bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1557: Loss of lncRNA XIST promote brain metastasis by reshaping tumor lipid metabolism via upregulation of ACSL4
Authors: Liu Yin , Smith Margaret R. , Wang Yuezhu , D’Agostino Ralph , Ruiz Jimmy , Kucera Gregory L. , Miller Lance D. , Li Wencheng , Chan Michael D. , Farris Michael , Zhao Dawen , Xing Fei
Published: March 2024

Metastatic disease is the main cause of cancer death, and the brain is one of the major sites of breast tumor metastasis. The median survival of breast cancer patients who developed brain metastases (BrM) is less than a year even with the advanced treatment such as stereotactic radiosurgery (SRS). Regardless of high clinical significance, the pathological mechanism of brain metastasis is still poorly understood. Previously, we found that loss of lncRNA XIST robustly promote metastasis and specially brain metastasis in breast cancer. However, the underlying molecular mechanism was not fully understood. In following study, we found that loss of XIST has significantly altered lipid metabolism of breast cancer cells specifically increasing lipid droplet amount and PUFA incorporation. Instead of de novo syntheses, XISTlow cancer cells acquire fatty acid by uptake from exogenous. We found that one X-linked gene, Acyl-CoA Synthetase Long Chain Family Member 4 (ACSL4) which are highly upregulated after loss of XIST is responsible for the altered lipid metabolism. ACSL4 activated the free polyunsaturated fatty acids (PUFAs) and lead to increased incorporation of PUFAs into phospholipids. On one hand, elevated ACLS4 expression leads to relative low PPAR pathway activation by decreasing the cellular free PUFA level which directly binds and activate PPAR. PPAR pathway is known to inhibit the expression of inflammatory cytokines which are important for cancer cells to establish brain metastasis. On the other hand, elevated ACSL4 expression enable cancer cells to metabolize the abundant PUFAs in the brain environment, thereby gaining survival advantage. However, increased PUFA incorporation into lipids especially phospholipids produce excess lipid ROS and sensitize cells to ferroptosis inducer such as RSL3. Our study has find out that brain microenvironment not only supports the outgrowth of XIST low cells by providing PUFAs for maintaining their metastatic properties but also sensitizes those cells to ferroptosis inducers, a potential therapy for treating this devastating disease.

Citation Format: Yin Liu, Margaret R. Smith, Yuezhu Wang, Ralph D’Agostino, Jimmy Ruiz, Gregory L. Kucera, Lance D. Miller, Wencheng Li, Michael D. Chan, Michael Farris, Dawen Zhao, Fei Xing. Loss of lncRNA XIST promote brain metastasis by reshaping tumor lipid metabolism via upregulation of ACSL4 [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 1557.
Abstract 1611: DNA methylation co-operates with genomic alterations during non-small cell lung cancer evolution
Authors: Gimeno-Valiente Francisco , Castignani Carla , Cadieux Elizabeth Cadieux L. , Mensah Nana E. , Chervova Olga , Jamal-Hanjani Mariam , McGranahan Nicholas , Beck Stephan , Demeulemeester Jonas , Tanic Miljana , Swanton Charles , Van Loo Peter , Kanu Nnennya
Published: March 2024

Aberrant DNA methylation patterns have been described in nearly all human cancers, yet their interplay with genomic alterations during tumor evolution is poorly understood. To explore this crosstalk, we performed reduced representation bisulfite sequencing on 217 tumor regions from 59 patients from the TRACERx study, all with matched adjacent normal tissue, to deconvolve tumor methylation rates. We combined two new metrics for integrative evolutionary analysis with DNA and RNA sequencing data. I-TMD (intra-tumoral methylation distance) quantifies intra-tumor DNA methylation heterogeneity. MR/MN classifies genes based on the rate of hypermethylation at regulatory (MR) versus non-regulatory (MN) CpGs, to identify driver genes exhibiting recurrent functional hypermethylation. We observed early DNA methylation of VIPR2 and ZNF714 co-occurring with driver mutations in CDKN2A and STK11, respectively. Finally, we found DNA methylation-linked dosage compensation of essential genes co-amplified with neighboring oncogenes. Our identification of hypermethylated driver genes under positive selection may open new avenues for therapeutic stratification of patients with non-small cell lung cancer.

Citation Format: Francisco Gimeno-Valiente, Carla Castignani, Elizabeth Cadieux L. Cadieux, Nana E. Mensah, Olga Chervova, Mariam Jamal-Hanjani, Nicholas McGranahan, Stephan Beck, Jonas Demeulemeester, Miljana Tanic, Charles Swanton, Peter Van Loo, Nnennya Kanu. DNA methylation co-operates with genomic alterations during non-small cell lung cancer evolution [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 1611.
Abstract 1640: The role of CDC20 in the progression of colorectal cancer
Authors: Abualsaud Nouran , Gazzaz Nada , Alhamid Amal , Alenizy Deemah , Alrfaei Bahauddeen M. , Alshehri Mana
Published: March 2024

