bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 7194: Targeting AXL and MCL-1 to eradicate lazertinib tolerance in EGFR-mutated NSCLC cells
Authors: Yamada Tadaaki , Matsui Yohei , Takayama Koichi
Published: March 2024

Lazertinib, a novel third-generation EGFR-tyrosine kinase inhibitor, has shown marked efficacy in patients with EGFR-mutant lung cancer. However, after various periods of therapeutic intervention, most patients eventually acquire resistance to lazertinib. A potential therapeutic approach to address this clinical issue is to overcome the initial drug resistance mechanism. To determine the underlying adaptive lazertinib resistance mechanisms, we evaluated signal transduction, cell apoptosis, and drug sensitivity in mutant EGFR-expressing non-small cell lung cancer (NSCLC) cells treated with lazertinib. The siRNA screening assay demonstrated that AXL knockdown significantly inhibited cell viability in the presence of lazertinib, indicating that AXL activation contributes to lazertinib resistance. However, long-term culture with a combination of lazertinib and AXL inhibitors eventually led to the proliferation of residual cells and increased MCL-1 expression, which was mediated by the nuclear translocation of the transcription factor YAP. Cell-based assays showed that triple therapy with an MCL-1 or YAP inhibitor, in combination with EGFR-TKI lazertinib, an AXL inhibitor, significantly reduced cell viability and increased apoptosis. These results demonstrate that AXL and YAP/MCL-1 signals contribute to the adaptive lazertinib resistance in EGFR-mutant NSCLC cells, suggesting that the initial dual inhibition of AXL and YAP/MCL-1 might be highly effective in eliminating lazertinib-resistant cells.

Citation Format: Tadaaki Yamada, Yohei Matsui, Koichi Takayama. Targeting AXL and MCL-1 to eradicate lazertinib tolerance in EGFR-mutated NSCLC 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 7194.
Abstract 7203: Anti-HDGF antibody attenuates the rise of resistance to EGFR tyrosine kinase inhibitor in NSCLC patient-derived xenograft tumors
Authors: Zhou Cindy Q. , Li Ariel , Ri Kaoru , Sultan Ahmed , Ren Hening
Published: March 2024

Mutant epidermal growth factor receptor (EGFR), a major oncogenic driver in non-small cell lung cancer (NSCLC), is found in the tumors of 15% (western countries) to 50% (Asian countries) of patients. EGFR-targeted therapy using tyrosine kinase inhibitors (TKIs) is a standard of care for those patients who developed metastatic or recurrent diseases. However, despite having an 80% initial response rate, most patients had partial tumor regression and their disease would progress when acquired resistance emerges. Thus, developing more effective treatment is an unmet need. The clinical response of these patients can be recapitulated in mouse models of patient-derived xenograft (PDX) tumor bearing sensitizing EGFR mutations. In this study, treating established PDX tumors with osimertinib, a third generation EGFR TKI, induced partial tumor regression (50% to 70% size reduction from baseline) followed by progression with a median progression-free survival (PFS) of 26 to 28 days. Interestingly, co-administering an antibody against hepatoma-derived growth factor (HDGF) with osimertinib resulted in enhanced tumor regression (98% to 100% size reduction from baseline) which translated into significantly extended animal survival with a median PFS of 103 or 135 days. Immunohistochemical and western blot examination of tumors collected at different treatment timepoints indicated that AKT/mTOR and MAPK pathways were reactivated after initial suppression in TKI monotherapy arm despite persistent EGFR inhibition. Since AKT/mTOR and MAPK pathways are key survival and proliferative signaling pathways, their reactivation can promote TKI tolerance of tumor cells and the emergence of TKI resistance. However, blocking HDGF attenuated the reactivation of these pathways which could partially explain the enhanced efficacy of osimertinib plus anti-HDGF antibody combination treatment seen in this study. Our results suggest tumor-derived HDGF could play a crucial role in the rise of acquired resistance to osimertinib. Identifying the exact cells and molecular pathways utilized by HDGF to promote tumor cell tolerance to TKI will help us understand how TKI sensitive tumor cells survive EGFR blockade and emerge as resistant cells.

Citation Format: Cindy Q. Zhou, Ariel Li, Kaoru Ri, Ahmed Sultan, Hening Ren. Anti-HDGF antibody attenuates the rise of resistance to EGFR tyrosine kinase inhibitor in NSCLC patient-derived xenograft 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 7203.
Abstract 7205: PLK1 inhibition overcomes PARP inhibitor resistance in triple-negative breast cancer
Authors: Siraj Abdul K. , Poyil Pratheesh Kumar , Padmaja Divya , Parvathareddy Sandeep Kumar , Alobaisi Khadija , Begum Rafia , Almalik Osama , Al-Dayel Fouad , Al-Kuraya Khawla S.
Published: March 2024

Patients with aggressive breast cancer (BC) subtypes usually do not have favorable prognosis despite improvements in treatment modalities. These cancers remain a major cause of morbidity and mortality in women globally. This has fostered a major effort to discover actionable molecular targets to treat these patients. Polo-like Kinase (PLK1) is one of these molecular targets that are under comprehensive investigation for the treatment of such tumors. However, its role in the pathogenesis of BC from Middle Eastern ethnicity has not been explored. Therefore, we examined the expression of PLK1 protein in a large cohort of more than 1500 Middle Eastern ethnicity BC by immunohistochemistry. Correlation with clinico-pathological parameters and the prognosis was performed. PLK1 overexpression was observed in 27.4% of all BC and was significantly associated with aggressive clinico-pathological markers. The antitumor effect of PLK1 and PARP inhibitors either alone or in combination was tested in two BRCA mutated, and one BRCA proficient TNBC cell lines. We showed that combined inhibition significantly reduced cell survival and induced apoptosis in TNBC cell lines. Furthermore, our data suggest that PLK1 inhibition overcomes PARP inhibitor resistance in TNBC cell lines. These findings would pave the way to explore the future use of PLK1 inhibitors in the clinical setting of PARPi-resistant patients.

