bluuebunny/crossref_metadata_2025 huggingface dataset:
Figure S6 from The Elongin BC Complex Negatively Regulates AXL and Marks a Differentiated Phenotype in Melanoma
Authors: Schieven Sebastiaan M. , Traets Joleen J.H. , Vliet Alex v. , Baalen Martijn v. , Song Ji-Ying , Guimaraes Marcos Da Silva , Kuilman Thomas , Peeper Daniel S.
Published: May 2023

Extended data on Figure 6: Low expression of ELOB/C is associated with dedifferentiation in human melanomas.
Figure S4 from The Elongin BC Complex Negatively Regulates AXL and Marks a Differentiated Phenotype in Melanoma
Authors: Schieven Sebastiaan M. , Traets Joleen J.H. , Vliet Alex v. , Baalen Martijn v. , Song Ji-Ying , Guimaraes Marcos Da Silva , Kuilman Thomas , Peeper Daniel S.
Published: May 2023

Extended data on Figure 4: Elongin B/C interact with AXL and loss of Elongin B/C stabilizes AXL protein levels.
Figure S1 from The Elongin BC Complex Negatively Regulates AXL and Marks a Differentiated Phenotype in Melanoma
Authors: Schieven Sebastiaan M. , Traets Joleen J.H. , Vliet Alex v. , Baalen Martijn v. , Song Ji-Ying , Guimaraes Marcos Da Silva , Kuilman Thomas , Peeper Daniel S.
Published: May 2023

Extended data on Figure 1: Whole genome-wide CRISPR-Cas9 screenidentifies several negative regulators of AXL.
Data from Activation of the JAK/STAT Pathway Leads to BRAF Inhibitor Resistance in BRAFV600E Positive Thyroid Carcinoma
Authors: Limberg Jessica , Egan Caitlin E. , Gray Katherine D. , Singh Mandeep , Loewenstein Zachary , Yang Yanping , Riascos Maria Cristina , Al Asadi Hala , Safe Parima , El Eshaky Steve , Liang Heng , Ullmann Timothy M. , Wang Weibin , Li Wei , Zhang Tuo , Xiang Jenny , Stefanova Dessislava , Jin Moonsoo M. , Zarnegar Rasa , Fahey Thomas J. , Min Irene M.
Published: May 2023

Abstract
A subset of thyroid cancers, recurrent differentiated thyroid cancers and anaplastic thyroid cancer (ATC), are difficult to treat by thyroidectomy and systemic therapy. A common mutation in thyroid cancer, BRAFV600E, has targetable treatment options; however, the results have been disappointing in thyroid cancers compared with BRAFV600E melanoma, as thyroid cancers quickly become resistant to BRAFV600E inhibitor (BRAFi). Here, we studied the molecular pathway that is induced in BRAFV600E thyroid cancer cells and patient-derived tumor samples in response to BRAFi, vemurafenib, using RNA-sequencing and molecular analysis. Both inducible response to BRAFi and acquired BRAFi resistance in BRAFV600E thyroid cancer cells showed significant activation of the JAK/STAT pathway. Functional analyses revealed that the combination of BRAFi and inhibitors of JAK/STAT pathway controlled BRAFV600E thyroid cancer cell growth. The Cancer Genome Atlas data analysis demonstrated that potent activation of the JAK/STAT signaling was associated with shorter recurrence rate in patients with differentiated thyroid cancer. Analysis of tumor RNA expression in patients with poorly differentiated thyroid cancer and ATC also support that enhanced activity of JAK/STAT signaling pathway is correlated with worse prognosis. Our study demonstrates that JAK/STAT pathway is activated as BRAFV600E thyroid cancer cells develop resistance to BRAFi and that this pathway is a potential target for anticancer activity and to overcome drug resistance that commonly develops to treatment with BRAFi in thyroid cancer.
Implications:
Dual inhibition of BRAF and JAK/STAT signaling pathway is a potential therapeutic treatment for anticancer activity and to overcome drug resistance to BRAFi in thyroid cancer.
Data from MYC/Glutamine Dependency Is a Therapeutic Vulnerability in Pancreatic Cancer with Deoxycytidine Kinase Inactivation-Induced Gemcitabine Resistance
Authors: Dash Suman , Ueda Takeshi , Komuro Akiyoshi , Amano Hisayuki , Honda Masahiko , Kawazu Masahito , Okada Hitoshi
Published: May 2023