Colorectal cancer (CRC) is the one of most common cancers and a major leading cause of cancer-related death worldwide. CDC20 is a key cell cycle regulator required during mitosis. Pathologically, CDC20 has been found to be overexpressed in cancer cells of various malignancies including breast, lung, brain and hepatic cancers and high level of CDC20 expression is associated with poor prognosis and disease progression in these cancers. Although it has been reported that CDC20 is associated with CRC progression and metastasis, it is still largely unknown how CDC20 regulates CRC cancer progression. Thus, the goal of this study is to identify the role of CDC20 in the progression of colorectal cancer. Our gene expression analysis revealed that CDC20 is highly expressed in colon cancer tissues compared to their adjacent normal colon in a cohort of CRC patients, suggesting the involvement of CDC20 in the CRC progression. To further understand the role of CDC20 in CRC progression, we experimentally targeted CDC20 genetically and pharmacologically. To perform CDC20 Loss of function studies, we screened various CRC cell lines for CDC20 protein levels and CDC20 highly expressing cell lines were utilized to establish CDC20-knockdown cells using shRNA targeting CDC20 and scrambled shRNA as controls. CDC20 Down-regulation levels were confirmed using both western blot and RT-PCR analysis. The effect of CDC20 knockdown/CRC cells on CRC cell proliferation was investigated using xCELLigence real-time cell analysis instrument and colony formation assay. Our results revealed that CDC20 knockdown CRC cells have lower proliferation capacity compared to the control, suggesting involvement of CDC20 in regulating tumorigenic phenotypes of CRC cells. Pharmacologically, we targeted CDC20 using a specific molecular inhibitor, Apcin and we assessed the Apcin treatment effect on cell viability and migration of CRC cells. Our results showed that Apcin significantly reduced CRC cell viability and migration in a dose-dependent manner. Taken together, our results suggest that CDC20 is a key regulator in the tumorigenic behavior of CRC and is considered a potential therapeutic target for treating patients with CRC.

Citation Format: Nouran Abualsaud, Nada Gazzaz, Amal Alhamid, Deemah Alenizy, Bahauddeen M. Alrfaei, Mana Alshehri. The role of CDC20 in the progression of 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 1640.
Abstract 1667: The role of CCN1 in mutant K-RAS addiction in pancreatic cancer
Authors: Kambhampati Anjali , De Archana , Haque Inamul , Banerjee Snigdha , Banerjee Sushanta K.
Published: March 2024

Mutant K-RAS addiction of pancreatic ductal adenocarcinoma cells (PDAC) coordinates their transformation, proliferation, and survival. Therefore, initially, it had an impression that targeting mutant K-RAS could be an ideal strategy to treat PDAC. However, after decades of studies, no effective RAS inhibitors reached the clinic, indicating that RAS-oncoprotein is an undruggable target in PDAC. Thus, identifying a new target linked with K-RAS signaling was most needed. Using genetically engineered cell lines and K-RAS-driven genetically engineered mouse models (KC or KPC) with or without pancreas-specific CCN1 conditional knockout background, we identified a positive feedback circuit between CCN1 and mutant K-RAS expression. Moreover, blocking this feedback via conditional knockout of CCN1 in the pancreas significantly reduced invasive phenotypes, PDAC growth, and metastasis in the lung in KC and KPC mice. Mechanistically, we found that the K-RAS-CCN1 feedback circuit is regulated by microRNA miR-145 via a feedforward mechanism. Collectively, these studies highlight the clinical potential of targeting CCN1 in PDAC. (VA Merit Grant supports this work)

Citation Format: Anjali Kambhampati, Archana De, Inamul Haque, Snigdha Banerjee, Sushanta K. Banerjee. The role of CCN1 in mutant K-RAS addiction in pancreatic 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 1667.
Abstract 1673: KRAS dependency, a gene editing approach
Authors: Marcireau Christophe , Lacroix Fréderic , Hoffmann Dietmar , Cindhuchao May , Calvet Loreley , Ruffin Yvette , Debussche Laurent
Published: March 2024

The RAS family genes encode small GTP-binding cytoplasmic proteins that are important signaling molecules. They regulate cell growth, survival and differentiation by coupling receptor activation to downstream effector pathways. Activating mutations of oncogenic RAS pathway genes are frequently detected in human cancers. The role of KRAS in tumor formation is not questionable. It’s implication in tumor maintenance is less well validated. The KRAS dependency is a key question to answer before to develop KRAS inhibitor. Targeted genome editing using CRISPR/Cas9 is a relatively new, revolutionary technology allowing for efficient and directed alterations of the genome. CRISPR is a genome-editing platform that makes use of the bacterially-derived endonuclease Cas9 to introduce DNA double-strand breaks at precise locations in the genome using complementary guide RNAs. These double strand breaks can be repaired by homologous recombination DNA repair mechanisms thank to a donor DNA template. By this way mutations can be introduced at desired loci, DNA fragment can be deleted or introduce at the desired location. We aimed at investigating the KRAS dependence and we applied the CRISPR-Cas9 technology to engineer isogenic cancer cells harboring a “conditional KRAS gene knockout" by exchanging the KRAS endogenous promoter. This promoter replacement approach can be used also to validate new targets.

