tbuckley/cabot-search huggingface dataset:
Abstract LB295: Unsaturated fatty acid synthesis is associated with poor prognosis and is differentially regulated by MYCN and tumor suppressor microRNAs in neuroblastoma
Authors: Dennis A. Sheeter, Secilia Garza, Hui Gyu Park, Lorraine-Rana Benhamou, Nikki R. Badi, Erika C. Espinosa, Kumar Kothapalli, J. Thomas Brenna, John T. Powers
Journal: Cancer Research (2024)

Abstract Dysregulated metabolism is a hallmark of cancer. While the role of glucose metabolism in cancer has been extensively studied, relatively little has been done to understand the role of poly-unsaturated fatty acids in cancer biology. To gain insight into their contribution to cancer progression we determined the expression patterns and outcome associations of both saturated and unsaturated fatty acid synthesis (UFAS) genes in pediatric neuroblastoma (NB), and fatty acid levels in NB cell lines derived from high-risk tumors. MYCN amplification and disruption of tumor suppressor miRNAs (TSmiR) function are central drivers of poor outcomes in NB. MYC, MYCN, and TSmiRs regulate glucose metabolism; however, their role in UFAS remains poorly understood. Using complementary analysis of publicly available genomic datasets and cultured NB cell measurements we examined the potential regulation of UFAS genes through MYCN and MYC activity and posttranscriptional regulation by TSmiRs. Here we show that de novo and UFAS pathway genes FASN, ELOVL6, SCD, FADS2, and FADS1 are upregulated in high-risk NB and are associated with poor prognosis. RNA-Seq analysis of eight human NB cell lines revealed parallel UFAS gene expression patterns. Consistent with this, we found that NB-related TSmiRs were predicted to extensively target these genes. Additionally, we observed that both MYC and MYCN upregulated UFAS pathway genes while suppressing TSmiR host gene expression, thereby creating a possible UFAS regulatory network between MYCN and TSmiRs in NB. Furthermore, using mass spectrometry analysis we found NB cells to be high in de novo synthesized omega 9 (ω9) unsaturated fatty acids and low in both ω6 and ω3. This finding provides a plausible means for NB to limit cell-autonomous immune stimulation and reactive oxygen species (ROS)-driven apoptosis from ω6 and ω3 unsaturated fatty acid derivatives, respectively. We propose a model in which the UFAS pathway, through novel regulation by MYCN and TSmiRs, plays a key role in neuroblastoma pathology with implications for other MYC-driven cancers. Citation Format: Dennis A. Sheeter, Secilia Garza, Hui Gyu Park, Lorraine-Rana Benhamou, Nikki R. Badi, Erika C. Espinosa, Kumar Kothapalli, J. Thomas Brenna, John T. Powers. Unsaturated fatty acid synthesis is associated with poor prognosis and is differentially regulated by MYCN and tumor suppressor microRNAs in neuroblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB295.
Abstract LB388: Super potent and efficacious ALK/ROS1/TRK inhibitor that overcomes multiple drug-resistant mutations
Authors: Li Xing, Jingbing Wang, Wei Zhu
Journal: Cancer Research (2024)

