bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of the Bolt Loosening Angle through Semantic Key Point Extraction Detection by Using an Hourglass Network
Authors: Ying Yu , Shichuan Wei , Wei Zhao
Published: May 2023

Damage in bolts, which are used as connecting fasteners in steel structures, affects structural safety. Sophisticated machine vision methods have been formulated for the detection of loose bolts, but their accuracy remains an area for improvement. In this paper, a method based on a stacked hourglass network is proposed for automatically extracting the key points of a bolt and for obtaining the bolt loosening angle by comparing the rotations of the key points before and after the bolt is damaged. A data set containing 100 images of key bolt loosening points was collected, and rotation was performed as data augmentation to yield 1800 images. Moreover, a method was designed for automatically annotating the augmented image data set. In this study, 70%, 10%, and 20% of the annotated image data set were used for training, validation, and testing, respectively. Subsequently, a neural network model based on a stacked hourglass network was established to train the annotated image data set. The detection results were evaluated in terms of normalized errors (NEs), percentage of correct key points (PCK), detection speed, and training time. In testing, the proposed method accurately and efficiently identified the bolt loosening angle, with a PCK value as high as 99.3%. The accuracy of the proposed method was also highly robust to different shooting distances, viewing angles, and illumination levels.
Supplementary Tables S1-S4 from Integrating Tumor-Intrinsic and Immunologic Factors to Identify Immunogenic Breast Cancers from a Low-Risk Cohort: Results from the Randomized SweBCG91RT Trial
Authors: Stenmark Tullberg Axel , Sjöström Martin , Niméus Emma , Killander Fredrika , Chang S. Laura , Feng Felix Y. , Speers Corey W. , Pierce Lori J. , Kovács Anikó , Lundstedt Dan , Holmberg Erik , Karlsson Per
Published: May 2023

Supplementary Table S1 Demographics of the training cohortsSupplementary Table S2 Immunscore modelSupplementary Table S3 Proliferative Index ModelSupplementary Table S4 Immunescore:Proliferative Index
Figure S1 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

Supplemental Figure 1. Myddosome signaling in normal human cerebral cortex.
supplementary table 1 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

supplementary table
Supplementary Data S1 from NPY Methylated ctDNA is a Promising Biomarker for Treatment Response Monitoring in Metastatic Colorectal Cancer
Authors: Janssens Katleen , Vanhoutte Greetje , Lybaert Willem , Demey Wim , Decaestecker Jochen , Hendrickx Koen , Rezaei Kalantari Hassan , Zwaenepoel Karen , Pauwels Patrick , Fransen Erik , Op de Beeck Ken , Van Camp Guy , Rolfo Christian , Peeters Marc
Published: May 2023

Supplementary data on the comparison of anti-EGFR therapy to anti-VEGF therapy.
Data from Zinc Finger MYND-Type Containing 8 (ZMYND8) Is Epigenetically Regulated in Mutant Isocitrate Dehydrogenase 1 (IDH1) Glioma to Promote Radioresistance
Authors: Carney Stephen V. , Banerjee Kaushik , Mujeeb Anzar , Zhu Brandon , Haase Santiago , Varela Maria L. , Kadiyala Padma , Tronrud Claire E. , Zhu Ziwen , Mukherji Devarshi , Gorla Preethi , Sun Yilun , Tagett Rebecca , Núñez Felipe J. , Luo Maowu , Luo Weibo , Ljungman Mats , Liu Yayuan , Xia Ziyun , Schwendeman Anna , Qin Tingting , Sartor Maureen A. , Costello Joseph F. , Cahill Daniel P. , Lowenstein Pedro R. , Castro Maria G.
Published: May 2023

AbstractPurpose:
Mutant isocitrate dehydrogenase 1 (mIDH1) alters the epigenetic regulation of chromatin, leading to a hypermethylation phenotype in adult glioma. This work focuses on identifying gene targets epigenetically dysregulated by mIDH1 to confer therapeutic resistance to ionizing radiation (IR).
Experimental Design:
We evaluated changes in the transcriptome and epigenome in a radioresistant mIDH1 patient-derived glioma cell culture (GCC) following treatment with an mIDH1-specific inhibitor, AGI-5198. We identified Zinc Finger MYND-Type Containing 8 (ZMYND8) as a potential target of mIDH1 reprogramming. We suppressed ZMYND8 expression by shRNA knockdown and genetic knockout (KO) in mIDH1 glioma cells and then assessed cellular viability to IR. We assessed the sensitivity of mIDH1 GCCS to pharmacologic inhibition of ZMYND8-interacting partners: HDAC, BRD4, and PARP.
Results:
Inhibition of mIDH1 leads to an upregulation of gene networks involved in replication stress. We found that the expression of ZMYND8, a regulator of DNA damage response, was decreased in three patient-derived mIDH1 GCCs after treatment with AGI-5198. Knockdown of ZMYND8 expression sensitized mIDH1 GCCs to radiotherapy marked by decreased cellular viability. Following IR, mIDH1 glioma cells with ZMYND8 KO exhibit significant phosphorylation of ATM and sustained γH2AX activation. ZMYND8 KO mIDH1 GCCs were further responsive to IR when treated with either BRD4 or HDAC inhibitors. PARP inhibition further enhanced the efficacy of radiotherapy in ZMYND8 KO mIDH1 glioma cells.
Conclusions:
These findings indicate the impact of ZMYND8 in the maintenance of genomic integrity and repair of IR-induced DNA damage in mIDH1 glioma.