Citation Format: Christophe Marcireau, Fréderic Lacroix, Dietmar Hoffmann, May Cindhuchao, Loreley Calvet, Yvette Ruffin, Laurent Debussche. KRAS dependency, a gene editing approach [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 1673.
Abstract 1697: Phase separation of BHLHE40 up-regulates SREBF1 and inhibits ferroptosis in pancreatic cancer cells
Authors: Cao Yizhi , Wang Xuelong , Liu Yang , Liu Pengyi , Qin Jiejie , Zhu Youwei , Zhai Shuyu , Shi Minmin , Wang Weishen , Deng Xiaxing , Peng Chenghong , Chen Hao , Ren Ruibao , Jiang Lingxi , Shen Baiyong
Published: March 2024

Pancreatic cancer (PCa) is one of the most lethal malignancies in human cancers. The enhanced infiltration of stromal tissue of PCa tumor microenvironment limits the identification of key tumor-specific transcription factors and epigenomic abnormalities in malignant epithelial cells. Integrated transcriptome and epigenetic multi-omics analysis of paired PCa organoids indicated that the basic helix-loop-helix transcription factor 40 (BHLHE40) was significantly upregulated in tumor samples. Increased chromatin accessibility at promoter region and enhanced mTOR pathway activity contribute to the elevated expression of BHLHE40. Integrated analysis of chromatin immunoprecipitation (ChIP)-seq, RNA-seq and high-through chromosome conformation capture (Hi-C) data together with chromosome conformation capture (3C) assay indicate that BHLHE40 not only regulates the sterol regulatory element-binding factor 1 (SREBF1) transcription as a classic transcription factor, but also links the enhancer and promoter regions of SREBF1 via forming liquid-liquid phase-separated droplets. Then, we find the BHLHE40-SREBF1-stearoyl-CoA desaturase (SCD1) axis protects PCa cells from ferroptosis, leading to the reduced accumulation of lipid peroxidation in cells. Moreover, SREBF1 inhibitor, Fatostatin, significantly suppresses the cell growth of PCa tumors with higher expression of BHLHE40. This study highlights the important roles of BHLHE40 mediated lipid peroxidation in inducing ferroptosis of PCa cells and provides a novel mechanism underlying the SREBF1 overexpression in PCa.

Citation Format: Yizhi Cao, Xuelong Wang, Yang Liu, Pengyi Liu, Jiejie Qin, Youwei Zhu, Shuyu Zhai, Minmin Shi, Weishen Wang, Xiaxing Deng, Chenghong Peng, Hao Chen, Ruibao Ren, Lingxi Jiang, Baiyong Shen. Phase separation of BHLHE40 up-regulates SREBF1 and inhibits ferroptosis in 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 1697.
Abstract 1701: ABI1 regulates prostate tumor plasticity through chromatin remodeling and transcriptional regulation
Authors: Kotula Leszek
Published: March 2024

Background: Prostate cancer remains a challenging issue affecting men worldwide. In contrast to localized disease, metastatic prostate cancer tumor is incurable. Progression to metastatic disease is characterized by tumor heterogeneity and plasticity regulated by epigenetic changes of tumor cells. While tumor heterogeneity is often associated with gene mutations, tumor plasticity is ascribed to transcriptional regulation and chromatin activity. The latter is modulated by treatment of prostate cancer leading to treatment resistance. Here, we identified a novel mechanism of epigenetic regulation in prostate cancer by an actin regulatory and signaling protein, Abelson Interactor 1 (ABI1).

Methods: To demonstrate the ABI1-DNA binding, we employed in vitro binding assays, NMR spectroscopy, and ChIP-seq. from cells expressing alternatively spliced isoforms of ABI1 that contain or lack the DNA binding HHR domain. To determine the ABI1 interactions with several transcriptional factors, we used immunoprecipitation and/or proximity ligation assay (PLA). We used ATAC sequencing to determine the chromatin accessibility in the presence or absence of ABI1 gene. RNA-seq established the activity of transcriptional factors and signaling pathways regulated by ABI1.

Results: Using NMR spectroscopy, we established that ABI1 demonstrated DNA binding dependent on the presence of alternatively spliced Exon 4. Exon 4 is located within the homeobox homology region (HHR). The DNA binding activity was confirmed using in vitro binding assays; the assay results confirmed the role of ABI1 HHR. Moreover, cells lacking ABI1 or expressing ABI1 lacking Exon 4 show low accessibility and activity of chromatin. In contrast, cells expressing ABI1 containing Exon 4 show active chromatin. RNA-seq analysis demonstrated that ABI1 regulated transcription in an Exon 4-dependent manner.

Conclusions: We uncovered a role of ABI1 in chromatin stability, that is dependent on the presence of the DNA binding region. Notably, ABI1's contribution to transcriptional activity occurs via a transient yet precisely defined interaction between its intrinsically disordered region and DNA. This regulatory control plays a pivotal role in managing tumor plasticity by establishing connections between the actin cytoskeleton, cellular signaling, and transcriptional regulation. Based on these findings, we propose that ABI1 functions as an epigenetic regulator, maintaining transcriptional homeostasis in prostate cancer.

Citation Format: Leszek Kotula. ABI1 regulates prostate tumor plasticity through chromatin remodeling and transcriptional regulation [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 1701.
Abstract 1717: RAS and PP2A co-regulated phosphosite on KDM1A dictates its substrate specificity & transcriptional outcome
Authors: Sharma Mukund , Aakula Anna , Kamila Jesse , Nätkin Reetta , Bonaldi Tiziana , Minucci Saverio , Nykter Matti , Westermarck Jukka
Published: March 2024

