bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5972: Antiangiogenic activity of FGFR inhibitor erdafitinib in urothelial carcinoma
Authors: Lim Seungtaek , Rha Sun Young , Bae Hyun Joo , Cho Sang Woo , Lee Jii Bum , Kim Tae Soo , Kang Sun Kyung , Kwon Woo Sun , Cho Nam Hoon , Choi Young Deuk , Kim Kunhong , Lee Hoi Young
Published: June 2022

Purpose: Fibroblast growth factors (FGFs) and fibroblast growth factor receptors (FGFRs) are implicated in tumor angiogenesis. Although erdafitinib showed efficacy in urothelial carcinoma (UC) patients harboring FGFR pathway alteration, the anti-angiogenic activity of this compound remains uncertain. Here, we investigated the suppression of UC growth by inhibiting angiogenesis with erdafitinib both in vitro and in vivo.

Materials and Methods: The inhibitory effect of erdafitinib on UC cells was evaluated by wound healing assay, transwell invasion assay, and zymography assay. Tubule formation assay and transwell migration assay was conducted to assess inhibitory effect of erdafitinib on endothelial cells (EC). Transwell migration assay to assess crosstalk of EC co-cultured with UC cell was also performed. For in vivo study, athymic nude mice bearing RT4 cells were randomly divided into a control group, and erdafitinib group. Tumors were then extracted for analysis such as immunohistochemistry.

Results: The results of wound healing assay and transwell invasion assay demonstrated that erdafitinib has inhibitory actions on the migratory and invasive potential of UC cells. Erdafitinib also suppressed tube formation and migratory potential of ECs. Transwell migration assay using EC co-cultured with RT4 showed that migration of EC was significantly inhibited by erdafitinib. For in vivo experiments, immuno-deficient mice (N=14) bearing RT4 xenografts were treated with or without erdafitinib (40mg/kg) orally three times a week for three weeks, and erdafitinib significantly suppressed tumor volumes and weight by 60.0% and 24.4%, respectively. The decrease of both CD31-positive and Ki-67-positive cells indicated that erdafitinib exerted anti-angiogenic activity.

Conclusion: This study demonstrated that erdafitinib has anti-angiogenic activities both in vitro and in vivo. It warrants further investigation for development of new therapeutic strategy.

Citation Format: Seungtaek Lim, Sun Young Rha, Hyun Joo Bae, Sang Woo Cho, Jii Bum Lee, Tae Soo Kim, Sun Kyung Kang, Woo Sun Kwon, Nam Hoon Cho, Young Deuk Choi, Kunhong Kim, Hoi Young Lee. Antiangiogenic activity of FGFR inhibitor erdafitinib in urothelial carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5972.
Abstract 5993: Inhibition of isorhapontigenin on migration and invasion of bladder cancer cells depends on Sestrin 2 and Beclin 1
Authors: Zhang Zhuo , Li Jingxia , Tu Huailu , Costa Max
Published: June 2022

Bladder cancer is the fourth most common cancer in men in the United States. It has been reported that about 83,730 new cases of bladder cancer and 17,200 deaths from bladder cancer occurred in 2021. Therefore, the discovery of new alternative medication becomes extremely important for reduction of cancer mortality. Isorhapontigenin (ISO), a phytopolyphenol, is derivative stilbene isolated from the Chinese herb Gnetum cleistostachyum. It has been reported that ISO exhibits multiple anticancer activities in human high grade invasive bladder cancer cells. Our previous study has demonstrated that ISO treatment increased methyltransferase 14, N6-adenosine-methyltransferase subunit (METTL14), subsequently decreased vimentin, a key member of epithelial mesenchymal transition (EMT), resulting in reduced invasion of bladder cancer T24T cells. Autophagy maintains normal cell homeostasis through the removal of oncogenic protein substrates, toxic unfolded proteins and damaged organelles. Tumor-promoting or tumor-inhibiting functions of autophagy depends on the cancer type and stage. Sestrin 2, a member of stress-inducible protein family which is essential for maintaining metabolic homeostasis, is involved in the autophagy initiation. Beclin 1, a key autophagy regulator, is involved in multiple stages of autophagy. The present study investigated the mechanisms of ISO-inhibited migration and invasion in bladder cancer cells by focusing on Sestrin 2 and Beclin 1 pathways. Our results showed that ISO treatment in bladder cancer T24T decreased both migration and invasion as assessed by using transwell assays. However, in T24T cells with Sestrin 2 knockdown or Beclin 1 knockdown ISO lost the inhibitory effect on migration and invasion. The results from immunoblotting analysis showed that knockdown of Sestrin 2 or Beclin 1 increased N-cadherin and vimentin, two important members of EMT. While treatment with ISO in T24T wildtype cells decreased N-cadherin and vimentin, ISO did not have any effect on N-cadherin or vimentin in T24T cells with Sestrin 2 or Beclin 1 knockdown. Furthermore, ISO treatment reduced protein levels of Atg7 and Bcl-2 in T24T wildtype cells. ISO failed to decrease Atg7 and Bcl-2 in those T24T cells with Sestrin 2 or Beclin 1 knockdown. The present study suggested that ISO inhibits migration and invasion of bladder cancer cells and the inhibition of ISO is dependent on Sestrin 2 and Beclin 1, and induction of autophagy by ISO reduces migration and invasion of bladder cancer cells. The present study provides evidence that ISO can be a candidate of chemotherapy.

