bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3665: Umbilical cord blood endothelial progenitor cell-derived extracellular vesicles control important endothelial cell functions
Authors: Fraj Sawssen Ben , Naserian Sina , Lorenzini Bileyle , Goulinet Sylvie , Mauduit Philippe , Uzan Georges , Haouas Houda
Published: April 2023

Background: Circulating endothelial progenitor cells (EPCs) play a pivotal role in vascular regeneration and the repair of diseases in which angiogenesis is required, including ischemia and tissue transplantation. Although they are a potentially valuable cell therapy tool, their clinical use remains limited due to suboptimal storage conditions and especially, immune rejection. Even if these cells have been shown to be tolerated by the immune system, their in vivo long-term effects still remain to be elucidated. EPC-derived extracellular vesicles (EPC-EVs) may be an attractive alternative to EPCs given their key role in cell-cell communication and expression of the same parental markers. In this study, we investigated the regenerative effects of umbilical cord blood EPC-EVs on EPCs in vitro.

Methods: EPCs were obtained from human umbilical cord blood (CB) and characterized by flow cytometry. After amplification, EPCs were cultured in a medium containing an EVs-depleted serum (EV-free medium). Then the conditioned medium was used to isolate the EVs with Tangential Flow Filtration (TFF). The EVs were characterized by a series of tests defining their size, number, and protein content. The regenerative effects of EPC-EVs on endothelial cells were investigated by analyzing cell migration, wound healing, and tube formation. We also analyzed the effect of EPC-EVs on endothelial cell inflammation and NO production.

Results: We showed that adding different doses of EPC-EVs on EPCs does not alter the basal expression of the endothelial cell markers CD31, CD144, and KDR, nor change their proliferative potential and NO production level. Furthermore, we demonstrated that EPC-EVs, when used at a higher than physiologic dose, create a mild inflammatory condition that activates EPCs and boosts their regenerative features like migration and tube formation functions.

Conclusions: Our results reveal for the first time that EPC-EVs, when used at a high dose, could enhance EPC regenerative functions without altering their endothelial identity.

Citation Format: Sawssen Ben Fraj, Sina Naserian, Bileyle Lorenzini, Sylvie Goulinet, Philippe Mauduit, Georges Uzan, Houda Haouas. Umbilical cord blood endothelial progenitor cell-derived extracellular vesicles control important endothelial cell functions. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3665.
Abstract 3678: Rewiring of amino acid metabolism in neurofibromatosis type 1-related tumors
Authors: La Spina Martina
Published: April 2023

Neurofibromatosis type 1 (NF1) is a tumor-predisposing genetic disorder caused by heterozygous mutations in the NF1 gene encoding for the tumor suppressor Neurofibromin. Biallelic NF1 inactivation in Schwann cells leads to the onset of neurofibromas, benign neoplasms that can cause severe medical complications and give rise to malignant peripheral nerve sheath tumors (MPNSTs), for which no treatment exists. Neurofibroma cells undergo bioenergetic changes required to sustain their malignant transformation. Our group has shown that inhibition of the mitochondrial chaperone TRAP1, a master metabolic regulator, hampers MPNST cell tumorigenicity. A growing number of evidence indicates that urea cycle (UC) dysregulation can redirect metabolic substrates to specific biosynthetic routes in many tumor cell types. We have found that a complete UC is absent in MPNST cell models, as they lack ornithine transcarbamylase (OTC), a key UC enzyme that converts ornithine into citrulline. In the absence of TRAP1, MPNST cells strongly reduce arginine levels and accumulate ornithine through the activity of the mitochondrial enzymes arginase 2 (ARG2) and ornithine aminotransferase (OAT). These changes can reverberate on glutamine and proline levels ultimately affecting extracellular matrix deposition, motility and ROS homeostasis, as well as on ornithine-dependent polyamine biosynthesis that can regulate cell growth and proliferation. Surprisingly, in the absence of TRAP1 MPNST cells also accumulate citrulline, even though they do not express either OTC or any nitric oxide synthase (NOS) isoform that converts arginine into citrulline. We ascribe citrulline production to the activity of dimethylarginine dimethylaminohydrolase (DDAH) enzymes, involved in the catabolism of asymmetric dimethylarginines. Induction of DDAHs indicates an elevated protein catabolism that could contribute to tune MPNST cell tumorigenicity. A thorough comprehension of the amino acid metabolism rewiring in NF1-related tumors may unveil new targetable liabilities of cancer cells to be exploited for the design of new effective therapeutic approaches.

