bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4527: TNG348 is synergistic with PARP inhibitors in tumor models with elevated replication stress
Authors: Simoneau Antoine , Wu Hsin-Jung , Pratt Charlotte , Comer Grace , Liu Shangtao , Meier Samuel , Khendu Tenzing , Choi Ashley , Zhang Hongxiang , Shen Binzhang , Whittington Douglas , Sudsakorn Sirimas , Zhang Wenhai , Yu Yi , Chen Yingnan , Haines Brian , Crystal Adam , Andersen Jannik N. , Maxwell John , Throner Scott
Published: March 2024

Defective maintenance of genomic integrity is a hallmark of cancer cells that can result from oncogene-induced replication stress and by loss of DNA repair mechanisms. DNA repair deficiencies and elevated replication stress present targetable vulnerabilities for cancer treatment. Notably, BRCA1/2 mutant and homologous recombination deficient (HRD) tumors cannot repair double-strand breaks by homologous recombination and rely on alternative pathways of DNA repair. PARP inhibitors (PARPi), which are a standard of care in many BRCA1/2 mutant tumors, cause synthetic lethality with BRCA1/2 mutation by inhibiting the DNA base excision repair pathway. Despite the clinical benefit of PARPi, they are not effective in every HRD tumor and the acquisition of PARPi resistance limits long-term response. TNG348, a selective allosteric inhibitor of the deubiquitinating enzyme USP1, was specifically designed to target HRD vulnerabilities through an alternative mechanism. We previously showed that the anti-tumor activity of USP1 inhibition results from disruption of the translesion synthesis DNA damage tolerance pathway, a mechanism of action that is functionally distinct from base excision repair targeted by PARPi. Our preclinical studies show that TNG348 is active in HRD models and strongly synergizes with PARP inhibitors to drive strong anti-tumor responses. We have identified replication stress as a predictive biomarker of TNG348 response using cell line profiling and genome-wide CRISPR screens. For example, overexpression of oncogenes known to induce replication stress sensitized to the TNG348 and PARPi combination both in vitro and in vivo. These data indicate that cancer-specific elevated DNA replication stress could contribute to tumor sensitivity to TNG348 and provide additional patient stratification strategies and opportunities for indication expansion.

Citation Format: Antoine Simoneau, Hsin-Jung Wu, Charlotte Pratt, Grace Comer, Shangtao Liu, Samuel Meier, Tenzing Khendu, Ashley Choi, Hongxiang Zhang, Binzhang Shen, Douglas Whittington, Sirimas Sudsakorn, Wenhai Zhang, Yi Yu, Yingnan Chen, Brian Haines, Adam Crystal, Jannik N. Andersen, John Maxwell, Scott Throner. TNG348 is synergistic with PARP inhibitors in tumor models with elevated replication stress [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 4527.
Abstract 4614: Inhibition of NEK2 promotes chemosensitivity and reduces primary effusion lymphoma burden
Authors: White Maria C. , Wong Jason P. , Damania Blossom
Published: March 2024

Non-Hodgkin lymphoma (NHL) is a common cancer in both men and women, and represents a significant cancer burden worldwide. Primary effusion lymphoma (PEL) is a subtype of NHL infected with Kaposi sarcoma-associated herpesvirus (KSHV). PEL is an aggressive and lethal cancer with no current standard of care, owing largely to its propensity to develop resistance to current chemotherapeutic regimens. Here, we report a reliance of PEL on the mitotic kinase, NEK2, for survival. Genetic and pharmacologic targeting of NEK2 resulted in caspase 3-mediated apoptotic cell death of PEL. Furthermore, inhibition of NEK2 significantly prolonged survival and reduced tumor burden in a PEL mouse model. We also report that the ABC transporter proteins, MDR1 and MRP, are most active in PEL and that NEK2 inhibition of PEL reduced the expression and activity of these ABC transporter proteins, which are known to mediate drug resistance in cancer. Additionally, NEK2 inhibition sensitized both viral and non-viral NHL to other chemotherapeutic agents such as rapamycin, resulting in enhanced cancer cell death. Overall, these data offer insight into the mechanisms underlying PEL survival and drug resistance, and suggest that NEK2 is a viable therapeutic target for PEL.

Citation Format: Maria C. White, Jason P. Wong, Blossom Damania. Inhibition of NEK2 promotes chemosensitivity and reduces primary effusion lymphoma burden [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 4614.
Abstract 4629: QClampTM Plex VEXAS syndrome UBA1 mutation detection assay: A noval XNA based assay to simultaneously detect eight UBA1 somatic mutations associated with VEXAS syndrome
Authors: Ma Yunqing
Published: March 2024