See related commentary by Sachdev et al., p. 1648
Data from Genomic Complexity Predicts Resistance to Endocrine Therapy and CDK4/6 Inhibition in Hormone Receptor–Positive (HR+)/HER2-Negative Metastatic Breast Cancer
Authors: Davis Andrew A. , Luo Jingqin , Zheng Tiantian , Dai Chao , Dong Xiaoxi , Tan Lu , Suresh Rama , Ademuyiwa Foluso O. , Rigden Caron , Rearden Timothy P. , Clifton Katherine , Weilbaecher Katherine , Frith Ashley , Tandra Pavan K. , Summa Tracy , Haas Brittney , Thomas Shana , Hernandez-Aya Leonel F. , Peterson Lindsay L. , Wang Xiaohong , Luo Shujun J. , Zhou Kemin , Du Pan , Jia Shidong , King Bonnie L. , Krishnamurthy Jairam , Ma Cynthia X.
Published: May 2023

AbstractPurpose:
Clinical biomarkers to identify patients unlikely to benefit from CDK4/6 inhibition (CDK4/6i) in combination with endocrine therapy (ET) are lacking. We implemented a comprehensive circulating tumor DNA (ctDNA) analysis to identify genomic features for predicting and monitoring treatment resistance.
Experimental Design:
ctDNA was isolated from 216 plasma samples collected from 51 patients with hormone receptor–positive (HR+)/HER2-negative (HER2−) metastatic breast cancer (MBC) on a phase II trial of palbociclib combined with letrozole or fulvestrant (NCT03007979). Boosted whole-exome sequencing (WES) was performed at baseline and clinical progression to evaluate genomic alterations, mutational signatures, and blood tumor mutational burden (bTMB). Low-pass whole-genome sequencing was performed at baseline and serial timepoints to assess blood copy-number burden (bCNB).
Results:
High bTMB and bCNB were associated with lack of clinical benefit and significantly shorter progression-free survival (PFS) compared with patients with low bTMB or low bCNB (all P < 0.05). Dominant APOBEC signatures were detected at baseline exclusively in cases with high bTMB (5/13, 38.5%) versus low bTMB (0/37, 0%; P = 0.0006). Alterations in ESR1 were enriched in samples with high bTMB (P = 0.0005). There was a high correlation between bTMB determined by WES and bTMB determined using a 600-gene panel (R = 0.98). During serial monitoring, an increase in bCNB score preceded radiographic progression in 12 of 18 (66.7%) patients.
Conclusions:
Genomic complexity detected by noninvasive profiling of bTMB and bCNB predicted poor outcomes in patients treated with ET and CDK4/6i and identified early disease progression before imaging. Novel treatment strategies including immunotherapy-based combinations should be investigated in this population.
Data from BRD9 Degradation Disrupts Ribosome Biogenesis in Multiple Myeloma
Authors: Kurata Keiji , Samur Mehmet K. , Liow Priscilla , Wen Kenneth , Yamamoto Leona , Liu Jiye , Morelli Eugenio , Gulla Annamaria , Tai Yu-Tzu , Qi Jun , Hideshima Teru , Anderson Kenneth C.
Published: May 2023

AbstractPurpose:
BRD9 is a defining component of the noncanonical SWI/SNF complex, which regulates gene expression by controlling chromatin dynamics. Although recent studies have found an oncogenic role for BRD9 in multiple cancer types including multiple myeloma, its clinical significance and oncogenic mechanism have not yet been elucidated. Here, we sought to identify the clinical and biological impact of BRD9 in multiple myeloma, which may contribute to the development of novel therapeutic strategies.
Experimental Design:
We performed integrated analyses of BRD9 in vitro and in vivo using multiple myeloma cell lines and primary multiple myeloma cells in established preclinical models, which identified the molecular functions of BRD9 contributing to multiple myeloma cell survival.
Results:
We found that high BRD9 expression was a poor prognostic factor in multiple myeloma. Depleting BRD9 by genetic (shRNA) and pharmacologic (dBRD9-A; proteolysis-targeting chimera; BRD9 degrader) approaches downregulated ribosome biogenesis genes, decreased the expression of the master regulator MYC, and disrupted the protein-synthesis maintenance machinery, thereby inhibiting multiple myeloma cell growth in vitro and in vivo in preclinical models. Importantly, we identified that the expression of ribosome biogenesis genes was associated with the disease progression and prognosis of patients with multiple myeloma. Our results suggest that BRD9 promotes gene expression by predominantly occupying the promoter regions of ribosome biogenesis genes and cooperating with BRD4 to enhance the transcriptional function of MYC.
Conclusions:
Our study identifies and validates BRD9 as a novel therapeutic target in preclinical models of multiple myeloma, which provides the framework for the clinical evaluation of BRD9 degraders to improve patient outcome.
Data from Influence of Genomic Landscape on Cancer Immunotherapy for Newly Diagnosed Ovarian Cancer: Biomarker Analyses from the IMagyn050 Randomized Clinical Trial
Authors: Landen Charles N. , Molinero Luciana , Hamidi Habib , Sehouli Jalid , Miller Austin , Moore Kathleen N. , Taskiran Cagatay , Bookman Michael , Lindemann Kristina , Anderson Charles , Berger Regina , Myers Tashanna , Beiner Mario , Reid Thomas , Van Nieuwenhuysen Els , Green Andrew , Okamoto Aikou , Aghajanian Carol , Thaker Premal H. , Blank Stephanie V. , Khor Victor K. , Chang Ching-Wei , Lin Yvonne G. , Pignata Sandro
Published: May 2023

