tbuckley/cabot-search huggingface dataset:
Abstract 6516: Single-cell protein activity inference reveals lymphocytic immune infiltration in diffuse intrinsic pontine glioma induced by focused ultrasound
Authors: Erin White, Hong-Jian Wei, Ester Calvo Fernández, Hanna Minns, Jovana Pavisic, Robyn Gartrell, Cheng-Chia Wu, Andrea Califano, Aleksandar Obradovic
Journal: Cancer Research (2024)

Abstract Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive pediatric brain tumor, located in the brainstem, and traditionally thought to be immune-excluded with no significant infiltration by cytotoxic T-cells, and therefore not amenable to immunotherapies. Focused ultrasound technology (FUS) for drug delivery is being investigated for DIPG in both preclinical and clinical trial settings. In this study, we sought to study the effects of FUS and radiation therapy (RT) on immune cell infiltration in DIPG tumors to assess their ability to alter the immune microenvironment and potentially enhance combination immunotherapies. Specifically, we generated single-cell RNAseq profiles for 27,780 cells from syngeneic orthotopic DIPG tumors (KPAP cell line containing H3K27M mutation, ATRX and P53 loss, and PDGFRA overexpression) after 14 days of tumor growth across the following treatment arms: vehicle control, FUS, and RT (n=2 each group). FUS was applied by 4-point sonication around the tumor with a pressure of 0.6 Mpa at days 8 and 11 post tumor implantation (PTI). RT was administered in fractions of 3 Gy daily from days 8 to 11 PTI (12Gy total). We leveraged a set of algorithms for network-based inference of regulatory protein activity to infer a set of context-matched gene regulatory networks from which protein activity can be inferred by expression of downstream targets. By this approach, we identified distinct clusters of immune cells segregating by cell type as inferred by singleR and activity of known lineage markers. Strikingly, we found that both RT and FUS significantly depleted a TGFb-expressing population of immune-suppressive macrophages as compared to vehicle controls. Importantly, FUS only additionally increased T-cell infiltration into the tumor micro-environment over three-fold as compared to vehicle controls, which was not observed in response to RT. Further protein validation is underway. This has significant implications for therapeutic combinations of FUS-mediated drug delivery with immune checkpoint inhibitors in DIPG, such that in addition to drug delivery, FUS-mediated immune modulatory effects may provide more proinflammatory response to enhance immunotherapy. Citation Format: Erin White, Hong-Jian Wei, Ester Calvo Fernández, Hanna Minns, Jovana Pavisic, Robyn Gartrell, Cheng-Chia Wu, Andrea Califano, Aleksandar Obradovic. Single-cell protein activity inference reveals lymphocytic immune infiltration in diffuse intrinsic pontine glioma induced by focused ultrasound [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 6516.
Abstract 4317: The role of autophagy in triple negative breast cancer
Authors: Sameh Gamal, Nefertiti A. El-Nikhely, Hesham Nematallah, Hesham M. Saeed
Journal: Cancer Research (2024)

Abstract Breast cancer (BC) remains a global health concern, being the most common cancer amongst women in the world, and the second-leading cause of cancer related death. Triple-negative breast cancer (TNBC) represents a challenging frontier in oncology, characterized by its aggressiveness and its unique molecular profile devoid of the known receptors. Its elusiveness lies in the inherent heterogeneity within its subtypes, contributing to diverse clinical behaviours and treatment responses. TNBC has also shown elevated basal autophagy level as a pro-survival mechanism to make up for the increased nutrients demand mandated by the high K-RAS signalling. To tackle such tumour, we chose an autophagy blocker in addition to multi-kinase inhibitor. The combination index calculated for the proposed drugs has shown promising results in reduction of cell viability more than each drug separately. Selectivity index proved the safety of our doses on normal fibroblast cells in contrast to two breast cancer cell lines (MDA-MB 231 &amp; MCF7). To further complement the findings, cell cycle arrest was witnessed at S phase which lead to apoptosis seen by flowcytometry and other expression analysis studies. Finally, Imaging studies and expression analysis on protein level have documented the apoptotic effects rendered by autophagy inhibition.Research endeavours continue to unravel the intricate landscape of TNBC, seeking novel avenues for targeted treatments, immunotherapies, and personalized medicine, aiming to transform the paradigm of care for those affected by this enigmatic form of breast cancer. As evident from the results, our combination has also managed to reduce the cells migration effectively which reflects that it can be initiated with aggressive metastatic tumours like TNBC. Citation Format: Sameh Gamal, Nefertiti A. El-Nikhely, Hesham Nematallah, Hesham M. Saeed. The role of autophagy in 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 4317.
Abstract 1919: Activity and affinity tuning next-generation immunotoxins for targeted therapy
Authors: Huazhu (Peter) Liang, Greg L. Beilhartz, Shi Bo Cao, Roman A. Melnyk
Journal: Cancer Research (2024)