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most life-threatening malignancies. Although the deoxycytidine analog gemcitabine has been used as the first-line treatment for PDAC, the primary clinical challenge arises because of an eventual acquisition of resistance. Therefore, it is crucial to elucidate the mechanisms underlying gemcitabine resistance to improve treatment efficacy. To investigate potential genes whose inactivation confers gemcitabine resistance, we performed CRISPR knockout (KO) library screening. We found that deoxycytidine kinase (DCK) deficiency is the primary mechanism of gemcitabine resistance, and the inactivation of CRYBA2, DMBX1, CROT, and CD36 slightly conferred gemcitabine resistance. In particular, gene expression analysis revealed that DCK KO cells displayed a significant enrichment of genes associated with MYC targets, folate/one-carbon metabolism and glutamine metabolism pathways. Evidently, chemically targeting each of these pathways significantly reduced the survival of DCK KO cells. Moreover, the pathways enriched in DCK KO cells represented a trend similar to those in PDAC cell lines and samples of patients with PDAC with low DCK expression. We further observed that short-term treatment of parental CFPAC-1 cells with gemcitabine induces the expression of several genes, which promote synthesis and transport of glutamine in a dose-dependent manner, which suggests glutamine availability as a potential mechanism of escaping drug toxicity in an initial response for survival. Thus, our findings provide insights into novel therapeutic approaches for gemcitabine-resistant PDAC and emphasize the involvement of glutamine metabolism in drug-tolerant persister cells.
Implications:
Our study revealed the key pathways involved in gemcitabine resistance in PDAC, thus providing potential therapeutic strategies.
Abstract A017: Deciphering the role of integrated stress response (ISR) in the developmental stages of mutant KRAS lung cancer
Authors: Diao Shiqi , Ghaddar Nour , Zou Jia Yi , Wang Shuo , Koromilas Antonis E.
Published: May 2023

Lung cancer is the leading cause of cancer death worldwide. Non-small cell lung cancer (NSCLC) constitutes 80% of all lung malignancies with 15-25% attributed to mutations in the KRAS gene. KRAS mutations expose cells to stress-inducing conditions, e.g., genotoxic, proteotoxic and metabolic stress, which disrupt normal proliferation and tissue homeostasis. Successful proliferation of tumors is dependent on stress-adaptive pathways, which promote growth and contribute to resistance to chemotherapeutic drugs. Thus, inhibition of the adaptation process is considered a suitable anti-tumor approach for the treatment of KRAS cancers including lung cancer. An important mechanism of adaptation to stress involves the phosphorylation of the translation initiation factor eIF2α at serine 52 (p-eIF2α). Increased p-eIF2α is the nodal point of the integrated stress response (ISR), a master regulator of translational and transcriptional reprogramming that determines survival and adaptation to stress. We demonstrated the tumorigenic function of p-eIF2α in a mouse model of mutant KRAS cancer (Nature Communications 2021). We delineate the role of the ISR in lineage diversity and tumor heterogeneity during KRAS LUAD progression by single-cell RNA sequencing (sc-RNA seq). As such, the ISR was found to drive high stemness and epithelial to mesenchymal transition (EMT) programs in KRAS LUAD cells. The ISR also employs a high-plasticity cell-state mechanism for successful lung tumor progression and evolution. The involvement of the ISR in the mentioned processes further emphasizes its role as master regulator of pro-tumorigenic pathways and highlights the therapeutic potential of ISR inhibitors as novel targets in KRAS lung cancer. Our recent findings demonstrate that increased p-eIF2α stimulates the activity of the gene trans-activator proteins YAP and TAZ in mutant KRAS lung tumors. Genetic approaches identify a stimulatory effect of p-eIF2 on the expression of YAP/TAZ-dependent genes with roles in proliferation and epithelial to mesenchymal transition (EMT) including genes of WNT signaling pathway. We provide strong evidence that stimulation of YAP/TAZ activity by p-eIF2α occurs, at least partially, through the upregulation of the transcription factor ATF4 in tumor cells. Our findings demonstrate that p-eIF2α is a focal point of different tumorigenic pathways, intimately implicated in mutant KRAS-mediated transformation and tumor resistance to mutant KRAS inactivation.

Citation Format: Shiqi Diao, Nour Ghaddar, Jia Yi Zou, Shuo Wang, Antonis E. Koromilas. Deciphering the role of integrated stress response (ISR) in the developmental stages of mutant KRAS lung 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 A017.
Abstract A027: Defining the role of PER1 and circadian rhythm dysregulation in KRAS/LKB1-mutant lung adenocarcinoma
Authors: Parker Rebecca E. , Koo Junghui , Dwivedi Bhakti , Marcus Adam I. , Gilbert-Ross Melissa
Published: May 2023

KRAS and LKB1 are frequently co-mutated in lung adenocarcinoma and characterize a particularly aggressive, metastatic, and treatment-resistant subtype of this disease. We recently published that the outputs of biological rhythm pathways downstream of the AMPK kinase are altered in KRAS/LKB1-mutant tumors. In a live-cell phenotyping screen we used RNAseq to identify the circadian clock genes PER1 and PER2 as uniquely upregulated in partially transformed and invasive KRAS/LKB1-mutant human bronchial epithelial cells. We have analyzed expression of individual circadian clock genes in KRAS-mutant and KRAS/LKB1-mutant patient tumors and found that expression of the PER genes, particularly PER1, is increased in the KRAS/LKB1 subtype of lung adenocarcinoma. At the protein level, PER1 expression is increased in KRAS/LKB1-mutant HBECs as compared to KRAS-mutant cells. Addback of wild-type LKB1 in A549 cells, which are KRAS/LKB1-mutant, results in a decrease in PER1 protein levels, confirming that LKB1 has a role in controlling PER1 levels. Multiple phosphorylation events lead to PER1 nuclear translocation to control its role as a transcriptional repressor in the core clock. In circadian-synced HBECs, PER1 enters the nucleus in KRAS-mutant cells, but remains cytosolic in KRAS/LKB1-mutant cells. In circadian-synced A549 cells, we also observed a lack of nuclear PER1 localization. Addback of wild-type LKB1 restored nuclear localization of PER1, as did expression of kinase-dead LKB1, suggesting that LKB1’s regulation of PER1 localization is kinase-independent. Our current and future experiments aim to determine how clock-controlled gene expression may be altered in KRAS/LKB1-mutant cells, what the functional impact of altered PER1 expression and localization is on growth of KRAS/LKB1-mutant tumors, and whether pharmacological manipulation of LKB1-related signaling pathways can restore nuclear localization of PER1.

