tbuckley/cabot-search huggingface dataset:
Abstract 290: The role of tumor stromal topography-regulated genes in modulating the cellular landscape of tumor stroma in breast cancer
Authors: Chia-Yi Su
Journal: Cancer Research (2024)

Abstract The tumor remodels the surrounding extracellular matrix fibers to become topographically aligned at the tumor front, further facilitating cancer cell migration. Our recent studies show that aligned tumor stromal topography promotes the detachment of breast cancer cells from the main tumor, then, in the following cell migration, upregulating genes such as genes encoding the cytochrome P450 family 1 subfamily A member 1 (CYP1) and inhibitor of DNA binding (ID) proteins. In this study, we further explored the role of topography-regulated genes in modulating the cellular landscape of tumor stroma. By analyzing the correlation of topography-regulated genes with stromal cell infiltration in bioinformatics databases, we found significant positive correlations between the RNA expression levels of most topography-regulated genes and the infiltration levels of cancer-associated fibroblasts and endothelial cells. Notably, the strongest correlation was between the expression level of ID3 and the infiltration levels of cancer-associated fibroblasts (r = 0.509) and endothelial cells (r = 0.506). Additionally, ID3 remained highly expressed in circulating tumor cells but exhibited low expression at distant metastatic sites. These findings suggest that genes regulated by tumor stromal topography, especially ID3, may play a role in neovascularization and fibrosis of the tumor microenvironment and the survival adaptation of cancer cells in circulation, thereby promoting metastasis. Citation Format: Chia-Yi Su. The role of tumor stromal topography-regulated genes in modulating the cellular landscape of tumor stroma in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 290.
Abstract 1334: Evaluation of NK cell combination therapies in mouse models of cancer
Authors: Katarzyna Franciszkiewicz, Pauline Rettman, Beatrice Gauthier, Laurence Noblet, Celine Nicolazzi, Andre Kunert, Rob Igarashi, Loreley Calvet, Valeria Fantin, Sukhvinder Sidhu
Journal: Cancer Research (2024)

Abstract Adoptive immunotherapy with natural killer (NK) cells has emerged as a promising innovative approach against hematological malignancies and solid tumors. To enhance the functional aspects of NK cells and to achieve stronger, sustained anti-tumor responses, combination strategies are under development. They are focused on optimization of NK cell potency, persistence and tumor targeting using monoclonal antibodies, multi-specific NK cell engagers and immune modulators like cytokines. SAR445419 is a universal off-the-shelf allogeneic human NK cell (hNK) product made using Sanofi’s proprietary platform with potential broad application across hematologic and solid tumor indications. We evaluated the therapeutic potential of these NK cells in combination with internal assets and standard of care treatments in preclinical mouse models. The studies were performed in immunodeficient NOG mouse strains transgenic for hIL-15, supporting long-term engraftment of functional hNK cells. We demonstrated the therapeutic advantage of NK cell combination with an anti-CD20 monoclonal antibody (mAb) in a disseminated lymphoma model. We also reported prolonged lifespan of leukemia-bearing animals treated with NK cells and pegenzileukin, a PEGylated non-alpha rhIL-2 variant engineered to preferentially bind to the IL-2 βγ receptors and promote NK cell function. The anti-tumor response correlated with pegenzileukin-induced increase in NK cell numbers in the blood. A combination of CD38KO NK cells with an anti-CD38 mAb was also investigated in a model of multiple myeloma (MM). FcγR-KO immunodeficient mice were used in these studies to limit the confounding contribution of residual murine immune cells engaging with the Fc-competent therapeutic antibody and to specifically detect hNK-cell mediated activity. The comparison of CD38KO versus WT NK cell numbers in the blood of animals treated with an anti-CD38 mAb showed a significant decrease in CD38-expressing NK cell count that was mitigated by the genetic deletion of CD38. Obtained results suggest that CD38KO NK cells are resistant to anti-CD38 mAb-mediated fratricide and provide a rationale for the combination of CD38KO NK cells with anti-an CD38 mAb against MM. Overall, these preclinical in vivo studies have a pivotal role in the evaluation of NK cell combination therapies against cancer and reveal their therapeutic potential. Citation Format: Katarzyna Franciszkiewicz, Pauline Rettman, Beatrice Gauthier, Laurence Noblet, Celine Nicolazzi, Andre Kunert, Rob Igarashi, Loreley Calvet, Valeria Fantin, Sukhvinder Sidhu. Evaluation of NK cell combination therapies in mouse models of cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1334.
