Acquisition Of Mutations Research Articles

Abstract B008: The polyclonal path towards malignant transformation in familial adenomatous polyposis

Abstract The widely accepted paradigm that cancer initiation is a monoclonal event has not been definitively resolved. This is largely due to the limitations of experimental systems to study cancer initiation, a definitively transient step in tumorigenesis. Individuals with familial adenomatous polyposis (FAP) possess a germline APC mutation, leading to hundreds of colonic polyps in adolescence and an eventual 100% lifetime risk of colorectal cancer. As such, total colectomies are performed once polyp burden becomes unmanageable and provide the resected colons from FAP donors provide a source of histologically normal mucosa, benign and dysplastic polyps, and, on rare occasions, adenocarcinomas, and serve as an exemplary model disease to understand human tumorigenesis. Through whole genome sequencing of 123 independent samples from six patients, we reveal the polyclonal origins of tumorigenesis in FAP. We characterize and contrast the genomic landscape and relative timing of driver mutation acquisition across normal to dysplastic and invasive colon tissue and compare this with multi-region sequencing data from sporadic colorectal cancers (CRC). We find that only early sporadic CRC drivers are common across the more heterogeneous premalignant stages. Selection, as assessed based on the ratio of nonsynonymous to synonymous mutations (dN/dS), is higher in benign than dysplastic FAP lesions and in sporadic adenomas relative to carcinomas. Phylogenetic reconstruction and pairwise sample comparisons reveal extensive heterogeneity and subclonal sharing within a patient’s benign and dysplastic lesions. Using a mechanistic mathematical model, we infer polyclonality for 90-100% of benign and 53-83% of dysplastic samples. Based on these findings, we propose a conceptual framework for the polyclonal origin of intestinal malignancies where inconsequential mutations, arising during colon formation in utero, are present across the colon and are valuable markers to uncover polyclonal ancestry. Citation Format: Ryan O. Schenck, Aziz Khan, Aaron M. Horning, Edward D. Esplin, HTAN Consortia, William J. Greenleaf, James M. Ford, Michael P. Snyder, Christina Curtis. The polyclonal path towards malignant transformation in familial adenomatous polyposis [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr B008.

Modeling stress-induced responses: plasticity in continuous state space and gradual clonal evolution.

Mathematical models of cancer and bacterial evolution have generally stemmed from a gene-centric framework, assuming clonal evolution via acquisition of resistance-conferring mutations and selection of their corresponding subpopulations. More recently, the role of phenotypic plasticity has been recognized and models accounting for phenotypic switching between discrete cell states (e.g., epithelial and mesenchymal) have been developed. However, seldom do models incorporate both plasticity and mutationally driven resistance, particularly when the state space is continuous and resistance evolves in a continuous fashion. In this paper, we develop a framework to model plastic and mutational mechanisms of acquiring resistance in a continuous gradual fashion. We use this framework to examine ways in which cancer and bacterial populations can respond to stress and consider implications for therapeutic strategies. Although we primarily discuss our framework in the context of cancer and bacteria, it applies broadly to any system capable of evolving via plasticity and genetic evolution.

Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies.

Viral populations in natural infections can have a high degree of sequence diversity, which can directly impact immune escape. However, antibody potency is often tested in vitro with a relatively clonal viral populations, such as laboratory virus or pseudotyped virus stocks, which may not accurately represent the genetic diversity of circulating viral genotypes. This can affect the validity of viral phenotype assays, such as antibody neutralization assays. To address this issue, we tested whether recombinant virus carrying SARS-CoV-2 spike (VSV-SARS-CoV-2-S) stocks could be made more genetically diverse by passage, and if a stock passaged under selective pressure was more capable of escaping monoclonal antibody (mAb) neutralization than unpassaged stock or than viral stock passaged without selective pressures. We passaged VSV-SARS-CoV-2-S four times concurrently in three cell lines and then six times with or without polyclonal antiserum selection pressure. All three of the monoclonal antibodies tested neutralized the viral population present in the unpassaged stock. The viral inoculum derived from serial passage without antiserum selection pressure was neutralized by two of the three mAbs. However, the viral inoculum derived from serial passage under antiserum selection pressure escaped neutralization by all three mAbs. Deep sequencing revealed the rapid acquisition of multiple mutations associated with antibody escape in the VSV-SARS-CoV-2-S that had been passaged in the presence of antiserum, including key mutations present in currently circulating Omicron subvariants. These data indicate that viral stock that was generated under polyclonal antiserum selection pressure better reflects the natural environment of the circulating virus and may yield more biologically relevant outcomes in phenotypic assays. Thus, mAb assessment assays that utilize a more genetically diverse, biologically relevant, virus stock may yield data that are relevant for prediction of mAb efficacy and for enhancing biosurveillance.

Sex-specific molecular differences in glioblastoma: assessing the clinical significance of genetic variants.

Glioblastoma multiforme (GBM) is one of the most aggressive types of brain cancer, and despite rigorous research, patient prognosis remains poor. The characterization of sex-specific differences in incidence and overall survival (OS) of these patients has led to an investigation of the molecular mechanisms that may underlie this dimorphism. We reviewed the published literature describing the gender specific differences in GBM Biology reported in the last ten years and summarized the available information that may point towards a patient-tailored GBM therapy. Radiomics analyses have revealed that imaging parameters predict OS and treatment response of GBM patients in a sex-specific manner. Moreover, gender-based analysis of the transcriptome GBM tumors has found differential expression of various genes, potentially impacting the OS survival of patients in a sex-dependent manner. In addition to gene expression differences, the timing (subclonal or clonal) of the acquisition of common GBM-driver mutations, metabolism requirements, and immune landscape of these tumors has also been shown to be sex-specific, leading to a differential therapeutic response by sex. In male patients, transformed astrocytes are more sensitive to glutaminase 1 (GLS1) inhibition due to increased requirements for glutamine uptake. In female patients, GBM is more sensitive to anti-IL1β due to an increased population of circulating granulocytic myeloid-derived suppressor cells (gMDSC). Moving forward, continued elucidation of GBM sexual dimorphism will be critical in improving the OS of GBM patients by ensuring that treatment plans are structured to exploit these sex-specific, molecular vulnerabilities in GBM tumors.

