterations, homozygous CDKN2A deletion, aneuploidy, and mutations in PTEN, TP53, PDGFRB, and/or PIK3CA. Eight patients (62%) died of disease, 4 were alive at the last follow-up, and 1 was lost to the follow-up. All primary tumors had worrisome features, including aggressive lineage subtype, high mitotic count, and/or high Ki-67 indices. Additional evidence of high-grade progression included immunohistochemical loss of neuroendocrine, transcription factor, and/or hormone markers. We conclude that metastatic PitNET is not the only high-grade form of pituitary NEN. If further confirmed, these histopathologic and/or molecular features could provide advanced warning of biological aggressiveness and be applied towards a future grading scheme.

Combined inhibition of CTPS1 and ATR is a metabolic vulnerability in p53-deficient myeloma cells.

In multiple myeloma, as in B-cell malignancies, mono- and especially bi-allelic TP53 gene inactivation is a high-risk factor for treatment resistance, and there are currently no therapies specifically targeting p53 deficiency. In this study, we evaluated if the loss of cell cycle control in p53-deficient myeloma cells would confer a metabolically actionable vulnerability. We show that CTP synthase 1 (CTPS1), which encodes a CTP synthesis rate-limiting enzyme essential for DNA and RNA synthesis in lymphoid cells, is overexpressed in samples from myeloma patients displaying a high proliferation rate (high MKI67 expression) or a low p53 score (synonymous with TP53 deletion and/or mutation). This overexpression of CTPS1 was associated with reduced survival in two cohorts. Using scRNA-seq analysis in 24 patient samples, we further demonstrate that myeloma cells in the S or G2/M phase display high CTPS1 expression. Pharmacological inhibition of CTPS1 by STP-B induced cell cycle arrest in early S phase in isogenic NCI-H929 or XG7 TP53 +/+, TP53 -/-, and TP53 R175H/R175H cells and in a TP53 -/R123STOP patient sample. The functional annotation of transcriptional changes in 10 STP-B-treated myeloma cell lines revealed a decrease in protein translation and confirmed the blockade of cells into the S phase. The pharmacological inhibition of ATR, which governs the intrinsic S/G2 checkpoint, in STP-B-induced S-phase arrested cells synergistically induced cell death in TP53 +/+, TP53 -/-, and TP53 R175H/R175H isogenic cell lines (Bliss score >15). This combination induced replicative stress and caspase-mediated cell death and was highly effective in resistant/refractory patient samples with TP53 deletion and/or mutation and in TP53 -/- NCI-H929 xenografted NOD-scid IL2Rgamma mice. Our in vitro, ex vivo, and in vivo data provide the rationale for combined CTPS1 and ATR inhibition for the treatment of p53-deficient patients.

