Mutant KRAS Protein Research Articles

Tunneling nanotubes mediate KRas transport: Inducing tumor heterogeneity and altering cellular membrane mechanical properties

Mutation in oncogene KRas plays a crucial role in the occurrence and progression of numerous malignant tumors. Malignancy involves changes in cell mechanics for extensive cellular deformation during metastatic dissemination. We hypothesize that oncogene KRas mutations are intrinsic to alterations in cellular mechanics that promote malignant tumor generation and progression. Here, we demonstrate the use of optical tweezers coupled with a confocal fluorescence imaging system and gene interference technique to reveal that the mutant KRas protein can be transported between homogeneous and heterogeneous tumor cells by tunneling nanotubes (TNTs), resulting in a significant reduction of membrane tension and acceleration of membrane phospholipid flow in the recipient cells. Simultaneously, the changes in membrane mechanical properties of the tumor cells also enhance the metastatic and invasive ability of the tumors, which further contribute to the deterioration of the tumors. This finding helps to clarify the association between oncogene mutations and changes in the mechanical properties of tumor cells, which provides a theoretical basis for the development of cancer treatment strategies. Statement of significanceHere, we present a laser confocal fluorescence system integrated with optical tweezers to observe the transfer of mutant KRasG12D protein from mutant cells to wild-type cells through TNTs. Malignancy involves changes in cell mechanics for extensive cellular deformation during metastatic dissemination. Our results demonstrate a significant decrease in membrane tension and an increase in membrane phospholipid flow in recipient cells. These alterations in mechanical properties augment the migration and invasive capabilities of tumor cells, contributing to tumor malignancy. Our findings propose that cellular mechanical properties could serve as new markers for tumor development, and targeting membrane tension may hold potential as a therapeutic strategy.

Endogenous oncogenic KRAS expression increases cell proliferation and motility in near-diploid hTERT RPE-1 cells

About 18% of all human cancers carry a mutation in the KRAS gene making it among the most sought-after anti-cancer targets. However, mutant KRas protein has proved remarkably undruggable. The recent approval of the first generation of RAS inhibitors therefore marks a seminal milestone in the history of cancer research. Inevitably though, it also raises the predictable challenges of limited drug efficacies and acquired resistance. Hence, new approaches that improve our understanding of the tumorigenic mechanisms of oncogenic RAS within more physiological settings continue to be essential. Here, we have employed the near-diploid human hTERT RPE-1 cells to generate isogenic cell lines in which one of the endogenous KRAS alleles carries an oncogenic KRAS mutation at glycine 12. Cells with a KRASG12V/+, KRASG12C/+, or KRASG12D/+ genotype, together with wild-type KRASG12G(WT)/+ cells, reveal that oncogenic KRAS.G12X mutations increase cell proliferation rate and cell motility and reduced focal adhesions in KRASG12V/+ cells. EGF-induced phosphorylation of ERK and AKT was comparable between KRASG12V/+, KRASG12C/+, KRASG12D/+, and KRASG12G(WT)/+ cells. Interestingly, KRASG12X/+ cells showed varying responses to distinct inhibitors with the KRASG12V/+ and KRASG12D/+ cells more sensitive to hydroxyurea and MEK inhibitors, U0126 and trametinib, but more resistant to PI3K inhibitor, PIK-90, than the KRASG12G(WT)/+ cells. A combination of low doses of hydroxyurea and U0126 showed an additive inhibition on growth rate that was greater in KRASG12V/+ than wild-type cells. Collectively, these cell lines will be a valuable resource for studying oncogenic RAS signalling and developing effective anti-KRAS reagents with minimum cytotoxicity on wild-type cells.

Abstract 5947: Discovery of ACE-47228211, a highly potent and selective SOS1 inhibitor

Abstract Dysregulation of receptor tyrosine kinase (RTKs) and KRAS signaling is the most frequent causes of cancer development and progression. SOS1 is one of the major guanine nucleotide exchange factors (GEFs) that facilitates the conversion of the inactive GDP-bound KRAS “off” state to the activated GTP-bound KRAS “on” state. SOS1 is therefore required for dysregulated RTKs, and wildtype and mutant KRAS proteins to drive cancer cells. In addition, SOS1 plays a crucial role in modulating the reactivation of the RAS/MAPK signaling upon the treatment of RAS/MEK/ERK inhibitors. Thus, blocking SOS1 and KRAS protein-protein interactions could be an effective strategy for targeting KRAS-MAPK driven cancers. Here, we report the discovery of a highly potent and orally bioavailable small molecule SOS1 inhibitor, ACE-47228211. This molecule has a unique novel scaffold. It exhibits an IC50 of 8.5 nM in the SOS1-KrasG12D (GDP) exchange assay and 5.0 nM in cellular ERK phosphorylation assay in H1957 cells. ACE-47228211 at 3 mg/kg (BID) demonstrated significant tumor growth inhibition in MiaPaca-2 KRAS G12C tumor model than MRTX0920 at 50 mg/kg (BID). When combined with Sotorasib (5 mg/kg QD), a Kras G12C inhibitor, ACE-47228211 at 3 mg/kg exhibited synergistic effect similar to MRTX0920 at 50 mg/kg. Further, ACE-47228211 demonstrated synergistic effects with EGFR and FGFR2 inhibitors in RTK mutant tumor models. ACE-47228211 has excellent ADME and physical properties with low risks of hERG, CYP inhibition and drug-drug interactions. The evaluation of ACE-47228211 in a safety panel of 87 targets and a kinase panel of >500 targets shows that this molecule has favorable selectivity and safety profiles. The molecule is currently in IND enabling stage of development. Citation Format: Junmei Wang, Wenqian Li, Sanjeev Kumar, Weitao Pan, Zhiming Wen, Tinggui Yin, Genshi Zhao, Kuo-Long Yu. Discovery of ACE-47228211, a highly potent and selective SOS1 inhibitor [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 5947.

