bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1162: Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia
Authors: Ferrer Miriam , Mourikis Nicholas , Davidson Emma E. , Kleeman Sam O. , Zaccaria Marta , Habel Jill , Rubino Rachel , Flint Thomas R. , Connell Claire M. , Lukey Michael J. , White Eileen P. , Coll Anthony P. , Venkitaraman Ashok R. , Janowitz Tobias
Published: April 2023

The dependency of cancer cells on glucose can be targeted with high-fat low-carbohydrate ketogenic diet (KD). However, hepatic ketogenesis is suppressed in IL-6 producing cancers, which prevents the utilization of this nutrient source as energy for the organism. In two IL-6 associated murine models of cancer cachexia we describe delayed tumor growth but accelerated onset of cancer cachexia and shortened survival when mice are fed KD. Mechanistically, we find this uncoupling is a consequence of the biochemical interaction of two simultaneously occurring NADPH-dependent pathways. Within the tumor, increased production of lipid peroxidation products (LPPs) and, consequently, saturation of the glutathione (GSH) system leads to ferroptotic death of cancer cells. Systemically, redox imbalance and NADPH depletion impairs the biosynthesis of corticosterone, the main regulator of metabolic stress, in the adrenal glands. Administration of dexamethasone, a potent glucocorticoid, improves food intake, normalizes glucose homeostasis and utilization of nutritional substrates, delays onset of cancer cachexia and extends survival of tumor-bearing mice fed KD, while preserving reduced tumor growth. Our study highlights that the outcome of systemic interventions cannot necessarily be extrapolated from the effect on the tumor alone, but that they have to be investigated for anti-cancer and host effects. These findings may be relevant to clinical research efforts that investigate nutritional interventions such as KD in patients with cancer.

Citation Format: Miriam Ferrer, Nicholas Mourikis, Emma E. Davidson, Sam O. Kleeman, Marta Zaccaria, Jill Habel, Rachel Rubino, Thomas R. Flint, Claire M. Connell, Michael J. Lukey, Eileen P. White, Anthony P. Coll, Ashok R. Venkitaraman, Tobias Janowitz. Ketogenic diet promotes tumor ferroptosis but induces relative corticosterone deficiency that accelerates cachexia [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 1162.
Abstract 121: In situ mutational mapping of tumor cells and tissues at subcellular resolution
Authors: Östlin Jessica , Chitnis Debashish , Olofsson Mimmi , Hernández-Neuta Iván , Kuhnemund Malte
Published: April 2023

In situ techniques enable studying cells and tissues within their cellular context. This is of great importance in cancer, often displaying genetic and phenotypic heterogeneity with distinct subclones harboring different capacity to grow and spread. It was recently shown that by spatially mapping dozens of mutations within tumor tissues, tumor evolution and microenvironmental impact could be studied at the subclonal level (1). We have developed an in situ technique that spatially maps multiple expressed mutations simultaneously at subcellular resolution. The technique is based on single-nucleotide discriminating probes hybridized to mRNA. Correctly hybridized probes get ligated, amplified by rolling circle amplification, and decoded on our Xenium In situ platform. The technique was validated in well characterized cell lines, targeting multiple single nucleotide variants of the KRAS codons 12 and 13. As a proof of concept, we then applied the technique on FFPE breast tumor tissue sections that were previously characterized by targeted NGS onco-gene panels on extracted tumor DNA. In addition to the 280 plex Xenium Human Breast Gene Expression Panel, we targeted several mutations in situ and successfully mapped their spatial distribution in the tumor tissue sections. In summary, we demonstrate that the Xenium In Situ technology can spatially resolve the genetic and phenotypic landscape of breast tumors. The technology will enable researchers to unravel tumor evolution, growth and spread as well as the microenvironmental impact in detail, potentially refining patient stratification and treatment decisions.

Citation Format: Jessica Östlin, Debashish Chitnis, Mimmi Olofsson, Iván Hernández-Neuta, Malte Kuhnemund. In situ mutational mapping of tumor cells and tissues at subcellular resolution [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 121.
Abstract 1231: A stochastic data-driven model predicts the timing and distribution of the epithelial-mesenchymal transition
Authors: Najafi Annice , Jolly Mohit K. , George Jason T.
Published: April 2023

