bluuebunny/crossref_metadata_2025 huggingface dataset:
Cross-lingual Text Reuse Detection at Document Level for English-Urdu Language Pair
Authors: Sharjeel Muhammad , Muneer Iqra , Nosheen Sumaira , Nawab Rao Muhammad Adeel , Rayson Paul
Published: May 2023

In recent years, the problem of Cross-Lingual Text Reuse Detection (CLTRD) has gained the interest of the research community due to the availability of large digital repositories and automatic Machine Translation (MT) systems. These systems are readily available and openly accessible, which makes it easier to reuse text across languages but hard to detect. In previous studies, different corpora and methods have been developed for CLTRD at the sentence/passage level for the English-Urdu language pair. However, there is a lack of large standard corpora and methods for CLTRD for the English-Urdu language pair at the document level. To overcome this limitation, the significant contribution of this study is the development of a large benchmark cross-lingual (English-Urdu) text reuse corpus, called the TREU (Text Reuse for English-Urdu) corpus. It contains English to Urdu real cases of text reuse at the document level. The corpus is manually labelled into three categories (Wholly Derived = 672, Partially Derived = 888, and Non Derived = 697) with the source text in English and the derived text in the Urdu language. Another contribution of this study is the evaluation of the TREU corpus using a diversified range of methods to show its usefulness and how it can be utilized in the development of automatic methods for measuring cross-lingual (English-Urdu) text reuse at the document level. The best evaluation results, for both binary (
F
1
= 0.78) and ternary (
F
1
= 0.66) classification tasks, are obtained using a combination of all Translation plus Mono-lingual Analysis (T+MA) based methods. The TREU corpus is publicly available to promote CLTRD research in an under-resourced language, i.e., Urdu.
Skin Lesion Intelligent Diagnosis in Edge Computing Networks: An FCL Approach
Authors: Shi Yanhang , Li Xue , Chen Siguang
Published: May 2023

In recent years, automatic skin lesion diagnosis methods based on artificial intelligence have achieved great success. However, the lack of labeled data, visual similarity between skin diseases, and restriction on private data sharing remain the major challenges in skin lesion diagnosis. In this article, first, we propose a federated contrastive learning framework to break down data silos and enhance the generalizability of diagnostic model to unseen data. Subsequently, by combining data features from different participated nodes, the proposed framework can improve the performance of contrastive training. To extract discriminative features during on-device training, we propose a contrastive learning based intelligent skin lesion diagnosis scheme in edge computing networks. Specifically, a contrastive learning based dual encoder network is designed to overcome training sample scarcity by fully leveraging unlabeled samples for performance improvement. Meanwhile, we devise a maximum mean discrepancy based supervised contrastive loss function, which can efficiently explore complex intra-class and inter-class variances of samples. Finally, the diagnosis simulations demonstrate that compared with existing methods, our proposed scheme can achieve superior accuracy in both on-device training and distributed training scenarios.
Enhancing RDF Verbalization with Descriptive and Relational Knowledge
Authors: Zhang Fan , Zhang Meishan , Liu Shuang , Sun Yueheng , Duan Nan
Published: May 2023

RDF verbalization has received increasing interest, which aims to generate a natural language description of the knowledge base. Sequence-to-sequence models based on Transformer are able to obtain strong performance equipped with pre-trained language models such as BART and T5. However, in spite of the general performance gain introduced by the pre-trained models, the performance of the task is still limited by the small scale of the training dataset. To address the problem, we propose two orthogonal strategies to enhance the representation learning of RDF triples. Concretely, two types of knowledge are introduced, i.e., descriptive knowledge and relational knowledge, respectively. The descriptive knowledge indicates the semantic information of self definition, and the relational knowledge indicates the semantic information learned from the structural context. We further combine the descriptive and relational knowledge together to enhance the representation learning. Experimental results on the WebNLG and SemEval-2010 datasets show that the two types of knowledge can both enhance the model performance, and their combination is able to obtain further improvements in most cases, providing new state-of-the-art results.
Ethernet Information Security Protocols Based on Industrial Control Wireless Sensor Networks
Authors: Yin Xiaobo , Zhang Shunxiang , Feng Li , Xu Guangyu
Published: May 2023

