bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3187: Understanding the role of cancer-associated fibroblasts (CAFs) on pathogenesis of KRAS mutated cancers by defining differences in the basal state proteome and secretome
Authors: Lau Rachel , Yu Lu , Roumeliotis Theodoros , Pickard Lisa , Stewart Adam , Choudhary Jyoti , Banerji Udai 
Published: June 2022

Abstract
Background: KRAS is commonly mutated in solid tumors. Cancer-associated fibroblasts (CAFs) are a key tumor stroma component, which can affect cancer progression and drug response. We hypothesized that defining the differential secreted proteins between CAFs and KRAS mutant-cancer cells could reveal potential mechanisms by which CAFs influence cancer progression and drug resistance.
Methods: We studied 12 cell lines: 3 KRAS mutant-colorectal cancer cell lines (H747, LIM2099 and SW620), 3 KRAS mutant-lung cancer cell lines (H1792, H2030 and H23), 3 KRAS mutant-pancreatic cancer cell lines (CAPAN1, DANG, MIAPACA2) and 3 CAF cell line models (colorectal and lung CAF and pancreatic stellate cells). We quantified proteins in cell lines and serum-free media after 24 hour incubation in cells using mass spectrometry in a multiplexed manner (12plex) in triplicates to characterize the proteome and the profile of secreted proteins (secretome), respectively. Prediction software (signalP, secretomeP, TMHMM) and databases (surfaceome and cell surface protein atlas) were used to annotate secreted or transmembrane proteins.
Results: Our proteome analysis quantified 9307 proteins. T-test between the cell types (CAF vs cancer) identified 1770 differentially expressed proteins, where 712 proteins were CAF-enriched. This included known CAF markers (e.g α smooth muscle actin) but also proteins not known to be CAF markers such as heat shock protein beta-5/6 (HSPB5/6). The secretome analysis identified 2330 secreted or transmembrane proteins where 202 were differentially expressed between cancer cells and CAFs. 190 proteins were CAF-enriched with the highest ranking being syndecan-2 (SDC2), collagen α-28(I) chain (COL28A1), decorin (DCN) and wnt family member 5B (WNT5B). Interestingly, basal proteome analysis of KRAS mutant-cancer cells showed expression of receptors corresponding to the CAF-enriched ligands, such as receptor tyrosine kinase-like orphan receptor 1/2 (ROR1/2) which respond to WNT5B. This suggests that CAF-enriched ligands may activate certain downstream pathways, including non-canonical WNT signaling, in KRAS mutant-cancer cells.
Conclusion: We undertook deep quantitative proteomics where we identified potential novel CAF markers HSPB5/6. We have also found proteins in the CAF secretome, such as WNT5B, which may drive drug resistance in KRAS mutant-cancer cells.
Citation Format: Rachel Lau, Lu Yu, Theodoros Roumeliotis, Lisa Pickard, Adam Stewart, Jyoti Choudhary, Udai Banerji. Understanding the role of cancer-associated fibroblasts (CAFs) on pathogenesis of KRAS mutated cancers by defining differences in the basal state proteome and secretome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3187.
Abstract 3195: Tumor inhibitory CAFs in CNS metastases
Authors: Simon Thomas , Buckley David , Salhia Bodour 
Published: June 2022

