bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 5852: Vimentin content associated with shear wave speed in hepatocellular carcinoma: Non-invasive identification of more aggressive tumor phenotypes
Authors: Cortes Andrea C. , Minamiguchi Kiyoyuki , Da Costa Lopez Patricia L. , Anfossi Simone , Malea L Williams , Stenkamp Maria S. , Avritscher Rony , Fowlkes Natalie W. 
Published: April 2023

Abstract
Tumor stromal heterogeneity can negatively impact immune surveillance and treatment outcomes. Current cross-sectional imaging tools rely solely on tumor size and perfusion to monitor therapy and fail to characterize tumor biomechanics. Shear-wave elastography has emerged as a non-invasive technique that can quantify stromal elasticity. The goal of the present study is to characterize the molecular underpinnings associated with shear wave elastography measurements in liver cancer. To this end, rat hepatoma cell line McA-RH7777 stably expressing green fluorescent protein genes (fluc/GFP) were implanted in the left liver lobe of Buffalo rats. Three weeks after tumor implantation, adequate tumor size was verified by B-mode ultrasound. A 7-color panel was developed to assess the percentage of vimentin, α-smooth muscle actin, IBA-1, S100A4, TGF-β, and glial fibrillary acidic protein (GFAP) in tumor sections. Shear wave elastography data was used to stratify tumor nodules as stiff or soft according to the mean value of the shear wave (3.05 versus 2,26 m/s). Our results showed two distinct tumor phenotypes. Stiffer tumors, as determined by higher shear wave speed measurements on ultrasound, were characterized by higher percentages of vimentin-positive cells, low S100A4 and IBA-1 macrophages expressing TGF-b, and intermediate expression of IBA-1 macrophages and GFAP cells. Slow shear wave speed, characteristic of softer tumors, displayed the opposite phenotype (two-factor ANOVA; P≤0.001). The most remarkable difference between stiffness phenotypes was the percentage of cells expressing vimentin, with a mean percentage in stiffer tumors of 26.54 compared with 13.68% in softer tumors (P&lt;0.003). Our results indicate that high expression of vimentin is highly correlated with increased shear wave speeds. Given the association between vimentin expression and epithelial-mesenchymal transition a marker of aggressive characteristics of tumor cells (increased migration and invasion), our findings suggest that longitudinal quantification of shear wave speed can be useful to assess functional changes in the stromal component and identify more aggressive tumor phenotypes with a higher likelihood of metastatic potential.
Citation Format: Andrea C. Cortes, Kiyoyuki Minamiguchi, Patricia L. Da Costa Lopez, Simone Anfossi, Williams Malea L, Maria S. Stenkamp, Rony Avritscher, Natalie W. Fowlkes. Vimentin content associated with shear wave speed in hepatocellular carcinoma: Non-invasive identification of more aggressive tumor phenotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5852.
Abstract 5863: Blockade of tumor glucocorticoid production inhibits Treg function and tumor growth
Authors: Otsuka Shizuka , Taves Matthew D. , Donahue Kaitlynn M. , Ashwell Jonathan D. 
Published: April 2023