Characteristics of Acute Myeloid Leukemia Patients with TP53 Alterations

Abstract Background TP53 is the most intensively studied gene in cancer. The vast majority of de novo AML patients have unaltered TP53 alleles; data from The Cancer Gene Atlas including adult patients with AML documented that ∼ 8% of cases harbor TP53 alterations. Objectives The objective of this study is to identify the features of TP53 alterations in acute myeloid leukemia (AML) patients, investigate its association with clinical findings, standard laboratory tests, morphological, cytogenetic and molecular profiles, and assess its influence on the overall outcome of patients on day 28 after induction therapy. Subjects and Methods The present study is an analytical observational study that was conducted on 60 de novo adult AML patients who presented to the Hematology/Oncology unit of Ain Shams University Hospitals. All patients’ samples were analyzed for TP53 deletion using LSI 17p13 FISH probe for detection of p53 deletion and they were further subjected to testing for TP53 Pro72Arg alterations by real time polymerase chain reaction. All patients were subjected to therapy and then followed up at day 28 to asses the outcome. Results Male gender and lower TLC were significantly associated with good outcome with (P-value ≤ 0.05). Patients with cytogenetic structural abnormalities showing 17q rearrangement showed significant association with bad outcome with (P-value ≤ 0.05) and t(8;21) was found to be highly significant in association with good outcome with (P-value&amp;lt; 0.01). FLT3ITD mutation was found to be highly significant in association with bad outcome with (P-value&amp;lt; 0.01). NPM mutation was significant in association with good outcome with (P-value ≤ 0.05). TP53 mutation was detected in 11.7 % of studied patients where 8.3% out of them were heterozygous mutation and 3.4% were homozygous. P53 mutation wassignificantly associated with advanced age, male gender and higher TLC with (P- value ≤ 0.05). Cytogenetic structural abnormalities including 11q23 rearrangement showed significant association with P53 mutation with (P-value ≤ 0.05) and t(8;21)+del 17p, del 17p&amp; -7 and del 17p only was found to be highly significant in association with p53 mutation with (P-value&amp;lt; 0.01). Normal karyotyping showed negative relation with P53 mutation with (P-value ≤ 0.05) where all patients who yielded normal karyotyping (35%) were negative for P53 alterations; that doesn't necessarily denote causation, but it's an observable pattern, and del 17p that was found to be highly significant in association with p53 mutation with (P-value&amp;lt; 0.01). P53 mutation was found to be highly significant in association with bad outcome with (P-value &amp;lt; 0.01). Unfavorable and Favorable risk stratification of ELN 2022 were found to be highly significant in association with p53 mutation with (P-value&amp;lt; 0.01). ELN 2022 risk stratification categories were found to be highly significant in association with patients’ outcomes with (P- value &amp;lt; 0.01). Conclusion TP53 alterations strongly identify high-risk AML patients with poor outcome in this study yet, this needs further investigation on larger sample size with longer follow up. Investigations of TP53 mutation especially in Adult AML may help with the selection of patients in need of intensive therapeutic strategy or may help with designation of new innovative targeted therapies. Key words Tp53, Mutation, Adult Acute Myeloid Leukemia.

Targeted BET inhibition with OPN-51107 synergizes with venetoclax in chronic lymphocytic leukemia

Chronic lymphocytic leukemia (CLL) remains incurable and its ability to acquire resistance to front-line therapeutics has proved challenging. Bromodomain and extra-terminal proteins, particularly bromodomain-containing protein 4 (BRD4), are integral to gene expression in CLL and offer a promising therapeutic target. In this study, we examined the activity of the BRD4 inhibitor OPN-51107 alone and in combination with the BCL-2 inhibitor, venetoclax, in CLL cell lines and patient-derived CLL samples. We demonstrate that OPN-51107 induces anti-tumor activity in both CLL cell lines and patient-derived samples, including relapsed/refractory (R/R) samples and those with high-risk features (i.e. ATM and/or TP53 deletions). Importantly, the combination of OPN-51107 and venetoclax exhibited synergistic cytotoxicity in ibrutinib-resistant CLL cells and patient-derived CLL samples regardless of R/R or deletion status. This study establishes the preclinical efficacy of using OPN-51107 and venetoclax in combination in therapy-resistant and/or high-risk CLL, lending support for its further development as a combination therapy.

Emerging advances in defining the molecular and therapeutic landscape of small-cell lung cancer.

Small-cell lung cancer (SCLC) has traditionally been considered a recalcitrant cancer with a dismal prognosis, with only modest advances in therapeutic strategies over the past several decades. Comprehensive genomic assessments of SCLC have revealed that most of these tumours harbour deletions of the tumour-suppressor genes TP53 and RB1 but, in contrast to non-small-cell lung cancer, have failed to identify targetable alterations. The expression status of four transcription factors with key roles in SCLC pathogenesis defines distinct molecular subtypes of the disease, potentially enabling specific therapeutic approaches. Overexpression and amplification of MYC paralogues also affect the biology and therapeutic vulnerabilities of SCLC. Several other attractive targets have emerged in the past few years, including inhibitors of DNA-damage-response pathways, epigenetic modifiers, antibody-drug conjugates and chimeric antigen receptor T cells. However, the rapid development of therapeutic resistance and lack of biomarkers for effective selection of patients with SCLC are ongoing challenges. Emerging single-cell RNA sequencing data are providing insights into the plasticity and intratumoural and intertumoural heterogeneity of SCLC that might be associated with therapeutic resistance. In this Review, we provide a comprehensive overview of the latest advances in genomic and transcriptomic characterization of SCLC with a particular focus on opportunities for translation into new therapeutic approaches to improve patient outcomes.

