bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract A015: Dynamics and lipid interactions of the RAS-RBD-CRD protein complex
Authors: Lightstone Felice C. , Carpenter Timothy S. 
Published: May 2023

Abstract
The high-resolution structure of the RAS G-domain complexed to the RBD and CRD domains of RAF provides critical insights into the assembly and conformation of the RAS-RAF signaling complex[1]. The influence and impact of the membrane on both the RAS and RAF proteins is a factor that we are just beginning to understand and appreciate. Molecular simulation is an ideal methodology to further study the complicated relationship between the membrane and associated proteins. Our recent work, using MuMMI[2] (Multiscale Machine-learned Modeling Infrastructure), investigated the different lipid compositions around KRAS4b and the interplay between the protein behavior and these membrane environments[3]. MuMMI uses machine learning to couple adjacent simulation scales and can be effectively scaled across some of the world’s largest high performance computing systems. The MuMMI multi-resolution framework has been expanded to include the RAF RBD-CRD domains. Here we present the overall simulation results from this latest MuMMI campaign. Tens of thousands of coarse-grained molecular dynamics simulations were completed, sampled from a variety of protein/lipid composition configurations. The orientations of the RAS-RBD-CRD complex on the membrane occupies distinct configurational states. Furthermore, the spatial patterns of lipid arrangements around these different protein states are also unique to each state. Interactions of the CRD with the membrane indicate the enrichment of very specific lipids in precise locations act to stabilize the complex. The extent, and size of the lipid ‘fingerprint’ imposed on the membrane by the RAS-RBD-CRD protein complex is significantly larger than observed for just the RAS protein on its own. We do not observe any statistically significant defined protein-protein orientations within the simulation ensemble. These observations indicate that spatial co-localize the RAS-RBD-CRD proteins in the same vicinity may be assisted by specific membrane environments. [1] Tran, Timothy H., et al. "KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation." Nature communications 12.1 (2021): 1-16. [2] Di Natale, Francesco, et al. "A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer." Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis. 2019. [3] Ingólfsson, Helgi I., et al. "Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins." Proceedings of the National Academy of Sciences 119.1 (2022): e2113297119.
Citation Format: Felice C. Lightstone, Timothy S. Carpenter. Dynamics and lipid interactions of the RAS-RBD-CRD protein complex [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 A015.
Abstract A019: The role of KRAS ubiquitination in lung cancer heterogeneity
Authors: Ivanisevic Tonci 
Published: May 2023

Abstract
Lung cancer is the most frequent cancer with an aggressive clinical course and high mortality rates. About 30% of non-small lung cancer is driven by activating mutations in KRAS (Kirsten rat sarcoma virus). KRAS signaling is tightly controlled through a series of post-transcriptional mechanisms, whereas dysregulation of KRAS activity is translated into heterogeneous clinical behavior. We, and others, have recently implicated leucine zipper-like transcriptional regulator 1 (LZTR1), an adaptor of the CUL3-containing E3 ligase complex, in the control of RAS ubiquitination. Heterozygous loss of LZTR1 is found in one-third of lung adenocarcinomas and co-occurs with oncogenic KRAS mutations, suggesting that LZTR1 loss could contribute to lung cancer by modulating KRAS signaling and affecting the drug response. Both WT and oncogenic KRAS mutant protein levels were modulated by LZTR1 according to a Global protein screen (GPS) scoring regulators of KRAS stability. LZTR1 also directly ubiquitinated mutant KRAS in lung cancer cells. To assess the impact of LZTR1 on KRAS-driven lung cancer, we then used the Kras-G12D mouse model. We found that either homozygous, or heterozygous knockout of Lztr1 cooperates with oncogenic KRAS and promotes tumor initiation and progression at early stages of lung cancer development. The observed phenotype arises from the changes of the immune tumor microenvironment mediated by the differential activation of RAL-B (Ras-related protein Ral-b) signaling in the absence of LZTR1. These results shed a novel light on the crosstalk between dysregulation of KRAS ubiquitination, paracrine communication exerted by the cancer cells through secreted cytokines, and the immune response in lung cancer, which has thwarted the effectiveness of therapy to date.
Citation Format: Tonci Ivanisevic. The role of KRAS ubiquitination in lung cancer heterogeneity [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 A019.
Abstract A039: RAS signaling strength determines phenotypic response in the colon
Authors: Moore Amanda R. , Carlos Sandra Melo , Storm Elaine E. , McGinnis Lisa M. , Malek Shiva , de Sauvage Frederic J. 
Published: May 2023

