bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5863: Double-negative prostate cancer emerges through a mixed basal, club, and hillock cell identity driven by KLF5
Authors: Pitzen Samuel , Qiu Yinjie , Munro Sarah , Dehm Scott
Published: March 2024

The purpose of this study was to characterize the phenotypes and drivers of therapy-induced lineage plasticity during the development of castration resistant prostate cancer (CRPC). While the majority of localized prostate cancer can be cured with surgery or radiation, metastatic disease is lethal. Therapies targeting the androgen receptor (AR) are initially effective, but eventually men will develop CRPC. About 70-75% of CRPC displays restored AR signaling (ARPC), while the remaining 25-30% display lineage plasticity evidenced by the emergence of AR-negative subtypes including those that display neuroendocrine (NE) markers, or double negative CRPC (DNPC) lacking both AR and NE markers. AR independent manifestations of CRPC represent a clinical challenge because no effective therapies are available and therapeutic targets are largely unknown. We analyzed publicly available bulk and single-cell RNA-seq datasets derived from clinical CRPC specimens to characterize the cellular identity of AR-negative tumors. Using a database of all known transcriptional regulators, we identified potential drivers of these phenotypes. We performed siRNA-mediated knockdown experiments in a model of DNPC to explore the extent to which the candidate regulators maintain AR-negative cell identity and sustain growth of DNPC prostate cancer cells. We identified a subset of CRPC tumors that co-express gene sets defining basal, club, and hillock cells in the benign prostate. This data supports the existence of epithelial cell lineage plasticity manifesting within CRPC tumors, as well as individual CRPC tumor cells, wherein AR-positive tumor cells transform to a phenotype encompassing basal, club, and hillock cell identities. We nominated the stem cell transcription factor KLF5 as a regulator of basal, club, and hillock cell identities in CRPC. In cell line models of DNPC, knock down of KLF5 inhibited cell growth and reduced the expression of genes defining basal, club, and hillock cell identities. This work links a prevalent and poorly-defined subtype of AR-negative CRPC to AR-negative epithelial cell types in benign prostate tissue. Inhibition of KLF5 and its downstream effectors could represent a therapeutic strategy to prevent or delay lineage plasticity and thereby extend patient response to AR-targeted therapies.

Citation Format: Samuel Pitzen, Yinjie Qiu, Sarah Munro, Scott Dehm. Double-negative prostate cancer emerges through a mixed basal, club, and hillock cell identity driven by KLF5 [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 5863.
Abstract 5874: Phenotypic plasticity of TKI resistance reprograms cytoskeleton organization through cadherin-catenin and integrin pathways
Authors: Ma Chun , Chen Jerry Chieh-Yu , Wang Mong-Lien
Published: March 2024

The acquired resistance to EGFR tyrosine kinase inhibitors (TKIs) restricts its clinical utility. Clinically, acquired resistance has been highly associated with epithelial-mesenchymal transition (EMT) traits. In this study, we characterized shared phenotypic plasticity features of TKI-resistant cells and aimed to find its key driver in three different cell lines harboring mutant EGFR. In vitro resistance cell lines were generated by dose-escalation exposure to osimertinib, a 3rd generation TKI, for more than 2 months. We employed canonical markers (E-cadherin, vimentin, pan-cytokeratin, and N-cadherin) along with additional markers (EpCAM and fibronectin) to define the EMT status of resistant cells. Moreover, cytoskeleton architecture (F-actin and Vimentin) was utilized to clarify the types of cell motility. Transcriptomics analysis illustrated enriched pathways at focal adhesion and adherens junction. Loss of adherens junction-related catenin (α-E-catenin, β-catenin, γ-catenin, p120 catenin) and aberrant activation of focal adhesion-related protein (p-FAK Y397 and Y576/57, p-Src Y416) confirmed the transcriptomics analysis of reduced contact inhibition and cell polarity. The resulting migration mode of resistant cells highly resembles ameboid movement. Mechanistically, we identified that YTHDF3, a metastasis-promoting regulator of mRNA methylation, destabilizes the mRNA of E-cadherin. Depletion of YTHDF3 in resistant cells reversed the cadherin-catenin pathway and distribution of vimentin and f-actin. In conclusion, resistant cells display ameboid-like movement resulting from loss of contact inhibition and aberrant activation of focal adhesion. Mechanistically, we identified that YTHDF3, a metastasis-promoting regulator of mRNA methylation, destabilizes the mRNA of E-cadherin. Depletion of YTHDF3 in resistant cells reversed the cadherin-catenin pathway and distribution of vimentin and f-actin. YTHDF3 serves as an RNA epitranscriptomic regulator that destabilizes CDH1 mRNA, thereby disrupting adherens junction formation and reducing integrin-mediated focal adhesion stabilization.

