tbuckley/cabot-search huggingface dataset:
Abstract 1276: Kindlin-2: a novel target of Parkin regulating cancer metastasis
Authors: Minjeong Yeon, Irene Bertolini, Dario C. Altieri
Journal: Cancer Research (2024)

Abstract Although targeted therapies in prostate cancer have clinically shown successful outcomes, resistance to these therapies and acquisition of lineage plasticity pose challenges for fully treating prostate cancer. Among several microscopic perspectives to solve these obstacles, much evidence has emerged indicating that mitochondria dynamics are closely associated with tumor metastasis and tumor progression in various types of cancer. The E3 ubiquitin ligase Parkin is associated with PINK1-mediated mitophagy, allowing cells to control mitochondria damages and generate the needed energy to survive in harsh physiological conditions. Interestingly, we found that Parkin potentially ubiquitinates proteins independently of PINK1-associated mitophagy. By SALIC analysis, we found that K681 and K582 of Kindlin-2 is one of the potential ubiquitination sites by Parkin in prostate cancer cells. Kindlin-2 is a cytoskeletal membrane protein and is a component of the focal adhesion complex. Computational modeling suggested that N-terminal region of Kindlin-2 binds to Parkin, with K581 and K582 of Kindlin-2 exposed outside for ubiquitination. Our studies showed that Kindlin-2 is ubiquitinated and degraded by wild-type Parkin but not by the catalytic site, C431S, mutant Parkin. Furthermore, K581A and K582A mutant Kindlin-2 did not exhibit poly-ubiquitination under conditions of Parkin overexpression. Surprisingly, in our immunofluorescence study, Kindlin-2 was recruited to the mitochondria and co-localized with Parkin. From a mitochondrial functional perspective, wild-type Kindlin-2 reduced mitochondria dynamics, whereas mutant Kindlin-2 didn’t in the presence of Parkin. This suggests that the cytoskeletal protein Kindlin-2 might play a role in mitochondrial dynamics that mediates tumor metastasis. Wild-type Kindlin-2 reduced both focal adhesion generation and decay, unlike mutant Kindlin-2 under Parkin-induced condition. Additionally, this pattern was observed in the single cell lamellipodia dynamics through live cell imaging. 2D and 3D cell invasive assays supported the evidence that Parkin decreases tumor metastatic potential by ubiquitinating Kindlin-2 and regulating mitochondria and focal adhesion dynamics. Our findings indicate that Parkin reduces tumor metastatic potential by ubiquitinating Kindlin-2 and demonstrate the possibility as a therapeutic agent for advanced and immune suppressive tumors. Furthermore, Parkin could be a promising agent for Parkin suppressed tumor patients in line with personalized cancer therapy development. Citation Format: Minjeong Yeon, Irene Bertolini, Dario C. Altieri. Kindlin-2: a novel target of Parkin regulating cancer metastasis [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 1276.
Abstract 3666: Multi-cancer early detection using metrics of DNA methylation based epigenetic instability
Authors: Sara-Jayne Thursby, Zhicheng Jin, Steve B. Baylin, Malcolm Brock, Thomas Pisanic, Hariharan Easwaran
Journal: Cancer Research (2024)

Abstract Cancers present significant changes in DNA methylation, which has proven to be highly useful in cell-free DNA (cfDNA) based cancer detection. Cancer epigenomes are marked by a high degree of intra- and inter-tumor epigenetic variation, indicative of the high level of epigenetic instability. However, the nature of the regions with high epigenetic instability and its utility as biomarker has not been explored. Here we developed a novel methodology and metric to measure the degree of epigenetic perturbation, termed the Epigenetic Instability Index (EII), for multiple cancer screening through cfDNA. Our novel methodology provides a sample specific score of epigenetic perturbation in relation to the expected normal state as opposed to only looking at CpG sites that change between samples. Through machine learning, we have elucidated 269 CpG-island regions which sufficiently capture the epigenetic instability in cancers. We have built classifier models using the EII metrics of these 269 regions and demonstrate that they can efficiently identify breast and lung cancer cases from cfDNA methylation data. Particularly, the models can differentiate even Stage IA of NSCLC with ~75% sensitivity at 95% specificity and early-stage breast cancer at ~68% sensitivity and 95% specificity. The EII metrics perform significantly better than metrics that measure absolute DNA methylation levels. Our studies highlight the potential of measuring epigenetic instability from cfDNA in any given sample in addition to traditional methods of methylation measurement for non-invasive screenings via liquid biopsies. Citation Format: Sara-Jayne Thursby, Zhicheng Jin, Steve B. Baylin, Malcolm Brock, Thomas Pisanic, Hariharan Easwaran. Multi-cancer early detection using metrics of DNA methylation based epigenetic instability [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 3666.
Abstract 2296: Liquid biopsy of cerebrospinal fluid in breast to brain metastases
Authors: Stephanie N. Shishido, Amelia Marvit, Saul Priceman, Jana Portnow, Peter Kuhn
Journal: Cancer Research (2024)