Citation Format: Rebecca E. Parker, Junghui Koo, Bhakti Dwivedi, Adam I. Marcus, Melissa Gilbert-Ross. Defining the role of PER1 and circadian rhythm dysregulation in KRAS/LKB1-mutant lung adenocarcinoma [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 A027.
Abstract A040: The SRG OncoRat supports growth of numerous RAS mutant cell lines, expanding pre-clinical RAS-inhibitor testing
Authors: Walton R. Grace , Begemann Diane , Dunn Cynthia , Steffey Valeria , Ross Abigail , Haque Razoanul , Noto Fallon K.
Published: May 2023

RAS family proteins are important drug targets in multiple cancers due to their central role in hypertrophic and pro-mitotic signaling. KRAS is a small GTPase that is activated in response to growth factors including HGF, TGFα, and EGF. KRAS then activates the MAP kinase (MAPK; RAF/MEK/ERK) signaling pathway, driving ERK translocation to the nucleus, and resulting in transcription of pro-mitotic and pro-growth genes. Additionally, KRAS contributes to PI3K/AKT/mTOR signaling, leading to transcriptional activation as well as hypertrophic protein synthesis via mTOR. We sought to validate several RAS mutant cell-derived tumor xenograft models in the SRG OncoRat. Cells were inoculated subcutaneously in the flank of SRG rats. To date, we have validated tumor growth using the HT-1080 fibrosarcoma NRAS mutant (Gln61Lys (c.181C>A)) cell line. We have also validated a suite of KRAS mutant lines in the SRG OncoRat, including: A-549 lung adenocarcinoma (Gly12Ser (c.34G>A)); NCI-H2122 NSCLC adenocarcinoma (Gly12Cys (c.34G>T)); MIA PaCa-2 pancreatic ductal adenocarcinoma and H-358 NSCLC adenocarcinoma (Gly12Cys (c.34G>T)); Capan-2 pancreatic ductal adenocarcinoma (Gly12Val (c.35G>T)); NCI-H441 NSCLC papillary adenocarcinoma (Gly12Val (c.35G>T)); NCI-H1734 NSCLC adenocarcinoma (Gly13Cys (c.37G>T)); and MDA-MB-231 breast adenocarcinoma (Gly13Asp (c.38G>A)). All cell lines showed robust and consistent tumor growth when injected subcutaneously into the SRG OncoRat. These models provide valuable tools for pre-clinical testing of RAS inhibition.

Citation Format: R. Grace Walton, Diane Begemann, Cynthia Dunn, Valeria Steffey, Abigail Ross, Razoanul Haque, Fallon K. Noto. The SRG OncoRat supports growth of numerous RAS mutant cell lines, expanding pre-clinical RAS-inhibitor testing [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 A040.
Abstract B020: Creating actionable neoantigens by design with KRAS(G12C) covalent inhibitors
Authors: Maso Lorenzo , Hattori Takamitsu , Araki Kiyomi , Koide Akiko , Rajak Epsa , Hayman James , Akkapeddi Padma , Bang Injin , Neel Benjamin G. , Koide Shohei
Published: May 2023

Covalent inhibitors against KRAS(G12C) represent major breakthroughs in the effort to directly and selectively target oncogenic RAS mutants. However, similar to other targeted therapies, they lack durability. Immune therapy can be curative, and fragments of RAS containing a G12 mutation can be presented by the major histocompatibility complex (MHC) and thus could serve neoantigens. However, it is challenging to achieve selective targeting with minimal differences for RAS G12 mutations in the context of the large MHC molecule. To overcome these challenges and unify targeted and immune therapies, we have established a platform technology that exploits the large changes produced by the conjugation of a covalent inhibitor to create distinct neoantigens that selectively mark cancer cells. We performed proof-of-concept experiments using the FDA-approved covalent inhibitors sotorasib and osimertinib, and we developed “HapImmune” antibodies that bind to drug-peptide conjugate/MHC complexes but not to the free drugs. HapImmune-based bispecific T cell engager selectively and potently kills sotorasib-resistant lung cancer cells upon sotorasib treatment. Notably, it is effective against KRAS(G12C) mutant cells with different HLA supertypes, HLA-A*02, A*03 and A*11, suggesting loosening of MHC restriction. We have determined the structures of several HapImmune antibodies bound to drug-peptide conjugate/MHC complexes using cryo-electron microscopy, which revealed the molecular basis of their antigen recognition and will guide further improvement of their potency and specificity. Furthermore, we have developed additional antibodies to other KRAS(G12C) drugs and other targets, demonstrating the expansive scope of HapImmune approach that can potentially utilize the vast possible combinations of covalent inhibitors and oncoproteins.