Abstract Abnormal activation of ALK, ROS1 and TRK is implicated in tumorigenesis, progression, invasion, and metastasis of malignancies through various mechanisms. The first generation TRK inhibitors including larotrectinib and entrectinib have limited applications due to acquired resistance in clinical settings. Multiple on-target mutations occur at the solvent-front, gatekeeper, and xDFG motif inside the ATP binding pocket of the TRK kinase domain. While some candidates under current clinical development aim to address the solvent-front mutation, they are ineffective against the xDFG mutations (e.g.NTRK1.G667X). There is strong unmet medical needs for next generation TRK inhibitors that can address resistance mutations. We employ the synergistic advantages of domain expertise and modern technology to accelerate early stage drug discovery. On our deep learning (DL) centric AI platform, extensive scientific computing supports large scale virtual screening, generative design, drug property prediction and multi-objective lead optimization. Only the optimized candidate compounds are passed along for synthesis and testing to save time and cost. In Ba/F3-TPM3 cellular assays, LB-2159 showed superior potencies that are hundreds to thousands of fold higher than larotrectinib and/or entrectinib, with IC50 values of 0.02 nM for NTRK1.WT, 0.3 nM for NTRK1.G595R and 0.88 nM for NTRK1.G667C. Similar cellular potencies were demonstrated for ALK and ROS1. In xenograft models LB-2159 at 10 mg/kg bid resulted in complete tumor regression in Ba/F3-TPM3-NTRK1-WT tumors, 96% TGI in Ba/F3-TPM3-NTRK1-G595R tumors, 84% TGI and 100% survival in mice bearing Ba/F3-TPM3-NTRK1-G667C tumors. The pharmacokinetic profiles of LB-2159 are overall favorable, demonstrating extended stability and half life. In vitro safety screens yielded clean profiles without any DDI signal or hERG liability. Preclinical safety evaluations exhibited good tolerance in rats. In multiple dose escalation studies LB-2159 was well tolerated at 50 mg/kg/day and beyond. Empowered by our proprietary AI platform, we have discovered the novel ALK/ROS1/TRK inhibitors that overcome clinically known resistance mutations. Our drug candidate exhibited good tolerance in animals in preclinical safety evaluations. In xenograft models that are resistant to current treatments the compound demonstrates strong tumor suppression efficacy. LB-2159 is advancing through IND enabling studies, and its preclinical profiles support the potential for best-in-class treatment for NTRK fusion-positive solid tumors. Citation Format: Li Xing, Jingbing Wang, Wei Zhu. Super potent and efficacious ALK/ROS1/TRK inhibitor that overcomes multiple drug-resistant mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB388.
Abstract LB093: Low IGFBP7 expression identifies a subset of breast cancers with favorable prognosis and sensitivity to IGF-1 receptor targeting with ganitumab: Data from I-SPY2 and SCAN-B
Authors: Christopher Godina, Michael N. Pollak, Helena Jernström
Journal: Cancer Research (2024)

Abstract Background and Hypothesis: To date, no IGF-1R targeting agent has shown clinical benefit in patients despite promising preclinical data. We hypothesized that Insulin-like growth factor binding protein-7 (IGFBP7) expression predicts response to Insulin-like growth factor-1 receptor (IGF-1R) targeting agents, for which there are no biomarkers predictive of efficacy. High IGFBP7 expression was previously associated with breast cancer progression. Materials and Methods: The predictive value of IGFBP7 expression was interrogated in I-SPY2 (NCT01042379) for pathological complete response (pCR) to neoadjuvant treatment and in SCAN-B (NCT02306096) for clinical outcome. In I-SPY2, IGFBP7 expression was examined as a predictor of pCR to neoadjuvant chemotherapy alone and separately to the combination of chemotherapy plus ganitumab (anti-IGF-1R antibody) and metformin. Odds ratios (OR) and hazard ratios (HR) with 95% confidence interval (CI) were calculated with logistic and Cox regression, respectively. Results: Higher IGFBP7 expression conferred lower odds of achieving pCR in the ganitumab/metformin plus chemotherapy arm, ORadj 0.38 (95% CI 0.17-0.80) but not in the chemotherapy-alone arm, adjusted OR 1.23 (95% CI 0.63-2.45; P interaction=0.016). In the ganitumab/metformin plus chemotherapy arm, 46.9% of patients with tumors in the lowest quartile of IGFBP7 expression achieved pCR compared to compared to only 5.6% in the highest quartile. In SCAN-B, higher IGFBP7 expression was associated with distant metastasis risk HRadj 1.41 (95% CI 1.16-1.73). Conclusion: Low IGFBP7 gene expression identifies a subset of breast cancer patients for whom the addition of ganitumab and metformin to chemotherapy results in a significantly improved pCR rate compared to neoadjuvant chemotherapy alone. Furthermore, we add to prior evidence that high IGFBP7 expression is predictive of poor outcome. Citation Format: Christopher Godina, Michael N. Pollak, Helena Jernström. Low IGFBP7 expression identifies a subset of breast cancers with favorable prognosis and sensitivity to IGF-1 receptor targeting with ganitumab: Data from I-SPY2 and SCAN-B [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB093.
Abstract LB366: KRASG12C inhibition enhances immunogenicity in KRASG12C-mutant colorectal cancer
Authors: Parasvi S. Patel, Jun Tian, Ferran Fece de la Cruz, Jacquelyn Curtis, Apekshya Panda, Tomonori Oka, Shadmehr Demehri, Moshe Sade-Feldman, Scott Koptez, Ryan B. Corcoran
Journal: Cancer Research (2024)