Citation Format: Zhuo Zhang, Jingxia Li, Huailu Tu, Max Costa. Inhibition of isorhapontigenin on migration and invasion of bladder cancer cells depends on Sestrin 2 and Beclin 1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5993.
Abstract 60: Functional mapping reveals widespread remodelling and unrecognized pathway dependencies in recurrent glioblastoma
Authors: Chokshi Chirayu R. , Brown Kevin , Venugopal Chitra , Moffat Jason , Singh Sheila K.
Published: June 2022

Glioblastoma is a highly fatal brain cancer. The underlying functional drivers of treatment resistance and disease recurrence are unclear. By applying a genome-wide CRISPR-Cas9 library to patient-derived glioblastoma stem cell models, we systematically map genetic dependencies in patient-matched pre-treatment primary and post-treatment recurrent tumor cells. These insights reveal a large-scale remodelling of genetic dependency profiles at disease recurrence, arming recurrent tumor cells with newly-acquired genetic drivers and further loss of tumor suppressors. These analyses support parallel tumor-intrinsic mechanisms of treatment resistance which rely on acquisition of immunosuppressive capacity, including a defective mismatch repair pathway, ablation of PTEN activity, and a novel combination of de novo mutations in SWI/SNF components. We map a multilayered genetic and functional response to drive tumor recurrence, identifying protein tyrosine phosphatase 4A2 (PTP4A2) as a novel driver of self-renewal, proliferation and tumorigenicity at glioblastoma recurrence. Mechanistically, genetic perturbation and a small molecule inhibitor of PTP4A2 results in greater survival and reduced tumor growth in patient-derived models of recurrent glioblastoma.

Citation Format: Chirayu R. Chokshi, Kevin Brown, Chitra Venugopal, Jason Moffat, Sheila K. Singh. Functional mapping reveals widespread remodelling and unrecognized pathway dependencies in recurrent glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 60.
Abstract 6025: Baseline cytokine profiling in naïve and tumor-bearing Balb/c and C57BL/6 Charles River mice
Authors: Munroe Kenneth , Eberle Christoph S. , Mihalek Robert , Festin Stephen
Published: June 2022

Background: Syngeneic studies are still the backbone of oncology research. These rely on immunocompetent mice to model anti-cancer immune responses elicited by experimental treatments. Cytokines mediate these responses through cell signaling, which contributes to an immunosuppressive milieu in the tumor microenvironment. Determining the secretion patterns of these protein modulators can help understand pathogenesis, disease progression and resistance to targeted therapies. To evaluate biological effects of potential interventions, we compared systemic cytokine activities in naïve and untreated tumor-bearing Balb/c and C57BL/6 mice.

Study Details: Charles River wild type Balb/c (n=9) and C57BL/6 (n=10) mice were used for all experiments. CT26 and B16.F10 tumor cell lines for inoculations were purchased from ATCC (Manassas, VA). Serum samples were collected from colon carcinoma (Balb/c) and melanoma (C57BL/6) bearing mice as well as tumor-free animals. For rapid multiplex measurements on the Meso Scale Discovery platform the V-PLEX Proinflammatory Panel 1 Mouse Kit was used (cat no. K15048D-1). IFN-γ, IL-1β, IL-2, IL-4, IL-5, IL-6, KC/GRO, IL-10, IL-12p70, and TNF-α were detected simultaneously by electrochemiluminescence within the manufacturer’s specification for each analyte.

Results: Sera from CT26 and B16.F10 tumor-bearing mice exhibited higher average concentrations of IFN-γ, IL1-β, IL-4, IL-10, KC/GRO and TNF-α, when compared to naïve mice of the Balb/c or C57BL/6 background, respectively; however, IL-2 production was found increased in tumor-bearing Balb/c and decreased in tumor-bearing C57BL/6 mice. Though known to be promoting tumor growth, IL-6 was only measurable in three out of ten B16.F10-bearing mice and below the limit of detection in CT26-bearing mice. IL-5 and IL-12 p70 levels showed no difference between CT26-bearing and naïve Balb/c mice, whereas both cytokines were elevated in the B16.F10 model over naïve C57BL/6 mice.

Conclusions: Circulating serum cytokines have been quantified in commonly used syngeneic mouse strains with and without tumor burden. These reference data provide baseline levels to compare soluble proinflammatory biomarkers suitable for assessing potential immunomodulatory effects of experimental cancer treatments in combination with other pharmacodynamic readouts.