VEXAS syndrome (acronym for Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) is a monogenic disease discovered in December 2020. It is an adult-onset systemic inflammatory disorder genetically characterized by somatic mutation of the UBA1 gene which encodes the ubiquitin like modifier activating enzyme 1. VEXAS patients have overlapping rheumatologic and hematologic manifestations, including increased risk for myelodysplastic syndrome (MDS). It is critically important to diagnose VEXAS syndrome, but UBA1 mutation test is still not commercially available. The three most frequent mutations of UBA1 gene are p.M41T(122T>C), p.M41V (c.121A>G), and p.M41L (c.121A>C) in codon 41 of exon 3. Other mutations including splice site mutations at exon 3 (c.118-2A>C, c.118-1G>C and c.118- 9_118-2del), p.S56F (c.167C>T) in codon 56 of exon 3, and p.S621C (c.1861A>T) in codon 621 of exon 16 have been reported. Based on XNA technology, we developed a QClampTM Plex platform to detect all the eight mutations in a single reaction with Luminex system. XNA technology enriches mutant target sequence in a PCR reaction by using synthetic DNA analog XNA (xenonucleic acid) to block wild type DNA. With spiking synthetic mutant DNA in GM24385 cell line DNA, we determined that this assay can detect mutations with a detection limit of variant allele frequency (VAF) for M41T at 0.1%, M41V at 0.1%, M41L at 0.25%, c.118-2A>C at 1%, c.118-1G>C at 1%, c.118- 9_118-2del at 1%, S56F at 0.25% and S621C at 1%, respectively, and specificity of 100% for all mutations. We tested saved DNA samples extracted from whole blood previously collected from suspected VEXAS patients and tested at the National Cancer Institute by Sanger sequencing, including 13 positive and 20 negative samples. Our assay detected all corresponding UBA1 mutations in the 13 positive patient samples, and did not detect UBA1 mutation in 18 of the 20 negative patient samples. Two of the 20 negative samples were also tested positive for UBA1 M41T and M41L on our assay, respectively, due to its significantly higher sensitivity than the Sanger sequencing platform, which has a detection limit of 15-20% VAF.

Citation Format: Yunqing Ma. QClampTM Plex VEXAS syndrome UBA1 mutation detection assay: A noval XNA based assay to simultaneously detect eight UBA1 somatic mutations associated with VEXAS syndrome [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 4629.
Abstract 4687: Primary study on the anticancer role of BAM15 in lung cancer cells
Authors: Zhang Mei-yin , Wang Yue-Ning , Zhou Yu-Feng , Wang Shuo-Cheng , Mai Shi-Juan , Wang Hui-Yun
Published: March 2024

Background: Lung cancer remains the leading cause of cancer-related death worldwide. Non-small cell lung cancer (NSCLC) accounts for about 80-85% of all lung cancer cases. BAM15, a mitochondrial uncoupler, is a potential therapeutic agent for many diseases, including obesity, diabetes, nonalcoholic fatty liver disease, Sepsis and cancers. However, there is no report on the anti-tumor role of BAM15 in NSCLC.

Methods: To investigate the direct anti-cancer effects of BAM15 in NSCLC, we examined its inhibitory role on cell proliferation of NSCLC cells using the Cell Counting Kit-8(CCK8), colony forming assays and EdU staining assays. The impact of BAM15 on the cell cycle and cell apoptosis of NSCLC cells was analyzed by flow cytometric. A xenotransplanted NSCLC model in mice were used to test the anticancer role of BAM15.

Result: Using the CCK8 assay, we found that the inhibitory role of BAM15 on the proliferation and colony formation of NSCLC cells is dose-dependent. The half maximal inhibitory concentration (IC50) values for cell proliferation were 2.71, 4.74, and 9.50 μM for A549, PC9, and H1299 NSCLC cells, respectively. The EdU staining assay demonstrated that BAM15 treatment significantly inhibited DNA synthesis in NSCLC cells. Flow cytometric analysis revealed that BAM15 arrested cell cycle at G2 phase in NSCLC cells and caused a striking increase in the percentage of apoptotic cells in NSCLC cells. The xenotransplanted NSCLC experiment indicated that BAM15 could significantly suppressed the growth of NSCLC tumors compared with the control tumors.

Conclusions: Our study demonstrates that BAM15 significantly inhibits cell proliferation and promotes apoptosis in NSCLC cells, indicating that BAM15 is a potential therapeutic candidate for the treatment of NSCLC.

Citation Format: Mei-yin Zhang, Yue-Ning Wang, Yu-Feng Zhou, Shuo-Cheng Wang, Shi-Juan Mai, Hui-Yun Wang. Primary study on the anticancer role of BAM15 in lung 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 4687.
Abstract 4704: Biochemical and cell-based assay platforms for development of RAF inhibitors against human cancers
Authors: Wu Jianghong , Wan Yong , Liang Shuguang , Gallagher Peter , Liang Li , Loch Christian , Ma Haiching
Published: March 2024