Abstract Up to 30% of patients with breast cancers will develop brain metastases, and this risk is especially high with HER2-positive cancers. For patients with central nervous system metastases, cerebrospinal fluid (CSF) liquid biopsies are a promising opportunity to monitor disease, inform treatment, and predict prognosis. This study explores the CSF liquid biopsy analytes from 3 patients with central nervous system metastases analyzed with the third generation non-enrichment high-definition single cell assay (HDSCA3.0) workflow. The detection of cellular analytes was compared between the CSF and matched peripheral blood (PB) samples. Circulating tumor cells (CTCs) were detected in the CSF but not the PB and were subsequently molecularly characterized by single cell genomics and targeted multiplexed proteomics to reveal a clonal population of phenotypically heterogeneous cells. There was a lack of concordance between CTCs and cfDNA of the CSF in the copy number alteration profiles. In an extracellular vesicle surface marker analysis of the CSF, there was a high signal among tetraspanin CD9/CD63/CD81, with CD81 signal the highest across all 3 patients. The data indicates that the CSF may be used as a diagnostic or potentially prognostic tool to measure and characterize disease burden. Citation Format: Stephanie N. Shishido, Amelia Marvit, Saul Priceman, Jana Portnow, Peter Kuhn. Liquid biopsy of cerebrospinal fluid in breast to brain metastases [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 2296.
Abstract 1045: A freely expandable 20-plex immuno-oncology antibody core panel for spatial biology experiments on human FFPE cancer sections: REAplex IO Core for MICS technology
Authors: Julia Femel, Eric C. DiBasio, Katrin Schönborn, Maximilian Büttner, Tim Düking, Markus Habich, Tanya Wantenaar, Stefan Eulitz, Andreas Bosio
Journal: Cancer Research (2024)

Abstract Spatial biology is integral to understanding the dynamics of immune cells, tumor microenvironment (TME), and therapeutic responses in cancer research. Ultra-high-plex immunofluorescence has transformed deep phenotyping and cell neighborhood analysis, providing unprecedented insight into complex and heterogeneous samples such as the TME. Many spatial biology platforms reduce operator hands-on time by automating image acquisition. However, determining the most appropriate markers to distinguish key cell types, finding application-compatible antibody clones and optimizing their dilution remains a tedious manual process. To streamline the panel-building process, we have developed a series of pre-defined, commercially available antibody panels for the MACSima™ Imaging Cyclic Staining (MICS) technology. So far, these have covered the spectrum from ultra-high-plex screening panels with up to 205 antibodies (REAscreen™ MAX) to the more focused REAscreen Immuno Oncology antibody panel with 61 cancer and immune-related antibodies for the comprehensive analysis of various different human FFPE samples. Here, we introduce a new, 20-plex, pre-defined antibody panel. Organized along essential marker groups, it can function as a stand-alone panel that allows the identification of the major tumor-infiltrating leukocyte populations with a focus on T-cells, and providing insight into TME architecture, tumor neovascularization, and cellular activity. Because it can be combined and expanded with any number of antibodies or even entire panel modules, it can be used as a standardized basis for highly multiplexed custom panels optimized for the research question at hand. We demonstrate its performance and broad applicability across several cancer types analyzed with the MICS technology. Finally, preset template examples for panel-specific data processing with MACS iQ View analysis software demonstrate the simplicity yet power of an integrated end-to-end workflow. Citation Format: Julia Femel, Eric C. DiBasio, Katrin Schönborn, Maximilian Büttner, Tim Düking, Markus Habich, Tanya Wantenaar, Stefan Eulitz, Andreas Bosio. A freely expandable 20-plex immuno-oncology antibody core panel for spatial biology experiments on human FFPE cancer sections: REAplex IO Core for MICS technology [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 1045.
Abstract 1472: APOBEC-induced non-coding hotspot mutations near <i>LEPROTL1</i> contribute to the tumorigenicity of bladder cancer via deregulation of <i>LEPROTL1</i>, <i>DCTN6</i> and <i>SARAF</i>
Authors: Bilal Lone, Kelly Butler, Alexandra Dobbins, Dhanusha Yesudhas, Arup Chakraborty, Evan Hickman, Salah Boudjadi, Andrea Apolo, Rouf Banday
Journal: Cancer Research (2024)