Abstract Classic cancer-associated receptors, such as EGFR and Her2, are often overexpressed on malignant cells relative to healthy cells. Numerous molecules have been developed to leverage this differential expression with the goal of developing specific and safe targeted therapies, including antibody-drug-conjugates and immunotoxins. The general schematic of these molecules is to fuse toxic payloads -either small molecules or proteins - with a targeting moiety that binds to the cancer-specific receptor. Despite the general success of this approach, even low levels of these receptors on healthy tissues result in on-target/off-tumor toxicity thus limiting the dose of therapeutic molecules available to tumors. Targeted therapies with greater on-tumor efficacy and reduced toxicity are urgently needed in order to further advance therapeutic outcomes. To achieve this, we set out to exploit the unique features of bacterial toxins as highly modular protein delivery systems to design next-generation targeted therapies. We demonstrate the capacity of the immunotoxin platform to deliver various therapeutic proteins, with distinct activities from inhibiting protein synthesis to degrading oncogenic signaling pathways, such as the RAS/MAPK pathway. Further, we show how modifying the affinity, valency, and specificity of the receptor-binding moieties, as well as tuning the enzymatic activity of the toxic enzyme payloads interact to affect the on-target efficacy and off-target toxicity of the targeted molecules. Altogether, these data demonstrate the potential of immunotoxins as highly flexible and tunable platforms for the development of a new class of anti-cancer therapeutics. Citation Format: Huazhu (Peter) Liang, Greg L. Beilhartz, Shi Bo Cao, Roman A. Melnyk. Activity and affinity tuning next-generation immunotoxins for targeted 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 1919.
Abstract 6943: Evolutionary dynamics under chemotherapy in small cell lung cancer: Insights from patient-derived xenotransplant models
Authors: Laura C. Kaiser, Marcel Schmiel, Agnieszka Ruminska, Nazanin Alavinejad, Christian Müller, Justinas Valiulis, Martin Peifer, Maria Cartolano, Roman K. Thomas, Julie George
Journal: Cancer Research (2024)

Abstract Introduction: The treatment of patients with small cell lung cancer (SCLC) represents a major medical challenge due to aggressive tumor growth and the poor 5-year overall survival rate of only 5%. SCLC tumors typically are remarkably sensitive to chemotherapy at the beginning; however, the subsequent rapid relapse of therapy-resistant tumors is a severe obstacle. We therefore aimed to decipher the molecular patterns guiding processes of evolutionary adaptation in SCLC as a consequence of therapeutic interventions. Methods: Over 100 patient-derived xenotransplant models were generated from clinical SCLC specimens capturing a wide range of genetic and molecular features as well as clinical phenotypes with regard to chemotherapy response. We recapitulated chemotherapy response in vivo for 32 models, and performed in-depth genome and single-cell transcriptome sequencing to thus dissect genomic evolutionary trajectories and transcriptional plasticity of therapy-naïve and relapsed tumors, which includes the study of multiregional and longitudinal samples. Results: The response to chemotherapy in vivo reflected the clinical response of the patients; however, several models of relapsed patients remained sensitive to treatment. Genomic studies of clonal dynamics indicated selection of subclones as a result of therapeutic pressure. In contrast, chemo-refractory tumors maintained their clonal composition after therapy. In agreement with genomic profiles, single-cell transcriptome data revealed a tremendous shift in expression profiles and composition of subpopulations. Furthermore, subclonal genomic events including copy number alterations were found to shape the transcriptional heterogeneity in tumors. Conclusion: Here, we demonstrate a comprehensive functional characterization of multi-regional tumor sites and longitudinal specimens acquired from patients with SCLC, in which we elucidate genomic and transcriptional heterogeneity as a consequence of therapy response. Overall, our data points to a complex interplay between sub-clonal genomic changes and transcriptional plasticity shaping therapy response in which pre-existing genomic alterations impact selection under therapy. Citation Format: Laura C. Kaiser, Marcel Schmiel, Agnieszka Ruminska, Nazanin Alavinejad, Christian Müller, Justinas Valiulis, Martin Peifer, Maria Cartolano, Roman K. Thomas, Julie George. Evolutionary dynamics under chemotherapy in small cell lung cancer: Insights from patient-derived xenotransplant models [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 6943.
Abstract 5053: Clinicopathologic and molecular genetic features of STAT3-mutated myeloid neoplasms
Authors: Matthew T. Ye, Zhuang Zuo, Steliana Calin, Fengxi Ye, Hua He, Wataru Kamata, M. James You
Journal: Cancer Research (2024)