Missense mutation of NRAS is associated with malignant progression in neurocutaneous melanosis

Neurocutaneous melanosis (NCM) is a rare congenital neurocutaneous syndrome characterized by congenital melanocytic nevus of skin and abnormal proliferation of leptomeningeal melanocytes. Early acquisition of post-zygotic somatic mutations has been postulated to underlie the pathogenesis of NCM. The pathogenesis of NCM remains to be fully elucidated, and treatment options have not been established. Here, we report for the first time, multiregional genomic analyses in a 3-year-old autopsied girl with leptomeningeal melanomatosis associated with NCM, in which a ventriculo-peritoneal (VP) shunt was inserted for the treatment of hydrocephalus. The patient expired six months after the onset due to respiratory failure caused by abdominal dissemination via VP shunt. We performed multiregional exome sequencing to identify genomic differences among brain and abdominal tumors, nevus, and normal tissues. A total of 87 somatic mutations were found in 71 genes, with a significantly large number of gene mutations found in the tumor site. The genetic alterations detected in the nevus were only few and not shared with other sites. Three mutations, namely GNAQ R183Q, S1PR3 G89S and NRAS G12V, considered pathogenic, were found, although S1PR3 mutations have not been previously reported in melanocytic tumors. GNAQ and S1PR3 mutations were shared in both tumor and normal sites. Moreover, the mutant allele frequencies of the two mutations were markedly higher in tumor sites than in normal sites, with copy-neutral loss-of-heterozygosity (CN-LOH) occurring in tumor. NRAS mutation was found only in the abdominal tumor and was thought to be responsible for malignant progression in the present case. Multiregional comprehensive genetic analysis may lead to discovering novel driver mutations associated with tumorigenesis and targeted therapy.

Clonal hematopoiesis of indeterminate potential (CHIP), treatment outcomes and adverse events in gastrointestinal cancers: A pooled analysis of clinical trial and real-world data.

169 Background: Clonal hematopoesis of indeterminate potential (CHIP) is the acquisition of somatic mutations leading to clonal expansion of hematopoietic stem cells and is a common incidental finding in circulating tumor DNA (ctDNA). Inflammation from these cells or a reduced marrow reserve may impact treatment outcomes or adverse events. We investigated the incidence of CHIP in ctDNA from patients with gastrointestinal (GI) cancers and explored its association with outcomes and adverse events (AEs). Methods: We collected ctDNA results from a local prospective metastatic colorectal cancer (mCRC) cohort (PREDICT-L) and ctDNA data from two randomized trials: CCTG CO.26 (durvalumab + tremelimumab [D+T] or best supportive care [BSC] in mCRC) and CCTG PA.7 (gemcitabine and nab-paclitaxel [GN] with or without D+T in metastatic pancreatic adenocarcinoma [mPDAC]). CHIP+ was defined as the presence of a variant of ≥2% variant allele frequency annotated in the ctDNA report in any of the genes DNMT3A, TET2, ASXL1 and ATM, and not annotated as germline by respective sequencing platforms. The first line of treatment after ctDNA was reviewed, and grade ≥3 or dose-limiting adverse events were documented. Results: The prevalence of CHIP varied from 10% to 18% (see table). CHIP+ patients were older than CHIP- in the CO.26 cohort (p=0.011), and ECOG was higher in CHIP+ patients in the PREDICT-L cohort. There was no difference between CHIP+/- patients with regards to sex. DNMT3A was the gene most frequently mutated in all three cohorts. There was no significant difference in PFS or OS between the CHIP+/- groups, both in those treated with chemotherapy (Chemo) or immunotherapy (IO). The most common AEs were rash, GI toxicities and bleeding/clotting abnormalities. There was no significant difference in the rates of AEs between the CHIP+/- groups for those treated with Chemo or IO. Conclusions: CHIP is a common alteration in ctDNA but did not impact PFS, OS, or the chance of developing an AE. [Table: see text]

Presumed Pathogenic Germ Line and Somatic Variants in African American Thyroid Cancer.

Background: African American (AA) thyroid cancer patients have worse prognoses than European Americans (EA), which has been attributed to both health care disparities and possible genetic differences. We investigated the impact of both germ line and somatic variants on clinical outcome in a cohort of AA nonmedullary thyroid cancer (NMTC) patients who had received therapeutic intervention from cancer centers. Methods: Whole-exome sequencing was performed on DNA from available blood/normal tissues (N = 37) and paired tumor samples (N = 32) collected from 37 and 29 AA NMTC patients, respectively. Variants with Combined Annotation Depletion Dependent (CADD) score of ≥20 and VarSome Clinical classification of likely pathogenic or pathogenic were classified as presumed pathogenic germ line or somatic variants (PPGVs/PPSVs). PPGVs/PPSVs in cancer-related genes and PPGVs in cardiovascular risk genes were further investigated, and PPGVs/PPSVs associated with African (AFR) ancestry were identified. Results: Among 17 PPGVs identified in 16 cancer predisposition or known cancer-related genes, only WRN was previously known to associate with NMTC predisposition. Among PPSVs, BRAFV600E was most the prevalent and detected in 12 of the 29 (41%) tumors. Examining PPGVs/PPSVs among three patients who died from NMTC, one patient who died from papillary thyroid carcinoma/anaplastic thyroid carcinoma (PTC/ATC) led us to speculate that the PPGV ERCC4R799W may have increased the risk of PPSV TP53R273H acquisition. Among PPGVs identified in 18 cardiovascular risk genes, PPGVs in SC5NA, GYG1, CBS, CFTR, and SI are known to have causal and pathogenic implications in cardiovascular disease. Conclusion: In this cohort, most AA-NMTC patients exhibit favorable outcomes after therapeutic intervention given at cancer centers, suggesting that health care disparity is the major contributor for worse prognoses among AA-NMTC patients. Nevertheless, the clinical impact of PPGVs that might facilitate the acquisition of TP53 tumor mutations, and/or PPGVs that predispose individuals to adverse cardiovascular events, which could be exacerbated by therapy-induced cardiotoxicity, needs to be further explored. Integrated analysis of PPGV/PPSV profiles among NMTC patients with different stages of disease may help to identify NMTC patients who require close monitoring or proactive intervention.

