tbuckley/cabot-search huggingface dataset:
Abstract 893: Studying the impact of CNVs on expression at single-cell resolution in HGSOC using autoencoders
Authors: Matias Marin Falco, Teemu Närhi, Erdogan Pekcan Erkan, Johanna Hynninen, Anna Vähärautio
Journal: Cancer Research (2024)

Abstract High-grade serous ovarian cancer (HGSOC) is one of the most lethal gynecological malignancies. Lack of common targetable oncogenic mutations has complicated the development of directed therapies to combat emerging resistance. This malignancy is mainly characterized by the mutation of gene TP53, which promotes genome instability for the emergence of extensive copy number variations (CNVs). However its impact on gene expression at the single-cell level is not well understood. In this study, we aim to investigate the effect of CNVs on transcriptomic signatures by taking advantage of variational autoencoders (VAE) ability for dimensionality reduction, unsupervised learning and feature extraction. The use of VAEs is becoming more popular for the analysis of scRNAseq data, and scVI is one of the most versatile VAE applications performing wide variety of tasks. Here, we used single-cell RNA sequencing (scRNA-seq) data from 90 longitudinal samples of 64 HGSOC patients and inferred CNVs in each cell using inferCNV, an established computational pipeline. Then, we modified scVI algorithm to allow the VAE to reconstruct CNVs from a latent space originated from gene expression profiles and viceversa. Our models were capable of reconstructing CNV profiles accurately from expression data and also remove batch effect. From these models we could observe how, after the integration of genomic information, the latent clusters produced from the transcriptomic space were influenced by the amplifications or deletions of certain genomic regions. Moreover, some of these clusters were characterized by the alteration of important oncogenes in HGSOC, such as KRAS and CCNE1, and allowed us to focus on the transcriptomic consequences of their amplifications. With the results from the approach presented here, we gained a more comprehensive picture of the impact of genomic alterations on HGSOC. As future work, we plan to validate of this results on external cohorts and link the identified signatures to clinically relevant features such as prognosis or chemotherapy response. Citation Format: Matias Marin Falco, Teemu Närhi, Erdogan Pekcan Erkan, Johanna Hynninen, Anna Vähärautio. Studying the impact of CNVs on expression at single-cell resolution in HGSOC using autoencoders [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 893.
Abstract 7193: ABCB1-mediated chemotherapeutic drug resistance is reversed by a potent p53-MDM2 inhibitor NVP-HDM201
Authors: Harsh Patel, Chaoyun Cai, Zhuoxun Wu, Qiuxu Teng, Hanli Li, Zhe-Sheng Chen
Journal: Cancer Research (2024)

Abstract The failure of chemotherapy in cancer persists as a result of overexpression of various ATP-binding cassette (ABC) transporters. ABCB1 is one such transporter that actively pumps out chemotherapeutic drugs and it is one of the reasons for multidrug resistance (MDR). In the last few years, activation of p53 has been targeted as a therapeutic strategy in the treatment of cancers. Siremadlin (NVP-HDM201) is a potent and selective inhibitor of p53-MDM2 interaction. The objective of this study was to explore the ability of HDM201 to reverse tumor MDR attributable to overexpression of ABC transporters. According to our findings, HDM201 significantly increased the sensitivity of ABCB1-overexpressing cells to ABCB1 substrates, such as colchicine and doxorubicin. We found that HDM201 reverses ABCB1-mediated MDR by interacting with ABCB1 and blocking its function without affecting the expression and cellular localization of ABCB1. Moreover, HDM201 promoted the accumulation of paclitaxel in cell lines that overexpress ABCB1. At both high and low doses, HDM201 increased the ATPase activity of ABCB1. The computational support for the cross-reactivity of this p53 inhibitor with human ABCB1 comes from docking simulation results that align with the binding conformation of HDM201 within the vast cavity of the transmembrane region of ABCB1. In conclusion, by blocking the transport function of ABCB1, HDM201 can reverse ABCB1-mediated MDR in vitro. Citation Format: Harsh Patel, Chaoyun Cai, Zhuoxun Wu, Qiuxu Teng, Hanli Li, Zhe-Sheng Chen. ABCB1-mediated chemotherapeutic drug resistance is reversed by a potent p53-MDM2 inhibitor NVP-HDM201 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7193.
Abstract 5387: Host-derived CCL2 drives prostate cancer bone metastasis <i>via</i> CCND2/STAT3 pathway
Authors: Jie Meng, Ming Chang, Siyuan Qin, Xin Huang, Weiping Liang, Haibo Tong, Jian Zhang
Journal: Cancer Research (2024)