Abstract
The 2-year survival rate for patients with central nervous system (CNS) metastases (CMs) remains below 2%. With the aim to define new therapeutic options, researchers have investigated how interactions between CM cells and the surrounding tumor microenvironment (TME) support metastatic progression. As an important component of the TME, cancer associated fibroblasts (CAFs) have largely been reported as tumor supportive. But new evidence for the high heterogeneity of the CAF compartment, including in vivo studies from our lab, showed that certain CAF subpopulations could exhibit tumor inhibitory capabilities. Interestingly, recent reports revealed that CAFs showing high expression of Immunoglobulin Superfamily containing Leucin Rich Repeat (ISLR) could show tumor inhibitory capabilities in both pancreatic ductal adenocarcinoma (PDAC) and colorectal cancer (CRC). Yet, despite the invaluable clinical potential of tumor inhibitory CAFs, the CAF compartment in the TME of CMs is still largely under described. Using CM patient tissue and CM patient-derived cell lines established in our lab, we performed single cell RNA sequencing (scRNA-seq) to define CAF subpopulations present in the TME of CMs. We identified distinct clusters characterized by differential expression of ISLR and tumor supportive CAF marker Actin Alpha 2, Smooth Muscle (ACTA2/α-SMA). CAF subpopulations were thus defined as follows: ISLRhigh/α-SMAlow, ISLRlow/α-SMAhigh, ISLRlow/α-SMAlow. Altogether, we hypothesized that ISLRhigh/α-SMAlow CAFs could act to restrain tumor progression in the TME of CMs, as opposed to potentially tumor supportive ISLRlow/α-SMAhighCAFs. ISLRhigh and ISLRlow CAFs were obtained through fluorescence-activated cell sorting (FACS) performed on one of our patient-derived CAF cell lines represented in all defined scRNA-seq clusters. ISLRhigh CAFs were validated to express lower levels of α-SMA (ISLRhigh/α-SMAlow CAFs) compared to ISLRlow cells (ISLRlow/α-SMAhigh CAFs). This mutually exclusive expression of ISLR and α-SMA in different CAF subpopulations is in accordance with recent data in PDAC and CRC and could indicate common underlying mechanisms driving the phenotype of each subpopulation. Further in vitro and in vivo experiments are currently underway in our lab to determine the tumor supportive capabilities of both ISLRhigh/α-SMAlow and ISLRlow/α-SMAhigh CAFs. Ultimately, we expect the current study to unravel the diverse and dynamic nature of CAFs in the TME of CMs, which is still largely unknown.
Citation Format: Thomas Simon, David Buckley, Bodour Salhia. Tumor inhibitory CAFs in CNS metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3195.
Abstract 3219: Changes and intra-individual reliability in computed tomography image-assessed adiposity and skeletal muscles areas after breast cancer surgery
Authors: Aduse-Poku Livingstone , Gopireddy Dheeraj , Henandez Mauricio , Lall Chandana , Divaker Joel , Falzarano Sara , Masood Shahla , Zhang Weizhou , Datta Susmita , Bian Jiang , Cheng Ting-Yuan David 
Published: June 2022

Abstract
Background: Levels of adiposity and skeletal muscles are prognostic indicators in breast cancer patients; however, data are limited on temporal changes in body composition, particularly in different densities of muscles, before and after mastectomy.
Objectives: We examined the change in CT-assessed adipose tissue and different density of skeletal muscle areas using a high-resolution segmentation method in breast cancer patients before and after surgery.
Methods: This study included 50 newly-diagnosed breast cancer patients who had taken CT scans before and after surgery. We analyzed their third lumbar (L3) CT images to measure the areas of adipose tissue and five-level (from very-high-density to very-low-density) skeletal muscle components. We assessed mean and percent changes in areas using paired t-test and calculated the intra-class correlation (ICC).
Results: Patients’ mean age at diagnosis was 58.3 (SD=12.5) years. The mean duration between scans was 591 (SD=537) days. There was a significant decrease in the areas of subcutaneous adipose tissue (mean change= -36.17 cm2, 11.72% decrease, p=0.029), total adipose tissue (mean change= -45.64 cm2, 10.18% decrease, p=0.032), and very-high-density muscle (mean change= -0.37 cm2, 11.08% decrease, p=0.010). The ratio of total adipose tissue and total skeletal muscle decreased from 3.67 to 3.32 after surgery (mean change= -0.36, 9.81% decrease, p=0.061). There was a strong correlation in adipose tissues and skeletal muscle areas of pre-and post-surgery scans taken within 3 years apart (ICC=0.802 to 0.999, all p&lt;0.05), but the correlations were attenuated in scans taken &gt;3 years apart (ICC = -0.055 to 0.738, all p&gt;0.05).
Conclusion: In this sample of breast cancer patients who have undergone surgery, there was a significant decrease in subcutaneous adipose tissues, total adipose tissues, and very-high-density muscle areas over time. Body composition assessed by CT images is reliable for a 3- year period involving breast cancer surgery. These findings serve as a baseline for prospective studies examining the impact of these changes on breast cancer outcomes.
Keywords: Adipose tissue, skeletal muscle, computed tomography scans, breast cancer, surgery
Citation Format: Livingstone Aduse-Poku, Dheeraj Gopireddy, Mauricio Henandez, Chandana Lall, Joel Divaker, Sara Falzarano, Shahla Masood, Weizhou Zhang, Susmita Datta, Jiang Bian, Ting-Yuan David Cheng. Changes and intra-individual reliability in computed tomography image-assessed adiposity and skeletal muscles areas after breast cancer surgery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3219.
Abstract 3249: Targeting polyploid giant cancer cells to overcome resistance to PARP inhibitors in ovarian cancer
Authors: Zhang Xudong , Yao Jun , Li Xiaoran , Niu Na , Liu Yan , Sood Anil K. , Liu Jinsong 
Published: June 2022

