N-ras Oncogene Research Articles

Mutational cooperativity of RUNX1::RUNX1T1 isoform 9a and oncogenic NRAS in zebrafish myeloid leukaemia.

RUNX1::RUNX1T1 (R::RT1) acute myeloid leukaemia (AML) remains a clinical challenge, and further research is required to model and understand leukaemogenesis. Previous zebrafish R::RT1 models were hampered by embryonic lethality and low penetrance of the malignant phenotype. Here, we overcome this by developing an adult zebrafish model in which the human R::RT1 isoform 9a is co-expressed with the frequently co-occurring oncogenic NRASG12D mutation in haematopoietic stem and progenitor cells (HSPCs), using the Runx1+23 enhancer. Approximately 50% of F0 9a+NRASG12D transgenic zebrafish developed signs of haematological disease between 5 and 14 months, with 27% exhibiting AML-like pathology: myeloid precursor expansion, erythrocyte reduction, kidney marrow hypercellularity and the presence of blasts. Moreover, only 9a+NRASG12D transplant recipients developed leukaemia with high rates of mortality within 40 days, inferring the presence of leukaemia stem cells. These leukaemic features were rare or not observed in animals expressing either the NRAS or 9a oncogenes alone, suggesting 9a and NRAS cooperation drives leukaemogenesis. This novel adult AML zebrafish model provides a powerful new tool for investigating the basis of R::RT1 - NRAS cooperativity with the potential to uncover new therapeutic targets.

IκBα kinase inhibitor BAY 11-7082 promotes anti-tumor effect in RAS-driven cancers

BackgroundOncogenic mutations in the RAS gene are associated with uncontrolled cell growth, a hallmark feature contributing to tumorigenesis. While diverse therapeutic strategies have been diligently applied to treat RAS-mutant cancers, successful targeting of the RAS gene remains a persistent challenge in the field of cancer therapy. In our study, we discover a promising avenue for addressing this challenge.MethodsIn this study, we tested the viability of several cell lines carrying oncogenic NRAS, KRAS, and HRAS mutations upon treatment with IkappaBalpha (IκBα) inhibitor BAY 11-7082. We performed both cell culture-based viability assay and in vivo subcutaneous xenograft-based assay to confirm the growth inhibitory effect of BAY 11-7082. We also performed large RNA sequencing analysis to identify differentially regulated genes and pathways in the context of oncogenic NRAS, KRAS, and HRAS mutations upon treatment with BAY 11-7082.ResultsWe demonstrate that oncogenic NRAS, KRAS, and HRAS activate the expression of IκBα kinase. BAY 11-7082, an inhibitor of IκBα kinase, attenuates the growth of NRAS, KRAS, and HRAS mutant cancer cells in cell culture and in mouse model. Mechanistically, BAY 11-7082 inhibitor treatment leads to suppression of the PI3K-AKT signaling pathway and activation of apoptosis in all RAS mutant cell lines. Additionally, we find that BAY 11-7082 treatment results in the downregulation of different biological pathways depending upon the type of RAS protein that may also contribute to tumor growth inhibition.ConclusionOur study identifies BAY 11-7082 to be an efficacious inhibitor for treating RAS oncogene (HRAS, KRAS, and NRAS) mutant cancer cells. This finding provides new therapeutic opportunity for effective treatment of RAS-mutant cancers.

Mutations found in cancer patients compromise DNA binding of the winged helix protein STK19

Serine/threonine protein kinase 19 (STK19) has been reported to phosphorylate and activate oncogenic NRAS to promote melanomagenesis. However, concerns have been raised about whether STK19 is a kinase. STK19 has also been identified as a putative factor involved in the transcription-coupled nucleotide excision repair (TC-NER) pathway. In this study, we determined the 1.32 Å crystal structure of human STK19. The structure reveals that STK19 is a winged helix (WH) protein consisting of three tandem WH domains. STK19 binds more strongly to double-stranded DNA and RNA (dsDNA/dsRNA) than to ssDNA. A positively charged patch centered on helix WH3-H1 contributes to dsDNA binding, which is unusual because the WH domain typically uses helix H3 as the recognition helix. Importantly, mutations of the conserved residues in the basic patch, K186N, R200W, and R215W, are found in cancer patients, and these mutations compromise STK19 DNA binding. Other mutations have been predicted to produce a similar effect, including two mutations that disrupt the nuclear localization signal (NLS) motif. These mutations may indirectly impact the DNA binding capacity of STK19 by interfering with its nuclear localization.

