tbuckley/cabot-search huggingface dataset:
Abstract 7560: Microsatellite instability (MSI) detection using flow-based sequencing
Authors: Gila Lithwick-Yanai, Hila Benjamin, Jorge Cano-Nistal, Shir Geisler, Ariel Jaimovich, Nika Iremadze, Dror Kessler, Ilya Soifer, Danit Lebanony, Keren Ben Simhon, Shlomit Gilad, Eti Meiri, Doron Lipson, Yosef E. Maruvka
Journal: Cancer Research (2024)

Abstract Background: Microsatellite instability (MSI) is an important genomic biomarker associated with various cancers and hereditary conditions. Accurate and efficient classification of MSI status is essential for diagnosis, prognosis, and treatment decisions. Different approaches for testing MSI have been presented in the literature, including NGS-based methods which either rely on comparison with a matched control sample, a set of reference control samples, or the reference genome (no control). In this study, we explore the feasibility of accurately identifying MSI status using the UG100 platform, which utilizes flow-based sequencing chemistry. Since MSI detection is typically based on long homopolymers, we examined here whether the flow-based sequencing data can be effectively used for MSI classification. Methods: We performed whole genome sequencing (WGS) on a cohort of 24 cell lines with known MSI status, as well as on 15 tumor tissue samples, encompassing various cancer types, including colon, lung, bladder, and endometrial cancer. To determine the MSI status, polyA/T homopolymer loci were considered. We measured the MSI status in these loci using two methods: 1) Counting short indel variants detected using somatic Deep Variant, in comparison with matched blood normal, and 2) a novel MSI score based on the difference of the polyA/T homopolymer length, in comparison to the reference genome. We assessed the ability to evaluate the score for the full sequenced coverage (~100X) as well as when limiting to exome boundaries, and when sampling down to 1X coverage. Results and Conclusions: We established the performance of the MSI score on the cell lines with known MSI status. The score was verified on cell line mixtures (simulating lower tumor purity) as well as on clinical samples from various tissue sources, including colon samples annotated as mismatch-repair deficient. We demonstrate the ability to use the cost-effective UG100 sequencing combined with the two methodologies to identify MSI-high samples in these scenarios. Citation Format: Gila Lithwick-Yanai, Hila Benjamin, Jorge Cano-Nistal, Shir Geisler, Ariel Jaimovich, Nika Iremadze, Dror Kessler, Ilya Soifer, Danit Lebanony, Keren Ben Simhon, Shlomit Gilad, Eti Meiri, Doron Lipson, Yosef E. Maruvka. Microsatellite instability (MSI) detection using flow-based sequencing [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 7560.
Abstract 7203: Anti-HDGF antibody attenuates the rise of resistance to EGFR tyrosine kinase inhibitor in NSCLC patient-derived xenograft tumors
Authors: Cindy Q. Zhou, Ariel Li, Kaoru Ri, Ahmed Sultan, Hening Ren
Journal: Cancer Research (2024)