Abstract RAS mutations are among the most prevalent oncogenic mutations, found in approximately 20% of human cancers. KRAS, the predominantly mutated isoform of RAS, is mutated in 40% of colorectal cancer (CRC) and leads to constitutive activation of the MAPK pathway and other downstream effectors. Despite recent FDA approval for KRASG12C selective inhibitor in non-small cell lung cancer, the response rate in CRC is below 20%, posing a challenge for treatment of these tumors. Several studies have implicated oncogenic KRAS signaling in creating an immunosuppressive tumor microenvironment; therefore, we hypothesized that KRAS inhibitors can enhance anti-tumor immunity, providing a rationale for their combination with immune checkpoint blockade. Using a syngeneic KRASG12C CRC mouse model with knockout of APC, TP53, and SMAD4, we examined tumor cell-intrinsic mechanism of cooperativity between KRAS inhibition and immune response. We found that combining KRASG12C inhibition with anti-PD1 produced a more substantial and sustained reduction in tumor volume compared with KRAS or PD-1 inhibition alone. KRASG12C inhibition led to a significant increase in CD3+CD8+ T cell infiltration compared with vehicle control. Single-cell RNA-sequencing corroborated our observations and revealed increased T cell infiltration in KRASG12C tumors following KRASG12C inhibition. Moreover, these T cells upregulated genes involved in interferon gamma production and T cell activation. Importantly, we observed a significant reduction in the Ras pathway genes, specifically in the tumor cell population, along with enrichment of genes involved in abnormal antigen presentation and MHC Class I peptide loading complex. Mechanistically, we found that KRASG12C inhibition activates the innate immune response, which subsequently induce Type I interferons that activate the expression of T cell-recruiting interferon stimulated genes like CXCL9, CXCL10, IFIT1, IFIT2, and IFIT3. Our data presents a connection between KRAS inhibition and anti-tumor immunity, providing insights into novel combination strategies for KRASG12C colorectal cancers. Citation Format: Parasvi S. Patel, Jun Tian, Ferran Fece de la Cruz, Jacquelyn Curtis, Apekshya Panda, Tomonori Oka, Shadmehr Demehri, Moshe Sade-Feldman, Scott Koptez, Ryan B. Corcoran. KRASG12C inhibition enhances immunogenicity in KRASG12C-mutant colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB366.
Abstract LB069: Repurposing anti-mesothelin CAR-NK immunotherapy against colorectal cancer
Authors: Erica Torchiaro, Marco Cortese, Alice D'Andrea, Consalvo Petti, Enzo Medico
Journal: Cancer Research (2024)

Abstract Colorectal cancer (CRC) is the third most common cancer worldwide, with highly variable prognosis and response to treatment. A large subset of patients does not respond to standard treatments or develops resistance. As an alternative, adoptive immunotherapy based on chimeric antigen receptor (CAR)-transduced immune cells has been proposed, however with significant adverse events. We therefore evaluated alternative CAR targets already tested in other tumour types, and employed the natural killer cell line NK-92 for CAR transduction because of its more favourable toxicity profile. As an alternative antigen, we considered mesothelin (MSLN), the most represented in CAR-based clinical studies for solid tumours. MSLN RNA expression was analysed in large series of CRC patient-derived xenografts (PDXs, n=500), cell lines (n=150) and tumours (n=640), to evaluate its distribution and to identify MSLN-overexpressing models. NK-92 cells were transduced with anti-MSLN CAR, and subsequently sorted and cloned. Activity of CAR-NK-92 cells against target-expressing ovarian and CRC cells was assessed in vitro and in vivo. Statistical significance of efficacy was evaluated by t-test. The large-scale expression analysis highlighted that about 10% of CRCs overexpress MSLN at levels comparable to those of ovarian cancer, a typical target of MSLN-CAR-based therapy. Intriguingly, MSLN overexpression is more frequent in the CRIS-B poor prognosis subtype and KRAS/BRAF-mutant CRC. Lentiviral transduction of NK-92 cells with the MSLN-CAR, followed by sorting and cloning, led to the identification of one clone, NK-92cl45, stably expressing the CAR and retaining the NK phenotype. As expected, the clone demonstrated significant in vitro and in vivo activity against ovarian cancer cells. When repurposed against models of CRC expressing high MSLN levels, it displayed comparable efficacy, both in vitro and in vivo. Specificity of NK-92cl45 was confirmed by the absence of activity on control models with low or absent MSLN. Our results provide preclinical evidence that a subset of colorectal cancers expressing high mesothelin levels can be effectively targeted by MSLN-CAR-based immunotherapy. The potential therapeutic impact of these findings is enhanced by the fact that frequently MSLN-overexpressing CRCs display worse prognosis and resistance to standard care. Citation Format: Erica Torchiaro, Marco Cortese, Alice D'Andrea, Consalvo Petti, Enzo Medico. Repurposing anti-mesothelin CAR-NK immunotherapy against colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB069.
Abstract SY35-02: Spatial mapping of mitochondrial networks in lung cancer
Authors: David B. Shackelford
Journal: Cancer Research (2024)