Citation Format: Abdul K. Siraj, Pratheesh Kumar Poyil, Divya Padmaja, Sandeep Kumar Parvathareddy, Khadija Alobaisi, Rafia Begum, Osama Almalik, Fouad Al-Dayel, Khawla S. Al-Kuraya. PLK1 inhibition overcomes PARP inhibitor resistance in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7205.
Abstract 7218: Venetoclax triggers apoptosis and augments the effectiveness of doxorubicin against acute myeloid leukemia cells
Authors: Aloudat Osama , Al Odat Omar S. , Budak-Alpdogan Tulin , Jonnalagadda Subash , Chen Yong , Pandey Manoj
Published: March 2024

Acute myeloid leukemia (AML) is a hematologic malignancy characterized by the clonal proliferation of immature blast cells in the peripheral blood and bone marrow. AML is the second most common type of childhood leukemia, and 50% to 60% of relapses occur within the first year of diagnosis. Chemotherapy side effects and resistance are becoming major clinical issues. Although anthracyclines are one of the most commonly used induction regimens for children with AML in the United States, clinicians avoid them due to adverse effects and clinical resistance issues. To address this clinical issue, we are looking for a novel AML approach to boost the usage of anthracyclines. Since Bcl-2 protein overexpression in AML is related to uncontrolled growth, poor prognosis, and chemoresistance. Multiple clinical trials have suggested combining venetoclax (a selective Bcl-2 inhibitor) with well-established medicines to boost efficacy and overcome resistance. We suggest that inhibiting Bcl-2 is a feasible strategy for increasing the use of anthracycline medicines. We proposed combining doxorubicin and venetoclax as an alternative approach for AML patients. In a panel of three AML cell lines, Kusami-1, U937, and THP-1, our western blot revealed that Kusami-1 had the highest expression of Bcl-2 proteins. Surprisingly, venetoclax causes Kusami-1 cell death and increases the efficacy of doxorubicin in a dose-dependent manner, suggesting that utilizing a lower clinical standard dose may avoid major adverse effects such as cardiotoxicity. Furthermore, the Annexin V Apoptosis Detection Kit indicated that venetoclax coupled with doxorubicin synergistically promoted total apoptosis in Kusami-1 cells. The combination medication shown promising and synergistic in vitro anti-leukemic action against AML cell lines and represents a potentially viable treatment option for AML patients. Future research will use the combination approach in AML cell lines, as well as in patient samples and in vivo experiments.

Citation Format: Osama Aloudat, Omar S. Al Odat, Tulin Budak-Alpdogan, Subash Jonnalagadda, Yong Chen, Manoj Pandey. Venetoclax triggers apoptosis and augments the effectiveness of doxorubicin against acute myeloid leukemia 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 7218.
Abstract 7223: A triplet therapeutic strategy targeting MEK, BCL-XL, and EGFR, for KRAS-mutant pancreatic ductal adenocarcinoma
Authors: Tushoski-Alemán Gerik W. , Crespin Alexandra J. , Oguejiofor Chibeze J. , McKean Jordan A. , Herremans Kelly M. , George Thomas J. , Allegra Carmen J. , Hughes Steven J. , Han Song
Published: March 2024

KRAS mutations drive over 90% of pancreatic cancers, but KRAS has been proven difficult to target. Downstream of KRAS, MEK inhibition in combination with BCL-XL inhibition is synthetically lethal and an effective treatment for gynecologic, but not colorectal malignancies. Like colorectal cancer, pancreatic cancer often exhibits aberrant HER/EGFR activity. We hypothesized that a triplicate regimen targeting MEK, BCL-XL, and EGFR/HER would be effective for pancreatic cancer. Trametinib (MEK inhibitor), Afatinib (pan-EGFR/HER inhibitor), and Navitoclax (BCL-XL inhibitor); or DT2216 (a BCL-XL/BCL-1 proteolysis targeting chimera, PROTAC) were explored using various combinatorial strategies. These drug combinations were tested using four primary human pancreatic cancer cell lines using live cell imaging (Incucyte) and an in vivo murine model. Group comparisons were analyzed using one-way ANOVAs, and adjusted p-values <0.05 were considered significant. We observed that no single-agent treatments were effective. MEK inhibition plus anti-BCL-XL (Trametinib + Navitoclax or Trametinib + DT2216) demonstrated efficacy in one of the four cell lines. We noted synergistic effects on reduced cell growth and increased cell death when EGFR/HER inhibition was included by the administration of Afatinib. The triplet combination resulted in synergistic effects in three of four cell lines with Navitoclax and four of four cell lines with DT2216 (q<0.05). This effect was confirmed with DT2216 inhibition of BCL-XL in an in-vivo murine model. In conclusion, our study shows that a combinatory strategy targeting MEK, BCL-XL, and pan-EGFR/HER receptor kinase shows significant synergistic effects in pancreatic cancer. Clinical trials that assess the efficacy and safety of this strategy for patients with KRAS-mutant pancreatic cancer are warranted. Our data also suggests that novel KRAS inhibitors as monotherapy are likely to fail.