Abstract Overexpression of tumor-derived CCL2 has been shown to partially promote prostate cancer (PCa) bone metastasis, but the function of host-derived CCL2 is not fully understood. We first developed a mouse model using intracardiac injection and obtained highly metastatic PCa cell subclones through in vivo selection. The highly metastatic tumor cells were injected intracardially into CCL2 knockout (CCL2 KO) mice and wild-type (WT) controls, and the tumor cell growth and metastasis were monitored weekly by bioluminescence imaging. The osteolytic lesions were evaluated by radiography, micro-computed tomography (microCT) and immunohistochemistry (IHC) staining. The cells in the bone microenvironment were analyzed by flow cytometry. Also, RNA sequencing (RNA-seq) analysis was performed on the cells either from CCL2 KO mice or WT controls. We found that a loss of host-derived CCL2 significantly retarded tumor growth in bone and prolonged mouse survival. In addition, bone density analysis revealed a decrease in osteolytic lesion in CCL2 KO mice, compared to WT controls. Systemically, CCL2 deficiency reduced the proportion of granulocyte-myeloid-derived suppressor cell (G-MDSC) populations with immunosuppressive function and decreased the PCa conditioned medium (CM)-induced osteoclast formation. The enrichment analysis revealed that the dysregulated genes in bone metastatic cells from CCL2 KO mice were significantly enriched in several biological processes, including vitamin metabolism, monoatomic anion homeostasis, immune response, and bone growth. Additionally, we also confirmed that the CCND2/STAT3 pathway is apparently suppressed in the cells from CCL2 KO mice. This study demonstrated that targeting the host-derived CCL2 might be a novel potential anti-metastatic approach. Supported by the NSFC projects (81972766, 81972420, 82173336), as well as grants from the Science and Technology Project of Shenzhen (JCYJ20190809161811237, JCYJ20210324104214040). Key words Host-derived CCL2; Prostate cancer; Bone metastasis; osteoclast; CCND2 Citation Format: Jie Meng, Ming Chang, Siyuan Qin, Xin Huang, Weiping Liang, Haibo Tong, Jian Zhang. Host-derived CCL2 drives prostate cancer bone metastasis via CCND2/STAT3 pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5387.
Abstract 6674: Fungi utilizes exocytosis pathway to facilitate the release of DAMPs from pancreatic cancer cells
Authors: Aftab Alam, Shyamananda Singh Mayengbam, Sharon Senchanthisai, Bektas Irmak, Prasenjit Dey
Journal: Cancer Research (2024)

Abstract Recent studies overwhelmingly show that microbiome is pervasive to tumor and play key role in immunotherapy response and reprograming tumor immune microenvironment (TIME). However, it remains unknown how microbiome facilitates the host-immune cell crosstalk and promote tumorigenesis. Our recent study in pancreatic ductal adenocarcinoma (PDAC) show that intratumor fungal microbiome facilitate the release of a damage associated molecular pattern (DAMP) molecule IL-33 from cancer cells. The secreted IL33 from cancer cells in turns recruits ILC2 and TH2 cells which promotes PDAC tumorigenesis. However, the mechanism of fungal mediated IL-33 release from PDAC cells remains unknown. Our follow up studies using high throughput integrated proteomic profiling and immunoprecipitation revealed a group of exocyst complex proteins interacting with IL-33 in the presence of fungus. The exocyst complex consists of eight sub-unit proteins that tethers the secretory vesicles to the plasma membrane and implicated in cellular exocytosis. We found EXOC6B a component of exocyst complex, modulates IL-33 release via exocytosis pathway from the PDAC cells. Genetic depletion of EXOC6B resulted in shunted IL-33 release and significantly abrogated PDAC tumor progression. Mechanistically, we found that mycobiome activates a non-canonical TLR2-CARD9 pathway, thereby driving IL-33 nucleocytoplasmic transport and exocytosis. This study identifies a unique mechanism of EXOC6B mediated release of IL-33 that expands our knowledge on how host-mycobiome interaction shapes PDAC tumor microenvironment by intricate molecular mechanism. Our study identifies EXOC6B as a new therapeutics target involved in the mycobiome driven IL-33 secretion in pancreatic cancer. Citation Format: Aftab Alam, Shyamananda Singh Mayengbam, Sharon Senchanthisai, Bektas Irmak, Prasenjit Dey. Fungi utilizes exocytosis pathway to facilitate the release of DAMPs from pancreatic cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6674.
Abstract 5727: ISM9682A, a novel and potent KIF18A inhibitor, shows robust antitumor effects against chromosomally unstable cancers
Authors: Jie Zhang, Feng Gao, Wei Zhu, Chenxi Xu, Xiaoyu Ding, Jing Shang, Junwen Qiao, Shan Chen, Xin Cai, Xiao Ding, Supriya Bavadekar, Sujata Rao, Man Zhang, Feng Ren, Alex Zhavoronkov
Journal: Cancer Research (2024)