RAS-mediated human cell transformation requires simultaneous inhibition of tumor suppressor phosphatase PP2A; however, the target phosphosites co-regulated by RAS and PP2A are poorly characterized. In this study, we describe the phosphoregulation of an epigenetic regulator, KDM1A, by RAS and PP2A. KDM1A is a lysine-specific demethylase that can act as a transcriptional activator or inhibitor, depending on its specific activity toward various histone marks. However, the post-translational modifications regulating the substrate specificity of KDM1A are poorly addressed. We found that KDM1A physically interacts with PP2A through a conserved binding motif, and that mutating the motif residues decreased its interaction with PP2A. Additionally, PP2A activation or RAS inhibition led to increased chromatin recruitment of KDM1A. This enhanced chromatin recruitment of KDM1A was recapitulated upon CRISPR/CAS9-mediated substitution of the PP2A/RAS-targeted serine to alanine. Using histone proteomics, we further identified that the RAS/PP2A-regulated phosphosite determines the substrate specificity of KDM1A. This is evidenced by an increased demethylation of histone H3K9me2/3, a marker of gene activation. The differential gene expression profile of the phosphorylation mutants of KDM1A predominantly showed increased gene expression, further validating our findings. The gene expression profiles of KDM1A phosphomutant RAS mutant cells demonstrate gene level specificity indicating that this newly discovered KDM1A phosphoswitch has an important role in specifying KDM1A function in cancer. Collectively, our results demonstrate that RAS and PP2A activities converge on phosphoregulation of epigenetic machinery in cancer cells. This RAS and PP2A co-regulated phosphosite on KDM1A dictates both its histone mark specificity and transcriptional outcome.

Citation Format: Mukund Sharma, Anna Aakula, Jesse Kamila, Reetta Nätkin, Tiziana Bonaldi, Saverio Minucci, Matti Nykter, Jukka Westermarck. RAS and PP2A co-regulated phosphosite on KDM1A dictates its substrate specificity & transcriptional outcome [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 1717.
Abstract 1738: Precise detection of benign and malignant renal tumor via epigenetic characteristics of urinary cell-free DNA
Authors: Kong Wen , Dong Hang , Tang Haoran , Du Pan , Jia Shidong , Zhang Jin
Published: March 2024

Early detection of clear cell renal cell carcinoma (ccRCC) and accurate differentiation between malignant and benign lesions pose clinical challenges. Profiling the epigenetic pattern of patients through liquid biopsy offers a promising strategy for non-invasive cancer identification. This study utilizes the methylation characteristics of urinary cell-free DNA to enhance the precise diagnosis of ccRCC. In this study, 32 patients with malignant RCC, 20 patients with benign kidney lesions, and 28 age- and sex-matched healthy donors were enrolled. Urine samples were collected and applied by PredicineEPIC assay to analyze the whole genome methylation profiles. We assessed the methylation differences on cancer-specific altered regions and constructed a machine learning model for malignant and benign classification. Beta values were calculated for differentially methylated regions identified through literature mining and our current work. These features carry methylation signals that are recognized by gradient boosting machine and used for classification training. The leave-one-out cross-validation method compensated for the shotage of sample size. The sensitivity and specificity of the optimal model in the training set are both greater than 0.97, and it can achieve an accuracy of 0.95 on the validation set. This performance surpasses traditional diagnostic methods such as contrast-enhanced CT and MRI. This study demonstrated the technical feasibility of leveraging epigenetics profiles to discriminate malignant from benign lesions, suggesting a promising liquid biopsy-based approach for the precise detection of renal cell carcinoma.

Citation Format: Wen Kong, Hang Dong, Haoran Tang, Pan Du, Shidong Jia, Jin Zhang. Precise detection of benign and malignant renal tumor via epigenetic characteristics of urinary cell-free DNA [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 1738.
Abstract 1741: AlidaBio EpiPlex: A platform for multiplexed detection of RNA modifications in clinical samples
Authors: Price Andrew , Miles Zachary , Chevillet John , Purse Byron , Gregory Richard I. , Stengel Gudrun
Published: March 2024

It is becoming increasingly appreciated that RNA modifications are widespread in development and homeostasis, regulating RNA stability and translation, and that alterations to these modifications are associated with cancer development and progression. Although 170 different RNA modifications have been identified using mass spectrometry, there is a paucity of convenient, validated tools immediately available to cancer researchers to explore these modifications using relevant clinical samples in sufficient numbers, and accurately determine their suitability for use as diagnostic or drug targets. In addition, most existing methods concentrate only on m6A, the most prevalent modification in mRNA. Alida Bio has developed an end-to-end assay platform with an integrated bioinformatics solution that detects multiple modifications in the same reaction. This platform exploits targeted, multiplexed barcoding to reveal the quantitative abundance of modified transcripts, co-localization of multiple RNA modifications to the same gene, and gene expression profiles. Alida Bio's mission is to equip translational researchers with tools that will significantly improve their understanding of gene regulation through seamless measurement of RNA modifications.

Citation Format: Andrew Price, Zachary Miles, John Chevillet, Byron Purse, Richard I. Gregory, Gudrun Stengel. AlidaBio EpiPlex: A platform for multiplexed detection of RNA modifications in clinical samples [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 1741.
Abstract 1748: Dearth of smoking-induced mutations in oncogene-driven NSCLCs despite smoking exposure
Authors: Huang Chen-Yang , Jiang Nanhai , Shen Meixin , Lai Gillianne , Tan Aaron C. , Jain Amit , Saw Stephanie P. , Ang Mei-Kim , Ng Quan Sing , Lim Darren Wan-Teck , Kanesvaran Ravindran , Tan Eng-Huat , Tan Wan Ling , Ong Boon-Hean , Chua Kevin L. , Anantham Devanand , Takano Angela , Lim Tony KH , Tam Wai Leong , Sim Ngak Leng , Skanderup Anders J. , Tan Daniel S.W. , Rozen Steven G.
Published: March 2024