This paper provides an in‐depth study and analysis of information security protocols for industrial Ethernet using wireless sensor networks. The optimal number of cluster heads for nonuniform subclustering is derived based on the sensor energy consumption model, and then, the EEUC contention radius formula is optimized to select candidate cluster heads with random values and energy as weights. A multihop approach based on the shortest offset is also proposed for intercluster information transmission. Experimental results show that the EEUC‐based improved cluster routing protocol proposed in this paper balances the node energy consumption and extends the network lifetime. In response to the problem that the coarsened hop value and average hop distance of the DV‐Hop localization algorithm cannot reflect the network topology, the improved DV‐Hop algorithm based on multicommunication radius and hop distance correction is proposed. Simulation experiments show that the improved algorithm based on multiple communication radius and hop count correction can significantly reduce the localization error and improve the accuracy of the algorithm. Aiming at the shortcomings of MRP with excessive risk concentration and transmission medium limitation, this paper proposes a fast self‐healing mechanism of industrial Ethernet with a multiexpert strategy. The PCP‐AP common platform architecture for openSAFETY sites is designed on the base sleeve of the implementation of the industrial Ethernet protocol Ethernet POWERLINK; the main communication part of POWERLINK is implemented through an FPGA hardware solution, and the openSAFETY site is implemented using AM335X high‐performance processor to implement openSAFETY security application functions. Finally, the article conducts field tests on the wireless signal information transmission, WSN data transmission, network connection, and power supply system in the system and compares and analyzes the data collected by the system with the monitoring data of the national control site. The data obtained by the system has real reliability. The communication module used is inexpensive, lightweight, and easy to operate. It can realize the collection of multiple pollution sources, and compared with traditional monitoring equipment, it avoids the difficulties of complicated wiring, difficult positioning of pollution sources, and restricted monitoring areas and largely reduces the investment in human and material resources.
Efficacy of Preemptive Dexamethasone versus Methylprednisolone in the Management of Postoperative Discomfort and Pain after Mandibular Third Molar Surgery: A Systematic Review and Meta-Analysis
Authors: Singh Anupam , Pentapati Kalyana Chakravarthy , Kodali Murali Venkata Rama Mohan , Smriti Komal , Patil Vathsala , Chowdhary Gandham Lekha , Gadicherla Srikanth
Published: May 2023

The corticosteroids have been used for preemptive management of surgical sequelae after mandibular third molar extraction. The aim of this article was to review the efficacy of methylprednisolone versus dexamethasone in the management of postsurgical pain, swelling, and trismus after mandibular third molar surgery. Randomized, double-blinded studies from PubMed, CINAHL, Scopus, DOSS, Cochrane central, and Web of Science were identified by using a search strategy. Randomized controlled trials evaluating the efficacy of use of dexamethasone versus methylprednisolone for mandibular third molar extraction were only considered. The studies involving the use of any other corticosteroid agent were excluded. Outcomes assessed were postoperative pain, the number of rescue analgesics required, swelling, trismus, and adverse events. The search strategy yielded 1046 articles for title and abstract screening, out of which only seven studies were included in the systematic review after full text screening. There was considerable heterogeneity between the studies with regards to the method as well as the parameters assessed. Risk of bias was low in three studies and unclear in other four studies. On pooled analyses, there was no significant difference with respect to pain, rescue analgesics, and swelling in the test and the control group. Forest plot analysis showed that dexamethasone had lesser trismus in early postoperative period (postoperative day 2) as compared to methylprednisolone. None of the included studies reported any adverse effects. Both the corticosteroids have similar efficacy in reducing the postoperative pain and swelling; however, dexamethasone showed statistically significant difference from methylprednisolone in reducing trismus (estimated standardized mean difference of −0.69 mm; 95% CI: −1.01 to −0.38;

p
<
0.0001

) in the early postoperative period. However, due to statistical heterogeneity, quality of the evidence for the review was low to moderate. Hence, more studies with larger study sample and low risk of bias are needed to confirm these results.
Supplementary Table S2 from Comparative Analysis of the Humoral Immune Response to the EBV Proteome across EBV-Related Malignancies
Authors: Argirion Ilona , Pfeiffer Ruth M. , Proietti Carla , Coghill Anna E. , Yu Kelly J. , Middeldorp Jaap M. , Sarathkumara Yomani D. , Hsu Wan-Lun , Chien Yin-Chu , Lou Pei-Jen , Wang Cheng-Ping , Rothman Nathaniel , Lan Qing , Chen Chien-Jen , Mbulaiteye Sam M. , Jarrett Ruth F. , Glimelius Ingrid , Smedby Karin E. , Hjalgrim Henrik , Hildesheim Allan , Doolan Denise L. , Liu Zhiwei
Published: May 2023