Abstract 5948: FMC-376 a dual inhibitor of ON and OFF states of KRASG12C is broadly active in PDX models of resistance

Abstract KRASG12C is a frequent activating mutation occurring in NSCLC, CRC, PDAC and other tumors that shifts KRAS into the active, GTP-bound (ON) state. KRAS was long considered undruggable until the recent discovery of single acting inhibitors, including those that bind the GDP-bound, inactive (OFF), state of KRASG12C. The most clinically advanced of these first-generation molecules have demonstrated clinical response rates of 37-43% and 6 to 7-month progression-free survival in lung cancer patients. While an important advance, a majority of cancers do not respond, and acquired resistance is common. FMC-376 is a next-generation dual inhibitor of both the ON and OFF states of KRASG12C with the potential to overcome resistance and deliver best-in-class durability of response. FMC-376 was discovered through the application of the FrontierTM platform, which integrates chemoproteomics, machine-learning, and covalent fragment-based drug discovery. FMC-376 is a highly selective, irreversible inhibitor of KRASG12C that covalently binds to the mutant cysteine in KRASG12C and directly blocks the ON and OFF states of the mutant KRAS protein leading to a complete, durable blockade of downstream signaling. This further translates into more durable tumor regressions in vivo in comparison to OFF state inhibitors like sotorasib. Clinical resistance to first-generation inhibitors that can only bind the OFF state of KRASG12C has been associated with multiple mechanisms that drive upregulation of ON state KRASG12C. These known drivers of resistance include activating co-mutation/amplification/fusions of receptor tyrosine kinases, amplification of KRASG12C and non-mutational mechanisms that lead to paradoxical activation of KRASG12C due to release of negative feedback control upon KRAS inhibition, often referred to as adaptive resistance. In addition, multiple mutations that may act independently of KRAS are also associated with resistance. These include mutation of KEAP1, CDKN2A, SMARCA4, PI3K, PTEN, MTOR, HRAS, NRAS, RAF, and MAPK. In vivo profiling of FMC-376 against a panel KRASG12C mutant patient derived xenograft (PDX) models of NSCLC, CRC and PDAC, has demonstrated that dual inhibition of both ON and OFF KRASG12C leads to complete suppression and regression of tumors carrying a broad spectrum of known genomic and non-genomic (adaptive) drivers of clinical resistance to OFF state KRASG12C inhibitors. FMC-376 a clinical stage dual inhibitor of ON and OFF state KRASG12C has the potential to overcome limitations of single acting and OFF state KRASG12C inhibitors. Citation Format: Yan Wang, Richard M. Neve, Jocelyn Staunton, Kevin R. Webster. FMC-376 a dual inhibitor of ON and OFF states of KRASG12C is broadly active in PDX models of resistance [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 5948.

Abstract 6717: Targeting mutant KRAS proteins with novel TCR-mimic fully human antibodies

Abstract Mutated KRAS proteins are ideal cancer targets, as they are expressed frequently and specifically in certain solid tumors. A large proportion of human colorectal cancer and pancreatic ductal adenocarcinoma express the tumor driver KRAS gene mutations G12V/G12D, but drugs targeting G12V/G12D are not available, revealing a huge unmet clinical need. While small molecules often fail to target the KRAS mutation G12V/G12D, T cell receptor-mimic (TCR-mimic) antibodies can specifically recognize KRAS mutations presented by human leukocyte antigen (HLA), opening up possibilities for targeting such intracellular antigens. Here, we discovered novel antibodies highly specific to G12V/HLA and G12D/HLA complexes by immunizing our proprietary RenTCR-mimicTM mice and using high-throughput Beacon-based screening. These TCR-mimic antibodies have higher affinities compared to endogenous TCRs, which may effectively reduce the possibility of tumor escape. Germline distribution analysis indicated their high sequence diversity, which suggests diverse epitope targeting. Although pancreatic cancer is extremely difficult to treat and has an extremely low KRAS mutant peptide-HLA complex density on the cell surface, our TCR-mimic antibodies exhibited potent in vitro tumor lysis activity when assembled into CD3 T cell engagers. Furthermore, these antibodies demonstrated convincing off-target safety. Together, our results indicate promising therapeutic potential of these KRAS mutation-targeted TCR-mimic antibodies for the treatment of solid tumors. Citation Format: Jun Du, Wanbo Tang, Xin Jiao, Limin Zhao, Pengfei Du, Yuqi Zhang, Jian Bao, Han Chen, Chaoshe Guo, W. Frank An. Targeting mutant KRAS proteins with novel TCR-mimic fully human antibodies [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 6717.