The RAF protein kinases are key intermediates in cellular signal transduction, functioning as direct effectors of the RAS GTPases and as the initiating kinases in the ERK cascade. In human cancer, RAF activity is frequently dysregulated due to mutations in the RAF family members (ARAF, BRAF, and CRAF) or to alterations in upstream RAF regulators, including RAS and receptor tyrosine kinases. The first and second generations of RAF inhibitors have yielded dramatic responses in malignant melanomas containing BRAF mutations; however, their overall usefulness has been limited by both intrinsic and acquired drug resistance. In addition, cancers with hyperactive RAS exhibit intrinsic resistance to these drugs. In particular, issues related to the dimerization of the RAF kinases can impact the efficacy of these compounds and are a primary cause of drug resistance. We have established biochemical HotSpotTM kinase assay, NanoBRETTM and NanoBITTM cell assay platforms for High Through Screening of kinase inhibitors. Here, we demonstrate that the 3rd generation of pan-RAF inhibitors LY3009120, LXH254, and Belvarafenib inhibit ARAF, BRAF, CRAF, BRAF(V600E), and CRAF(R391W) kinase activity in biochemical HotSpotTM assay. Our NanoBRETTM target engagement and NanoBITTM cellular assay data show that LY3009120, LXH254, and Belvarafenib bind to KRAS(G12C) primed BRAF and CRAF, and block BRAF and CRAF dimerization. Furthermore, our results show these inhibitors can block the downstream ERK phosphorylation in cellular HTRF assay and induce caspase-3/7 activation in Western blot assay in the triple negative breast cancer MDA-MB-231 cells. Taken together, our results indicate the biochemical HotSpotTM kinase activity assay, and NanoBRETTM target engagement and NanoBITTM cellular assays can serve as great platforms to facilitate RAF drug discovery against human cancers.

Citation Format: Jianghong Wu, Yong Wan, Shuguang Liang, Peter Gallagher, Li Liang, Christian Loch, Haiching Ma. Biochemical and cell-based assay platforms for development of RAF inhibitors against human 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 4704.
Abstract 4716: First-in-class peroxiredoxin 3 (PRX3) inhibitor RSO-021 triggers mesenchymal-to-epithelial transition in mesothelioma
Authors: Messier Terri , Gibson Victoria , Seward David J. , Baitei Essa Y. , Jordan Peter Wells , Poile Charlotte , Dzialo Joanna , Bzura Aleksandra , Kutywayo Kudzayi , Nakas Apostolos , Naumov George N. , Fennell Dean A. , Cunniff Brian
Published: March 2024

Mesothelioma, a lethal cancer associated with asbestos exposure, lacks effective drug therapy particularly in the relapsed treatment setting. Epithelial-to-mesenchymal transition (EMT) confers an aggressive sarcomatoid phenotype capable of invasion, metastasis, and drug resistance. Pharmacological targeting of EMT could favorably alter the progression and treatment of mesothelioma. We identified a geospatial transcriptomic gradient between adjacent epithelioid and sarcomatoid regions in patient-derived biphasic mesotheliomas involving hypoxia tolerance, TGF-β, mitochondrial oxidative phosphorylation, and EMT. Mesothelioma cells rely on buffering of mitochondrial oxidative stress through the expression and activity of mitochondrial peroxiredoxin 3 (PRX3), which is covalently inactivated by the first-in-class inhibitor RSO-021, now under investigation in the phase 1/2 MITOPE clinical trial (NCT05278975). To better understand the pharmacodynamics of RSO-021, transcriptomic profiles of drug sensitive and resistant biphasic mesothelioma cell lines were generated. Differential analysis revealed that RSO-021 induced up-regulation of ROS response and apoptosis signaling, while down-regulating TGF-β and EMT markers, WNT signaling, and TEAD target genes. Additionally, we observed altered expression of the mesothelioma specific EMT genes Col5A2, mesothelin and VISTA. Resistance to RSO-021 conferred significant proliferative defects and was reversible upon RSO-021 removal, however the down-regulation of EMT genes was conserved, suggesting an irreversible mesenchymal-to-epithelial transition. In summary PRX3 is a clinically actionable drug target, inhibition of which correlates with EMT modulation. This activity suggests a mechanism to alter mesothelioma progression and prevent the emergence of the most aggressive mesothelioma phenotype.

Citation Format: Terri Messier, Victoria Gibson, David J. Seward, Essa Y. Baitei, Peter Wells Jordan, Charlotte Poile, Joanna Dzialo, Aleksandra Bzura, Kudzayi Kutywayo, Apostolos Nakas, George N. Naumov, Dean A. Fennell, Brian Cunniff. First-in-class peroxiredoxin 3 (PRX3) inhibitor RSO-021 triggers mesenchymal-to-epithelial transition in mesothelioma [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 4716.
Abstract 4741: Targeting sorafenib-resistant HCCs by protein X-armed T cell immunotherapy
Authors: Ngo Mai-Huong Thi , Chen Michael , Lan Pei-Chi , Chuang Kuo-Hsiang , Huang Yen-Hua
Published: March 2024