Abstract
PARP inhibitors (PARPi) offer major clinical benefit for patients with ovarian or other cancers, especially those with deficiencies in the homologous recombination DNA repair pathway. However, most patients with advanced cancer eventually acquire resistance to PARPi, and the mechanisms by which tumors escape PARPi therapy are still not fully understood. Here, we report that treatment with the PARPi olaparib induces the formation of polyploid giant cancer cells (PGCCs) in ovarian and breast cancer cell lines (Hey, SKOV3, MCF-7), three human high-grade serous cancer (HGSC)-derived organoids, and HGSC patient-derived xenografts. Live-cell fluorescence time-lapse tracking of ovarian cancer cells labeled with FUCCI (fluorescent ubiquitination cell-cycle indicator) or histone H2B-mCherry/α-tubulin-EGFP revealed that PGCCs primarily developed from the endoreplication of diploid cancer cells after exposure to sublethal concentrations of olaparib. PGCCs exhibited markers of senescent cells; however, they were able to escape senescence to generate mitotically competent daughter cells via budding, multipolar mitosis, and acytokinetic mitosis following olaparib withdrawal. PGCCs and derived daughter cells conferred resistance to olaparib-induced cytotoxicity, which could be blocked by the anti-progesterone drug mifepristone. Whole transcriptome analysis by RNA sequencing of ovarian cancer cell lines and ovarian cancer-derived organoids showed activation of a senescence-associated secretory phenotype with upregulated cytokines and chemokines and downregulation of MYC signaling in PGCCs. Mifepristone/olaparib combination therapy significantly mitigated tumor growth in patient-derived xenograft models with acquired resistance to olaparib. Thus, targeting of PGCCs may represent a promising approach to overcome PARPi resistance in recurrent ovarian cancer.
Citation Format: Xudong Zhang, Jun Yao, Xiaoran Li, Na Niu, Yan Liu, Anil K. Sood, Jinsong Liu. Targeting polyploid giant cancer cells to overcome resistance to PARP inhibitors in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3249.
Abstract 3250: Microbial metabolite, Urolithin A acts as chemo-sensitizing adjuvant in conventional drug therapies via modulation of drug transporters and EMT markers
Authors: Ghosh Sweta , Singh Rajbir , Vanwinkle Zachary M. , Guo Haixun , Vemula Praveen K. , Goel Ajay , Haribabu Bodduluri , Jala Venkatakrishna Rao 
Published: June 2022

Abstract
Colon cancer is the third leading cause in cancer related deaths in United States of America. Chemoresistance (drug resistance) of tumors is the primary reason for the failure of chemotherapy and a major cause of mortality in colon cancer. The molecular mechanisms involved in chemoresistance or methods to chemosensitization of cancer cells to chemotherapy remain elusive. Recent studies suggest that gut microbiota and microbial metabolites play a crucial role in the development and progression of colon cancer. Urolithin A (UroA) is a gut microbial metabolite derived from ellagitannin/ellagic acid rich-diets such as pomegranate and berries. Here, we identified that UroA and its novel structural analogue (UAS03) chemosensitize 5FU resistant (5FUR) colon cancer cells to 5FU treatment. Our data suggested that combination of 5FU with UroA or UAS03 significantly reduced cell viability of 5FUR colon cancer cell lines with combination index (CI) less than 1 suggesting their synergism. Moreover, UroA or UAS03 in combination with 5FU significantly inhibited 5FUR colon cancer cell proliferation, migration as well as induced apoptosis. Mechanistically, UroA or UAS03 treatment down regulated drug transporters (MDR1, BCRP and MRP2) leading to decreased efflux of drug (e.g., 5FU) and potentially responsible for chemosensitization. Furthermore, treatment with these compounds also modulated EMT makers (e.g., downregulated Snail and β-catenin; upregulated ZO-1 and E-cadherin) to reduce EMT transition. Treatment of UroA or UAS03 in combination with 5FU significantly reduced the growth of 5FUR-tumor xenografts in NRGS mice. Taken together, utilization of UroA or UAS03 in combination with 5FU treatment may provide better therapeutic options for 5FUR colon cancer alleviation.
Citation Format: Sweta Ghosh, Rajbir Singh, Zachary M. Vanwinkle, Haixun Guo, Praveen K. Vemula, Ajay Goel, Bodduluri Haribabu, Venkatakrishna Rao Jala. Microbial metabolite, Urolithin A acts as chemo-sensitizing adjuvant in conventional drug therapies via modulation of drug transporters and EMT markers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3250.
Abstract 3288: The use of in vitro assays to assess and measure gene therapy immunogenicity
Authors: Schockaert Jana , Janss Thibaut J. , Lamy Juliette , Mazy Aurélie , Boelen Ellen , Lefevre Simon , Pattijn Sofie 
Published: June 2022