Abstract
The RAS (KRAS, NRAS and HRAS) genes are the most frequently mutated in cancer and are highly specific to tissue type by isoform and codon, yet the underlying cause for this selection is unknown. Mutations in KRAS, but not NRAS, frequently occur and act as oncogenic events in colorectal cancer. Biochemically, activating mutations in RAS increase the abundance of the GTP-bound active state, however, the position and substitution of the mutated amino acid affect the ‘on’ and ‘off’ rates of the RAS-GTP/GDP cycle. Alterations in codon 61 result in the largest accumulation of RAS-GTP. While this leads to robust pathway activation, codon 61 mutations are rarely observed in KRAS-mutant colorectal cancers. To study the effect of the isoform and codon mutations in colorectal tumor formation, we engineered mouse models to express codon 12 or 61 mutations in Kras and Nras. Our mouse models recapitulate the clinical RAS isoform and allelic selection. We found Kras G12D provided the greatest proliferative effect. To further understand this allelic selection, we investigated the interplay between RAS signaling strength and intestinal epithelial cell composition. We observed a correlation between RAS signaling strength and induction of stem cell differentiation. Together, our data provide insights to the preference for KRAS mutations in human colorectal cancers and provides a rationale for allelic selection.
Citation Format: Amanda R. Moore, Sandra Melo Carlos, Elaine E. Storm, Lisa M. McGinnis, Shiva Malek, Frederic J. de Sauvage. RAS signaling strength determines phenotypic response in the colon [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 A039.
Abstract B014: Phenotypic CRISPR genome-wide screening for the discovery of genetic regulators of allele-specific mutant KRAS
Authors: Hu Xiyue , Singh Randy , Kelley Shana 
Published: May 2023

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 B030: Using the ResCu system for preclinical testing of KRAS G12C inhibitors
Authors: Ruiz Victor M. , Hill Lindsay , Gadde Manasa , Bulow Christopher , Morri Maurizio , Goldner Nicholas 
Published: May 2023

Abstract
Introduction: Recent colorectal cancer trials with KRAS G12C inhibitors have faced resistance challenges, and a preclinical model is needed to test resistance inhibition strategies. Experimental Methods: We have developed a novel culturing system, ResCu, that allows for long-term culture of cells without the need for passaging, enabling us to determine treatment resistance that can develop over time in a physiologically relevant system that conserves the resistance pathways found in patients. Using this system, we evolved resistance to a KRAS G12C inhibitor, sotorasib, after only two weeks of culture. The evolved cells were characterized for cross-resistance and cross-sensitivity by exposing these cells to a panel of drugs for seven days. Cell viability was assessed by luminescence. Based on the drug screen results, the sotorasib evolved cells were further evolved to additional drug classes to identify novel therapeutic combinations. Whole population and single-cell transcriptomic analysis were used to identify resistance mechanisms and synthetic lethality. Results: Using the ResCu system, we evolved resistance to sotorasib, a KRAS G12C inhibitor, and other drugs in combination with sotorasib. We identified a synergistic combination of sotorasib and a secondary inhibitor that initially suppressed resistance in the sotorasib evolved cells. We identified potential mechanisms underlying this synergy using transcriptomic analysis to enable future mechanistic characterization. Subsequently, the ResCu system drove resistance evolution to the sotarasib synergistic combination. We identified splicing alterations associated with this resistance. Conclusion: We have developed a novel resistance culturing system, ResCu, that allows for preclinical testing of KRAS G12C inhibitors and determines the most promising compounds for inhibiting specific resistance pathways. This system allows for long-term culturing of cells without passaging, thereby maintaining the various phenotypes of the original populations that are commonly lost in traditional passaging cultures.
Citation Format: Victor M. Ruiz, Lindsay Hill, Manasa Gadde, Christopher Bulow, Maurizio Morri, Nicholas Goldner. Using the ResCu system for preclinical testing of KRAS G12C 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 B030.
Abstract IA08: Direct covalent inhibitors of mutant K-Ras
Authors: Shokat Kevan M. 
Published: May 2023

Abstract
Somatic mutations in the small GTPase K-Ras are the most common activating lesions found in human cancer, and are generally associated with poor response to standard therapies. Efforts to directly target this oncogene have faced difficulties due to its picomolar affinity for GTP/GDP and the absence of known allosteric regulatory sites. I will discuss the development of small molecules that irreversibly bind to a common oncogenic mutant, K-Ras G12C. These compounds rely on the mutant cysteine for binding and therefore do not affect the wild type protein (WT). New covalent molecules targeting K-Ras G12S and G12D are currently under development and will be discussed. I will also discuss reactivation of mutant p53 (Y220C) to leverage the natural anti-tumor effects of tumor suppressors.
Citation Format: Kevan M. Shokat. Direct covalent inhibitors of mutant K-Ras [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 IA08.
Abstract IA12: Developing combinatorial therapies for KRAS-driven cancers
Authors: Cichowski Karen 
Published: May 2023