Abstract Mitochondria are critical to the governance of metabolism and bioenergetics in cancer cells. The mitochondria form highly organized networks, in which their outer and inner membrane structures define their bioenergetic capacity. However, in vivo studies delineating the relationship between the structural organization of mitochondrial networks and their bioenergetic activity have been limited. Here we present an in vivo structural and functional profiling of mitochondrial networks and bioenergetic phenotypes in non-small cell lung cancer (NSCLC) using an integrated platform comprised of positron emission tomography (PET) imaging, respirometry and 3-dimensional scanning block-face electron microscopy (3D SBEM). Interestingly, the diverse bioenergetic phenotypes and metabolic dependencies we identified in NSCLC tumors align with distinct structural organization of mitochondrial networks present. Further, we discovered that mitochondrial networks are organized into distinct compartments within tumor cells. In tumors with high rates of oxidative phosphorylation (OXPHOSHI) and fatty acid oxidation we identified peri-droplet mitochondrial networks wherein mitochondria contact and surround lipid droplets. In contrast, we discovered that in tumors with low rates of OXPHOS (OXPHOSLO), high glucose flux regulated i) peri-nuclear localization of mitochondria, ii) structural remodeling of cristae and iii) mitochondrial respiratory capacity. Our findings suggest that in NSCLC, mitochondrial networks are compartmentalized into distinct subpopulations that govern the bioenergetic capacity of tumors. Structure-and-function studies defining the relationship between mitochondrial architecture and metabolic dependencies may hold promise as strategies to profile metabolic liabilities unique to lung cancer subtypes. We anticipate that coupling PET imaging with 3D SBEM will have dynamic applications beyond that of lung cancer and enrich our understanding of how mitochondrial bioenergetics impact human disease. Citation Format: David B. Shackelford. Spatial mapping of mitochondrial networks in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr SY35-02.
Abstract LB204: EHMT1 mediates cellular motility in embryonal rhabdomyosarcoma by activating SOX8 expression
Authors: Dipanwita Das, Upasana Bajaj, Jia Yu Leung, Nurul Fateha Binti Abdul Rashi, Vinay Tergaonkar, Reshma Taneja
Journal: Cancer Research (2024)

Abstract Embryonal Rhabdomyosarcoma (ERMS) stands as the prevailing subtype of Rhabdomyosarcoma (RMS), the most prevalent pediatric soft tissue sarcoma. With a survival rate below 20% in the metastatic stage, RMS lacks targeted drug therapies, emphasizing the need for novel treatment avenues. Genomic analyses have unveiled a low incidence of somatic mutations in RMS, highlighting the substantial role of epigenetic modifiers in oncogenesis.This investigation focuses on EHMT1's involvement in ERMS oncogenesis. Our findings illuminate EHMT1 as a pivotal contributor to the migratory and invasive capabilities of ERMS cells, both in vitro and in vivo. Transcriptomic analysis following EHMT1 depletion unveils significant alterations in pathways crucial for cell migration and invasion. Specifically, the transcription factor SOX8, essential for cellular motility, experiences a substantial reduction upon EHMT1 loss. Notably, the phenotypic effects of EHMT1 loss are mirrored upon SOX8 depletion.Further RNA-Sequencing of SOX8-depleted cells exposes the downregulation of multiple integrin genes. Mechanistically, we delineate EHMT1's role in the upregulation of SOX8 through the regulation of BRD4 expression, influencing its occupancy at the promoter. This study unravels a novel EHMT1-SOX8 axis as a key driver of metastasis in ERMS, providing valuable insights for potential therapeutic interventions in this challenging clinical landscape. Citation Format: Dipanwita Das, Upasana Bajaj, Jia Yu Leung, Nurul Fateha Binti Abdul Rashi, Vinay Tergaonkar, Reshma Taneja. EHMT1 mediates cellular motility in embryonal rhabdomyosarcoma by activating SOX8 expression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB204.
Abstract LB280: Enhancing glioblastoma radiotherapy by COMT inhibition
Authors: Meng Jiao, Christopher J. Pirozzi, Chen Yu, Xuhui Bao, Mengjie Hu, Dong Pan, Sejiro Littleton, Nathan Reynolds, Daniel R. Saban, Fang Li, Chuan-yuan Li
Journal: Cancer Research (2024)