Abstract KIF18A belongs to the kinesin-8 subfamily and is a plus-end-directed motor, which regulates kinetochore microtubules dynamics to control mitotic chromosome alignment and spindle tension. Studies have shown that genetic depletion or pharmacological inhibition of KIF18A is a promising therapeutic approach for cancers, exhibiting high chromosomal instability (CIN-high), without having a significant impact on the normal division of euploid cells. Here, we report the discovery and preclinical evaluation of ISM9682A, a novel KIF18A inhibitor with excellent potency and high selectivity. ISM9682A is a potent KIF18A inhibitor with a single-digit nanomolar IC50 value and exhibits high selectivity over other kinesin family members. In addition, ISM9682A demonstrated excellent monotherapy anti-proliferative activity, with single-digit nanomolar IC50 values, in high-grade serous ovarian carcinoma (HGSOC) as well as in triple-negative breast cancer (TNBC) aneuploid cell lines with p53 mutation. Notably, ISM9682A exhibited a prolonged drug-target residence time indicated by both enzymatic and cellular assays. Consistent with the in vitro findings, ISM9682A displayed significant anti-tumor efficacy with a robust pharmacodynamic response (pH3, mitotic marker; γH2AX, DNA damage marker) in OVCAR3 and HCC1806 CDX models in a dose-dependent manner. In addition to its robust biological potency and high selectivity, ISM9682A exhibits favorable drug-like properties, including desirable in vitro ADMET characteristics and excellent in vivo exposure, clearance, as well as good oral bioavailability across multiple preclinical species. Collectively, these findings highlight the potential of ISM9682A as a novel and highly potent KIF18A inhibitor for the treatment of CIN-high cancers. Citation Format: Jie Zhang, Feng Gao, Wei Zhu, Chenxi Xu, Xiaoyu Ding, Jing Shang, Junwen Qiao, Shan Chen, Xin Cai, Xiao Ding, Supriya Bavadekar, Sujata Rao, Man Zhang, Feng Ren, Alex Zhavoronkov. ISM9682A, a novel and potent KIF18A inhibitor, shows robust antitumor effects against chromosomally unstable cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5727.
Abstract 3484: Mechanism of BRAF V600E resistance revealed by cell panel screening and bioinformatics
Authors: Kaiqiang Hu, Qiuyuan Yang, Pengwei Pan, Fang He
Journal: Cancer Research (2024)

Abstract The BRAF V600E mutation is pivotal target in the treatment of melanoma. Dabrafenib, one of the most potent inhibitors approved by the FDA, exhibits differential sensitivity across different cancer types. To explore the underlying mechanisms responsible for the resistance of certain cancers to Dabrafenib, we tested a panel of 20 BRAF V600E positive cancer cell lines. Our results showed that 15 of these cell lines demonstrated sensitivity to Dabrafenib, whereas the remaining 5 exhibited resistance. We then investigated the correlation between Dabrafenib potency and gene expression patterns based on public high throughput sequencing data via bioinformatics methods. The results uncovered that the cell lines resistant to Dabrafenib showed low expression of MAP3K1, alongside with elevated expression of G0S2 and PIK3CG. These alterations are known to promote tumor cell proliferation, migration, and invasion, thereby contributing to a reduced sensitivity to BRAF inhibitors. Subsequent in vitro experiments validated the findings derived from our analysis. This unbiased, bioinformatics-driven approach provides valuable insight into the reasons behind treatment resistance and aids in the development of next-generation treatment approaches for inhibitor-resistant cancers. Citation Format: Kaiqiang Hu, Qiuyuan Yang, Pengwei Pan, Fang He. Mechanism of BRAF V600E resistance revealed by cell panel screening and bioinformatics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3484.
Abstract 6678: Microbial regulation of anti-tumor immunity in colorectal cancer
Authors: Charlie Chung, Elif Ozcelik, Jill Habel, Jialin Zhang, Yihan Qin, Libia Garcia, Joseph Merrill, Taemoon Chung, Scott Lyons, Zeli Shen, James G. Fox, Peter Westcott, Semir Beyaz
Journal: Cancer Research (2024)