Abstract
The RAS pathway is one of the most commonly deregulated pathways in human cancer. Approximately 30% of all tumors harbor activating mutations in either KRAS, NRAS or HRAS, and even more possess alterations in other genes that enhance RAS signaling. While RAS was thought to be undruggable for decades, agents that directly inhibit KRAS and/or specific KRAS oncoproteins have now been developed. Nevertheless, not all patients respond to current clinical agents and responses are often temporary. As such there is an urgent need to develop more effective therapies for these malignancies, which will likely require combinatorial approaches. Vertical strategies designed to target different nodes within the RAS pathway to achieve deeper suppression represents one promising approach. However, additional options are emerging, which may circumvent challenges associated with potent pathway suppression. In this presentation, two promising combinatorial strategies for KRAS mutant lung and colon cancer will be discussed. Importantly, by dissecting the mechanism by which these agents function we have uncovered nodal points of convergence between distinct oncogenic pathways, which represent key therapeutic vulnerabilities, and have identified biomarkers that can be used for patient selection.
Citation Format: Karen Cichowski. Developing combinatorial therapies for KRAS-driven 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 IA12.
Abstract PR05: The role of the RAS GTPase RIT1 in RASopathies and cancer
Authors: Castel Pau 
Published: May 2023

Abstract
RAS oncoproteins are drivers of tumor initiation and progression and therapies targeting these directly or their downstream pathways have resulted in unprecedented clinical benefit in cancer. However, recent advances in genomic medicine have revealed that many of the known RAS oncoproteins and cancer-associated mutations are also involved in the pathogenesis of a group of congenital disorders termed RASopathies. Our research is aimed at understanding the role of these oncoproteins at the biochemical and signaling level and we develop novel mouse models that allow us to study RAS oncoproteins in the context of cancer and genetic syndromes. Our recent work has focused on the non-classical RAS protein RIT1, a poorly understood GTPase expressed in most tissues. Pathogenic variants in RIT1 are found somatically in some cancers, such as lung and bladder adenocarcinoma, myeloid leukemias, and in the germline of individuals with Noonan syndrome, the most common RASopathy. Our lab recently demonstrated that, in contrast to classical RAS proteins, RIT1 appears to be mostly regulated through proteasomal degradation by interacting with a complex formed by the substrate adaptor protein LZTR1 and the RING E3 Ubiquitin Ligase Cullin3. We found that this complex is conserved in lower organisms and is necessary for the proper regulation of RIT1 protein levels. In addition, we have also found that RIT1 binds directly to the spindle assembly checkpoint protein MAD2 and its dysregulation leads to increased mitotic length and aneuploidy. Taking advantage of genetically-engineered mice, we have also generated models for RIT1-driven disorders, including Noonan syndrome, lung cancer, and leukemia. Finally, we have recently investigated the mechanisms that underlie RIT1-dependent RAF-MEK-ERK activation and proposed novel therapies that could be used for Noonan syndrome and other cancers. Overall, our work provides novel insights into the regulation, function, and pathogenesis of the RAS-like protein RIT1
Citation Format: Pau Castel. The role of the RAS GTPase RIT1 in RASopathies and 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 PR05.
Abstract A20: Inflammation remodels the immune microenvironment in acute myeloid leukemia
Authors: Lasry Audrey , Nadorp Bettina , Fornerod Maarten , Nicolet Deedra , Wu Huiyun , Walker Christopher J , Sun Zhengxi , Witkowski Matthew T , Tikhonova Anastasia N , Guillamot Maria , Cayanan Geraldine , Yeaton Anna , Gruber Tanja A , Eisfeld Ann-Kathrin , Aifantis Iannis 
Published: May 2023

