tbuckley/cabot-search huggingface dataset:
Abstract 6931: Characterization of cancer evolution landscape based on accurate detection of somatic mutations in single tumor cells
Authors: Muchun Niu, Yang Zhang, Jiayi Luo, Jefferson C. Sinson, Alastair M. Thompson, Chenghang Zong
Journal: Cancer Research (2024)

Abstract Accurate detection of somatic mutations in single tumor cells is greatly desired as it allows us to quantify the single-cell mutation burden and construct the mutation-based phylogenetic tree. Here we developed scNanoSeq chemistry and profiled 842 single cells from 21 human breast cancer samples. The majority of the mutation-based phylogenetic trees comprise a characteristic stem evolution followed by the clonal sweep. We observed the subtype-dependent lengths in the stem evolution. To explain this phenomenon, we propose that the differences are related to different reprogramming required for different subtypes of breast cancer. Furthermore, we reason that the time that the tumor-initiating cell took to acquire the critical clonal-sweep-initiating mutation by random chance set the time limit for the reprogramming process. We refer to this model as a reprogramming and critical mutation co-timing (RCMC) subtype model. Next, in the sweeping clone, we observed that tumor cells undergo a branched evolution with rapidly decreasing selection. In the most recent clades, effectively neutral evolution has been reached, resulting in a substantially large number of mutational heterogeneities. Integrative analysis with 522-713X ultra-deep bulk whole genome sequencing (WGS) further validated this evolution mode. Mutation-based phylogenetic trees also allow us to identify the early branched cells in a few samples, whose phylogenetic trees support the gradual evolution of copy number variations (CNVs). Overall, the development of scNanoSeq allows us to unveil novel insights into breast cancer evolution. Citation Format: Muchun Niu, Yang Zhang, Jiayi Luo, Jefferson C. Sinson, Alastair M. Thompson, Chenghang Zong. Characterization of cancer evolution landscape based on accurate detection of somatic mutations in single tumor 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 6931.
Abstract 3986: Exploring nonsense-mediated decay inhibition as a novel approach to improve immunogenicity in small cell lung cancer
Authors: Lucia A. Torres Fernández, Volker Böhm, Lukas Maas, Anna Schöllhorn, Joel Kaufmann, Joshua D'Rozario, Laura Kaiser, Niels Gehring, Martin Peifer, Cécile Gouttefangeas, Roman K. Thomas, Julie George
Journal: Cancer Research (2024)

Abstract Cancer immunotherapy has revolutionized the field of oncology and is one of the most promising treatments for lung cancer. Small cell lung cancer (SCLC) is highly aggressive and patients often relapse due to chemotherapy resistance. In the recent years, chemotherapy has been combined with immune checkpoint inhibition (ICI) for SCLC treatment, leading to improved responses in some patients, but also leaving a high number of non-responders to address. Paradoxically, SCLC has one of the highest tumor mutational burden, including remarkably abundant frameshifts (FS) which could create highly immunogenic neoantigens (NeoAg). However, FS-harbouring transcripts are often degraded via Nonsense-Mediated Decay (NMD). We therefore aimed to inhibit the NMD pathway to increase the immunogenicity of SCLC. Our lab has so far profiled the mutational landscape of more than 400 SCLC patients and generated over 100 patient-derived xenotransplant models. We analyzed genome and transcriptome sequencing data of multiple tumors to interrogate the NMD target repertoire in SCLC. We determined tumor-specific mutations and predicted NeoAg based on the HLA-I-binding ability of mutant peptides. Upon NMD inhibiton, we validated the expression and presentation of NeoAg via transcriptomics, proteomics and HLA-I-immunopeptidomics. NMD-sensitive mutated transcripts included a wide range of somatic alterations beyond FS-mutations, suggesting an overall increase of potential tumor-specific NeoAg. We furthermore evaluated immunogenicity after NMD perturbation employing in vitro co-cultures as well as immunocompetent in vivo mouse models. Inhibition of NMD in tumor cells resulted in an HLA-I-dependent enhancement of T cell-mediated tumor killing in vitro, and in vivo experiments showed reduced tumor growth accompanied by increased immune infiltration upon controlled induction of NMD inhibition. Altogether, NMD inhibition in SCLC led to an upregulation of NeoAg expression in tumor cells accompanied by enhanced T cell responses in vitro and in vivo. Our strategy provides a novel approach for the treatment of low immunogenic tumors which could be combined with ICI to enhance the efficacy of immunotherapy. Citation Format: Lucia A. Torres Fernández, Volker Böhm, Lukas Maas, Anna Schöllhorn, Joel Kaufmann, Joshua D'Rozario, Laura Kaiser, Niels Gehring, Martin Peifer, Cécile Gouttefangeas, Roman K. Thomas, Julie George. Exploring nonsense-mediated decay inhibition as a novel approach to improve immunogenicity in small cell lung 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 3986.