Citation Format: Gerik W. Tushoski-Alemán, Alexandra J. Crespin, Chibeze J. Oguejiofor, Jordan A. McKean, Kelly M. Herremans, Thomas J. George, Carmen J. Allegra, Steven J. Hughes, Song Han. A triplet therapeutic strategy targeting MEK, BCL-XL, and EGFR, for KRAS-mutant pancreatic ductal adenocarcinoma [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 7223.
Abstract 7328: Relationship between PIN3 16bp duplication of TP53 and HPV in HIV women in Mali
Authors: Maiga Mamoudou , Diakite Brehima , Kassogue Yaya , Traore Ban , Kassogue Oumar , Kamate Bakarou , Traore Cheick B. , Holl Jane L. , Hou Lifang
Published: March 2024

Background: TP53 polymorphisms can influence the immune response to HPV, affecting TP53's role in cell cycle regulation and apoptosis, crucial for controlling HPV infection and preventing cancer.

Objective: Explore the link between TP53 PIN3 16-bp duplication and HPV infection in HIV-positive Malian women.

Methods: This study explored the link between PIN3 16-bp duplication polymorphism of TP53 and HPV infection in 50 HIV-positive women in Mali. Data included surveys, self-sampled vaginal swabs, and blood collection. HPV typing used GeneXpert, and PIN3 genotyping utilized AS-PCR.

Results: Participants, primarily >30 years (92%), had a mean age of 43.30 ± 10.332 years. HPV prevalence was 36%, with P3 being the most common subtype (30.8%). PIN3 genotypic frequencies were A1A1 (50%), A1A2 (34%), and A2A2 (10%). History of sexually transmitted infections correlated with higher mutation rates (37.8% A1A2, 10.8% A2A2). A2A2 genotype prevalence was higher in HIV-positive women with specific HPV subtypes (P5, P4, HPV16, P3, P18/45). A1A2 genotype was observed in 60% of HPV subtype P3 cases and 20% of P4 and P18/45 cases.

Conclusion: These results suggest a link between TP53 gene polymorphisms and susceptibility to different HPV subtypes in HIV-positive women, warranting further research into their functional implications and impact on HPV-related diseases in this population.

Keywords: TP53 polymorphism, HPV, HIV, Malian population

Citation Format: Mamoudou Maiga, Brehima Diakite, Yaya Kassogue, Ban Traore, Oumar Kassogue, Bakarou Kamate, Cheick B. Traore, Jane L. Holl, Lifang Hou. Relationship between PIN3 16bp duplication of TP53 and HPV in HIV women in Mali [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 7328.
Abstract 7347: A transcriptome correlation network analysis of the high grade serous ovarian tumor immune microenvironment
Authors: Carey Kaylin M. , Dammer Eric B. , Young Corey , Singh Rajesh , Griffen Ti'ara , Lillard James W.
Published: March 2024

High Grade Serous Ovarian Cancer (HGSOC) affects many women and is the most common and lethal histopathological type of ovarian cancer. The molecular subtypes delineated by TCGA–mesenchymal, proliferative, immunoreactive, and differentiated subtypes, offer a sophisticated and innovative framework for HGSOC classification. These subtypes not only provide a detailed molecular characterization but also contribute to understanding the HGSOC Tumor Immune Microenvironment (TIME), comprised of both immune and tumor cells. The interplay within the TIME significantly influences pro- or anti-tumor responses, creating an important link between molecular landscape and dynamic immune-tumor interactions. Currently, there is a lack of understanding for the key drivers of clinical outcomes, molecular phenotypes, and diagnostic biomarkers for HGSOC. Here, we answer the question, does immune cell type, and proportion, drive clinical and molecular subtyping of primary HGSOC? Primary ovarian tumor samples from The Cancer Genome Atlas, TCGA (n=358) samples were collected and RNA-sequenced. FPKM values were used to construct the Weighted Gene Correlation Network Analysis (WGCNA), Gene Ontology (GO) and Proportion Estimations of Immune and Cancer cells (EPIC). Enrichment of HGSOC network module overlaps using a Fischer Exact Test were used to identify novel components of HGSOC progression that were significantly associated with clusters of highly correlated gene expression profiles, HGSOC stage, grade, and molecular phenotypes. We show genes associated with T cell proliferation (CD84) and B cell regulation (CD37), epithelial to mesenchymal transition (DOCK2), adaptor proteins present in T cells and myeloid cells (LCP2), inflammatory and metabolic signaling modulators (AIF1,CD53, SASH3), immunosuppressors of T lymphocytes and dendritic cells (FGL2), cell proliferation (PI3K) and relevant tertiary lymphoid structure gene (TNFAIP8L2) significantly correlated with HGSOC progression in both estimated tumor and proportions of immune cells. Future studies aim to confirm phosphorylation cascades associated with the aggressive molecular phenotypes of HGSOC and immune cell pathobiology.