The challenge of diagnosing and classifying eosinophilia and eosinophil disorders: A review.

Eosinophilia is a feature of multiple conditions, both hematologic and non-hematologic, and may be associated with organ damage. The pathogenesis of eosinophilia can follow two distinct pathways. Primary eosinophilia is caused by a cell-intrinsic mechanism originating from clonal expansion of eosinophils through acquisition of a somatic mutation, such as FIP1L1-PDGFRA. In recent years, great progress has been made in the field of pathogenesis and molecularly targeted therapy of neoplastic eosinophilia. The diagnostic procedure should include, among other things, morphologic analysis of blood and bone marrow samples, cytogenetics and fluorescence in situ-hybridization tests to detect evidence of an acute or chronic myeloid or lymphoid disorder. Secondary eosinophilia follows a cell-extrinsic mechanism as a response to exogenous cytokines. In most clinical cases, peripheral blood eosinophilia is reactive and typically associated with non-hematological disorders such as infections, allergic conditions, connective tissue disorders, vasculitis, malignancy, or endocrinopathies. Nonetheless, the cause of most cases of hypereosinophilic syndrome remains unknown. In this article, we present a short review focused on differential diagnosis of eosinophilia and eosinophilic disorders. The diagnosis of eosinophilia is a challenge for physicians; thus this review may be useful in clinical practice.

A Novel CRISPR/Cas9-mediated Mouse Model of Colon Carcinogenesis

Background & AimsHuman sporadic colorectal cancer (CRC) results from a multistep pathway with sequential acquisition of specific genetic mutations in the colorectal epithelium. Modeling CRC in vivo is critical for understanding the tumor microenvironment. To accurately recapitulate human CRC pathogenesis, mouse models must include these multi-step genetic abnormalities. Aims: Generate a sporadic CRC model that more closely mimics this multi-step process and use this model to study the role of a novel Let7 target PLAGL2 in CRC pathogenesis. MethodsWe generated a CRISPR/Cas9 somatic mutagenesis mouse model that is inducible and multiplexed for simultaneous inactivation of multiple genes involved in CRC pathogenesis. We used both a doxycycline-inducible transcriptional activator and a dox-inactivated transcriptional repressor to achieve tight, non-leaky expression of the Cas9 nickase. This mouse has transgenic expression of multiple guide RNAs to induce sporadic inactivation in the gut epithelium of four tumor suppressor genes commonly mutated in CRC, Apc, Pten, Smad4 and Trp53. These were crossed to Vil-LCL-PLAGL2 mice which have Cre-inducible overexpression of PLAGL2 in the gut epithelium. ResultsThese mice exhibited random somatic mutations in all four targeted tumor suppressor genes, resulting in multiple adenomas and adenocarcinomas in the small bowel and colon. Crosses with Vil-LCL-PLAGL2 mice demonstrated that gut-specific PLAGL2 overexpression increased colon tumor growth. ConclusionsThis conditional model represents a new CRISPR/Cas9-mediated mouse model of colorectal carcinogenesis. These mice can be used to investigate the role of novel, previously uncharacterized genes in CRC, in the context of multiple commonly mutated tumor suppressor genes and thus more closely mimic human CRC pathogenesis.

Molecular and Functional Key Features and Oncogenic Drivers in Thymic Carcinomas.

Thymic epithelial tumors, comprising thymic carcinomas and thymomas, are rare neoplasms. They differ in histology, prognosis, and association with autoimmune diseases such as myasthenia gravis. Thymomas, but not thymic carcinomas, often harbor GTF2I mutations. Mutations of CDKN2A, TP53, and CDKN2B are the most common thymic carcinomas. The acquisition of mutations in genes that control chromatin modifications and epigenetic regulation occurs in the advanced stages of thymic carcinomas. Anti-angiogenic drugs and immune checkpoint inhibitors targeting the PD-1/PD-L1 axis have shown promising results for the treatment of unresectable tumors. Since thymic carcinomas are frankly aggressive tumors, this report presents insights into their oncogenic drivers, categorized under the established hallmarks of cancer.