Non-small cell lung cancers (NSCLCs) in non-smokers are mostly driven by mutations in the oncogenes EGFR, ERBB2, and MET, and fusions involving ALK and RET. We term these “non-smoking-related oncogenes” (NSROs). NSRO-driven tumors account for approximately half of NSCLCs in East Asia, and, alarmingly, their age-adjusted incidence is increasing for unknown reasons. In addition to occurring in non-smokers, NSRO-driven tumors also occur in smokers. However, the clonal architecture and genomic landscape of these tumors remain largely unexplored. Here, we investigated genomic and transcriptomic alterations in 173 tumor sectors from 48 patients with NSRO-driven or typical-smoking NSCLCs. Overall, NSRO-driven NSCLCs in smokers and non-smokers had similar genomic landscapes and clonal architectures that were distinct from those in typical-smoking NSCLCs. Surprisingly, even in patients with prominent smoking histories, the mutational signature caused by tobacco smoking was essentially absent in NSRO-driven NSCLCs. We confirmed this unexpected finding in two large NSCLC data sets from other geographic regions. However, we observed differences in the tumor transcriptomes of NSRO-driven NSCLCs in smokers and non-smokers, with tumors in smokers displaying higher transcriptomic activities related to regulation of the cell cycle. This suggested that smoking does have an impact on tumor phenotype in NSCRO-driven NSCLC, likely through non-genetic mechanisms. We concluded that NSRO-driven NSCLCs, whether in non-smokers or smokers, constitute an important disease entity that is very different from typical-smoking NSCLC.

Citation Format: Chen-Yang Huang, Nanhai Jiang, Meixin Shen, Gillianne Lai, Aaron C. Tan, Amit Jain, Stephanie P. Saw, Mei-Kim Ang, Quan Sing Ng, Darren Wan-Teck Lim, Ravindran Kanesvaran, Eng-Huat Tan, Wan Ling Tan, Boon-Hean Ong, Kevin L. Chua, Devanand Anantham, Angela Takano, Tony KH Lim, Wai Leong Tam, Ngak Leng Sim, Anders J. Skanderup, Daniel S.W. Tan, Steven G. Rozen. Dearth of smoking-induced mutations in oncogene-driven NSCLCs despite smoking exposure [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 1748.
Abstract 1765: The genetic landscape of head and neck cancer using brush biopsy
Authors: John Evit , Lesluyes Tom , Baker Toby , Tarabichi Maxime , Van Loo Peter , Zhao Xiao
Published: March 2024

Oral premalignant lesions (OPLs) with genomic alterations have a heightened risk of evolving into oral squamous cell carcinoma (OSCC). Currently, genomic data are obtained through invasive tissue biopsy. Brush biopsy has been utilized for diagnosing dysplasia but its effectiveness in reflecting the complete genomic landscape of OPLs remains uncertain. This study investigates the potential of brush biopsy samples in accurately reconstructing the genomic profile of OPLs. The evolution and heterogeneity were assessed by assessing SNVs, copy number analysis, and subclonal architecture reconstruction of paired tissue-brush biopsy samples of oral epithelium, dysplastic lesion, and OSCC lesion. We found that brush biopsy accurately reflects the genomic landscape of oral lesions, mirroring about 90% of SNVs and comparable CNA profiles found in tissue biopsies. Genomic profiling with brush biopsy was tissue-specific, as SNVs identified in OPL or OSCC lesions were not found in adjacent normal mucosa. Shared SNVs and CNAs were observed between OPL and OSCC samples. This suggested a common ancestor giving rise to these lesions. Subclonal architecture reconstruction confirmed that both lesion types shared a common ancestor clone and then diverged evolutionarily. These findings underscore the potential of brush biopsies in accurately reconstructing the genomic profile of OPL and OSCC, highlighting their usefulness in understanding the biological processes involved in tumor evolution.

Citation Format: Evit John, Tom Lesluyes, Toby Baker, Maxime Tarabichi, Peter Van Loo, Xiao Zhao. The genetic landscape of head and neck cancer using brush biopsy [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 1765.
Abstract 1818: Novel efficient isolation and water-soluble prodrug preparation of anti-cancer natural product narciclasine
Authors: Kornienko Alexander , Rutledge Ryan
Published: March 2024

Narciclasine is a promising anti-cancer agent produced by plants of the family Amaryllidaceae. Narciclasine has been shown to be a potent anti-cancer agent against a variety of cancers carrying dismal outcomes, including glioblastoma, non-small cell lung cancer, and non-Hodgkin’s lymphoma. It is particularly effective in animal studies of brain cancer both primary, such as glioblastoma, metastatic tumors to the brain, such as melanoma and non-small cell lung cancer. Its isolation from plants has generally been accompanied with variable success as it depends on the plant species, their location and the time of plant collection. In this study, an optimized procedure for the extraction of narciclasine yielding 300 mg/kg of dried plant material. This represents a crucial step towards the development of optimized narciclasine derivatives, as the price of narciclasine from commercial sources ranges from $100-$500 per milligram. Additionally, clinical advancement of narciclasine and its derivatives has been severely thwarted, potentially owing to its sparing water-solubility. Insolubility in water makes administration at therapeutic dosages difficult and can lead to unfavorable pharmacokinetic and pharmacodynamic characteristics. To this effort, the synthesis of five prodrug esters of narciclasine is presented, with the target of a water-soluble narciclasine prodrug.