Abstract Colorectal cancer (CRC) is the 3rd leading site of cancers and cause of cancer cell death. Although Immunotherapies revolutionized cancer therapy, the majority of CRC patients, particularly with metastatic disease, do not respond to the treatments. This necessitates a better mechanistic understanding of the tumor-immune cell interactions in the context of CRC. Microbiome influences multiple biological aspects of the host including immune responses against cancers. Here, we show that the gut microbiome influences cancer MHC-I and -II expression levels and restricts tumor progression and metastasis, resulting in longer survival in 3 different CRC models and two different mouse strains. We found that the anti-tumor effects are dependent on T cells and B cells. Interestingly, depletion of B cell negated anti-metastatic effects of gut microbiome. Mechanistically, MHC-II expression in cancer cells mediates the anti-tumor effects of the microbiome. MHC-II upregulation on human CRC organoids enhances cancer-immune cell interactions and associated apoptosis, demonstrating an anti-tumor role and significance of MHC-II in human CRC. Thus, gut microbes that enhance MHC-II antigen presentation promotes anti-tumor immunity and may be utilized to enhance efficacy of immunotherapy in metastatic CRC. Citation Format: Charlie Chung, Elif Ozcelik, Jill Habel, Jialin Zhang, Yihan Qin, Libia Garcia, Joseph Merrill, Taemoon Chung, Scott Lyons, Zeli Shen, James G. Fox, Peter Westcott, Semir Beyaz. Microbial regulation of anti-tumor immunity in colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6678.
Abstract 6717: Targeting mutant KRAS proteins with novel TCR-mimic fully human antibodies
Authors: Jun Du, Wanbo Tang, Xin Jiao, Limin Zhao, Pengfei Du, Yuqi Zhang, Jian Bao, Han Chen, Chaoshe Guo, W. Frank An
Journal: Cancer Research (2024)

Abstract Mutated KRAS proteins are ideal cancer targets, as they are expressed frequently and specifically in certain solid tumors. A large proportion of human colorectal cancer and pancreatic ductal adenocarcinoma express the tumor driver KRAS gene mutations G12V/G12D, but drugs targeting G12V/G12D are not available, revealing a huge unmet clinical need. While small molecules often fail to target the KRAS mutation G12V/G12D, T cell receptor-mimic (TCR-mimic) antibodies can specifically recognize KRAS mutations presented by human leukocyte antigen (HLA), opening up possibilities for targeting such intracellular antigens. Here, we discovered novel antibodies highly specific to G12V/HLA and G12D/HLA complexes by immunizing our proprietary RenTCR-mimicTM mice and using high-throughput Beacon-based screening. These TCR-mimic antibodies have higher affinities compared to endogenous TCRs, which may effectively reduce the possibility of tumor escape. Germline distribution analysis indicated their high sequence diversity, which suggests diverse epitope targeting. Although pancreatic cancer is extremely difficult to treat and has an extremely low KRAS mutant peptide-HLA complex density on the cell surface, our TCR-mimic antibodies exhibited potent in vitro tumor lysis activity when assembled into CD3 T cell engagers. Furthermore, these antibodies demonstrated convincing off-target safety. Together, our results indicate promising therapeutic potential of these KRAS mutation-targeted TCR-mimic antibodies for the treatment of solid tumors. Citation Format: Jun Du, Wanbo Tang, Xin Jiao, Limin Zhao, Pengfei Du, Yuqi Zhang, Jian Bao, Han Chen, Chaoshe Guo, W. Frank An. Targeting mutant KRAS proteins with novel TCR-mimic fully human antibodies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6717.
Abstract 5396: Vascularized gastric cancer 3D co-culture model using a microphysiological system as an oncolytic virus testing platform
Authors: YeLin Kim, Youngsook Song, Yeongmin Choi, Jinhwan Jang, Suryong Kim, Tsung-Li Liu, Kyusuk Baek, Keunhee Oh, Seunghyun Ma, Tae Soo Kim, Woo Sun Kwon, Sanghee Yoo, Jee Hung Kim, Sun Young Rha
Journal: Cancer Research (2024)