Design, synthesis, and evaluation of novel quindoline derivatives with fork-shaped side chains as RNA G-quadruplex stabilizers for repressing oncogene NRAS translation

NRAS mutation is the second most common oncogenic factor in cutaneous melanoma. Inhibiting NRAS translation by stabilizing the G-quadruplex (G4) structure with small molecules seems to be a potential strategy for cancer therapy due to the NRAS protein's lack of a druggable pocket. To enhance the effects of previously reported G4 stabilizers quindoline derivatives, we designed and synthesized a novel series of quindoline derivatives with fork-shaped side chains by introducing (alkylamino)alkoxy side chains. Panels of experimental results showed that introducing a fork-shaped (alkylamino)alkoxy side chain could enhance the stabilizing abilities of the ligands against NRAS RNA G-quadruplexes and their anti-melanoma activities. One of them, 10b, exhibited good antitumor activity in the NRAS-mutant melanoma xenograft mouse model, showing the therapeutic potential of this kind of compounds.

Abstract 1674: Inhibition of oncogenic nras signaling in acute myeloid leukemia cell lines through directed transcriptome alterations

Abstract Oncogenic mutations in genes involved in proliferative signaling are hallmarks of malignant transformation. The Ras family of signal transducing proteins are involved in the activation of several proliferative pathways and therefore are found to be oncogenically mutated in a variety of cancer types. The NRAS-directed pathways resulting in Erk1/2 activation are dysregulated in a significant percentage of acute myeloid leukemia (AML), metastatic melanoma, Hodgkin lymphoma, and thyroid cancers. The consequence of oncogenic NRAS signaling is the establishment of a transcriptome commanding constitutive proliferation and survival. It has long been known that phorbol ester treatment of AML cell lines, resulting in activation of protein kinase C (PKC), causes phenotypic changes that include cell cycle arrest, myeloid differentiation, and apoptosis. The paradox is that numerous studies identify PKC as an activator of RAS/ERK signaling. Here we show that phorbol ester treatment of NRAS-driven AML cell lines results in the transcriptional upregulation of genes encoding negative regulators of RAS signaling including DUSP1,2,4,5,6, SPRY2, SPRED1, RASA1, PEA15, RPS6KA1, and RASSF5. Additionally, phorbol ester treatment eventually results to ERK1/2 inactivation through dephosphorylation. Several of these negative regulators, when overexpressed in AML cell lines, dampen proliferation, and induce senescence. We propose that the induction of RAS negative regulators alters the AML transcriptome to a non-proliferative state in part through the transcriptional regulation of genes such as CDKN1A, CDKN2B, ZFP36L1, and MYC. As gene therapy strategies develop, designed to provide negative regulators of proliferative signaling pathways that are repressed in the malignant cell, we imagine the RAS/ERK pathway as a target for transcriptome reprogramming. Citation Format: Michael Roberts, Sophia Kovatsis, Amelia Harper, Megan Cravinho, Kishan Mangru, Sher Bahadur, Keagan Hesse, Katy Meta, Cuong Nguyen. Inhibition of oncogenic nras signaling in acute myeloid leukemia cell lines through directed transcriptome alterations [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 1674.

Mechanisms of Melanoma Progression and Treatment Resistance: Role of Cancer Stem-like Cells.

Melanoma is the third most common type of skin cancer, characterized by its heterogeneity and propensity to metastasize to distant organs. Melanoma is a heterogeneous tumor, composed of genetically divergent subpopulations, including a small fraction of melanoma-initiating cancer stem-like cells (CSCs) and many non-cancer stem cells (non-CSCs). CSCs are characterized by their unique surface proteins associated with aberrant signaling pathways with a causal or consequential relationship with tumor progression, drug resistance, and recurrence. Melanomas also harbor significant alterations in functional genes (BRAF, CDKN2A, NRAS, TP53, and NF1). Of these, the most common are the BRAF and NRAS oncogenes, with 50% of melanomas demonstrating the BRAF mutation (BRAFV600E). While the successful targeting of BRAFV600E does improve overall survival, the long-term efficacy of available therapeutic options is limited due to adverse side effects and reduced clinical efficacy. Additionally, drug resistance develops rapidly via mechanisms involving fast feedback re-activation of MAPK signaling pathways. This article updates information relevant to the mechanisms of melanoma progression and resistance and particularly the mechanistic role of CSCs in melanoma progression, drug resistance, and recurrence.