Insights into brain tumor diagnosis: exploring in situ hybridization techniques.

Diagnosing brain tumors is critical due to their complex nature. This review explores the potential of in situ hybridization for diagnosing brain neoplasms, examining their attributes and applications in neurology and oncology. The review surveys literature and cross-references findings with the OMIM database, examining 513 records. It pinpoints mutations suitable for in situ hybridization and identifies common chromosomal and gene anomalies in brain tumors. Emphasis is placed on mutations' clinical implications, including prognosis and drug sensitivity. Amplifications in EGFR, MDM2, and MDM4, along with Y chromosome loss, chromosome 7 polysomy, and deletions of PTEN, CDKN2/p16, TP53, and DMBT1, correlate with poor prognosis in glioma patients. Protective genetic changes in glioma include increased expression of ADGRB3/1, IL12B, DYRKA1, VEGFC, LRRC4, and BMP4. Elevated MMP24 expression worsens prognosis in glioma, oligodendroglioma, and meningioma patients. Meningioma exhibits common chromosomal anomalies like loss of chromosomes 1, 9, 17, and 22, with specific genes implicated in their development. Main occurrences in medulloblastoma include the formation of isochromosome 17q and SHH signaling pathway disruption. Increased expression of BARHL1 is associated with prolonged survival. Adenomas mutations were reviewed with a focus on adenoma-carcinoma transition and different subtypes, with MMP9 identified as the main metalloprotease implicated in tumor progression. Molecular-genetic diagnostics for common brain tumors involve diverse genetic anomalies. In situ hybridization shows promise for diagnosing and prognosticating tumors. Detecting tumor-specific alterations is vital for prognosis and treatment. However, many mutations require other methods, hindering in situ hybridization from becoming the primary diagnostic method.

The Psychoneurologic Symptom Cluster and Its Association With Breast Cancer Genomic Instability.

To phenotype the psychoneurologic (PN) symptom cluster in individuals with metastatic breast cancer and associate those phenotypes with individual characteristics and cancer genomic variables from circulating tumor DNA. This study included 201 individuals with metastatic breast cancer recruited in western Pennsylvania. A descriptive, cross-sectional design was used. Symptom data were collected via the MD Anderson Symptom Inventory, and cancer genomic data were collected via ultra-low-pass whole-genome sequencing of circulating tumor DNA from participant blood. Three distinct PN symptom phenotypes were described in a population with metastatic breast cancer: mild symptoms, moderate symptoms, and severe mood-related symptoms. Breast cancer TP53 deletion was significantly associated with membership in a moderate to severe symptoms phenotype (p = 0.013). Specific cancer genomic changes associated with increased genomic instability may be predictive of PN symptoms. This finding may enable proactive treatment or reveal new therapeutic targets for symptom management.