Citation Format: Chun Ma, Jerry Chieh-Yu Chen, Mong-Lien Wang. Phenotypic plasticity of TKI resistance reprograms cytoskeleton organization through cadherin-catenin and integrin pathways [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 5874.
Abstract 5892: SCUBE3 promotes therapy resistance in triple negative breast cancer
Authors: Singh Deepika , Medina Daisy , Onyeagucha Benjamin , Mojidra Rahul , Subbarayallu Panneerdoss , Taylor Alex , Lyu Dongwen , Timilsina Santosh , Venkata Prabhakar Pitta , Nirzhor Saif S R , Abdulsahib Shahad M. , Do Trong Phat , Chen Yidong , Vadlamudi Ratna , Rao Manjeet K.
Published: March 2024

Introduction: The development of novel targeted therapies is urgently required for improving the outcome of triple negative breast cancer (TNBC) patients. Chemotherapy is the common treatment option for TNBC. However, resistance and tumor relapse remain the major obstacles hindering the effectiveness of chemotherapeutic agents in cancer patients. Therefore, identifying genes/factors that sensitize breast cancer cells to chemotherapeutic agents could improve treatment outcome in patients. Here we report Signal peptide CUB domain EGF-like 3 (SCUBE3) genes as a novel therapeutic adjuvant that can improve the efficacy of doxorubicin, a chemotherapeutic agent commonly used in treating breast cancer patients.

Methods: Unbiased high-throughput loss of function genomic screen was performed on breast cancer cells in the presence or absence of doxorubicin. Breast cancer cells lines (MDA-MB-231 and MDA-MB-468) were purchased from the American Type Culture Collection and cultured in standard medium. Breast cancer cells were transfected either with SCUBE3 overexpression plasmid or shRNA specific to SCUBE3. These overexpression/knockdown breast cancer cells were analyzed for cell viability, migration, invasion, colony formation, cell cycle, apoptosis assays, western blotting, and in vivo tumor xenograft study.

Results: Our finding demonstrated that SCUBE3 promotes breast cancer cell progression as knockdown of SCUBE3 inhibited the ability of breast cancer cells to form colony, migrate, and invade, while overexpression of SCUBE3 promoted tumor growth in preclinical mouse models. Our results revealed that SCUBE3 mediates its protumor effects by regulating genes involved in growth and survival in the MAPK pathway, DNA damage surveillance pathway including RAD51 and FOXM1, and apoptotic pathway including Mcl-1. We demonstrated that SCUBE3 promotes tumor growth and progression by interacting with and activating several oncoproteins.

Conclusions: Overall, our data suggests that SCUBE3 can be a potent therapeutic target for treating TNBC patients.