Supplementary Table S2 shows summary of participant characteristics
Supplementary Table S1 from Rural, Large Town, and Urban Differences in Optimal Subspecialty Follow-up and Survivorship Care Plan Documentation among Childhood Cancer Survivors
Authors: Noyd David H. , Janitz Amanda E. , Baker Ashley A. , Beasley William H. , Etzold Nancy C. , Kendrick David C. , Oeffinger Kevin C.
Published: May 2023

Rural-Urban Commuting Area (RUCA) codes, definitions, and categories (adapted from https://www.ers.usda.gov/data-products/rural-urban-commuting-area-codes/ and https://depts.washington.edu/uwruca/ruca-uses.php)
Supplementary Figure S3 from Rural, Large Town, and Urban Differences in Optimal Subspecialty Follow-up and Survivorship Care Plan Documentation among Childhood Cancer Survivors
Authors: Noyd David H. , Janitz Amanda E. , Baker Ashley A. , Beasley William H. , Etzold Nancy C. , Kendrick David C. , Oeffinger Kevin C.
Published: May 2023

Subanalysis and geographical map for Oklahoma City Urban, non-Oklahoma City urban, large town, and small town/isolated rural areas in Oklahoma.
Supplementary Figure S2 from Rural, Large Town, and Urban Differences in Optimal Subspecialty Follow-up and Survivorship Care Plan Documentation among Childhood Cancer Survivors
Authors: Noyd David H. , Janitz Amanda E. , Baker Ashley A. , Beasley William H. , Etzold Nancy C. , Kendrick David C. , Oeffinger Kevin C.
Published: May 2023

Directed acyclic graph of the potential associations between rurality at time of diagnosis and survivors with Passport for Care
Supplementary Figure 6 from Prevalence and Prognostic Significance of Malnutrition in Patients with Brain Metastasis
Authors: Liu Zheran , Zhang Yu , Pei Yiyan , He Yan , Yu Jiayi , Zhang Renjie , Wang Jingjing , Chong Weelic , Hai Yang , Peng Xingchen , Fang Fang
Published: May 2023

Supplementary Figure 6 Kaplan-Meier curves for overall survival in patients who received chemotherapy and radiotherapy.
Table S6A from Linking Physical Activity to Breast Cancer Risk via Inflammation, Part 1: The Effect of Physical Activity on Inflammation
Authors: Swain Christopher T.V. , Drummond Ann E. , Milne Roger L. , English Dallas R. , Brown Kristy A. , Lou Makayla W.C. , Boing Leonessa , Bageley Amy , Skinner Tina L. , van Roekel Eline H. , Moore Melissa M. , Gaunt Tom R. , Martin Richard M. , Lewis Sarah J. , Lynch Brigid M.
Published: May 2023

Supplementary Table 6A presents findings of individual parallel group RCTs
Table S1 from Linking Physical Activity to Breast Cancer Risk via Inflammation, Part 1: The Effect of Physical Activity on Inflammation
Authors: Swain Christopher T.V. , Drummond Ann E. , Milne Roger L. , English Dallas R. , Brown Kristy A. , Lou Makayla W.C. , Boing Leonessa , Bageley Amy , Skinner Tina L. , van Roekel Eline H. , Moore Melissa M. , Gaunt Tom R. , Martin Richard M. , Lewis Sarah J. , Lynch Brigid M.
Published: May 2023

Supplementary Table 1 presents the search terminology used in the systematic review
Figure S5A from Linking Physical Activity to Breast Cancer via Inflammation, Part 2: The Effect of Inflammation on Breast Cancer Risk
Authors: Lou Makayla W.C. , Drummond Ann E. , Swain Christopher T.V. , Milne Roger L. , English Dallas R. , Brown Kristy A. , van Roekel Eline H. , Skinner Tina L. , Moore Melissa M. , Gaunt Tom R. , Martin Richard M. , Lewis Sarah J. , Lynch Brigid M.
Published: May 2023