Citation Format: Martina La Spina. Rewiring of amino acid metabolism in neurofibromatosis type 1-related tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3678.
Abstract 3679: DNAJB1-PRKACA fusion in fibrolamellar hepatocellular carcinoma induces glutamine addiction and an immunosuppressive tumor microenvironment
Authors: Kamdar Zeal , Lopez-Vidal Tamara , Howe Kathryn , Munjal Kabeer , Saeed Ali , Zabransky Daniel , Shu Daniel , Longway Gabriella , Kartalia Emma , Leatherman James , Mohan Aditya , Khare Pratik , Zhang Cissy , Le Anne , Pearce Erika , Furth Mark , Baretti Marina , Leone Robert , Jaffee Elizabeth , Yarchoan Mark
Published: April 2023

Fibrolamellar hepatocellular carcinoma (FLC) is a rare and often lethal form of liver cancer that primarily affects children and young adults. A fusion between DNAJB1, a heat shock chaperone protein, and PRKACA, the catalytic domain of protein kinase A (PKA) has been identified as a signature genomic event in FLC, but the effect of this fusion on the tumor immune microenvironment is not understood. We created an orthotopic, syngeneic model of FLC (TIBx-FLC) by inducing the DNAJB1-PRKACA fusion in a murine hepatoblastoma-derived cell line (TIBx). CD8 T cells isolated from TIBx-FLC tumors demonstrated markedly impaired activation as compared to CD8 T cells isolated from control TIBx tumors. We investigated metabolic programming as a potential mechanism for DNAJB1-PRKACA immunosuppression in FLC. Labeled glucose metabolomics performed on TIBx-FLC and TIBx tumor cells demonstrated a metabolic shift away from aerobic metabolism to an increased glucose contribution towards the hexosamine biosynthetic pathway and purine synthesis, which requires glutamine as a nitrogen source. As compared to the parental TIBx cell line, the TIBx-FLC cell line demonstrated high sensitivity to glutamine antagonism in vitro, consistent with glutamine addiction. Systemic treatment of BALB/c mice bearing TIBx-FLC tumors with JHU-083, a glutamine antagonist, in combination with immune checkpoint inhibitor therapy enhanced survival as compared to vehicle or monotherapy. These data identify altered glutamine metabolism as a target in FLC, and may provide an explanation for immune suppression seen in the FLC tumor microenvironment.

Citation Format: Zeal Kamdar, Tamara Lopez-Vidal, Kathryn Howe, Kabeer Munjal, Ali Saeed, Daniel Zabransky, Daniel Shu, Gabriella Longway, Emma Kartalia, James Leatherman, Aditya Mohan, Pratik Khare, Cissy Zhang, Anne Le, Erika Pearce, Mark Furth, Marina Baretti, Robert Leone, Elizabeth Jaffee, Mark Yarchoan. DNAJB1-PRKACA fusion in fibrolamellar hepatocellular carcinoma induces glutamine addiction and an immunosuppressive tumor microenvironment. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3679.
Abstract 3717: Defining the mechanism of ER receptor transcription complex activity and its effect on epigenetic modulations using super resolution microscopy
Authors: Akhshi Tara , Brown Myles
Published: April 2023

Estrogen Receptor α (ERα) is expressed in ER+ breast cancers, one of the leading causes of death among women. Despite effectiveness of endocrine therapy, a significant number of patients experience resistance to these treatments. One of the major hurdles is lack of comprehensive information about ERα transcriptional complex activity. While biochemical assays have improved our knowledge significantly, it is critical to imply techniques that allow direct visualization of ERα activity and gain spatiotemporal information. We used super resolution microscopy to examine the mechanism of ERα transcriptional activity. We showed that ERα interactions with its co-activators (P300, SRC-3), is influenced upon administration of Tamoxifen and Fulvestrant, an effect that is lost in cells carrying multination in ERα ligand binding site. Additionally mutant cells are no longer able to recruit ERα co-inhibitor (NCORI). Using STORM microscopy, we showed estrogen treatment caused an “open” chromatin (H3K27ac) structure which may represent active areas of gene expression, while Tamoxifen and Fulvestrant treatments caused chromatin to form “closed” structures which likely represent close and inactive phase of chromatin.

Citation Format: Tara Akhshi, Myles Brown. Defining the mechanism of ER receptor transcription complex activity and its effect on epigenetic modulations using super resolution microscopy. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3717.
Abstract 3748: Epstein-Barr virus BART lncRNAs induce IKZF3/Aiolos to maintain EBV latency and promote tumorigenicity in nasopharyngeal carcinoma
Authors: He Songtao , Liu Jiayan , Wing-Yee Mok Bobo , Tsao Sai Wah , Chen Honglin
Published: April 2023

Epstein-Barr virus (EBV) maintains latency in its associated tumors, including nasopharyngeal carcinoma (NPC), expressing very few viral proteins but abundant levels of noncoding RNAs (mainly EBERs and BARTs) in NPC cells. We found that IKZF3/Aiolos is a downstream target of BART lncRNAs in NPC cells. The functions of BART lncRNAs and IKZF3 in EBV latency and pathogenesis of NPC remain elusive. In this study, meta-analysis of eight EBV-associated studies showed that IKZF3/Aiolos was consistently upregulated in EBV-infected NPC cells. Our study further showed that transcription of IKZF3/Aiolos is highly upregulated in EBV-infected NPC cells and clinical tissue samples due to the action of EBV encoded BART lncRNAs, with IKZF3/Aiolos was expressed at higher levels in late stage (stage III & IV) NPC patients than in early stage (stage I & II) disease. Secondly, we found that IKZF3/Aiolos was upregulated in BART-activated NPC cells but downregulated in BART-knockdown NPC cells. In addition, this study further demonstrated that IKZF3/Aiolos modulates transcription of EBV BZLF1 and the cellular gene, LRIG1, to maintain EBV latency and promote NPC tumorigenesis in vitro and in vivo. Our results showed that the EBV lytic reactivator BZLF1 was upregulated in IKZF3/Aiolos knockout or Aiolos inhibitor-treated NPC cells. ChIP-qPCR, immunoprecipitation and immunofluorescence analyses further revealed that IKZF3/Aiolos induces H3K27 deacetylation to silence expression of BZLF1 and maintain EBV latency in NPC cells. Moreover, functional analyses and western blotting showed that IKZF3/Aiolos inhibited the tumor suppressor, LRIG1, to upregulate expression and phosphorylation of the cellular proto-oncogene Erb-B2 for NPC pathogenesis. Sphere- and colony-formation assays demonstrated that IKZF3/Aiolos enhances growth of NPC cells in vitro, and in vivo experiments further showed that IKZF3/Aiolos promotes tumorigenicity of NPC cells in NOD mice. Mechanically, we found that the expression of EBV lytic reactivator BZLF1 and cellular LRIG1 were negatively regulated by BART lncRNA/IKZF3/Aiolos regulatory machinery in NPC cells, while Erb-B2 was positively regulated, which indicated that IKZF3/Aiolos is a new biomarker for NPC and may lead to the development of novel diagnostic tests and treatments for NPC.