A Top-Down Proteomic Assay to Evaluate KRAS4B-Compound Engagement.

Development of new targeted inhibitors for oncogenic KRAS mutants may benefit from insight into how a given mutation influences the accessibility of protein residues and how compounds interact with mutant or wild-type KRAS proteins. Targeted proteomic analysis, a key validation step in the KRAS inhibitor development process, typically involves both intact mass- and peptide-based methods to confirm compound localization or quantify binding. However, these methods may not always provide a clear picture of the compound binding affinity for KRAS, how specific the compound is to the target KRAS residue, and how experimental conditions may impact these factors. To address this, we have developed a novel top-down proteomic assay to evaluate in vitro KRAS4B-compound engagement while assessing relative quantitation in parallel. We present two applications to demonstrate the capabilities of our assay: maleimide-biotin labeling of a KRAS4BG12D cysteine mutant panel and treatment of three KRAS4B proteins (WT, G12C, and G13C) with small molecule compounds. Our results show the time- or concentration-dependence of KRAS4B-compound engagement in context of the intact protein molecule while directly mapping the compound binding site.

Abstract B080: Mutant-selective KRASG12D(ON) inhibitor suppresses proliferation in vitro and tumor growth in vivo of KrasG12D GEMM-derived PDAC organoids

Abstract KRAS is the most frequently mutated oncogene in pancreatic ductal adenocarcinoma (PDAC), with KRASG12D driving initiation and progression of ~40% of tumors. Mutant KRAS proteins exist predominantly in the GTP-bound (RAS(ON)) state, leading to excessive downstream signaling via interaction with effectors such as RAF kinases. RMC-9805 is an orally bioavailable, mutant-selective covalent inhibitor of the active state of KRASG12D. RM-044, used here, is the corresponding representative preclinical tool compound. RM-044, KRASG12D and cyclophilin A form a stable, high affinity tri-complex resulting in the disruption of interactions with downstream KRAS effectors and suppression of KRASG12D(ON) signaling. RM-044 decreased RAS pathway activity and inhibited proliferation in multiple human KRASG12D PDAC cell lines in vitro. While these data are encouraging, we sought to study models that more faithfully represent the heterogeneity and complex tumor microenvironment found in the tumors of patients with KRASG12D PDAC. To address this, we generated and characterized pancreatic organoids from the lox-STOP-lox-KrasG12D genetically engineered mouse model (GEMM) and introduced expression of the KrasG12D mutation and p53 loss (KP) through a vector containing a p53 sgRNA and Cre recombinase. GEMM-derived KP pancreatic organoid lines treated with RM-044 showed concentration-dependent proliferation inhibition in vitro. KP organoids were implanted orthotopically into mouse pancreas leading to the development of PDAC tumors in immunocompetent mice. Histopathological examination of KP organoid derived tumors revealed molecular and phenotypic features translatable to the tumors of patients with PDAC. In this orthotopic model, oral administration of RM-044 inhibited MAPK pathway activation and led to deep and durable tumor growth suppression at a well-tolerated dose. In summary, mutant-selective, covalent inhibition of KRASG12D(ON) inhibits cell proliferation and drives tumor growth suppression in both human and murine preclinical models of KRASG12D PDAC. The generation of preclinical models that allow for in-depth translational analyses of KRASG12D(ON) inhibition in vitro and in vivo can support identification of optimal therapeutic regimens. Collectively, these preclinical results indicate that direct targeting of KRASG12D(ON) in PDAC has the potential to translate into clinical benefit for patients with pancreatic cancer. Citation Format: Mark P. Labrecque, Lingyan Jiang, Nicole Nasholm, Biswadeep Nayak, Xinxing Yu, Avian Song, Caroline Weller, James W. Evans, Maria Paz Zafra, Marie Parsons, Marie Menard, Lukas E. Dow, Jingjing Jiang, Ida Aronchik, Mallika Singh. Mutant-selective KRASG12D(ON) inhibitor suppresses proliferation in vitro and tumor growth in vivo of KrasG12D GEMM-derived PDAC organoids [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Pancreatic Cancer; 2023 Sep 27-30; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(2 Suppl):Abstract nr B080.