The Epithelial-Mesenchymal Transition (EMT) is a key contributor to cancer metastasis and morbidity. During this process, epithelial cells acquire migratory and stem-like characteristics, which allow them to travel through vasculature and form distant metastases in a secondary organ site via the reverse process of MET. Initially thought of as a binary process, it is now well established that cells can be stably arrested en route to EMT in an intermediate hybrid state (H) with characteristics falling on a spectrum between the epithelial (E) and mesenchymal (M) phenotypes. This non-transient intermediate state is stabilized by phenotypic stability factors and is associated with more tumor aggressiveness, worse treatment response, and patient outcomes. Although abundant time-course single-cell RNA sequencing data exists, enabling dynamical single-cell analysis of EMT, current methods of EMT state inference are optimized on microarray data. Thus, there is a large need for a computational framework that infers and predicts the E, H, and M fractions at transient and steady states from single-cell RNA sequencing data. Here, we introduce a fully stochastic continuous-time Markov model to predict the dynamics of EMT transitions from time-course data. We fit our continuous-time model on a multi-replicate time-course flow cytometry data of MCF10A cell line where TGF is withdrawn at different days following treatment for each replicate. We then demonstrate that our model is extendable to time-course single-cell RNA sequencing data utilizing a novel data-driven pipeline. Our data-driven pipeline infers the three E, H, and M trajectories from time-dependent and dose-dependent single-cell RNA sequencing data. We confirm our trajectories accurately reflect the E, H, and M states via gene-set enrichment analysis. We find the fraction of cells in each state at stationary distribution using our data-driven pipeline and show that they match the predictions of a previous simulation study. By applying the stochastic model to time-course single-cell RNA sequencing trajectories of four cancer cell lines (A549, MCF7, OVCA420, and DU145), we show that the stochastic model accurately predicts context-specific EMT dynamics over time. Our model is the first RNA sequencing-based method for tracking EMT from longitudinal data at the single-cell resolution and therefore is of immediate utility for studying metastatic signatures in cancer.

Citation Format: Annice Najafi, Mohit K. Jolly, Jason T. George. A stochastic data-driven model predicts the timing and distribution of the epithelial-mesenchymal transition [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 1231.
Abstract 1236: Direct interaction between cancer cells and fibroblasts drives epithelial-to-mesenchymal plasticity (EMP)
Authors: Dhungel Nilu , Dragoi Ana-Maria
Published: April 2023

The tumor microenvironment (TME), composed of immune cells and fibroblasts, blood vessels, signaling molecules and extracellular matrix, is the source of important cues that govern epithelial-to-mesenchymal (EMT) transition and facilitate the acquisition of aggressive traits by cancer cells. It is now recognized that EMT is not a binary program, and cancer cells rarely switch to a fully mesenchymal phenotype. Rather, cancer cells exist in multiple hybrid epithelial/mesenchymal (E/M) states responsible for cell population heterogeneity, which is advantageous for the ever-changing environment during tumor development and metastasis. How are these hybrid states generated and maintained is not fully understood. We show that direct interaction between small cell lung carcinoma cells (SCLC) and lung fibroblasts induces a hybrid EMT phenotype in cancer cells in which several mesenchymal genes involved in receptor interaction with the extracellular matrix (ECM) and ECM remodeling are upregulated while epithelial genes such as E-cadherin remain unchanged. We also demonstrate that several core EMT-regulating transcription factors (EMT-TFs) are upregulated in cancer cells during direct contact with fibroblasts, as is Yes-associated protein (YAP1), a major regulator of the Hippo pathway. Further, we show that these changes are transient and reverse to the initial state once the interaction is disrupted. Altogether, our results provide evidence that tumor cells’ direct contact with the fibroblasts in the TME initiates a signaling cascade responsible for hybrid E/M states of cancer cells. These hybrid states are maintained during the interaction and possibly contribute to therapy resistance and immune evasion, while interference with direct contact will result in slow recovery and a switch to the initial states.

Citation Format: Nilu Dhungel, Ana-Maria Dragoi. Direct interaction between cancer cells and fibroblasts drives epithelial-to-mesenchymal plasticity (EMP) [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 1236.
Abstract 1254: Acetyl-coA distribution devote STAT3 related neuronal methylation phenotype and pro-inflammatory niche in gastric cancer
Authors: Low Jie-Ting , Chuang Yu-Ming , Lee Yu-Ting , Chan Michael Wing-Yan
Published: April 2023

STAT3 activation is important in the development of gastric cancer (GCA), but its role in DNA methylation is not fully understood. STAT3-mediated DNA methylation is controlled by K685 acetylation, we therefore hypothesized that distribution of acetyl-CoA could affect the role of STAT3 in DNA methylation. Here, by methylation microarray from GCA patients and cells depleted with STAT3, we identified a STAT3-related CpG island methylator phenotype (CIMP), located at neuronal genes (neuronal CIMP). Further TCGA RNA-Seq identified neuronal CIMP+ve to be positively associated with the expression and higher cyto/mito ratio of acetyl-CoA synthetase (ACSS2). Intriguingly, patients with neuronal-CIMP +ve or higher cyto/mito ratio of ACSS were associated with a better survival, suggesting a different role of acetyl-STAT3. As STAT3 pathway plays a key role in chemokine response, we also analyze whether neuronal-CIMP contributes to anti-tumor immune response. Surprisingly, CIMP +ve patients correlated with pro-inflammatory niche, including activated CD4 + T cells and M1 macrophages. In conclusion, neuronal-CIMP may be a biomarker to predict patient’s immune responses in GCA.