Citation Format: Songtao He, Jiayan Liu, Bobo Wing-Yee Mok, Sai Wah Tsao, Honglin Chen. Epstein-Barr virus BART lncRNAs induce IKZF3/Aiolos to maintain EBV latency and promote tumorigenicity in nasopharyngeal carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3748.
Abstract 3752: The role of miR-200 in anaplastic thyroid cancer aggressiveness
Authors: Huth Hugo , Fuziwara César , Kimura Edna
Published: April 2023

Anaplastic Thyroid Cancer (ATC) is the most aggressive and lethal of all thyroid cancer histotypes, characterized by undifferentiated, highly proliferative and invasive cells, which are intrinsically resistant to conventional treatment. Deregulation of microRNAs (miRNAs), a group of small non-coding RNAs that post-transcriptionally regulates protein expression, has been linked with cancer development. Specifically, the miR-200 family has been postulated to control the balance between epithelial and mesenchymal cell states through Epithelial-Mesenchymal Transition (EMT), a critical process for tumor metastasis. Previous results showed that miR-200c, a member of miR-200 family, is downregulated in ATC, but the biological effect of its deregulation remains unclear. Therefore, this study aims to evaluate the antitumor effect of miR-200c on ATC cell aggressiveness. Using plasmid overexpression, we induced miR-200c upregulation in KTC2 (KTC2-200c) and SW1736 (SW-200c) cells to analyze its role in cell differentiation, proliferation, migration, and EMT markers expression. Light microscope images showed that KTC-200c and SW-200c cells presented an epithelial morphology in contrast with the control group which displayed mesenchymal morphology. Analysis by qPCR and western blot of KTC-200c and SW-200c cells showed that upregulation of miR-200c expression enhanced mRNA and protein expressions of the epithelial marker E-cadherin, while diminished the mRNAs and protein levels of the mesenchymal markers N-cadherin and ZEB1/2. Additionally, KTC2-200c and SW-200c presented reduced cell colony formation and cell proliferation, and reduced cell migration visualized by wound healing assay and transwell assay. In conclusion, this study evidences the tumor suppressor role of miR-200 in controlling ATC cell aggressiveness. Grants from FAPESP (2021/12284-0, 2019/17282-5, 2019/25116-8) and CNPq (311210/2021-0).

Citation Format: Hugo Huth, César Fuziwara, Edna Kimura. The role of miR-200 in anaplastic thyroid cancer aggressiveness. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3752.
Abstract 3754: The cell- and non-cell autonomous actions of UCA1 dysregulation in hypopharyngeal cancer
Authors: Wu Li-Wha
Published: April 2023

Long non-coding RNAs (lncRNAs), encoding noncoding transcripts greater than 200 nucleotides, are multifunctional regulator of gene expression and play vital roles in various biological processes. Urothelial cancer-associated 1 (UCA1) is one such molecule and found to be dysregulated in the development of several cancer types, including those in bladder, colon, stomach, lung and breast. One previous study showed that an upregulation of UCA1 expression profile in hypopharyngeal cancer tissues relative to their adjacent normal counterparts significantly negated overall survival among these cancer patients. However, the molecular mechanism whereby UCA1 played any role in HPC, a subtype of head and neck cancer and often detected in advanced stages, remains elusive. In this report, we showed that ectopic UCA1 expression promoted cell migration and invasion while reducing cell proliferation. The increase of migration and invasion was accompanied by partial epithelial mesenchymal transition. By contrast, UCA1 depletion had the opposite effect. In addition to the presence of UCA1 in the culture medium (CM) and a stimulatory effect of CM derived from UCA1-OE cells on cell migration and invasion, we found a predominant nuclear localization of UCA1 in HPC cells. PTBP3, a RNA-binding protein, was identified as a novel interacting partner of UCA1 by RNA pulldown and mass spectrometry. PTBP3 silencing significantly reduced UCA1 mRNA expression, suggesting a regulatory role in UCA1 stability. While mapping the interacting domains between UCA1 and PTBP3, we are also in the process of identifying the involvement of UCA1-PTBP3 axis in hypopharyngeal carcinogenesis. We hope to validate if UCA1 can serve as a novel therapeutic target against or diagnostic marker for hypopharyngeal cancer.