Abstract In bladder cancer, APOBEC3 deaminases are major drivers of genomic mutagenesis, with most of these mutations occurring in synonymous or non-coding regions of the genome. The impact of these mutations on tumorigenesis has not been explored. This study aimed to investigate two non-coding hotspot mutations, likely induced by APOBEC3A near LEPROTL1—chr8: 29,952,919 G&amp;gt;A and chr8: 29,952,921 C&amp;gt;T—in bladder cancer. Using dual-luciferase reporter assays, we found that these mutations enhance both promoter and enhancer activities. Employing multi-omics approaches, including RNA-seq, ChiP-seq, and Hi-C, identified LEPROTL1, DCTN6, and SARAF as target genes co-regulated by a common enhancer where these hotspot non-coding mutations manifest. Isogenic cell lines, generated through CRISPR-mediated base editing to introduce these mutations, exhibited upregulation of target genes, and displayed oncogenic characteristics, such as increased cell growth, proliferation, invasiveness, and resistance to cisplatin. Moreover, these mutations exert their effect on cell proliferation by promoting cell cycle progression. These results suggest that recurrent non-coding somatic mutations upstream of LEPROTL1 disrupt the coregulation pattern of the three genes, thereby promoting bladder tumorigenesis. Citation Format: Bilal Lone, Kelly Butler, Alexandra Dobbins, Dhanusha Yesudhas, Arup Chakraborty, Evan Hickman, Salah Boudjadi, Andrea Apolo, Rouf Banday. APOBEC-induced non-coding hotspot mutations near LEPROTL1 contribute to the tumorigenicity of bladder cancer via deregulation of LEPROTL1, DCTN6 and SARAF [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 1472.
Abstract 4326: CDK7/CDK9 mediates transcriptional regulation to prime cancer cell paraptosis
Authors: Ling-Chu Chang, Shih-Kai Chiang, Shuen-Ei Chen
Journal: Cancer Research (2024)

Abstract The mechanisms underlying progression in cell paraptosis are largely unknown. CPYPP, cyclosporin A, and curcumin incited cytoplasmic vacuolization and induced paraptosis in breast cancer cells. The paraptotic program evolved with reactive oxygen species (ROS) provocation and overactivation of proteostatic dynamics to elicit transcriptional regulation involved in redox homeostasis and proteostasis. Pharmacological and genetic approaches suggested that cyclin-dependent kinase (CDK) 7/9 drives paraptotic progression in a reciprocally-dependent manner with heat shock proteins (HSPs). Proteostatic stress as accumulated cysteine-thiols, HSPs, ubiquitin-proteasome system, endoplasmic reticulum stress, and unfolding protein response, as well as ROS provocation primarily within the nucleus enforced CDK7/CDK9-Rpb1 (RNAPII subunit B1) activation by potentiating its interaction with HSPs and protein kinase R (PKR) in a forward loop to amplify the transcriptional regulation and thereby exacerbate proteotoxicity leading to overt paraptosis. Xenograft mouse with OECM-1 cells further confirmed the paraptotic induction against tumor growth. A novel regulatory paradigm that activation of CDK7/CDK9-Rpb1 by nuclear proteostatic stress mediates transcriptional regulation to prime cancer cell paraptosis therefore was concluded. Citation Format: Ling-Chu Chang, Shih-Kai Chiang, Shuen-Ei Chen. CDK7/CDK9 mediates transcriptional regulation to prime cancer cell paraptosis [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 4326.
Abstract 6429: Critical role of elevated TMEM176B gene expression in humanized patient-derived xenografts mouse models of triple negative breast cancer
Authors: Yujeong Her, Jihui Yun, Woohang Heo, Jong-Il Kim, Han-Byoel Lee, Wonshik Han, Hyeong-Gon Moon
Journal: Cancer Research (2024)