10141-GMC-13 MULTIREGIONAL GENOMIC ANALYSIS: A NOVEL APPROACH FOR DETECTING PATHOGENIC DRIVER MUTATION ASSOCIATED WITH MALIGNANT PROGRESSION IN NEUROCUTANEOUS MELANOSIS

Abstract Neurocutaneous melanosis (NCM) is a rare congenital neurocutaneous syndrome characterized by congenital melanocytic nevus of skin and abnormal proliferation of leptomeningeal melanocytes. Early acquisition of post-zygotic somatic mutations has been postulated to underlie the pathogenesis of NCM. The pathogenesis of NCM remains to be fully elucidated and treatment options have not been established. Here, we report for the first time, multiregional genomic analyses in a 3-year-old autopsied girl with leptomeningeal melanomatosis associated with NCM, in which a ventriculo-peritoneal shunt was inserted for the treatment of hydrocephalus. The patient expired six months after the onset due to respiratory failure caused by abdominal dissemination via ventriculo-peritoneal shunt. We performed multiregional exome sequencing to identify genomic differences among brain and abdominal tumors, nevus, and normal tissues. A total of 87 somatic mutations were found in 71 genes, with a significantly large number of gene mutations found in the tumor site. The genetic alterations detected in the nevus were only few and not shared with other sites. Three pathogenic mutations, GNAQ R183Q, S1PR3 G89S and NRAS G12V were found. GNAQ and S1PR3 mutations were shared in both tumor and normal sites. Moreover, the mutant allele frequencies of the two mutations were markedly higher in tumor sites than in normal sites. NRAS mutation was found only in the abdominal tumor and was thought to be responsible for malignant progression in the present case. Multiregional comprehensive genetic analysis may lead to discover novel driver mutations associated with tumorigenesis and targeted therapy.

Loss of CD20 expression as a mechanism of resistance to mosunetuzumab in relapsed/refractory B-cell lymphomas

AbstractCD20 is an established therapeutic target in B-cell malignancies. The CD20 × CD3 bispecific antibody mosunetuzumab has significant efficacy in B-cell non-Hodgkin lymphomas (NHLs). Because target antigen loss is a recognized mechanism of resistance, we evaluated CD20 expression relative to clinical response in patients with relapsed and/or refractory NHL in the phase 1/2 GO29781 trial investigating mosunetuzumab monotherapy. CD20 was studied using immunohistochemistry (IHC), RNA sequencing, and whole-exome sequencing performed centrally in biopsy specimens collected before treatment at predose, during treatment, or upon progression. Before treatment, most patients exhibited a high proportion of tumor cells expressing CD20; however, in 16 of 293 patients (5.5%) the proportion was <10%. Analyses of paired biopsy specimens from patients on treatment revealed that CD20 levels were maintained in 29 of 30 patients (97%) vs at progression, where CD20 loss was observed in 11 of 32 patients (34%). Reduced transcription or acquisition of truncating mutations explained most but not all cases of CD20 loss. In vitro modeling confirmed the effects of CD20 variants identified in clinical samples on reduction of CD20 expression and missense mutations in the extracellular domain that could block mosunetuzumab binding. This study expands the knowledge about the occurrence of target antigen loss after anti-CD20 therapeutics to include CD20-targeting bispecific antibodies and elucidates mechanisms of reduced CD20 expression at disease progression that may be generalizable to other anti-CD20 targeting agents. These results also confirm the utility of readily available IHC staining for CD20 as a tool to inform clinical decisions. This trial was registered at www.ClinicalTrials.gov as #NCT02500407.

Abstract A037: Mechanisms of resistance to BAY 2927088, the first reversible inhibitor targeting EGFR exon 20 insertion mutations in non-small cell lung cancer

Abstract Molecular therapies targeting EGFR-mutant non-small cell lung cancer (NSCLC) have dramatically improved prognosis for patients with the classical activating mutations, L858R and exon 19 deletion. However, tumors harboring EGFR exon 20 insertions have been historically more difficult to target. Agents such as amivantamab and mobocertinib have recently been granted accelerated approval for treatment of lung cancer patients with exon 20 insertions, but agents with an improved selectivity profile versus wild-type EGFR are still needed. BAY 2927088, currently in phase I clinical trials, is a novel reversible inhibitor that targets EGFR exon 20 insertion mutations with decreased activity towards wild-type EGFR. Although most patients with advanced EGFR-mutant NSCLC eventually progress due to acquired resistance to EGFR inhibitors, the mechanisms of resistance to BAY 2927088 are currently unknown. Using two different methods of in vitro resistance generation by inhibitor treatment of sensitive cell lines, we identified mechanisms of intrinsic and acquired resistance to BAY 2927088 and other EGFR inhibitors. Incubation with a high concentration of inhibitor selected for drug-tolerant persister cells that underwent a transcriptional state transition resembling EMT (epithelial-mesenchymal transition). Conversely, gradual escalation of inhibitor concentrations resulted in acquisition of oncogenic NRAS mutations. In a parallel approach, we performed a deep mutational scanning assay of the EGFR D770_N771insSVD kinase domain, replacing each amino acid with every other possible amino acid, identifying both known and novel mutations that cause resistance to BAY 2927088 and other EGFR inhibitors. As expected, the C797S mutation was enriched as a mechanism of acquired resistance only to irreversible EGFR exon 20 insertion inhibitors. Surprisingly, the T790M gatekeeper mutation was found to cause resistance to all EGFR exon 20 insertion inhibitors tested, including irreversible inhibitors. Several novel resistance mutations clustering predominantly in exons 20 and 21 were also identified. Citation Format: Gizem Karsli Uzunbas, Quinn McVeigh, Akansha Gupta, Stephanie Hoyt, Kristen Doucette, Hasmik Keshishian, Steven Carr, Xiaoping Yang, David Root, Andrew D Cherniack, Franziska Siegel, Stephan Siegel, Matthew Meyerson, Heidi Greulich. Mechanisms of resistance to BAY 2927088, the first reversible inhibitor targeting EGFR exon 20 insertion mutations in non-small cell lung cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A037.