O09 Targeted genetic therapy for congenital melanocytic naevi

Abstract Severe cases of congenital melanocytic naevi (CMN) are associated with substantial cutaneous and neurological morbidity and an excess childhood mortality from melanoma. Effective treatments are lacking. This mosaic disorder is caused most commonly by a heterozygous oncogenic variant NRAS c.181C>A, p.(Q61K). As NRAS has multiple downstream effectors we have sought to treat this disease by precision genetic therapy rather than downstream pathway inhibition, hypothesising that silencing of the oncogenic allele may remove cellular protection from RAS induced apoptosis. Using a lead siRNA selected for allele specificity and fewest off-target effects on RNAseq (siNRASQ61K) we show here significant selective knockdown of variant mRNA expression and knockdown of NRAS protein levels. A single treatment to primary naevus cell cultures leads to normalisation of MAPK pathway activation, reduction in proliferation rate, and importantly, triggering of apoptosis. We go on to demonstrate that receptor-targeted lipid nanoparticles (RTNPs) successfully protect siRNA from degradation, deliver cargo to naevus cells in patient skin explants and improve naevus cell targeting. A single intradermal injection of siNRASQ61K-RTNPs into transgenic mice harbouring humanised NRASQ61K(Tyr::NRASQ61K) confirms significant selective knockdown of the variant NRAS allele in vivo.Successful targeting of variant NRAS and triggering of naevus cell apoptosis now paves the way for clinical trials of this genetic therapy for CMN.

A gain-of-function p53 mutant synergizes with oncogenic NRAS to promote acute myeloid leukemia in mice.

We previously demonstrated that a subset of acute myeloid leukemia (AML) patients with concurrent RAS pathway and TP53 mutations have an extremely poor prognosis and that most of these TP53 mutations are missense mutations. Here, we report that, in contrast to the mixed AML and T cell malignancy that developed in NrasG12D/+ p53-/- (NP-/-) mice, NrasG12D/+ p53R172H/+ (NPmut) mice rapidly developed inflammation-associated AML. Under the inflammatory conditions, NPmut hematopoietic stem and progenitor cells (HSPCs) displayed imbalanced myelopoiesis and lymphopoiesis and mostly normal cell proliferation despite MEK/ERK hyperactivation. RNA-Seq analysis revealed that oncogenic NRAS signaling and mutant p53 synergized to establish an NPmut-AML transcriptome distinct from that of NP-/- cells. The NPmut-AML transcriptome showed GATA2 downregulation and elevated the expression of inflammatory genes, including those linked to NF-κB signaling. NF-κB was also upregulated in human NRAS TP53 AML. Exogenous expression of GATA2 in human NPmut KY821 AML cells downregulated inflammatory gene expression. Mouse and human NPmut AML cells were sensitive to MEK and NF-κB inhibition in vitro. The proteasome inhibitor bortezomib stabilized the NF-κB-inhibitory protein IκBα, reduced inflammatory gene expression, and potentiated the survival benefit of a MEK inhibitor in NPmut mice. Our study demonstrates that a p53 structural mutant synergized with oncogenic NRAS to promote AML through mechanisms distinct from p53 loss.

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.

Acute Myeloid Leukemia (AML) from Older HSCs Is Resistant to Chemotherapy and Has an Altered DNA Damage Response

Acute myeloid leukemia (AML) is an aggressive malignancy that leads to the accumulation of immature myeloid precursors, resulting in progressive marrow failure and death. AML arises from the hematopoietic stem cell (HSC), either directly or through an early myeloid precursor. HSCs must survive for the entire human lifespan to provide the 200+ billion blood cells that are produced daily. They are subjected to the entirety of the aging process. Further, while AML is diagnosed in every age range, it disproportionately affects older patients, with a median age at diagnosis of 68. Older age, typically defined as 60 years of age or older, is a powerful, poor prognostic factor. Clinical trials show an estimated 5-year survival of less than 10% in these patients. Ten-year survival is even worse with one study estimating 2.4% of patients over 60 years of age alive at ten years when treated with chemotherapy. Importantly, this poor outcome is the result of disease that is significantly more resistant to therapy. Even though this clinical data is well known the underlying mechanisms of therapy resistance in older AML are unknown. To address this, we generated genetically identical AML cells from fetal, 12-week-old (Young) or 24-month-old (Old) murine HSCs. Retroviral vectors were used to express the oncogenic MLL-ENL fusion protein and NRas G12D. AML was confirmed by morphology, immunophenotype and all AML cells were lethal when injected into syngeneic recipients. Old AML cells demonstrated reduced autophagy, decreased NAD levels and impaired mitochondria consistent with a significant effect of biological aging. When treated with DNA damaging chemotherapy, Old AML cells were significantly more resistant than either Young or Fetal cells to both cytarabine and the anthracycline doxorubicin. To examine the DNA damage response AML cells were treated with doxorubicin and stained for the early DNA damage marker gH2AX. Old AML cells generated significantly more gH2AX than either Fetal or Young AML cells (Figure 1). We next examined the induction of p53 in response to treatment and in contrast to the gH2AX results Old AML cells induced the least amount of p53 in response to doxorubicin treatment (Figure 2). This data demonstrates that Old AML cells were more adept at recognizing DNA damage but least likely to induce p53 in response to it suggesting a difference in DNA repair. To better understand these differences RNA sequencing was performed and differentially expressed genes (DEGs) identified. When Fetal and Young AML cells were compared, no DEGs reached the false discovery threshold for significance, demonstrating that Fetal and Young AMLs have highly similar gene expression profiles. In contrast, when Old AML cells were compared to either Young or Fetal cells, hundreds of highly significant DEGs were identified, and KEGG pathway enrichment analysis revealed that several DNA repair pathways were significantly upregulated in Old AML. These include base excision repair (FDR p= 8.60E-06), mismatch repair (FDR p=3.26E-05), and nucleotide excision repair (FDR p= 0.00043). To further validate these pathways, the Beat AML TCGA dataset was assessed for the prognostic effect of increased expression of key genes in these pathways. Patients with increased expression of these genes had a trend toward worse survival (p=0.07) consistent with these pathways being clinically relevant. These data suggest that AML arising in older patients may overexpress DNA damage repair pathways leading to chemotherapy resistance and poor outcomes. Additional work on ways to increase sensitivity to Old AML cells is in progress.