Abstract
Glucocorticoids (GCs) are steroid hormones with potent immunosuppressive properties. GCs are primary produced from cholesterol in the adrenals via the de novo synthetic pathway. In some tissues, however, there is also a recycling pathway in which the enzyme 11β-HSD1 generates GCs from the inactive metabolites dehydrocorticosterone (rodent) or cortisone (human). Here we find that multiple tumor types produce GCs via 11β-HSD1 in vitro and in vivo. We used CRISPR/Cas9 technology to knock out Hsd11b1 in GC-producing tumor cell lines and found that lack of 11β-HSD1 in B16 melanoma, Panc02 pancreatic adenocarcinoma, and MC38 colon carcinoma lines reduced their growth in vivo. Reduced tumor growth corresponded with increased expression of the activation marker CD44 and production of the effector cytokines IFNγ and TNFα by tumor-infiltrating CD8+ T cells (TILs). Rather than directly suppressing effector cell function, recent findings have suggested that GCs instead act primarily by activating Treg cells, and that these Treg are responsible for inhibition of effector cell function. Consistent with this, we found that tumor-derived GCs upregulate Treg expression of miRNA-342, which downregulates the mTOR component Rictor and activates Treg activity. A role of tumor-derived GCs in enhancing Treg function was demonstrated by inoculating tumor cells into mice with Treg-specific glucocorticoid receptor deficiency (GRFoxp3Cre mice). Notably, growth of tumors was reduced in GRFoxp3Cre mice, along with increased CD8+ TIL activation. Importantly, pharmacologic inhibition of 11β-HSD1 reduced WT tumor growth to the same degree as knockout of 11β-HSD1, and rendered immunotherapy-resistant tumors susceptible to inhibition with anti-PD-1 antibodies. Given that 11β-HSD1 expression is upregulated in many human tumors, these data suggest that its inhibition, which has been accomplished in a number of phase 3 clinical trials for other indications and is well-tolerated, may be beneficial in their treatment.
Citation Format: Shizuka Otsuka, Matthew D. Taves, Kaitlynn M. Donahue, Jonathan D. Ashwell. Blockade of tumor glucocorticoid production inhibits Treg function and tumor growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5863.
Abstract 5868: Uncovering key microenvironmental features for immunotherapy response at the subclonal level in pancreatic cancer
Authors: Yen Er-Yen , Ho I-Lin , Li Chieh-Yuan , Dyke Charles , Jiang Shan , Citron Francesca , Attanasio Sergio , Shah Rutvi , Chen Ko-Chien , Draetta Giulio , Viale Andrea 
Published: April 2023

Abstract
The lack of suitable experimental approaches to investigate and model functional heterogeneity in vivo has had a profound negative impact on our understanding of how heterogeneity affects the response to immunotherapy. To bridge this technological gap, we leverage a new platform that visualizes the spatial architecture of subclones and microenvironments. To study heterogeneous populations of cells and their clonal dynamics in vivo, we performed barcode lineage tracing with next-generation sequencing analysis. It allows a quantitative evaluation of the spatial distribution and temporal clonal dynamic in vivo with multiple pharmacological perturbations, such as immune checkpoint blockade (ICB). We found that treatment with a PD1 inhibitor, despite a limited effect on tumor volume, induced dramatic changes in tumor clonal architecture. Furthermore, we revealed that subclones from well-defined geographical domains in vivo share differential behavior upon immune checkpoint blockade (ICB). By visualizing 40 different markers with multiplexed staining technology, we further identified that the microenvironment also exhibits a high level of spatial heterogeneity. Therefore, we coupled spatial barcode sequencing with high-content imaging and revealed the differential microenvironment feature of sensitive and resistant clones. We will further explore the mechanisms of immune evasion at the subclonal level. Through isolation and deep characterization of clonal lineages endowed with a distinct ability to engage the immune response, we hope to identify new vulnerabilities to overcome resistance to ICB.
Citation Format: Er-Yen Yen, I-Lin Ho, Chieh-Yuan Li, Charles Dyke, Shan Jiang, Francesca Citron, Sergio Attanasio, Rutvi Shah, Ko-Chien Chen, Giulio Draetta, Andrea Viale. Uncovering key microenvironmental features for immunotherapy response at the subclonal level in pancreatic cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5868.
Abstract 5872: Spatial immunophenotypes contribute to predict survival of triple-negative breast cancer assessed as Miller-Payne grade 4 and N0 after neoadjuvant therapy
Authors: Ma Jianli , Deng Yuwei , Chen Dawei , Li Xiaomei , Yu Zhiyong , Wang Haibo , Zhong Lei , Li Yingjie , Wang Chengqin , Zhou Xiaoping , Li Xiang , Zhang Qingyuan , Yu Jinming 
Published: April 2023