Hepatocellular carcinoma (HCC) is the most common type of liver cancer globally, ranking fourth according to the World Health Organization's GLOBOCAN database. Sorafenib and lenvatinib are single-drug therapies used for advanced HCC, but only around 30% of patients benefit from them, and drug resistance typically develops within a few months. Our previous study has demonstrated the specific IL-6-IGF-1R-YAP signaling in regulating the stemness expressions, tumor metastasis, and drug-resistance of the sorafenib resistant HCC (2015 Clinical Cancer Res, 2019 J Exp Clinical Cancer Research, 2021 Cancers, 2023 Cancers). In advance our previous study, this study aims to develop a novel immune therapeutic strategy for sorafenib-resistant HCC treatment. We found, when compared to peri-tumor tissues, the immunohistochemical staining showed a high co-expression of both protein X and PD-L1 in liver tumor tissues (6.25%, n=32 versus 28.125%, n = 64, respectively). To further confirm this observation, we used in vitro cell line models with sorafenib-naïve HCCs (HepG2215_N, Hep3B_N, Huh7_N, and PLC5_N) and sorafenib-resistant HCCs (HepG2215_R, Hep3B_R, Huh7_R, and PLC5_R) in this study. As PD-L1 on tumor cells can dampen T cell cytotoxicity, we generated CD3/protein X bispecific antibodies, which can bind to both CD3 and protein X, and coupled them to T cells (Arm-T cells) and normal T cells (N-T cells). We tested their cytotoxic effects on sorafenib-resistant HCCs using the sorafenib-resistant HepG2215_R cells, co-cultured with Arm-T cells and N-T cells for 24 hours. Our results showed that Arm-T cells exhibited a significantly stronger cytotoxic effect on sorafenib-resistant HepG2215_R cells, with several notable findings: (1) The binding time of Arm-T cells to HepG2215_R cells was significantly longer than that of N-T cells (248.9 ± 146.6 minutes, n=23 versus 28.3 ± 13.49 minutes, n=24); (2) The cytotoxicity of Arm-T cells was significantly higher than that of N-T cells (29.7 ± 2.3% versus 13.6 ± 3.3%); and (3) The secreted levels of INFγ and TNFα by Arm-T cells were significantly higher than those of N-T cells (138.1 ± 7.2 ng/ml and 34.6 ± 0.7 ng/ml versus 31.4 ± 2.5 ng/ml and 3.6 ± 1.1 ng/ml, respectively). These findings were also consistent when using Hep3B-R cells (data not shown). To summarize, our study shows that Arm-T cells possess strong cytotoxic abilities against sorafenib-resistant HCC. These findings have implications for developing effective immuno-therapeutic strategies for patients with sorafenib-resistant HCCs.

Citation Format: Mai-Huong Thi Ngo, Michael Chen, Pei-Chi Lan, Kuo-Hsiang Chuang, Yen-Hua Huang. Targeting sorafenib-resistant HCCs by protein X-armed T cell immunotherapy [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 4741.
Abstract 4742: Targeting the RNA-binding protein LARP1 overcomes therapeutic resistance in ovarian cancer
Authors: Elsayed Abdelrahman M. , Amero Paola , Bayraktar Emine , Sood Anil K. , Lopez-Berestein Gabriel , Rodriguez-Aguayo Cristian
Published: March 2024

La-related protein 1 (LARP1) is an RNA-binding protein that plays a pivotal role in regulating mRNA on a post-transcriptional level. Overexpression of LARP1 has been detected in multiple cancers substantiating the critical role of LARP1 as a driver for cancer progression. This study aims to investigate the downstream target pathways regulated by LARP1 and to determine the impact of LARP1 targeting on the resistance to cisplatin and olaparib therapy in ovarian cancer (OC). Analysis of The Cancer Genome Atlas OC dataset, reverse phase protein array, in vitro functional and mechanistic experiments, and a xenograft OC mouse model using OVCAR8 cell line were executed. Our results revealed that overexpression of LARP1 is negatively correlated with progression-free survival in OC patients. Furthermore, LARP1 knockdown using two independent small interfering RNAs (siRNAs) suppressed cell growth, invasion, and migration, and ameliorated cisplatin resistance in vitro. Mechanistic analyses identified AXL as a target of LARP1 and this finding was further supported clinically in which co-overexpression of LARP1 and AXL is associated with poor prognosis in OC. Furthermore, LARP1 knockdown resulted in reduced phosphorylation of mTOR, AKT, and SRC with no significant effect on FAK. In vivo, administration of 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine (DOPC) nanoparticles loaded with LARP1-siRNA suppressed tumor growth and improved the response to cisplatin and olaparib in a xenograft OC mouse model. In conclusion, LARP1 acts as an oncogenic RNA-binding protein in OC, and targeting LARP1 may represent an innovative therapeutic approach for ameliorating resistance to chemotherapy and targeted therapy in OC.

Keywords: RNA-binding proteins; cisplatin resistance; olaparib resistance; chemotherapy resistance; LARP1; ovarian cancer.

Citation Format: Abdelrahman M. Elsayed, Paola Amero, Emine Bayraktar, Anil K. Sood, Gabriel Lopez-Berestein, Cristian Rodriguez-Aguayo. Targeting the RNA-binding protein LARP1 overcomes therapeutic resistance in ovarian 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 4742.
Abstract 4754: Targeted inhibition of the HNF1A/SHH axis by triptolide overcomes paclitaxel resistance in non-small cell lung cancer
Authors: Li Peichao , Li ngbing , Yang Lingxiao , Liu Lei , Zhao Xiaogang
Published: March 2024