Abstract 2248: Diminished survival in patients with pancreatic ductal adenocarcinoma is linked with residence in redlined neighborhoods
Authors: Vignesh Vudatha, Devon Freudenberger, Christopher Liu, Leopoldo Fernandez, Jose Trevino
Journal: Cancer Research (2024)

Abstract Redlining refers to the practice of classifying neighborhoods with racial minorities and low-income residents as “hazardous” for investors. This discriminatory practice by the Home Owners’ Loan Corporation (HOLC) has been shown to impact patient cancer incidence and outcomes in breast, lung, cervical, and colorectal cancers. In this study, we evaluate the impact of HOLC status on pancreatic ductal adenocarcinoma (PDAC) outcomes in Virginia. The Virginia Department of Health Cancer Registry was queried for adult patients diagnosed with pancreatic ductal adenocarcinoma from 2009-2018. The HOLC grade (A: best, B: still desirable, C: definitely declining, D: hazardous) of each patient’s address was determined using the University of Richmond Inequality map. Patient demographics, treatment, and survival data were compared by HOLC Grade via descriptive statistics, bivariate and multivariate analysis. 394 patients were identified (A: 24 (6.1%), B: 54 (13.7%), C: 198 (50.3%), D: 118 (29.9%)). There was no association between patient age, sex, insurance status, receipt of therapy, or smoking history and HOLC status. Patient race was significantly associated with HOLC status with more Black patients living in areas with worse HOLC grades compared to White patients (p&amp;lt;0.001). Survival analysis demonstrated that lack of surgery and chemotherapy (p&amp;lt;0.0001), metastatic disease (p&amp;lt;0.0001), and residential status in areas of HOLC grade D (p=0.012) were associated with worse survival. Based on Cox regression analysis, patients who lived in areas with HOLC grade B (adjusted HR 0.70; CI 0.49-0.98) and C (adjusted HR 0.74; CI 0.58-0.95) had improved survival compared to those living in areas with HOLC grade D. Additionally, age greater than 65, metastatic disease, and lack of treatment were associated with worse survival. Residence in a redlined neighborhoods can play a significant role in pancreatic ductal adenocarcinoma outcomes. Location in a “hazardous” area in Virginia is associated with worse survival in PDAC patients. Disparities in socioeconomics, housing, education, and food accessibility in these areas likely play a role in shaping these outcomes. Future studies are warranted to further investigate this disparity in care. Citation Format: Vignesh Vudatha, Devon Freudenberger, Christopher Liu, Leopoldo Fernandez, Jose Trevino. Diminished survival in patients with pancreatic ductal adenocarcinoma is linked with residence in redlined neighborhoods [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2248.