Citation Format: Li-Wha Wu. The cell- and non-cell autonomous actions of UCA1 dysregulation in hypopharyngeal cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3754.
Abstract 3762: A novel lncRNA, GTF2A1-AS1, is required for cell cycle progression and cell proliferation
Authors: Goldstein Yael , Nizri-Megnaji Tali , Ginsberg Doron
Published: April 2023

Long noncoding RNAs (lncRNAs) are major regulators of many cellular processes including cell cycle progression, cell proliferation and tumorigenesis. In this study, we identify a novel lncRNA, GTF2A1-AS1, and reveal its effects on cell cycle progression and cancer growth. Inhibition of GTF2A1-AS1 expression alters cell cycle distribution, leading to a decrease in the number of G1 cells and a concomitant increase in all other stages of the cell cycle, and in particular S phase, suggesting its involvement in the regulation of G1/S transition. Accordingly, knock down of GTF2A1-AS1 enhances G1 phase exit upon release from a late G1 block. In agreement with its suggested role in G1/S transition, prolonged silencing of GTF2A1-AS1 enhances proliferation of human cancer cells. GTF2A1-AS1 RNA is mostly nuclear and its gene is localized upstream to the protein-coding gene GTF2A1. GTF2A1-AS1 functions in trans to repress the expression of EIF5A2 and HOXA13. Knockdown of either EIF5A2 or HOXA13 rescues the effects of GTF2A1-AS1 silencing on cell proliferation, indicating that it functions mainly by modulating the levels of these two proteins. In agreement with the effect of GTF2A1-AS1 silencing on cell cycle progression and cell proliferation, low levels of GTF2A1-AS1 are associated with reduced survival in brain cancer patients. In conclusions, our data identify GTF2A1-AS1 as a novel lncRNA that regulates cell-cycle progression and cell proliferation and has a potential role in human cancer.

Citation Format: Yael Goldstein, Tali Nizri-Megnaji, Doron Ginsberg. A novel lncRNA, GTF2A1-AS1, is required for cell cycle progression and cell proliferation. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3762.
Abstract 3773: DeMixMir: deconvolution of microRNA sequencing data from heterogeneous tumor samples
Authors: Montierth Matthew , Nemeth Kinga , Tao Xinghua , Calin George , Wang Wenyi
Published: April 2023

Measuring tumor heterogeneity is a key issue in modern clinical oncology, with relevance to understanding cancer progression, resistance to therapy, and recurrence. Studies of the transcriptomic landscape in cancer have rapidly advanced in scale, enabled by novel methods and advancing technologies. One such novel method is TmS, a computational estimate of tumor-specific total messenger RNA content from heterogeneous tumor samples, which is calculated by combining genomic and transcriptomic deconvolutions. We have previously shown TmS as a promising pan-cancer biomarker for patient prognosis. Given the fruitful study of tumor cell total messenger RNA content, a logical extension is to investigate the utility of estimating tumor cell content of other RNA species. MicroRNAs (miRNAs) are small noncoding RNAs that regulate mRNA expression, and their dysregulation is a hallmark feature observed across cancers. A computational method to derive tumor cell total miRNA content from bulk sequencing data is especially needed since miRNAs cannot yet be reliably profiled at single cell resolution. Here we develop and benchmark DeMixMir, a new expansion of our reference-free transcriptomic deconvolutional model DeMixT, in order to recover tumor-specific miRNA proportions from mixed samples. For benchmarking, we generated an artificially mixed dataset of small RNA sequencing consisting of a total of 30 samples that were made by mixing HS-5 fibroblast cells with either wildtype or Dicer1 knockout HCT116 colorectal cancer cells. The tumor and fibroblast cell lines were mixed at 5 different proportions, to simulate a broad spectrum of tumor/nontumor cell mixing scenarios, with three independent replicates generated at each mixing ratio. DeMixMir demonstrated high accuracy in estimating the tumor-specific miRNA proportions in both the wildtype and the Dicer1 knockout mixtures. We further calculated tumor cell total miRNA content using DeMixMir output. Our proof-of-concept study suggests estimating tumor cell total miRNA content across tumor tissues at scale is feasible and likely valuable for advancing understanding of the complex roles miRNAs play in the cancer ecosystem.

Citation Format: Matthew Montierth, Kinga Nemeth, Xinghua Tao, George Calin, Wenyi Wang. DeMixMir: deconvolution of microRNA sequencing data from heterogeneous tumor samples. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3773.
Abstract 3781: NF-κB classical and alternative signaling differentially regulate miRNA expression in ovarian cancer
Authors: Kamdar Rahul D. , Harrington Brittney S. , Korrapati Soumya , Attar Emma , Wong Nathan , House Carrie D. , Annunziata Christina M.
Published: April 2023