Abstract B022: A non-conserved histidine residue on KRAS drives paralog selectivity of the KRAS G12D inhibitor MRTX1133

Abstract The discovery of small molecule inhibitors against mutant KRAS protein has been a breakthrough in targeted therapy. MRTX1133 is the first non-covalent inhibitor with selectivity for the mutant KRAS G12D protein. Using isogenic cell lines expressing single Ras allele to test the selectivity of this compound, we found that in addition to KRAS G12D, MRTX1133 shows significant activity against several other KRAS mutants as well as wildtype KRAS protein. In contrast, MRTX1133 exhibits no activity against both G12D and wildtype forms of HRAS and NRAS proteins. Functional analysis revealed that the selectivity of MRTX1133 towards KRAS is associated with its binding to histidine 95 on KRAS, a residue that is not conserved in HRAS and NRAS. Reciprocal mutation of amino acid 95 among the three Ras paralogs resulted in reciprocal change in their sensitivity towards MRTX1133. Thus, histidine 95 is an essential selectivity handle for MRTX1133 towards KRAS. This knowledge could aid the development of other KRAS-selective inhibitors. (Funding: this research was supported by the Intramural Research Program of the National Cancer Institute, NIH) Citation Format: Miles Keats, John Han, Yeon-Hwa Lee, Chih-Shia Lee, Ji Luo. A non-conserved histidine residue on KRAS drives paralog selectivity of the KRAS G12D inhibitor MRTX1133 [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr B022.

Abstract B014: Phenotypic CRISPR genome-wide screening for the discovery of genetic regulators of allele-specific mutant KRAS

Abstract Kirsten rat sarcoma viral oncogene homolog (KRAS) is the most frequently mutated oncogene detected in 30% of all human cancers. Drugs that can impede the function of oncogenic KRAS offer exceptional therapeutic value. However, direct targeting KRAS is challenging due to its protein structure that lacks deep binding pockets for small-molecule inhibitors. Despite the recent success in targeting the G12C allele, targeted therapy for another hotspot mutant – G12V mutant KRAS has not been described. Here, we utilize CRISPR-Cas9 based genome-wide knockout screens and leverage a high-throughput microfluidic cell sorting platform to identify genes that regulate mutant KRAS harboring G12V mutation. The screens were conducted in two colorectal cancer cell lines HT29 and SW480, expressing wild-type KRAS and homozygous G12V KRAS, respectively. We have identified a list of genes whose loss-of-function reduces wild-type or mutant G12V KRAS protein expression. Our top gene identified from the mutant KRAS screen - denoted as selective-mutant KRAS modulator (SMKM) has shown promising results in selectively decreasing G12V KRAS protein expression. Through multiple assays including live cell imaging, western blot, flow cytometry, and proteomic analysis in SMKM knockout cells and SMKM inhibitor-treated cells. We found highly selective reduction in G12V KRAS protein expression. More importantly, genetically or pharmacologically inhibiting SMKM has demonstrated anti-tumor activity. We conducted cell viability assays including CellTiter-glo, MTT, and clonogenic assay. We treated a panel of G12V KRAS mutant and wild-type KRAS cell lines with SMKM inhibitor and found significantly reduced cell viability in G12V KRAS mutant cell lines across colorectal and lung cancer. To further demonstrate the downstream impact on mutant KRAS signaling, secondary assays including western blot and Lumit immunoassay were conducted. We observe a reduction in the aberrant phospho-ERK and phospho-AKT signaling in SMKM inhibitor treated cells. Our in vivo efficacy trial using heterozygous G12V KRAS lung cancer NCI-H441 xenograft model has shown SMKM inhibition significantly reduces tumor growth and increases the survival rate. Together, these data indicate the feasibility of selectively targeting G12V KRAS with SMKM inhibition. Lastly, our results provide a first-in-class small molecule oral inhibitor based selective protein clearance as an effective anti-G12V mutant KRAS therapeutic strategy. Citation Format: Xiyue Hu, Randy Singh, Shana Kelley. Phenotypic CRISPR genome-wide screening for the discovery of genetic regulators of allele-specific mutant KRAS [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr B014.

Abstract PR01: Structural plasticity of KRAS oncogenic mutants – A case of misleading conclusions from GTP analogues