Supplementary Figure 5A presents the forest plots for adiponectin and breast cancer risk, by menopausal status
Figure S1B from Linking Physical Activity to Breast Cancer via Inflammation, Part 2: The Effect of Inflammation on Breast Cancer Risk
Authors: Lou Makayla W.C. , Drummond Ann E. , Swain Christopher T.V. , Milne Roger L. , English Dallas R. , Brown Kristy A. , van Roekel Eline H. , Skinner Tina L. , Moore Melissa M. , Gaunt Tom R. , Martin Richard M. , Lewis Sarah J. , Lynch Brigid M.
Published: May 2023

Supplementary Figure 1B presents forest plots for CRP and breast cancer risk, excluding studies where exogenous hormone use status was unknown
Data from Prevalence and Prognostic Significance of Malnutrition in Patients with Brain Metastasis
Authors: Liu Zheran , Zhang Yu , Pei Yiyan , He Yan , Yu Jiayi , Zhang Renjie , Wang Jingjing , Chong Weelic , Hai Yang , Peng Xingchen , Fang Fang
Published: May 2023

AbstractBackground:
Malnutrition is a severe but modifiable risk factor for cancers. However, the relationship between malnutrition and the survival of patients with brain metastases has not been fully revealed. We aimed to evaluate the prevalence of malnutrition and assess its prognostic value on patients with brain metastases
Methods:
We retrospectively recruited 2,633 patients with brain metastases between January 2014 and September 2020. Three malnutrition scores were used to evaluate patients’ malnutrition status at their first admission, including controlling nutritional status, the nutritional risk index, and the prognostic nutritional index. The association between malnutrition and overall survival (OS) was estimated.
Results:
The three malnutrition scores were associated with each other and with body mass index (BMI). Malnutrition assessed by any of the three scores was significantly associated with poor OS. All three malnutrition scores were better indicators than BMI, and adding malnutrition scores to the Graded Prognostic Assessment (GPA) scoring system could significantly improve the accuracy of prognosis prediction.
Conclusions:
Malnutrition monitoring using any of the three malnutrition scores on patients’ first admission could be a better survival indicator for patients with brain metastases compared with BMI alone.
Impact:
Malnutrition is a more significant indicator of survival stratification compared with BMI. Adding malnutrition to the GPA score system achieves better survival prediction.
Data from Oral IRAK-4 Inhibitor CA-4948 Is Blood-Brain Barrier Penetrant and Has Single-Agent Activity against CNS Lymphoma and Melanoma Brain Metastases
Authors: Von Roemeling Christina A. , Doonan Bently P. , Klippel Kelena , Schultz Daniel , Hoang-Minh Lan , Trivedi Vrunda , Li Chenglong , Russell Rylynn A. , Kanumuri Raju S. , Sharma Abhisheak , Tun Han W. , Mitchell Duane A.
Published: May 2023