Citation Format: Jie-Ting Low, Yu-Ming Chuang, Yu-Ting Lee, Michael Wing-Yan Chan. Acetyl-coA distribution devote STAT3 related neuronal methylation phenotype and pro-inflammatory niche in gastric 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 1254.
Abstract 1288: NRP1 exon 4-skipping variant promotes colorectal cancer metastasis by secreted exosomes and activated endosomal signals
Authors: Gu Yiwei , Huang Xiuping , Ye Qing , She Qing-Bai
Published: April 2023

Neuropilin-1 (NRP1) is a transmembrane glycoprotein that acts as a critical co-receptor for tyrosine kinase receptors in growth factor signaling in both physiological and pathological context. The characterization of the NRP1 variants generated by alternative splicing mechanisms has provided profound insights into our understanding of the regulation of NRP1 function in cancer growth, angiogenesis, invasion and metastasis as well as for the modulation of therapeutic outcomes. Here, we identified a novel human NRP1 splice variant resulting from the skipping of exon 4 (NRP1-ΔE4) in colorectal cancer (CRC). We found that NRP1-ΔE4 was largely expressed in CRC and significantly correlated with CRC progression. Furthermore, NRP1-ΔE4 exhibited increased endocytosis/recycling activity via secreted exosomes and decreased levels of degradation, leading to accumulation on endosomes. In addition, NRP1-ΔE4 enhanced interactions with the Met and β1-integrin receptors, resulting in Met/β1-integrin co-internalization and co-accumulation on endosomes. This provided persistent endosomal signals to activate the FAK/p130Cas pathway, thereby promoting CRC cell migration, invasion and metastasis. Blocking exosome secretion, endocytosis or endosomal Met/β1-integrin/FAK signaling using genetic and pharmacological approaches profoundly inhibited the oncogenic effects of NRP1-ΔE4. Taken together, these findings reveal a unique function of NRP1-ΔE4 in the regulation of endocytic trafficking for CRC cell dissemination.

Citation Format: Yiwei Gu, Xiuping Huang, Qing Ye, Qing-Bai She. NRP1 exon 4-skipping variant promotes colorectal cancer metastasis by secreted exosomes and activated endosomal signals [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 1288.
Abstract 1291: Signaling pathways modulated by lncRNA UCA1 during anchorage-independent growth in colorectal cancer
Authors: Leslie Sophia , Doxtater Kyle D. , Lopez Samantha , Ezell Kristopher , Anilkumar Adithya , Sanchez Amayrani , Hafeez Bilal , Oraby Tamer , Jaggi Meena , Loy Timothy , Chauhan Subhash , Tripathi Manish K.
Published: April 2023

Colorectal cancer (CRC) is the second deadliest cancer, and over 40-50% of patients develop metastasis during their fight against the disease. CRC survival rate drops from 90% to 14% when the condition is contained within the colon vs. when found at distant sites within the body. Metastasis is a multistep process and one of the critical steps for cancer cells to acquire anoikis resistance to survive after detachment from the primary sites and travel through the circulatory and lymphatic systems to distant target organs. Thus, understanding the molecular players involved in the anoikis process and metastasis could be vital for improving the survival of CRC patients. The aberrant expression of a long noncoding RNA (lncRNA) urothelial carcinoma-associated 1 (UCA1) has been identified in CRC. However, its role in metastasis processes is not yet well defined. Our preliminary results in the anchorage-independent growth (anoikis model) demonstrate increased expression of lncRNA UCA1. Moreover, the overexpression of lncRNA UCA1 led to high expression of stemness markers SOX2 and Kaiso, along with increased survival of anchorage-independent cells, which indicates a potential mechanistic role of UCA1 in anoikis resistance. Thus, in this study, we propose elucidating the role(s) of UCA1 and its associated signaling pathways during anoikis resistance. We hypothesize that the overexpression of lncRNA UCA1 enhances CRC metastasis through anoikis resistance-associated signaling pathways. We will utilize Isogenic CRC cell lines SW480 (oncogenic) and SW620 (metastatic) to understand the mechanistic regulation of anoikis resistance. Lentiviral transduced stable overexpression (SW480+UCA1//GFP) and knockdown (SW620+CRISPRgUCA1) cell lines have been utilized for this study. After subjecting these cell lines (along with control) to anchorage-independent growth conditions, cell cycle, pro-survival, anti-apoptotic, stemness, and glucose metabolism factors will be analyzed through RT-PCR, Digital Droplet PCR (ddPCR), western blot, and FACS analyses. Utilizing the same model, we will examine lncRNA UCA1 linked anoikis resistance specific phosphorylation profiles of kinases, their protein substrates using the Proteome Profiler Phospho-Human Phospho-Kinase Array.

Citation Format: Sophia Leslie, Kyle D. Doxtater, Samantha Lopez, Kristopher Ezell, Adithya Anilkumar, Amayrani Sanchez, Bilal Hafeez, Tamer Oraby, Meena Jaggi, Timothy Loy, Subhash Chauhan, Manish K. Tripathi. Signaling pathways modulated by lncRNA UCA1 during anchorage-independent growth in colorectal 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 1291.
Abstract 1298: Single cell analysis of breast cancer progression and metastasis to lymph nodes reveals cancer cell plasticity and MHC class II-mediated immune regulation
Authors: Lei Pin-Ji , Pereira Ethel , Andersson Patrik , Amoozgar Zohreh , Van Wijnbergen Jan Willem , O'Melia Meghan J. , Zhou Hengbo , Chatterjee Sampurna , Ho William Wee , Posada Jessica M. , Kumar Ashwin Srinivasan , Morita Satoru , Chuang Charlie , Ergin Ilgin , Jones Dennis , Huang Peigen , Beyaz Semir , Padera Timothy P.
Published: April 2023