Abstract STAT3 is a key transcription factor that can mediate cancer progression through phosphorylation or gain-of-function mutations. STAT3 mutations have been mainly associated with large granular lymphocytic T-cell leukemia. Whereas STAT3 activation is common in myeloid neoplasms, it is primarily mediated through STAT3 phosphorylation. STAT3 mutation has only rarely been reported in myeloid neoplasms. We assessed the clinicopathologic and molecular genetic features of 32 STAT3-mutated myeloid neoplasms. Twenty (62.5%) cases were classified as acute myeloid leukemia (AML), 7 (21.9%) as myelodysplastic syndrome (MDS), and 5 (15.6%) as chronic myelomonocytic leukemia (CMML). It is of note that STAT3 mutation was not detected in myeloproliferative neoplasms (MPN). STAT3 mutations were detected at the initial diagnosis in 22 of 25 (88%) cases, suggesting STAT3 mutation is an early event in pathogenesis. However, STAT3 mutations represented the dominant clone in only 6 (18.8%) cases, all classified as AML. Most are missense mutations, located at the SH2 domain. The median variant allele frequencies were 6.8%, 4.6% and 3.1% for AML, MDS and CMML, respectively, and in a case of CMML, the VAF increased from 2.4% to 34.8% upon leukemic transformation. STAT3 mutation was accompanied by co-existing mutations in all cases, with SRSF2 (40.6%), TET2 (40.6%), ASXL1 (37.5%), and SETBP1 (34.4%) being most common. Cases with STAT3 mutations were usually associated with morphologic dysplasia and increased blasts. Monosomy 7/del7q was the most common cytogenetic abnormality, seen in 11 (34.4%) cases. With a median follow-up of 24.5 months, 21 patients died, 6 had persistent disease, and 5 achieved complete remission. We summarize that STAT3 mutation is present in a variety of myeloid neoplasms, but not seen in MPN. It is often an early events and always with concurrent mutations. It may play an important role in the pathogenesis and progression of myeloid neoplasms by activating JAK-STAT pathway, and may serve as a potential therapeutic target. Citation Format: Matthew T. Ye, Zhuang Zuo, Steliana Calin, Fengxi Ye, Hua He, Wataru Kamata, M. James You. Clinicopathologic and molecular genetic features of STAT3-mutated myeloid neoplasms [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 5053.
Abstract 4953: A proposal to extend standardized organ mapping antibody panels (OMAPs) to integrate protein and RNA analysis in spatial biology
Authors: Werner Müller, Julia Femel, Emily Neil, Dongju Park, Rebecca C. Hennessey, Eric C. DiBiasio, Michael DiBuono, Hanna Lafayette, Erica Lloyd, Hsinyi Lo, Alex Makrigiorgos, Sameh Soliman, Dominic Mangiardi, Paurush Praveen, Silvia Rüberg, Fabian Staubach, Ryan Hindman, Thomas Rothmann, Hansueli Meyer, Tanya Wantenaar, Jinling Wang, Robert Pinard, Andreas Bosio
Journal: Cancer Research (2024)