Abstract
Objectives Some Miller-Payne 4 and N0 patients with triple-negative breast cancer (TNBC) after neoadjuvant chemotherapy (NACT) who had better survival should avoid treatment escalation. We aimed to identify these patients based on spatial distributions of immunophenotypes at initial diagnosis.
Methods We retrospectively analyzed 272 TNBC patients with Miller-Payne grade 4/5 and N0 for tumor-infiltrating lymphocytes (TILs) in relation to clinical survival. The spatial immunophenotypes were analyzed by multiplexed ion beam imaging by time of flight combined with proteomic. A prognostic classifier was established by the random forest algorithm.
Results The 5-year disease-free survival (DFS) was 63.8% for Miller-Payne 4 and 83.0% for Miller-Payne 5 (p=0.003), and overall survival (OS) was 71.0% and 85.5% respectively (p=0.007). High TILs were significantly associated with better DFS and OS in the Miller-Payne 4 patients (both p=0.016). Spatially, Miller-Payne 4 with good prognosis exhibited inflamed phenotype, with dominant CD8+ T cells on tumor center, few scattered CD68+ myeloid-derived cells far away from T cells, and deposit of increased lymphocyte activate molecules. Miller-Payne 4 with poor prognosis presented excluded phenotype, with few CD8+ T cells restricted to invasive margin, high density of CD14+CD68+CD11c+ myeloid cells with related molecules. These spatial immunophenotypes provided a good classifier model (AUC=0.975) to identify Miller-Payne 4 patients with different prognosis. We also observed similar signatures in Miller-Payne 5.
Conclusion Spatial immunophenotypes may indicate the prognosis in TNBC assessed as Miller-Payne 4 and N0.
Citation Format: Jianli Ma, Yuwei Deng, Dawei Chen, Xiaomei Li, Zhiyong Yu, Haibo Wang, Lei Zhong, Yingjie Li, Chengqin Wang, Xiaoping Zhou, Xiang Li, Qingyuan Zhang, Jinming Yu. Spatial immunophenotypes contribute to predict survival of triple-negative breast cancer assessed as Miller-Payne grade 4 and N0 after neoadjuvant therapy. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5872.
Abstract 5893: Suppression of anti-tumor immunity by the Fusobacterium nucleatum protease fusolisin
Authors: Shhadeh Amjad , Dassa Liat , Fahoum Jamal , Haj Nicole , Wiener Reuven , Mandelboim Ofer , Bachrach Gilad 
Published: April 2023

Abstract
Fusobacterium nucleatum is an oral pathogen associated with periodontal disease, preterm births and the exacerbation of colorectal, esophageal, pancreatic, and breast cancers. F. nucleatum was previously found to inhibit killing of cancer cells by natural killer (NK) cells and tumor infiltrating T cells by inducing the NK cells killing-suppressing receptors TIGIT and CEACAM1. In this study, we show that the incubation of F. nucleatum with primary human natural killer (NK) cells causes the cleavage of the activating receptors CD16, NKp44 and NKp46 by fusolisin. Fusolisin is a fusobacterial outer-membrane, auto-transporter, serine protease and to date the only functional protease found in F. nucleatum. We previously showed that fusolisin is essential for fusobacterial growth in culture. High expression of a functional recombinant fusolisin in E. coli was enabled using codon optimization and replacement of the fusolisin's signal peptide with that of the E. coli OmpA. Recombinant fusolisin was found to cleave the same NK-activating receptors degraded by F. nucleatum. Cleavage of these activating receptors by fusolisin inhibited NK cells activity including killing of tumor cells in-vitro and in-vivo. Our results provide a new bacterial protease-dependent mechanism in which tumors colonized by F. nucleatum are protected from NK cells attack by exploiting fusolisin proteolytic activity. Importantly, our previous and current results suggest that fusolisin might serve to target for tumor-colonized fusobacteria.
Citation Format: Amjad Shhadeh, Liat Dassa, Jamal Fahoum, Nicole Haj, Reuven Wiener, Ofer Mandelboim, Gilad Bachrach. Suppression of anti-tumor immunity by the Fusobacterium nucleatum protease fusolisin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5893.
Abstract 5994: INX-315, a potent and selective CDK2 inhibitor, demonstrates robust antitumor activity in CCNE1-amplified cancers
Authors: Trub Alec G. , Bisi John E. , Dietrich Catherine , Taylor Michael , Strum Jay C. , Goel Shom , Roberts Patrick J. 
Published: April 2023