Abstract B164: ASTX029 is a dual mechanism ERK1/2 inhibitor with activity in models of MAPK-inhibitor resistance

Abstract Clinical efficacy of RAF, MEK1/2 (MEK) and KRASG12C inhibitors has been demonstrated in MAPK-activated cancers. However, response is often short-lived due to resistance mechanisms, which commonly confer reactivation of ERK1/2 (ERK). As the primary downstream effector of the MAPK pathway, ERK is an attractive therapeutic target for overcoming resistance to upstream inhibition. ASTX029 is a potent and selective dual-mechanism ERK inhibitor. Due to its distinctive ERK-binding mode, ASTX029 inhibits both ERK catalytic activity and the phosphorylation of ERK by MEK. It is currently in Phase 1/2 trial in patients with advanced solid tumors (NCT03520075). Here we demonstrate the potent activity of ASTX029 in models of acquired MAPK inhibitor resistance. Two MAPK inhibitor-resistant models were generated by continuous culture of A375 (BRAFV600E -mutant melanoma) cells in the presence of the BRAF inhibitor vemurafenib (A375R) or by introduction of an NRASQ61K mutation (A375-NRASQ61K). The A375-NRASQ61K and A375R cell lines were resistant to vemurafenib in cell proliferation assays (IC50 &amp;gt;3 µM and &amp;gt;10 µM respectively, compared to IC50 110 nM in parental A375 cells). They were also less sensitive to the MEK inhibitor selumetinib (IC50 270 nM and 1000 nM, respectively, compared to IC50 43 nM in parental A375). Both models were highly sensitive to ASTX029, with proliferation assay IC50 values of 12 nM (A375-NRASQ61K) and 7.2 nM (A375R), values which were not significantly different to the ASTX029 IC50 of parental A375. ASTX029 inhibited MAPK signalling in both models, whereas vemurafenib and selumetinib had no effect. Treatment of A375R tumour-bearing mice with 50 mg/kg bid vemurafenib (which causes significant tumor growth inhibition in parental A375 xenografts), did not result in significant tumor growth inhibition. In contrast, 75 mg/kg qd ASTX029 conferred significant anti-tumor activity (P&amp;lt; 0.001). The acquisition of MEK mutations is a known resistance mechanism to RAF, MEK and KRASG12C inhibitors. We performed a CRISPR-tiling screen on MEK1 and identified mutations that conferred resistance to MEK inhibitors. The identified MEK1 mutations either caused MEK activation (indicated by elevated pERK levels) or were predicted to prevent MEK inhibitor binding (supported by MEK1 structural analysis). All mutations conferred resistance to selumetinib (7- to 200-fold increase in cell proliferation IC50 values relative to parental cells). Mutations predicted to prevent MEK inhibitor binding were sensitive to vemurafenib and the pan-RAF inhibitor LY3009120, whereas those that caused MEK1 activation were resistant (5- to 10-fold increase in cell proliferation IC50 relative to parental cells). However, they were all sensitive to ASTX029 (IC50 values of 4 to 17 nM). We conclude that the MAPK inhibitor resistance mechanisms described did not confer resistance to ASTX029. These data highlight the therapeutic potential of ASTX029 for the treatment of cancers, which have acquired resistance to inhibitors of upstream components of the MAPK pathway. Citation Format: Zhiqiang Zhang, Christopher Hindley, Andrea Biondo, Nicola Wallis, John Lyons, Joanne Munck. ASTX029 is a dual mechanism ERK1/2 inhibitor with activity in models of MAPK-inhibitor resistance [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B164.

Abstract B029: Investigating therapeutic strategies to promote immune rejection of KRAS G12C inhibitor-resistant sub-populations in lung cancer

Abstract Oncogenic KRAS signaling not only instigates aberrant growth in cancer cells but can further induce inhibitory effects on anti-tumor immune responses. Hence, recently developed KRAS G12C inhibitors (G12Ci) have the potential to alleviate immune suppression in the tumor microenvironment (TME) and reshape the therapy responses for patients with a KRAS G12C driver mutation. However, rewiring of oncogenic signaling circuits and acquisition of further mutations allows cancer cells to rapidly evolve drug resistance. In fact, clinical trial data from the recently approved G12Ci, adagrasib and sotorasib, showed a median progression-free survival in non-small cell lung cancer of just 7 months. In this project, we investigate how to combat G12Ci-resistant subpopulations in lung tumors by engaging an anti-tumor immune response. We mimic the development of drug resistance by combining traced isogenic G12C- and G12D-mutant lung cancer cells, where the KRAS G12D mutant cells are inherently resistant to G12Ci. By alleviating RAS-driven immune suppression and potentially inducing immunogenic cell death of G12Ci-responsive cells, we aim to further potentiate an adaptive immune response targeting the drug-resistant population. We found that G12Ci as monotherapy drives therapy resistance by giving the drug-resistant subpopulation a proliferative advantage. On the other hand, combining G12Ci with immunotherapy or a SHP2 inhibitor potentiated an adaptive immune response to induce complete eradication of both G12C and G12D KRAS mutant cancer cell populations and also immune memory towards drug-resistant KRAS G12D cells in mice. However, when repeating the combination treatment in Rag1 −/− mice, which lack B- and T-cells, there were no complete responders. Histopathological analysis of tumor sections in immune-competent mice revealed a strong T-cell infiltration in the TME of tumors treated with combination therapies. Although understanding the mechanistic changes in the TME induced by combination therapies is ongoing, these results indicate a role for the adaptive immune response in targeting G12Ci drug-resistant subpopulations. Understanding these underlying mechanisms will contribute to combating the development of drug resistance in patients by enhancing treatment regimens that promote immune-mediated destruction of drug-resistant tumor cell sub-populations. Citation Format: Mona Tomaschko, Miriam Molina-Arcas, Christopher Moore, Sareena Rana, Sophie de Carne, Panayiotis Anastasiou, Claire Pillsbury, Andrea de Castro, Julian Downward. Investigating therapeutic strategies to promote immune rejection of KRAS G12C inhibitor-resistant sub-populations in lung cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor Immunology and Immunotherapy; 2023 Oct 1-4; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Immunol Res 2023;11(12 Suppl):Abstract nr B029.