Citation Format: Kaylin M. Carey, Eric B. Dammer, Corey Young, Rajesh Singh, Ti'ara Griffen, James W. Lillard. A transcriptome correlation network analysis of the high grade serous ovarian tumor immune microenvironment [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 7347.
Abstract 7355: Integration analysis of lncRNAs and R-loops in 3D genome organization and gene regulation in the cancer genome
Authors: Wang Shengyuan , Wang Zhenjia , Wang Yuh-Hwa , Li Hui , Stukenburg Peter Todd , Zang Chongzhi
Published: March 2024

Existing evidence shows that some long non-coding RNAs (lncRNAs) can recruit chromatin regulators and form R-loops to mediate CCTCC-binding factor (CTCF) binding at topologically associated domain (TAD) boundaries to activate transcription of target genes. However, it remains unclear to what extent such lncRNA-dependent chromatin organization events occur genome-wide in normal and cancer cells. By curated public data of lncRNA, CTCF, RAD21 profiles and integrative analysis of multi-omics data using innovative computational approaches, we investigated global associations of lncRNAs and R-loops with activities of transcription factors and chromatin regulators in gene expression regulations across multiple human cell types. We developed a comprehensive computational pipeline for cross-cell-type analysis of lncRNA and protein-coding gene expression profiles and transcription factor binding profiles. We identified a total of 542 candidate genomic regions where lncRNAs play a pivotal role in regulating target genes by facilitating CTCF/cohesin binding. R-loops are enriched at CTCF/cohesin binding sites, suggesting their potential contribution to CTCF binding. Additionally, our findings underscore the significant cell-type specificity of CTCF binding patterns across the genome. This work adds knowledge to cancer genome organization and gene regulation, and builds foundations for further functional and mechanistic studies of lncRNAs and R-loops in the human genome.

Citation Format: Shengyuan Wang, Zhenjia Wang, Yuh-Hwa Wang, Hui Li, Peter Todd Stukenburg, Chongzhi Zang. Integration analysis of lncRNAs and R-loops in 3D genome organization and gene regulation in the cancer genome [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 7355.
Abstract 7356: 3 UTR variations in esophageal squamous cell carcinoma in African Americans
Authors: Erkizan Ceyda , Wadleigh Robert
Published: March 2024

Esophageal squamous cell carcinoma (ESCC) predominantly affects African Americans (AA). Esophageal Cancer (EC) consists of two major histological subtypes: esophageal adenocarcinoma and squamous cell carcinoma. ESCC ranks among the most lethal cancers and is particularly aggressive among AA, comprising about 75% of total ESCC patients. The 5-year survival rate for localized EC in AA patients is 25%; in contrast, the survival rate for EC patients of Caucasian origin is 48%. However, for metastatic disease, the survival rate decreases dramatically to 5% regardless of race. To conduct an extensive mutation screening, we performed whole exome sequencing (WES) in 10 paired AA ESCC and control tissues. Mutations included nonsynonymous mutations in multiple genes and copy number variations. Here, we report on further analysis of the WES data to identify 3 UTR noncoding region alterations, comprising the highest proportion of noncoding variations. Whole exome sequencing was performed using Agilent SureSelect XT Human All Exon V6 + UTR kit on matched normal-tumor samples from 10 AA patients (nine males and one female) with advanced-stage ESCC. The ages of patients ranged from 53 to 80 years. All patients, except for one, reported tobacco use and alcohol consumption. Our analysis yielded 5378 variants in noncoding regions in our cohort. The most variations were found in the 3UTR location, with 46% of all noncoding variations. In our dataset, variations in the 3UTR region of 48 genes were predicted by CScape to assert an oncogenic effect. The highest ten oncogenic predictive scores are for ETV1, FOXO3, MSI2, TCF7L2, KAT6A, FOXO1, IRF4, TRIM24, ELK4, and FGFR1 genes. Approximately 2500 genes having 3’UTR variations are over-presented in intracellular signaling and cell-cell communications, transcriptional regulation of pluripotent stem cells by OCT4, SOX2, NANOG, generic RNA polymerase II transcription, RHO GTPase cycle, and regulation of cytoskeletal remodeling. The combined effects of noncoding and coding region mutations may largely impact poor prognosis in AA with ESCC and yield targets for developing candidate therapeutics.

Citation Format: Ceyda Erkizan, Robert Wadleigh. 3 UTR variations in esophageal squamous cell carcinoma in African Americans [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 7356.
Abstract 7359: Priority targets in pancreatic cancer
Authors: Nwosu Zeribe Chike , di Magliano Marina Pasca , Lyssiotis Costas
Published: March 2024

Pancreatic ductal adenocarcinoma (PDAC) is a drug resistant and lethal cancer. To better understand this disease, we separately analyzed five published human PDAC microarrays, determined the differential genes in each dataset and defined a gene as ‘consistent’ if it is ‘upregulated’ or ‘downregulated’ in >4 datasets (adjusted P<0.05). We identified 2,010 consistently upregulated- and 1,928 downregulated genes, over 50% of which were previously uncharacterized in PDAC. These genes span multiple processes, including cell cycle, immunity, transporters, metabolism, signaling, transcription factors and epigenetics. - with cell cycle and glycolysis being the most altered. Many consistent genes correlated with tumor subtype, proliferation, metastasis, and ~41% predicted survival, notably, OGN, PLOD2, DIAPH3, C2orf40, ADM, UPP1, ZNF189, DCBLD2, PLAG1, and glycolysis genesALDOA, GAPDH, PKM and LDHA. We identified 451 high priority targets, including 185 upregulated genes (notably in cell cycle and glycolysis) whose knockdown suppressed PDAC cell growth in prior RNAi screen studies. Our results represent an important milestone in the quest for mechanisms, drug targets and biomarkers and could enable the discovery of novel mechanisms and therapies in PDAC.