Citation Format: Kenneth Munroe, Christoph S. Eberle, Robert Mihalek, Stephen Festin. Baseline cytokine profiling in naïve and tumor-bearing Balb/c and C57BL/6 Charles River mice [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6025.
Abstract 6049: Identifying shared features of low-H3K27me3 pediatric brain tumors
Authors: Pun Matthew , Pratt Drew , Venneti Sriram
Published: June 2022

Brain tumors have the worse survival rates of all childhood malignancies, and a better understanding of their biology is needed for therapeutic development. Two especially devastating subtypes of pediatric brain tumors—diffuse midline gliomas, H3K27M-mutant (DMGs) and posterior fossa ependymomas, group A (PFAs) are both characterized by a hallmark of global reduction of histone 3 lysine 27 trimethylation, a mark associated with transcriptional repression. DMGs primarily harbor mutations of histone 3 (H3K27M) that inhibit the function of the H3 methyltransferase enhancer of zeste homolog 2 (EZH2)-containing polycomb repressive complex (PRC2). Most PFAs overexpress EZH inhibitory protein (EZHIP), resulting in a similar effect on PRC2 activity. Intriguingly, a small subset of DMGs found to be lacking H3K27M mutations express EZHIP, and a fraction of histological PFAs lacking EZHIP expression harbor H3K27M mutations. Given the highly similar putative driving alterations and epigenetic features in these two tumor types, we undertook a systematic evaluation of the clinical and molecular features of each tumor class to elucidate additional shared features and potential targetable vulnerabilities. We performed detailed analyses of genomic aberrations, gene expression, and epigenomic landscapes to identify key similarities and differences in tumor biology. From preliminary studies, our findings demonstrate similar H3K27me3 landscapes with convergence of residual tri-methylated loci between PFA and DMG tumors. We additionally found shared recurrent copy number gain of the long arm of chromosome 1 (1q) and identified several 1q genes whose expression correlated with survival differences in cohorts of both tumors. Together, these findings better define the commonalities and differences of these highly aggressive, low-H3K27me3 pediatric brain tumors and will provide a framework for understanding which therapeutic strategies may translate from one tumor to the other.

Citation Format: Matthew Pun, Drew Pratt, Sriram Venneti. Identifying shared features of low-H3K27me3 pediatric brain tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6049.
Abstract 6050: JMJD6 regulates super-enhancer mediated transcriptional dependencies in group 3 medulloblastoma
Authors: Kling Matthew , Ray Sutapa , Coulter Don W. , Chaturvedi Nagendra
Published: June 2022

Medulloblastoma (MB) is a heterogenous cerebellar tumor that comprises four molecular and clinically significant subgroups. MB is the most common brain malignancy in children with a five-year survival of 70%, however, Group 3 MB patients have the poorest survival due to the amplification of MYC and overexpression of key oncogenes that underly the Group 3 phenotype. Recently, epigenetic modifications bearing super-enhancer, H3K27ac, marks have been suggested to contribute to transcriptional dependencies that define Group 3 MB and represents an emerging target for therapeutic intervention. Currently, the mechanism that establishes and maintains these modifications to the DNA architecture remains unclear. In our study, we hypothesize that an epigenetic modifying protein, JMJD6, regulates the promoter-pause release associated with super-enhancer mediated oncogene addiction in Group 3 MB. This hypothesis is based on evidence in the literature showing that JMJD6 regulates the transcriptional pause release at enhancer regions. Moreover, the promoter-pause release has been shown to be critical for super-enhancer mediated transcription. In our preliminary studies, we demonstrate elevated levels of JMJD6 in Group 3 MB and survival analysis indicating JMJD6 as a predictor for poor prognosis in MB patients. Immunoprecipitation revealed that JMJD6 forms complexes with proteins involved in maintaining and regulating the promoter-pause at super-enhancers. Inducible knockdown of JMJD6 decreased MYC expression, cellular proliferation and stemness in vitro while inhibiting tumor formation and promoting survival in mice. Together, these studies identify JMJD6 as a promising therapeutic target for treating aggressive epigenetically driven Groups 3 MB tumors.

Citation Format: Matthew Kling, Sutapa Ray, Don W. Coulter, Nagendra Chaturvedi. JMJD6 regulates super-enhancer mediated transcriptional dependencies in group 3 medulloblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6050.
Abstract 6109: Clonal relationship of B cells between tertiary lymphoid structures (TLSs) and tumor infiltrating lymphocytes (TILs) in advanced endometrial cancer
Authors: Suzuki Haruka , Hamanishi Junzo , Qin Meng , Ukita Masayo , Ueda Akihiko , Kawahara Shunsuke , Yamanoi Koji , Miyamoto Taito , Takamatsu Shiro , Taki Mana , Hosoe Yoko , Kobayashi Takashi , Yamaguchi Ken , Mandai Masaki
Published: June 2022

Objective: Tertiary lymphoid structures (TLSs) are known to be a marker of peripheral inflammation. While high densities of TLSs were reported to be associated with longer patient survival in several cancer types, there is no direct evidence where B cells in TLSs(TLBs) are derived from and whether these clones are consistent with tumor infiltrating B cells (TIBs), in endometrial cancer.

Methods: We analyzed the pathological distribution of TLSs and TIBs in human endometrial cancer samples using immunohistochemistry of a series of B cell markers and evaluated the relationship with patients’ clinical outcomes. Additionally, we micro-dissected six pairs of tumor nests and their neighbor TLSs and analyzed the clonal consistency between TLBs and TIBs using the sequencing of complementarity-determining region (CDR) of B cell receptor (BCR).

Results: In 104 patients with endometrial cancer, TLSs were detected in 81 patients (78%), and the absence of TLS was related to worse progression-free survival (PFS) (HR, 0.15, P <0.01). Among TLS-detected cases, the high number of TIBs was significantly associated with better PFS (P<0.05). BCR analyses in the six patients found that three patients with advanced stage had a unique B cell clones in common between TLBs and TIBs, while the other three patients with early stage did not have any common B cell clones. The frequency of common B cell clones in the former three patients were 10.3% (5250/51146 reads), 9.7% (1873/19369 reads) and 3.0% (1034/34618 reads).