Exploring the In Vitro and In Vivo Therapeutic Potential of BRAF and MEK Inhibitor Combination in NRAS-Mutated Melanoma.

Patients with NRAS-mutant metastatic melanoma often have an aggressive disease requiring a fast-acting, effective therapy. The MEK inhibitor binimetinib shows an overall response rate of 15% in patients with NRAS-mutant melanoma, providing a backbone for combination strategies. Our previous studies demonstrated that in NRAS-mutant melanoma, the antitumor activity of the MEK inhibitor binimetinib was significantly potentiated by the BRAFV600E/K inhibitor encorafenib through the induction of ER stress, leading to melanoma cell death by apoptotic mechanisms. Encorafenib combined with binimetinib was well tolerated in a phase III trial showing potent antitumor activity in BRAF-mutant melanoma, making a rapid evaluation in NRAS-mutant melanoma imminently feasible. These data provide a mechanistic rationale for the evaluation of binimetinib combined with encorafenib in preclinical and clinical studies on NRAS-mutant metastatic melanoma. The combination of BRAFi plus MEKi was tested in a monolayer culture of patient-derived cell lines and in corresponding patient-derived tissue slice cultures of NRAS-mutant melanoma. To investigate the treatment in vivo, NSG (NOD. Cg-PrkdcscidIl2rgtm1Wjl/SzJ) mice were subcutaneously injected with three different BRAF wild-type melanoma models harboring oncogenic NRAS mutations and treated orally with encorafenib (6 mg/kg body weight, daily) with or without binimetinib (8 mg/kg body weight, twice daily). In parallel, an individual healing attempt was carried out by treating one patient with an NRAS-mutated tumor. Encorafenib was able to enhance the inhibitory effect on cell growth of binimetinib only in the cell line SKMel147 in vitro. It failed to enhance the apoptotic effect found in two other NRAS-mutated cell lines. Encorafenib led to a hyperactivation of ERK which could be reduced with the combinational treatment. In two of the three patient-derived tissue slice culture models of NRAS-mutant melanomas, a slight tendency of a combinatorial effect was seen which was not significant. Encorafenib showed a slight induction of the ER stress genes ATF4, CHOP, and NUPR1. The combinational treatment was able to enhance this effect, but not significantly. In the mouse model, the combination therapy of encorafenib with binimetinib resulted in reduced tumor growth compared to the control and encorafenib groups; however, the best effect in terms of tumor growth inhibition was measured in the binimetinib therapy group. The therapy showed no effect in an individual healing attempt for a patient suffering from metastatic, therapy-refractory NRAS-mutated melanoma. In in vitro and ex vivo settings, the combination therapy was observed to elicit a response; however, it did not amplify the efficacy observed with binimetinib alone, whereas in a patient, the combinational treatment remained ineffective. The preclinical in vivo data showed no increased combinatorial effect. However, the in vivo effect of binimetinib as monotherapy was unexpectedly high in the tested regimen. Nevertheless, binimetinib proved to be advantageous in the treatment of melanoma in vivo and led to high rates of apoptosis in vitro; hence, it still seems to be a good base for combination with other substances in the treatment of patients with NRAS-mutant melanoma.

Adoptive Transfer of T Cells Genetically Engineered to Express T-Cell Receptors Targeting Neoantigens Arising from p53 and Ras Hotspot Mutations in Hematologic Malignancies