Citation Format: Zeribe Chike Nwosu, Marina Pasca di Magliano, Costas Lyssiotis. Priority targets 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 7359.
Abstract 7364: Comprehensive multi-omics analysis for resectable hepatocellular carcinoma uncovers biomarkers to predict microvascular invasion
Authors: Kang Incheon , Kwon Woo Young , Lee Sung Hwan
Published: March 2024

Introduction: Microvascular invasion (MVI) is a well-known prognostic factor in predicting cancer relapse after curative resection of resectable hepatocellular carcinoma (HCC).Therefore, there is a clear unmet need for a precision strategy based on cancer-specific multi-omics features to predict the MVI feature at the initial diagnosis of HCC.

Methods: Using gene expression profiling for resected human HCC (Discovery cohort, n=240), we identified the transcriptomic signature predicting the MVI feature. Comprehensive analyses were performed using the dataset from the cancer dependency map (DepMap) project, including cancer-specific molecular characterization with multi-omics data, and drug sensitivity with compound screening, and integrative in-silico prediction methods to uncover MVI. The transcriptomic signature predicting the MVI feature were validated in independent translational cohorts (TCGA-LIHC; n=373, KOREA; n=188, TOKYO; n=183, MODENA; n=78, ZHONGSHAN; n=159).

Results: The MVI signature with 1028 genes was identified from robust statistical testing from the discovery cohort, and robust validation for the prediction performance of the MVI signature showed significant accuracy in the validation cohort (AUC=0.865, p<0.01). Multi-omics analysis revealed aggressive tumor biology associated with the MVI signature and specified biomarkers.

Conclusions: Integrative multi-omics profiling for resectable HCC uncovers biomarkers to predict MVI. A novel combination of biomarkers performs in sorting out the tumor with aggressive tumor biology. A precision strategy to discover resectable tumors beneficial from surgical resection can be established from consecutive clinical trials based on this translational study.

Citation Format: Incheon Kang, Woo Young Kwon, Sung Hwan Lee. Comprehensive multi-omics analysis for resectable hepatocellular carcinoma uncovers biomarkers to predict microvascular 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 7364.
Abstract 7399: Development of a reproducible AI-based spatial biomarker of the tumor immune infiltrate on H&E slides
Authors: Di Proietto Valentina , El-Khoury Jean , Adjadj Benjamin , Gillet Lucie , Marteau Ulysse , Schutte Kathryn , Von Loga Katharina
Published: March 2024

Background: The immune infiltrate in the tumor microenvironment (TME) has been shown to be associated with prognosis in several studies. However, a comprehensive assessment of the TME composition is not performed in routine practice due to the lack of standardized methods and tools for quantification. The aim of our study is to develop a reproducible, artificial intelligence (AI)-based, spatial biomarker of the tumor related immune response to predict patients outcome on routine Hematoxylin & Eosin (H&E) slides. To the best of our knowledge, this is the first study that implements a robust H&E pipeline to assess, across multiple cohorts, the prognostic power and the added-value of a spatial marker in comparison to non-spatial measures such as the overall lymphocytes density on the slide.

Methods: We trained AI models on both publicly available (NuCLS and Lizard) and proprietary datasets to automatically detect cells and tissue types on H&E stained Whole Slide Images of cancers from different origins.

We used these models on TCGA COAD and TCGA BRCA and computed spatial measures related to the lymphocyte densities in the tumor core versus the invasive margin as well as the immune infiltration in the tumor stroma (in between tumor islets) versus in the tumor islets themselves.

Univariate and multivariate survival analysis is performed through repeated cross-validation. A log-rank test on the stratified groups is performed for each evaluated marker, using the median value as cutoff.

Preliminary results on TCGA-COAD and TCGA-BRCA show that spatial markers of the tumor-related immune response are individually associated with overall survival, reinforcing findings from prior studies emphasizing the importance of the spatial relationship between tumor and immune cells. Multivariate analysis with both linear and non-linear models is currently ongoing across selected cohorts.

Citation Format: Valentina Di Proietto, Jean El-Khoury, Benjamin Adjadj, Lucie Gillet, Ulysse Marteau, Kathryn Schutte, Katharina Von Loga. Development of a reproducible AI-based spatial biomarker of the tumor immune infiltrate on H&E slides [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 7399.
Abstract 7428: S2Map: An online interactive analytical platform for quantitative signal measurement of cell Secretion Signal Map
Authors: Yue Zongliang , Zhou Lang , Huang Fengyuan , Chen Pengyu
Published: March 2024

Cell communication is predominantly governed by secreted proteins, whose diverse secretion patterns often signify underlying physiological irregularities. Unraveling the intricacies of these secreted signals at the single-cell level is crucial for a comprehensive understanding of regulatory mechanisms involving various molecular agents. To elucidate the array of cell secretion signals, encompassing both anisotropic and isotropic biomolecular cues from individual immune cells or disparate cell types, we introduce the Secretion Signal Map (S2Map). S2Map is an innovative online interactive analytical platform that incorporates qualitative metrics, the signal inequality index (SII) and the signal coverage index (SCI), which are exquisitely sensitive in facilitating the measurement of dissymmetry and diffusion of cumulative signals and signal dynamics in temporal analysis. S2Map's innovation lies in its depiction of signals through real-time secretion hotspots, and cumulative secretion contour lines, complemented by the visualization of potential cell secretion signal velocities via stream plots generated by regression models. We evaluated the SII and SCI performance in distinguishing the simulated signal diffusion model. Presently, S2Map hosts a repository of 12 datasets that map single-cell and two-cell secretion dynamics. These datasets serve as a resource to explore secretion signal types. We anticipate that S2Map will be a powerful approach to delve into the complexities of physiological systems, providing insights into the regulation of protein production, such as cytokines at the remarkable resolution of single cells. The S2Map server is publicly accessible via https://au-s2map.streamlit.app/.

