bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1071: Tipifarnib synergizes with TKIs in clear cell renal cell carcinoma models
Authors: Gatchalian Jovylyn , Kessler Linda , Chan Stacia , Burrows Francis , Malik Shivani 
Published: April 2023

Abstract
Clear cell renal cell carcinoma (ccRCC) is a highly vascularized tumor type, primarily due to loss of the Von Hippel-Lindau (VHL) gene, which is observed in ~88% of ccRCC cases. Deletion of VHL stabilizes hypoxia-inducible factor alpha protein (HIFα) to drive the hypoxic transcriptional response, including induction of VEGF and PDGF2 that mediate tumor angiogenesis. Anti-angiogenic tyrosine kinase inhibitors (TKIs) such as sunitinib and axitinib have demonstrated therapeutic benefit in patients with ccRCC by exploiting the critical dependency of ccRCC tumors on the vasculature for oxygen, nutrients, and growth factors. However, resistance to TKIs is commonly observed, leading to clinical relapse. Here, we report that the combination of the farnesyltransferase inhibitor (FTI), tipifarnib, and any of several anti-angiogenic TKIs results in deeper and more durable responses in the VHL-mutant 786-O CDX model and an RCC PDX model, compared to TKI alone. While the anti-angiogenic TKIs or tipifarnib alone merely slowed or occasionally arrested tumor growth, the TKI-tipifarnib combination induced marked tumor regressions in all treated animals. To investigate the mechanism of action, VHL-mutant RCC cell lines were subjected to hypoxia (1% O2) in vitro to mimic the hypoxic conditions induced by TKIs in vivo and were treated with tipifarnib to evaluate tipifarnib’s impact on signaling pathways in hypoxia-exposed cells. In the Caki2 cell line, hypoxia initially reduced mTOR signaling, but it rebounded strongly after 24 hours in hypoxia, suggesting that mTOR pathway reactivation is a potential mechanism of resistance to TKIs. Addition of tipifarnib blocked hypoxia-induced mTOR reactivation. Mechanistically, tipifarnib potently inhibits the farnesylation, and hence the activity, of an obligate farnesylated protein RHEB, a positive regulator of mTOR, suggesting that the synergy may arise through RHEB inhibition in this model. The mechanistic data in cell lines suggest that tipifarnib’s ability to inhibit mTOR reactivation observed in ccRCC cell lines under hypoxic stress contributes to the enhanced treatment durability observed in vivo. Because FTIs are pleiotropic drugs, there are likely additional cell intrinsic mechanisms that may influence synergy with TKIs. Further in vitro and in vivo studies are underway to establish the scope and mechanistic underpinnings of TKI-tipifarnib effects and strengthen the therapeutic rationale for combining TKIs with tipifarnib in the treatment of patients with ccRCC.
Citation Format: Jovylyn Gatchalian, Linda Kessler, Stacia Chan, Francis Burrows, Shivani Malik. Tipifarnib synergizes with TKIs in clear cell renal cell carcinoma models [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 1071.
Abstract 2268: Single cell RNA sequencing defines dynamic immune cell subsets in serial colon and peripheral blood samples in a patient with checkpoint inhibitor-induced colitis
Authors: Mann Jacqueline E. , Lucca Liliana , Austin Matthew , Merkin Ross D. , Aizenbud Lilach , Herold Kevan , Robert Marie , Kluger Harriet M. 
Published: April 2023