Citation Format: Lorenzo Maso, Takamitsu Hattori, Kiyomi Araki, Akiko Koide, Epsa Rajak, James Hayman, Padma Akkapeddi, Injin Bang, Benjamin G. Neel, Shohei Koide. Creating actionable neoantigens by design with KRAS(G12C) covalent inhibitors [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 B020.
Abstract B033: Wild-type RAS signaling is an essential therapeutic target in RAS-mutated cancers
Authors: Sealover Nancy , Finniff Bridget , Kortum Robert
Published: May 2023

Single-agent targeting of RAS-mutated cancers using RAF/MEK/ERK or PI3K/AKT pathway inhibitors is ineffective; blocking one pathway relieves negative feedback control of RTK signaling and hyperactivates parallel effector pathways. While combined MEK and PI3K inhibition is effective in preclinical models, toxicity of this combination prevents its clinical use. Alternative strategies for treating RAS-mutated cancers are essential. Therapeutics directly targeting mutated RAS proteins have the potential to spare normal cellular function thereby lessening overall toxicity. Unfortunately, direct RAS inhibition as a monotherapy does not fully block RAS effector signaling. RAS proteins show differential activation of RAF and PI3K pathways: KRAS potently activates RAF but poorly activates PI3K, whereas HRAS effectively activates PI3K but poorly activates RAF. Further, mutant RAS inhibition relieves negative feedback controls leading to rapid hyperactivation of RTK−WT RAS signaling. A more comprehensive understanding of the interplay between mutant RAS and RTK−WT RAS signaling is essential to developing rational therapeutic approaches to treat RAS-mutated cancers. We found that WT RAS enhanced mutant RAS-driven transformation by activating RAS effectors poorly engaged by mutated RAS. Further, inhibition of RAS effectors activated poorly by mutant RAS synergized with and limited resistance to mutant HRAS and KRAS inhibitors. The mutant HRAS inhibitor tipifarnib blocked PI3K signaling and synergized with MEK inhibitors in HRAS-mutated cancer cell lines; covalent KRASG12C inhibitors blocked MEK signaling and synergized with PI3K inhibitors in KRASG12C-mutated cell lines. Synergy between inhibitors of mutant RAS and RAS effectors was dependent on intact RTK/WT RAS signaling and was lost in both RASless or SOSless MEFs. These results should inform the design of clinical trials for patients with RAS-mutated cancers.

Citation Format: Nancy Sealover, Bridget Finniff, Robert Kortum. Wild-type RAS signaling is an essential therapeutic target in RAS-mutated cancers [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 B033.
Abstract B036: Treatment modalities in KRAS-driven cancer
Authors: Tyson Darren R. , Singh Neetu , Bhavar Prashant K. , Sarma Partha Pratim , Surampudi Uday Kumar , Katike Sathish
Published: May 2023

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 B038: Preclinical efficacy of KRASG12C inhibitors in models of pediatric cancer
Authors: Price Hannah , Stauffer Stacey , Powell Katie , Baker Andrew , Perciaccante Andrew , Hernandez Edjay Ralph , Odeniyide Patience , Pratilas Christine , Burgan William , Jenkins Lisa , Rossman Kent L. , Yohe Marielle
Published: May 2023

Directly targeting RAS is a desirable approach for treating RAS-mutated tumors because direct RAS inhibitors block all RAS effector pathways simultaneously. Recently, several groups have developed agents that directly target KRAS by covalently modifying KRASG12C. KRAS is commonly altered in adult malignancies such as lung, pancreatic, and colorectal adenocarcinoma, but is less commonly altered in pediatric cancer. However, rare pediatric tumors harboring K-, H-, or NRASG12C are observed. The efficacy of KRASG12C inhibitors in pediatric malignancies is currently unknown, and the ability of these drugs to modify H- and NRASG12C has been incompletely characterized. Here we show that the KRASG12C inhibitors AMG 510, MRTX849, and ARS-1620 slow the release of GDP from H-, N-, and KRASG12C in vitro. Using RASless MEFs, we show that the activity of AMG 510 is specific for H-, N- or KRASG12C, while MRTX849 has both G12C and RAS-independent effects on cell viability. The KRASG12C inhibitors decreased cell viability in KRAS-mutant cell lines derived from patients with the pediatric solid tumor neuroblastoma. MRTX849 was more potent than AMG 510 in neuroblastoma cell lines but was less efficacious and less G12C-specific. The KRASG12C inhibitors also decreased cell viability in an NRASG12C-mutant T-cell ALL cell line derived from an adolescent patient but only MTRX849 decreased cell viability in an HRASG12C-mutant rhabdomyosarcoma cell line. These results suggest that KRASG12C inhibitors may be a treatment option for pediatric patients with H-, N- or KRASG12C mutant solid tumors or leukemia. Future studies will be aimed at testing the efficacy of these inhibitors in xenograft models of pediatric cancer and identifying non-RAS targets of MRTX849.