Conclusion: TLSs and TIBs are associated with better prognosis in endometrial cancer. Common B cell clones were found in the advanced stage cases, suggesting that B cells may have gradually acquired immunospecificity in TLSs.

Citation Format: Haruka Suzuki, Junzo Hamanishi, Meng Qin, Masayo Ukita, Akihiko Ueda, Shunsuke Kawahara, Koji Yamanoi, Taito Miyamoto, Shiro Takamatsu, Mana Taki, Yoko Hosoe, Takashi Kobayashi, Ken Yamaguchi, Masaki Mandai. Clonal relationship of B cells between tertiary lymphoid structures (TLSs) and tumor infiltrating lymphocytes (TILs) in advanced endometrial cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6109.
Abstract 6123: High-fat diets promote lung metastasis of breast cancer by activating lung fibroblasts
Authors: Chen Huiping , Huang Penghan , Chen Jianing , Song Erwei
Published: June 2022

Metastasis is the main cause of patient death among many tumor types including breast cancer and breast cancer patients with obesity have higher risk of distant metastases during 10-year follow-up. Diet is one of the main and manageable factors that cause obesity and regular intake of high-fat diets can induce obesity. In addition, fibroblasts, as the most abundant stromal cell type in tumor microenvironment, are involved in cancer metastasis. However, the role of fibroblasts and the downstream mechanism in metastasis of patients with high-fat diet remains unclear. In this study, we fed MMTV-PyMT transgenic mice with high-fat diet to obtain a high-fat tumorigenesis model, and isolate primary lung fibroblasts and then coculture them with breast cancer cells to explore the interaction. We found that a high-fat diet can significantly promote progression of primary breast cancer and lung metastasis, and that before weight difference shows, there is a different chemotactic influence of lung fibroblasts on breast cancer cell between high-fat diet and normal diet group. And we observed increased chemotactic function of primary lung fibroblasts in high-fat diet group. Moreover, tumor cells treated with primary lung fibroblasts in high-fat diet group show increased ability of adhesion, suggesting that high-fat diet chemoattracts breast cancer cell colonization by activating lung fibroblasts. Collectively, we explored the functional differences of lung fibroblast and the key factors for the lung colonization of recruited breast cancer cells. Our findings suggest that dietary patterns are associated with the risk of breast cancer metastasis and targeting activated fibroblasts in pre-metastatic microenvironment may serve as potential early therapeutic strategy to reduce breast cancer lung metastasis.

Citation Format: Huiping Chen, Penghan Huang, Jianing Chen, Erwei Song. High-fat diets promote lung metastasis of breast cancer by activating lung fibroblasts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6123.
Abstract 6156: High-fat diet-induced gut dysbiosis promotes prostate cancer growth through mast cells and histamine 1 receptor
Authors: Fujita Kazutoshi , Matsushita Makoto , Motooka Daisuke , Hase Takuaki , Banno Eri , De Velasco Marco , Kato Taigo , Kawashima Atsunari , Uemura Motohide , Nakamura Shota , Tsujikawa Kazutake , Morii Eiichi , Yoshimura Kazuhiro , Uemura Hirotsugu
Published: June 2022

Introduction and Objective High-fat diet (HFD) induce prostate inflammation and promote cancer growth. However, the mechanism of this inflammation has not been entirely clear. We provide the evidence of new histamine-mediated mechanism and the crucial role of the gut microbiota on HFD-induced prostate cancer (PCa) growth.

Methods We compared between HFD-fed and control diet (CD)-fed prostate-specific Pten KO mice at 22 weeks of age as PCa models. HFD-fed mice were given histamine receptor antagonist. Tumor growth was evaluated by prostate weight and Ki67 staining. Gut microbiota compositions were analyzed by 16S rRNA gene sequencing. Histamine signaling in PCa was assessed at gene and protein level.

Results HFD significantly increased prostate weight (0.25 vs. 0.46g, P = 0.01) and Ki67-positive cancer cell ratio (0.15 vs. 0.36, P = 0.01). cDNA microarray of PCa showed that expression of Hdc encoding histidine decarboxylase (HDC), which is responsible for histamine production, was upregulated in HFD-fed mice (Fold change = 2.71). The elevated expression of Hdc was also confirmed by quantitative PCR (P < 0.01). Infiltrating mast cells highly produced HDC protein, and mast cell counts around cancer foci were significantly increased in HFD-fed mice. Fexofenadine (Fexo), an H1 blocker, inhibited HFD-induced PCa growth, while ranitidine, an H2 blocker, had no inhibitory effect. Fexo reduced MDSC counts and suppressed IL6-STAT3 signaling in PCa of HFD-fed mice. In vitro, both histamine and Fexo did not affect the proliferation of DU145. HFD altered the composition of gut microbiota, and Shannon index suggesting diversity of gut microbiota was reduced in HFD-fed mice. Serum lipopolysaccharide (LPS) levels were elevated in 11-week-old HFD-fed mice, and LPS injection resulted in upregulation of Hdc in PCa.

Conclusions We found that HFD caused gut microbiota dysbiosis and elevated systemic LPS level, which could promote inflammatory PCa progression through mast cells and histamine H1 receptor signaling. These results suggest the existence of “Gut-Prostate Axis.”