The tumor suppressor gene p53 and the oncogenes NRAS and KRAS (shortened to Ras) are frequently mutated in many difficult-to-treat hematologic malignancies including myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), and relapsed multiple myeloma. Driver mutations in p53 and Ras are associated with treatment-refractory malignancies. There are no Food and Drug Administration (FDA)-approved therapies specifically targeting hematologic malignancies with p53 or Ras mutations. Some missense mutations in p53 and Ras lead to immunogenic peptides (neoepitopes) that are presented by human leukocyte antigens (HLA). Members of our group have identified T-cell receptors (TCRs) targeting some of these neoepitopes and used T cells expressing these TCRs as treatments for epithelial tumors (Levin et al. Clin Cancer Res, 2021 and Kim et al. Cancer Immunol Res, 2022). Adoptively transferred T cells expressing some of these TCRs have caused objective responses of advanced epithelial cancers in patients. Here, we report preclinical experiments with T cells genetically engineered to target neoantigens arising from p53 and Ras mutations in hematologic malignancies. p53 mutations occur in approximately 5-10% of de novo AML, 25-50% of treatment-related or complex-karyotype MDS/AML, 5-10% of multiple myeloma, and 25% of plasma cell leukemia. Mutations in Ras occur in 15-20% of AML and 20% of multiple myeloma. Our TCR panel targets neoepitopes arising from 2 of the 5 most common p53 mutation sites and 2 of the 3 most common Ras mutation sites . The human leukocyte antigen (HLA) restriction of these TCRs is shown along with the HLA frequencies ( Table 1). In all experiments, human donor peripheral blood mononuclear cells were activated in culture with an anti-CD3 antibody. Two days later, T cells were transduced with a gamma-retroviral vector encoding a neoepitope-specific TCR. Presence of mutations in target cell lines was confirmed by DNA sequencing. Cell lines which did not naturally express the appropriate HLA were transduced with a gamma-retroviral construct encoding the HLA. We assessed the general specificity of TCRs for each targeted neoepitope. For each neoepitope-specific TCR, T cells expressing the TCR were cultured overnight with target cell lines expressing the neoepitope plus the HLA targeted by that TCR. We cultured T cells from the same cultures with 12 to 16 negative-control target cell lines that lacked the appropriate mutation and/or HLA. Negative control cell lines were from a variety of human tissues. Enzyme-linked immunosorbent assays (ELISA) performed on the culture supernatants showed that IFN-gamma release was much higher when T cells expressing a neoepitope-specific TCR were cultured with target cells having both the targeted mutation and the appropriate HLA (Table 1). We conducted another set of experiments to evaluate the neoepitope-specificity of the TCRs. For each neoepitope, COS7 cells with the appropriate HLA were transfected with plasmids encoding either wild-type or mutant versions of p53 or Ras differing from wild-type by 1 amino acid. The COS7 cells were cultured with T cells expressing the appropriate TCR. IFN-gamma was released in a neoepitope-specific manner. Higher levels of T-cell degranulation and interleukin-2 release occurred when T cells expressing neoepitope-specific TCRs were cultured with target cells having the targeted mutation and HLA versus target cells lacking the appropriate mutation and/or HLA. We evaluated efficacy of the T53-R175H-A2 TCR in vivo. Immunocompromised NOD-scid common gamma-chain-deficient mice received intravenous injections of the KMS26-luciferase multiple myeloma cell line, which naturally expresses HLA-A*02:01 and the p53 R175H mutation. One week later when all mice had detectable tumor burdens, mice received either 10 million R175H-targeted T cells, T cells expressing an irrelevant TCR, or untransduced T cells. All groups received 3 doses of interleukin-2. Mice treated with R175H-targeted T cells cleared the tumor while mice in all other groups had progressive tumor growth (Figure 1). In vivo studies of additional TCRs are in progress. In conclusion, we have demonstrated activity of neoantigen-targeted T cells against hematologic malignancies in preclinical models. We plan to evaluate adoptively transferred autologous T cells targeting p53 and Ras mutations in an upcoming clinical trial.

RAB27B controls palmitoylation-dependent NRAS trafficking and signaling in myeloid leukemia.

RAS mutations are among the most prevalent oncogenic drivers in cancers. RAS proteins propagate signals only when associated with cellular membranes as a consequence of lipid modifications that impact their trafficking. Here, we discovered that RAB27B, a RAB family small GTPase, controlled NRAS palmitoylation and trafficking to the plasma membrane, a localization required for activation. Our proteomic studies revealed RAB27B upregulation in CBL- or JAK2-mutated myeloid malignancies, and its expression correlated with poor prognosis in acute myeloid leukemias (AMLs). RAB27B depletion inhibited the growth of CBL-deficient or NRAS-mutant cell lines. Strikingly, Rab27b deficiency in mice abrogated mutant but not WT NRAS-mediated progenitor cell growth, ERK signaling, and NRAS palmitoylation. Further, Rab27b deficiency significantly reduced myelomonocytic leukemia development in vivo. Mechanistically, RAB27B interacted with ZDHHC9, a palmitoyl acyltransferase that modifies NRAS. By regulating palmitoylation, RAB27B controlled c-RAF/MEK/ERK signaling and affected leukemia development. Importantly, RAB27B depletion in primary human AMLs inhibited oncogenic NRAS signaling and leukemic growth. We further revealed a significant correlation between RAB27B expression and sensitivity to MEK inhibitors in AMLs. Thus, our studies presented a link between RAB proteins and fundamental aspects of RAS posttranslational modification and trafficking, highlighting future therapeutic strategies for RAS-driven cancers.