Immunoglobulin D-Lambda Multiple Myeloma Initially Presenting in the Sphenoid Sinus, Orbital Apex, and Skull Base: A Systematic Review with a Case Report

Abstract Objectives Multiple myeloma (MM) with initial manifestations in the sphenoid sinus, orbital apex, and skull base is exceedingly rare. A systematic review was conducted to investigate the epidemiology and advancements. Methods Relevant cases were identified by searching CNKI, WanFang Data, CQVIP databases, PubMed, Embase, and Web of Science. Additionally, we present a case of IgD-λ (immunoglobulin D-lambda) MM with initial symptoms of dizziness, unilateral pain, blindness, and ophthalmoplegia, leading to a 4-month overall survival. Strictly based on PRISMA standards, we included and summarized existing cases and reflected our case. Results Our systematic review includes 34 case reports, revealing 67.6% of patients initially presented with diplopia and 44.1% underwent endoscopic procedures, notably with only two cases of IgD-λ subtype. In our case, we performed an endoscopic wide trans-ethmoidal sphenoidotomy and biopsy of the skull base and orbital apex lesion. Postoperative pathology confirmed a highly active plasmacytoma, clinically diagnosed as IgD-λ MM with a TP53 deletion mutation and multiple extramedullary metastases. A range of diagnostic tools was employed, including hemoglobin, immunoglobulin, urinary protein analysis, positron emission tomography-computed tomography (CT), bone marrow cytology, and gene detection. Conclusion The subtle clinical manifestations of IgD-λ MM in the paranasal sinuses and skull base hinder early diagnosis. There is a paucity of literature describing MM initially presenting in these locations. CT/magnetic resonance scans are necessary to identify characteristic bone destruction. An endoscopic approach is popular for tissue biopsy. Bone marrow biopsy with a smear, serum or urine protein electrophoresis, and immunofixation electrophoresis are crucial upon the appearance of target organ damage.

Abstract IA018: Vulnerabilities of TP53-mutated AML and therapeutic implications

Abstract Acute myeloid leukemia (AML) is a complex and genetically diverse with an overall survival rate of less than 32%. Despite the remarkable success of targeted therapy in mediating remission, the emergence of acquired resistance remains a major clinical challenge to overcome. The prevailing understanding of acquired resistance identifies successive genetic changes as the primary cause.TP53 mutations are found in 70-80% of acute myeloid leukemia (AML) patients with complex karyotypes and associated with resistance towards both conventional chemotherapy and newly approved venetoclax plus azacytidine (VEN/AZA) combination. By using CRISPR-Cas9-edited isogenic AML cells harboring, mutation (6 missense mutations) or deletion (KO) of TP53, we found that TP53 mutant/KO cells are less sensitive to etoposide or VEN-AZA induced apoptosis compared to WT without defect in G1 arrest. Surprisingly, we found that TP53-mutant and TP53-wild-type (WT) isogenic AML cells and primary tumors (n=40) had comparable mitochondrial outer membrane permeabilization (MOMP) at baseline, despite the key role of TP53 in transcriptionally activating proapoptotic regulators of MOMP (such as BAX, PUMA, and NOXA). Based on these findings, we hypothesize that the targets downstream of mitochondrial permeabilization drive resistance to HMA/VEN combinations in TP53 mutant disease. By leveraging unbiased bulk RNA-seq and proteomics, and whole genome CRISPR-cas9 screen we identified IAPs as functional vulnerability. Collectively we reveal novel chemoresistance mechanisms in TP53 mutant/KO downstream of MOMP and provide a targeting strategy to improve existing therapy by targeting non-transcriptional function of TP53 in overcoming therapy resistance. Citation Format: Shruti Bhatt. Vulnerabilities of TP53-mutated AML and therapeutic implications [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr IA018.

Cannabidiol reverts the malignant phenotype of hepatocellular carcinoma cells via the GPR55/TP53/MAPK axis