Citation Format: Kazutoshi Fujita, Makoto Matsushita, Daisuke Motooka, Takuaki Hase, Eri Banno, Marco De Velasco, Taigo Kato, Atsunari Kawashima, Motohide Uemura, Shota Nakamura, Kazutake Tsujikawa, Eiichi Morii, Kazuhiro Yoshimura, Hirotsugu Uemura. High-fat diet-induced gut dysbiosis promotes prostate cancer growth through mast cells and histamine 1 receptor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6156.
Abstract 6167: Pancreatic tumor environmental nutrients alter SREBP-mediated lipid homeostasis and drive reliance on extracellular lipids for growth
Authors: Jonker Patrick , Muir Alexander
Published: June 2022

Both the cell-intrinsic metabolic network and the uniquely altered cell-extrinsic tumor microenvironment dictate tumor metabolism. However, while much is known about how cell-intrinsic factors regulate tumor metabolism, the effects of cell-extrinsic factors remain poorly understood. In particular, despite evidence that tumor nutrient availability extrinsically regulates tumor metabolism, further investigation has been hindered by the lack of models to study physiological nutrient availability in vitro.To accurately model the tumor nutrient microenvironment, our group quantified nutrient availability in pancreatic ductal adenocarcinoma (PDAC) tumor perfusate and created a medium to mimic this in vitro, called tumor interstitial fluid medium (TIFM). We compare the effects of TIFM-culture to maintenance in conventional culture medium (RPMI-1640) as a control for standard laboratory conditions. Using this model, I found that TIFM-cultured PDAC cells downregulate lipid synthesis, making TIFM-cultured cells uniquely reliant upon extracellular lipid uptake for growth. Analysis of murine PDAC tumors confirms downregulated lipogenesis in vivo, suggesting cell-extrinsic nutrients render lipogenesis dispensable—and lipid uptake necessary—for PDAC tumor growth. Notably, this contrasts studies in conventional culture media that claim lipogenesis is critical for PDAC growth.I am currently working to: (1) understand how the nutrient microenvironment alters lipid metabolism and (2) determine the extracellular lipids and transporters pancreatic cancer cells require for growth. Regarding the first question, transcriptomic analysis of TIFM-cultured cells revealed significant deactivation of SREBPs, master regulators of intracellular lipid and sterol synthesis, suggesting cell-extrinsic nutrient cues suppress lipogenesis by altering SREBP signaling. I am currently investigating which TIFM nutrients alter this signaling. I am also performing lipidomics analysis and lipid transporter knockdown experiments to identify lipids and transporters that TIFM-cultured cells require for growth. Collectively, these experiments will clarify the role extracellular nutrients play in driving changes to PDAC lipid metabolism and may suggest novel therapeutic treatment options for PDAC patients.

Citation Format: Patrick Jonker, Alexander Muir. Pancreatic tumor environmental nutrients alter SREBP-mediated lipid homeostasis and drive reliance on extracellular lipids for growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6167.
Abstract 6181: Cell line panel with HIBIT tagged endogenous proteins to accelerate PROTAC drug discovery
Authors: Zhai Yunpeng , Tan Ming , Liu Defu , Wang Guoqian , Ning Jinying , Hao Feng
Published: June 2022

Recent years have seen great advancement of targeted protein degradation technology, in particular, proteolysis targeting chimeras (PROTACs) are now widely used in developing therapeutics for treating cancer. A PROTAC is a heterobifunctional small molecule with three distinct moieties: a ligand to bind a targeted protein of interest (POI), a second ligand to recruit E3 ubiquitin ligase to form a ternary complex, and a linker for bridging the two ligands. Through the E3 ubiquitin ligase pathway, properly designed PROTACs can effectively degrade POIs with high specificity, which can be pathogenic proteins, thus regulate related pathways and inhibit tumor growth. Currently, there is no high-throughput biochemical assay to measure the POI degradation in vitro, hindering the application of the PROTAC technology. Here we report the development of a high-throughput cell based assay to quantitatively measure the endogenous drug target degradation induced by PROTACs. This assay encompasses over 800 cancer cell lines, many of which are CRISPR-engineered ones on common drug targets. A unique feature of our assay is the incorporation of HiBiT short sequence tags on either N-terminal or C-terminal of endogenous protein in E3 ligase matched cell line through site-specific gene homologous recombination technology. By highly specific and sensitive detection of HiBiT tag content in cell lysates with biochemical assay, we can determine target protein degradation by PROTAC treatment. We demonstrate the utility of the assay on a wide array of drug targets including RAS, LDHA, BTK and HPK1, and show that it can accelerate PROTAC drug discovery.