Citation Format: Hannah Price, Stacey Stauffer, Katie Powell, Andrew Baker, Andrew Perciaccante, Edjay Ralph Hernandez, Patience Odeniyide, Christine Pratilas, William Burgan, Lisa Jenkins, Kent L. Rossman, Marielle Yohe. Preclinical efficacy of KRASG12C inhibitors in models of pediatric 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 B038.
Abstract B040: Designed sensors reveal normal and oncogenic Ras signaling in endomembranes and condensates
Authors: Zhang Jason Z. , Nguyen William H. , Rose John C. , Ong Shao-En , Maly Dustin J. , Baker David
Published: May 2023

While Ras is known to dynamically shuttle around the cell, the activity, mechanism of activation, and function of non-plasma membrane-localized Ras is unclear due to lack of suitable tools. To address these questions, we used the Latching Orthogonal Cage-Key pRotein (LOCKR) switch platform to generate first-in-class intracellular sensors for endogenous Ras activity (Ras-LOCKR-S) and signaling-dependent proximity labelers (Ras-LOCKR-PL). We find that: 1) Receptor activation leads to endogenous Ras signaling at endomembranes, which is enhanced by golgi-localized guanine exchange factors. 2) Recruitment of SAM68 and MARCKS to oncogenic condensates fuels local Ras signaling and cell growth. 3) Major Vault Protein drives RasG12C inhibitor resistance by enhancing signaling at the golgi and altering mitochondrial metabolism. Together, these results highlight the importance of non-plasma membrane Ras signaling (endomembranes and condensates), and our new sensors should accelerate the discovery of new therapeutic targets.

Citation Format: Jason Z. Zhang, William H. Nguyen, John C. Rose, Shao-En Ong, Dustin J. Maly, David Baker. Designed sensors reveal normal and oncogenic Ras signaling in endomembranes and condensates [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 B040.
Abstract IA09: Allelic specificity: The key to NRAS-mutant melanoma initiation?
Authors: Burd Christin E.
Published: May 2023

The reason why different NRAS mutants are enriched in each tumor type is unclear. We made a suite of conditional, Nras knock-in models (LSL-Q61R, -K, -L, -H, -P, -Q; G12D and G13D, -R) to test whether melanocyte transformation is dependent upon functions specific to the NRAS mutants found in human melanoma (Q61R and K). Spontaneous melanomas were rare in mice expressing Nras mutants infrequently observed in human melanoma (G12D, G13D, G13R, Q61H, or Q61P). However, melanocyte-specific Nras Q61R or Q61K expression induced rapid melanoma onset with high penetrance. Cohorts of mice carrying one LSL-Nras Q61R and one LSL-Nras Q61K, -L, -H, -P, or -Q allele were used to evaluate potential interactions between Nras mutants. These combinations initiated tumors with kinetics intermediate to those of mice homozygous for either allele (Nras Q61R or 61X) except in the case of Nras Q61Q/Q61R mice, which rarely developed tumors. Genomic and in vitro analyses revealed that the melanoma-initiating potential of each NRAS mutant directly correlated with enhanced MAPK signaling. Together, these data establish that functions specific to the most common NRAS mutants in human melanoma are needed to initiate the disease.

Citation Format: Christin E. Burd. Allelic specificity: The key to NRAS-mutant melanoma initiation? [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 IA09.
Abstract IA20: The impact of RAS inhibition on tumor immune evasion
Authors: Downward Julian
Published: May 2023

The approval of two KRAS G12C mutant-specific inhibitory drugs, sotorasib and adagrasib, has markedly improved the treatment of lung cancer patients harbouring KRAS G12C oncogenic mutations. However, development of acquired drug resistance is very common after initial responses, and impact on overall survival is small. Additional therapies will therefore need to be combined with KRASG12C inhibitors if long-term cures are to be achieved. Due to the immunosuppressive nature of the signaling network controlled by oncogenic KRAS, targeted KRAS G12C inhibition can indirectly affect anti-tumour immunity. This has served as a rationale for combination with immune checkpoint blockade (ICB), which we have shown leads to additional therapeutic benefit in immunogenic/hot, but not immune evasive/cold, pre-clinical lung tumour models. However, in clinical trials in KRAS G12C mutant lung cancer, combination of KRAS G12C inhibitors with PD-(L)1 blockade has yet to show improved outcome, either due to toxicities or lack of efficacy, possibly linked to prior progression on immunotherapy. Study of the response of KRAS G12C mutant lung tumours to KRAS G12C inhibitory drugs using spatial and multi-omic technologies has highlighted the role of particular populations of immune cells in the tumor microenvironment in impeding immune attack on the tumor. In immune evasive lung cancer, following KRAS G12C inhibitor treatment a community of cells is identified within the tumor containing dendritic cells, CD8+ T cells and dying tumor cells, which appears to function as an antigen presentation hub. This community is restrained by T reg cells, whose coordinate targeting markedly improves the impact of KRAS G12C inhibitors. In an immunogenic/hot mouse model of KRAS G12C mutant lung cancer, tertiary lymphoid structures are seen along with tumor-binding antibodies, which target endogenous retrovirus (ERV) envelope glycoproteins on the tumor cells. ERV-targeting B cell responses are amplified by ICB in both humans and mice, and by targeted KRAS G12C inhibition in the murine model. ERV-reactive antibodies exert anti-tumour activity that extend survival in the murine model and ERV expression predicts the outcome of ICB in human lung adenocarcinoma. Rational, mechanism-based exploitation of the impact of KRAS inhibition on tumor immune evasion provides opportunities for successful combination therapy of RAS mutant cancers.