Paclitaxel resistance is commonly associated with a poor prognosis in non-small cell lung cancer (NSCLC) patients, and there are no promising pharmacological treatments for paclitaxel resistance. Here, we constructed human NSCLC-derived paclitaxel-resistant cell lines as an effective tool to explore the mechanisms of chemoresistance. We discovered that triptolide, a monomer compound extracted from Tripterygium wilfordii Hook F, was able to reverse paclitaxel resistance by reducing ABCB1 expression in vivo and in vitro. Through high-throughput sequencing, we found that the SHH-initiated Hedgehog signaling pathway played an important role in this process. More importantly, triptolide could directly target HNF1A, a transcription factor of SHH, and inhibited HNF1A/SHH expression, ensuing in attenuation of Hedgehog signaling. Clinically, we found a positive correlation between HNF1A and SHH expression in both NSCLC tumor tissue microarrays and cancer network databases. These findings illuminated a novel molecular mechanism through which triptolide effectively targets and inhibits HNF1A, thereby impeding the activation of the Hedgehog signaling pathway and reducing the expression of ABCB1. This finding indicated the potential clinical application of triptolide and provided promising prospects in targeting the HNF1A/SHH pathway as a therapeutic strategy for NSCLC patients with paclitaxel resistance.

Citation Format: Peichao Li, ngbing Li, Lingxiao Yang, Lei Liu, Xiaogang Zhao. Targeted inhibition of the HNF1A/SHH axis by triptolide overcomes paclitaxel resistance in non-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 4754.
Abstract 4826: Cancer mortality attributable to area-level socioeconomic inequalities in Japan from 2015 to 2020
Authors: Ito Yuri , Nakaya Tomoki , Inoue Manami , Sobue Tomotaka , Nakagama Hitoshi
Published: March 2024

Background: In the 3rd Healthy Japan 21 and the 4th National Cancer Plan, the government focused on reducing health inequalities. However, current monitoring of socioeconomic inequalities in cancer is still insufficient to set the targets for the plan. To prioritize strategy aimed at reducing socioeconomic inequalities in cancer mortality, we estimated the population attributable risk fraction (PAF) and excess death due to socioeconomic inequalities, by sex, age group and cancer site.

Method: We used the areal deprivation index (ADI) to establish area-based socioeconomic status. We categorized municipalities to ADI quintile weighted by the size of population, Q1 is the least deprived and Q5 the most deprived group. Excess death due to socioeconomic inequalities was calculated by the difference between observed number of deaths and expected death of Q2 to Q5 group with Q1 as standard population. We used cancer mortality data obtained from vital statistics in 2015-2020.

Results: In total, about 12000 male and 2800 female excess deaths per year due to socioeconomic inequalities were estimated; that is 5.5% and 1.8% as PAF. PAF due to socioeconomic inequalities limited to premature death, less than 75 years old, was estimated as 7.6% in men and 3.3% in women. By age group, the 0-39 years group showed the largest PAF at 15.7% in men and 16.6% in women. In men of all age groups, except 0-39 years, lung cancer was the highest excess death due to socioeconomic inequalities. For women, some cancer sites (breast, ovary, esophagus) showed an opposite association, Q1 was the highest mortality group. Therefore, total excess death was lower than in men. In women of all ages, the highest rate of excess death due to socioeconomic inequalities was gallbladder cancer. For the 0-39 years group, a high rate of excess death in stomach, leukemia, and cervical cancer was observed.

Discussion: Excess death and PAF due to socioeconomic inequalities differed by sex and age group. A greater impact of socioeconomic inequality on cancer mortality was observed in men than in women. Among women, further attention should be paid to areal variation of cancer death related to socioeconomic inequalities, based on the different area-based indices.

Citation Format: Yuri Ito, Tomoki Nakaya, Manami Inoue, Tomotaka Sobue, Hitoshi Nakagama. Cancer mortality attributable to area-level socioeconomic inequalities in Japan from 2015 to 2020 [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 4826.
Abstract 4897: Personalized cell surface target identification from pan-cancer RNA-seq and proteomics profiling of tumors
Authors: Marino Giacomo B. , Deng Eden Z. , Clarke Daniel J.B. , Ma Weiping , Wang Pei , Resnick Adam C. , Ma'ayan Avi
Published: March 2024

In its third phase, the Clinical Proteomic Tumor Analysis Consortium (CPTAC) program collected pan-cancer data from 1,069 patients profiling the transcriptome, proteome, and phospho-proteome of tumors and adjacent tissues from ten cancer types. To identify potential immunotherapeutic candidates from this CPTAC cohort, we searched for cell-surface proteins that are highly expressed in tumor subtypes compared to their expression in normal tissues and cell types from ARCHS4 and the Genotype-Tissue Expression (GTEx) resources. For each cancer type, tumor samples were first clustered into subtypes based on RNA-seq data, and then cell surface targets were prioritized for each cluster. These targets were subsequently confirmed for high protein expression in the tumor subtypes. Tumor samples were also processed by their classification into immune subtypes to identify targets specific to hot (CD8+/IFNG+) and cold (CD8-/IFNG-) tumors of each cancer type. For each cancer type, the computational pipeline identified ~30 cell surface proteins that are highly expressed in the tumor and lowly expressed across tissues and cell types in both the ARCHS4 and GTEx backgrounds. Many of these targets are also robustly differentially expressed at the proteome level. Several targets were shared across tumor types, including VTCN1 and TMPRSS4. Altogether, this rational approach to identify potential targets demonstrates a pipeline that can be applied for personalized cancer diagnosis and therapeutic development.