Abstract Introduction: Angiogenesis is a critical aspect of cancer growth and metastasis. Consequently, inhibiting angiogenesis has garnered substantial attention in oncology research. JX-594 (pexastimogene devacirpvec; Pexa-Vec®), engineered from the Wyeth vaccine strain, has emerged as an attractive oncolytic virotherapy and demonstrated oncolytic, immunotherapeutic, and tumor vasculature-disrupting capacities. In our previous study, we found that JX-594 reduced the amount of vasculature in gastric tumors using a xenograft mouse model. In the present study, we investigate the effect of JX-594 on tumor vasculature using an in vitro human cell 3D co-culture model of vascularized gastric cancer, to determine if this tool provides improved accuracy in evaluating the mechanism of action and biological activity of JX-594 as compared to traditional animal models. Methods: The Curio-Spheroid chip is a Microphysiological System (MPS) that can grow tumor organoids or spheroids in 3D using physiologically relevant hydrogels and culturing them with other human cell types such as fibroblasts, endothelial cells, and immune cells. We evaluated nine human gastric cancer cell lines (YCC-18, YCC-19, YCC-22, YCC-30, YCC-32, YCC-38, Hs746T, NUGC-3, SNU-620) for their ability to form spheroids and induce angiogenesis inside Curio-Spheroid chips. We selected YCC-32 for the oncolytic virus testing. Serial increases of M.O.I (multiplicity of infection) of JX-594 disrupted the tumor-induced angiogenesis in a dose-dependent manner. Results: JX-594 treatment of the YCC-32 spheroid resulted in decreased levels of Ki-67 and cytopathic effects in a dose-dependent manner inside the Curio-Spheroid MPS system. Angiogenesis was observed surrounding the spheroid when co-cultured with endothelial cells and fibroblasts. JX-594 decreased YCC-32 spheroid-induced angiogenesis in a dose-dependent manner in the vascularized gastric cancer 3D co-culture model. Conclusion: JX-594 had an inhibitory effect on tumor-induced angiogenesis in our vascularized gastric cancer in vitro 3D human cell co-culture model, demonstrating the utility of the platform as a tool to interrogate the effects of an oncolytic virus on both tumor cell killing and tumor-induced angiogenesis. Citation Format: YeLin Kim, Youngsook Song, Yeongmin Choi, Jinhwan Jang, Suryong Kim, Tsung-Li Liu, Kyusuk Baek, Keunhee Oh, Seunghyun Ma, Tae Soo Kim, Woo Sun Kwon, Sanghee Yoo, Jee Hung Kim, Sun Young Rha. Vascularized gastric cancer 3D co-culture model using a microphysiological system as an oncolytic virus testing platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5396.
Abstract 572: Identifying potential therapeutic targets through gene expression analysis of peritoneal cavity cells in gastric cancer with peritoneal dissemination
Authors: Yukihiko Hiroshima, Wataru Kawase, Itaru Hashimoto, Shizune Onuma, Hayato Watanabe, Mitsuhiro Furuta, Takashi Oshima, Yohei Miyagi
Journal: Cancer Research (2024)

Abstract Background: Peritoneal dissemination (PD) is the primary mode of metastasis in gastric cancer (GC) and is strongly associated with a poor prognosis. However, the mechanisms underlying PD formation in GC remain largely unknown.Methods and Results: In this study, we collected peritoneal washings from three cytology-positive (CY1) and five cytology-negative (CY0) gastric cancer patients undergoing laparotomy. We performed RNA sequencing on cell components in the peritoneal washings and identified 13 genes that were differentially expressed and upregulated in the CY1 group. Among these genes, we focused on thrombospondin 1 (THBS1) and 2 (THBS2). We evaluated their expression levels in 317 patients with gastric or gastroesophageal junction cancer who underwent primary curative resection at the Kanagawa Cancer Center between January 2002 and December 2012. Patients were stratified into two groups based on the median expression values of these genes, and Kaplan-Meier analysis was conducted. THBS2 expression was found to be inversely associated with disease-free survival (DFS) (p = 0.041), peritoneal dissemination-specific DFS (p = 0.041), and overall survival (OS) (p = 0.041) in the study cohort. In contrast, THBS1 expression did not exhibit a significant association with any of the aforementioned outcomes.Conclusion: Our results suggest that THBS2 expression in gastric cancer tissues may serve as a useful independent prognostic factor for patients, potentially playing a crucial role in the formation of PD. Citation Format: Yukihiko Hiroshima, Wataru Kawase, Itaru Hashimoto, Shizune Onuma, Hayato Watanabe, Mitsuhiro Furuta, Takashi Oshima, Yohei Miyagi. Identifying potential therapeutic targets through gene expression analysis of peritoneal cavity cells in gastric cancer with peritoneal dissemination [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 572.