KRAS and NRAS Translation Is Increased upon MEK Inhibitors-Induced Processing Bodies Dissolution

Overactivation of the mitogen-activated protein kinase (MAPK) pathway is a critical driver of many human cancers. However, therapies directly targeting this pathway lead to cancer drug resistance. Resistance has been linked to compensatory RAS overexpression, but the mechanisms underlying this response remain unclear. Here, we find that MEK inhibitors (MEKi) are associated with an increased translation of the KRAS and NRAS oncogenes through a mechanism involving dissolution of processing body (P-body) biocondensates. This effect is seen across different cell types and is extremely dynamic since removal of MEKi and ERK reactivation result in reappearance of P-bodies and reduced RAS-dependent signaling. Moreover, we find that P-body scaffold protein levels negatively impact RAS expression. Overall, we describe a new feedback loop mechanism involving biocondensates such as P-bodies in the translational regulation of RAS proteins and MAPK signaling.

Genome-wide maps of UVA and UVB mutagenesis in yeast reveal distinct causative lesions and mutational strand asymmetries.

Ultraviolet (UV) light primarily causes C > T substitutions in lesion-forming dipyrimidine sequences. However, many of the key driver mutations in melanoma do not fit this canonical UV signature, but are instead caused by T > A, T > C, or C > A substitutions. To what extent exposure to the UVB or UVA spectrum of sunlight can induce these noncanonical mutation classes, and the molecular mechanism involved is unclear. Here, we repeatedly exposed wild-type or repair-deficient yeast (Saccharomyces cerevisiae) to UVB or UVA light and characterized the resulting mutations by whole genome sequencing. Our data indicate that UVB induces C > T and T > C substitutions in dipyrimidines, and T > A substitutions that are often associated with thymine-adenine (TA) sequences. All of these mutation classes are induced in nucleotide excision repair-deficient cells and show transcriptional strand asymmetry, suggesting they are caused by helix-distorting UV photoproducts. In contrast, UVA exposure induces orders of magnitude fewer mutations with a distinct mutation spectrum. UVA-induced mutations are elevated in Ogg1-deficient cells, and the resulting spectrum consists almost entirely of C > A/G > T mutations, indicating they are likely derived from oxidative guanine lesions. These mutations show replication asymmetry, with elevated G > T mutations on the leading strand, suggesting there is a strand bias in the removal or bypass of guanine lesions during replication. Finally, we develop a mutation reporter to show that UVA induces a G > T reversion mutation in yeast that mimics the oncogenic NRAS Q61K mutation in melanoma. Taken together, these findings indicate that UVA and UVB exposure can induce many of the noncanonical mutation classes that cause driver mutations in melanoma.

Abstract 1431: Sprouty 2 expression attenuates proliferation in nras-driven acute myeloid leukemia cell lines

Abstract Oncogenic mutations in the NRAS gene are found in many cancers including a subset of acute myeloid leukemias (AML). Established AML cell lines exhibiting hyperactive signaling through the RAS-RAF-MEK-ERK pathway show constitutive ERK activation generating a transcriptome that mediates escape from programmed cell death and continuous proliferation. It has been established that exposure of many AML cell lines to phorbol esters such as phorbol-12-myristate-13-acetate (PMA) mediates cell cycle arrest, myeloid differentiation, and apoptosis. This effect seems counterintuitive given that PMA irreversibly activates protein kinase C (PKC), which enhances ERK activity leading to transcriptional upregulation of target genes controlled by ERK activated transcription factors, many of which promote proliferation. Here we define a set of PMA response genes in AML cell lines driven by oncogenic NRAS that encode negative regulators of RAS-RAF-MEK-ERK signaling, including SPRY2, RASA1, DUSP 5, and DUSP6. Additionally, we show that overexpression of SPRY2 alone attenuates proliferation by inhibiting ERK activation and altering the AML cell transcriptome through the activation of genes encoding members of the AP-1 transcription factor family, FOS, JUNB, and JUND, and the cyclin-CDK inhibitors CDKN1A and CDKN2B. We hypothesize that oncogenic NRAS signaling is overridden by PMA treatment through the activation of ERK target genes that ultimately inhibit the MAPK-ERK pathway, such as SPRY2. Finally, we show that SPRY 2 expression in AML patient samples represents a survival prognostic indicator where higher expression levels correlate with improved overall survival. Citation Format: Michael Roberts, Sher Bahadur, Coltin Albitz, Jae Chung, Samantha Garcia, Cuong Nguyen, Sophia Kovatsis. Sprouty 2 expression attenuates proliferation in nras-driven acute myeloid leukemia cell lines [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 1431.