Citation Format: Giacomo B. Marino, Eden Z. Deng, Daniel J.B. Clarke, Weiping Ma, Pei Wang, Adam C. Resnick, Avi Ma'ayan. Personalized cell surface target identification from pan-cancer RNA-seq and proteomics profiling of tumors [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 4897.
Abstract 4899: Interface-guided phenotyping of coding variants in the transcription factor RUNX1
Authors: Ozturk Kivilcim , Panwala Rebecca , Sheen Jeanna , Ford Kyle , Jayne Nathan , Zhang Dong-Er , Hutter Stephan , Haferlach Torsten , Ideker Trey , Mali Prashant , Carter Hannah
Published: March 2024

Understanding the consequences of single amino acid substitutions in cancer driver genes remains an unmet need. Perturb-seq provides a tool to investigate the effects of individual mutations on cellular programs. Here we deploy SEUSS, a Perturb-seq like approach, to generate and assay mutations at physical interfaces of the RUNX1 Runt domain. We measured the impact of 115 mutations on RNA profiles in single myelogenous leukemia cells and used the profiles to categorize mutations into three functionally distinct groups: wild-type (WT)-like, loss-of-function (LOF)-like and hypomorphic. Notably, the largest concentration of functional mutations (non-WT-like) clustered at the DNA binding site and contained many of the more frequently observed mutations in human cancers. Hypomorphic variants shared characteristics with loss of function variants but had gene expression profiles indicative of response to neural growth factor and cytokine recruitment of neutrophils. Additionally, DNA accessibility changes upon perturbations were enriched for RUNX1 binding motifs, particularly near differentially expressed genes. Overall, our work demonstrates the potential of targeting protein interaction interfaces to better define the landscape of prospective phenotypes reachable by amino acid substitutions.

Citation Format: Kivilcim Ozturk, Rebecca Panwala, Jeanna Sheen, Kyle Ford, Nathan Jayne, Dong-Er Zhang, Stephan Hutter, Torsten Haferlach, Trey Ideker, Prashant Mali, Hannah Carter. Interface-guided phenotyping of coding variants in the transcription factor RUNX1 [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 4899.
Abstract 5182: Exploiting tumor RNA-sequencing data for prediction of immune checkpoint inhibition response
Authors: Mestdagh Pieter , Van Dam Pieter-Jan , De Baene Frederick , Fierro Carolina , Van Hoof Elise , Rivière Emmanuel , Dangreau Hanne , Van Cauwenberge Reindert , Vandesompele Jo
Published: March 2024

Immune checkpoint inhibitors (ICI) have become the standard of care as a first- or second-line systemic treatment for patients with various cancer types. Unfortunately, many patients do not respond to this treatment and the occurrence of immune-related adverse events varies widely. There is an urgent need for robust predictive biomarkers for ICI response to identify patients with likely clinical benefit from this costly treatment. Several biomarkers, aimed at predicting response to ICI, have been proposed, including PD-L1 expression, tumor mutation burden (TMB), infiltration of cytotoxic T-cells in the tumor, Microsatellite Instability (MSI) and expression of various immune gene signatures. However, these individual biomarkers have suboptimal performance and multiple complementary omics technologies are required to properly quantify them. Integration of these multi-omic biomarkers has proven valuable in increasing the accuracy and robustness of ICI response prediction.We have developed a computational pipeline that determines the expressed mutation burden (eTMB), MSI status, fraction of infiltrating immune cells and various immune gene expression signatures directly from the RNA-sequencing profile of the tumor. Each biomarker is quantified using a dedicated algorithm that applies machine learning (eTMB and MSI) or computational deconvolution (infiltrating immune cells) and integrates external data sources to maximize performance. Algorithm performance has been validated on large cohorts of tumor RNA-sequencing data with matching gold standard quantification of said biomarkers.

As a proof of concept, we applied our pipeline to tumor RNA-sequencing data of 45 gastric cancer patients treated with pembrolizumab. Responders showed significantly higher eTMB scores and were enriched among the MSI-H patients. Fractions of CD8 T-cells and M1 Macrophages, together with interferon gamma and cytotoxic T-cell gene expression signatures, were significantly increased in responders. Notably, integrating these biomarkers into a single prediction model improved prediction of response to checkpoint inhibition therapy compared to predictions based on eTMB or MSI alone.

Taken together, our approach enables the quantification of various ICI response biomarkers from a single omics layer (RNA-sequencing) and can contribute to ICI response prediction.