Abstract The HubMap consortium has developed a new standard to report on normal histological samples using multicolor immunofluorescence imaging. An Organ Mapping Antibody Panel (OMAP) currently describes in a table the antibodies used, the cycle number assigned to a given reagent, and provides the rationale for using a particular antibody to better understand features of the tissue. This table is accompanied by antibody validation templates that show example images from the tissue described for the OMAP table. In addition, links to existing databases, gene symbols, the antibody features and colors are included. For each tissue, a further table called "Anatomical Structures, Cell Types, plus Biomarkers" (ASCT+B), which contains structures of the tissue, cell types in a given tissue structure, key RNA transcripts for a given cell type, and antibody stains as used in the OMAP table, is created. So far, this process has not been established for spatial multiomic datasets including protein and RNA detected on the same tissue section. We have extended spatial biology methodology to combine cyclic RNA transcript detection with cyclic antibody-based protein detection using the MACSima Imaging Cyclic Staining (MICS) technology as well as H&amp;E-staining on the same tissue section. For such datasets, the current OMAP data table needs to be extended by adding information on the RNA detection, cycle IDs and RNA validation templates, demonstrating the correct performance of a given RNA probe detection. This poster will demonstrate a proposal to extend the OMAP table structure on an extended version of the “tonsil OMAP (OMAP-10)”, which was published on the Zenodo data repository page (https://zenodo.org/records/7875938). In addition, we will apply this extended OMAP to a colorectal cancer sample, to highlight the applicability and relevance of the OMAP structure for tumor tissue. Citation Format: Werner Müller, Julia Femel, Emily Neil, Dongju Park, Rebecca C. Hennessey, Eric C. DiBiasio, Michael DiBuono, Hanna Lafayette, Erica Lloyd, Hsinyi Lo, Alex Makrigiorgos, Sameh Soliman, Dominic Mangiardi, Paurush Praveen, Silvia Rüberg, Fabian Staubach, Ryan Hindman, Thomas Rothmann, Hansueli Meyer, Tanya Wantenaar, Jinling Wang, Robert Pinard, Andreas Bosio. A proposal to extend standardized organ mapping antibody panels (OMAPs) to integrate protein and RNA analysis in spatial biology [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 4953.
Abstract 4991: Radiotherapy-induced immunological and therapeutic response depends on stem-like TCF-1+PD-1+CD8+ T-cells
Authors: Hakan Köksal, Michael Herbst, Nicola Marti, Maries van den Broek
Journal: Cancer Research (2024)

Abstract Radiotherapy is a frequently used treatment for cancer. Recent data, including ours, showed that radiotherapy promotes an inflammatory response in the tumor that supports tumor-specific immunity, and in fact, the efficacy of radiotherapy in pre-clinical models depends on CD8+ T-cells. According to our preliminary data, the response to radiotherapy is independent of de novo recruited CD8+ T-cells, suggesting that radiation drives differentiation and proliferation of preexisting intratumoral CD8+ T-cells. Intratumoral CD8+ T-cells are heterogeneous concerning phenotype and function. Under conditions of chronic stimulation by antigen, a subset of CD8+ T-cells expressing PD-1 and the transcription factor TCF-1 was described. These so-called stem-like CD8+ T-cells, which give rise to effector cells, were shown to be essential for the clinical response to PD-1 blockade. How radiotherapy influences the different CD8+ T-cell subsets in the tumor microenvironment has not been comprehensively investigated. We propose that the efficacy of radiotherapy depends on the presence of stem-like CD8+ T-cells, presumably by giving rise to effector cells. To address this, we selectively depleted TCF-1+ cells from tumor-bearing mice immediately before radiotherapy. Subsequently, we correlated tumor regression with the immunological response using single-cell analyses of intratumoral CD8+ T-cells. In the absence of TCF-1+ cells, we found a reduced efficacy and reduced number of intratumoral effector cells after radiotherapy. We currently analyze our single-cell RNA-sequencing data and expect to discover novel radiotherapy-induced pathways in CD8+ T-cells that contribute to therapeutic efficacy. Citation Format: Hakan Köksal, Michael Herbst, Nicola Marti, Maries van den Broek. Radiotherapy-induced immunological and therapeutic response depends on stem-like TCF-1+PD-1+CD8+ T-cells [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 4991.
Abstract 6493: CRISPR-directed prime editing sensitizes EGFR inhibitor by correcting oncogenic KRAS mutants In NSCLC
Authors: Qingxiao Fang, Chao Yang, Chongbiao Huang, Hongwei Wang, Jun Yu, Jihui Hao
Journal: Cancer Research (2024)