Abstract 5799: SPINK1-induced tumor plasticity provides a therapeutic window for chemotherapy in hepatocellular carcinoma

Abstract Intratumor molecular heterogeneity of hepatocellular carcinoma (HCC) is partly attributed to the presence of cancer stem cells (CSCs), which we now know represents a critical root of tumor recurrence and chemotherapy resistance. CD133 is known to represent an important functional marker of liver CSCs. We have demonstrated CD133 to enrich following chemotherapy treatment, while CD133/Prom1-depletion would enhance sensitivity of HCC tumors to chemotherapy. Yet unfortunately, CD133 is not specific to HCC, but is also expressed in normal regenerating liver. Identifying critical factors expressed specifically in liver CD133+ CSCs, but not in liver normal CD133+ stem/progenitor cells may offer important therapeutic opportunities overcoming chemoresistance in HCC. RNA-seq profiling comparing sorted CD133+ and CD133- subsets of normal regenerating liver induced by DDC diet and HCC induced by either N-nitrosodiethylamine (DEN)/carbon tetrachloride (CCl4) or hydrodynamic tail vein injection of oncogenic plasmids AKT and NRAS identified Serine Peptidase Inhibitor Kazal Type I (SPINK1) to be distinctly expressed in the HCC CD133+ subpopulation but not in normal regenerating liver CD133+ subpopulation. SPINK1 overexpression in HCC clinical samples is correlated with a poor prognosis. Expression of SPINK1 increased during early liver progenitor development, peaked during the premature hepatocyte stage, decreased during hepatocyte maturation and increased progressively from well-differentiated to poorly differentiated HCCs. Enhanced transcriptional activity of SPINK1 was mediated by promoter binding of the epithelial cell-specific transcription factor ELF3, which like CD133, were both increased following chemotherapy treatment. SPINK1 inhibition by lentiviral-based knockdown or a specific monoclonal antibody (mAb) mitigated tumor initiation, self-renewal and chemoresistance. Mechanistically, secretory SPINK1 bound to epidermal growth factor receptor (EGFR) activating MEK/ERK signaling and consequently promoting the formation of CDK4/6-cyclin D1 complex to phosphorylate Rb and release E2F2, allowing the cells to overcome G1/S checkpoint promoting cell cycle progression as well as transcribing stemness, oncogenic dedifferentiation and chemoresistance-related genes. Collectively, our findings suggest SPINK1 to play a critical role in hepatocarcinogenesis and that SPINK1 mAb may represent a novel therapeutic option for the treatment of HCC, targeting at the CD133+ CSC tumor roots and overcoming chemoresistance. Citation Format: Ki-Fong Man, Lei Zhou, Ying-Tung Lam, Jun Yu, Jing-Ping Yun, Xin-Yuan Guan, Ming Liu, Stephanie Ma. SPINK1-induced tumor plasticity provides a therapeutic window for chemotherapy in hepatocellular carcinoma [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 5799.

Abstract 3808: MicroRNA-206 drives antitumor immunity by disrupting the communication between Kupffer cells and Tregs

Abstract Kupffer cells (KCs) account for 15% of the total liver cells. However, their roles in hepatocellular carcinoma (HCC) is poorly described. Clec4fCre-tdTomato knock-in mice expressing Cre recombinase and tdTomato-NLS under the KC-specific Clec4f promoter were hydrodynamically injected with oncogenic AKT and Nras (AKT/Ras) to induce HCC. A LoxP-stop-LoxP (LSL) system was used to express miR-206 in KCs of mice. AKT activation was observed in hepatocytes and KCs of HCC patients. Hydrodynamic injection (HDI) of AKT/Ras led to activation of AKT signaling in KCs and hepatocytes. AKT/Ras mice developed lethal HCC within 6-8 weeks post injection. Activation of AKT signaling led to M2 polarization of KCs, increased hepatic Tregs and exhaustion of CTLs. MicroRNA (miR) profiling revealed that AKT/Ras impaired miR-206 biogenesis in KCs by driving translation of Yin Yang 1 (YY1), a transcription repressor of miR-206. HDI of miR-206 into AKT/Ras mice fully prevented HCC, while all control mice died of HCC 6-8 weeks post injection. However, HDI of miR-206 only transfected ~ 20% of hepatocytes, indicating that it is unreasonable to conclude that the full prevention of HCC in AKT/Ras/miR-206 mice is caused by inhibited proliferation of HCC cells. We, therefore, posited that miR-206-mediated recovery of immune surveillance, at least in part, accounted for the full prevention of HCC in AKT/Ras/miR-206 mice. We next used the LSL system to overexpress miR-206 in KCs of Clec4fCretdTomato mice injected with AKT/Ras. KC-specific expression of miR-206 fully prevented HCC in AKT/Ras mice, while 100% control mice died of HCC. Mechanistically, AKT signaling in KCs drove CCL22 (C-C motif chemokine ligand 22) production by phosphorylating β-catenin that activates transcription of Ccl22. In contrast, miR-206 disrupted β-catenin signaling by targeting LEF1 (lymphoid enhancer-binding factor 1), an “architectural” transcription factor of β-catenin. CCL22 recruits Tregs. Indeed, KC-specific expression of miR-206 led to elevated CCL22, M2 to M1 transition of KCs, reduced hepatic Tregs, and elevated CTLs. Depletion of CTLs in AKT/Ras mice fully offset the ability of miR-206 to prevent HCC. Conclusions: AKT-educated KCs initiate Treg recruitment via a regulatory loop consisting of YY1, β-catenin/LEF1, miR-206, and CCL22; once this loop is activated, AKT activates β-catenin axis, which drives CCL22 production, Treg recruitment and HCC growth; while KC-specific expression of miR-206 reversed this process by blocking β-catenin axis in KCs. miR-206 represents a novel immunotherapy against HCC. Citation Format: Guisheng Song, Ningning Liu. MicroRNA-206 drives antitumor immunity by disrupting the communication between Kupffer cells and Tregs. [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 3808.