Citation Format: Pieter Mestdagh, Pieter-Jan Van Dam, Frederick De Baene, Carolina Fierro, Elise Van Hoof, Emmanuel Rivière, Hanne Dangreau, Reindert Van Cauwenberge, Jo Vandesompele. Exploiting tumor RNA-sequencing data for prediction of immune checkpoint inhibition response [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 5182.
Abstract 5246: Therapeutic efficacy of glypican-3 peptide-linked chimeric antigen receptor-macrophages in hepatocellular carcinoma
Authors: Leung Wing Hei , Leung Oi Ning , Wong Tsun Ting , Lee Kin Wah
Published: March 2024

Hepatocellular carcinoma (HCC) is the third most lethal cancer and sixth most diagnosed cancer worldwide. Recently, chimeric antigen receptor-T cell (CAR-T) therapy has been demonstrated to be a promising immunotherapy for the treatment of hematologic malignancies such as leukemia. However, its application in solid tumors has proven to be challenging. To overcome this limitation, chimeric antigen receptor-macrophages (CAR-Ms) have emerged as a new immunotherapy against solid cancers, capitalizing on the unique attributes of macrophages in penetrating the tumor microenvironment, promoting antigen presentation, and priming T cells. Traditionally, CAR-M therapy involves the transfer of an edited CAR gene into macrophages via viral infection. However, this method is expensive, involves tedious procedures, and has long-term safety concerns. In the present study, we employed peptides to mimic the genetic approach for producing CAR-Ms to reduce the above uncertainties. To achieve this, we developed a novel bioconjugation method called the phthalaldehydeamine capture (PAC) reaction to produce peptidic CAR-Ms (pCAR-Ms) targeting Glypican-3 (GPC3) in HCC cells. This was achieved by linking GPC3 specific peptides to Raw264.7 murine macrophages. Using an in vitro co-culture system, we demonstrated the specificity and efficacy of pCAR-Ms against GPC3, as evidenced by a significant increase in the number of phagocytosed cells with high GPC3 expression when compared to their low-expression counterparts, by flow cytometry and confocal microscopy. The specificity of pCAR-Ms was further proven in GPC3-knockdown HCC cells, with a significant decrease in the phagocytic rate. Using an HCC xenograft model derived from MHCC97L cells, we confirmed the specific homing of pCAR-Ms to tumor sites via intravenous injection of lipopolysaccharide (LPS)-differentiated pCAR-Ms. Strikingly, pCAR-Ms suppressed HCC tumor growth when compared with untagged macrophages and PBS control. In conclusion, we provided evidence of the potency and specificity of non-viral-based pCAR-Ms in targeting HCC with simple and short production time and increased flexibility.

Citation Format: Wing Hei Leung, Oi Ning Leung, Tsun Ting Wong, Kin Wah Lee. Therapeutic efficacy of glypican-3 peptide-linked chimeric antigen receptor-macrophages in hepatocellular 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 5246.
Abstract 5280: Minimizes T cells DNA damage induced by PARP inhibitors and enhances its anti-tumor efficacy
Authors: Liu Jiahao , Jiao Xiaofei , Mu Wei , Li Huayi , Zhu Li , Zhao Xuejiao , Mills Gordon B. , Gao Qinglei , Fang Yong
Published: March 2024

Background: Poly (ADP-ribose) polymerase (PARP) inhibitors have emerged as promising targeted therapies for ovarian and breast cancer. The sustained remission induced by PARP inhibitors largely depends on T cell activity. However, the direct effects of PARP inhibitors on T cells, as well as their precise impact on T cell DNA integrity and subsequent anti-tumor immune responses, have not been fully elucidated.

Method & Result: Following treatment with 25 μM olaparib or 15 μM niraparib for 48 hours, T cell viability decreased by 39.20% and 41.89%, respectively. Reduced proliferation and increased cell death were also observed, as indicated by reduced Ki-67 and elevated cleaved Caspase-3 levels. RNA sequencing further revealed a significant enrichment of DNA damage pathways in T cells after olaparib treatment, which was validated by elevated γH2AX levels in T cells using western blots and immunofluorescence. To assess PARP inhibitor-induced DNA damage in clinical settings, paired ovarian cancer samples pre- and post-niraparib monotherapy were obtained from the NANT trial (NCT04507841). Post-treatment tumor samples exhibited a higher number of γH2AX+ T cells compared to their pre-treatment counterparts. To identify the key protein mediating T cell inhibition induced by PARP inhibitors, a whole genomic CRISPR knock-out screening was conducted in human T cells, revealing an enrichment of sgRNAs targeting PARP1 after PARP inhibitor treatment. This outcome was further confirmed by the knockout of PARP1 in human T cells in vitro, leading to the restored viability and reduced levels of DNA damage after olaparib treatment. Importantly, following cytosine base editors (CBEs) of PARP1 in CAR-T cells, improved anticancer activity was observed both in vitro and in two ovarian cancer patient-derived xenografts (PDX) models when combined with PARP inhibitors.

Conclusion: This study observed that PARP inhibitors can cause significant DNA damage in human T cells, resulting in cell death, inhibited proliferation, and impairment of anti-cancer immunity. PARP1 was identified as the target for PARP inhibitor-induced T cell death, and its knockout or point mutation led to improved anticancer efficacy of T cells when used in combination with PARP inhibitors. [JH Liu and XF Jiao contributed equally as co-first authors.]