Abstract
Background: Immune checkpoint inhibition is an increasingly popular strategy for the management of numerous malignancies. Unfortunately, severe inflammatory toxicities affect up to 60% of patients, often leading to treatment discontinuation in settings where few alternative therapies are available to control disease. Checkpoint inhibitor induced colitis is a common toxicity for which the underlying mechanisms are poorly defined.
Methods: To better understand the changing colon-specific and peripheral immune environments over the course of disease progression and treatment, we collected blood and colon tissue from a Merkel Cell carcinoma patient who developed colitis after treatment with pembrolizumab. We performed 10X Genomics single cell RNA sequencing on samples collected before, during and after checkpoint inhibition and various interventions to mitigate toxicity.
Results: We identified both shared and colon-exclusive clonal expansion of T cells defined by distinct transcriptional programs, including cytotoxicity, memory, and proliferation markers, at various stages of the disease process. These clones decreased dramatically in the colon after infliximab and vedolizumab therapies.
Conclusions: We identified several distinct T cell subsets as potential drivers of colitis in the colon. T cell clones that potentially recognize colonic tissue with a high degree of specificity can be harnessed for therapeutic intervention. Our findings emphasize the need for a more detailed understanding of the immune environment in the colon and suggest the potential for peripheral blood as a readout for immune activity during CPI treatment.
Citation Format: Jacqueline E. Mann, Liliana Lucca, Matthew Austin, Ross D. Merkin, Lilach Aizenbud, Kevan Herold, Marie Robert, Harriet M. Kluger. Single cell RNA sequencing defines dynamic immune cell subsets in serial colon and peripheral blood samples in a patient with checkpoint inhibitor-induced colitis [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 2268.
Abstract 259: Fully automated targeted sequencing sample prep on open platform liquid handlers
Authors: Wahba Ashraf , Bao Yun , Wang Heng , Watson Kinnari , Zhao Grace Q. , Lin Shengrong 
Published: April 2023

Abstract
To accommodate the growing demands of sample throughput, reliability, and reduced hands-on time of targeted sequencing, automation is critical. The implementation of sample preparation automation is limited by several factors — complicated protocols and long incubation times. As an industry first, Avida’s Point-n-Seq™ hybridization-based targeted sequencing kit solution features 1 hr hybridization time and PCR free capture which enables full automation on a broad range of open platform liquid handlers, from the economical Opentrons (OT-2) to the high throughput Hamilton (Microlab Star).
We report a walk-away targeted sequencing sample-prep solution based on the highly efficient chemistry of our Point-n-Seq technology. This strategy supports PCR-free capture for variant detection. A sequencing-ready captured library is prepared in 6 hours, with just 25 minutes of hands-on time. More importantly, a PCR-free protocol increases sequence uniformity, decreases amplicon bias as well as GC-bias, and eliminates the need for purification and quantification before capture. We have demonstrated the feasibility of automated workflows using 40 ng of genomic DNA with panel sizes ranging from 20 Kb to 2 Mb. Using a comprehensive oncology panel containing 500 genes to analyze Horizon oncology cfDNA (30 ng) or FFPE gDNA (40 ng) reference standards, we demonstrated reliable detection of SNV and structural variations with allele frequency matching the expected values. The Point-n-Seq technology enables fully automated targeted sequencing sample prep on open platform liquid handlers, enhancing accuracy and reliability while reducing hands-on time. The one hour hybridization time makes hybridization more economical on the liquid handler when compared to off-instrument for overnight/longer hybridization. This automated solution greatly accelerates the development of fast, simple, and accurate genomic profiling assays. Furthermore, Point-n-Seq targeted methylation sequencing and targeted RNA assays can also be easily adapted to the same automation platforms for research and clinical applications.
Citation Format: Ashraf Wahba, Yun Bao, Heng Wang, Kinnari Watson, Grace Q. Zhao, Shengrong Lin. Fully automated targeted sequencing sample prep on open platform liquid handlers [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 259.
Abstract 2622: Targeting Rac/Cdc42 GTPases to overcome HER2-targeted therapy resistance
Authors: Reyes Miciely Cristal Aponte , Vega Luis E. Velazquez , Dharmawardhane Suranganie 
Published: April 2023