Tumor-draining lymph nodes are critical sites for generating tumor antigen-specific T cells and are associated with durable immune responses. However, lymph nodes are often the first site of metastasis and lymph node metastases portend worse outcomes. Through cross species single cell gene expression analysis of breast cancer progression and metastasis to lymph nodes, we uncovered features that define the heterogeneity, plasticity, and immune evasion of cancer cells. Notably, a subpopulation of metastatic cancer cells in the lymph node were marked by high levels of MHC class II (MHC-II) gene expression both in mice and humans. Mechanistically, the IFN-γ and JAK/STAT signaling pathways mediate MHC-II expression in cancer cells. Ablation of IFNGR1/2 or CIITA, the transactivator of MHC-II, in cancer cells prevented tumor progression. Interestingly, MHC-II+ cancer cells lacked co-stimulatory molecule expression, engendered the expansion of regulatory T cells and blunted CD4+ effector T cells in the tumor draining lymph nodes and favor tumor progression. Overall, our data suggests that cancer cell plasticity during breast cancer progression and metastasis to lymph nodes endows metastatic cells with the ability to avoid immune surveillance. These data provide the basis for new opportunities to therapeutically stimulate anti-cancer immune responses against local and systemic metastases.

Citation Format: Pin-Ji Lei, Ethel Pereira, Patrik Andersson, Zohreh Amoozgar, Jan Willem Van Wijnbergen, Meghan J. O'Melia, Hengbo Zhou, Sampurna Chatterjee, William Wee Ho, Jessica M. Posada, Ashwin Srinivasan Kumar, Satoru Morita, Charlie Chuang, Ilgin Ergin, Dennis Jones, Peigen Huang, Semir Beyaz, Timothy P. Padera. Single cell analysis of breast cancer progression and metastasis to lymph nodes reveals cancer cell plasticity and MHC class II-mediated immune regulation [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 1298.
Abstract 1347: PAUF stimulates monocytes and induces their differentiation into tumor-associated macrophages
Authors: Jiang Fen , Kim Yeon Jeong , Park Yun Yong , Kang Tae Heung , Koh Sang Seok
Published: April 2023

Background: One of the main reasons for the failure of cancer treatments is that the biological function of therapeutic target molecules is only studied in cancer cells. Therefore, the dynamic and complex interactions between cancer and stromal cells in the tumor microenvironment (TME) should be investigated. TME-specific stromal cells include various cells, with tumor-associated macrophages (TAMs) being one of the major players. TAM are differentiated from monocytes, as immature monocytes recognize molecules derived from infected cells or foreign substances, become activated, and may differentiate into anti-tumoral M1 macrophages or pro-tumoral M2 macrophages (called TAMs). TAMs induce immune evasion of cancer cells in the TME, leading to active proliferation and metastasis of cancer cells. The presence of TAMs in the TME is associated with poor prognosis in various cancers.

PAUF is a protein that is secreted by cancer cells, and it exerts tumor-promoting effects through autocrine and paracrine mechanisms. Compared to the autocrine actions, the paracrine effects of PAUF on immune cells in the TME are less understood.

Objective: This study aimed to evaluate 1) the role of PAUF as a TME modulator, and specifically, a TAM inducer and 2) the potentiality of PAUF antibody as a blocker of TAM transformation.

Methods and Results: In a monocyte-PAUF co-culture system, PAUF (tested at two concentrations, 0.1 and 0.5 μg/mL) demonstrated strong chemoattractant effects on monocytes (~400% of that caused by PBS), which were blocked by TLR2/4 inhibitors. PAUF also induced differentiation of monocytes into macrophages, which were identified to be TAM, using flow cytometric analysis and ELISA method. Moreover, these PAUF-induced TAM demonstrated T cell suppressing capacities. Finally, in a CFPAC-1 human cancer orthotopic mouse model, a humanized monoclonal PAUF-antibody diminished 60-70% of infiltrated TAM (p<0.01), quantified using an immunofluorescence assay (IFA).

Conclusion: In conclusion, this study provides direct evidence that PAUF can differentiate monocytes into TAM of immune-suppressing functions, and the PAUF neutralization-induced TAM infiltration blocking suggests potential combination use of PAUF antibody with immunotherapeutics for cancer treatments.