Abstract Objective: In the cancer research, a highly promising in vivo platform for personalized treatment involves the adoption of an advanced approach—specifically, the grafting of patient-derived xenografts (PDX) onto humanized mouse models. These models capture distinctive aspects of interaction with the human immune system and the tumor microenvironment (TME). In this study, we have engineered humanized triple-negative breast cancer (TNBC) PDX models to observe alterations in differentially expressed genes, thereby enhancing our understanding of the intricacies of personalized treatment in this context. Method: We utilized two TNBC PDX models established for the humanized models, where CD34+ hematopoietic stem cells were transplanted into immunodeficient mice. RNA sequencing was performed to identify altered gene expression in humanized PDX models compared to NSG PDXs. Additionally, we generated stable cell lines overexpressing TMEM176B in MDAMB231 and Hs578T cells, and we knocked down TMEM176B in 4T1 cells using recombinant techniques Results: In the humanized model, the growth of PDX tumors did not show a significantly faster or markedly different rate compared to previous studies. However, upon conducting RNA sequencing in the PDX model, the expression of the TMEM176B gene was consistently downregulated. Consequently, we transfected and observed that the increased expression of TMEM176B in MDAMB231 and Hs578T cell lines resulted in enhanced cell proliferation in vitro. Transplanting MDAMB231 cells overexpressing TMEM176B into athymic nude mice resulted in accelerated tumor growth. The study further investigates the expression of TMEM176B in an immune-competent environment by knocking down the gene in 4T1 cells or transplanting the control group into a balb/c mouse model. Tumors with TMEM176B knockdown exhibited inhibited growth, increased CD3+ T cell infiltration, and significant inhibition when treated with anti-PD-L1 compared to the control group. Conclusion: This research demonstrates the utility of PDX models, particularly humanized PDX models, in studying the complexities of cancer biology and the tumor microenvironment. The findings regarding TMEM176B and its role in tumorigenesis and immune responses in triple-negative breast cancer provide valuable insights for further research and potential therapeutic interventions. Citation Format: Yujeong Her, Jihui Yun, Woohang Heo, Jong-Il Kim, Han-Byoel Lee, Wonshik Han, Hyeong-Gon Moon. Critical role of elevated TMEM176B gene expression in humanized patient-derived xenografts mouse models of triple negative breast 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 6429.
Abstract 5520: β2 adrenergic receptor signaling promotes colorectal cancer liver metastasis
Authors: Yixuan Zhang, Jintian Chen, Thomas Ting Hei Chan, Huanyu Wang, Jiahuan Lu, Jingqing Li, Jingying Zhou
Journal: Cancer Research (2024)