Cannabidiol (CBD) has antioxidant and anti-inflammatory activities. However, the anti-tumor effect of CBD on hepatocellular carcinoma (HCC) remains unclear. Here, we investigated whether CBD displays anti-tumorigenic effects in HCC cells and whether it could reduce tumorigenesis and metastases in vivo. First, this study treated HCC cells with different concentrations of CBD, followed by analyzing the changes in the proliferative, apoptotic, migratory and invasive abilities. The effects of CBD on the growth and metastasis of HCC cells in vivo were verified by tumorigenesis and metastasis assays. Subsequently, the target genes of CBD were predicted through the SwissTarget website and the genes differentially expressed in cells after CBD treatment were analyzed by microarray for intersection. The enrichment of the pathways after CBD treatment was analyzed by KEGG enrichment analysis, followed by western blot validation. Finally, rescue assays were used to validate the functions of genes as well as pathways in the growth and metastasis of HCC cells. A significant weakening of the ability of HCC cells to grow and metastasize in vitro and in vivo was observed upon CBD treatment. Mechanistically, CBD reduced GRP55 expression in HCC cells, along with increased TP53 expression and blocked MAPK signaling activation. In CBD-treated cells, the anti-tumor of HCC cells was restored after overexpression of GRP55 or deletion of TP53. CBD inhibits the MAPK signaling activation and increases the TP53 expression by downregulating GRP55 in HCC cells, thereby suppressing the growth and metastasis of HCC cells.

Modeling and therapeutic targeting of t(8;21) AML with/without TP53 deficiency

Acute myeloid leukemia (AML) with t(8;21)(q22;q22.1);RUNX1-ETO is one of the most common subtypes of AML. Although t(8;21) AML has been classified as favorable-risk, only about half of patients are cured with current therapies. Several genetic abnormalities, including TP53 mutations and deletions, negatively impact survival in t(8;21) AML. In this study, we established Cas9+ mouse models of t(8;21) AML with intact or deficient Tpr53 (a mouse homolog of TP53) using a retrovirus-mediated gene transfer and transplantation system. Trp53 deficiency accelerates the in vivo development of AML driven by RUNX1-ETO9a, a short isoform of RUNX1-ETO with strong leukemogenic potential. Trp53 deficiency also confers resistance to genetic depletion of RUNX1 and a TP53-activating drug in t(8;21) AML. However, Trp53-deficient t(8;21) AML cells were still sensitive to several drugs such as dexamethasone. Cas9+ RUNX1-ETO9a cells with/without Trp53 deficiency can produce AML in vivo, can be cultured in vitro for several weeks, and allow efficient gene depletion using the CRISPR/Cas9 system, providing useful tools to advance our understanding of t(8;21) AML.

Abstract NG02: Distinct genomic and immunologic tumor evolution in germline TP53-driven breast cancers

Abstract NG02: Distinct genomic and immunologic tumor evolution in germline TP53-driven breast cancers

Abstract 973: Plasma androgen receptor (AR) copy number gain at progression in patients randomized in the STAMPEDE phase 3 abiraterone acetate, prednisolone (AAP) and enzalutamide (ENZ) trial: An ancillary biomarker study