Damage mapping techniques and the light they have shed on canonical and atypical UV photoproducts.

Ultraviolet (UV) light is a pervasive threat to the DNA of terrestrial organisms. UV light induces helix-distorting DNA lesions, primarily cyclobutane pyrimidine dimers (CPDs) that form between neighboring pyrimidine bases. Unrepaired CPD lesions cause cytosine-to-thymine (C>T) substitutions in dipyrimidine sequences, which is the predominant mutation class in skin cancer genomes. However, many driver mutations in melanoma (e.g., in the BRAF and NRAS oncogenes) do not fit this UV mutation signature. Recent studies have brought to light the intriguing hypothesis that these driver mutations may be induced by infrequent or atypical UV photoproducts, including pyrimidine 6-4 pyrimidone photoproducts (6-4PP) and thymine-adenine (TA) photoproducts. Here, we review innovative methods for mapping both canonical and atypical UV-induced photoproducts across the genome.

Prognostic role of NRAS-related pharmacogenetics in metastatic papillary thyroid carcinoma

Saha et al. deserve appreciation for addressing the enigmatic issue of tumor pharmacogenetics in thyroid cancer, through the interesting case, “NRAS mutation in differentiated thyroid cancer,” published in the Molecular Tumor Board section of the previous issue of the journal.[1] They have nicely narrated the chronological events in the natural history, response to biological therapy, and related genetics in a patient with papillary thyroid carcinoma. We have few pertinent comments and queries. First, NRAS mutation is the most common mutation reported in follicular adenomas, follicular thyroid cancer, and the follicular variant of papillary thyroid cancer, among the RAS gene (H, N, K) family.[2] Second, the genetic mechanisms of thyroid cancer cell biology are complex including genetic, epigenetic, sequential, evolving, and superadded mutations leading to clonal evolution. Third, the expanding genetic database, especially after next-generation sequencing studies, has shifted the clinical paradigm to predicting the natural history, tumor biology, response to radioidodine therapy, and response to biological therapy based on these molecular footprints.[3] Fourth, the ultimate aim of predicting prognosis, response of residual disease, response of metastasis, and influence of biological therapy on re-differentiation are the latest areas of active research in cancer tumor science. Fifth, the dramatic regression of progressive, refractory metastatic recurrences as reported in this case, is a very rare and interesting phenomenon. Such a favorable response in thyroid cancer has been reported in the past, but the biological reason is speculative.[4] It has been shown that suppression of oncogenic NRAS has induced apoptosis in human melanoma cell lines.[5] Sixth, thyroid cancer genetics are not static, but dynamically evolving, as shown in the sequential genetic mechanisms influencing the adenoma-carcinoma sequence, de-differentiation of papillary thyroid cancer to anaplastic thyroid cancer, and re-differentiation of thyroid cancer tissues.[2] Lastly, a single universal gene panel including common genes associated with thyroid cancer such as RAS, BRAF, and RET/PTC rearrangements for routine clinical use, is the need of the hour. Such a panel, for prognosticating and treating papillary thyroid cancer, is an ambitious target for future thyroid cancer management. The present paper would have been enhanced by a pathophysiological explanation of the role of NRAS pharmacogenetics in papillary thyroid cancer. A paragraph on the plausible reasons for the good response to downstream biological therapies targeting MEK, ERK, mTOR, and P13K genes would have added more value. The possible reasons could include pharmacogenetics, induced apoptosis, or other as-yet-unknown causes. Financial support and sponsorship Nil. Conflicts of interest There are no conflicts of interest.