Abstract Mutant epidermal growth factor receptor (EGFR), a major oncogenic driver in non-small cell lung cancer (NSCLC), is found in the tumors of 15% (western countries) to 50% (Asian countries) of patients. EGFR-targeted therapy using tyrosine kinase inhibitors (TKIs) is a standard of care for those patients who developed metastatic or recurrent diseases. However, despite having an 80% initial response rate, most patients had partial tumor regression and their disease would progress when acquired resistance emerges. Thus, developing more effective treatment is an unmet need. The clinical response of these patients can be recapitulated in mouse models of patient-derived xenograft (PDX) tumor bearing sensitizing EGFR mutations. In this study, treating established PDX tumors with osimertinib, a third generation EGFR TKI, induced partial tumor regression (50% to 70% size reduction from baseline) followed by progression with a median progression-free survival (PFS) of 26 to 28 days. Interestingly, co-administering an antibody against hepatoma-derived growth factor (HDGF) with osimertinib resulted in enhanced tumor regression (98% to 100% size reduction from baseline) which translated into significantly extended animal survival with a median PFS of 103 or 135 days. Immunohistochemical and western blot examination of tumors collected at different treatment timepoints indicated that AKT/mTOR and MAPK pathways were reactivated after initial suppression in TKI monotherapy arm despite persistent EGFR inhibition. Since AKT/mTOR and MAPK pathways are key survival and proliferative signaling pathways, their reactivation can promote TKI tolerance of tumor cells and the emergence of TKI resistance. However, blocking HDGF attenuated the reactivation of these pathways which could partially explain the enhanced efficacy of osimertinib plus anti-HDGF antibody combination treatment seen in this study. Our results suggest tumor-derived HDGF could play a crucial role in the rise of acquired resistance to osimertinib. Identifying the exact cells and molecular pathways utilized by HDGF to promote tumor cell tolerance to TKI will help us understand how TKI sensitive tumor cells survive EGFR blockade and emerge as resistant cells. Citation Format: Cindy Q. Zhou, Ariel Li, Kaoru Ri, Ahmed Sultan, Hening Ren. Anti-HDGF antibody attenuates the rise of resistance to EGFR tyrosine kinase inhibitor in NSCLC patient-derived xenograft tumors [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 7203.
Abstract 4069: IL12-expressing genetically engineered myeloid cells remodel the stromal dense and T cell poor tumor microenvironment and premetastatic niche of F42010 murine osteosarcoma
Authors: Kailey Jackett, Alice Browne, Sabina Kaczanowska, Miranda Clements, Rosandra Kaplan, Kristin Wessel, Brendan Ball, James Cronk
Journal: Cancer Research (2024)

Abstract Treatment options for patients with metastatic and recurrent osteosarcoma are poor. The development of immunotherapies for osteosarcoma has been hindered by the lack of immunocompetent preclinical models that recapitulate the stromal dense, myeloid-rich, T cell poor, and overall immunosuppressive microenvironment of human osteosarcoma. We hypothesized that the syngeneic murine osteosarcoma model F42010 may serve as a useful immunocompetent preclinical model of osteosarcoma suitable for developing novel immunotherapies for osteosarcoma. To test this, we used flow cytommetry, bulk RNA sequencing, and immunohistochemistry to characterize the stromal and immune compartments of this model. We found that the F42010 osteosarcoma model recapitulates the ECM-rich and immunosuppressive nature of human osteosarcoma primary tumor and pre-metastatic microenvironments, characterized by increased myeloid infiltrate expressing suppressive markers and lymphocyte exhaustion. Finally, we used this model to test the utility of a myeloid immunotherapy for osteosarcoma, IL-12 secreting genetically engineered myeloid cells (IL12-GEMys) that can reverse immune suppression in the pre-metastatic niche and tumor microenvironment. IL12-GEMy treatment augmented immune activation and significantly extended survival by delaying tumor growth. Our findings highlight that the F42010 osteosarcoma model effectively replicates key features of the osteosarcoma tumor microenvironment and is a valuable model for developing novel tumor microenvironment and pre-metastatic niche modulating immunotherapies for osteosarcoma. Citation Format: Kailey Jackett, Alice Browne, Sabina Kaczanowska, Miranda Clements, Rosandra Kaplan, Kristin Wessel, Brendan Ball, James Cronk. IL12-expressing genetically engineered myeloid cells remodel the stromal dense and T cell poor tumor microenvironment and premetastatic niche of F42010 murine osteosarcoma [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 4069.
Neuroactive metabolites and bile acids are altered in extremely premature infants with brain injury
Authors: Manuel Pristner, Daniel Wasinger, David Seki, Katrin Klebermaß-Schrehof, Angelika Berger, David Berry, Lukas Wisgrill, Benedikt Warth
Journal: Cell Reports Medicine (2024)

The gut microbiome is associated with pathological neurophysiological evolvement in extremely premature infants suffering from brain injury. The exact underlying mechanism and its associated metabolic signatures in infants are not fully understood. To decipher metabolite profiles linked to neonatal brain injury, we investigate the fecal and plasma metabolome of samples obtained from a cohort of 51 extremely premature infants at several time points, using liquid chromatography (LC)-high-resolution mass spectrometry (MS)-based untargeted metabolomics and LC-MS/MS-based targeted analysis for investigating bile acids and amidated bile acid conjugates. The data are integrated with 16S rRNA gene amplicon gut microbiome profiles as well as patient cytokine, growth factor, and T cell profiles. We find an early onset of differentiation in neuroactive metabolites between infants with and without brain injury. We detect several bacterially derived bile acid amino acid conjugates in plasma and feces. These results provide insights into the early-life metabolome of extremely premature infants.
Abstract 7579: Dual inhibition of enhancer of zeste homolog 1 2 induces pyroptosis, modulates oncogenic signaling pathways &amp; sensitizes hepatocellular carcinoma to valemetostat &amp; docetaxel treatments
Authors: Asmaa Elkhder Harira, Adham Maher, Ahmed Sultan
Journal: Cancer Research (2024)