Abstract Addition of ENZ or AAP to androgen deprivation therapy (ADT) as first-line treatment for advanced prostate cancer improves survival compared to ADT alone. Genomic alterations in AR associate with resistance to ENZ/AAP when started for castration-resistant prostate cancer (CRPC). We aimed to test whether early use of AAP/ENZ altered the incidence of AR alterations at progression. Between July 2014 and March 2016, 1976 patients with metastatic or high-risk locally advanced prostate cancer were randomized to ADT or ADT+ENZ+AAP in the STAMPEDE trial (NCT00268476). Consenting patients were given the option to donate blood for the ancillary biomarker study at trial-defined progression and prior to start of the next line of treatment. We focused on patients who progressed within 4 years from the end of recruitment (early progressors), as these patients represent the greatest unmet need. We obtained plasma DNA at emergence of CRPC from 115 early progressors (ADT n=63, ADT+ENZ+AAP n=52). We performed liquid biopsy-focused, custom, high-coverage targeted enrichment sequencing (PCF-SELECT, Orlando et al, NAR Cancer 2022). We used a bespoke computational pipeline, leveraging allelic imbalance and fragmentome analysis, to detect circulating tumor DNA (ctDNA) in plasma samples and copy number changes. Of 108 samples that passed quality control, 94 were positive for tumor (ADT n=52, ADT+AAP+ENZ n=42). The detection rate and ctDNA fractions were similar between the two treatment groups [ADT: 86.7% (52/60), mean ctDNA fraction 0.18; ADT+ENZ+AAP: 87.5% (42/48), mean ctDNA fraction 0.21; p=0.34]. The proportion of plasma with detectable ctDNA and AR gain was significantly higher with ADT+AAP+ENZ vs ADT alone (15/42, 35.7% vs 8/52, 15.4%, p=0.03). We then implemented the same approach on plasma collected from patients progressing on ENZ started for metastatic CRPC in a prospective Phase 3b trial (PRESIDE, NCT02288247): we confirmed a high prevalence of AR gain in plasma samples with detectable ctDNA (47.7%, 95% CI 38.8-54.9) in the CRPC setting. Significant copy number aberrations in relevant prostate cancer-related genes/pathways (deletions of TP53, RB1, PTEN or DNA repair genes, or gain of PI3K/AKT1) were identified in 9 out of 42 evaluable samples in the ADT group and 18 out of 38 evaluable samples in the ADT+ENZ+AAP group (21.4% vs 47.4%, p=0.014). Treatment with ADT+ENZ+AAP increases detection of plasma AR gain at emergences of CRPC in early progressors compared to ADT alone. Detection of plasma AR gain increases at progression on ADT+ENZ regardless of the treatment setting. The impact of early use of ENZ/AAP on the detection of copy number aberrations, especially homozygous deletions, in other prostate cancer-related genes in plasma requires further investigation. Citation Format: Gianmarco Leone, Francesco Orlando, Suparna Thakali, Sharanpreet Lall, Daniel Wetterskog, Anna Wingate, Noel W. Clarke, Nicholas D. James, Francesca Demichelis, Gerhardt Attard. Plasma androgen receptor (AR) copy number gain at progression in patients randomized in the STAMPEDE phase 3 abiraterone acetate, prednisolone (AAP) and enzalutamide (ENZ) trial: An ancillary biomarker study [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 973.

Abstract A029: Development of a new iPSC-derived organoid platform to model FTE-derived HGSOC onset and progression

Abstract A029: Development of a new iPSC-derived organoid platform to model FTE-derived HGSOC onset and progression

Genomic profile analysis of leiomyomas with bizarre nuclei and fumarate hydratase deficient leiomyomas: Strengths, weaknesses, and limitations of array-CGH interpretation.

A close relationship has been demonstrated between genomic complexity and clinical outcome in uterine smooth muscle tumors. We studied the genomic profiles by array-CGH of 28 fumarate hydratase deficient leiomyomas and 37 leiomyomas with bizarre nuclei (LMBN) from 64 patients. Follow-up was available for 46 patients (from three to 249 months, mean 87.3 months). All patients were alive without evidence of disease. For 51 array-CGH interpretable tumors the mean Genomic Index (GI) was 16.4 (median: 9.8; from 1 to 57.8), significantly lower than the mean GI in LMS (mean GI 51.8, p < 0.001). We described three groups: (1) a group with FH deletion (24/58) with low GI (mean GI: 11 vs. 22,4, p = 0.02), (2) a group with TP53 deletion (17/58) with higher GI (22.4 vs. 11 p = 0.02), and (3) a group without genomic events on FH or TP53 genes (17/58) (mean GI:18.3; from 1 to 57.8). Because none of these tumors recurred and none showed morphological features of LMS we concluded that GI at the cut-off of 10 was not applicable in these subtypes of LM. By integration of all those findings, a GI <10 in LMBN remains a valuable argument for benignity. Conversely, in LMBN a GI >10 or alteration in tumor suppressor genes, should not alone warrant a diagnosis of malignancy. Nine tumors were tested with Nanocind CINSARC® signature and all were classified in low risk of recurrence. We propose, based on our observations, a diagnostic approach of these challenging lesions.