Citation Format: Alexander Kornienko, Ryan Rutledge. Novel efficient isolation and water-soluble prodrug preparation of anti-cancer natural product narciclasine [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 1818.
Abstract 1839: Proteomic and glycoproteomic differences associated with prostate cancer in urine
Authors: Shamsher Nikhiya , Garcia-Marques Fernando , Bermudez Abel , Flory Mark R. , Pitteri Sharon J.
Published: March 2024

Background and Aims: Prostate cancer is one of the most common cancers affecting men in the United States, with ~288,300 new cases and 34,700 deaths in 2023 alone. Prostate-specific antigen (PSA), the most widely used prostate cancer biomarker, lacks specificity and sensitivity, leading to unnecessary biopsies, overdiagnosis, and overtreatment. There is an urgent unmet clinical need to find new biomarkers that can distinguish patients with benign disease from those with prostate cancer. Urine is an attractive source for these biomarkers as prostate-derived proteins are more highly concentrated in urine than in blood. To better understand both global proteomic and glycoproteomic molecular signatures that could lead to improved diagnostics for prostate cancer, we analyzed urine samples from unaffected men, men with benign prostatic hyperplasia (BPH), and men with prostate cancer.

Methods: Urine samples (N = 58 total) were collected from unaffected men (N = 17), men with BPH (N = 24), and men with prostate cancer (N = 17). Samples were digested with trypsin and analyzed with high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS) for shotgun proteomics analysis. Association with cancer was determined through supervised analysis using Pearson correlation. For glycoproteomics analysis, intact glycopeptides were enriched using strong anion exchange-electrostatic repulsion hydrophilic interaction chromatography, fractionated using high pH reversed-phase chromatography, and analyzed with LC-MS/MS. Association with the three conditions was determined through several rounds of supervised analysis using Pearson correlation.

Results: In total, 3542 human proteins were identified, and 78 proteins (p < 0.01) were significantly associated with prostate cancer. The glycolysis pathway and lysosome pathway were enriched in samples from men with prostate cancer. In the glycoproteomics analysis, 36 proteins (p < 0.05) had altered glycan diversity in one of the three conditions, and the complement and coagulation cascade pathway and the lysosome pathway were highly enriched. Six proteins (p < 0.05) had significantly increased glycan diversity in the cancerous samples than in the BPH and normal samples.

Conclusions: This study identifies a set of interesting proteomic and glycoproteomic differences in urine from men with prostate cancer compared to BPH and non-cancer samples, which warrant further investigation in additional sample cohorts as potential novel biomarkers.

Citation Format: Nikhiya Shamsher, Fernando Garcia-Marques, Abel Bermudez, Mark R. Flory, Sharon J. Pitteri. Proteomic and glycoproteomic differences associated with prostate cancer in urine [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 1839.
Abstract 1846: Integrative histopathologic, proteomic, phosphoproteomic, genomic, and transcriptomic characterization of renal cell carcinoma
Authors: Kwon Woo Sun , Kim Chang Gon , Koo Harim , Bae Woo Kyun , Hwang Eu Chang , Ham Won Sik , Cho Nam Hoon , Sa Jason K. , Park Jong Bae , Rha Sun Young
Published: March 2024

Although histologically defined subtypes exist, renal cell carcinoma (RCC) is a heterogenous disease, resulting in various treatment outcomes and prognosis. Here, we conduct comprehensive profiling of RCC with histopathologic, proteomic, phosphoproteomic, genomic, and transcriptomic analyses on tumor and paired adjacent normal tissues from 113 patients. RCC tumors are distinctly separated from corresponding normal tissues through multi-omics clustering, a distinction further supported by pathway analysis. In addition, various hallmarks of cancer were differentially observed at the individual patient level, highlighting the intertumoral heterogeneity of RCC. Proteomic subtyping classifies RCC tumors into four subtypes (C1-4) with distinct phosphoproteomic, genomic, and transcriptomic characteristics with prognostic and predictive implications. Among these subtypes, C1-3 were almost composed of clear cell RCC (ccRCC; 96.8%), whereas C4 was composed of non-clear cell RCC (nccRCC) or other types of cancer (100.0%). Among each subtype, C1 (N=37) exhibits the strongest adaptive immune response and angiogenesis with favorable prognosis after surgical resection. C2 (N=39) was characterized with enrichment in DNA repair pathways and alteration in VHL (100.0%) along with BAP1 (24.0%) genes. C3 (N=19) was associated with enrichment in inflammatory response with dismal prognosis and therapeutic resistance to tyrosine kinase inhibitors targeting vascular endothelial growth factor receptors. C4 (N=18) was exclusively enriched with nccRCC with active mitochondrial and oxidation phosphorylation. Transglutaminase 2 (TGM2), a crosslinking enzyme, is identified as a potential marker with therapeutic implication for ccRCC. Collectively, this study reports a large-scale multi-omics-based approach of RCC, providing insights into biologic underpinning and evidence for rational treatment selection as well as linking the multi-omics-derived phenotypes to clinical outcomes of ccRCC.