Abstract HCC is a global health concern, with chemotherapy resistance and patient recurrence posing significant challenges to liver cancer treatment. EZH2 is a crucial part of the polycomb repressive complex 2 (PRC2). It, along with its homolog EZH1, is a focus for cancer therapeutic targets. Dysregulation of EZH1/2 can cause cancer development due to significant changes in geneexpression. The current study aims to investigate the interaction between EZH1/2 and oncogenic signals responsible for HCC progression and pyroptosis induction. Two cell lines, HepG2 and SK-Hep1, were subjected to two FDA-approved drugs, Valemetostat (Val) and Docetaxel (Doc), to determine the impact of EZH1/2 on tumorigenicity and drug resistance. The WST-1 assay was utilized to gauge cell proliferation. The results indisputablydemonstrated a synergistic effect of the drugs after 48 h of treatment. The inhibition of viability was attributed to apoptosis induction in both tested cell lines, and the maximum effect was observed in the combined treatment as compared to either the control or each drug alone. Furthermore, our datashowed activation of caspase-3, upregulation of BAX, indicating apoptotic induction, and downregulation of Bcl-2, Bcl-XL, AKT, S6k, oncogenic β-catenin, and Stat3 protein expression levels, suggesting a modulation of oncogenic signaling pathways at the protein level. After 24 h of Val/Doc treatment, pyroptosis was observed, characterized by cell swelling and bubbles on themembrane and a significant release of lactate dehydrogenase, indicating pyroptotic cell cytotoxicity. The antitumor effects and pyroptosis were enhanced by using a dual inhibitor, UNC1999, for EZH1/2, resulting in a marked increase in the sensitivity of tested cells to the Val/Doc treatment invitro. The present study unequivocally demonstrated that dual inhibition of EZH1/2 acts as a potent sensitizer of HCC cells to Val/Doc treatment, which might be a promising therapeutic approach for inducing cellular pyroptosis in HCC cell lines. Citation Format: Asmaa Elkhder Harira, Adham Maher, Ahmed Sultan. Dual inhibition of enhancer of zeste homolog 1 2 induces pyroptosis, modulates oncogenic signaling pathways &amp; sensitizes hepatocellular carcinoma to valemetostat &amp; docetaxel treatments [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 7579.
Abstract 7545: Epigenetic plasticity in rewiring DNMT1/UHRF1-RB1- NFkB signaling circuit regulates asbestos-induced mesothelial malignant transformation
Authors: Sichuan Xi, Xinwei Wu, David M Straughan, Eden C Payabyab, Haitao Wang, Ruihong Wang, Mary Zhang, Shamus R. Carr, Chuong D. Hoang, David S. Schrump
Journal: Cancer Research (2024)