Citation Format: Zongliang Yue, Lang Zhou, Fengyuan Huang, Pengyu Chen. S2Map: An online interactive analytical platform for quantitative signal measurement of cell Secretion Signal Map [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 7428.
Abstract 753: CEACAM1 induces microbiome and metabolite driven diversion of TGF-β signaling to promote colon cancer
Authors: Bhowmick Krishanu , Ohshiro Kazufumi , Xiang Xiyan , John Sahara , Yang Xiaochun , Idicula Kevin , Beauchemin Nicole , Mazumder Raja , Crandall Keith A. , Hassan Mohammad I. , Mohammad Taj , Mishra Lopa
Published: March 2024

Background: Colon cancer is rising in younger individuals in the United States. Potential causal factors are altered diets and gut microbiomes. Yet key signaling pathways, host-microbe interactions, and metabolites such as ammonia in cancer remain unclear. CEACAM1 responds to pathogenic microbes, interacts with the TGF-β/SPTBN1 and levels are raised in invasive colon cancer. Alterations in the TGF-β pathway occur ~40% of human GI cancers, and mouse models with disrupted TGF-β signaling (Tgfbr2−/−, Smad4+/−Sptbn1+/−, and Tgfb1−/−) develop colorectal cancer (CRC) that is dependent upon an altered gut microbiome. Our previous studies indicate the lipid metabolites (reactive aldehydes) form toxic adducts with cleaved SPTBN1 and divert TGF-β signaling to pro-oncogenic process. Poor prognosis CRC is associated with raised levels of microbial metabolites, such as ammonia. Thus, we hypothesized that “the intricate relationships among pathogen-binding CEACAM1, the gut microbiome, metabolites such as ammonia, and βII-Spectrin drive colon cancer development”.

Methods: We examined gut microbiota composition, immune cell population, inflammation, and cancers in Smad4+/−Sptbn1+/− and Sptbn1LSKO mice fed a normal chow diet or a high-fat diet (HFD). We evaluated CEACAM1 and TGF-β member alterations in in CRCs using TCGA datasets. Alphafold-based molecular modeling predicted interaction sites between βII-Spectrin and CEACAM1 was followed by functional studies.

Results: Increased CEACAM1 levels with alterations in TGF-β members were associated with lower survival (TCGA). Mice with disrupted TGF-β signaling (Smad4+/−Sptbn1+/−) develop CRC, have high CEACAM1 levels, and an altered gut microbiome signature. CEACAM1 interacts with βII-Spectrin, and levels are restored to normal in βII-Spectrin LSKO which restores the gut microbiome and blocks inflammation and cancer. Ammonia induces CASPASE-3 mediated cleavage of βII-Spectrin, forms toxic adducts and divert TGF-β signaling to pathological pro-oncogenic signaling, triggering CRC.

Conclusion: We have found a critical role for CEACAMs in CRC cancer development, through diverting the TGF-β signaling pathway to a pro-oncogenic phenotype. CEACAM1 and βII-Spectrin are attractive therapeutic targets for CRC.

Citation Format: Krishanu Bhowmick, Kazufumi Ohshiro, Xiyan Xiang, Sahara John, Xiaochun Yang, Kevin Idicula, Nicole Beauchemin, Raja Mazumder, Keith A. Crandall, Mohammad I. Hassan, Taj Mohammad, Lopa Mishra. CEACAM1 induces microbiome and metabolite driven diversion of TGF-β signaling to promote colon 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 753.
Abstract 7560: Microsatellite instability (MSI) detection using flow-based sequencing
Authors: Lithwick-Yanai Gila , Benjamin Hila , Cano-Nistal Jorge , Geisler Shir , Jaimovich Ariel , Iremadze Nika , Kessler Dror , Soifer Ilya , Lebanony Danit , Simhon Keren Ben , Gilad Shlomit , Meiri Eti , Lipson Doron , Maruvka Yosef E.
Published: March 2024

Background: Microsatellite instability (MSI) is an important genomic biomarker associated with various cancers and hereditary conditions. Accurate and efficient classification of MSI status is essential for diagnosis, prognosis, and treatment decisions. Different approaches for testing MSI have been presented in the literature, including NGS-based methods which either rely on comparison with a matched control sample, a set of reference control samples, or the reference genome (no control). In this study, we explore the feasibility of accurately identifying MSI status using the UG100 platform, which utilizes flow-based sequencing chemistry. Since MSI detection is typically based on long homopolymers, we examined here whether the flow-based sequencing data can be effectively used for MSI classification.