Citation Format: Woo Sun Kwon, Chang Gon Kim, Harim Koo, Woo Kyun Bae, Eu Chang Hwang, Won Sik Ham, Nam Hoon Cho, Jason K. Sa, Jong Bae Park, Sun Young Rha. Integrative histopathologic, proteomic, phosphoproteomic, genomic, and transcriptomic characterization of renal cell carcinoma [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 1846.
Abstract 1863: α-ABN501, a novel antibody targeting claudin-3, demonstrates the potential to be a new therapeutic option for small cell lung cancer
Authors: Choi Jae , Hong Sunghyun , Park Ha Yeon , Kim Jaemun , Lee Sangin , Seo Myeung-Ryun , Bang Sang-Beom , Shin Hyo-Jin , Jeong Kwang-il , Yang Hobin , Hong Sungyoul , Choi Jun Young , Kim Na Young , Shin Young Kee , Lee Saehyung
Published: March 2024

Small Cell Lung Cancer (SCLC) is the most aggressive and lethal type of lung cancer, characterized by a poor prognosis, with a 5-year survival rate of only 7% for overall SCLC patients. Limited treatment options such as chemotherapy and immune-checkpoint inhibitor therapy are available for SCLC patients, very often followed by rapid recurrence and metastasis. Thus, new effective treatment options for SCLC remain high unmet medical needs. Overexpression of claudin-3 (CLDN3), one of the tight junction proteins, is observed in various types of cancers. The abnormal conformation of tumor cell growth leads to the external exposure of CLDN3, in contrast, the normal cells that maintain high polarity do not expose CLDN3 externally. Therefore, CLDN3 could be a potential therapeutic target and biomarker. Based on the analysis of the expression pattern of CLDN3 using a single-cell RNA sequencing dataset derived from SCLC patients, we found that CLDN3 could be a superior and unique target of SCLC compared to others (e.g., DLL3 and B7H3). Hence, we developed a fully human monoclonal antibody, afucosylated ABN501 (α-ABN501), which has high specificity and strong affinity to CLDN3-expressing cells. The α-ABN501 antibody showed CLDN3-dependent killing effects against the SCLC cells, expressing different levels of CLDN3, as assessed via the antibody-dependent cellular cytotoxicity (ADCC) assay wherein using NK cells expressing CD16a (NK-92MI-CD16a), peripheral blood mononuclear cells (PBMC), and primary NK cells. Further, the efficacy study in the CLDN3-expressing SCLC cell derived xenograft mouse model revealed that α-ABN501 was highly efficacious in inhibition of tumor growth. Collectively, we elucidated that the ADCC activity of α-ABN501 was dependent on the expression level of CLDN3 and especially specific to the SCLC cells, which underlines significant suppression of tumor growth. Present study data sets suggest that the α-ABN501 can be a potential new therapeutic option for SCLC. In addition, the α-ABN501 antibody is currently under way of development into new drug platforms for further applications.

Citation Format: Jae Choi, Sunghyun Hong, Ha Yeon Park, Jaemun Kim, Sangin Lee, Myeung-Ryun Seo, Sang-Beom Bang, Hyo-Jin Shin, Kwang-il Jeong, Hobin Yang, Sungyoul Hong, Jun Young Choi, Na Young Kim, Young Kee Shin, Saehyung Lee. α-ABN501, a novel antibody targeting claudin-3, demonstrates the potential to be a new therapeutic option for small cell lung 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 1863.
Abstract 1876: Development of therapeutic antibodies targeting the GLUT-1 transporter to restrict cancer cell growth
Authors: Tahk Siret , Virumae Kai , Anton Korneelia , Hermet Paule , Pau Robin , Plaas Mario , Abel Maiken , Belitškin Denis , Galdieri Luciano , Garner Steven , Krings Jillian , Collver Kaleb , Schultz Emily , Powers Kaitlyne , King Alastair , Neethling Francisca , Planken Anu , Ustav Mart , Terya Joan , Mannik Andres , Ustav Mart
Published: March 2024

Background: Upregulated glucose metabolism is one of the strategies cancer cells use to fuel their abnormal cell growth and division. Targeting the cancer-specific glucose transporter GLUT-1 is a promising approach to restrict glucose uptake and challenge the metabolic needs of tumor cells. Antibodies, as opposed to small molecule inhibitors, are an attractive modality to therapeutically target complex muti-pass membrane transporters. Here we report the development of antibodies that very specifically block the function of only GLUT-1.

Methods: Monoclonal antibodies against GLUT-1 were generated using virus-like particles. For immunization, chickens were used as they are evolutionarily distant from mammals and can produce antibodies with prolonged CDR3-s in VH, which could facilitate their binding to the limited extracellular region of GLUT-1. Antibody discovery was performed with HybriFree B cell cloning technology followed by functional screens with 2-deoxyglucose uptake interference or cell proliferation measurements.

Results: The discovered antibodies specifically bind to GLUT-1 with low nanomolar EC50 values and do not target other glucose transporters. The lead candidate, ICO-33, inhibits glucose uptake and rewires the metabolism of GLUT-1-dependent cancer cells to rely on oxidative phosphorylation. This results in a significantly synergistic cancer proliferation inhibition with ICO-33 and OXPHOS inhibitor combinations in doses that do not inhibit proliferation as single agents. ICO-33 and OXPHOS inhibitor treatment is well-tolerated and demonstrates a drastic tumor growth inhibition in in vivo colorectal and pancreatic cancer models.

Conclusions: We describe the discovery of highly specific monoclonal antibodies targeting GLUT-1. We further demonstrate that the restriction of the much-needed glucose uptake by ICO-33 makes cancer cells highly susceptible to OXPHOS inhibitor co-therapy both in vitro and in vivo, validating the antibody as a promising candidate for clinical development.