AbstractPurpose:
An ongoing challenge in cancer is the management of primary and metastatic brain malignancies. This is partly due to restrictions of the blood-brain barrier and their unique microenvironment. These challenges are most evident in cancers such as lymphoma and melanoma, which are typically responsive to treatment in systemic locations but resistant when established in the brain. We propose interleukin-1 receptor-associated kinase-4 (IRAK-4) as a potential target across these diseases and describe the activity and mechanism of oral IRAK-4 inhibitor CA-4948.
Experimental Design:
Human primary central nervous system lymphoma (PCNSL) and melanoma brain metastases (MBM) samples were analyzed for expression of IRAK-4 and downstream transcription pathways. We next determined the central nervous system (CNS) applicability of CA-4948 in naïve and tumor-bearing mice using models of PCNSL and MBM. The mechanistic effect on tumors and the tumor microenvironment was then analyzed.
Results:
Human PCNSL and MBM have high expression of IRAK-4, IRAK-1, and nuclear factor kappa B (NF-κB). This increase in inflammation results in reflexive inhibitory signaling. Similar profiles are observed in immunocompetent murine models. Treatment of tumor-bearing animals with CA-4948 results in the downregulation of mitogen-activated protein kinase (MAPK) signaling in addition to decreased NF-κB. These intracellular changes are associated with a survival advantage.
Conclusions:
IRAK-4 is an attractive target in PCNSL and MBM. The inhibition of IRAK-4 with CA-4948 downregulates the expression of important transcription factors involved in tumor growth and proliferation. CA-4948 is currently being investigated in clinical trials for relapsed and refractory lymphoma and warrants further translation into PCNSL and MBM.
Data from Pilot Study of Recurrent Ewing's Sarcoma Management with Vigil/Temozolomide/Irinotecan and Assessment of Circulating Tumor (ct) DNA
Authors: Anderson Peter , Ghisoli Maurizio , Crompton Brian D. , Klega Kelly S. , Wexler Leonard H. , Slotkin Emily K. , Stanbery Laura , Manning Luisa , Wallraven Gladice , Manley Meghan , Horvath Staci , Bognar Ernest , Nemunaitis John
Published: May 2023

AbstractPurpose:
Treatment options for recurrent or refractory Ewing's sarcoma (ES) are limited. Vigil is a novel autologous tumor cell therapy expressing bi-shRNA furin/GMCSF plasmid, which previously demonstrated monotherapy activity in advanced ES. Herein we report safety and evidence of benefit to Vigil for ES as potential treatment.
Patients and Methods:
In this pilot trial, eligible patients with recurrent or refractory ES who failed initial standard-of-care therapy received treatment with temozolomide (TEM) 100 mg/m2/day oral and irinotecan (IRI) 50 mg/m2/day oral, Days 1 to 5, in combination with Vigil (1 × 106–107 cells/mL/day intradermal, Day 15), every 21 days (Vigil/TEM/IRI). Objective response rate (ORR) by RECIST v1.1, progression-free survival (PFS), and overall survival (OS) were assessed. Circulating tumor (ct) DNA analysis was done by patient-specific droplet digital PCR on baseline and serially collected on-treatment samples.
Results:
Eight of 10 enrolled patients were evaluable for safety and efficacy (mean age 24.6; 12.6–46.1 years old); 2 did not receive Vigil. Seven of 8 patients previously received TEM/IRI. No Vigil-related adverse events were reported. Common ≥Grade 3 chemotherapy-related toxicity included neutropenia (50%) and thrombocytopenia (38%). We observed two partial response patients by RECIST; both showed histologic complete response without additional cancer therapy. Median PFS was 8.2 months (95% confidence interval, 4.3–NA). Five patients showed stable disease or better for ≥6 months. Patient-specific EWS/FLI1 ctDNA was detectable in all 8 evaluable patients at baseline. Changes in ctDNA levels corresponded to changes in disease burden.
Conclusions:
Results demonstrated safety of combination Vigil/TEM/IRI.
Figure S4 from Bone Marrow Mesenchymal Stem Cells Induce Metabolic Plasticity in Estrogen Receptor–Positive Breast Cancer
Authors: Buschhaus Johanna M. , Rajendran Shrila , Chen Siyi , Wharram Bryan L. , Bevoor Avinash S. , Cutter Alyssa C. , Humphries Brock A. , Robison Tanner H. , Farfel Alex P. , Luker Gary D.
Published: May 2023

Figure S4. Validation of FRET reporters for intracellular glucose and ATP. Pseudocolor scale depicts high (red) and low (blue) CFP lifetime. Scale bar = 50 µm. Symbols show pair-wise comparisons with ****p<0.0001 using one-way ANOVA. A) Representative images and box and whiskers plots of intracellular glucose in MCF7 monocultures with 0-, 5-, or 25-mM glucose. B) Representative images and box and whiskers plots of intracellular ATP in MCF7 monocultures before and after addition of oligomycin.
Figure S7 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

Modulation of AXL neither affects cell proliferation nor sensitivity to MEK inhibition.
Data 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