Abstract 171: Chemotherapeutic agent, cisplatin, influences the proportion of TREM2 (+) M2 macrophages in the TME of LUAD
Authors: Yoon Jin Cha, Min Kyung Park, Yoon Soo Chang
Journal: Cancer Research (2024)

Abstract Background: Triggering receptor expressed on myeloid cells (TREM2) serves as an immune signaling hub that senses and interacts with a wide range of ligands arising from damaged tissues in pathologic conditions. Despite TREM2’s diverse role in casting immune suppressive environment, the effects of chemotherapy on tumor microenvironment (TME), TREM2 and their interactions are not well established. In this study, we aimed to investigate the characteristics of TREM2 (+) Mφ within the lung TME (Tu), focusing on the impact of chemotherapy on the immune dynamics of lung adenocarcinoma (LUAD). Method: Changes in the number and distribution of Mφ subclusters in normal appearing lung tissue (NL) and Tu were examined using open-source single cell RNA sequencing (scRNA-seq) datasets and immunofluorescent staining of lung cancer-induced Kras-G12D mouse tissue. Clinical measures affecting the expression of TREM2 were explored using the TCGA-LUAD and -LUSC datasets, and the effects of anticancer drugs and the apoptotic cells on Mφ were observed by differentiating THP1 cells into M0, M1, and M2. Results: scRNA-seq analysis on LUAD datasets showed that Mφ were the second most abundant cell population that constitutes the lung TME, and the proportion of Mφ in the Tu decreases compared to NL. Among the Mφ subclusters in Tu, a subcluster which specifically increased in Tu shows enrichment of apoptotic cell clearance gene sets, including TREM2. In lung cancer induced Kras-G12D mouse, compared to NL the Tu has an increase in M2 proportion, showing the characteristics of interstitial Mφ in addition with overexpression of TREM2 and enrichment of monocyte chemotaxis gene set enrichment. Among TCGA-LUAD, the high TMB group has low TREM2 expression, and the proportion of TREM2 (+) M2 in the Tu decreases in cisplatin-treated Kras-G12D mouse Tu, suggesting the expression of TREM2 in M2 is suppressed by either cisplatin treatment itself or active immunity in Tu. Additionally, we are going to observe the effect on TREM2 expression by adding cisplatin treated A549-GFP cells or cisplatin alone, to the THP-1 cells that were differentiated into M0, M1, or M2 state. Conclusion: In addition to changes in the lung immune environment due to the tumor, anticancer treatment changes in the characteristics of M2 in TME, in terms of decrease in TREM2 (+) Mφ fraction. Considering that TREM2 plays a central inhibitory role in the tumor immune environment, the effect of anticancer chemotherapeutic agents should be considered in the development TREM2 targeting agents. Citation Format: Yoon Jin Cha, Min Kyung Park, Yoon Soo Chang. Chemotherapeutic agent, cisplatin, influences the proportion of TREM2 (+) M2 macrophages in the TME of LUAD [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 171.