Abstract LB_A05: Coadministration of AZD 4573 and gilteritinib exhibits a potent activity in FLT3 inhibitor-sensitive and -resistant AML cells

Abstract Acute myeloid leukemia (AML) is caused by the sequential acquisition of mutations that regulate multiple cellular pathways, indicating that multiple pathways must be coordinately inhibited for a successful therapy in this disease. Transcriptomics analysis suggest that exposure of AML cells to the selective CDK9 inhibitor AZD4573 led to activation of multiple survival pathways including MAPK, PI3K, and STAT suggesting that disruption of these signaling pathways may potentiate this agent activity. Notably, combined treatment with AZD4573 and the FLT3 inhibitor gilteritinib resulted in a robust suppression of cell growth and a marked induction of apoptosis in various AML cell lines, particularly those with FLT3 mutations. These were associated with a marked induction of apoptosis reflected by increased Annexin V/PI positivity and cleavage in caspase 3 and its substrate PARP. Importantly, combined treatment was also highly effective in FLT3 mutants AML cells that exhibit significant resistance to various FLT3 inhibitors including gilteritinib. Combined treatment led to a profound disruption of critical survival signaling pathways including MEK/ERK, STAT, and PI3K/AKT pathways. Combined treatment also significantly disrupted the balance between the proapoptotic and anti-apoptotic Bcl-2 members as reflected by downregulation of MCL1 and upregulated of Bim protein levels. Importantly, GILT/AZD4573-induced cell death was fully prevented when Bax and Bak were knocked out using CRISPR system, suggesting that the anti-AML activity of this regimen proceeds mainly via the mitochondrial apoptotic pathway. Finally, using a systemic acute myeloid leukemia xenograft model, co-administration of gilteritinib and AZD4573 sharply reduced leukemia growth and markedly prolonged mice survival. Collectively, these findings demonstrate that dual inhibition of CDK9 and FLT3 exhibits a potent anti-leukemic efficacy in vitro and in vivo. These findings also indicate that this strategy warrants further attention in FLT3-dependent acute myeloid leukemias. Citation Format: Mohamed Rahmani, Baraa Khalid Salah, Burcu Yener, Bassam Mahboub, Steven Grant. Coadministration of AZD 4573 and gilteritinib exhibits a potent activity in FLT3 inhibitor-sensitive and -resistant AML cells [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_A05.

Correlation of TCR Repertoire Diversity with Myeloid Gene Mutations in Chronic and Advanced Phase Myeloproliferative Neoplasms

Introduction: Myeloproliferative neoplasms (MPN) are characterized by a chronic phase (CP), with indolent clinical behavior and, in 10-30% of cases, progression to advanced phases (AP), with aggressive behavior and compromised prognosis. Numerous factors have been associated with progression to AP, including the acquisition of mutations in recurrently mutated myeloid genes (1,2). On the other hand, decreased diversity in the T-cell receptor (TCR) repertoire has been associated with worse prognosis in solid tumors. The purpose of this work is to study the correlation between the acquisition of mutations in myeloid genes and the diversity of the TCR repertoire in chronic and advanced myeloproliferative neoplasms. Methods: Patients with chronic CP and AP myeloproliferative neoplasms were selected. The selected patients underwent an NGS panel of 48 myeloid genes. Only pathogenic (P) or likely pathogenic (LP) variants were considered. In parallel, the study of the TCR repertoire by NGS with the panel “AmpliSeq for Illumina Immune Repertoire Plus, TCR beta Panel” (Illumina™) was performed on the available samples. Finally, the obtained data were correlated. The study was approved by the local ethics committee. Results: A total of 22 patients were selected, 10 in CP and 12 in AP. Regarding diagnosis, 8 were polycythemia vera (PV), 4 essential thrombocythemia (ET), 6 secondary myelofibrosis (MFS) (1 to PV and 5 to ET), 2 systemic mastocytosis (MS) and 1 primary myelofibrosis (MFP). Eighty percent were male and the mean age was 68 years. The AP patients were significantly older (74 vs. 62 years of age, p&amp;lt;0,001). Regarding the myeloid NGS panel result, 41 mutations were found in 19 patients. Fourteen percent of the patients had no mutation, 36% had an isolated driver mutation and 50% had additional mutations. Of these, 9% were in CP and 81% were in AP. The most recurrently mutated genes were JAK2 (45.4%), CALR (18.2%), ASXL1, IDH2, SRSF2, IDH2 (all 13.6%), MPL and KIT (both 9.1%). Regarding the results of the TCR repertoire, it was possible to perform the study in 11 patients, 4 in CP and 7 in AP. Only 6/11 had results of sufficient quality to allow analysis. Of these 6 patients, 3 were in CP and 3 in AP. As can be seen in Figure 1, the diversity of the TCR between CP patients and PC patients was different. Thus, while the pattern of diversity in the CP phase shows the expected distribution, the diversity in AP shows a characteristic pattern. Conclusions: APs of MPNs show an abnormal TCR diversity pattern. This pattern may be related to the acquisition of myeloid gene mutations in AP. To our knowledge, this is the first study demonstrating an alteration in TCR diversity in AP and opens the door to future fields of research.