Citation Format: Yunpeng Zhai, Ming Tan, Defu Liu, Guoqian Wang, Jinying Ning, Feng Hao. Cell line panel with HIBIT tagged endogenous proteins to accelerate PROTAC drug discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6181.
Abstract 6207: Ba/F3 kinase mutant cell panel, a powerful cell model for the discovery and development of inhibitors for kinase specific mutation
Authors: Wang Yu , Peng Yao , Tang Yao , Zhou Lin , Ning Jinying , Hao Feng
Published: June 2022

Although over 70 protein kinase inhibitors have been approved by FDA since 2001, the protein kinase is still the hot target class of molecularly targeted cancer therapy because of the discovery of new driver kinase fusion mutation and a large number of secondary kinase mutations after the inhibitor treatment in cancer patients with the sequencing technology advancement, the need for new generation specific small molecule kinase inhibitors is still unmet, and it urge the industry to development more accurate, efficient kinase cellular assay models.Ba/F3 line is a popular cell model because many protein kinases and their mutants can transform the Ba/F3 cells to be growth independent of exogenous IL-3 supplement, while their inhibitors can antagonize these effects. Our group have generated a large of cell line panel with over 300 different well validated (sequencing, Western Blot and inhibitor test) Ba/F3 kinase cell lines for kinase inhibitor screening and development, covering several hot kinases, such as EGFR, EML-ALK, FLT3, NTRK, ROS1, HER, BCR-ABL, RET, FGFR1, FGFR2, FGFR3, FGFR4, KRAS, cMET, et al. Except used in in vitro high-throughput compound screening, most of the transformed Ba/F3 lines can grow well in immune-deficient mice and were also used to evaluate the efficacy of drug candidate and its downstream signaling in vivo. Our data indicate that our Ba/F3 cell line panel is a powerful cell model for new kinase inhibitor discovery and development.

Citation Format: Yu Wang, Yao Peng, Yao Tang, Lin Zhou, Jinying Ning, Feng Hao. Ba/F3 kinase mutant cell panel, a powerful cell model for the discovery and development of inhibitors for kinase specific mutation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6207.
Abstract 6210: Loss of inflammation-related genes and inflammation inhibitors effectively targets ER- breast cancer cell metastasis
Authors: Song Chaeun (Christine) , Lowe Val J. , Lee SeungBaek
Published: June 2022

The anti-estrogen tamoxifen is a highly effective hormonal therapy for hormonal (HR+) breast cancer patients. However, the estrogen receptor-negative, progesterone receptor-positive (ER-/PR+) subtype does not receive the benefits of tamoxifen. Therefore ER-/PR+ breast cancer have a poor clinical outcome, but drug development for ER-/PR+ breast cancer is not well studied. Here, we found that gene expression in ER-/PR+ HR+ breast cancer is positively related to triple negative breast cancer (TNBC) and not HR+ breast cancer using 4,319 breast cancer patients database. Especially, inflammation-related genes, A20/TNFAIP3, CDC20 and CASP1/Caspase-1, which are highly expressed in TNBC, are also upregulated in ER-/PR+ HR+ breast cancer. Suppression of A20/TNFAIP3, CDC20 and CASP1 inhibit cancer cell growth and metastasis in ERα KO (ER-/PR+) cell lines. Interestingly, loss of ERα in HR+ cell lines is not responsive to tamoxifen, but highly sensitive to inflammation inhibitor, Ac-YVAD-CHO. In in vitro and ex vivo models, inflammation inhibitor specifically blocks ER-/PR+ tumor proliferation and migration. These findings suggest that the inflammation inhibitor might be the first potential target therapy for ER-/PR+ HR breast cancer patients.

Citation Format: Chaeun (Christine) Song, Val J. Lowe, SeungBaek Lee. Loss of inflammation-related genes and inflammation inhibitors effectively targets ER- breast cancer cell metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6210.
Abstract 6265: Do epigenetic outliers impact racial disparities in colorectal cancer
Authors: Ghosh Jayashri , Schultz Bryant M. , Chan Joe , Wultsch Claudia , Shureiqi Imad , Chow Stephanie , Doymaz Ahmet , Varriano Sophia , Driscoll Melissa , Muse Jen , Kleiman Frida E. , Krampis Konstantinos , Issa Jean-Pierre J. , Sapienza Carmen
Published: June 2022

African Americans (AA) have a higher incidence and mortality rate for colorectal cancer (CRC) compared to Caucasians. DNA methylation profiling on normal colon mucosa from 77 CRC patients and 68 patients without cancer (controls) of AA and Caucasian descent identified a distinct subgroup of CRC patients (11AA and 4 Caucasians) who are statistical “outliers” at a large number of CpGs. Such highly epigenetically disrupted CRC patients are termed “Outlier Methylation Phenotype” (OMP). Comparison of methylome profiles of CRC patients and controls revealed that AA CRC patients have greater disruption of the normal colon methylome than do Caucasian patients. A large fraction of the overall methylation differences found between CRC patients and controls is attributable to OMPs. Estimation of epigenetic ages shows that OMPs have lower epigenetic ages compared to their chronological ages. In other words, OMPs undergo epigenetic age deceleration. Comparison of normal colon mucosa transcription profiles of OMP cancer patients with those of non-OMP cancer patients indicates genes whose promoters are hypermethylated in the OMP patients are also transcriptionally down-regulated, and that many of the genes most affected are involved in interactions between epithelial cells, the mucus layer, and the microbiome. Analysis of 16S RDNA profiles suggests that normal colon mucosa of OMPs are enriched in bacterial genera associated with CRC risk, advanced tumor stage, chronic intestinal inflammation, malignant transformation, nosocomial infections and KRAS mutations. In conclusion, our study suggests a distinct epigenetically disrupted OMP group in CRC that are responsible for disrupted methylome, altered gene expression and microbial dysbiosis. Furthermore, a higher frequency of OMPs among African Americans (11/42) than among Caucasians (5/35) may contribute to observed racial disparities in CRC incidence and outcome.