The NF-κB signaling pathway has been shown to contribute to epithelial ovarian cancer (EOC) through its classical and alternative pathways, characterized by the RelA and RelB transcription factors respectively. Previous studies have highlighted the role of RelA in sustaining the proliferative cancer cell population, while RelB aids in promoting the survival of chemoresistant, stem-like tumor-initiating cells (TICs) that promote disease relapse. In further characterizing the downstream effects of NF-κB signaling on EOC, we hypothesize NF-κB signaling differentially regulates the expression of several microRNAs (miRNAs) to promote TIC survival and proliferation through its classical and alternative pathways. miRNAs comprise a subset of small, noncoding RNAs that regulate gene expression, making them amenable for therapeutic targeting. Inducible shRNA stably expressed in OV90 EOC cells to knockdown RelA or RelB were analyzed by miR-seq to identify the differential expression of miRNAs in cells grown in TIC vs adherent (adh) conditions. Several miRNAs were differentially expressed in these conditions with RelA or RelB knockdown; we identified and validated the expression of two candidate miRNAs: hsa-miR-452-5p and hsa-miR-335-5p. We observed the decreased expression of hsa-miR-452-5p when either RelA or RelB is knocked down, while also observing the increased expression of hsa-miR-335-5p when RelA is knocked down. By inhibiting miR-452-5p in conjunction with disrupting NF-κB activity, we found changes in cell viability, sphere formation, and expression of the stem cell marker ALDH. Understanding the role of miRNA signaling in the context of NF-κB will better define the transcriptional roles of RelA and RelB in EOC. Ongoing work will further characterize the downstream targets of these miRNAs as potential therapeutic targets.

Citation Format: Rahul D. Kamdar, Brittney S. Harrington, Soumya Korrapati, Emma Attar, Nathan Wong, Carrie D. House, Christina M. Annunziata. NF-κB classical and alternative signaling differentially regulate miRNA expression in ovarian cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3781.
Abstract 3824: Remodeling of anaplastic thyroid cancer cell signaling and immune landscape by natural alkaloid berberine
Authors: Jarboe Tara , Kopec Kaci , DeSouza Nicole R. , Geliebter Jan , Tiwari Raj K. , Li Xiu-Min
Published: April 2023

Anaplastic thyroid cancer (ATC) is universally diagnosed as Stage IV with a five-year-survival of 4%, illuminating its dreadful prognosis. ATC is undifferentiated, has an inflammatory tumor microenvironment (TME), and metabolic dysregulation. As it is refractory to all established therapies, we propose a novel therapeutic - Berberine (BBR), a natural plant alkaloid, with numerous cellular targets that can potentially reprogram ATC’s aggressive phenotype. This research comprehensively examines the multitarget efficacy of BBR. Following initial dose response studies, all assays used 100µM concentration of BBR or DMSO vehicle control for 24-hour exposure. To model the ATC tumor microenvironment, monocyte cell line U937 cells were activated and polarized into a proinflammatory macrophage phenotype. In the presence of berberine at the activation and polarization stages, 33 soluble inflammatory mediators were downregulated in the conditioned media compared to controls. Targeting the aggressiveness of anaplastic disease, berberine slowed proliferation by 50% selectively in ATC cells from 48 to 72 hours, while sparing the immortalized normal thyroid cells. BBR also delayed wound healing by 30% in ATC cells after 24, 48, and 72 hours. These observations were substantiated by Western blot analysis of ATC and immortalized normal cells where BBR decreased phosphorylation of MEK, ERK, and ribosomal protein S6, crucial downstream regulators of the pro-proliferative and pro-survival pathways and increased phosphorylation of AMPKα, activating its anti-tumor and regulatory effects. Validation of in vitro findings via RNA-Seq was conducted by Genewiz from Azenta Life Sciences and Qiagen’s Ingenuity Pathway Analysis was used for in silico modeling. Greater than 400 significantly differentially expressed genes were identified suggesting that BBR regulates mitochondrial metabolism, cholesterol biosynthesis, glycometabolism, apoptosis, inflammation, and proliferation. BBR’s ability to alleviate inflammatory mediators in the TME, depress overactive cell signaling, and regulate metabolism to make it a more targetable cancer reveals it as an interesting candidate to prime ATC for combination therapy.

Citation Format: Tara Jarboe, Kaci Kopec, Nicole R. DeSouza, Jan Geliebter, Raj K. Tiwari, Xiu-Min Li. Remodeling of anaplastic thyroid cancer cell signaling and immune landscape by natural alkaloid berberine. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3824.
Abstract 3923: Identification of membrane-expressed CAPRIN-1 as a novel and universal cancer target and generation of a therapeutic anti-CAPRIN-1 antibody TRK-950
Authors: Okano Fumiyoshi , Saito Takanori , Minamida Yoshitaka , Kobayashi Shinichi , Ido Takayoshi , Miyauchi Yasushi , Wasai Ukei , Ke Jiang , Aicher Alexandra , Heeschen Christopher , Yonehara Tetsu
Published: April 2023

Specific targets for cancer treatment are highly desirable, but still remain to be discovered. While previous reports suggested that CAPRIN-1 localizes in the cytoplasm, here we now show that part of this molecule is strongly expressed on the cell membrane surface in most solid cancers, but not normal tissues. Notably, the membrane expression of CAPRIN-1 extended to the subset of highly tumorigenic cancer stem cells and EMT induced metastatic cancer cells. In addition, we revealed that cancer cells with particularly high CAPRIN-1 surface expression exhibited enhanced tumorigenicity. We generated a therapeutic humanized anti-CAPRIN-1 antibody (TRK-950), which strongly and specifically binds to various cancer cells and shows anti-tumor effects via engagement of immune cells. TRK-950 was further developed as a new cancer drug and a series of pre-clinical studies demonstrates its therapeutic potency in a tumor bearing mouse model and safety in a relevant cynomolgus monkey model. Together our data demonstrate that CAPRIN-1 is a novel and universal target for cancer therapies. A phase I clinical study of TRK-950 (NCT02990481) has been completed and a phase Ib study (combination with approved drugs) is currently underway (NCT03872947).