Abstract 2851: Characterization of neogenes in desmoplastic small round cell tumors
Authors: Danh Truong, Justin Magrath, Sean Lee, Joseph Ludwig
Journal: Cancer Research (2024)

Abstract Desmoplastic Small Round Cell Tumor (DSRCT) is a rare, soft tissue sarcoma caused by the EWS::WT1 fusion protein (FP). The FP acts as an aberrant transcription factor with oncogenic properties. Recently, oncogenic chimeric transcription factors (OCTF), such as EWS::WT1, were discovered to induce the expression of novel transcripts in otherwise silent genomic regions. These neogenes (NGs) are highly specific to each OCTF and not detected in normal tissue. 37 NGs were found to be associated with the EWS::WT1 FP.We explored the NGs to characterize their expression and regulation in a cohort of MD Anderson Cancer Center patients. We annotated and counted the NGs from the bulk RNA-seq data of 37 specimens. After fusion detection, only 22/37 specimens harbored the EWS::WT1 FP. We found that only the same 22 specimens robustly expressed DSRCT-specific NGs. Interestingly the NGs were heterogeneously expressed, suggesting that there may be patient-specific differences. Single-nucleus RNA-sequencing (snRNA-seq) of Ewing sarcoma (ES), CIC::DUX4 sarcoma (CDS), DSRCT, and osteosarcoma revealed that only the three sarcomas driven by an OCTF robustly expressed NGs. Notably, the DSRCT-specific NGs were only expressed in DSRCT. Similarly, ES and CDS only expressed their subtype-specific NGs. Given the robust expression of the DSRCT-specific NGs in DSRCT, we asked if the EWS::WT1 FP regulated the expression of the NGs. Knockdown (KD) of the EWS::WT1 FP in four DSRCT cell lines showed a consistent reduction in DSRCT-specific NGs. While there was variability in NG expression and EWS::WT1 FP KD sensitivity, we identified seven NGs decreased by at least 75% in all four cell lines and an additional eight NGs with 75% reduction across three cell lines. BOD-DSRCT and SK-DSRCT2 had the largest number of NGs reduced after KD, with 25/37 and 20/37 NGs with 75% expression reduction, respectively. EWS::WT1 FP has two known isoforms generated by alternative splicing in the WT1 domain that includes or excludes three amino acids, lysine, threonine, and serine (KTS) between zinc fingers 3 and 4, producing E+KTS and E-KTS isoforms. By transducing one or both isoforms into the mesothelial cell line LP9, we found 3/37 NGs were induced by the E+KTS isoform and 17/37 were induced by the E-KTS isoform, suggesting that the E-KTS isoform is primarily responsible for NG expression. Current work is underway investigating the relationship between EWS::WT1 FP binding and NG expression and the potential for NG to produce novel peptides that could serve as DSRCT immunotherapy targets. Citation Format: Danh Truong, Justin Magrath, Sean Lee, Joseph Ludwig. Characterization of neogenes in desmoplastic small round cell 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 2851.
Abstract 2527: PD-L1 regulation by Dual Oxygenase 2 (DUOX2), a reactive oxygen species (ROS) producing enzyme in gastric cancers
Authors: France Carrier, Mariana B. Martins
Journal: Cancer Research (2024)

Abstract Immune checkpoint inhibitors have shown outstanding activities in some cancers, but their efficacy is rather variable with limited long-term response in most patients while others do not respond well or even develop resistances. The oxidative state of the tumor and its microenvironment plays a critical role in this response and highlights the importance of better understanding the role of redox enzymes in response to immunotherapy. In fact, Reactive Oxygen Species (ROS) effectors can either up or down regulate PD-L1 expression depending on their targets and mechanisms of action. Our data indicate that DUOX2, an NADPH enzyme involved in the production of H2O2, is expressed in about forty percent of human gastric cancers and is significantly increased in esophageal cancers. Moreover, DUOX2 expression in human gastric and esophageal cancer cells corresponds to down regulation of the immune checkpoint PD-L1. Conversely, down regulation of DUOX2 increases PD-L1, HIF-1α and c-Myc expression in these cells. To better understand the role of DUOX2 in the production of ROS and how it interferes with the expressions of HIF-1α and PD-L1, we also evaluated its effects on the ROS scavenger glutathione (GSH) and the ROS generating Ceramide in cells expressing or not DUOX2. The down regulation of DUOX2 reduced by more than half Ceramide levels and significantly increased GSH levels. This is consistent with the known effect of H2O2 on Ceramide generation through sphingomyelin hydrolysis and H2O2 inhibitory effect on HIF-1α binding and accumulation of HIF-1α protein. Because HIF-1α is a known regulator of PD-L1, DUOX2 expression on some tumors could thus interfere with PD-L1 expression through generation of H2O2. Moreover, because HIF-1α and PD-L1 expression contribute to radio-resistance, DUOX2 expression could sensitize cancer cells to radiation therapy. On the other hand, tumors lacking DUOX2 expression would be expected to be more sensitive to immunotherapy targeting PD-1 and/or PD-L1. DUOX2 expression thus appears to hold significant potential as a valuable biomarker to guide therapeutic decisions regarding radiation or immuno-therapy. Citation Format: France Carrier, Mariana B. Martins. PD-L1 regulation by Dual Oxygenase 2 (DUOX2), a reactive oxygen species (ROS) producing enzyme in gastric cancers [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 2527.