Abstract
High expression of the receptor tyrosine kinase AXL is implicated in epithelial-to-mesenchymal transition, cancer progression, and therapy resistance. For example, AXL is abundant in BRAF mutant melanomas progressing on targeted BRAF/MEK inhibition. Therefore, AXL is thought to represent an attractive therapeutic target. This notwithstanding, little is known about the mechanisms governing expression of AXL. Here, we describe a FACS-based whole-genome-wide CRISPR-Cas9 screen to uncover regulators of AXL expression. We identified several genes, inactivation of which led to increased AXL expression. Most remarkable was the identification of five components that associate with the Elongin B/C heterodimer. Elongin B/C engage in multiple protein–protein interactions, including the transcription factor complex subunit Elongin A, the von Hippel-Lindau (VHL) tumor suppressor protein, and members of the SOCS-box protein family. The screen identified ELOB, ELOC, SOCS5, UBE2F, and RNF7, each of which we demonstrate to serve as an inhibitor of AXL expression. Although the AXL promoter contains hypoxia response elements and Elongin B/C are found in the VHL complex, Elongin B/C unexpectedly regulate AXL independently of hypoxia. Instead, we demonstrate that the Elongin BC complex interacts with AXL through ELOB, and contributes to proteasomal AXL turnover. RNA-sequencing and IHC analyses of melanoma patient-derived xenografts and clinical samples revealed a negative association between Elongin B/C and dedifferentiation. Together, the Elongin BC complex regulates AXL and marks a differentiated melanoma phenotype.
Implications:
This study identifies the Elongin BC complex as a key regulator of AXL expression and marker of melanoma differentiation.
Data from Exosomal lincROR Promotes Docetaxel Resistance in Prostate Cancer through a β-catenin/HIF1α Positive Feedback Loop
Authors: Jiang Xingkang , Xu Yong , Liu Ranlu , Guo Shanqi
Published: May 2023

Abstract
Emerging evidence has suggested that patients with metastatic prostate cancer will become resistant after receiving docetaxel (DTX) chemotherapy, but the specific regulatory mechanism is still unclear. lincROR is an important oncogenic long noncoding RNA which plays an important role in regulating tumor carcinogenesis and metastasis; however, the underlying mechanism of lincROR functioning in the DTX resistance process of prostate cancer remains largely unknown. In the current study, we found that lincROR is highly expressed in DTX-resistant prostate cancer cell lines and was associated with poor DTX response in patients with metastatic prostate cancer. By using loss- and gain-of-function experiments revealed that lincROR promotes prostate cancer cells growth and DTX resistance in vitro and in vivo. Mechanistic studies demonstrated that lincROR specifically interacts with and stabilizes MYH9 protein, which enhances β-catenin/hypoxia-inducible factor 1-alpha (HIF1α) pathways. Besides, HIF1α could bind with the promoter region of lincROR to activate its transcription, thus forming the lincROR/MYH9/HIF1α positive feedback loop. Moreover, lincROR could be packaged into exosomes in an heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1)-dependent manner and then disseminated chemoresistance phenotype to receipt cells. Overall, our study provides evidence supporting exosome-mediated lincROR activates the β-catenin/HIF1α positive feedback loop by targeting MYH9 protein, which may be exploited for anticancer therapy.
Implications:
Our findings suggest that targeting hypoxia stress and chemoresistance for therapeutic purposes and lincROR could promote the improvement of treatment responses in patients with DTX-resistant prostate cancer.
Abstract A006: Chromatin remodeling as a potential epigenetic mechanism of tolerance to KRAS loss
Authors: Martins Flavia , Machado Ana L. , Carvalho Patricia D. , Carvalho Joana , Matthiesen Rune , Backman Vadim , Velho Sergia
Published: May 2023