Abstract 7128: Novel Ku-DNA binding inhibitors impact on the cellular and <i>in vivo</i> DNA damage response to radio- and radiomimetic-therapy
Authors: Pamela L. Mendoza-Munoz, Dineshsinha Chauhan, Navnath S. Gavande, Joseph R. Dynlacht, Joy E. Garrett, John J. Turchi
Journal: Cancer Research (2024)

Abstract DNA-PK, the DNA-dependent protein kinase, is a validated target for cancer therapeutics that plays a central role in the non-homologous end joining (NHEJ) DNA repair pathway and the DNA damage response (DDR). NHEJ is a key mechanism of DNA double-strand breaks (DSB) repair, especially those induced by ionizing radiation (IR). Ku 70/80 heterodimer is required as initiator in this process, acting as an essential DNA-binding component of DNA-PK that senses DNA damage. Blocking the DNA-PK kinase activity in combination with DSB inducing agents has been widely used as a therapeutic strategy to drive clinical efficacy of radiation therapy for cancer treatment. We have reported a unique approach of DNA-PK inhibition by developing Ku-DNA binding inhibitors (Ku-DBi’s), small molecule inhibitors that target the interaction between Ku70/80 and DNA. Ku-DBi’s demonstrated a direct interaction with Ku70/80, a potent inhibition of Ku-DNA binding and DNA-PK catalytic activity, and in vitro and cellular NHEJ inhibitory activity. This results in the potentiation of non-small cell lung cancer (NSCLC) cellular sensitivity to DSB generating therapies, as a function of inhibiting DNA-PKcs autophosphorylation and dysregulation of signaling to the DDR. In this study, we have expanded our structure activity relationship analyses to focus on optimizing selectivity, cellular uptake and Ku inhibitory activity. The new series of Ku-DBi’s include oxindole derivatives of the X80 core structure that achieve these goals. These novel compounds display increased cellular uptake while retaining potent Ku inhibitory activity and enhanced cellular inhibition on DNA-DSB repair. Ku-DBi’s optimization has enabled in vivo analyses of Ku-DBi - ionizing radiation combination therapy in human xenograft models of non-small cell lung cancer. The impact of Ku-DBi treatment on therapeutic efficacy, toxicity, Ku/DNA-PK inhibition, and DDR signaling will be presented. These data represent a significant advance in the development of Ku-DNA binding inhibitors and their therapeutic intervention for cancer treatment. Citation Format: Pamela L. Mendoza-Munoz, Dineshsinha Chauhan, Navnath S. Gavande, Joseph R. Dynlacht, Joy E. Garrett, John J. Turchi. Novel Ku-DNA binding inhibitors impact on the cellular and in vivo DNA damage response to radio- and radiomimetic-therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7128.
Abstract 2247: Cellular senescence as a potential mechanism underlying differences in chemoresistance between lung cancer cell lines derived from African-American and Caucasian patients
Authors: Nina Semenova, Camille C. Robertson, Juan S. Yakisich, Robyn R. Ayscue, Anand K. Iyer, Neelam Azad
Journal: Cancer Research (2024)

Abstract Lung cancer remains the leading cause of cancer-related deaths world-wide. Statistical data reveals significant difference in both lung cancer incidence and death rate between African-American (AA) and Caucasian (CA) populations in the United States. Although these disparities can be partially attributed to socio-economical reasons, the biological mechanisms underlying them are poorly understood. In this study, we compared the chemoresistance of cell lines derived from tumor tissues obtained from AA patients (H23, H292) versus CA patients (A549, H460). The cell lines were treated with FDA-approved anti-cancer drugs as well as with cardenolide analogues previously reported by our group to have anti-cancer properties. Irrespectively of drug class, cellular senescence appeared to develop more abundantly in cells derived from AA patients. However, AA-derived cell lines manifested higher drug resistance in comparison to CA-derived ones, especially to cardenolide analogues. Recovery experiments in drug-free media revealed faster and more efficient re-growth after long-term (2 weeks) drug treatment in AA-derived cell lines. Taken together, the data provides a potential role for cellular senescence as mechanism of the differential chemoresistance observed between AA and CA lung cancer cell lines, revealing new potential targets for anti-cancer therapy. Citation Format: Nina Semenova, Camille C. Robertson, Juan S. Yakisich, Robyn R. Ayscue, Anand K. Iyer, Neelam Azad. Cellular senescence as a potential mechanism underlying differences in chemoresistance between lung cancer cell lines derived from African-American and Caucasian patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2247.