Abstract
Cyclin-dependent kinases (CDK) are a family of serine/threonine kinases that heterodimerize with regulatory subunits called cyclins to drive cell cycle progression. Uncontrolled cellular proliferation is a hallmark of cancer commonly driven by dysregulated kinase activity of specific CDK family members, including cyclin-dependent kinase 2 (CDK2). Aberrant CDK2 activity most frequently occurs through amplification of CCNE1 and/or overexpression of its protein product cyclin E1, which is a canonical binding partner of CDK2. Overexpression of cyclin E1 is observed in many solid tumors including in patients with high grade serous ovarian cancer (HGSOC), gastric cancer, and ER-positive breast cancer patients whose tumors have progressed on a prior CDK4/6 inhibitor regimen. Selective inhibition of CDK2 is thus a compelling therapeutic approach to regain cell cycle control. Here, we report preclinical data supporting the development of INX-315 for patients with cancers in which proliferation is CDK2-dependent. INX-315 is a potent inhibitor of CDK2/cyclin E (0.6 nM biochemical IC50) with high selectivity over other CDK family members in both biochemical and intracellular NanoBRET assays. In CCNE1-amplified human ovarian and gastric cancer cell lines, INX-315 potently inhibited Rb phosphorylation, induced a G1 cell cycle arrest, and inhibited proliferation. INX-315 also showed potent anti-proliferative activity in luminal breast cancer cell lines that had been cultured in CDK4/6 inhibitor (+/- anti-estrogen therapy) for prolonged periods to the point of developing drug resistance. While these cell lines did not readily respond to either CDK4/6 or CDK2 inhibition alone, combination treatment again suppressed Rb phosphorylation, accompanied by G1 arrest and a senescent-like phenotype. Lastly, in CCNE1-amplified xenograft models of ovarian and gastric carcinomas, INX-315 inhibited Rb-phosphorylation and induced tumor regression. These data demonstrate INX-315 to be a potent and selective CDK2 inhibitor that may benefit patients with CDK2/cyclin E driven cancers.
Citation Format: Alec G. Trub, John E. Bisi, Catherine Dietrich, Michael Taylor, Jay C. Strum, Shom Goel, Patrick J. Roberts. INX-315, a potent and selective CDK2 inhibitor, demonstrates robust antitumor activity in CCNE1-amplified cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5994.
Abstract 6041: Investigating metabolic dependencies of group 3 medulloblastoma
Authors: Dang Derek , Smith Kyle S. , Panwalkar Pooja , McKolay John , Animasahun Olamide , Achreja Abhinav , Nagrath Deepak , Northcott Paul A. , Venneti Sriram 
Published: April 2023

Abstract
Medulloblastomas (MB) are the most common pediatric brain malignancy. Transcriptomic, genomic, and epigenomic insights have stratified these tumors into four distinct subtypes: SHH, WNT, Group 3 and Group 4. Of the four subtypes, Group 3 tumors bear the worst prognosis. Each MB subtype is distinguished by their unique transcriptome profile and epigenetic landscape. Metabolic reprogramming is a hallmark of cancer and allows cells to actively promote the utilization of nutrients to support their uncontrolled proliferation. We identified distinct transcriptional metabolic profiles in medulloblastomas. We found that Group 3 MB show upregulation of key anabolic pathways. We then cross-referenced these data from comprehensive single-cell RNA sequencing profiles of cerebellar developmental niches. We found that Group 3 MB exhibits metabolic signature similar that of early progenitors, rhombic lip progenitors, and cerebellar ventricular zone derivatives. Finally, we identify DLAT, the E2 subunit of the pyruvate dehydrogenase complex, as a uniquely upregulated gene in Group 3 MB. Knockdown of DLAT inhibited tumor growth in-vitro and in-vivo suggesting a potential targets for future therapeutic regimens.
Citation Format: Derek Dang, Kyle S. Smith, Pooja Panwalkar, John McKolay, Olamide Animasahun, Abhinav Achreja, Deepak Nagrath, Paul A. Northcott, Sriram Venneti. Investigating metabolic dependencies of group 3 medulloblastoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6041.
Abstract 6044: Identification and molecular characterization of cancer cells survived under glucose starvation
Authors: Nesher Elimelech , Levi Bar , Levy Hadas , Cohen-Harazi Raichel , Koman Igor 
Published: April 2023