Abstract
Acute myeloid leukemia (AML) is a hematopoietic malignancy with poor prognosis and limited treatment options. Here we provide a comprehensive single cell RNA-Sequencing census of the bone marrow immune microenvironment in adult and pediatric AML patients. We characterize unique inflammation signatures in a subset of AML patients, associated with inferior outcomes. We identify atypical B cells, a dysfunctional B cell subtype enriched in high-inflammation AML patients, as well as an increase in CD8+ GZMK+ and regulatory T cells, accompanied by a reduction in T cell clonal expansion. We derive an inflammation-associated gene score (iScore) that associates with poor survival outcomes in AML patients. Addition of the iScore refines current risk stratifications for AML patients and may enable identification of patients in need of more aggressive treatment. This work provides a first framework for classifying AML patients based on their immune microenvironment and a rationale for consideration of the inflammatory state in clinical settings.
Citation Format: Audrey Lasry, Bettina Nadorp, Maarten Fornerod, Deedra Nicolet, Huiyun Wu, Christopher J Walker, Zhengxi Sun, Matthew T Witkowski, Anastasia N Tikhonova, Maria Guillamot, Geraldine Cayanan, Anna Yeaton, Tanja A Gruber, Ann-Kathrin Eisfeld, Iannis Aifantis. Inflammation remodels the immune microenvironment in acute myeloid leukemia [abstract]. In: Proceedings of the AACR Special Conference: Acute Myeloid Leukemia and Myelodysplastic Syndrome; 2023 Jan 23-25; Austin, TX. Philadelphia (PA): AACR; Blood Cancer Discov 2023;4(3_Suppl):Abstract nr A20.
ОСОБЛИВОСТІ ФОРМУВАННЯ ІМУННОЇ ВІДПОВІДІ ПІСЛЯ ВАКЦИНАЦІЇ ВІД COVID-19
Authors: Кисельова Г. Л. , Анастасій І. А. , Тонковид О. Б. , Ісаєв В. М. , Воронова К. В. , Шевель І. І. , Сідорова І. В. , Карпеченко С. В. , Панченко А. А. 
Published: May 2023

Мета оцінити особливості імунної відповіді у вакцинованих від COVID-19 серед співробітників ТОВ «МЛ «ДІЛА», дослідити рівні таких моніторингових показників, як імуноглобуліни М та G при застосуванні різних вакцин.
Матеріали і методи. У 603 співробітників, вакцинованих від COVID-19 препаратами CoronaVac, Pfizer-BioNTech, AstraZeneca, Moderna, досліджено імунну відповідь шляхом визначення імуноглобулінів класу М і G до різних білків-мішеней коронавірусу (білка S шипоподібного, білка N нуклеокапсидного), напівкількісним та кількісним методами на імунохемілюмінесцентному аналізаторі.
Результати досліджень та їх обговорення. Встановлено наявність імунної відповіді у 99,2 % вакцинованих, порівняно зі 73,3 % співробітників, які перенесли COVID-19. Усі вакциновані виробляють захисні антитіла, незалежно від історії захворювання на COVID-19 до вакцинації. Ці антитіла утримуються принаймні протягом 4 міс., демонструючи певні коливання їх кількості, залежно від виду отриманої вакцини. Найстабільніший рівень антитіл забезпечує РНК вакцина Pfizer-BioNTech.
Висновки. Встановлена тривалість імунної відповіді (за результатами визначення антитіл) засвідчує ефективність вакцинації та доцільність застосування бустерних доз вакцини.
CLINICAL AND PATHOGENETIC FEATURES OF DAMAGE TO THE NERVOUS SYSTEM AT THE INITIAL CLINICAL STAGES OF HIV-INFECTION
Authors: Sosnovenko D. S. , Chemych O. M. , Chemych M. D. 
Published: May 2023

The aim of the study – investigating the features of clinical symptoms in HIV-positive people in the early stages of the disease and their pathogenetic justification.
The study used theoretical methods based on the analysis and synthesis of studying the information of the modern world from the PubMed and Scopus databases, clinical observations, as well as deductive-inductive methods.
Conclusions. As a result of the war in Ukraine, the epidemiological control of infectious diseases on the territory of the country was violated. HIV-infection and the absence or atypicality of its clinical symptoms in infected patients deserve special attention, which is based on a detailed understanding of the pathological processes of neuroAIDS. Damage to astrocyte cells disrupts the connection of cells of the structural and functional complex of the brain with other cells and forms the fundamental basis for understanding clinical symptoms. Most often in the form of: neuropsychic, cognitive somatic and neurological disorders. The pathogenic effect of the virus contributes to spasm of cerebral microvessels, is the cause of local hypoxic lesions, microstrokes, and in late cases – lacunar cerebral infarcts. The active involvement of brain cells in the pathogenesis of HIV-infection has been confirmed by many studies. Along with standard diagnostic methods, it is advisable to use psychoneurological and cognitive tests and scales.
A number of shortcomings have been identified that can reduce the reliability of diagnostic studies when establishing a diagnosis.
Understanding the pathogenetic picture will allow choosing «indicators» for the general diagnostic scheme and increasing the probability of establishing the correct diagnosis, adjusting ART and predicting the further development of the disease.