Abstract 7120: Investigating PARP1 selective inhibitor DSB1559 efficacy in BRCA1-associated triple negative breast cancer
Authors: Adam Nelson, Kelly F. Zheng, Carlos Wanderley, Daniel E. Michaud, Phillip M. Cowley, Gillian M. Campbell, Barry E. McGuinness, Alan Wise, Jennifer Guerriero
Journal: Cancer Research (2024)

Abstract Background: Poly (ADP-ribose) polymerase inhibitors (PARPi) have improved outcomes of BRCA-associated breast cancer. However, toxicity can limit patient response as well as the ability to be combined with other therapeutics. Current PARPi broadly inhibit members of the PARP protein family, however only inhibition of PARP1 is needed for PARPi-mediated cell death. As inhibition of PARP2 is associated with hematological toxicity seen in PARPi patients, selectively inhibiting PARP1 may reduce PARPi toxicity and lead to better outcomes for patients. Here we characterize and test the efficacy of the PARP1 selective inhibitor (PARP1i) DSB1559 compared to Olaparib in BRCA1-associated triple negative breast cancer (TNBC). Methods: NanoBRET, PARylation, and pharmacokinetic/pharmacodynamic assays were performed to examine DSB1559 potency, PARP family selectivity, and in vivo behavior. Immunocompetent FVB/n mice bearing BRCA1-deficient TNBC (CMV-Cre;Brca1f/f;Trp53f/f) tumors were treated daily with PARPi (Olaparib) or PARP1i (DSB1559) for 60 days and followed for survival. CellTiter-Glo and qPCR assays were used to examine DSB1559 effect on cell viability and STING activation, respectively. Results: DSB1559 is a novel and potent PARP1 inhibitor which has superior selectivity for PARP1 compared to Olaparib and PARP1i AZD5305. DSB1559 has highly desirable physico-chemical and in vitro ADME properties, which translate to high oral bioavailability and moderate clearance in rodent PK studies. Additionally, DSB1559 demonstrated superior tumor residence time and tumor/plasma ratio compared to AZD5305. Compared to Olaparib, DSB1559 significantly increased STING activation and reduced cell viability in BRCA1-associated murine TNBC cells. BRCA1-associated TNBC-bearing immune-competent mice treated with DSB1559 had significantly reduced tumor growth and increased overall survival (median survival 74 days) compared to Olaparib (median survival 18 days). Analysis of changes in the tumor microenvironment are ongoing. Conclusions: Taken together, DSB1559 is a highly selective PARP1 inhibitor that demonstrates superior efficacy compared to Olaparib in a BRCA1-associated immune-competent TNBC model. Citation Format: Adam Nelson, Kelly F. Zheng, Carlos Wanderley, Daniel E. Michaud, Phillip M. Cowley, Gillian M. Campbell, Barry E. McGuinness, Alan Wise, Jennifer Guerriero. Investigating PARP1 selective inhibitor DSB1559 efficacy in BRCA1-associated triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7120.