Abstract RAS mutations occur in approximately 20% of human cancers including the majority of pancreatic ductal adenocarcinoma (PDAC), half of colorectal cancers, and a third of all lung cancers. In cases of oncogenic activating RAS mutations, GTP hydrolysis is impaired, and the protein is preferentially held in the active GTP-bound state. When activated, RAS triggers multiple proliferative signaling cascades, including the MAPK/ERK and PI3K pathways, to induce cell growth, division, and differentiation. In solution, RAS exists in two interconverting GTP-bound conformational states, State 1 (inactive) and State 2 (active). State 2 is the active conformation since it binds to RAS Binding Domain (RBD) of effector proteins. Though the State 1 conformation is GTP-bound, it is unable to bind effectors and represents an inactive KRAS conformation. This State 1/State 2 equilibrium is closely coupled to the conformations (γ1 and γ2) exhibited by the γ-phosphate of GTP and its analogues. Solution-state 31P NMR spectroscopy captures and quantifies the γ1 and γ2 peaks representing State 1 and State 2 (Spoerner M et al., JBC 2010). We have initiated solution-state NMR investigation to determine the structural differences between wild-type (WT) and oncogenic mutant KRAS proteins (G12C, G12D, G12V, Q61L, and G13D) when bound to GTP and GppNHp. We quantified the State 1/State 2 equilibrium using 31P NMR. Our results show that GppNHp-bound KRAS proteins harboring oncogenic mutations differentially modulate the State 1/State 2 conformational equilibria resulting in remarkable divergence in conformational populations compared to WT protein; a notion for presence of mutation induced structural plasticity. Much work on the structural biology, biophysics and biochemistry of KRAS proteins is done when bound to the non-hydrolysable GTP analogue, GppNHp. Strikingly, our 31P NMR results show that GTP-bound KRAS elicits significant variations in State 1 and State 2 populations in comparison to GppNHp-bound proteins. These data suggest GppNHp binding induces a significant increase in the State 1 population; an observation that does not translate into GTP-bound KRAS. Our results provide additional insights into the differential binding affinities seen between WT/mutant KRAS and effector proteins (e.g., Hunter JC et al., Mol Cancer Res 2015) as well as interpretation for State 1 conformations in KRAS crystal structures when bound to mostly GppNHp and not GTP. We have also applied this 31P NMR approach to the evaluation of KRAS small molecule inhibitors that shift the population equilibrium to the State 1 (inactive) conformation in the protein-ligand complex. This demonstrates an intriguing therapeutic opportunity and novel mechanism of action that we are further exploring as part of our drug discovery pipeline. Citation Format: Alok K. Sharma, Marcin Dyba, Dominic Esposito, Bin Wang, Pedro J. Beltran, Eli Wallace, Dwight Nissley, Frank McCormick, Anna E. Maciag. Structural plasticity of KRAS oncogenic mutants – A case of misleading conclusions from GTP analogues [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr PR01.

Abstract B036: Treatment modalities in KRAS-driven cancer

Abstract KRAS is the most common RAS isoform, found to be altered in 22% of RAS-mutated cancers. The mutant protein is found most prevalently in pancreatic cancer followed by colorectal, non-small cell lung cancer and other solid tumors. Due to its structural complexity, KRAS remained “undruggable” for several decades. Recently, the discovery of a specific protein binding pocket has led to the development of small molecule inhibitors that potently bind and inhibit KRAS downstream signalling. The accelerated FDA approval of sotorasib and adagrasib for treatment of NSCLC patients harbouring KRASG12C-mutation and further clinical evaluation of several other inhibitors of KRASG12C are under investigation, however emergence of resistance and limited efficacy beyond non-small cell lung cancer is a major concern. Targeting KRAS mutations other than KRASG12C (i.e., without a mutant-specific cysteine residue) with small molecules, has been considered much more challenging, especially for developing covalent inhibitors. Small molecule targeting of KRASG12D (e.g. MRTX1133), is under active preclinical investigation and small molecule drugs that target other KRAS-activating mutations (G12S, G12R and G12V) are being intensely explored. A variety of novel alternative approaches are also being investigated to target tumors driven by mutant KRAS, such as (i) targeting complementary signalling pathways (ii) enhancing mutant KRAS protein degradation using PROTACS, (iii) developing pan-KRAS small molecules inhibitors, (iv) anti-KRAS immune cell-based therapies, (v) small interfering RNAs to block mutant KRAS expression and (vi) anti-KRAS vaccines. Here, we aim to provide a comprehensive overview of current status and future prospect of these modalities, in the context of RAS-mutated cancers. Citation Format: Darren R. Tyson, Neetu Singh, Prashant K. Bhavar, Partha Pratim Sarma, Uday Kumar Surampudi, Sathish Katike. Treatment modalities in KRAS-driven cancer [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr B036.

Abstract 1481: MAPK and NF-kappaB signaling converge on the epigenome to transcriptionally activate genes involved in pancreatic cancer metastasis

Abstract Pancreatic ductal adenocarcinoma (PDAC) is the most prevalent and highly aggressive type of pancreatic neoplasm. Unfortunately, most patients will present with unresectable, locally advanced, or metastatic disease at the time of diagnosis. Current treatment methods (gemcitabine and nab-paclitaxel, FOLFIRINOX) are not sufficient for patients with late-stage disease and only modestly improve survival. Difficulties in treating PDAC lie in the characteristics of PDAC tumors. They are highly heterogeneous, have multiple signaling pathway alterations, and are highly metastatic with a dense tumor microenvironment (TME). Hence, PDAC remains one of the most lethal malignancies with a 5-year survival rate below 10%.The KRAS mutation is a hallmark of PDAC, occurring early in 95% of pancreatic neoplasms. The mutant KRAS protein constitutively activates the mitogen-activated protein kinase (MAPK) signaling pathway to sustain PDAC pathogenesis. Although the mutant KRAS gene is the initiating molecular alteration, chronic inflammation accelerates PDAC progression to a highly aggressive and therapy-resistant cancer. Our study shows that MAPK and the nuclear factor kappa-light-chain-enhancer of activated B (NF-κB) inflammatory signaling pathway synergize to promote PDAC progression. Live cell imaging analysis of PDAC cell lines after the simultaneous hyperactivation of MAPK and NF-κB signaling by epidermal growth factor (EGF) and tumor necrosis factor alpha respectively (TNF alpha), showed significant increases in cell migration. An integrated genome-wide epigenetic and transcriptomic analysis (ChIPseq and RNAseq) after the simultaneous stimulation of both pathways revealed significant increases in the occupancy of the active mark, H3K27ac. This was observed around transcription start sites of a subset of genes involved in cell polarity, migration, and subtype switch, processes known to be important for tumor aggressiveness. Epigenome mapping of the transcription factors FOSL1 and RELA, which are downstream targets of the MAPK and NF-κB signaling pathways respectively, show their co-occupancy in the H3K27ac-enriched regions. Furthermore, loss-of-function approaches show the synergistic effect of both MAPK and NF-κB hyperactivation on the migration capacity in vitro and in vivo. Based on these observations, we aim to delineate the molecular mechanism involved in the synergism, investigate the role of the TME, and decipher the signaling interactions between PDAC tumor cells and cells of the TME. This study is the first comprehensive analysis of the synergism between MAPK and NF-κB signaling and will provide novel insights into the development of mechanism-based therapeutic approaches. Citation Format: Joana E. Aggrey-Fynn, Feda H. Hamdan, Alexander Q. Wixom, Thomas L. Ekstrom, Steven A. Johnsen. MAPK and NF-kappaB signaling converge on the epigenome to transcriptionally activate genes involved in pancreatic cancer metastasis [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 1481.