Citation Format: Fumiyoshi Okano, Takanori Saito, Yoshitaka Minamida, Shinichi Kobayashi, Takayoshi Ido, Yasushi Miyauchi, Ukei Wasai, Jiang Ke, Alexandra Aicher, Christopher Heeschen, Tetsu Yonehara. Identification of membrane-expressed CAPRIN-1 as a novel and universal cancer target and generation of a therapeutic anti-CAPRIN-1 antibody TRK-950. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3923.
Abstract 3927: Genome-wide screening and validation of molecular targets and biomarkers for lung cancer
Authors: Daigo Yataro , Takano Atsushi , Nakamura Yusuke
Published: April 2023

The number of lung cancer patients who respond well to currently available standard therapies is still small, new molecular targeted therapies with companion diagnostics are eagerly needed. We have been developing new molecular therapies targeting oncoproteins with their cancer biomarkers as follows, i) To identify strongly expressed genes in 120 lung cancers by genome-wide gene expression profile analysis, ii) To verify the candidate genes for their scarce expression in 23 normal organs, iii) To validate the clinicopathological significance of their protein expression by tissue microarray covering about 400 lung cancers (non-small cell lung cancers (NSCLCs) and SCLCs), iv) To examine their importance in the growth and/or invasion of cancer cells by siRNA, small molecule inhibitor, cell permeable peptides targeting their function and/or antibody assays, and v) To analyze the oncogenic function of the target molecules. By this system, we identified 50 oncoproteins and selected a LSERT (lung cancer-specific receptor tyrosine kinase) as a candidate. Immunocytochemical and immunohistochemical analyses confirmed that LSERT protein was expressed in cytoplasm and cytoplasmic membrane of lung cancer cells, but it was hardly expressed in normal lung cells. Strong LSERT expression was associated with poorer prognosis for surgically-treated NSCLC patients, and it was an independent prognostic factor. Exogenous expression of LSERT increased the cell growth and invasion probably through its elevated kinase activity and subsequent phosphorylation of downstream proteins. Inhibition of LSERT expression by siRNAs or treatment with anti-LSERT antibody suppressed the growth of lung cancer cells. Our genome-wide screening might be a useful approach to identify target molecules for developing new therapeutics and diagnostics. LSERT could be a candidate cancer biomarker and therapeutic target for lung cancer.

Citation Format: Yataro Daigo, Atsushi Takano, Yusuke Nakamura. Genome-wide screening and validation of molecular targets and biomarkers for lung cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3927.
Abstract 3974: Discovery and validation of therapeutic targets in immune cells by mass spectrometry-based proteomics
Authors: Au Yu-Wah , Satijn David , Mehnert Martin , Lachaud Amaury , Feng Yuehan , Vowinckel Jakob , Bon Hélène
Published: April 2023

Immuno-oncology (IO) has substantially improved the survival of cancer patients over the past several years encouraging the discovery of novel IO targets which are typically proteins expressed on the surface of immune cells. Sensitive quantification of proteins in complex biological samples is routinely achieved by immunoassays that use antibodies specific to target proteins. Such approaches can be a limitation in IO drug discovery and development as de novo development of antibodies is associated with long lead times, high costs, and high failure rates.

Protein quantification using mass spectrometry (MS) is agnostic to species and matrices and removes the barriers of availability or specificity of antibody-based assay. Further, MS proteomics workflows can support both large scale discovery studies but also represent an attractive alternative to targeted quantitative studies.

The main purpose of this work is to assess the performance of the TrueDiscovery™ and TrueSignature™ MS-proteomics platforms for the deep proteome and surfaceome profiling of human primary and immortalized immune cells compared to flow cytometry solutions. We assess the number of quantified proteins and specifically the coverage of immune cell marker proteins in primary human immune cells across cell count groups from 2 million down to 2500 immune cells. In addition, we compared the quantification of a multiplexed surface antigens panel using TrueSignature™ and QIFI® flow cytometry platforms.

We found that the applied MS-based proteomics workflows achieve high sensitivity and robustness in detection and quantification of immune cell markers down to 2500 primary immune cells. Additionally, we observed a strong correlation of the quantitative data derived from our MS-based proteomics workflows with flow cytometry supporting the substitution of immunoassays by MS-based proteomics workflows in target discovery and validation.