Abstract
Tumors are heterogeneous, consisting of different cell subpopulations to allow tumor survival in variable conditions. We observed the survival of a small percentage of HCT116 cells under glucose starvation. We hypothesized that these cells represent a previously undescribed subpopulation able to adjust their metabolism in the absence of glucose. Here we aimed to characterize the metabolic and molecular properties allowing these cells to survive. We propagated individual clones from HCT116 cells and further analyzed a single clone descendants were able to survive glucose starvation. Biochemical and molecular analyses were performed under standard glucose conditions, under glucose starvation during adaptation period, and under glucose starvation after resumption of proliferation. Metabolic analysis by Seahorse revealed that surviving cells completely shifted their metabolism from glycolysis to oxidative phosphorylation. LC-MS metabolomics analysis revealed that during senescence-like adaptation the cells accumulate metabolites required for NAD synthesis. FAD, a co-factor involved in the TCA cycle, was not found in the dormant cells, while higher levels of carnosine, essential for ROS elimination, were observed. The metabolic shift toward enhanced oxidative phosphorylation was accompanied by increased production of ROS leading to DNA damage, reflected in an upregulation of the genes NUPR, ST6GAL1, and EGRF as observed by RNAseq. Cells that resumed proliferation were also characterized by enhanced expression of DNA damage repair genes and upregulated subunits of ATP-synthase, a key enzyme in oxidative phosphorylation. We suggest that cells predisposed to effective DNA repair have more time and capabilities to adjust their metabolism and to survive.
Citation Format: Elimelech Nesher, Bar Levi, Hadas Levy, Raichel Cohen-Harazi, Igor Koman. Identification and molecular characterization of cancer cells survived under glucose starvation. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6044.
Abstract 6050: Analysis of diverse metabolic pathways using bioluminescent cell-based assays
Authors: Leippe Donna , Karassina Natasha , Valley Mike , Sylvester Kayla , Vidugiriene Jolanta 
Published: April 2023

Abstract
Cellular energy metabolism is a complex system of many interconnected metabolic pathways that govern both cell health and function. Cancer cells are adept at quickly switching between metabolic pathways to adapt to nutrient limitations in the environment, enhancing their growth advantages while negatively impacting other cells in the tumor microenvironment such as immune cells. To facilitate metabolic characterization of cancer cells, we developed assays for detection of metabolites involved in key pathways, such as glycolysis and glutaminolysis, using a bioluminescent NADH detection technology coupled to specific dehydrogenases. We have now extended these assays to include metabolites involved in glycogen, lipid, ketone body and amino acid metabolism, as well as intermediates in the TCA cycle such as malate, isocitrate, and 2-hydroxyglutarate. A second core bioluminescent hydrogen peroxide detection system was also used to develop an assay for pyruvate. Here we describe the use of these assays to measure metabolite levels in cell lysates and cell culture media collected from cancer cell lines plated in 96- or 384-well plates and in 2D or 3D cultures. Changes in metabolite levels were monitored in response to altered media composition and drug treatments. Levels were also compared between different cell lines. In comparative studies of glioblastoma cell lines, 2-hydroxyglutarate production was higher in cells expressing mutant isocitrate dehydrogenase. By reconfiguring the NADH detection technology to measure cellular enzyme activity rather than metabolite levels, we were able to detect activity of dehydrogenases that participate in the glycolysis pathway, the TCA cycle, and pentose phosphate pathway. Assays for cellular malate dehydrogenase, isocitrate dehydrogenase and other dehydrogenase enzymes were sensitive, requiring ≤ 400 lysed cells per assay. The expanded collection of bioluminescent assays provides a way to quickly characterize the metabolic states and behaviors of cancer cells to help identify pathways that may present therapeutic targets.
Citation Format: Donna Leippe, Natasha Karassina, Mike Valley, Kayla Sylvester, Jolanta Vidugiriene. Analysis of diverse metabolic pathways using bioluminescent cell-based assays [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6050.