Abstract 2852: Novel combination therapy with a KAT6A/B inhibitor together with retinoids induces irreversible differentiation of neuroblastoma cells
Authors: Nina Weichert-Leahey, Alla Berezovskaya, Mark Zimmerman, Brian J. Abraham, Adam W. Durbin, A Thomas Look
Journal: Cancer Research (2024)

Abstract Neuroblastoma is a pediatric tumor of the peripheral sympathetic nervous system derived from migratory neural crest cells that have committed to become sympathetic neuroblasts, but their definitive differentiation is blocked. Neuroblastoma cell identity depends on the adrenergic core regulatory circuit (CRC) of transcription factors that collaborate with MYCN to drive cell proliferation and the oncogenic gene expression program. Retinoic acid is used as differentiation therapy for patients with high-risk neuroblastoma, with the goal to block proliferation and drive sympathetic neuronal differentiation. We recently showed that retinoic acid re-organizes the enhancer landscape of neuroblastoma and promotes a new retino-sympathetic cell state characterized by MYCN downregulation, proliferative arrest, and sympathetic neuronal differentiation. However, the effects of retinoic acid on epigenetic rewiring of the adrenergic CRC and suppression of MYCN expression are reversible in vitro and in vivo, leading to tumor re-growth when the retinoic acid is withdrawn. Therefore, we sought to determine if retinoid-induced differentiation can be forced to progress to irreversible neuronal maturation by the addition of inhibitors of epigenetic modifying enzymes. Here, we conducted a drug screen of epigenetic modifying drugs alone and in combination with retinoic acid to determine their effects on neuroblastoma cell growth and differentiation. In this screen, we found that an inhibitor of the histone H3K23 acetyltransferases KAT6A/B, PF-9363, synergistically inhibits neuroblastoma cell growth in combination with retinoic acid. Moreover, retinoid-resistant neuroblastoma cell lines can be sensitized to retinoic acid when combined with a KAT6 inhibitor. Importantly, this combination treatment renders the differentiated cell state irreversible, such that it is maintained after retinoic acid is withdrawn, with continued suppression of the adrenergic CRC and MYCN expression. In conclusion, the retino-sympathetic differentiated cell state induced by retinoic acid in neuroblastoma becomes irreversible when the cells are also treated with an inhibitor of the KAT6A/B histone H3K23 acetyltransferases, implicating the essential role of these enzymes in restoring the proliferative immature progenitor phenotype in adrenergic neuroblastoma cells. Citation Format: Nina Weichert-Leahey, Alla Berezovskaya, Mark Zimmerman, Brian J. Abraham, Adam W. Durbin, A Thomas Look. Novel combination therapy with a KAT6A/B inhibitor together with retinoids induces irreversible differentiation of neuroblastoma 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 2852.