Abstract The exact mechanisms underlying the causal relationship between asbestos exposure and malignant mesothelioma (MM) have yet to be elucidated. Widespread genomic and epigenomic alterations are being implicated in rewiring of oncogenic signaling networks which may contribute to initiation and progression of MM. In the present study, we examined the molecular profiles of mesothelial cells exposed to asbestos in-vitro and found that asbestos-induced activation of DNMT1/UHRF1 mediated epigenetic repression of RB1 in normal mesothelial cells as well as mesothelioma cells via promoter-specific methylation mechanisms. RB1, as a noncanonical transcription factor, was capable of also negatively modulating the transcriptional activities of DNMT1/UHRF1 mesothelium and mesothelioma. Functioning as one of the downstream effectors of RB1, NFkB was also involved in the transcriptional regulation of DNMT1/UHRF1 directly in a promoter-selective manner and played a pivotal role in the acute as well as chronic functional and phenotypic changes of mesothelial cells following asbestos exposure. Pharmacological interference of the dysregulated RB1-DNMT1/UHRF1- RB1-NFkB signaling circuit constitutively arrested the invasive growth of MPM cells. In-vivo studies using FVB genetic background wild-type and Bap1+/- mice further revealed involvement of epigenetically dysregulation of the RB1-DNMT1/UHRF1- RB1-NFkB signaling circuit during asbestos-induced malignant transformation of mesothelial cells. Taken together, our data are the first to describe that asbestos epigenetically rewires the RB1-DNMT1/UHRF1- RB1-NFkB signaling circuit during mesothelioma development and suggest potential novel strategies to reverse these epigenetic perturbations for MPM treatment in the clinic. Citation Format: Sichuan Xi, Xinwei Wu, David M Straughan, Eden C Payabyab, Haitao Wang, Ruihong Wang, Mary Zhang, Shamus R. Carr, Chuong D. Hoang, David S. Schrump. Epigenetic plasticity in rewiring DNMT1/UHRF1-RB1- NFkB signaling circuit regulates asbestos-induced mesothelial malignant transformation [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 7545.
Abstract 3697: Proof-of-concept study to enumerate large oncosomes using the RareCyte CTC platform
Authors: Eszter Papp, Jo Vandesompele, Peter B. Vermeulen, Luc Y. Dirix, Mark Kockx
Journal: Cancer Research (2024)

Abstract Introduction: Large oncosomes (LO) are produced by tumor cells and can be detected in blood from cancer patients. The clinical utility of enumerating and characterizing LOs along with CTCs has been demonstrated, especially in settings where CTC counts are low. The RareCyte CTC platform has the potential to capture LOs along with CTCs. We performed a pilot study to evaluate the RareCyte CTC platform’s potential to analyze LOs using established preanalytical procedures. Methods: Metastatic breast cancer patients’ (N=10) blood smears labelled with RarePlex® Enumeration panel kit were re-evaluated to identify objects with LO-like characteristics at 10x magnification, along with negative control slides (N=5). LO-like objects were annotated and re-scanned at 40x magnification using the CyteFinder® imaging instrument. After establishing the criteria for LO identification, LO enumeration was performed on a cohort of MBC patients (N=6). Sets of five blood smear slides stained with the RarePlex® Enumeration panel kit were reviewed and LO counted. Total LO counts were established by extrapolating LO counts to 7.5 mL plasma. Pearson correlation was used to determine the level of correlation between LO counts and previously obtained CTC counts. Results: The established identification criteria enabled the consistent enumeration of LOs at 10X magnification. Total LO count was 9.6 on the negative control slides. In MBC patients the mean total LO count was 306.2 (range 3.2 - 792). There was a significant positive correlation between LO and CTC count (r=0.855, p=0.3). In samples with CTC&amp;gt;0 (N=3), the average total LOs count was 588, about six times higher than CTC count. In CTC=0 patient samples (N=3) the mean total LO count was 24.3 (range 3.2-36). Conclusions: We report a novel protocol to quantify large oncosomes using the RareCyte CTC platform using established preanalytical workflows. The strong CK/EpCam staining in LOs and the strong correlation of LO count with CTC count indicates their tumoral origin. Due to their higher abundance, LOs combined with CTCs offer a more sensitive tool for treatment response monitoring. Due to its broad range, LO counts in patients with CTC=0 may reveal therapy response dynamics undetectable with CTC enumeration alone. Ongoing work focuses on the parallel detection and integrated evaluation of HER2 by immunofluorescent staining of CTCs and LOs, along with digital PCR based HER2 quantification using cfDNA from matched blood plasma samples. Citation Format: Eszter Papp, Jo Vandesompele, Peter B. Vermeulen, Luc Y. Dirix, Mark Kockx. Proof-of-concept study to enumerate large oncosomes using the RareCyte CTC platform [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 3697.
Abstract 258: An organoid model for investigating Lynch syndrome tumorigenesis
Authors: Caroline Guild, Christopher Heinen, Samantha Nadeau
Journal: Cancer Research (2024)