Abstract There is an urgent unmet medical need to discover novel therapeutics to enhance the efficacy of glioma radiotherapy. Here we assessed the roles of catechol - o - methyltransferase COMT, a key enzyme in dopamine metabolism and a drug target for Parkinson's disease, in glioma treatment. Analysis of TCGA data showed significantly higher COMT expression levels in glioma versus normal brain tissues. Inhibition of COMT by genetic knockout or FDA - approved COMT inhibitors significantly sensitized glioma cells to radiotherapy in vitro and murine glioma in vivo. Mechanistically, COMT inhibition in glioblastoma cells led to mitochondria dysfunction and increased mitochondrial RNA release into the cytoplasm, activating the cellular antiviral dsRNA sensing pathway and type I IFN response. Elevated type I IFNs stimulated microglial cells′ phagocytic capacity, enhancing radiotherapy efficacy. Because of the long - established safety record of the COMT inhibitors, our findings provide a solid rationale to evaluate them in combination with radiotherapy in glioma patients. Citation Format: Meng Jiao, Christopher J. Pirozzi, Chen Yu, Xuhui Bao, Mengjie Hu, Dong Pan, Sejiro Littleton, Nathan Reynolds, Daniel R. Saban, Fang Li, Chuan-yuan Li. Enhancing glioblastoma radiotherapy by COMT inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB280.
Abstract LB126: Generation of a novel ROR1 x CD3 bispecific T-cell engager for better tumor killing and minimal cytokine release
Authors: Danqing Wu, Shiyong Gong, Xuan Wu, Gaowa Naren, Liqin Dong, Stephan Lensky, Chengbin Wu
Journal: Cancer Research (2024)

Abstract Receptor tyrosine kinase-like orphan receptor 1 (ROR1) expression is a highly specific tumor associated antigen expressed in multiple hematological malignancies and solid tumors. EMB-07 is a novel monovalent asymmetrical tandem Fab (MAT-Fab) antibody composed of two different Fab fragments targeting ROR1 and CD3ε respectively, and a “knob-in-hole” Fc fragment maintaining FcRn binding and Ig-like pharmacokinetics in vivo. To avoid light chain miss-pairing, the anti-ROR1 light chain was directly connected to the N-terminus of the anti-CD3 heavy chain. The ROR1 binding arm has a high affinity of 0.52 nM and recognizes a membrane distal epitope, which is different from a reference BiTE molecule currently in clinical trial. In comparison with this BiTE molecule, EMB-07 showed similar tumor killing efficacy to ROR1 expressing tumor cell lines while it induced much lower levels of cytokines both in vitro and in vivo. Moreover, comparing with a clinical stage ROR1-vc-MMAE ADC, EMB-07 demonstrated ~500-fold increased tumor lysis potency in vitro. In PD-1 resistant tumor xenograft mice models, EMB-07 showed potent tumor growth inhibition and synergistic activity in combination with PD-1 blockade. In a preclinical GLP toxicological study, EMB-07 was well tolerated in cynomolgus monkeys with no evidence of lethality, life-threatening toxicity, or obvious EMB-07-related macroscopic and histopathological adverse findings up to 50 mg/kg. By using a highly specific IHC clone, we validated membrane-associated ROR1 expression in multiple tumor types, including triple negative breast cancer, ovarian cancer, endometrial cancer, lung adenocarcinoma, and pancreatic cancer, while the observation of its expression in normal tissues is very limited. This study supports the clinical development of EMB-07 for treating multiple solid tumors with ROR1 expression. A FIH study of EMB-07 in locally advanced/metastatic solid tumors or relapse/refractory lymphoma is currently ongoing (NCT05607498). Citation Format: Danqing Wu, Shiyong Gong, Xuan Wu, Gaowa Naren, Liqin Dong, Stephan Lensky, Chengbin Wu. Generation of a novel ROR1 x CD3 bispecific T-cell engager for better tumor killing and minimal cytokine release [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB126.