Citation Format: Julian Downward. The impact of RAS inhibition on tumor immune evasion [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 IA20.
Abstract IA25: Systematic interrogation of KRAS function
Authors: Hahn William C.
Published: May 2023

Oncogenic mutations of KRAS occur frequently in pancreas, lung and colon cancers. Recent efforts to target particular KRAS alleles or RAS effector pathways has led to clinical responses but resistance to therapy limits the effectiveness of these therapies. To understand the role of KRAS in tumor initiation and maintenance, we have used systematic approaches to understand dependencies in KRAS-driven cancers. Specifically, we have used genome scale gain and loss of function screens to interrogate pathways necessary for the survival of KRAS-driven cancers. We have identified genes that required for the survival of KRAS-driven cancers and that canonical RAS signaling proteins have multiple functions. Together these on-going approaches provide new insights into KRAS signaling and identify potential targets for combination therapies for KRAS driven cancers.

Citation Format: William C. Hahn. Systematic interrogation of KRAS function [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 IA25.
Abstract PR07: Oncogenic Kras signaling shapes the tumor microenvironment in lung adenocarcinoma
Authors: Baliira Rachael K. , Opsahl Emily Lasse , McLintock Elyse , Donahue Katelyn L. , Barravacchia Ivana , Magliano Marina Pasca di , Galbán Stefanie
Published: May 2023

Despite advancements in targeted therapy and immunotherapy, lung cancer remains the leading cause of cancer-related deaths in both men and women worldwide, with an estimated 2.2 million deaths each year. At 85%, non-small cell lung cancer (NSCLC) is by far the most common subtype, comprising adenocarcinomas and lung squamous cell carcinoma. Mutations in Kirsten rat sarcoma viral oncogene homolog (KRAS), epidermal growth factor receptor (EGFR) and anaplastic lymphoma receptor tyrosine kinase (ALK) genes are common, with the worst overall survival in KRAS mutant adenocarcinoma patients. About 40% of lung tumors with KRAS mutations also harbor mutations in tumor protein p53 gene (TP53), a tumor suppressor gene. KrasG12C and KrasG12D are both prevalent mutations in lung cancer. Sotorasib, a KrasG12C inhibitor, was recently approved for treatment of NSCLC. However, only 37% of patients have an objective response to Sotorasib, with a median duration of just 11 months. The KrasG12D inhibitor MRTX1133 is entering clinical trials; elucidating the mechanism of action for potential resistance is imperative to design combination treatment approaches. While cell-intrinsic mechanisms of resistance in epithelial oncogenic KRASG12D (Kras*) are well studied, our group and others have shown that KRASG12D also extrinsically regulates the tumor microenvironment (TME) in pancreatic cancer. Whether and how this oncogene regulates the TME of lung cancer is less understood. To study the crosstalk between epithelial lung cells expressing oncogenic KRAS and the surrounding TME, we have established a triple transgenic murine model of Kras*-driven NSCLC, wherein both lung epithelial-specific expression of Kras* and expression of mutant TP53R172H (Tp53*) can be controlled in an inducible and reversible manner. Our preliminary data show that expression of Kras* drives tumor growth, while Kras* depletion results in regression, even in the presence of Tp53*. Here we interrogate how Kras* modulates the TME in lung adenocarcinomas. Harnessing scRNA sequencing, immunohistochemistry, and multiple biochemical approaches, we will provide insight into changes in stromal and immune contexture upon Kras* depletion in mice.

Citation Format: Rachael K. Baliira, Emily Lasse Opsahl, Elyse McLintock, Katelyn L. Donahue, Ivana Barravacchia, Marina Pasca di Magliano, Stefanie Galbán. Oncogenic Kras signaling shapes the tumor microenvironment in lung adenocarcinoma [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 PR07.
Supplementary Table S2 from Validation of an Abridged Breast Cancer Risk Prediction Model for the General Population
Authors: Spaeth Erika L. , Dite Gillian S. , Hopper John L. , Allman Richard
Published: May 2023

Supplementary Table S2 shows the study eligibility criteria
Supplementary Methods S1 from Validation of an Abridged Breast Cancer Risk Prediction Model for the General Population
Authors: Spaeth Erika L. , Dite Gillian S. , Hopper John L. , Allman Richard
Published: May 2023

Supplementary Methods S1 describes the calculation of the risk scores
Supplementary Figure S1 from Validation of an Abridged Breast Cancer Risk Prediction Model for the General Population
Authors: Spaeth Erika L. , Dite Gillian S. , Hopper John L. , Allman Richard
Published: May 2023

Supplementary Figure S1 shows the distributions of the 5-year risks for affected and unaffected women for each model
Supplemental Table 1 from Stressful Life Events, Social Support, and Incident Breast Cancer by Estrogen Receptor Status
Authors: Lawrence Wayne R. , McDonald Jasmine A. , Williams Faustine , Shiels Meredith S. , Freedman Neal D. , Lin Ziqiang , Magnani Jared W.
Published: May 2023