Citation Format: Siret Tahk, Kai Virumae, Korneelia Anton, Paule Hermet, Robin Pau, Mario Plaas, Maiken Abel, Denis Belitškin, Luciano Galdieri, Steven Garner, Jillian Krings, Kaleb Collver, Emily Schultz, Kaitlyne Powers, Alastair King, Francisca Neethling, Anu Planken, Mart Ustav, Joan Terya, Andres Mannik, Mart Ustav. Development of therapeutic antibodies targeting the GLUT-1 transporter to restrict cancer cell growth [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 1876.
Abstract 1885: Developing a biparatopic anti-ROR1 antibody drug conjugate BR111 for hematological and solid tumor treatment
Authors: Zhao Xiaobei , Zhu Jie , Wu zhenhua , Li Yiqun , Li Jing , Zhou Yaqiong , Nie Lei , Wang Haibin , Chen Gang
Published: March 2024

ROR1 is a type I transmembrane protein that belongs to the ROR family. It is a receptor for Wnt family signaling molecules Wnt5a, and plays a critical role in various cellular processes, such as cell proliferation, survival, and migration. Being an oncofetal protein, ROR1 exhibits limited expression in most normal tissues. However, it is abnormally expressed in various hematological and solid cancers, contributing to the development and progression of many types of cancer. Due to its overexpression in cancer, ROR1 presents as a highly attractive target for antibody-drug conjugate (ADC) therapy. The current clinical results of ROR1 ADCs have been promising in treating patients with relapsed and/or refractory (R/R) hematologic malignancies.

BR111 is anti-ROR1 ADC that consists of a biparatopic antibody, stably conjugated to an antimitotic agent. The biparatopic antibodies demonstrate superior binding affinity to ROR1-expressing cancer cells compared to single epitope antibodies. Notably, our unique and innovative conjugation platform CysX™, not only prevents payload detachment during circulation and reducing the off-target toxicity, but also enables a uniformed drug-to-antibody ratio (DAR) of 4.

Both in vitro and In vivo studies have highlighted the remarkable antitumor activity of BR111. Preclinical data have shown great safety profile in cynomolgus monkeys. BR111 demonstrated a wider therapeutic window for cancer treatment, outperforming the lead anti-ROR1 ADC currently in phase II/IIl trial. The promising outcome holds great potential as a therapeutic treatment for hematological and solid cancers, offering a better safety profile. BR111 has great potential in further clinical evaluations.

Citation Format: Xiaobei Zhao, Jie Zhu, zhenhua Wu, Yiqun Li, Jing Li, Yaqiong Zhou, Lei Nie, Haibin Wang, Gang Chen. Developing a biparatopic anti-ROR1 antibody drug conjugate BR111 for hematological and solid tumor treatment [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 1885.
Abstract 1901: Disitamab vedotin, a clinical stage HER2-directed antibody-drug conjugate, shows potent antitumor activity as a monotherapy in preclinical urothelial cancer models
Authors: Hein Renee , Willis Kelsi , LoMastro Gina , Vasaikar Suhas , Gupta Vinita , Snead Katie , Sandall Sharsti , Kulukian Anita
Published: March 2024

Disitamab vedotin (DV, RC48-ADC) is an antibody-drug conjugate (ADC) that selectively delivers cytotoxic drug to HER2-expressing cancer cells. DV is composed of disitamab, a HER2-directed monoclonal antibody, and a vedotin linker-payload system, which enables conjugation of the microtubule-disrupting agent monomethyl auristatin E (MMAE) to the antibody via a protease-cleavable linker. The proposed mechanism of action (MOA) of DV occurs through direct cytotoxicity of HER2-expressing tumor cells following internalization of DV and intracellular release of MMAE. DV may also induce antitumor activity through bystander-mediated cytotoxicity of neighboring cells and via the inhibition of HER2 signaling pathways. Moreover, cellular response to MMAE includes the induction of immunogenic cell death and recruitment of immune cells to the tumor site. DV is currently being evaluated globally in subjects with HER2-expressing locally advanced or metastatic urothelial carcinoma (la/mUC) and has gained conditional approval in China following an overall response rate of 50.5% (pooled analysis from studies NCT03507166 and NCT03809013). RNA sequencing data from a large cohort of urothelial cancer patient tumors revealed expression of HER2 in many urothelial tumors; however, the relationship between HER2 expression and efficacy of DV is not well understood. Here, we sought to evaluate the antitumor activity of DV monotherapy in preclinical urothelial cancer models with varying levels of HER2 expression. Multiple patient-derived xenografts (PDX) and patient-derived 3D in vitro urothelial cancer models showed potent antitumor response to DV monotherapy in tumors with varying HER2 expression levels including HER2-low tumors. Overall, these findings support ongoing clinical trials in subjects with HER2-expressing la/mUC and provide scientific rationale to further explore DV monotherapy in HER2-positive and HER2-low urothelial cancer clinical settings.

Citation Format: Renee Hein, Kelsi Willis, Gina LoMastro, Suhas Vasaikar, Vinita Gupta, Katie Snead, Sharsti Sandall, Anita Kulukian. Disitamab vedotin, a clinical stage HER2-directed antibody-drug conjugate, shows potent antitumor activity as a monotherapy in preclinical urothelial cancer models [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 1901.