AbstractPurpose:
To explore whether patients with BRCA1/2-mutated or homologous recombination deficient (HRD) ovarian cancers benefitted from atezolizumab in the phase III IMagyn050 (NCT03038100) trial.
Patients and Methods:
Patients with newly diagnosed ovarian cancer were randomized to either atezolizumab or placebo with standard chemotherapy and bevacizumab. Programmed death-ligand 1 (PD-L1) status of tumor-infiltrating immune cells (IC) was determined centrally (VENTANA SP142 assay). Genomic alterations, including deleterious BRCA1/2 alterations, genomic loss of heterozygosity (gLOH), tumor mutation burden (TMB), and microsatellite instability (MSI), were evaluated using the FoundationOne assay. HRD was defined as gLOH ≥ 16%, regardless of BRCA1/2 mutation status. Potential associations between progression-free survival (PFS) and genomic biomarkers were evaluated using standard correlation analyses and log-rank of Kaplan–Meier estimates.
Results:
Among biomarker-evaluable samples, 22% (234/1,050) harbored BRCA1/2 mutations and 46% (446/980) were HRD. Median TMB was low irrespective of BRCA1/2 or HRD. Only 3% (29/1,024) had TMB ≥10 mut/Mb, and 0.3% (3/1,022) were MSI-high. PFS was better in BRCA2-mutated versus BRCA2–non-mutated tumors and in HRD versus proficient tumors. PD-L1 positivity (≥1% expression on ICs) was associated with HRD but not BRCA1/2 mutations. PFS was not improved by adding atezolizumab in BRCA2-mutated or HRD tumors; there was a trend toward enhanced PFS with atezolizumab in BRCA1-mutated tumors.
Conclusions:
Most ovarian tumors have low TMB despite BRCA1/2 mutations or HRD. Neither BRCA1/2 mutation nor HRD predicted enhanced benefit from atezolizumab. This is the first randomized double-blind trial in ovarian cancer demonstrating that genomic instability triggered by BRCA1/2 mutation or HRD is not associated with improved sensitivity to immune checkpoint inhibitors.

See related commentary by Al-Rawi et al., p. 1645
Data from Impact of Biomarker-Matched Therapies on Outcomes in Patients with Sarcoma Enrolled in Early-Phase Clinical Trials (SAMBA 101)
Authors: Carmagnani Pestana Roberto , Moyers Justin T. , Roszik Jason , Sen Shiraj , Hong David S. , Naing Aung , Herzog Cynthia E. , Fu Siqing , Piha-Paul Sarina A. , Rodon Jordi , Yap Timothy A. , Karp Daniel D. , Tsimberidou Apostolia M. , Pant Shubham , Zarzour Maria A. , Ratan Ravin , Ravi Vinod , Benjamin Robert S. , Lazar Alexander J. , Wang Wei-Lien , Daw Najat , Gill Jonathan B. , Harrison Douglas J. , Lewis Valerae O. , Roland Christina L. , Patel Shreyaskumar R. , Livingston J. Andrew , Somaiah Neeta , Ludwig Joseph A. , Conley Anthony P. , Hamerschlak Nelson , Gorlick Richard , Meric-Bernstam Funda , Subbiah Vivek
Published: May 2023

AbstractPurpose:
Developing new therapeutics for any of the more than 100 sarcoma subtypes presents a challenge. After progression from standard therapies, patients with sarcoma may be referred for enrollment in early-phase trials. This study aimed to investigate whether enrollment in biomarker-matched early-phase clinical trials leads to better outcomes for patients with advanced sarcoma.
Experimental Design:
In this retrospective analysis, investigational treatment characteristics and longitudinal survival outcomes were analyzed in patients with biopsy-confirmed sarcoma enrolled in early-phase trials at MD Anderson Cancer Center from May 2006 to July 2021.
Results:
Five hundred eighty-seven patients were included [405 soft tissue, 122 bone, 60 gastrointestinal stromal tumor (GIST); median of three prior lines of therapy]. Most common subtypes were leiomyosarcoma (17.2%), liposarcoma (14.0%), and GIST (10.2%). Molecular testing was available for 511 patients (87.1%); 221 patients (37.6%) were treated in matched trials. Overall response rate was 13.1% matched compared with 4.9% in unmatched (P < 0.001); the clinical benefit rate at 6 months was 43.9% vs. 19.9% (P < 0.001). Progression-free survival was longer for patients in matched trials (median, 5.5 vs. 2.4 months; P < 0.001), and overall survival was also superior for patients in matched trials (median, 21.5 vs. 12.3 months; P < 0.001). The benefit of enrollment in matched trials was maintained when patients with GIST were excluded from the analysis.
Conclusions:
Enrollment in biomarker-matched early-phase trials is associated with improved outcomes in heavily pretreated patients with metastatic sarcoma. Molecular testing of tumors from patients with advanced sarcoma and enrollment in matched trials is a reasonable therapeutic strategy.
Data from Integrating Tumor-Intrinsic and Immunologic Factors to Identify Immunogenic Breast Cancers from a Low-Risk Cohort: Results from the Randomized SweBCG91RT Trial
Authors: Stenmark Tullberg Axel , Sjöström Martin , Niméus Emma , Killander Fredrika , Chang S. Laura , Feng Felix Y. , Speers Corey W. , Pierce Lori J. , Kovács Anikó , Lundstedt Dan , Holmberg Erik , Karlsson Per
Published: May 2023