Citation Format: Fen Jiang, Yeon Jeong Kim, Yun Yong Park, Tae Heung Kang, Sang Seok Koh. PAUF stimulates monocytes and induces their differentiation into tumor-associated macrophages [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 1347.
Abstract 1373: Cell-in-cell mediated entosis reveals a progression mechanism in pancreatic cancer
Authors: Song Jianlu , Ruze Rexiati , Chen Yuan , Xu Ruiyuan , Yin Xinpeng , Wang Chengcheng , Zhao Yupei
Published: April 2023

Pancreatic cancer (PC) is a deadly malignancy with high intra-tumoral heterogeneity and lacks effective therapeutics. Entosis is a non-apoptotic regulated cell death mediated by cell-in-cell (CIC) structures. However, the impact of entosis on PC progression needs to be determined. This study analyzes the expression levels and prognostic values of entosis-related regulators in public datasets. It identifies that these regulators are commonly upregulated in PC and associated with worse prognosis. We further find that the entotic CIC structures detected in PC specimens have a possible correlation with PC metastases. We enrich a cell population of PC cells undergoing entotic CIC using fluorescence-activated cell sorting (FACS), and several oncogenes, such as NET1, ALDH3A1, PLAT, GALNT5, and FAM3C, were defined as the marker genes of this population using single-cell RNA sequencing (scRNA-seq) analysis. Functionally, this population demonstrates enhanced cell proliferation, migration, invasion, anoikis resistance, sphere formation in vitro, and tumorigenicity in vivo. Moreover, NET1 (neuroepithelial cell transforming gene 1) overexpression promotes cell proliferation, migration, invasion, anoikis resistance, CIC formation, cell competition in vitro, and tumorigenicity in vivo of PC cells. NTE1 is also associated with unfavorable prognosis for PC patients. These results indicate that entosis may play a vital oncogenic role in PC progression. PC cells generate a highly “progressive” subpopulation marked by NET1 via entotic CIC. NET1 is a newly validated gene related to entosis. Targeting entotic processes may be a potential therapeutic option for PC.

Citation Format: Jianlu Song, Rexiati Ruze, Yuan Chen, Ruiyuan Xu, Xinpeng Yin, Chengcheng Wang, Yupei Zhao. Cell-in-cell mediated entosis reveals a progression mechanism in pancreatic 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 1373.
Abstract 1383: Mechanisms of ATG9 mediated aggrephagy initiation
Authors: Madhusanka Deshan , McEwan Colton , Broadbent David , Schmidt Jens , Andersen Joshua
Published: April 2023

Highly biosynthetic cancer cells produce proteins at a rate that may exceed the capacity of protein folding machinery, resulting in an accumulation of misfolded proteins that are poly-ubiquitinated and clustered into phase-separated ‘ubiquitin-rich’ condensates. These condensates are the initiation point for a form of autophagy called aggrephagy, which maintains cancer cell homeostasis by degrading the misfolded protein condensates via the lysosome. Aggrephagy is a cancer cell vulnerability, yet its mechanisms are poorly understood, particularly the mechanisms by which autophagy machinery recognizes the ubiquitin-rich condensates to initiate aggrephagy. Among 15 core autophagy proteins, ATG9A is the only multi-pass transmembrane protein and is essential for all known forms of autophagy. Recent evidence indicates that ATG9A is a lipid scramblase, in complex with ATG2A, that channels lipids to a growing autophagosome, which ultimately engulfs the ubiquitin-rich condensate. However, the mechanism of ATG9A recruitment to these condensates is not understood. Our data indicate that genetic or chemical manipulations of cells that cause ubiquitin-rich condensates to accumulate causing a corresponding accumulation of ATG9A. Furthermore, the induction of artificial ubiquitin-rich condensates, composed of chains of M1-linked ubiquitin, is sufficient to recruit ATG9A. Using a CRISPR knockout and reconstitution approach, we show that ATG9A is essential for assembling other autophagy machinery at ubiquitin-rich condensates. Together, our data support a model in which ATG9A recruitment is the initiating step for aggrephagy. Furthermore, our data suggest a signal or molecular pattern within the condensate promotes ATG9A recruitment to initiate aggrephagy. Our current work focuses on identifying features of ATG9A and components of the ubiquitin-rich condensate that cooperate to recruit ATG9A to these sites of aggrephagy initiation.

Citation Format: Deshan Madhusanka, Colton McEwan, David Broadbent, Jens Schmidt, Joshua Andersen. Mechanisms of ATG9 mediated aggrephagy initiation [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 1383.
Abstract 1396: The HOX family gene signature predicts prognosis and indicates immune infiltrates in pediatric gliomas
Authors: Zhao Qianhao , Su Junyan
Published: April 2023

Background: Pediatric gliomas (PGs) are highly aggressive and predominantly occur in young children. Homeobox (HOX) family genes are transcription factors that play a crucial role in anterior-posterior body axis patterning during embryonic development. This study aimed to propose a novel HOX-related signature of PGs to predict patients’ prognosis and immune infiltrate characteristics.

Methods: Multiple levels of data (whole-exome sequencing, mRNA-sequencing, and single-cell RNA-sequencing) of 571 PGs obtained from publicly available databases were utilized to reveal the relationship among abnormal expression of HOX family genes, prognosis, tumor immune infiltration, clinical features, and genomic features in PGs. A total of 39 HOX family genes were utilized to identify heterogeneous subtypes using consensus clustering. Then a random forest-supervised classification algorithm and a nearest shrunken centroid algorithm were performed to develop a prognostic signature in the training group and validated in two test groups and an independent cohort.