Methods: We performed whole genome sequencing (WGS) on a cohort of 24 cell lines with known MSI status, as well as on 15 tumor tissue samples, encompassing various cancer types, including colon, lung, bladder, and endometrial cancer. To determine the MSI status, polyA/T homopolymer loci were considered. We measured the MSI status in these loci using two methods: 1) Counting short indel variants detected using somatic Deep Variant, in comparison with matched blood normal, and 2) a novel MSI score based on the difference of the polyA/T homopolymer length, in comparison to the reference genome. We assessed the ability to evaluate the score for the full sequenced coverage (~100X) as well as when limiting to exome boundaries, and when sampling down to 1X coverage.

Results and Conclusions: We established the performance of the MSI score on the cell lines with known MSI status. The score was verified on cell line mixtures (simulating lower tumor purity) as well as on clinical samples from various tissue sources, including colon samples annotated as mismatch-repair deficient. We demonstrate the ability to use the cost-effective UG100 sequencing combined with the two methodologies to identify MSI-high samples in these scenarios.

Citation Format: Gila Lithwick-Yanai, Hila Benjamin, Jorge Cano-Nistal, Shir Geisler, Ariel Jaimovich, Nika Iremadze, Dror Kessler, Ilya Soifer, Danit Lebanony, Keren Ben Simhon, Shlomit Gilad, Eti Meiri, Doron Lipson, Yosef E. Maruvka. Microsatellite instability (MSI) detection using flow-based sequencing [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 7560.
Abstract 7576: Exemestane and its primary metabolite 17-hydroexemestane inhibit synergically the tumor growth of ER/AR positive breast cancer tumors
Authors: Santacana-Font Gemma , Kedra Darek , del Carmen García-Macías Maria , Cornelus-Reitsma Laurens , Lyngra Marianne , Sauer Torill , Kristensen Vessela , Hurtado Antoni , Geisler Jürgen
Published: March 2024

Exemestane, an aromatase inactivator of the third generation, plays a crucial role in breast cancer therapy by targeting the P450 aromatase enzyme and, thus, decreasing estrogen synthesis. Exemestane (Aromasin™) is currently the only steroidal aromatase inactivator widely used in clinical routine treatment of ER+ breast cancer in all phases of the disease in a global perspective. However, the complex mechanisms underlying its therapeutic effects, besides being an aromatase inhibitor, remain incompletely understood. In this study, we employed a combination of human samples and in vitro data to unveil a compelling insight: Exemestane (EXE) and its primary metabolite, 17β-hydroxyexemestane (HEXE), exhibit potent inhibitory effects on tumor growth when present together in patient serum. Our biochemical analysis establishes a critical threshold—20% HEXE metabolite of the total EXE in patient serum—to trigger a tumor growth inhibition exceeding 90%, as evidenced by Ki67 staining. Mechanistically, our data reveals that both HEXE and EXE bind to the Androgen Receptor (AR), triggering a synergistic activation that induces a transcriptional program leading to cell death while diminishing the intracellular signaling activated by the oncogene Ras. Notably, patients with tumors characterized by a minimum of 20% AR+ epithelial cancer cells stand to benefit the most from exemestane and HEXE. Intriguingly, the binding of AR to chromatin in tumors gives rise to a molecular signature capable of distinguishing responsive from non-responsive patients to both EXE and HEXE. Collectively, our findings elucidate a dual therapeutic role for Exemestane in selected patients: it not only restrains estrogen-driven proliferation by estrogen suppression but also stimulates cell death by establishing a specific interactome with the AR at the genomic level. These insights suggest that both EXE and HEXE are necessary to achieve the best therapeutic effects in ER+/AR+ breast cancer tumors. Moreover, our findings suggest that AR-expression and targeting should be investigated further to potentially add novel strategies to our existing algorithms in ER+/AR+ MBC.

Citation Format: Gemma Santacana-Font, Darek Kedra, Maria del Carmen García-Macías, Laurens Cornelus-Reitsma, Marianne Lyngra, Torill Sauer, Vessela Kristensen, Antoni Hurtado, Jürgen Geisler. Exemestane and its primary metabolite 17-hydroexemestane inhibit synergically the tumor growth of ER/AR positive breast cancer 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 7576.
Abstract 7579: Dual inhibition of enhancer of zeste homolog 1 2 induces pyroptosis, modulates oncogenic signaling pathways & sensitizes hepatocellular carcinoma to valemetostat & docetaxel treatments
Authors: Harira Asmaa Elkhder , Maher Adham , Sultan Ahmed
Published: March 2024

HCC is a global health concern, with chemotherapy resistance and patient recurrence posing significant challenges to liver cancer treatment. EZH2 is a crucial part of the polycomb repressive complex 2 (PRC2). It, along with its homolog EZH1, is a focus for cancer therapeutic targets. Dysregulation of EZH1/2 can cause cancer development due to significant changes in geneexpression. The current study aims to investigate the interaction between EZH1/2 and oncogenic signals responsible for HCC progression and pyroptosis induction. Two cell lines, HepG2 and SK-Hep1, were subjected to two FDA-approved drugs, Valemetostat (Val) and Docetaxel (Doc), to determine the impact of EZH1/2 on tumorigenicity and drug resistance. The WST-1 assay was utilized to gauge cell proliferation. The results indisputablydemonstrated a synergistic effect of the drugs after 48 h of treatment. The inhibition of viability was attributed to apoptosis induction in both tested cell lines, and the maximum effect was observed in the combined treatment as compared to either the control or each drug alone. Furthermore, our datashowed activation of caspase-3, upregulation of BAX, indicating apoptotic induction, and downregulation of Bcl-2, Bcl-XL, AKT, S6k, oncogenic β-catenin, and Stat3 protein expression levels, suggesting a modulation of oncogenic signaling pathways at the protein level. After 24 h of Val/Doc treatment, pyroptosis was observed, characterized by cell swelling and bubbles on themembrane and a significant release of lactate dehydrogenase, indicating pyroptotic cell cytotoxicity. The antitumor effects and pyroptosis were enhanced by using a dual inhibitor, UNC1999, for EZH1/2, resulting in a marked increase in the sensitivity of tested cells to the Val/Doc treatment invitro. The present study unequivocally demonstrated that dual inhibition of EZH1/2 acts as a potent sensitizer of HCC cells to Val/Doc treatment, which might be a promising therapeutic approach for inducing cellular pyroptosis in HCC cell lines.