AbstractPurpose:
The local immune infiltrate's influence on tumor progression may be closely linked to tumor-intrinsic factors. The study aimed to investigate whether integrating immunologic and tumor-intrinsic factors can identify patients from a low-risk cohort who may be candidates for radiotherapy (RT) de-escalation.
Experimental Design:
The SweBCG91RT trial included 1,178 patients with stage I to IIA breast cancer, randomized to breast-conserving surgery with or without adjuvant RT, and followed for a median of 15.2 years. We trained two models designed to capture immunologic activity and immunomodulatory tumor-intrinsic qualities, respectively. We then analyzed if combining these two variables could further stratify tumors, allowing for identifying a subgroup where RT de-escalation is feasible, despite clinical indicators of a high risk of ipsilateral breast tumor recurrence (IBTR).
Results:
The prognostic effect of the immunologic model could be predicted by the tumor-intrinsic model (Pinteraction = 0.01). By integrating measurements of the immunologic- and tumor-intrinsic models, patients who benefited from an active immune infiltrate could be identified. These patients benefited from standard RT (HR, 0.28; 95% CI, 0.09–0.85; P = 0.025) and had a 5.4% 10-year incidence of IBTR after irradiation despite high-risk genomic indicators and a low frequency of systemic therapy. In contrast, high-risk tumors without an immune infiltrate had a high 10-year incidence of IBTR despite RT treatment (19.5%; 95% CI, 12.2–30.3).
Conclusions:
Integrating tumor-intrinsic and immunologic factors may identify immunogenic tumors in early-stage breast cancer populations dominated by ER-positive tumors. Patients who benefit from an activated immune infiltrate may be candidates for RT de-escalation.
Type 2 Diabetes Mellitus and Efficacy Outcomes from Immune Checkpoint Blockade in Patients with Cancer
Authors: Cortellini Alessio , D'Alessio Antonio , Cleary Siobhan , Buti Sebastiano , Bersanelli Melissa , Bordi Paola , Tonini Giuseppe , Vincenzi Bruno , Tucci Marco , Russo Alessandro , Pantano Francesco , Russano Marco , Stucci Luigia Stefania , Sergi Maria Chiara , Falconi Martina , Zarzana Maria Antonietta , Santini Daniele , Spagnolo Francesco , Tanda Enrica T. , Rastelli Francesca , Giorgi Francesca Chiara , Pergolesi Federica , Giusti Raffaele , Filetti Marco , Lo Bianco Francesca , Marchetti Paolo , Botticelli Andrea , Gelibter Alain , Siringo Marco , Ferrari Marco , Marconcini Riccardo , Vitale Maria Giuseppa , Nicolardi Linda , Chiari Rita , Ghidini Michele , Nigro Olga , Grossi Francesco , De Tursi Michele , Di Marino Pietro , Queirolo Paola , Bracarda Sergio , Macrini Serena , Inno Alessandro , Zoratto Federica , Veltri Enzo , Spoto Chiara , Vitale Maria Grazia , Cannita Katia , Gennari Alessandra , Morganstein Daniel L. , Mallardo Domenico , Nibid Lorenzo , Sabarese Giovanna , Brunetti Leonardo , Perrone Giuseppe , Ascierto Paolo A. , Ficorella Corrado , Pinato David J.
Published: May 2023

Purpose:

No evidence exists as to whether type 2 diabetes mellitus (T2DM) impairs clinical outcome from immune checkpoint inhibitors (ICI) in patients with solid tumors.

Experimental Design:

In a large cohort of ICI recipients treated at 21 institutions from June 2014 to June 2020, we studied whether patients on glucose-lowering medications (GLM) for T2DM had shorter overall survival (OS) and progression-free survival (PFS). We used targeted transcriptomics in a subset of patients to explore differences in the tumor microenvironment (TME) of patients with or without diabetes.

Results:

A total of 1,395 patients were included. Primary tumors included non–small cell lung cancer (NSCLC; 54.7%), melanoma (24.7%), renal cell (15.0%), and other carcinomas (5.6%). After multivariable analysis, patients on GLM (n = 226, 16.2%) displayed an increased risk of death [HR, 1.29; 95% confidence interval (CI),1.07–1.56] and disease progression/death (HR, 1.21; 95% CI, 1.03–1.43) independent of number of GLM received. We matched 92 metformin-exposed patients with 363 controls and 78 patients on other oral GLM or insulin with 299 control patients. Exposure to metformin, but not other GLM, was associated with an increased risk of death (HR, 1.53; 95% CI, 1.16–2.03) and disease progression/death (HR, 1.34; 95% CI, 1.04–1.72). Patients with T2DM with higher pretreatment glycemia had higher neutrophil-to-lymphocyte ratio (P = 0.04), while exploratory tumoral transcriptomic profiling in a subset of patients (n = 22) revealed differential regulation of innate and adaptive immune pathways in patients with T2DM.

Conclusions:

In this study, patients on GLM experienced worse outcomes from immunotherapy, independent of baseline features. Prospective studies are warranted to clarify the relative impact of metformin over a preexisting diagnosis of T2DM in influencing poorer outcomes in this population.
Uncoupling CD4+ TIL-Mediated Tumor Killing from JAK-Signaling in Melanoma
Authors: Draghi Arianna , Presti Mario , Jensen Agnete W.P. , Chamberlain Christopher A. , Albieri Benedetta , Rasmussen Anne-Christine K. , Andersen Mads H. , Crowther Michael D. , Svane Inge Marie , Donia Marco
Published: May 2023

Purpose:

Impaired MHCI-presentation and insensitivity to immune effector molecules are common features of immune checkpoint blockade (ICB)-resistant tumors and can be, respectively, associated with loss of β2 microglobulin (B2M) or impaired IFNγ signaling. Patients with ICB-resistant tumors can respond to alternative immunotherapies, such as infusion of autologous tumor-infiltrating lymphocytes (TIL). CD4+ T cells can exert cytotoxic functions against tumor cells; however, it is unclear whether CD4+ T-cell responses can be exploited to improve the clinical outcomes of patients affected by ICB-resistant tumors.

Experimental Design:

Here, we exploited CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 gene editing to reproduce immune-resistant tumor phenotypes via gene knockout (KO). To determine the role of cytotoxic CD4+ TILs in ICB-resistant tumors, we investigated CD4+ TIL-mediated cytotoxicity in matched pairs of TILs and autologous melanoma cell lines, used as a model of patient-specific immune-tumor interaction. Around 40% of melanomas constitutively express MHC Class II molecules; hence, melanomas with or without natural constitutive MHC Class II expression (MHCIIconst+ or MHCIIconst−) were used.