Citation Format: Yu-Wah Au, David Satijn, Martin Mehnert, Amaury Lachaud, Yuehan Feng, Jakob Vowinckel, Hélène Bon. Discovery and validation of therapeutic targets in immune cells by mass spectrometry-based proteomics. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3974.
Abstract 4044: Development of UCT-01-097, a novel orally available ERK1/2 inhibitor for the treatment of ERK1/2 dependent cancers
Authors: O'Brien Neil A. , McDermott Martina S. , O'Boyle Brendan M. , Reeves Corey M. , Bartberger Michael , Loson Oliver , Chau Kevin , Hong Jenny J. , Jia Weiping , Kamranpour Naeimeh , Luo Tong , Ayala Raul , Madrid Athena M. , Glaspy John A. , Stoltz Brian M. , Slamon Dennis J.
Published: April 2023

The MAPK signaling pathway is the most commonly mutated and/or dysregulated pathway in cancer. Strategies to target it have yielded some success with inhibitors against KRASG12C and BRAF, and to a lesser extent, MEK1/2. However, the impact of these molecules is often limited by toxicity and rapid and diverse mechanisms of resistance; both adaptive and/or acquired. For example, treatment with MAPK pathway targeting agents results in compensatory activation of the downstream mediator ERK1/2 and enables tumors to subvert the targeted therapy. Thus, targeting ERK1/2 provides promising potential advantages in overcoming and/or preventing adaptive and acquired resistance. We evaluated multiple preclinical and clinically staged ERK1/2 inhibitors—including ERAS-007 and BVD-523—in a 500+ cell line screening platform and identified cancers with subpopulations that are sensitive to this class of inhibitor. KiNativ analyses helped to inform the differences in sensitivity/selectivity that we observed between each ERK1/2 inhibitor. Comprehensive molecular profiling of the cell lines at baseline allowed us to screen for potential molecular markers of sensitivity/resistance to these compounds. Using this platform, we have developed a novel, potent ERK1/2 small molecule inhibitor, UCT-01-097, with improved selectivity over other clinically staged inhibitors. These data, coupled with the broad spectrum of in vitro responses, suggests an improved therapeutic index with this molecule. UCT-01-097 shows kinase selectivity in both cell free and in-cell assays and robust efficacy in panel of pancreatic PDX models. Inhibition of xenograft tumor growth was achieved using both daily dosing and intermittent dosing schedules. We have successfully submitted a regulatory IND and are currently enrolling a Phase 1 clinical trial in advanced solid tumors for treatment with UCT-01-097 (NCT04761601).

Citation Format: Neil A. O'Brien, Martina S. McDermott, Brendan M. O'Boyle, Corey M. Reeves, Michael Bartberger, Oliver Loson, Kevin Chau, Jenny J. Hong, Weiping Jia, Naeimeh Kamranpour, Tong Luo, Raul Ayala, Athena M. Madrid, John A. Glaspy, Brian M. Stoltz, Dennis J. Slamon. Development of UCT-01-097, a novel orally available ERK1/2 inhibitor for the treatment of ERK1/2 dependent cancers. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4044.
Abstract 410: Tumor heterogeneity via AXL activation on primary resistance to EGFR tyrosine kinase inhibitors in EGFR mutated lung cancer
Authors: Yamada Tadaaki , Nakamura Ryota , Fujii Hiroyuki , Yaoi Takeshi , Itoh Kyoko , Tokuda Shinsaku , Takayama Koichi
Published: April 2023

Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are the standard treatments for patients with advanced non-small cell lung cancer (NSCLC) harboring EGFR mutations. However, some patients show primary resistance to EGFR-TKIs at the first-line treatment setting. AXL, a member of the TAM family of receptor tyrosine kinase, was reported to be involved in primary resistance to EGFR-TKIs for EGFR mutated NSCLC patients. In the present study, we investigated spatial tumor heterogeneity using autopsy specimens from EGFR mutated NSCLC patients, showing primary resistance to erlotinib plus ramucirumab. qPCR analysis showed that the AXL mRNA expression levels differed in each metastatic site. In addition, the AXL expression levels were likely to negatively correlate with the efficacy of erlotinib plus ramucirumab therapy. The analysis of patient-derived cell lines, established from left pleural effusion before initiation of the treatment, showed that the combination of EGFR-TKIs and an AXL inhibitor remarkably inhibited cell viability compared with EGFR-TKI monotherapy or combination with ramucirumab. Our observations suggested that tumor AXL expression might play a critical role in progression of spatial tumor heterogeneity and primary resistance to EGFR-TKIs for EGFR mutated NSCLC patients.

Citation Format: Tadaaki Yamada, Ryota Nakamura, Hiroyuki Fujii, Takeshi Yaoi, Kyoko Itoh, Shinsaku Tokuda, Koichi Takayama. Tumor heterogeneity via AXL activation on primary resistance to EGFR tyrosine kinase inhibitors in EGFR mutated lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 410.
Abstract 4240: Tumor PD-L1 induction associated with dietary protein restriction is modulated by PERK activation
Authors: Cordova Ricardo , Colligan Sean , Rupert Chris , Wek Ronald , Staschke Kirk , Pili Roberto
Published: April 2023