Citation Format: Asmaa Elkhder Harira, Adham Maher, Ahmed Sultan. Dual inhibition of enhancer of zeste homolog 1 2 induces pyroptosis, modulates oncogenic signaling pathways & sensitizes hepatocellular carcinoma to valemetostat & docetaxel treatments [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 7579.
Abstract 7585: Targeting of 7 or 24 dehydrocholesterol reductase decreases cancer progression in head and neck cancer
Authors: Lee Bok-Soon , Choi Ji-Hye , Kim Hyo Jeong , Roh Jin , Padilla Joselyn , Brock Kennedy Davis , Jang Jeon Yeob , Woo Hyun Goo , Kim Chul-Ho , Lee Jiyoung
Published: March 2024

The elevated expression of cholesterol metabolism has been associated with many cancer including head and neck squamous cell carcinoma (HNSCC). However, the molecular mechanisms between cholesterol biosynthesis and head and neck cancer have not yet been studied. In this study, we identified upregulation of dehydrocholesterol reductase such as DHCR7 or DHCR24 in HNSCC compared with adjacent normal tissues from the same patients using RNA sequencing data. We observed protein expression level of DHCR7 or DHCR24 in head and neck cancer cell lines through Western blotting. We also checked high expression of DHCR7 or DHCR24 in HNSCC tissues from patients using immunohistochemistry assays. Yet, when DHCR7 or DHCR24 was knocked down using siRNA, the viability of HNSCC cells was decreased in MTT assays. In parallel, we adapted small inhibitory drugs; AY9944 for DHCR7 inhibition and Triparanol or SH-42 for DHCR24 inhibition. Treatment of AY9944, Triparanol, or SH-42 also resulted in decreased viability of HNSCC cells. Moreover, when we used a cholesterol blocker, MCD, the cell viability was decreased, whereas the cells overcame cell death by adding the combination of cholesterol and LDL. Taken together, we concluded that head and neck cancer requires DHCR7 and DHCR24 activity involved in cholesterol metabolism for cancer growth. Our data suggest that targeting DHCR7 or DHCR24 using AY9944, Triparanol or SH-42 is one of the potential strategies that will definitely help with cancer treatment for head and neck cancer.

Citation Format: Bok-Soon Lee, Ji-Hye Choi, Hyo Jeong Kim, Jin Roh, Joselyn Padilla, Kennedy Davis Brock, Jeon Yeob Jang, Hyun Goo Woo, Chul-Ho Kim, Jiyoung Lee. Targeting of 7 or 24 dehydrocholesterol reductase decreases cancer progression in head and neck 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 7585.
Abstract 7597: Therapeutic potential of ketogenic diet as an adjuvant to lenvatinib treatment in hepatocellular carcinoma
Authors: Zhang Minghe , Lee Terence Kin-Wah , Ma Stephanie , Tong Man
Published: March 2024

Hepatocellular carcinoma (HCC) has been a major public health concern worldwide for decades because of its high mortality rates and poor prognosis, which are attributable to frequent tumor relapse and limited treatment regimens. Lenvatinib is one of the tyrosine kinase inhibitors approved for first-line treatment of advanced HCC, but its efficacy remains modest. Growing evidence suggest that the unsatisfactory survival benefits of lenvatinib could be attributed to the acquired drug resistance developed in HCC patients. In this study, we aim to explore the intrinsic metabolic vulnerability which could be exploited to enhance the treatment efficacy of lenvatinib in HCC. Our previous study showed that loss of tyrosine catabolism accompanied with a reduced downstream ketone metabolite beta-hydroxybutyrate (BHB) supports HCC initiation. To explore the therapeutic value of BHB in potentiating lenvatinib treatment in HCC, tyrosine catabolism-suppressing HCC cells were treated with BHB. We found that BHB treatment suppressed cell proliferation, increased cellular reactive oxygen species and potentiated the efficacy of lenvatinib treatment. Similar tumor-suppressive effect was observed when BHB was administered in vivo in mice bearing HCC patient derived xenograft. Combination treatment of lenvatinib and ketogenic diet which induces BHB level could drastically attenuate tumor development in immunocompetent mice bearing hepatic tumors. This study presents a potentially translatable combination treatment regimen to potentiate the therapeutic efficacy of lenvatinib in advanced HCC.

Citation Format: Minghe Zhang, Terence Kin-Wah Lee, Stephanie Ma, Man Tong. Therapeutic potential of ketogenic diet as an adjuvant to lenvatinib treatment 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 7597.