Abstract
Breast cancer is the most common cancer in women. Breast cancer is categorized by the overexpression (or lack thereof) of estrogen receptors (ER+/-), progesterone receptors (PR+/-) or human epidermal growth factor 2 receptors (HER2+/-). Specifically, HER2+ breast cancer is one of the most aggressive subtypes, comprising ~20% of all cases. Overexpression of the HER2 receptor leads to active downstream signaling that results in cell proliferation and metastasis. Clinically, this problem has been tackled by targeting the HER2 receptor with antibodies (e.g., Trastuzumab, Pertuzumab) and (or) tyrosine kinase inhibitors (TKIs; e.g., Lapatinib). However, patients may present with intrinsic or acquired resistance to these therapies. Molecular mechanisms of resistance to HER2 targeted therapy include activating mutations, alterations in downstream effectors, and compensation from other growth factor receptors. The active signaling sequelae from such mechanisms converge on the activation of guanine nucleotide exchange factors (GEFs) that regulate the GTPases Rac and Cdc42. These GTPases are critical for cell migration/invasion and have been correlated with poor prognosis in breast cancer patients. Therefore, targeting the activation of Rac/Cdc42 is a rational strategy to overcome HER2-targeted therapy resistance. Previously, we characterized the dual Rac/Cdc42 inhibitor MBQ-167 with IC50s of 103nM and 78nM for Rac and Cdc42, respectively. Our objective is to test MBQ-167 as an alternative to overcome HER2-targeted therapy resistance. To test the hypothesis that MBQ-167 will overcome HER2 therapy resistance, metastatic trastuzumab resistant HER2 overexpressing cells were treated with vehicle or individual or combined Trastuzumab and MBQ-167. Rac activity was determined by pulldown assays for active (GTP-bound) Rac, and viability was tested by MTT assays. Additionally, we measured apoptosis via caspase 3/7 activity and western blotted for the active signaling sequelae downstream of Rac. MBQ-167 reduced Rac activity and downstream signaling, as well as cell viability with a GI50 of 78nM after 72 hours, while caspase activity was increased after 24 hours of treatment. The results presented herein show the utility of the Rac/Cdc42 inhibitor MBQ-167 in overcoming HER2-targeted therapy resistance.
Citation Format: Miciely Cristal Aponte Reyes, Luis E. Velazquez Vega, Suranganie Dharmawardhane. Targeting Rac/Cdc42 GTPases to overcome HER2-targeted therapy resistance [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 2622.
Abstract 3188: Patient-derived TAC01-HER2 TAC T cells produced in Cocoon® Platform is highly functional in models of solid tumors
Authors: Wang Ling , Xu Stacey X. , Benatar Tania , Randhawa Ritu R. , Ip Philbert , Lal Prabha , Nitya-Nootan Thanyashanthi , Ravensbergen Laura , MacGregor Heather , Prosser Suzy , Sengupta Sadhak , Helsen Christopher W. , Bader Andreas G. 
Published: April 2023

Abstract
Background:
The T cell antigen coupler (TAC) is a novel, proprietary chimeric receptor that facilitates the re-direction of T cells to tumor cells and activates T cells by co-opting the endogenous T cell receptor complex with the goal to elicit a safe and durable anti-tumor response. TAC01-HER2, a first-in-class TAC T product targeting HER2 (ERBB2), has entered a Phase I/II clinical trial in patients with HER2-positive solid tumors. Here, we characterized the TAC T cell phenotypes and anti-tumor activity of TAC01-HER2 manufactured using leukocytes from Phase I/II patients in nonclinical in vitro and in vivo assays.
Materials and Methods:
TAC T cell proliferation, activation, and phenotype of patient-derived TAC01-HER2 were assessed by flow cytometric analysis. In vitro anti-tumor cytotoxicity was assessed via a real-time microscopy-based co-culture assay, and in vivo anti-tumor activity of TAC01-HER2 was assessed in mice engrafted with established solid HER2-expressing human tumors.
Results:
Complex phenotype analysis showed that patient-derived TAC01-HER2 products consisted of a high percentage of memory T cells similar to products generated from healthy donors. Patient-derived products had significant proportions of CD4 and CD8 T cells, with CD4 being the predominant population in several of these. In a 5-day in vitro potency assay, patient-derived products showed effective tumor cell killing at low E:T rations (1:1 to 1:20) which was comparable to product generated from healthy donors. Similarly, intravenous administration of patient-derived TAC01-HER2 in mice carrying HER2-positive tumors xenografts led to a complete and sustained tumor clearance.
Conclusion:
The in vitro and in vivo data confirm the potency of patient-derived TAC01-HER2 against HER2-expressing solid tumor models. This work combined with other biomarkers may help correlate nonclinical potency with clinical outcomes.
Citation Format: Ling Wang, Stacey X. Xu, Tania Benatar, Ritu R. Randhawa, Philbert Ip, Prabha Lal, Thanyashanthi Nitya-Nootan, Laura Ravensbergen, Heather MacGregor, Suzy Prosser, Sadhak Sengupta, Christopher W. Helsen, Andreas G. Bader. Patient-derived TAC01-HER2 TAC T cells produced in Cocoon® Platform is highly functional in models of solid tumors [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 3188.
Abstract 3532: Activator protein-1 (AP-1) signaling inhibits the growth of Ewing sarcoma cells in response to DNA replication stress
Authors: Gordon David , Croushore Emma , Koppenhafer Stacia , Goss Kelli , Geary Elizabeth 
Published: April 2023