Abstract Liver is the most common site for cancer metastases, which may be attributed to the hepatic immunosuppressive microenvironment. Recent studies have highlighted the immunomodulatory and tumor-supportive roles of neurotransmitter-receptor signals in various cancers. Given that various neurotransmitter receptors are expressed in the liver, we aimed to investigate their possible involvement in the metastatic-prone liver microenvironment. Single-cell RNA sequencing analysis identified ADRB2, which encodes β2-adrenergic receptor (β2-AR), as the top-upregulated neurotransmitter receptor gene in colorectal cancer (CRC) and liver metastasis in patients with CRC liver metastasis (CRLM). Co-immunofluorescence (co-IF) staining confirmed the colocalization of β2-AR with myeloid cell marker CD11b instead of T cell marker CD3 and NK cell marker CD56 in patients with CRLM. Consistently, we observed the upregulation of CD11b/β2-AR double-positive cells in the liver tissues from mice bearing CRC or CRLM compared to naïve mice through co-IF staining. High-dimensional flow cytometry analysis further revealed that β2-AR was mainly expressed in macrophages and myeloid-derived suppressor cells (MDSCs). Treatment of CRC-tumor bearing mice with pan β-AR inhibitor propranolol and β2-AR specific inhibitor showed a potential to reduce liver metastatic incidence without suppressing primary CRC. Mechanistically, β2-AR activation may upregulate the expression of S100a8/9 to enhance the immunosuppressive activity of macrophages and MDSCs, thereby promoting CRC liver metastasis. Taken together, our findings reveal the potential of targeting β2-AR signaling for the prevention and treatment of liver metastasis. This project is supported by the Hong Kong University Grants Committee through the General Research Fund (14104820, 14107622, 24110323) and the Strategic Seed Funding for Collaborative Research Scheme (SSFCRS) from the Chinese University of Hong Kong. Conflict of interest: The authors declare no conflict of interest. Citation Format: Yixuan Zhang, Jintian Chen, Thomas Ting Hei Chan, Huanyu Wang, Jiahuan Lu, Jingqing Li, Jingying Zhou. β2 adrenergic receptor signaling promotes colorectal cancer liver metastasis [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 5520.
Abstract 3008: Loss of Rab25 accompanied by NRAS activation cooperatively mediates the tumorigenic transformation in melanoma
Authors: Samikshya Kandel, Krishna Rao
Journal: Cancer Research (2024)

Abstract Background: Ras oncogene activation is a common and often essential event in cancer development, including melanoma. Ras mutation is present in 20-30% of melanomas and remains an undrugged target. NRAS mutation is the most frequent Ras isoform activated in melanoma, with more than 80% cases of Q61 substitutions, and is closely associated with tumor aggressiveness. Rab25 is a ubiquitously expressed small GTPase protein with a context-dependent role in cancer pathophysiology. Its role remains undiscovered in the case of melanoma. Rab25 deep deletion can be seen in portions of melanoma in databases such as the Cancer Genome Atlas and Cbioportal. Interestingly, Rab25 has a consensus sequence homologous with the binding site of Q61 mutant Ras. We propose that the loss of Rab25 in melanocytes accompanied by Ras oncogenic activation are significant events in melanoma development, and restoration of Rab25 can potentially inhibit constitutively activated N-RAS; Rab25 serves as a tumor suppressor in melanoma genesis. Objectives: To discover the role of Rab25 in melanoma, we studied Rab25 expression via mRNA and protein levels in different melanoma cell lines and screened biopsy-proven melanoma samples through immunohistochemistry in 61 different melanoma sections. Further, to see the tumor suppressive mechanism of Rab25 in vitro, we transduced selected cell lines Rab25. Results: There is an 87% and 62.7% reduction in Rab25 mRNA level in NRASQ61R(SKMEL-2) and NRASQ61L type (WM1366) melanoma cell lines, respectively, also reflected in Rab25 protein level, and statistically significant at p-value &amp;lt;0.005, using student’s T-test. Further, Rab25, prominent in adjacent normal tissues, was significantly lost in biopsy-proven melanoma tissues, with an H-score ranging from 13.28 to 91.77% and 0.00 to-11.24 % for normal skin tissue and melanoma section, respectively, and a negative correlation of -0.350, indicating a promising association of Rab25 loss with the progression of melanoma. Conclusion: There is a loss of Rab25 in NRAS mutant melanoma with cancer progression. We saw a significant increase in Rab25 expression among the transduced sublines of NRAS mutant melanoma cell lines at the mRNA level, which will be further assessed through western blotting, cell proliferation assay, trans well migration assay, soft-agar colony formation assay to confirm NRAS mutant melanoma cell behavior. We will attempt to deliver a liposomally encapsulated six-peptide sequence to therapeutically inhibit the mutant NRAS. Citation Format: Samikshya Kandel, Krishna Rao. Loss of Rab25 accompanied by NRAS activation cooperatively mediates the tumorigenic transformation in melanoma [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 3008.