KRAS-targeted inhibition yielded promising, yet far from ideal, clinical responses, revealing that cancer cells easily bypass KRAS loss. Therefore, we aim to understand how mutant KRAS cancer cells tolerate so well the loss of a key oncogene to which they were addicted to. KRAS expression was silenced through siRNAs in colorectal cancer (CRC) cell lines that carry KRAS mutations. The proteome characterization was obtained by mass spectrometry and the expression of significantly altered proteins was validated by western blotting. Chromatin states were investigated using electron microscopy. Upon KRAS inhibition, there was a significant reduction in the cell number, accompanied by changes in cell cycle, thus supporting KRAS-dependency. Proteomics analysis revealed that KRAS inhibition-tolerant cells upregulated several proteins associated with the extracellular exosome or nuclear compartments. Molecular function and biological process gene ontology terms revealed an up-regulation of proteins mainly associated with binding activities (RNA, protein, nucleosome, and core promoter binding) as well as gene expression regulation, mRNA splicing and processing, and nucleosome assembly and repositioning. In addition, the proteomics data also revealed an upregulation of proteins associated with active chromatin states. Moreover, KRAS-silenced persister cells also presented alterations in some histone post-translational modifications and in chromatin packing, both suggesting that transcription is impacted. Overall, our results suggest an epigenetic mechanism underlying tolerance to KRAS inhibition that involves chromatin structural changes and transcription alterations, which we are currently pursuing.

Citation Format: Flavia Martins, Ana L. Machado, Patricia D. Carvalho, Joana Carvalho, Rune Matthiesen, Vadim Backman, Sergia Velho. Chromatin remodeling as a potential epigenetic mechanism of tolerance to KRAS loss [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 A006.
Abstract A015: Dynamics and lipid interactions of the RAS-RBD-CRD protein complex
Authors: Lightstone Felice C. , Carpenter Timothy S.
Published: May 2023

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

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

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

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 B027: Bioluminescence resonance energy transfer (BRET) as a tool for assessing mutant KRAS-effector affinity and drug efficacy
Authors: Rigby Megan , Columbus John , Wall Vanessa , Esposito Dominic , Turbyville Thomas , Simanshu Dhirendra , Nissley Dwight , McCormick Frank , Maciag Anna
Published: May 2023

KRAS mutations occur in roughly 15% of cancer patients, with KRAS G12D, KRAS G12V, and KRAS G12C substitutions constituting the majority of these cases. Cancer types also display puzzling preferences for certain RAS mutations; for instance, 49% of pancreatic ductal carcinomas (PDAC) are driven by KRAS G12D substitutions compared to 35% of colon adenocarcinomas (COAD) and 17% of lung adenocarcinomas (LUAD)1. In contrast, KRAS G12C mutations drive only 3% of PDAC and 10% of COAD, but 41% of LUAD cases1. Some of this discrepancy can be explained by mutagen exposure, as there is evidence that tobacco smoke carcinogens drive the predominance of KRAS G12C mutations in lung cancer. However, it is possible that inherent functional differences between the mutant proteins also contribute to such preferences across cancer types. These oncogenic substitutions do endow subtle and unique differences in biochemical properties, but it is unknown whether this translates to differences in cellular signaling potential. KRAS activates the MAPK and PI3K signaling pathways by binding directly to RAF1 or the p110 catalytic subunit of PI3K. These interactions are important signaling nodes that result in cellular proliferation, survival, movement, differentiation, and immune evasion, and therefore drive cancer when constitutively activated by mutant KRAS. Biochemical assessments of relative effector affinity between KRAS mutants lack crucial elements present in a cellular environment, such as GDP/GTP ratios, membrane interactions, subcellular localization, and engagement with other proteins. Here, we optimize a cell-based Bioluminescent Resonance Energy Transfer (BRET) system in HEK293T cells using NanoLuc- and mVenus-tagged proteins to quantify relative effector affinities between KRAS mutants. We assess the affinities of KRAS4b G12C, KRAS4b G12D, and KRAS4b WT for effectors p110α and RAF1(52-188), along with RAS binding deficient control mutants p110α T208D/K227A and RAF1(52-188)R89L, and show statistical differences in effector engagement between the wildtype and mutant proteins. We also demonstrate the efficacy of this optimized system as a drug screening tool by assessing compounds in clinical development for their ability to disrupt mutant KRAS-effector interactions within a cellular environment. 1Prior IA, Hood FE, Hartley JL. The frequency of Ras mutations in cancer. Cancer Research 2020.

Citation Format: Megan Rigby, John Columbus, Vanessa Wall, Dominic Esposito, Thomas Turbyville, Dhirendra Simanshu, Dwight Nissley, Frank McCormick, Anna Maciag. Bioluminescence resonance energy transfer (BRET) as a tool for assessing mutant KRAS-effector affinity and drug efficacy [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 B027.
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

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

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

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.