Citation Format: Jayashri Ghosh, Bryant M. Schultz, Joe Chan, Claudia Wultsch, Imad Shureiqi, Stephanie Chow, Ahmet Doymaz, Sophia Varriano, Melissa Driscoll, Jen Muse, Frida E. Kleiman, Konstantinos Krampis, Jean-Pierre J. Issa, Carmen Sapienza. Do epigenetic outliers impact racial disparities in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6265.
Abstract 6283: Reannotation and normalisation of Infinium 850k data for improved analysis of methylation at enhancers and non-coding RNAs
Authors: Bizet Martin , Defrance Matthieu , Calonne Emilie , Bontempi Gianluca , Fuks François , Jeschke Jana
Published: June 2022

In this study, we evaluated the MethylationEPIC BeadChip (850k) technology for enhancer methylation analysis with respect to RRBS, both high-throughput technologies commonly used to screen large patient cohorts. We developed and applied a new approach to re-annotate the 850k data, which greatly improved the association of probes to enhancers and show that 850k targets more enhancers than RRBS. We further investigated the reproducibility of the two technologies and applied various existing normalization methods to 850k data that reduce variability between replicates and variability with other technologies. We thereby showed that normalization methods developed for 450k greatly reduced variability in 850k data to a level below that of highly variable RRBS data. We finally performed differential methylation analysis with 850k data from breast cancer samples applying our new re-annotation method and highlight that the majority of differentially methylated cytosines were detected with probes specific to the 850k mapping to enhancers, confirming the deregulation of enhancer methylation in breast cancer. In summary, our study provides a new annotation for the 850k array, which greatly increases the number of cytosines mapping to enhancers and therefore allows for the improved analysis of enhancer methylation. Overall, we conclude that the 850k array allows for detection of methylation changes in regions not covered by previous Infinium arrays and is the best choice, as compared to RRBS, for high-throughput analysis of enhancer methylation in large clinical cohorts.

Citation Format: Martin Bizet, Matthieu Defrance, Emilie Calonne, Gianluca Bontempi, François Fuks, Jana Jeschke. Reannotation and normalisation of Infinium 850k data for improved analysis of methylation at enhancers and non-coding RNAs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6283.
Abstract 633: Delineating tumor-neural communication in brain metastasis with spatiotemporal transcriptomic analysis and multi-cellular crosstalk modeling
Authors: Wang Xin , Zhu Ying , Sheng Jianting , Zhao Hong , Wong Stephen
Published: June 2022

Brain metastases are diagnosed in 20-40% of all cancer patients. Despite the advancements in neurosurgery, radiotherapy, and chemotherapy, one-year survival of metastatic brain tumor patients still within a single digit such that brain metastases constitute about 20% of annual cancer deaths. These facts clearly indicate a critical need for better understanding of mechanisms that promote the growth of brain metastases. Emerging data, including ours, indicate that different types of metastatic cancer cells leverage dissimilar sets of neurotransmitters to favor their outgrowth in the brain. However, there are over sixty types of neurotransmitters in the brain being synthesized and released by various types of neural cells, we need a systemic investigation of how they mediate the pathogenesis of brain metastases in concert. Since neurotransmitters, gliotransmitters, neurotrophic factors, and neural cytokines, called neuroactive substances, are the most abundant and key intercellular communication signals in the brain, we hypothesize that tumor cells leverage these neuroactive substances to assimilate into neural circuitry via communicating with neural cells including neurons, astrocytes, microglia, oligodendrocyte, and others, in promoting the vicious circle of tumor-neural crosstalk during brain metastasis development. By performing spatial transcriptomics analysis on mouse brain sections bearing metastatic tumors, we found that tumor lesions at different locations and even tumor-surrounding areas in the brain regions could be differentiated into different cellular clusters based on gene transcriptomic expressions. We further predicted several paracrine and autocrine signaling between and within tumors as well as tumor-surrounding neural niches in different tumor locations (e.g., centers or edges), of different tumor sizes, and at various tumor development stages, using our Cell-Cell Communication Explorer (CCC-Explorer) modeling software. Functional experiments were conducted to demonstrate that cell type-specific depletion of the secreted NSs deactivated the activities of corresponding receptors and downstream signaling in co-cultured metastatic brain tumor cells. Characterizing spatiotemporal tumor-neural crosstalk in the brain metastatic niche would provide a new strategy in the development of novel and effective therapeutics of brain metastases.

Citation Format: Xin Wang, Ying Zhu, Jianting Sheng, Hong Zhao, Stephen Wong. Delineating tumor-neural communication in brain metastasis with spatiotemporal transcriptomic analysis and multi-cellular crosstalk modeling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 633.
Abstract 6339: Deep plasma proteomics at scale enabling proteogenomic analyses in a lung cancer (NSCLC) study
Authors: Zamanighomi Mahdi , Guturu Harendra , Wang Jian , Alavi Amir , Brown Tristan , Hornburg Daniel , Hasan Moaraj , Ferdosi Shadi , Motamedchaboki Khatereh , Donovan Margaret , Platt Theodore , Benz Ryan , Siddiqui Asim , Batzoglou Serafim
Published: June 2022

Our ~20,000 genes encode over one million protein variants, given alternative splice forms, allelic variation, and protein modification. Though large-scale genomics studies have expanded our understanding of biology, similarly, scaled deep and untargeted proteomics studies of biofluids have remained impractical due to complex workflows. To address this need, we have previously described Proteograph࣪, a novel platform that leverages the protein-corona interactions of nanoparticles for deep and untargeted proteomic sampling at scale.