Results:

CD4+ TIL-mediated cytotoxicity was not affected by B2M loss but was dependent on the expression of CIITA. MHCIIconst+ melanomas were killed by tumor-specific CD4+ TILs even in the absence of IFNγ-mediated MHCII upregulation, whereas IFNγ was necessary for CD4+ TIL-mediated cytotoxicity against MHCIIconst- melanomas. Notably, although tumor-specific CD4+ TILs did not kill JAK1KO MHCIIconst- melanomas even after IFNγ stimulation, sensitivity to CD4+ TIL-mediated cytotoxicity was maintained by JAK1KO MHCIIconst+ melanomas.

Conclusions:

In conclusion, our data indicate that exploiting tumor-specific cytotoxic CD4+ TILs could help overcome resistance to ICB mediated by IFNγ-signaling loss in MHCIIconst+ melanomas.

See related commentary by Betof Warner and Luke, p. 3829
Direct-to-Patient Clinical Trials: One Small Step or a Giant Leap?
Authors: Desai Aakash , Subbiah Vivek
Published: May 2023

Genome driven precision oncology has transformed the landscape of multiple cancers. However, access barriers exist. A recent study exemplified a direct-to-patient outreach program via social media through the implementation of a global program that offered free tumor genomic testing with a focus on rare cancers.

See related article by Doe-Tetteh et al., p. 2445
Data 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

Abstract
Cancer cells reprogram energy metabolism through metabolic plasticity, adapting ATP-generating pathways in response to treatment or microenvironmental changes. Such adaptations enable cancer cells to resist standard therapy. We employed a coculture model of estrogen receptor–positive (ER+) breast cancer and mesenchymal stem cells (MSC) to model interactions of cancer cells with stromal microenvironments. Using single-cell endogenous and engineered biosensors for cellular metabolism, coculture with MSCs increased oxidative phosphorylation, intracellular ATP, and resistance of cancer cells to standard therapies. Cocultured cancer cells had increased MCT4, a lactate transporter, and were sensitive to the MCT1/4 inhibitor syrosingopine. Combining syrosingopine with fulvestrant, a selective estrogen receptor degrading drug, overcame resistance of ER+ breast cancer cells in coculture with MSCs. Treatment with antiestrogenic therapy increased metabolic plasticity and maintained intracellular ATP levels, while MCT1/4 inhibition successfully limited metabolic transitions and decreased ATP levels. Furthermore, MCT1/4 inhibition decreased heterogenous metabolic treatment responses versus antiestrogenic therapy. These data establish MSCs as a mediator of cancer cell metabolic plasticity and suggest metabolic interventions as a promising strategy to treat ER+ breast cancer and overcome resistance to standard clinical therapies.
Implications:
This study reveals how MSCs reprogram metabolism of ER+ breast cancer cells and point to MCT4 as potential therapeutic target to overcome resistance to antiestrogen drugs.
Abstract A012: Exploring the role of adaptive amino acid responses in Ras-driven leukemia progression and therapy
Authors: Zhang Ji , Claude Rodney , Srivastava Sankalp , Batra Sandeep , Zhong Minghua , Dave Utpal , Wek Ronald C.
Published: May 2023

Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer, affecting the lymphoid cells of both B and T lineages. Most ALL cells are auxotrophic for asparagine, a nonessential amino acid for protein synthesis, due to the low expression of asparagine synthetase (ASNS), a rate limiting enzyme for de novo biosynthesis of asparagine. As a result, standard ALL treatment takes advantage of this vulnerability by giving patients L-asparaginase, a bacterial enzyme that depletes the circulating asparagine. However, previous work from our lab and others have shown that some ALL cells become resistance to L-asparaginase treatment through the induction of ASNS expression. Mechanistically, amino acid starvation actives the general control nonderepressible 2 (GCN2) kinase, leading to the accumulation of ATF4 transcriptional factor. ATF4, in turn, is recruited to the promoter of the ASNS gene to activate its transcription. However, the role of GCN2 kinase in the process of leukemogenesis under nutrient limiting environment has not been established. In this study, our goal is to use a mouse model of T-ALL driven by mutant KRas to determine the role of GCN2 in leukemogenesis and the therapeutic response to L-asparaginase treatment.

Citation Format: Ji Zhang, Rodney Claude, Sankalp Srivastava, Sandeep Batra, Minghua Zhong, Utpal Dave, Ronald C. Wek. Exploring the role of adaptive amino acid responses in Ras-driven leukemia progression and therapy [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 A012.
Abstract B005: RAS inhibitors to treat luminal B breast cancer
Authors: Clarke Geoff , Donninger Howard , Jigo Raphael , Arshad Tariq , von Baby Becca , Ferrill Rachel , Sabo Mike , Burlison Joe , Trent John
Published: May 2023

Since RAS mutations are rare in Breast Cancer, RAS has not traditionally been considered as an important driver of this disease. However, RAS signaling pathways are frequently hyper-activated in breast cancers and genetic/epigenetic inactivation of RAS negative regulators (GAPs) is common. This is particularly true for Luminal B breast cancer.   Luminal breast cancer makes up the majority of Breast Cancers, ~ 65% of cases.   The Luminal B form makes up around 1/3 of these. Although current therapeutic options for luminal A (surgery, endocrine therapy) can be reasonably effective, Luminal B tumors are much more dangerous. These tumors are less sensitive to therapy in the first place and have a high frequency of relapse.   Moreover, Luminal B tumors tend to occur more frequently in younger women and have a higher incidence of metastasis. One recent analysis has shown that Luminal B cancers have little better overall survival rates than the notorious triple negative breast cancers. Therefore, better therapies for Luminal B breast cancer are urgently required. One approach may be to target the hyper-active wild-type RAS oncoprotein that drives many of these tumors. We have in used in silico library screening followed by Medicinal Chemistry optimization to develop a series of novel small molecules that bind to all three main RAS proteins and block RAS function. We have validated the agents by using Microscale Thermophoresis binding procedures to quantify recombinant protein interaction. We used 3D growth inhibition and protein-based RAS signaling assays to quantify the biological action of the agents. Finally, we validated one of the more effective agents in vivo against a Luminal B cell line xenograft. This may be the first example of an effective anti-RAS therapy in breast cancer. It serves as proof of principal for the use of ant-RAS drugs in Luminal B disease. As basal breast cancers often exhibit loss of function of the RAS GAP called NF1, this strategy may have applications beyond Luminal B disease.