Abstract Lynch syndrome (LS) is the most common inherited predisposition for developing colon cancer and is caused by germline variants in mismatch repair (MMR) genes. Still, the mechanism of tumorigenesis in these patients is unknown. An LS patient inherits one defective copy of an MMR gene. At some point in their lifetime, the remaining wild-type allele is lost in a cell rendering it entirely MMR deficient. MMR deficiency increases mutational rate and the chance of acquiring mutations in an oncogene or tumor suppressor that drive tumor initiation. However, loss of MMR in cells also leads to increased resistance to certain forms of DNA damage. Thus, our question is whether this phenotype imparts a selective advantage in colonic cells that may lead to clonal expansion of MMR-deficient cells as a first step towards tumorigenesis in LS patients. To test this, we are using stem cell-derived human colonic organoids and CRISPR gene editing to examine competition between MMR-deficient (MMRd) and MMR-proficient (MMRp) colonic cells over time. We have initially observed that MMRd stem cells are much more efficient at generating colonic organoids that grow larger and survive longer, consistent with our hypothesis of a selective advantage. To mimic the spontaneous loss of heterozygosity that occurs in LS patients’ colonic crypts, we are forming organoids from differentially labeled MMRd and MMRp stem cells. Live fluorescent imaging of individual organoids is used to quantify changes in cell population over time. Preliminary data indicate that MMRd cells can outgrow MMRp cells resulting in a shift in the ratio of green to red cells over a two-week time period while challenged with a DNA-damaging agent. These results suggest that loss of MMR function imparts an immediate selective advantage in colonic cells in response to DNA damage. Citation Format: Caroline Guild, Christopher Heinen, Samantha Nadeau. An organoid model for investigating Lynch syndrome tumorigenesis [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 258.
Abstract 3393: Deciphering colorectal cancer: A model to study sex-based differences and role of estrogen amidst obesity
Authors: Prachi Wele, Haifei Shi, Xian Wu
Journal: Cancer Research (2024)

Abstract Worldwide statistics indicate that obesity is increasing globally, mostly due to the consumption of Western diet. The literature points out that obesity is a potent risk factor for the development of colorectal cancer (CRC). Interestingly, CRC incidence is higher in men compared to women, and the sex hormone estrogen protects reproductive-age females from CRC despite obesity. In this project, we aim to understand the sex-based differences and protective role of estrogen in obesity-influenced CRC. An improved mouse model was devised where the effects of obesity and estrogen in CRC could be meticulously studied. We deployed 4-5-week-old male and female FVB/NJ mice and performed either sham surgery (males and females) or bilateral ovariectomy (OVX) (females). Post one week of recovery, all mice were randomly sub-grouped into either low-fat diet (LFD, 10% fat) or high-fat diet (HFD, 60% fat) groups, weekly injected with a colon-specific carcinogen azoxymethane (AOM; 5 mg/kg for week 1, 10 mg/kg for weeks 2-6), and cyclically every 4-5 days injected 17-beta-estradiol (E2; 4 μg/mouse) to a group of OVX mice for the study period of 22 weeks. The body weight of all mice was tracked every week. A whole-body composition analysis after 22 weeks showed that males and OVX females are more obese compared to females with sham surgery and OVX females with E2 injection (OVX+E2), respectively. Additionally, mice on HFD had a higher body weight compared to those on LFD; however, the absence of estrogen in OVX females led them to have higher body weight compared to sham and OVX+E2 females. Moreover, a significant difference was observed in the tumor size between males and females, females and OVX females, and OVX and OVX+E2 females. Study models have rarely incorporated both sex-dependent differences and diet-induced obesity in understanding CRC. With the current study model, it is anticipated to learn more about these differences at molecular, cellular, and metabolic levels. Acknowledgments: 1) NIH/NCI R15 [To HS, XW]; 2) Miami University CFR Faculty Research Grants [To HS, XW, JZ]; 3) Miami University's College of Education, Health, and Society Interdisciplinary Research Seed Grant [To HS, XW, JZ]; 4) Sigma Xi Grants in Aid Research [To PW]; and 5) We thank Jazzminn Hembree (Director of Laboratory Animal Resources, Miami University) and Laboratory Animal Resources, Dr. Jiangjiang Zhu (Department of Human Sciences, Ohio State University), Dr. Jing Zhang (Department of Statistics), and Dr. Ramiro Malgor (Director of Histology Core Facility, Ohio University) Citation Format: Prachi Wele, Haifei Shi, Xian Wu. Deciphering colorectal cancer: A model to study sex-based differences and role of estrogen amidst obesity [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 3393.