Functional Ex-Vivo Testing Combined with Machine Learning Predicts Clinical Response to Azacitidine+Venetoclax in AML

Background: The combination of Venetoclax + hypomethylating agents such as Azacitidine (Ven/Aza) has revolutionized the treatment of Acute Myeloid Leukemia (AML). Ven/Aza is currently the standard of care for patients with newly diagnosed AML who are not candidates for intensive chemotherapy (IC), as well as a recurrent therapeutic choice for IC-relapsed/refractory patients. Despite widespread adoption, the predictive biomarkers of Ven/Aza response/resistance available today are not sufficiently conclusive (Griffioen et al. Cancers 2022). In fact, a current hot topic in the field is whether Ven/Aza can also become a frontline therapy for fit patients as an alternative to IC. Several worldwide studies are addressing this issue, including an ongoing clinical trial named “Survival of the Fittest” exploring this concept in the US (NCT04801797). An open question is whether functional ex-vivo testing could become a powerful actionable tool that overcomes limitations presented by genetic and molecular indicators. Aim &amp; Methods: In this study, we utilized an innovative ex-vivo functional platform of Patient Micro Avatars (PMAs) developed at OncoPrecision (García et al, Blood 2022 140 (Supplement 1): 13027-13028) to assess the predictive power for Ven/Aza treatment in a cohort of 11 AML patients. Patient-Derived Cells (PDCs) were obtained from the patients' PBMCs and Ven/Aza activity was assessed using high-throughput flow cytometry. An in-house Machine Learning (ML) tool was developed to identify the optimal variables that predict clinical outcome (Complete Remission: Yes/No). Clusters of predictive Response/Non-Response were defined by analyzing a cohort of &amp;gt;60 previously profiled AML patients and by leveraging the two most predictive populational features generated by the platform that better correlate with clinical outcome from &amp;gt;12,000 combinations of variables. Results: Our findings revealed differential ex-vivo activity of Ven/Aza in AML, with remarkably contrasting outcomes that defined clearly separate clusters of response (Figure - Left Panel). Such ML clustering led to 80% Overall Predictive Power and 100% Positive Predictive Value, meaning that all the patients for whom the platform predicted response achieved complete clinical remission. Moreover, by comparing the performance of other targeted therapies such as Gilteritinib, as well as IC regimens such as AraC-FaraA-IDA, side by side we were able to identify patients for whom Ven/Aza is the optimal regimen (e.g., Patient #169), and others for whom IC or Gilteritinib emerge as more promising therapeutic options (e.g., Patient #170) (Figure - Right Panel). Conclusions: This work presents a groundbreaking approach to predict Aza/Ven responders versus non-responders in AML. Combining the phenotypic outcomes of functional ex-vivo testing with ML tools presents the opportunity to more comprehensively predict response to cutting-edge therapies such as Ven/Aza than traditional genetic testing. This potential is particularly compelling for therapeutic schemes not directly associated with the acquisition of genetic mutations.

Identifying PTPRJ As a Novel Mediator of CEBPA-Mutated AML

10-20% of acute myeloid leukaemia (AML) cases in children and adults carry mutations in the transcription factor CCAAT/enhancer binding protein alpha (CEBPA). CEBPA is transcribed from a single exon and produces two isoforms, p30 and p42, with characteristic mutations, either frameshift mutations in the N-terminal portion ( CEBPA Nterm) leading to production of only the p30 isoform, or in frame mutations in the C-terminal portion ( CEBPA Cterm), disrupting DNA binding. The most frequent secondary driver mutation in CEBPA-mutated AML, is the second allele of CEBPA. Additionally, in rare germline CEBPA cases, the founding mutation is usually CEBPA Nterm, with allindividuals showing acquisition of a second hit mutation in the CEBPA Cterm on the alternate CEBPA allele at the time of AML diagnosis, which has near 100% penetrance in these families. This highlights a strong selective pressure for this very specific biallelic mutation pattern. We have developed zebrafish models with germline cebpa Nterm and cebpa Cterm mutations that faithfully recapitulates the disease, with all homozygous and double heterozygous mutants showing loss of mature myeloid cells, and impaired survival. All double or compound mutants die by 10 weeks of age, with haematopoietic stem and progenitor cell (HSPC) expansion, and leukaemia in around 30% of these animals. Our model also demonstrates distinct phenotypes for cebpa Nterm and cebpa Cterm mutations during developmental haematopoiesis prior to leukaemia onset. We observed that cebpa Nterm and cebpa Cterm mutations have opposite effects on the expression of c-myb, a transcription factor expressed by proliferating HSPC, from 3 days post fertilization. cebpa Nterm/Nterm mutants show an increase in c-myb while cebpa Cterm/Cterm show reduced c-myb expression during development. To uncover the mechanisms by which cebpa Nterm and cebpa Cterm effect HSPCs we undertook RNASeq of sorted Tg(cd41:eGFP) lo HSPCs from fish of all possible genotype combinations. We identified both shared and unique expression profiles between genotypes. We also identified 4 genes that that were differentially regulated in both cebpa Nterm/Nterm and cebpa Cterm/Cterm HSPC, but in opposing vectors (upregulated in cebpa Cterm/Cterm and downregulated in cebpa Nterm/Nterm) (Figure 1). We hypothesised that these 4 genes are candidate drivers of selective pressure for the common CEBPA Cterm/Ntermmutation combination in human AML, and thus the malignant phenotype it confers. One of these candidate genes, PTPRJ, has also recently been identified as a frequently mutated gene in CEBPA-mutated AML in children thereby validating the relevance of our dataset and our approach. To define the effects of these 4 candidate genes we then conducted an F0 CRISPR knock-out screen in all cebpa mutant combinations in our zebrafish model, using c-myb expression as a phenotypic readout. We identified ptprja as our primary candidate gene and showed that loss of ptprja alone and in combination with cebpa Cterm/+ reduced expression of c-myb but had no effect on expression of c-myb in cebpa Cterm/Cterm, indicating that ptprja loss reduces c- myb-expressing HSPC and that this is dependent on functional cebpa DNA binding. We then examined the impact of ptprja knockout in juvenile zebrafish. Homozygous and double heterozygous mutants develop a pre-leukaemia expansion of HSPC before they succumb to death. We showed that that loss of ptprja in cebpa Cterm/Cterm fish accelerates this pre-leukaemic expansion of Tg(cd41:eGFP) lo HSPCs in 4 week fish (Figure 2). We also showed an opposing effect in the cebpa Nterm/Nterm mutants at 2 weeks, where loss of ptprja resulted in decreased pre-leukemic expansion of HSPC. These data indicate a role for PTPRJ in mediating HSPC expansion in CEBPA-mutated AML and suggest that PTPRJ may mediate the mechanism of clonal selection in those with a CEBPA mutation that drives the acquisition of a second CEBPA mutation on the opposing allele, leading to the common CEBPA Cterm/Nterm in patients with CEBPA-mutated AML.