Abstract
Introducing the gene therapy product into human cells requires a vector that will deliver the gene into the cells and incorporate those genes into the gene expression mechanism in those cells. One of the issues is the induction of an unwanted immune response that can have an influence on the efficacy and potency of the treatment. Additionally, pre-existing immunity towards AAV and CRISPR can also neutralize the therapeutic effect. Comprehensive assessment of human immune responses to gene therapy candidates includes characterization of humoral and cellular immunogenicity specific for both the viral vector and the expressed transgene (protein) product before and after dose administration. In vitro assays such as dendritic cell activation and T cell proliferation assays can be used to assess this unwanted immunogenicity in an early phase. Additionally, innate assays such as dendritic cell activation assays can be used for the evaluation of potential impurities and innate response inducing contaminants. Sensitive Fluorospot assays can be used to monitor patient’ specific immunogenicity both at the T and B cell level. The advantage of the Fluorospot technology is the sensitivity to detect responses on a single cell level and measure up to 4 analytes simultaneously. For all in vitro assays, the quality and functionality of the primary cells is important to assure reproducibility and solid assay performance.
Citation Format: Jana Schockaert, Thibaut J. Janss, Juliette Lamy, Aurélie Mazy, Ellen Boelen, Simon Lefevre, Sofie Pattijn. The use of in vitro assays to assess and measure gene therapy immunogenicity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3288.
Abstract 331: Pre-clinical evaluation in endocrine resistant breast cancer of a novel antibody-drug conjugate targeting cell surface cleaved Amphiregulin
Authors: Lofgren Kristopher A. , Sreekumar Sreeja , Jenkins E. Charles , Ernzen Kyle J. , Kenny Paraic A. 
Published: June 2022

Abstract
The EGFR ligand, Amphiregulin, is a key proliferative effector of estrogen receptor signaling in breast cancer and also plays a role in other malignancies. Amphiregulin is a single-pass transmembrane protein proteolytically processed by TACE/ADAM17 to release the soluble EGFR ligand, leaving a residual transmembrane stalk that is subsequently internalized. Here, we report the development of an antibody drug conjugate, GMF-1A3-MMAE, targeting an AREG neo-epitope revealed following ADAM17-mediated cleavage. The antibody does not interact with uncleaved Amphiregulin, providing a novel means of targeting cells with high rates of Amphiregulin shedding. Using fluorescent dye conjugation, we demonstrated that the antibody is internalized by cancer cells in a manner dependent on the presence of cell surface cleaved Amphiregulin. Antibodies conjugated with monomethyl auristatin E (MMAE) were cytotoxic in vitro and induced rapid regression of established breast tumor xenografts in immunocompromised mice. We also show that these antibodies recognize the Amphiregulin neo-epitope in formalin fixed paraffin embedded tumor tissue, suggesting their utility as a companion diagnostic for patient selection. Among ER-positive (n = 88) and ER-negative (n = 50) tumors evaluated, the proportions of tumors exhibiting medium/high intensity staining with 1A3 were essentially equivalent (69.3% v 70%, respectively). These data provide proof-of-principle that cell surface proteolytic cleavage products can represent good targets for antibody drug conjugate development and highlight the potential of using this antibody drug conjugate against tumors shedding high levels of Amphiregulin.
Citation Format: Kristopher A. Lofgren, Sreeja Sreekumar, E. Charles Jenkins, Kyle J. Ernzen, Paraic A. Kenny. Pre-clinical evaluation in endocrine resistant breast cancer of a novel antibody-drug conjugate targeting cell surface cleaved Amphiregulin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 331.
Abstract 3331: Effective multitargeted kinase inhibitors for metastatic castration-resistant prostate cancer predicted by integrative systems-based modeling
Authors: Bello Thomas , Paindelli Claudia , Diaz-Gomez Luis , Mikos Antonios , Nelson Peter , Gujral Taranjit , Dondossola Eleonora 
Published: June 2022