Results: Here, we first identified 39 HOX family genes significantly differentially expressed in PGs compared to adjacent normal tissues. Then the individuals with PGs were then divided into two heterogeneous clusters (cluster 1 and cluster 2) based on HOX family gene expression profiles. Cluster 2 showed higher total mutation counts, lower immune infiltration, and worse prognosis than cluster 1. Finally, we constructed a four-hub-HOX gene signature (including HOXA2, HOXA6, HOXC5, and HOXC6) based on the cluster for subtype prediction applying a random forest supervised classification algorithm and a nearest shrunken centroid algorithm. The signature was revealed to be an independent prognostic factor for patients with PGs by multivariable Cox regression analysis.

Conclusion: Our results provide a novel method for the prognosis classification of PGs. The findings also suggest that the four-hub-HOX gene signature is a new biomarker for the prognosis of patients with PGs, allowing for more accurate survival prediction.

Citation Format: Qianhao Zhao, Junyan Su. The HOX family gene signature predicts prognosis and indicates immune infiltrates in pediatric gliomas [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 1396.
Abstract 1488: The FOXA2 contributes to tumor proliferation and invasion via HGF mediated ERK signaling pathway in human gastric cancer
Authors: Jung Jiyoon , Koh Sungae , Lee Kyunghee
Published: April 2023

Background: FOXA1 and FOXA2, members of the forkhead transcription factor family, are critical for epithelial differentiation in many endoderm-derived organs and important regulators in body homeostasis. It has been shown that FOXA2 plays an important role in tumorigenesis and carcinogenesis in glioma, breast cancer, hepatoma, and others. However, FOXA2 has not yet been elucidated on the tumorigenesis, proliferation, and invasion of human gastric cancer, and needs to be researched and discovered. In this study, the HGF-mediated association of FOXA2, extracellular signal-regulated protein kinase (ERK), and matrix metalloproteinase 9 (MMP9) and cancer cell proliferation and invasion were investigated in two types of human gastric cancer cell lines.

Methods: In this study, cell culture, cDNA microarray analysis, western blotting, Real-time Polymerase chain reaction, Zymography, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, FOXA2 knock-down with short hairpin RNA (shRNA), chromatin immunoprecipitation assay, Standard two chamber invasion assay.

Results: First, we confirmed that the expression level of FOXA2 was up-regulated by HGF (hepatocyte growth factor) in human gastric cancer cells. To identify the associated pathway of HGF-induced FOXA2 about ERK, MMP9 expression, the cells were treated with PI3K (Phosphoinositide 3-kinase) inhibitor (LY294002) and then analyzed by Western blotting. The role of FOXA2 associated with MMP9 and ERK was determined by knockdown cell of FOXA2. FOXA2-sh RNA cells showed a decreased level of MMP9 and ERK. HGF-mediated cell proliferation and invasion were decreased in FOXA2 knockdown cell.

Conclusions: These results suggest that FOXA2 plays an important role in cell proliferation and metastasis in hepatocellular carcinoma, and FOXA2 may be a novel target for the prevention of progression and treatment of human gastric cancer.

Citation Format: Jiyoon Jung, Sungae Koh, Kyunghee Lee. The FOXA2 contributes to tumor proliferation and invasion via HGF mediated ERK signaling pathway in human gastric 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 1488.
Abstract 1512: Evolution of large copy number variants in breast cancer through genetic network rewiring
Authors: Kuzmin Elena , Monlong Jean , Bourgey Mathieu , Lesluyes Tom , Barker Toby , Morin Genevieve , Zou Dongmei , Schwartz Michael , Yang Yang , Pacis Alain , Martinez Constanza , Kuasne Hellen , Fortier Anne-Marie , Li Rui , Kleinman Claudia , Huang Sidong , van Loo Peter , Ragoussis Jiannis , Bourque Guillaume , Park Morag
Published: April 2023

Large chromosomal alterations are common in cancer and often show preferential gain or loss across many cancer types indicating their selective advantage. Triple negative breast cancer (TNBC) exhibits complex mutational spectrum without common oncogenic drivers yet displays consistent loss of large chromosomal regions. Here, we characterize selection pressures that maintain a recurrently deleted region of chromosome 4p in TNBC. We used bulk WGS phylogenetic analysis of TNCB PT/PDX panel to show that chr4p deletion is an early event in tumor evolution. We used scRNAseq gene expression and inferred copy number analysis to show that chr4p loss is associated with a proliferative state. This finding was confirmed by a combination of RNA in situ hybridization and immunofluorescence. We then tested the dosage sensitivity of genes residing within this region by individual and dual overexpression in TNBC PDX-derived cell lines and control normal cell line by assessing their effect on cell proliferation. The overexpression of genes within chr4p elicited a strong cell proliferation defect in cancer but not normal cell line models. We also characterized an unknown gene within chr4p region as a novel member of the STRIPAK complex. Genome-wide pooled ORFeome library screens identified a global pattern of background-specific dosage sensitive regions. Our study shows that large chromosomal deletions are maintained due to evolutionary early genetic network rewiring rendering multiple genes within such regions to be dosage sensitive. Ultimately, this work enhances our understanding of genetic events that modulate TNBC.