Abstract
Ribonucleotide reductase (RNR) is the rate-limiting enzyme in the synthesis of deoxyribonucleoside triphosphates (dNTPs) and is required for DNA replication and the repair of DNA damage. Multiple types of cancer, including Ewing sarcoma tumors, are sensitive to RNR inhibitors or a reduction in the levels of either the RRM1 or RRM2 subunits of RNR. However, the polypharmacology and off-target effects of RNR inhibitors has complicated the identification of the precise mechanisms that regulate sensitivity and resistance to this class of drugs. Consequently, we used a conditional knockout (CRISPR/Cas9) and rescue approach to target RRM1 in Ewing sarcoma cells and identified that loss of RRM1 results in upregulation of the expression of multiple members of the activator protein-1 (AP-1) transcription factor complex, including c-Jun and c-Fos. This upregulation of AP-1 is mediated, in part, by SLFN11, which is expressed at high levels in Ewing sarcoma tumor and other pediatric sarcomas. Notably, the inducible expression of c-Jun and c-Fos in Ewing sarcoma cells impairs cell growth, downregulates the expression of the stem cell factor Sox2, and upregulates markers of cellular differentiation. In addition, small-molecule inhibitors of RNR, including gemcitabine and hydroxyurea, and HDAC inhibitors, which reduce the level of the RRM1 protein, also activate this AP-1 signaling pathway in Ewing sarcoma cells. Overall, these results provide novel insight into the critical pathways activated by loss of RNR activity and the mechanisms of action of inhibitors of RNR.
Citation Format: David Gordon, Emma Croushore, Stacia Koppenhafer, Kelli Goss, Elizabeth Geary. Activator protein-1 (AP-1) signaling inhibits the growth of Ewing sarcoma cells in response to DNA replication stress. [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 3532.
Abstract 378: Ferritin regulates oxaliplatin sensitivity and immunosuppression in pancreatic ductal adenocarcinoma
Authors: Chiu Ching-Feng 
Published: April 2023

Abstract
Oxaliplatin, a third-generation of platinum analog, has been used for the treatment of colorectal, gastric, and advanced pancreatic ductal adenocarcinoma (PDAC); however, its relatively high toxicity reduced its efficacy in clinical use. Recently, we found that organic cation transporter 2 (OCT2) expression is positively correlated to Oxaliplatin sensitivity in PDAC cells and better survival outcomes in PDAC patients with chemotherapy, suggesting that OCT2 level is important not only in predicting sensitivity to oxaliplatin but also in guiding dose adjustments to minimize toxicity. Here, we observed the significance of serum Ferritin as a prognostic marker for pancreatic cancer, and further identified Ferritin heavy chain (FTH1) down-regulated OCT2 level and reduced Oxaliplatin sensitivity of advanced PDAC cells in vitro and in vivo. Our study reveals the negative correlation between FTH1 and OCT2 levels in PDAC database analysis and reducing FTH1 expression with Deferasirox (DFX), which is an agent that has been widely used for patients with iron overload, reversed OCT2 expression and Oxaliplatin sensitization in metastatic PDAC cells. Additionally, we identified that exosomal Ferritin/FTH1 from PDAC cells may enhance M1-type to M2-type macrophage polarization to build up immunosuppression in the tumor microenvironment.
Citation Format: Ching-Feng Chiu. Ferritin regulates oxaliplatin sensitivity and immunosuppression in pancreatic ductal adenocarcinoma [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 378.
Abstract 3830: The anticancer activity of a water-soluble extract from the leaves of the indigenous Southern African plant Tulbaghia violacea against a triple negative breast cancer cell line
Authors: Hull Rodney , Dlamini Zodwa , Penny Clement , Alaouna Mohammed 
Published: April 2023