Using Proteograph࣪ in a non-small cell lung cancer (NSCLC) cohort, we previously conducted a deep interrogation of plasma from 141 subjects: 61 early-stage NSCLC subjects and 80 non-cancer controls. We identified 2,499 plasma proteins, with 1,992 present in ≥ 25% of the samples. Leveraging this data, we created a biomarker classifier distinguishing NSCLC from controls with area under the receiver operating characteristic curve of 0.911. In this study, we now re-analyze the data with the more sensitive DIA-NN software to enhance protein depth while preserving the accuracy of the classifier. In addition, to show the added value of our platform in combination with genomic data, we integrate previously sequenced exome data with our proteomic data to build a multi-modal proteogenomic deep learning classifier. Our results outline proteogenomic workflows for robust biomarker discovery and cohort subtyping.

The Proteograph࣪ platform interrogates the plasma proteome at previously impractical combinations of scale, depth and coverage, and enables the development of improved classification models and the study of proteogenomics.

1Blume et al. Nat. Comm. (2020)

Citation Format: Mahdi Zamanighomi, Harendra Guturu, Jian Wang, Amir Alavi, Tristan Brown, Daniel Hornburg, Moaraj Hasan, Shadi Ferdosi, Khatereh Motamedchaboki, Margaret Donovan, Theodore Platt, Ryan Benz, Asim Siddiqui, Serafim Batzoglou. Deep plasma proteomics at scale enabling proteogenomic analyses in a lung cancer (NSCLC) study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6339.
Abstract 6352: Ascites derived exosomes promote progression of advanced gastric cancers
Authors: Hyung Sujin , Ko Jihoon , Lee In-kyung , Jeon Noo Li , Lee Jeeyun
Published: June 2022

Gastric cancer (GC) with peritoneal metastasis accompanied by a sequential buildup of malignant ascites currently has no curative therapy; accordingly, developing novel biomarkers is critical for reducing the severity of this disease. Recently, the significance of exosomes as a biomarker has gradually increased; exosomes act as a critical mediator of cell-cell intracellular communication in cancer progression. In this study, we characterized exosomes derived from ascites (ExoAscites) of four patients with GC; the high concentration of ExoAscites was observed with the morphology of round-cup shape. Our results showed that ExoAscites were actively endocytosed into cancer spheroid with time. The tropism of ExoAscites showed a predominance to GC rather than stromal cells.Furthermore, their importance on cancer invasiveness and angiogenesis are verified in the 3D microfluidic cancer spheroid model. Interestingly, tumor progression was gradually promoted by treatment with increasing ExoAscites concentrations. Collectively, these results support the view that exosomes from ascites fluids act as mediators of the tumor microenvironment, thus providing conditions favorable for future tumor progression.

Citation Format: Sujin Hyung, Jihoon Ko, In-kyung Lee, Noo Li Jeon, Jeeyun Lee. Ascites derived exosomes promote progression of advanced gastric cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6352.
Abstract 6370: Assessing the effect of blocking CCL2-CCR2 axis on breast cancer brain metastasis
Authors: Duan Yimin , Qi Yutao , Zhang Lin , Yuan Xiangliang , Yu Dihua
Published: June 2022

Among the 300,000 newly diagnosed breast cancer patients every year, 5~20% of them will develop symptomatic brain metastasis, whose 1-year survival rate is lower than 20%. Our group previously reported that brain tumor microenvironment (TME)-mediated PTEN downregulation in brain metastatic tumor cells increases the secretion of the chemokine CCL2, which enhances the infiltration of CCR2+ bone marrow derived myeloid cells, eventually promoting brain metastasis outgrowth. However, the mechanism of CCL2-CCR2 axis promoting brain metastasis is not clear, and the efficacy of targeting either CCR2 or CCL2 remained to be assessed. Here we show that Ccr2 antagonism significantly blocked Ccr2high myeloid cells trafficking in the blood and infiltration into the brain TME. However, Ccr2 antagonism did not sufficiently impede breast cancer brain metastasis in multiple preclinical models. Nevertheless, knocking down CCL2 or targeting CCL2 exhibited significant inhibition of brain metastasis growth. Subsequent analysis of the brain TME through mass cytometry demonstrated dramatically decreased infiltration of both Ccr2high and Ccr2low myeloid cell populations in the CCL2 targeted group, implying that the Ccr2low myeloid cells are also involved in promoting brain metastasis growth. Our data highlights the differential responses between targeting CCR2 or CCL2 in multiple preclinical brain metastasis models, which direct us to explore the function of Ccr2low myeloid cells in regulating brain metastasis progression. Our findings also suggest that carefully choosing between CCR2 or CCL2 as a target to control brain metastasis is important in clinical practice.

Citation Format: Yimin Duan, Yutao Qi, Lin Zhang, Xiangliang Yuan, Dihua Yu. Assessing the effect of blocking CCL2-CCR2 axis on breast cancer brain metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6370.