Citation Format: Elena Kuzmin, Jean Monlong, Mathieu Bourgey, Tom Lesluyes, Toby Barker, Genevieve Morin, Dongmei Zou, Michael Schwartz, Yang Yang, Alain Pacis, Constanza Martinez, Hellen Kuasne, Anne-Marie Fortier, Rui Li, Claudia Kleinman, Sidong Huang, Peter van Loo, Jiannis Ragoussis, Guillaume Bourque, Morag Park. Evolution of large copy number variants in breast cancer through genetic network rewiring [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 1512.
Abstract 1513: A multi-sample study reveals the evolution and heterogeneity in high-grade serous ovarian cancer
Authors: Wong Siao-Han , Doberstein Kai , Marmé Frederik , Brors Benedikt
Published: April 2023

Ovarian cancer is a heterogeneous disease and high-grade serous carcinoma (HGSC) accounts for 70% of them. The pathogenesis of HGSC had remained obscure until the identification of its tubal origin; however, the carcinogenesis process remains largely underexplored. Meanwhile, targeted therapy using poly(ADP-ribose) polymerase (PARP) inhibitors have revolutionized the treatment of HGSCs and emphasizes the importance of patient stratification. Nonetheless, current clinical trials use different assays and a consensus approach for patient stratification is still lacking.

In this study, whole genome sequencing technique was used to profile tumor-normal sample pairs, including some related tumors collected from different anatomical sites. This yields a multi-sample cohort comprising 55 pre-treatment samples from 33 HGSC patients and is suitable for addressing questions about molecular stratification and tumor pathogenesis.

We first recapitulated two reported HGSC subgroups (H-HRD and H-FBI) in our cohort. Comprehensive analyses were conducted on genomic scars ranging from mutations, indels, structural variants and copy numbers. Our data suggests that the genomic subgroups are characterized by different extent and onset timing of homologous recombination repair defect (HRD) as well as CCNE1 activation. Of note, H-HRD group showed higher levels of copy number-based HRD score, which often serves as a surrogate biomarker for PARP inhibitor treatment response.

On the other hand, tumor evolutionary trajectory was reconstructed based on in silico methods capable of inferring relative timing of genetic alterations. This highlights an early bifurcation of carcinogenesis paths in this HGSC dichotomy, despite a common scenario of a very early TP53 mutation, an often early whole genome duplication and a chromosomal instability phenotype seen eventually.

Overall, these findings corroborate the concept of tumor-intrinsic genomic phenotypes by providing mechanistic underpinnings from the aspect of tumor evolution. This provides the rationale for studying HGSC disease biology in different contexts and formulating questions about subtype-specific pathogenesis and vulnerabilities. Translationally, it also holds the promise for better identifying the patient subset that might benefit from PARP inhibitor treatment.

Citation Format: Siao-Han Wong, Kai Doberstein, Frederik Marmé, Benedikt Brors. A multi-sample study reveals the evolution and heterogeneity in high-grade serous 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 1513.
Abstract 1547: The urokinase plasminogen activator receptor-associated protein (uPARAP) is an attractive target for the development of antibody-drug conjugates (ADCs) for treatment of mesenchymal malignancies
Authors: Barkholt Pernille , Wozniak Agnieszka , Wang Chao-Chi , Lee Che-Jui , De Kock Lore , Engelholm Lars H. , Lynch Carmel , Mumberg Dominik , Schöffski Patrick
Published: April 2023

Background: Soft tissue sarcoma (STS) is a complex family of rare malignancies with high unmet medical need. uPARAP is an endocytic receptor expressed at low levels on selected mesenchymal cell types, which internalizes fragments of collagen and transfers them to the lysosome for degradation. Besides its physiological role, uPARAP is considered a critical modulator of the tumor microenvironment. Here, for the first time, we explored the molecular epidemiology of uPARAP in sarcoma tissue to validate this receptor as target for the development of ADCs in this indication.

Methods: uPARAP expression was assessed in STS-specific tissue microarrays by immunohistochemistry in tissue samples from more than three hundred individual donors. Stainings were assessed by histopathologic scoring and grouped into high, medium and low expressing subgroups.

Results: uPARAP was found to be strongly over-expressed in a high percentage of cases of common STS, with variations in terms of incidence and level of expression between histological subtypes. High uPARAP expression was found in fibro- (86% of cases), synovial (84%), dedifferentiated lipo- (68%), pleomorphic lipo- (65%), myxofibro- (59%), leiomyo- (49%), and myxoid liposarcoma (24%). Work is ongoing in additional sarcoma subtypes.

Conclusions: Based on protein expression uPARAP is an attractive emerging therapeutic target for the development of uPARAP-binding ADCs in a broad range of mesenchymal malignancies. In addition, expression of uPARAP in STS may serve as a potential marker for patient selection in early clinical studies with uPARAP-targeting ADCs.