Ras protein abundance correlates with Ras isoform mutation patterns in cancer

Activating mutations of Ras genes are often observed in cancer. The protein products of the three Ras genes are almost identical. However, for reasons that remain unclear, KRAS is far more frequently mutated than the other Ras isoforms in cancer and RASopathies. We have quantified HRAS, NRAS, KRAS4A and KRAS4B protein abundance across a large panel of cell lines and healthy tissues. We observe consistent patterns of KRAS > NRAS»HRAS protein expression in cells that correlate with the rank order of Ras mutation frequencies in cancer. Our data provide support for the model of a sweet-spot of Ras dosage mediating isoform-specific contributions to cancer and development. We suggest that in most cases, being the most abundant Ras isoform correlates with occupying the sweet-spot and that HRAS and NRAS expression is usually insufficient to promote oncogenesis when mutated. However, our results challenge the notion that rare codons mechanistically underpin the predominance of KRAS mutant cancers. Finally, direct measurement of mutant versus wildtype KRAS protein abundance revealed a frequent imbalance that may suggest additional non-gene duplication mechanisms for optimizing oncogenic Ras dosage.

Adagrasib: First Approval.

Adagrasib (KRAZATI™) is an orally available, potent, irreversible, small molecule inhibitor of KRAS G12C mutant isoform being developed by Mirati Therapeutics for the treatment of solid tumours harbouring KRAS G12C oncogenic driver mutation, including non-small cell lung cancer (NSCLC) and colorectal cancer (CRC). Adagrasib covalently binds to the mutant cysteine in KRAS G12C and locks the mutant KRAS protein in its inactive state, thereby preventing downstream signalling without affecting wild-type KRAS protein. In December 2022, adagrasib received its first approval in the USA for the treatment of adults with KRAS G12C-mutated locally advanced or metastatic NSCLC (as determined by an FDA approved test) who have received ≥1 prior systemic therapy. It was approved under accelerated approval based on objective response rate and duration of response, and its continued approval for this indication may be contingent upon verification and description of a clinical benefit in a confirmatory trial(s). The drug is under regulatory review for NSCLC in the European Union and is in development for CRC in the US. Clinical studies of adagrasib in solid tumours, including CRC, are underway in several countries. This article summarizes the milestones in the development of adagrasib leading to this first approval for KRAS G12C-mutated locally advanced or metastatic NSCLC.

Identification of potential inhibitor targeting KRAS mutation in Papillary Thyroid Carcinoma through molecular docking and dynamic simulation analysis

Thyroid cancer is a predominant form of endocrine malignancy, which destabilizes the metabolic rate of the body. The rapid increase in the incidence rate of thyroid cancer in recent years has aroused great concern to be investigated and diagnosed at an early stage. This study aimed to analyze the pathogenic mutations in thyroid cancer to identify their potential inhibitors for therapeutic targets. RAS genes are the most common oncogenes, which encode proteins that play an essential role in cell signaling and have been frequently mutated in different cancer types. The mutation in these genes causes abnormal cell growth and fails to respond to death signals. In this study, we identified the most significant mutations in the RAS genes; thus, the highly pathogenic mutations were curated from thyroid cancer patients and analyzed for their pathogenicity effect. The physicochemical analysis predicted mutation in wild-type KRAS protein had adapted negative charge on single base substitution of G12D that may easily cause loss of interactions and result in critical differences in the structure and function of the protein. Furthermore, the native KRAS protein was mutated and screened against a library of druggable compounds from the ZINC drug repository. The molecular docking analysis revealed that G12D mutant KRAS protein form best-docked complex with Naldemedine with the highest binding affinity. The dynamic simulation results further justified the stability of Naldemedine as a potential inhibitor with high efficiency in MMPBSA value of −45.4867 kcal/mol of being treated as a potential drug for papillary thyroid carcinoma. Further in vivo and in vitro validation of Naldemedine and its efficiency as a drug for the targeted pathogenic KRAS mutation is required.