Abstract 7118: FANCA promoteshomologous recombinationby facilitating DR-Loop formation
Authors: Fang Li, Haibo Yang, Boya Gao, Liang Luo, Alyan Zafar, Fenghua Yuan, Li Lan, Yanbin Zhang, Liang Luo, Alyan Zafar, Fenghua Yuan, Yanbin Zhang
Journal: Cancer Research (2024)

Abstract Homologous recombination (HR), a fundamental DNA double-strand break (DSB) repair pathway, is a universal mechanism employed by cells to accurately mend breaks in both strands of the DNA helix, ensuring genomic stability. Displacement loops, commonly referred to as D-loops, play a crucial role as intermediate structures in HR. Furthermore, recent studies indicate that the unique DNA: RNA three-stranded structure, known as R-loops, may serve as a starting point for homologous pairing and contribute significantly to enhancing HR efficiency by promoting D-loop formation. Besides, the formation of R-loops might assist in recruiting DNA repair proteins, especially those related to HR, thereby accelerating the repair of damaged sites.In this study, we find that highly purified human FANCA protein anneals synthetic single-stranded RNA (ssRNA) and ssDNA species to R-loops and binds R-loop substrates with high affinity, preferring guanine-rich sequences in vitro. In comparison, FANCA exhibits both a weaker capacity to form D-loops and a lower affinity for binding to D-loops in vitro. We then use the DART (damage at RNA transcription site) system to reveal the colocalization of FANCA with R-loops in a highly transcribed genomic locus upon DNA damage in cells. Next, we further demonstrate FANCA's participation in forming R-loops in the initial DSB repair stage and assisting in removing R-loops later. Additionally, we uncover FANCA's ability to aid in the generation of R-loops at specific DNA DSB sites within transcriptionally active regions in both Tet-DR-GFP U2OS cells and DIvA (DSB inducible via AsiSI) cells. Importantly, the R-loop formation ability of FANCA is independent of the Fanconi Anemia (FA) pathway. In conclusion, our findings indicate that FANCA, independent of the FA pathway, can enhance HR in non-transcriptionally active DNA DSB sites through D-loop formation. Furthermore, FANCA significantly elevates transcription-Coupled Homologous Recombination (TC-HR) efficiency by catalyzing the formation of DNA: RNA hybrids, generating temporary R-loops at DNA damage sites and thereby contributing to genomic stability maintenance. Citation Format: Fang Li, Haibo Yang, Boya Gao, Liang Luo, Alyan Zafar, Fenghua Yuan, Li Lan, Yanbin Zhang, Liang Luo, Alyan Zafar, Fenghua Yuan, Yanbin Zhang. FANCA promoteshomologous recombinationby facilitating DR-Loop formation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7118.
Abstract 6269: Assessment of new generation endocrine therapies for the treatment of breast to bone metastasis
Authors: Emily Kate Zboril, Julia E. Altman, Nicole S. Hairr, Rachel K. Myrick, Amy L. Olex, Mikhail G. Dozmorov, J. Chuck Harrell
Journal: Cancer Research (2024)

Abstract Estrogen receptor (ER) signaling is the main driver of tumorigenesis in ER+ breast cancers by inducing proliferation and survival through genomic and non-genomic means, therefore inhibition of ER signaling has been a mainstay of treatment for decades. Roughly 30 percent of patients will develop treatment-refractory recurrence or metastasis within their lifetime, which may include metastasis to the bone, lung, liver, and brain. Although advances in treatment approaches have prolonged average progression free survival, metastatic breast cancer remains incurable. A new endocrine therapy, Elacestrant, has been approved by the FDA for the treatment of ER+, ESR1-mutant advanced or metastatic breast cancer. The mechanism of action of Elacestrant involves both degradation of ER and modulation of ER signaling through non-degradative means. The central hypothesis of this study was that Elacestrant may prolong progression free survival in animal models of breast to bone metastasis, because modulation of ER in the bone would decrease the incidence of osteoporosis which is induced by other endocrine therapies. However, we discovered that prolonged Elacestrant treatment induces destruction of the trabecular bone structure and increased adipocyte mass within the bone, consistent with an osteoporotic phenotype. Ongoing studies will seek to determine if other endocrine therapies will provide better protection to the bone architecture while reducing metastatic burden in animal models. Additionally, we will evaluate organotropic efficacy of new endocrine therapies on multi-organ metastasis to determine if utility is contingent upon the metastatic site. Citation Format: Emily Kate Zboril, Julia E. Altman, Nicole S. Hairr, Rachel K. Myrick, Amy L. Olex, Mikhail G. Dozmorov, J. Chuck Harrell. Assessment of new generation endocrine therapies for the treatment of breast to bone metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6269.