Citation Format: Geoff Clarke, Howard Donninger, Raphael Jigo, Tariq Arshad, Becca von Baby, Rachel Ferrill, Mike Sabo, Joe Burlison, John Trent. RAS inhibitors to treat luminal B breast 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 B005.
Abstract IA06: Targeting the ERK-MYC signaling network for the treatment of KRAS-mutant cancers
Authors: Der Channing J.
Published: May 2023

KRAS is mutationally activated in 95% of pancreatic ductal adenocarcinomas (PDAC) and essential for maintenance of PDAC tumorigenic growth. The recent clinical evaluation of inhibitors of one KRAS mutant (KRASG12C) supports the therapeutic value of direct targeting of KRAS for PDAC treatment. However, this mutant comprises less than 2% of KRAS mutations in PDAC. Therefore, we have evaluated direct inhibitors of the predominant KRAS mutations (G12D, G12V and G12R) in PDAC. Additionally, both innate and treatment-associated resistance mechanisms will limit the effectiveness of direct KRAS inhibitors. Genomic sequencing analyses of patients who relapsed on KRASG12C inhibitors suggest that reactivation of KRAS effector signaling comprises one major mechanism of resistance. We determined that activation of MEK-ERK but not AKT activation alone is sufficient to drive resistance to KRASG12C/D inhibitors. However, our recent clinical evaluation of direct ERK inhibition in PDAC found that toxicity limited the effectiveness of this therapeutic approach. These observations prompted our studies to complete a system-wide determination of the molecular mechanisms by which ERK signaling supports KRAS-dependent PDAC growth. First, we determined the KRAS-ERK regulated transcriptome, kinome, total proteome and phosphoproteome in KRAS-mutant PDAC. We identified KRAS-dependent gene signature (677 KRAS-dependent and 1,051 KRAS-suppressed genes) that diverged significantly from the classical Hallmark KRAS gene signature. We identified 5,117 ERK-dependent phosphosites on 2,252 proteins, of which 88% and 67%, respectively, were not previously associated with ERK. Second, since a major consequence of ERK signaling involves activation of MYC-regulated gene transcription, we also determined the MYC-dependent transcriptome (2,086 MYC-dependent and 2,403 MYC-suppressed genes) that include 80 protein kinases. Together, these analyses define a highly complex and dynamic ERK-regulated signaling network that deregulates cell cycle progression, RHO GTPase function and metabolism to support KRAS-dependent PDAC growth.

Citation Format: Channing J. Der. Targeting the ERK-MYC signaling network for the treatment of KRAS-mutant 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 IA06.
Abstract IA10: K-RAS hyperexchange mutants in colorectal cancer
Authors: Haigis Kevin
Published: May 2023

K-RAS can be functionally activated by reducing its ability to catalyze the hydrolysis of GTP and/or by increasing its nucleotide exchange activity. Cancer-associated mutations that increase exchange – termed hyperexchange mutants – are relatively rare and exhibit unique structural, biochemical, and biologic properties relative to hydrolysis mutants. The most common hyperexchange mutant is Ala146Thr, which exhibits a 10-fold increase in exchange activity relative to wild-type K-RAS while not significantly affecting GTP hydrolysis. This mutant is relatively common in colorectal cancer, but exceedingly rare in pancreatic cancer. The hyperexchange property of K-RASA146T leads to relatively low steady state levels of K-RAS-GTP, which underlies the tissue specific oncogenic activity of the mutant. Another hyperexchange mutant, K-RASA59T, is unique in that it uses the gamma-phosphate of GTP to phosphorylate Thr59 in the active site. This mutant also exhibits attenuated MAPK signaling, but through a distinct mechanism. K-RAS proteins with oncogenic substitutions at position 59 fail to properly engage RAF proteins and cannot induce B-RAF/C-RAF dimers. As a result, residue 59 mutants require cooperating mutations in other MAPK pathway genes in order to be fully oncogenic. This obligate cooperativity is borne out in the genetics of human cancers and in genetically engineered mouse models. In summary, hyperexchange mutants represent a class of oncogenic forms of K-RAS that exhibit distinct biochemically properties and attenuated MAPK. As such, this class of mutants may be sensitive to therapeutic approaches that are not effective in cancers expressing stronger forms of oncogenic K-RAS.

Citation Format: Kevin Haigis. K-RAS hyperexchange mutants in colorectal 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 IA10.
Abstract IA17: Use of RAS isoforms in nerve tumors
Authors: Ratner Nancy , Hu Liang , Pundavela Jay , Epstein Jonathan A.
Published: May 2023