Citation Format: Jiahao Liu, Xiaofei Jiao, Wei Mu, Huayi Li, Li Zhu, Xuejiao Zhao, Gordon B. Mills, Qinglei Gao, Yong Fang. Minimizes T cells DNA damage induced by PARP inhibitors and enhances its anti-tumor efficacy [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 5280.
Abstract 5396: Vascularized gastric cancer 3D co-culture model using a microphysiological system as an oncolytic virus testing platform
Authors: Kim YeLin , Song Youngsook , Choi Yeongmin , Jang Jinhwan , Kim Suryong , Liu Tsung-Li , Baek Kyusuk , Oh Keunhee , Ma Seunghyun , Kim Tae Soo , Kwon Woo Sun , Yoo Sanghee , Kim Jee Hung , Rha Sun Young
Published: March 2024

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 5402: Understanding the role of exercise in lymphatic vessel regulation in melanoma
Authors: Tirumala Priya , Lee Jonghae , Schadler Keri L.
Published: March 2024

Exercise has been demonstrated to be an effective method to remodel tumor blood vessels and to improve immune cell infiltration in multiple tumor models in mice. However, it is unclear whether aerobic exercise alters lymphatic vasculature in tumors. The lymphatic system plays an important role in tumor growth and metastasis because it regulates interstitial fluid pressure via lymph flow and immune cell trafficking, in conjunction with blood vessels. Lymphatic vessels are particularly important during metastasis because tumor cells frequently escape the primary tumor through lymphatic vasculature to establish the first site of metastasis in the lymph nodes. Here, we evaluated the effect of aerobic exercise on lymphatic vessels and lymphatic endothelial cell junctions in melanoma in male C57BL/6J mice. BP melanoma cells derived from transgenic mice with BrafV600E/+ and Pten−/− mutations were injected subcutaneously. Mice were assigned to no exercise and exercise groups when tumors reached ~30 mm3. The exercise group completed treadmill running at 12 meters/minute for 45 minutes for 5 consecutive days with 2 days of rest per week for 2 weeks before tumor harvest. Tumor lymphatic endothelial cells were identified by LYVE-1, endothelial tight junctions by ZO-1, and nuclei were identified by DAPI using immunofluorescence staining on frozen tumors. The number of total lymphatic vessels, elongated vessels( >100 µm), open lumens, and co-localization of ZO-1 with LYVE-1 was quantified on 6 random images per tumor using NIH Image J software. ANOVA and t-test were used to conduct statistical analysis (p < 0.05). Tumors from exercised mice had higher lymphatic vessel density (p=0.002) and more open lumens (p=0.001). Surprisingly, tumors from exercised mice had fewer ZO-1 positive vessels (p=0.015) and lower co-localization of ZO-1 and LYVE-1 (p = 0.0185) than tumors from non-exercised mice, suggesting fewer stable endothelial cell junctions in lymphatic vessels. The higher lymphatic vessel density and higher number of open lumens present in tumors from exercised mice may contribute to an exercise-induced improved anti-tumor immune response, which has been previously reported. However, the lower ZO-1 expression on lymphatic endothelial cells in tumors from exercised mice may indicate lymphatic vasculature dysfunction and/or hyper-permeability. Further work is needed to assess the functional changes in tumor lymphatic vasculature by exercise, and how these changes impact the anti-tumor immune response and metastasis.

Citation Format: Priya Tirumala, Jonghae Lee, Keri L. Schadler. Understanding the role of exercise in lymphatic vessel regulation 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 5402.
Abstract 5419: Claudin-7 mediates Rab25-induced suppression of colon cancer cell invasion
Authors: Cho Su Jin , Jeong Bo Young , Yoon Se-Hee , Park Chang Gyo , Lee Hoi Young
Published: March 2024

Ras-related protein 25 (Rab25) is a member of small GTPase, and growing evidence demonstrates the context-dependent roles of Rab25 in cancer progression. While Rab25 aggravates cancer cell invasion in ER-positive breast, ovarian, and gastric cancers, Rab25 is under-expressed and suppresses colon and triple-negative breast cancer progression. Claudins are major components of tight junctions, and disruption of claudins is implicated in tumorigenesis. Among 27 known members of the claudin family, claudin-7 is suggested to suppress colon cancer progression. Previously, we identified that Rab25 induces endothelial-mesenchymal transition (EMT) and invasiveness of several types of cancer cells through activating the β1 integrin/epidermal growth factor receptor (EGFR)/Snail signaling cascades. However, little is known about the underlying mechanism of Rab25-induced tumor suppression. In the present study, we identify the critical role of claudin-7 in Rab25-induced suppression of colon cancer invasion. 3D Matrigel and modified Boden chamber were used to assess the invasiveness of colon cancer cells. Wound-healing assay was used to analyze colon cancer cell migration. 3D Matrigel was used to analyze tumor growth. Immunoblotting was used to assess the protein expression. Rab25 induced claudin-7 expression in colon cancer cells through protein stabilization. In addition, the enforced expression of claudin-7 not only reduced the EGFR/Ras signaling activity and Snail expression but also attenuated colon cancer cell invasion. However, silencing of claudin-7 expression rescued the tumor suppressive role of Rab25, thereby increasing colon cancer cell invasiveness. Collectively, our data demonstrate for the first time that Rab25 reduces the EGFR/Ras/Snail signaling activity and inhibits colon cancer cell invasion by upregulating claudin-7 expression.

Citation Format: Su Jin Cho, Bo Young Jeong, Se-Hee Yoon, Chang Gyo Park, Hoi Young Lee. Claudin-7 mediates Rab25-induced suppression of colon cancer cell invasion [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 5419.