The Association of SEPTIN6 Mutations with Pediatric Myelodysplasia

Septin family proteins belong to the RAS-like GTPase superclass and are considered as a structural element of the cytoskeleton. They are evolutionarily conserved and are important in cytokinesis, polarity, cell cycle, vesicle trafficking, and exocytosis. They are implicated in T and B cell lymphomas; and acute myeloid leukemias, where they frequently act as fusion partners with the Mixed-Lineage Leukemia (MLL) gene. Previously, we described two non-syndromic patients with severe neutropenia which progressed to myelodysplastic syndrome (MDS) (Renella et al. AJH, 2022, Mohamad et al. ASH, 2022). Next-generation sequencing revealed both patients (P1 and P2) to have novel X-linked germline mutations in codon 428 of the SEPTIN6 gene (P1: SEPTIN6 c.1282T&amp;gt;C; P2: SEPTIN6 c.1282T&amp;gt;A). One of these patients (P1) had an additional somatic stop-gain mutation (P1: SEPTIN6 c.43C&amp;gt;T) of unclear function. Both patient germline mutations were predicted to add 9 amino acids to the C-terminal end creating a novel mutated SEPTIN6 protein. Since SEPTIN6 is located on the X-chromosome and expression of these mutated proteins occurred in males, no wild-type protein was present in the patient cells. To further explore the biological relevance of these mutations, single base-pair gene editing was used to introduce the (P1: T&amp;gt;C) mutation into normal male donor CD34+ cells. Morphological studies demonstrated that SEPTIN6 edited cells had enlarged, multi-nucleated and dysplastic nuclei; and reduced clonogenic activity. To further assess the effect of the T&amp;gt;C mutation on hematopoietic stem cell (HSC) function, the SEPTIN6 edited cells were transplanted into immunocompromised NSGW mice. Analysis of peripheral blood demonstrated reduced chimerism in edited recipients (4.27% +/-3.4%) compared to controls (20.56% +/-6.2%, mean+/- SD, p= 0.0008) indicating a functional HSC defect upon mutation acquisition. Bulk mRNA sequencing demonstrated changes in ribosome, DNA replication, homologous recombination and mismatch repair pathways which imply DNA damage and cell cycle defects (Figure 1). To examine the potential dominant negative vs haploinsufficiency role of these mutations, we introduced the mutated SEPTIN6 (P1: SEPTIN6 c.1282T&amp;gt;C) cDNA into wild type human male CD34+ cells. Morphological studies demonstrated enlarged cells with multi-nucleated and dysplastic nuclei. Moreover, clonogenic assays demonstrated that cells containing both the mutated and wild type protein had reduced number of colonies (17.7+/- 5.5) compared to controls (127+/- 13.7, mean+/- SD, p &amp;lt;0.0001). This indicates that the mutated SEPTIN6 protein has a dominant negative effect over the wild type protein. We hypothesized that the somatic stop-gain mutation in the patient (P1) genome may mitigate the deleterious effects of the primary germline SEPTIN6 c.1282T&amp;gt;C mutation. To test this hypothesis, and determine the effect of each individual mutation, we created lentivirus vectors which contained a shmiR against the native SEPTIN6 mRNA and also contained (a) the germline P1: SEPTIN6 c.1282T&amp;gt;C mutation (M2 mutation) alone, or (b) the germline M2 mutation and the somatic stop-gain mutation (P1: M1+M2 mutation) in tandem, or (c) germline P2: SEPTIN6 c.1282T&amp;gt;A (M3 mutation). The wild type SEPTIN6 gene was reintroduced as a control. Clonogenic assays demonstrated that SEPTIN6 knockdown in human CD34+ cells caused no significant change in progenitor activity (Table 1). Furthermore, introduction of the M2 or the M3 germline mutants in SEPTIN6 knocked down cells caused a reduction in the total number of colonies, especially the number of GM colonies with no change in the number of BFU-E colonies (Table 1). This data validates our previous experiments performed with single base pair gene editing in human CD34+ cells. Interestingly, introduction of the stop-gain M1 mutation along with the M2 mutation (M1+M2) reversed the reduced clonogenic activity seen with expression of the M2 mutation (Table 1). This indicates that the M1 mutation by introducing an early stop codon creates a SEPTIN6 knockdown effect and rescues hematopoietic function from the deleterious M2 mutation. Overall, our data demonstrates the acquisition of de novo gain of function mutations in the SEPTIN6 gene in myelopoiesis and suggests deleterious effects on engrafting hematopoietic stem cells. These mutations are associated with the development of MDS in two pediatric patients.