Citation Format: Pernille Barkholt, Agnieszka Wozniak, Chao-Chi Wang, Che-Jui Lee, Lore De Kock, Lars H. Engelholm, Carmel Lynch, Dominik Mumberg, Patrick Schöffski. The urokinase plasminogen activator receptor-associated protein (uPARAP) is an attractive target for the development of antibody-drug conjugates (ADCs) for treatment of mesenchymal malignancies [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 1547.
Abstract 1570: Novel Myc-dependent compound DL78 selectively induces mitotic catastrophe and cell death in high grade serous ovarian cancer
Authors: Teitel Jessica , Cusato Michele , Farah Margaret , Gandhi Agharnan , Lee Pil , White Andrew , Takyi-Williams John , Wen Bo , Da Rocha Andre Monterio , DiFeo Analisa
Published: April 2023

While the rates of new cases and deaths for high grade serous ovarian cancer (HGSC) have declined steadily in the past decade, HGSC remains the fifth leading cause of cancer death in women. As many patients succumb to chemoresistance, there is a need to uncover novel targeted drugs. One way to do so is by drug repurposing. A computational screen, DrugPredict, led to the discovery that amiodarone, an antiarrhythmic, is a potent apoptosis-inducer and Myc-degrader in numerous patient-derived ovarian cancer cell lines. In search of a more selective, but less toxic compound, structure-activity relationship was applied to identify DL78. Due to its structural differences, DL78 is considered to be independent of amiodarone. DL78 lacks hERG activity, retains Myc regulation, and gains selective anticancer properties. This compound produces significant cell death selectively in patient-derived HGSC cells, including isogenic cisplatin-resistant lines, but does not harm non-transformed fallopian tube cells. Cancer cells treated with DL78 arrest prior to anaphase and showcase microtubule abnormalities and upregulation of mitotic regulators. The prolonged arrest leads to loss of Myc, mitotic catastrophe, and apoptosis selectively in the HGSC cells, while fallopian tube cells can cycle normally. DL78’s activity is confirmed to be dependent on Myc expression because targeted inhibition of Myc decreases its potency and prevents the DL78-induced cell cycle arrest. Finally, pharmacokinetic analysis shows that DL78 saturates the tumor following intraperitoneal injection, yet drug concentrations in the blood and liver present at normal levels. Overall, these phenotypes do not show with amiodarone treatment, suggesting that structurally different DL78 performs through a different mechanism. Further classification of this tumor-selective compound may reveal targeted ovarian cancer vulnerabilities.

Citation Format: Jessica Teitel, Michele Cusato, Margaret Farah, Agharnan Gandhi, Pil Lee, Andrew White, John Takyi-Williams, Bo Wen, Andre Monterio Da Rocha, Analisa DiFeo. Novel Myc-dependent compound DL78 selectively induces mitotic catastrophe and cell death in high grade serous 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 1570.
Abstract 1594: SMARCA2 (BRM) degraders promotes differentiation and inhibit proliferation in AML models
Authors: Agarwal Anjana , Osinubi Olusola Peace , Vykuntam Komali , Fultang Norman , Bhagwat Neha , Heiser Diane , Vaddi Kris , Ito Koichi , Scherle Peggy
Published: April 2023

Dysregulated cellular differentiation is a major pathological feature of myeloid malignancies such as acute myeloid leukemia (AML). Targeting cellular differentiation programs has emerged as a novel therapeutic approach to treat patients with AML. Advantages of such differentiation therapy may include fewer systemic side-effects as well as opportunities to target leukemic stem cells (LSCs) and a broader range of clonal populations, likely resulting in lower frequencies of resistance and relapse in AML patients. The success of ATRA and decitabine in subsets of AML patients has proven that inducing differentiation can play a critical role in long-term durable responses. More agents targeting epigenetic regulators have been increasingly studied as differentiation inducers, including LSD1, DNMT1, Menin, and BET inhibitors. Recently, targeting SWI/SNF chromatin remodeling complexes has also been shown to regulate key leukemic gene expression signatures and induce AML differentiation. Small molecule inhibitors as well as gene knockdown for ATP-dependent SWI/SNF subunits SMARCA2 (BRM) and SMARCA4 (BRG1) are associated with re-direction of oncogenic transcriptional regulation to drive cellular differentiation and apoptosis in AML models. We have previously described the activity of highly potent, bispecific SMARCA2 degraders that efficiently promote SMARCA2 protein degradation in preclinical models. In the present study, we investigated the effects of our SMARCA2 selective degraders in AML models. Treatment with SMARCA2 degraders significantly inhibits AML cell line proliferation in vitro with IC50 ranging from 10 to 50 nM. In the SMARCA2 degrader treated cells, expression of PU.1 (SPI1), a key transcription factor in myeloid leukemias, was downregulated. In an in vivo OCI-AML3 xenograft model, treatment with a SMARCA2 selective degrader showed moderate tumor growth inhibition accompanied by robust increases in monocytic maturation markers CD11b and CD14. Further analyses of SMARCA2 degrader effects on global transcriptome and AML immunophenotypes as well as combination effects with other therapies are currently in progress. These findings highlight the potential of SMARCA2 degraders to target AML differentiation blocks and to improve the effectiveness of other therapeutic agents such as decitabine and venetoclax in AML patients.

Citation Format: Anjana Agarwal, Olusola Peace Osinubi, Komali Vykuntam, Norman Fultang, Neha Bhagwat, Diane Heiser, Kris Vaddi, Koichi Ito, Peggy Scherle. SMARCA2 (BRM) degraders promotes differentiation and inhibit proliferation in AML 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 1594.