Supplemental Table 1: Describes the Stressful Life Events and Social Support scales used in the study.
Supplemental Figure 1 from Stressful Life Events, Social Support, and Incident Breast Cancer by Estrogen Receptor Status
Authors: Lawrence Wayne R. , McDonald Jasmine A. , Williams Faustine , Shiels Meredith S. , Freedman Neal D. , Lin Ziqiang , Magnani Jared W.
Published: May 2023

Supplemental Figure 1: Presents the flow chart of women that participated in the observational study that were included in the analytical sample.
Supplementary Table S4 from Simple Prediction Model for Colorectal Serrated Polyps: Development and External Validation Study in U.S. Prospective Cohorts
Authors: Lyu Zhangyan , Hang Dong , He Xiaosheng , Wu Kana , Cao Yin , Rosner Bernard , Chan Andrew T. , Ogino Shuji , Li Ni , Dai Min , Giovannucci Edward L. , Song Mingyang
Published: May 2023

Supplementary Table S4: NRI and IDI of the risk prediction models for high-risk SPs.
Supplementary Table S3 from Precision Cut Lung Slices as a Preclinical Model for Non–Small Cell Lung Cancer Chemoprevention
Authors: Sompel Kayla , Smith Alex J. , Hauer Caroline , Elango Alamelu P. , Clamby Eric T. , Keith Robert L. , Tennis Meredith A.
Published: May 2023

Supplementary Table S3 lists antibody combinations used for immune cell detection in Figure 5.
Supplementary Figure S3 from Simple Prediction Model for Colorectal Serrated Polyps: Development and External Validation Study in U.S. Prospective Cohorts
Authors: Lyu Zhangyan , Hang Dong , He Xiaosheng , Wu Kana , Cao Yin , Rosner Bernard , Chan Andrew T. , Ogino Shuji , Li Ni , Dai Min , Giovannucci Edward L. , Song Mingyang
Published: May 2023

Supplementary Figure S3: The calibration plot of the simple risk prediction model for a composite endpoint of high-risk high-risk serrated polyps (SPs) and high-risk conventional adenoma (HRAs) across deciles of predicted risk in women and men.
Supplementary Figure S2 from Precision Cut Lung Slices as a Preclinical Model for Non–Small Cell Lung Cancer Chemoprevention
Authors: Sompel Kayla , Smith Alex J. , Hauer Caroline , Elango Alamelu P. , Clamby Eric T. , Keith Robert L. , Tennis Meredith A.
Published: May 2023

Supplementary Figure S2 shows a dot blot for Figure 4C.
Data from Stressful Life Events, Social Support, and Incident Breast Cancer by Estrogen Receptor Status
Authors: Lawrence Wayne R. , McDonald Jasmine A. , Williams Faustine , Shiels Meredith S. , Freedman Neal D. , Lin Ziqiang , Magnani Jared W.
Published: May 2023

Abstract
Chronic stress affects immune function and hormonal signaling and has been hypothesized to be associated with breast cancer, although results from the few prior studies are mixed and have not examined potential differences by estrogen receptor (ER) status. Using the Women's Health Initiative study, we included 76,951 postmenopausal women followed for events for a median of 16.7 years to investigate the association between baseline self-reported stressful life events and incident breast cancer by ER status and whether the association was modified by social support. We generated Cox proportional hazards models adjusting for demographic, clinical, lifestyle/behavioral, and social factors to estimate HRs and 95% confidence intervals (95%CI). The mean age was 63 (SD, 7.3), and majority of participants were White race (83.5%) and married or in a marriage-like relationship (63.0%). In analyses stratified by ER status, there was no relationship between stressful life events and ER-positive breast cancer. In contrast, compared with women in the lowest quartile, those in higher quartiles had an increased risk of ER-negative breast cancer, where those in quartile 4 had the highest risk (Quartile 4 vs. Quartile 1; HR = 1.30; 95%CI, 1.01–1.68; Ptrend = 0.050). Moreover, associations were stronger for the highest versus lowest quartile of stressful life events among widowed women (HR = 2.39; 95%CI, 1.29–4.44; Pinteraction<0.001). Association between stressful life events and ER-negative breast cancer was not modified by social support. In this cohort of postmenopausal women, higher experiences of prediagnostic stressful life events were associated with increased risk of ER-negative breast cancer.
Prevention Relevance:
Epidemiologic studies on the association between psychosocial stress and breast cancer risk remain inconsistent, while investigation of whether the association differs by ER status is limited. In this prospective cohort of postmenopausal women, high experiences of stressful life events were positively associated with ER-negative disease but not ER-positive.
Supplementary Table S9 from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: May 2023

Supplementary Table S9 shows the gene set enrichment analysis gene set that corresponds to Figure S6A.
Supplementary Table S4 from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: May 2023

Supplementary Table S4 shows the list of custom minipool sgRNA target genes.
Supplementary Table S2 from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: May 2023

Supplementary Table S2 shows the quantification of (R)-2HG in TF-1 cells.
Supplementary Table S1 from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: May 2023