Neurofibromatosis Type I (NF1) is a common genetic disorder caused by mutations in the NF1 gene, which encodes a RAS-GAP. NF1 loss of function renders patients susceptible to tumors including NF1-/- benign neurofibromas, which can transform into atypical neurofibromas with NF1 and CDKN2A loss, and then lethal malignant peripheral nerve sheath tumors with NF1. CDKN2A, and PRC2 component loss. NF1 mutations are also common in many sporadic cancers. NF1 loss is known to increase or prolong wild type RAS activation, but the relative contribution of RAS paralogs (classical H-, N-, K-RAS and non-classical R-RAS, TC21, MRAS) to NF1 nerve tumorigenesis remains unknown. Our goal was to define the critical RAS paralog mediating the effect of NF1 protein deficiency due to NF1 mutations in neurofibromas and atypical neurofibromas, and to test whether targeting specific RAS paralogs might provide therapeutic strategies. Our data shows that KRAS is activated in RAS protein in NF1-deficient human and mouse Schwann cells (SCs), and in atypical Schwann cells. We find that a PKC agonist, prostratin, known to kill KRAS mutant cells, also selectively kills NF1 mutant Schwann cells in vitro and in mouse neurofibromas, and reduces tumor growth in a xenograft model of atypical neurofibroma. Prostratin acts through use of a subset of PKC isoforms. We anticipate that these findings can ultimately be used to develop an effective RAS targeting therapy for NF1 tumor prevention and treatment. Supported by: NIH R37 NS083580 and R01 NS12082 (N.R.), CancerFree KIDS (N.R.) and a Strauss Fellow Award (L.H.).

Citation Format: Nancy Ratner, Liang Hu, Jay Pundavela, Jonathan A. Epstein. Use of RAS isoforms in nerve tumors [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 IA17.
Abstract IA19: Oncogenic KRAS and the regulation of the pancreatic cancer microenvironment.
Authors: Magliano Marina Pasca di
Published: May 2023

Pancreatic ductal adenocarcinoma, the most common form of pancreatic cancer, is characterized by almost universal presence of oncogenic KRAS. A key characteristic of pancreatic cancer is the abundant accumulation of tumor microenvironment, rich in infiltrating immune cells and an extensive fibroblast population. Pancreatic cancer is preceded by precursor lesions known as Pancreatic Intraepithelial Neoplasia (PanIN); PanIN formation is accompanied by the formation of a pre-TME. Analysis of donor pancreas from healthy individual revealed that PanIN is common in human samples, and accompanied by pre-TME accumulation in human samples. We sought to determine whether oncogenic KRAS drives accumulation and maintenance of the pre-TME. For this purpose, we utilized the iKRAS mouse model of pancreatic cancer, which allows tissue-specific, inducible and reversible activation of KRASG12D, the most common mutant form in human pancreatic cancer. Activation of oncogenic KRAS in iKRAS mice leads to PanIN formation. We observed that fibroblast activation occurs upon KRAS activation and precedes the formation of overt lesions. Further, epithelial oncogenic KRAS is required to maintain fibroblast reprogramming in PanIN. To comprehensively understand changes in fibroblasts, we used single cell RNA sequencing, and observed that the fibroblast transcriptional program is extrinsically regulated by epithelial oncogenic KRAS. The reprogramming process can be modeled in vivo using conditioned media from pancreatic cancer cells expressing oncogenic KRAS, and is mediated by JAK/STAT3 signaling in fibroblasts. We then sought to determine whether the extrinsic effects of oncogenic KRAS induced reprogramming of fibroblasts at distal sites. We chose to study the lung, which is a common site of metastasis for pancreatic cancer. Our data show that lung fibroblasts are activated following expression of oncogenic KRAS in the pancreas; fibroblast activation is accompanied by phospho-Stat3 signaling, a readout of the JAK/Stat3 pathway, and precedes metastasis outgrowth in the pancreas. Thus, oncogenic KRAS extrinsically reprograms the local and systemic environments, possibly facilitating metastatic spread of pancreatic cancer.

Citation Format: Marina Pasca di Magliano. Oncogenic KRAS and the regulation of the pancreatic cancer microenvironment. [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 IA19.
Abstract IA21: Immune rewiring of mutant Ras tumors: Mechanisms and translational implications
Authors: Bar-Sagi Dafna
Published: May 2023

Oncogenic mutations in KRas are found in more than 90% of pancreatic tumors. These mutations are acquired at an early stage of disease and, in experimental models, have been shown to be essential for tumor initiation, progression and maintenance. Studies from our lab have shown that the growth of oncogenic KRas harboring pancreatic tumors is associated with an immuo-suppressed state that is established via the dynamic interplay between the tumor cells and the immune milieu. Molecular dissection of the mechanisms that mediate this interplay reveals the engagement of a transcriptional program that drives the expression of a plethora of cytokines and chemokines. This presentation will focus on a subgroup of cytokines and the role they play in activating specific immunosuppressive pathways. The implication of our findings to disease progression and therapeutic intervention will be discussed.

Citation Format: Dafna Bar-Sagi. Immune rewiring of mutant Ras tumors: Mechanisms and translational implications [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 IA21.
Abstract PR09: KRAS-targeted PROTAC degraders are broadly efficacious against KRAS-dependent tumor models
Authors: Smith Kathryn , Lopez-Arroyo Andrea , Berk Jason , Hegan Peter , Nower Peter , Tice Samantha , Moutran Aurelie , Pizzano Jennifer , Dowtin Amanda , Bookbinder Mark , Bortolon Elizabeth , Cadelina Greg , Karim Fazlul , Digianantonio Katie , Bekes Miklos , Medina Jesus
Published: May 2023

KRAS is genomically altered in about one third of all human tumors. Due to its central role in oncogenesis, many attempts have been made in the last four decades to drug mutant KRAS, either directly or indirectly. Despite recent advances in targeting KRAS using small molecule inhibitors, the majority of KRAS alterations do not yet have an existing targeted therapy, and where inhibitors are available, resistance rapidly emerges. Thus, novel approaches to drugging KRAS are needed. Eliminating mutant KRAS using a targeted protein degradation approach may lead to superior efficacy relative to inhibiting the protein. KRAS PROTAC® degraders that selectively target the G12D mutant form of KRAS were identified and profiled in KRAS-dependent cancer models. In vitro, PROTAC degraders targeting the G12D mutant degrade KRAS with picomolar potency, robustly suppress MAPK and PI3K/AKT signaling, induce apoptosis, and have antiproliferative activity that is superior to known inhibitors. These molecules are selective for mutant KRAS G12D, neither degrading wild-type KRAS nor the related isoforms HRAS and NRAS. In vivo, these degraders can eliminate >95% of mutant KRAS from relevant xenograft models, induce apoptosis, and lead to tumor regression. Consistent with the extended pharmacodynamics often observed with PROTAC degraders, a single dose of a G12D PROTAC results in prolonged KRAS degradation and significant pERK suppression up to one week after administration. Combined, these data show that degrading mutant KRAS G12D in tumors is highly efficacious and may have advantages over inhibition, making it an exciting potential new approach for the treatment of KRAS mutant cancers.