Abstract
Metastatic castration-resistant prostate cancer (CRPC) is an advanced subtype of prostate cancer (PCa) with limited therapeutic opportunities. Here, we applied an unbiased systems-based modeling approach called Kinome Regularization (KiR) to identify candidate kinase inhibitors (KIs) for the treatment of CRPC. KiR is a method of target deconvolution that harnesses the polypharmacology of KIs to identify critical kinases involved in a specific cellular activity (i.e., cell proliferation). By computationally integrating the results of a functional drug screen with prior biochemical knowledge, we generated KiR models for a panel of PCa cell lines that predict KIs effective at abrogating CRPC cell growth and proliferation. Two predicted KIs (PP121 and SC-1) showed significant inhibition of PCa cell growth and kinase-mediated growth factor signaling in vitro and in primary subcutaneous tumors. However, therapy resistance emerged in bone metastases, as identified by analysis in a 3D in vitro engineered bone mimetic environment and in tumors implanted in mouse bones. A combination of PP121 and SC-1 with standard-of-care chemotherapy overcame the resistance, enhancing both tumor response and mouse survival. These results suggest that combining multi-targeted KIs with chemotherapy may represent an effective strategy for CRPC treatment.
Overall, our findings demonstrate the application of a multidisciplinary strategy that blends bench science with machine-learning approaches for rapidly identifying KIs that result in desired phenotypic effects.
Citation Format: Thomas Bello, Claudia Paindelli, Luis Diaz-Gomez, Antonios Mikos, Peter Nelson, Taranjit Gujral, Eleonora Dondossola. Effective multitargeted kinase inhibitors for metastatic castration-resistant prostate cancer predicted by integrative systems-based modeling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3331.
Abstract 3340: Small molecule mediated stabilization of PP2A modulates the homologous recombination pathway and potentiates DNA damage-induced cell death
Authors: Avelar Rita A. , Armstrong Amy , Narla Goutham , DiFeo Analisa 
Published: June 2022

Abstract
High Grade Serous Carcinoma (HGSC) is the most lethal ovarian cancer subtype and accounts for approximately 60% of all ovarian tumors. Despite recent advances in drug development and increased understanding of genetic alterations that drive HGSC progression, mortality has not declined, highlighting the need for novel therapies. PARP inhibitors (PARPi) have become the mainstay of HGSC targeted therapy research given that these tumors are driven by a high degree of genomic instability resulting from the combination of fast DNA replication rates and numerous defects in the DNA-damage response (DDR) pathway. Nonetheless, only ~25% of these patients initially respond to treatment and a significant percentage eventually relapses with resistant disease. Here, we discovered that a Small Molecule Activator of Protein Phosphatase 2A (PP2A) (SMAP-061) induces apoptosis in both established and patient-derived HGSC cell lines as well as in genetically distinct Patient-Derived Xenograft (PDX) mouse models. Interestingly, we also uncovered that several genes that make-up the heterotrimer PP2A tumor suppressor protein are heterozygously lost in more than 95% of HGSC tumors, second only to p53. Mechanistically, we show that stabilization of PP2A protein by SMAP-061 inhibits the Homologous Recombination (HR) pathway via the direct inhibition of RAD51, ultimately leading to chronic accumulation of DNA damage and thus programmed cell death. Furthermore, we found that SMAP-061’s ability to inhibit HR potentiated the effects of PARP inhibition and resulted in synergistic cell death in both HR proficient and deficient models. These studies emphasize the potential of PP2A activators to expand the patient population that can benefit from PARPi therapies and possibly overcome PARPi resistance. In sum, our data highlights a new role of PP2A in regulating the DDR pathway in HGSC and supports the use of SMAPs in both HR proficient and deficient HGSC tumors.
Citation Format: Rita A. Avelar, Amy Armstrong, Goutham Narla, Analisa DiFeo. Small molecule mediated stabilization of PP2A modulates the homologous recombination pathway and potentiates DNA damage-induced cell death [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3340.