Supplementary Table S1 shows the frequencies of TET2 and IDH mutations in clonal myeloid disorders.
Supplementary Figure S6 from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: May 2023

Transcriptional analysis of primary AML patient samples.
Supplementary Figure S2 from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: May 2023

Inhibition of KDM5 enzymes by the (R)- and (S)-enantiomers of 2-hydroxyglutarate.
Supplementary Figure S10 from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: May 2023

Prolonged exposure to MLL inhibitor VTP50469 does not affect the proliferation of TF-1 cells grown under cytokine-rich conditions.
Supplementary Data: list of figures and tables from (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers
Authors: Gunn Kathryn , Myllykoski Matti , Cao John Z. , Ahmed Manna , Huang Bofu , Rouaisnel Betty , Diplas Bill H. , Levitt Michael M. , Looper Ryan , Doench John G. , Ligon Keith L. , Kornblum Harley I. , McBrayer Samuel K. , Yan Hai , Duy Cihangir , Godley Lucy A. , Koivunen Peppi , Losman Julie-Aurore
Published: May 2023

List of supplementary figures and tables.
Supplementary Table S9 from In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target
Authors: Vujovic Ana , de Rooij Laura , Chahi Ava Keyvani , Chen He Tian , Yee Brian A. , Loganathan Sampath K. , Liu Lina , Chan Derek C.H. , Tajik Amanda , Tsao Emily , Moreira Steven , Joshi Pratik , Xu Joshua , Wong Nicholas , Balde Zaldy , Jahangiri Soheil , Zandi Sasan , Aigner Stefan , Dick John E. , Minden Mark D. , Schramek Daniel , Yeo Gene W. , Hope Kristin J.
Published: May 2023

Table S9 shows the (a) differentially expressed transcripts and (b) altered pathways as identified by GSEA from the ELAVL1 knockdown human primary AML RNA-sequencing data set.
Supplementary Table S3 from In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target
Authors: Vujovic Ana , de Rooij Laura , Chahi Ava Keyvani , Chen He Tian , Yee Brian A. , Loganathan Sampath K. , Liu Lina , Chan Derek C.H. , Tajik Amanda , Tsao Emily , Moreira Steven , Joshi Pratik , Xu Joshua , Wong Nicholas , Balde Zaldy , Jahangiri Soheil , Zandi Sasan , Aigner Stefan , Dick John E. , Minden Mark D. , Schramek Daniel , Yeo Gene W. , Hope Kristin J.
Published: May 2023

Table S3 shows clinical information for all AML patient specimens used in this study.
Supplementary Figure S7 from In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target
Authors: Vujovic Ana , de Rooij Laura , Chahi Ava Keyvani , Chen He Tian , Yee Brian A. , Loganathan Sampath K. , Liu Lina , Chan Derek C.H. , Tajik Amanda , Tsao Emily , Moreira Steven , Joshi Pratik , Xu Joshua , Wong Nicholas , Balde Zaldy , Jahangiri Soheil , Zandi Sasan , Aigner Stefan , Dick John E. , Minden Mark D. , Schramek Daniel , Yeo Gene W. , Hope Kristin J.
Published: May 2023

Supplemental Figure S7 shows the expression profile of TOMM34 in normal human bone marrow and across different AML and CML data sets. The effects of TOMM34 depletion on human primary AML cells in vitro and validation of TOMM34 knockdown and overexpression is shown.
Supplementary Figure S6 from In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target
Authors: Vujovic Ana , de Rooij Laura , Chahi Ava Keyvani , Chen He Tian , Yee Brian A. , Loganathan Sampath K. , Liu Lina , Chan Derek C.H. , Tajik Amanda , Tsao Emily , Moreira Steven , Joshi Pratik , Xu Joshua , Wong Nicholas , Balde Zaldy , Jahangiri Soheil , Zandi Sasan , Aigner Stefan , Dick John E. , Minden Mark D. , Schramek Daniel , Yeo Gene W. , Hope Kristin J.
Published: May 2023

Supplemental Figure S6 shows the GSEA of ELAVL1 depletion in mouse RN2c and human primary AML cells, ELAVL1 subcellular localization in mouse and human AML, the qRT-PCR of ELAVL1 targets in MS-444-treated RN2c cells, and the integrative analysis of the mouse RNA-seq and eCLIP-seq.
Supplementary Figure S3 from In Vivo Screening Unveils Pervasive RNA-Binding Protein Dependencies in Leukemic Stem Cells and Identifies ELAVL1 as a Therapeutic Target
Authors: Vujovic Ana , de Rooij Laura , Chahi Ava Keyvani , Chen He Tian , Yee Brian A. , Loganathan Sampath K. , Liu Lina , Chan Derek C.H. , Tajik Amanda , Tsao Emily , Moreira Steven , Joshi Pratik , Xu Joshua , Wong Nicholas , Balde Zaldy , Jahangiri Soheil , Zandi Sasan , Aigner Stefan , Dick John E. , Minden Mark D. , Schramek Daniel , Yeo Gene W. , Hope Kristin J.
Published: May 2023

Supplemental Figure S3 shows the generation of the bcCML mouse model and the effects of ELAVL1 on normal bone marrow in vivo.