Tumor cells rely on the Integrated Stress Response (ISR) to adapt to different environmental and physiological stresses. The ISR is comprised of four eIF2 kinases that sense different stresses and catalyze phosphorylation of the alpha subunit of eIF2. This results in inhibition of global translation initiation, but at the same time results in preferential translation of select mRNA transcripts in order to relieve stress. Recent work has suggested that programmed death-ligand 1 (PD-L1), a cell surface protein commonly upregulated by tumors to evade the immune system, may be translationally regulated by the ISR in cancer. PD-L1 interaction with immune-checkpoint receptor programmed death-1 (PD-1) leads to the negative regulation of T cell activation and inhibitors that block the PD-L1/PD-1 interaction are widely used to treat different cancers. The ISR may serve as a novel therapeutic target to modulate PD-L1 protein levels and treat immune-evasive cancers. Our group has previously reported that dietary protein restriction increases the anti-tumor effect of PD-1 inhibition in the RENCA kidney cancer mouse model. Here, we show that in the RENCA model, phospho-PERK and phospho-eIF2α protein levels correlate with PD-L1 induction associated with dietary protein restriction. This is supported by TCGA data that shows a correlation between PERK and PD-L1 mRNA levels in different genitourinary cancers. In vitro, activation of the eIF2 kinases PERK and GCN2 by ER stress and amino acid starvation, respectively, in both RENCA cells and prostate cancer cells, leads to induction of PD-L1 protein without changing mRNA levels, suggesting preferential translation under stress conditions. Inhibiting PERK using selective inhibitors blocked ER stress-induced induction of PD-L1. These data support the notion that PD-L1 is induced by dietary protein restriction and is translationally regulated by the ISR. Modulating PD-L1 protein levels in immune-evasive tumors by targeting the ISR in the context of dietary protein restriction may enhance the anti-tumor response to immune checkpoint inhibitors.

Citation Format: Ricardo Cordova, Sean Colligan, Chris Rupert, Ronald Wek, Kirk Staschke, Roberto Pili. Tumor PD-L1 induction associated with dietary protein restriction is modulated by PERK activation. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4240.
Abstract 4299: Gene expression based machine learning classifier to predict and validate cancer type in patient derived xenograft (PDX) models
Authors: Andrews Warren , Do Long , Nakashima Jonathan
Published: April 2023

Patient derived xenografts (PDX) are increasingly utilized in translational research and drug development. Characterizing the genomic features of PDX is essential to establishing reliable models for cancer research. Despite great interest, problems remain in PDX tumor data banks including improper cancer type diagnosis and sample mix-ups. In an effort to improve annotation and quality of PDX models, we developed a machine learning model trained on gene expression data from The Cancer Genome Atlas (TCGA). We then applied the model to corresponding data collected from nearly 300 Certis PDX models plus publicly available data from NCI’s Patient-Derived Models Repository (PDMR). The model shows high precision and variable recall and provides a fast and accurate method for cancer type diagnosis.

Citation Format: Warren Andrews, Long Do, Jonathan Nakashima. Gene expression based machine learning classifier to predict and validate cancer type in patient derived xenograft (PDX) models. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4299.
Abstract 4334: Clever-1/PD-L1 ratio predicts response to Bexmarilimab, a novel macrophage-guided immunotherapy, in immune deprived cancers
Authors: Björkman Mari L. , Vuorinen Elisa M. , Jalkanen Juho , Fjällskog Marie-Louise , Koivunen Jussi , Huttunen Teppo , Hollmén Maija , Bono Petri
Published: April 2023

Introduction: Clever-1 is an immunosuppressive scavenger receptor expressed on tumor associated macrophages. High levels of Clever-1 are associated with poor survival, T-cell exclusion and dysfunction, and immunotherapy resistance. Bexmarilimab (FP-1305) is a novel humanized anti-Clever-1 IgG4-antibody capable of promoting an immune switch, potentially leading to intratumoral proinflammatory responses in patients. In a first-in-human all-comer single agent Phase I/II study in advanced solid tumors (NCT03733990) approximately 30% of patients in hepatocellular carcinoma, cutaneous melanoma and cholangiocarcinoma achieved immune activation, characterized by an IFNg response, which led to a survival benefit (ASCO 2022). Here, we show that patients getting a therapy benefit have immunologically cold tumors with low PD-L1 staining and high Clever-1 staining.

Methods: Pre-treatment tumor samples were immunohistochemically stained for Clever-1 (4G9, Santa Cruz) using Ventana platform and scored by % of intratumoral positive cells out of all viable cells and PD-L1 (22C3, Agilent) with combined positivity scoring (CPS). Ratio (PD-L1/Clever-1) at baseline was compared using non-parametric Wilcoxon-test according to clinical benefit.

Results: 23 successful baseline biopsies and stainings were obtained, 6 per cutaneous melanoma, 11 per cholangiocarcinoma and 1 per hepatocellular carcinoma, from patients treated with bexmarilimab. Patients had received an average of three previous lines of therapy. At baseline, patients that saw a clinical benefit (CBR) from bexmarilimab had average PD-L1/Clever-1 ratio of 0.2 compared to 4.4 (p=0.042, Wilcoxon nonparametric test) in patients that did not respond to the treatment.

Conclusion: PD-L1/Clever-1 IHC staining ratio may be used to predict bexmarilimab responding patients. These patients have a low PD-L1 staining and low IFNg levels as reported previously, and are often refractory to checkpoint inhibitors and other T cell activating agents. Bexmarilimab provides a novel therapy option for a tumor group that is otherwise poorly responsive to immune therapies.

Citation Format: Mari L. Björkman, Elisa M. Vuorinen, Juho Jalkanen, Marie-Louise Fjällskog, Jussi Koivunen, Teppo Huttunen, Maija Hollmén, Petri Bono. Clever-1/PD-L1 ratio predicts response to Bexmarilimab, a novel macrophage-guided immunotherapy, in immune deprived cancers. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4334.