Abstract 252: Functional and lineage atlas of salivary gland regeneration charted by rapid in vivo gene targeting
Authors: Qiwen Gan, Zhe Ying
Journal: Cancer Research (2024)

Abstract The crucial function of the salivary gland of keeping the oral cavity lubricated to facilitate breathing, swallowing, and lingual communication is often compromised following cancer radiotherapies. Due to the ultra-high radiosensitivity and low regeneration potential of the salivary epithelium, radiation-induced damage is largely permanent, representing a major clinical challenge. To solve this problem, we have developed a scalable rapid gene targeting system in the murine salivary gland using in-utero injection of lentiviruses. This allows us to transduce ectodermal progenitors of salivary glands with high efficiency and full randomness. Barcoded lentiviral lineage tracing suggests that every major salivary gland originated from a defined number of progenitors, each progenitor-derived clone has relatively equal expansion potential during development and equally contributes to regeneration post radiation challenge. This observation indicates that the major salivary glands of a single mouse can be used as a platform to study lineage dynamics or test up to ~2600 different genetic conditions during regeneration. With this robust approach in hand, we identified major barriers to salivary gland regeneration from among hundreds of differentially regulated signaling pathways and genes post-irradiation. Based on these discoveries, we are currently in the process of 1) Understanding the molecular mechanisms underlying the top regeneration barriers; 2) Dissecting the cell fate dynamics of salivary gland regeneration with or without regeneration barriers; and 3) Testing if we can restore the salivary gland in situ via combinatorial removal of regeneration barriers. Our work will provide unbiased functional and lineage roadmaps of post-irradiation salivary gland regeneration and potentially serve as the cornerstones of future therapeutic interventions. Citation Format: Qiwen Gan, Zhe Ying. Functional and lineage atlas of salivary gland regeneration charted by rapid in vivo gene targeting [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 252.
Abstract 2130: Glioblastoma-derived extracellular vesicle cargo as a reporter of drug delivery and effect
Authors: Valerie DeLuca, Nanyun Tang, Nathaniel Hansen, Anjali Raju, Charles Shaffer, Yue Hao, Terry C. Burns, Jann N. Sarkaria, Ian Parney, Patrick Pirrotte, Kendall Van Keuren-Jensen, Michael E. Berens
Journal: Cancer Research (2024)

Abstract The selectivity of the blood-brain-barrier (BBB) can prevent therapeutics from reaching the brain, and this may contribute to the high failure rate of new drugs for tumors like glioblastoma (GBM) and brain metastasis. The capacity to detect BBB penetrance in real-time in a noninvasive manner would arguably aid the rate of therapeutic development. Extracellular vesicles, which are membrane bound particles secreted by all cell types in the body, have potential as a neuro pharmacodynamic reporter given that their protein and RNA cargo reflect the originating cell population. We hypothesized that the exposure of GBM cells to therapy results in altered EV cargo, and that the detection of this shift can be leveraged as a liquid biopsy from patients during early clinical trials to determine BBB penetrance and tumor engagement. To identify cargo shifts indicative of treatment, we exposed four short-term patient derived glioma cell lines to arsenic trioxide (an idiopathic toxin), MLN4924 (a neddylation inhibitor), and the alkylating agent temozolomide, then harvested EVs for unbiased mass spectrometry and RNA sequencing. Interestingly, we identified conserved upregulated and downregulated protein and RNA species across cell lines and across drug treatments, despite the diverse mechanisms of action. Candidate proteins were further validated by mesoscale immunoassays and exoview evaluation of tetraspanin-captured EVs. RNA species were validated by qRT-PCR. Overall, we demonstrate that GBM-derived EV cargo changes in response to therapy, supporting the development of EVs as a reporter of drug delivery in GBM. Ongoing and future work is focused on identifying enrichment handles in order to selectively evaluate GBM-derived EV cargo from patient biofluids. Thus far, B7H3, PTPRZ1, EGFRvII and IL13Ra2 have been screened as putative handles. Success in this pursuit could substantially enhance findings and accelerate drug testing in early-stage clinical trials in brain tumor patients by reporting drug accessibility to the tumor and engagement with drug targets. Citation Format: Valerie DeLuca, Nanyun Tang, Nathaniel Hansen, Anjali Raju, Charles Shaffer, Yue Hao, Terry C. Burns, Jann N. Sarkaria, Ian Parney, Patrick Pirrotte, Kendall Van Keuren-Jensen, Michael E. Berens. Glioblastoma-derived extracellular vesicle cargo as a reporter of drug delivery and effect [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 2130.