Citation Format: Kathryn Smith, Andrea Lopez-Arroyo, Jason Berk, Peter Hegan, Peter Nower, Samantha Tice, Aurelie Moutran, Jennifer Pizzano, Amanda Dowtin, Mark Bookbinder, Elizabeth Bortolon, Greg Cadelina, Fazlul Karim, Katie Digianantonio, Miklos Bekes, Jesus Medina. KRAS-targeted PROTAC degraders are broadly efficacious against KRAS-dependent tumor models [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 PR09.
Data 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

Abstract
Accurate breast cancer risk prediction could improve risk-reduction paradigms if thoughtfully used in clinical practice. Identification of at-risk women is the first step in tailoring risk screening and risk-reduction protocols to women's needs. Using the UK Biobank, we validated a simple risk model to predict breast cancer risk in the general population. Our simple breast cancer risk (BRISK) model integrates a combination of impactful breast cancer-associated risk factors including extended family history and polygenic risk allowing for the removal of moderate factors currently found in comprehensive traditional models. Using two versions of BRISK, differing by 77-single-nucleotide polymorphisms (SNP) versus 313-SNP polygenic risk score integration, we found improved discrimination and risk categorization of both BRISK models compared with one of the most well-known models, the Breast Cancer Risk Assessment Tool (BRCAT). Over a 5-year period, at-risk women classified ≥3% 5-year risk by BRISK had a 1.829 (95% CI = 1.710–1.956) times increased incidence of breast cancer compared with the population, which was higher than the 1.413 (95% CI = 1.217–1.640) times increased incidence for women classified ≥3% by BCRAT.
Prevention Relevance:
In this prospective population-based cohort study, we show the improved performance of a new risk assessment model compared with a gold-standard model (BCRAT). The classification of at-risk women using this new model highlights the opportunity to improve risk stratification and implement existing clinical risk-reduction interventions.
Data from Molecular evolution of classic Hodgkin lymphoma revealed through whole genome sequencing of Hodgkin and Reed Sternberg cells
Authors: Maura Francesco , Ziccheddu Bachisio , Xiang Jenny Z. , Bhinder Bhavneet , Rosiene Joel , Abascal Federico , Maclachlan Kylee H. , Eng Kenneth Wha. , Uppal Manik , He Feng , Zhang Wei , Gao Qi , Yellapantula Venkata D. , Trujillo-Alonso Vicenta , Park Sunita I. , Oberley Matthew J. , Ruckdeschel Elizabeth , Lim Megan S. , Wertheim Gerald B. , Barth Matthew J. , Horton Terzah M. , Derkach Andriy , Kovach Alexandra E. , Forlenza Christopher J. , Zhang Yanming , Landgren Ola , Moskowitz Craig H. , Cesarman Ethel , Imielinski Marcin , Elemento Olivier , Roshal Mikhail , Giulino-Roth Lisa
Published: May 2023

Abstract
The rarity of malignant Hodgkin and Reed Sternberg (HRS) cells in classic Hodgkin lymphoma (cHL) limits the ability to study the genomics of cHL. To circumvent this, our group has previously optimized fluorescence-activated cell sorting to purify HRS cells. Using this approach we now report the whole genome sequencing landscape of HRS cells and reconstruct the chronology and likely etiology of pathogenic events leading to cHL. We identified alterations in driver genes not previously described in cHL, APOBEC mutational activity, and the presence of complex structural variants including chromothripsis. We found that high ploidy in cHL is often acquired through multiple, independent chromosomal gains events including whole genome duplication. Evolutionary timing analyses revealed that structural variants enriched for RAG motifs, driver mutations in B2M, BCL7A, GNA13, and PTPN1, and the onset of AID driven mutagenesis usually preceded large chromosomal gains. This study provides a temporal reconstruction of cHL pathogenesis.
LONG-COVID ТА АСОЦІЙОВАНІ УРАЖЕННЯ СЕРЦЕВО-СУДИННОЇ ТА НЕРВОВОЇ СИСТЕМ
Authors: Світайло В. С. , Чемич М. Д. , Саєнко О. С.
Published: May 2023

З метою вивчення особливостей клінічного перебігу Long-COVID здійснили огляд наукових публікацій, які містять дані про Long-COVID як окремий патологічний стан, актуальну інформацію про його прояви, та деякі патофізіологічні механізми, що призводять до розвитку уражень серцево-судинної і нервової систем.

Висновки. Визначення терміну Long-COVID як окремого стану у перебігу коронавірусної хвороби відбувалось у кілька етапів. Симптоми Long-COVID пов’язані з ураженням майже всіх систем органів. Ураження серцево-судинної системи є одними з домінуючих, при цьому є дані, що механізм таких уражень пов’язаний з порушеннями у системі згортання крові з утворенням мікротромбів. Також ураження серцево-судинної системи є основною причиною смерті хворих з Long-COVID. Співвідношення за статтю у випадку уражень серцево-судинної системи однакове, у той час як ураження нервової системи, інших органів та систем відбувається переважно у жінок. Деякі з існуючих даних вже знайшли додаткове підтвердження у результатах останніх досліджень, інші потребують його.