Abstract EGFR inhibitor has been demonstrated with huge therapeutic potential in advanced non-small cell lung cancer (NSCLC), while the patients carrying KRAS mutation had poor response to EGFR inhibitor. KRAS mutation is the most frequent molecular alteration found in advanced NSCLC, which is associated with a poor prognosis without available targeted therapy. Previous research showed that CRISPR-directed prime editor could induce unconstrained correction for KRAS mutants (KRASG12D, KRASG12C, KRASG12V). Accordingly, it would be a promising strategy to combine PE-based genetic therapy with EGFR inhibitor for enhanced therapy in NSCLC. Here,we selected several PE variants with reported highly efficient reverse transcriptase, among which eEc48-based PE6a showed the highest editing efficiency toward KRAS mutation. The lentivirus-mediated PE6a editing inhibited cell proliferation and invasion in vitro and in vivo. After that, EGFR inhibitor combined with PE6a was employed in patient-derived organoid (PDO) model carrying diverse KRAS mutants. We found that PE6a editing significantly inhibited PDO proliferation compared to EGFR inhibitor alone and control. Correspondingly, the transcriptome sequencing also showed that the cell apoptosis, cell growth and cell motility signaling were inhibited upon PE6a editing. Our findings demonstrated that the PE-directed genetic therapy could sensitize EGFR inhibitor in NSCLC, providing an alternative choice for NSCLC patients carrying KRAS mutant. Citation Format: Qingxiao Fang, Chao Yang, Chongbiao Huang, Hongwei Wang, Jun Yu, Jihui Hao. CRISPR-directed prime editing sensitizes EGFR inhibitor by correcting oncogenic KRAS mutants In NSCLC [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 6493.
Abstract 6525: Modulating the immune response in cholangiocarcinoma: Targeting sulfatase-2 for therapeutic intervention
Authors: Tayla R. Brooks, Nellie Campbell, Melanie Keim, Lewis R. Roberts
Journal: Cancer Research (2024)

Abstract Cholangiocarcinoma (CCA) is an aggressive epithelial malignancy of the bile ducts. Recent reports have suggested a rise in the incidence of CCA globally. Current treatments for CCA have limited effectiveness, with only 20-30% response rates in patients with advanced cancer. Thus, there is a growing need to investigate new therapeutic targets for CCA. The tumor microenvironment (TME) is a potential target for novel therapies. The TME plays an important role in progression and metastasis of cancer through facilitating immune escape. Recent studies have demonstrated potential roles for heparan sulfate proteoglycans (HSPGs) in tumorigenesis. Sulfatase 2 (SULF2) is a heparan sulfate editing sulfatase that removes the 6-O sulfate moiety within the heparan sulfate (HS) chains and alters the affinity of HS chains for growth factors and cytokines and their receptors, thus modulating HSPG function in cell signaling pathways. HSPG specific sulfatases have been recently identified as a potential therapeutic target in CCA. We aimed to assess the effects of anti-Sulfatase-2 antibody on immune cells in the tumor microenvironment of syngeneic CCA xenografts in C57BL6 mice. Mice bearing syngeneic CCA xenografts were treated with an anti-sulf2 antibody, and the tumors compared to untreated control xenografts. After treatment, the tumors were harvested and analyzed by Cytometry by time of flight (Cytof) to identify changes in the types and numbers of immune cells in the tumor xenografts. Treatment with anti-sulf2 antibody resulted in a decrease in immunosuppressive cells such as tumor associated macrophages (TAMs) and myeloid derived suppressor cells (MDSC) compared to the control. There was also an increase in anti-tumor cells such as T-cells and NK cells, suggesting that suppressing sulf-2 in the microenvironment can shift the TME toward an anti-tumorigenic rather than a pro-tumorigenic environment. In summary, our work demonstrates the potential to target Sulfatase 2 as a therapeutic mechanism for immunomodulation of the tumor microenvironment. Future experiments to determine the relationship between specific clinical phenotypes and the number, activities and types of immune cells seen in the TME, and experiments in other hepatobiliary cancers models, such as hepatocellular carcinoma and gallbladder cancer, will be conducted. Citation Format: Tayla R. Brooks, Nellie Campbell, Melanie Keim, Lewis R. Roberts. Modulating the immune response in cholangiocarcinoma: Targeting sulfatase-2 for therapeutic intervention [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 6525.