Abstract B057: KRAS mutant-specific protein interactions reveal mechanisms in pancreatic cancer tumorigenesis and metabolic regulation

Abstract Pancreatic ductal adenocarcinoma (PDAC) is the third most deadly human cancer in the US with a five-year survival rate of 11%. KRAS is mutated in over 95% of PDAC patients and is a key driver of tumorigenesis. Despite the promise of targeted inhibition of the RAF-MEK-ERK MAPK signaling pathway, arguably the most critical KRAS-mediated signaling pathway, clinical trials targeting MEK/ERK signaling as a single-agent therapy have been unsuccessful, indicating the role of additional KRAS-specific signaling pathways. The most frequent KRAS mutations in PDAC are KRAS G12D (40%), KRAS G12V (33%) and KRAS G12R (17%). However, the KRAS G12R mutation is rare in lung and colorectal cancers (<1%), suggesting the presence of KRAS mutant-specific signaling, which remains poorly understood. While mutagenic processes may drive the observed mutation frequency data, many studies have demonstrated that mutant KRAS protein signaling drives the overall observed mutational frequencies. In agreement with this observation, the KRAS Q61L mutant is predicted to occur in PDAC but is rarely detected in the patient population. Therein, we hypothesize that mutation-specific signaling promotes tumorigenesis and that determination of the KRAS mutant-specific interactomes that promote pancreatic tumorigenesis in KRAS G12R yet hinder oncogenic fitness in KRAS Q61L will provide insight into the development of KRAS mutation-selective therapies in PDAC. Thus, we used doxycycline-inducible KRAS constructs combined with BioID proximity labeling to determine the mutant-selective interactomes of four KRAS mutant proteins in an isogenic immortalized pancreatic cell line. While we detected significant overlap in effector signaling, numerous mutant-selective differences were detected, including pathways regulating endocytosis and autophagy. Interestingly, the PDAC tumor microenvironment has been shown to have limited nutrient availability, which promotes macropinocytosis, the nonselective uptake of proteins and molecules from extracellular spaces, and autophagy, a mode of cellular recycling, to promote tumor proliferation. To replicate this environment in cell culture, we utilized a minimal glucose medium supplemented with albumin, a large protein that is absorbed via macropinocytosis. We show that this altered cell culture medium preferentially drives increased macropinocytosis and resistance to MEK MAPK and autophagy inhibition in KRAS G12R-mutant PDAC. Furthermore, while KRAS G12R PDAC cell lines continue to proliferate in the absence of glucose, many KRAS G12D mutant PDAC cell lines fail to sustain proliferation. To determine alternative potential therapeutic vulnerabilities, we have performed an RNA sequencing screen in high and low glucose medium, which has exposed an increase in receptor tyrosine kinase signaling and a reprogramming of metabolic processes in the tricarboxylic acid cycle. These studies provide a rationale for the limited success of MEK/ERK therapies in the clinic and we propose novel treatment strategies for KRAS G12R PDAC patients with elevated macropinocytosis. Citation Format: Guy Aaron Hobbs, Rachel Burge, Amanda Linke, Kamala Sundararaj, John P. O'Bryan. KRAS mutant-specific protein interactions reveal mechanisms in pancreatic cancer tumorigenesis and metabolic regulation [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B057.

Abstract 1887: Discrimination of aggressive tumor profiles in lung adenocarcinomas using activity based protein profiling by SWATH/DIA-MS mode

Abstract (a) Activity-based proteome profiling (ABPP) probes combined with mass spectrometry (MS) is the tool of functional proteomics for the quantification of catalytically active enzymes. Here, we applied a depletion-dependent ABPP for serine hydrolase (SH) profiling in 30-μm thickness cryosections of optimal-cutting-temperature (OCT)-embedded tissue of advanced lung adenocarcinomas (LUAD). (b) For the proof-of-concept, we profiled SH activities in advanced LUAD disease. We retrospectively analyzed hydrolase activity differences with prognostic values related to aggressive phenotype based on clinical data collected over the course of disease progression. Interestingly, detection of proteins correlating by active-enzyme capture uncover their functional links with the metabolic SHs related to the enhanced palmitoylation-depalmitoylation cycle of lipoproteins in aggressive LUAD. In contrast, the standard DDA-MS analysis of on-bead-depleted enzymes detected 95 SH’s of which less than 60 enzymes were quantified based on spectral counting. (c) We found enhanced activities of dozen SHs in all LUAD tumors. Remarkably, the activity of 11 hydrolases emphasized by IAH1, ABHD12, LYPLA2 and MST1 discriminate aggressive tumors at the time of diagnosis. Functional analysis leveraging enzymes and associated co-depleted proteins revealed catabolic processing of lipoproteins and enrichment of enzymes displaying increased de-palmitoylase activities. This is interesting because multiple isoforms of RAS protein (K-RAS, H-RAS and N-RAS), the most frequently mutated oncogene in human cancers including LUAD (i.e. 30% of LUADs contain somatic K-Ras mutation), attain oncogenic properties only in depalmitoylated state which favor protein intracellular trafficking by detachment from hydrophobic plasma membrane. In line, mutant K-Ras protein co-localize on outer mitochondrion membrane and interact with glycolytic enzymes (hexokinase-1 and -2) only in depalmitoylated state. This interaction induce K-Ras oncogenic properties and increased glucose uptake and glycolysis even in the presence of abundant oxygen (Warburg effect). Curiously, we observed co-depletion of mitochondrial proteins including glycolytic hexokinase 2 with several lipases displaying increase depalmitoylase activity in short LUAD survivals. (d) Surprisingly, an evident disagreement in the activity of enzymes involved in lipolysis and protein depalmitoylation (i.e. IAH1, ABHD12, LYPLA2) was discovered between LUAD survival subtypes. These essential metabolic differences were uncovered by our standard proteomic analysis and to our knowledge have not been reported. Since the inhibitors of serine lipases are promising targets in other RAS-mutant carcinomas, this metabolic vulnerabilities discovered in aggressive LUAD can be explored as promising therapeutic strategies in lung cancer. Citation Format: Tatjana Sajic, Stephan Arni, Rudolf Aebersold, Sven Hillinger. Discrimination of aggressive tumor profiles in lung adenocarcinomas using activity based protein profiling by SWATH/DIA-MS mode [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1887.