Abstract
Triple negative breast cancer (TNBC) is difficult to treat and leads to a low five-year survival rate.In South Africa, a sizable percentage of the population still relies on traditional plant-based medicine. One of these plants, Tulbaghia violacea), has traditionally been used to treat cancer. In order to establish the usefulness of both methanol and water-soluble extracts from the leaves of this plant, extracts were used to treat a TNBC cell. Cytotoxicity assays were carried out to establish the IC50 values against the TNBC cell line. These concentrations were used to carry out assays to study the ability of these extracts to inhibit cell migration, invasion, as well as the effect of these extracts on the cell cycle and their ability to induce apoptosis in these cells. Finally, the antioxidant activity of these cells was assayed. The IC50 values for the water and methanol soluble extracts was determined to be 400 and 820 µg/mL respectively. Due to the high IC50 value and inconsistent performance of the methanol soluble extract, further studies focussed on the water-soluble extract. Treatment of the TNBC cells with the water-soluble extract led to an increase in apoptosis, with the extract causing approximately 82% of the TNBC cells to undergo apoptosis compared to only 32% of the normal breast cells. This extract also significantly decreased the ability of the TNBC cells to migrate or penetrate abasement membrane in scratch and invasion assays. These results demonstrate that the water-soluble extract from T. violacea leaves contains compounds that are able to preferentially induce apoptosis in TNBC cells while also inhibiting the ability of these cells to metastasize. The exact molecular make up of this extract will need to be determined on order to develop the extract as a potential therapy for TNBC.
Citation Format: Rodney Hull, Zodwa Dlamini, Clement Penny, Mohammed Alaouna. The anticancer activity of a water-soluble extract from the leaves of the indigenous Southern African plant Tulbaghia violacea against a triple negative breast cancer cell line. [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 3830.
Abstract 6057: Association of liver cancer and chronic liver disease with urinary glyphosate and its metabolites in Thailand
Authors: Patel Daxesh P. , Pupacdi Benjarath , Rabibhadana Siritida , Toulabi Leila , Haznadar Majda , Dalal Bhavik , Khan Mohammed , Stone Joshua , Bhudhisawasdi Vajarabhongsa , Lertprasertsuke Nirush , Chotirosniramit Anon , Pairojkul Chawalit , Auewarakul Chirayu U. , Sricharunrat Thaniya , Phornphutkul Kannika , Sangrajrang Suleeporn , Budhu Anuradha , Mahidol Chulabhorn , Wang Xin W. , Gonzalez Frank J. , Ruchirawat Mathuros , Loffredo Christopher A. , Harris Curtis C. ,   TIGER-LC Consortium
Published: April 2023

Abstract
Background: Glyphosate, the primary weed-killing ingredient in Roundup®, is the most widely used herbicide worldwide. The World Health Organization’s International Agency for Research on Cancer (IARC) Monographs Program classified glyphosate is a probable human carcinogen (Group 2A), capable of causing human cancer under some circumstances.
Methods: We analyzed urine specimens from 848 sequential patients with liver cancer and matched non-cancer controls from five different regional hospitals in Thailand. Gas chromatography electrospray ionization mass spectrometry (GC-ESI/MS) technique was used to measure glyphosate and its metabolites aminomethylphosphonic acid (AMPA) and phosphoric acid (PPA) to study their levels in hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (CCA), and chronic liver disease (CLD) in comparison to matched population controls.
Findings: Significantly higher levels of glyphosate were found in CLD patients compared to cancer cases and population controls, while significantly elevated levels of both AMPA and PPA were observed in HCC and CLD patients. Glyphosate and its metabolites were also detected at low to moderately high levels in convenience samples of food products and drinking water.
Interpretation: These results raise concern about the potential role of glyphosate in chronic human liver disease and cancer.
Citation Format: Daxesh P. Patel, Benjarath Pupacdi, Siritida Rabibhadana, Leila Toulabi, Majda Haznadar, Bhavik Dalal, Mohammed Khan, Joshua Stone, Vajarabhongsa Bhudhisawasdi, Nirush Lertprasertsuke, Anon Chotirosniramit, Chawalit Pairojkul, Chirayu U. Auewarakul, Thaniya Sricharunrat, Kannika Phornphutkul, Suleeporn Sangrajrang, Anuradha Budhu, Chulabhorn Mahidol, Xin W. Wang, Frank J. Gonzalez, Mathuros Ruchirawat, Christopher A. Loffredo, Curtis C. Harris, TIGER-LC Consortium . Association of liver cancer and chronic liver disease with urinary glyphosate and its metabolites in Thailand [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 6057.