Activating KRAS and GNAS mutations in heterotopic submucosal glands of the stomach.

The heterotopic submucosal gland (HSG) is a common incidental finding in gastrectomy specimens. The majority of HSGs are small incidental lesions, which are also known as gastritis cystica profunda. However, larger lesions may appear as an inverted growth of well-organized mucosa referred to as gastric inverted polyps. To determine whether genetic alterations are involved in HSG development, we analyzed 63 gastric HSG lesions using targeted next-generation sequencing and immunohistochemistry. Histologically, HSG lesions consistently had areas of pyloric gland differentiation with variable extent of foveolar differentiation. Although the background mucosa showed intestinal metaplasia in most cases (98%), intestinal-type epithelium was seen in only one HSG lesion (2%). Sequencing analysis identified activating KRAS, BRAF, CTNNB1, and GNAS mutations in 34 (54%), 1 (2%), 1 (2%), and 7 (11%) lesions, respectively. HSG lesions harboring a KRAS mutation were more likely to present extensive foveolar differentiation (P = 0.013) and absence of parietal cells (P = 0.0081). Five HSG lesions had a dysplastic component, and concordant genetic alterations were detected between the non-dysplastic and dysplastic areas of two lesions that were successfully analyzed. Immunohistochemical staining demonstrated diffuse expression of mutant KRAS protein in lesions with the most common genetic alteration, KRAS G12D. Our study demonstrated that a major proportion of HSGs were proliferative lesions associated with oncogenic mutations, with more than half of lesions harboring activating KRAS mutations.

Identification of MRTX1133, a Noncovalent, Potent, and Selective KRASG12D Inhibitor.

KRASG12D, the most common oncogenic KRAS mutation, is a promising target for the treatment of solid tumors. However, when compared to KRASG12C, selective inhibition of KRASG12D presents a significant challenge due to the requirement of inhibitors to bind KRASG12D with high enough affinity to obviate the need for covalent interactions with the mutant KRAS protein. Here, we report the discovery and characterization of the first noncovalent, potent, and selective KRASG12D inhibitor, MRTX1133, which was discovered through an extensive structure-based activity improvement and shown to be efficacious in a KRASG12D mutant xenograft mouse tumor model.

In silico comparative analysis of KRAS mutations at codons 12 and 13: Structural modifications of P-Loop, switch I&II regions preventing GTP hydrolysis

KRAS mutation is prevalent in around 30% of all cancers and is an undruggable molecular target. Of seven mutations at codon 12 and 13, only one, the G12C mutant is finally proven to be druggable, as evidenced by the recent USFDA approval of sotorasib. Investigation of other small molecules targeting G12C and G12D are undergoing clinical trials. Understanding the fine structural details is a prerequisite to design specific inhibitors which also requires in depth molecular exploration. We used bioinformatics as a tool to analyze the KRAS protein's GTP (guanosine triphosphate) binding dynamics when mutated. KRAS undergoes significant conformational changes, affecting GTP binding conformation within the active site pocket of KRAS due to high torsional strains, hydrophobicity, and altered Switch I and II regions. GTP molecule for wildtype had a low torsional strain of 10.71, and is the only molecule, in comparison to KRAS mutant bound GTP, to have a glycine at position 10 interacting with its nitrogenous base. All mutant KRAS proteins lacked the interaction of glycine with the nitrogenous base. The binding affinity of wildtype (WT) KRAS for the gamma-phosphate was lower in scoring compared to the mutated KRAS protein in multiple analyses. This study provides an insight to the GTP-KRAS protein binding details that are important to define parameters required to be explored to design the appropriate inhibitor for each different type of mutant KRAS protein.