Citation Format: Deepika Singh, Daisy Medina, Benjamin Onyeagucha, Rahul Mojidra, Panneerdoss Subbarayallu, Alex Taylor, Dongwen Lyu, Santosh Timilsina, Prabhakar Pitta Venkata, Saif S R Nirzhor, Shahad M. Abdulsahib, Trong Phat Do, Yidong Chen, Ratna Vadlamudi, Manjeet K. Rao. SCUBE3 promotes therapy 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 5892.
Abstract 5912: Rational design of a small-molecule inhibitor targeting the allosteric site of sos1 in oncogenic k-ras pancreatic cancer
Authors: Duan Xin , Evelyn Chris R , Biesiada Jacek , Johnson James F , Seibel William L. , Meller Jaroslaw , Zheng Yi
Published: March 2024

Oncogenic Kras signaling is a key therapeutic target in human cancers. Ras activation is catalyzed by guanine nucleotide exchange factors (GEFs), of which SOS1 is a major player that transduces receptor tyrosine kinase signaling to Ras. In addition to recently devised oncogenic Kras targeting small molecule inhibitors, disrupting the catalytic interaction between Ras and SOS1 has emerged as an attractive therapeutic strategy in working synergistically with Kras inhibitors and overcoming resistance. Previous studies have demonstrated an active “feed forward” loop of active Kras binding to the allosteric site of SOS1 that further stimulates SOS1 catalytic activation of wild type H/N/Kras, which is required for oncogenic Kras driven tumorigenesis. Here we have developed a rational approach that combines virtual screening with experimental screening to identify small molecule inhibitors that target the allosteric site of SOS1 to suppress oncogenic Kras mediated SOS1-regulated wild-type Ras activities. Unlike SOS1 catalytic site inhibitors which can have significant toxicity due to their ability to inhibit normal Ras signaling function, the lead SOS1 allosteric inhibitors developed in our laboratory binds to the allosteric site of SOS1 and blocks active Ras interaction with SOS1: we found these inhibitors can competitively suppresses SOS1-Ras interaction at the SOS1 allosteric site and dose-dependently inhibits the feed-forward SOS1 GEF activity. Mutagenesis and structure-activity relationship studies mapped the site of action to the SOS1 allosteric site, and preliminarily defined the chemical moieties in the inhibitor essential for the activity. The inhibitor showed dose-dependent and selective efficacy in inhibiting WT Ras activity, downstream signaling activities, and associated cell proliferation in KRAS mutation cells but not KRAS wild-type cells. Compared to the SOS1 catalytic inhibitor, BI3406, our inhibitors showed better selectivity for KRAS mutant pancreatic cancer cells vs. WT KRAS cells. These studies establish a proof of principle for the rational design of small molecule inhibitors targeting an oncogenic Kras specific allosteric site of SOS1 and provide a novel therapeutic concept to target KRAS-driven tumors more effectively.

Citation Format: Xin Duan, Chris R Evelyn, Jacek Biesiada, James F Johnson, William L. Seibel, Jaroslaw Meller, Yi Zheng. Rational design of a small-molecule inhibitor targeting the allosteric site of sos1 in oncogenic k-ras 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 5912.
Abstract 5941: Small molecule NSC59984 synergizes with PARP inhibitors in BRCA1 wild type ovarian cancer
Authors: Zhang Shengliang , Zhou Lanlan , Zhang Leiqing , Pinho-Schwermann Maximilian , Carneiro Benedito , Sedivy John , El-Deiry Wafik S.
Published: March 2024

PARP inhibitors (PARPi) targeting poly (ADP-ribose) polymerase are the first clinically approved drugs designed to apply synthetic lethality in BRCA1 mutant/deficient cancer. However, the treatment can cause reversion of BRCA mutation which results in drug resistance. To explore new strategies to improve antitumor efficacy of PARPi, we applied PARPi in combination with a small molecule NSC59984 for cancer therapy. NSC59984 is a small molecular targeting mutant p53 degradation and activating p73 via ROS-ERK2-MDM2 pathway. The treatments with radiation or hydrogen peroxide showed that NSC59984 enhanced DNA comet tails and gamma-H2AX, correlated to reduction of rad51 foci in cancer cells. These results suggest that NSC59984 impairs DNA damage repair via abrogation of homologous recombination (HR). We further applied the combinational treatment of NSC59984 and PARPi in BRCA1 wild-type ovarian cancer cells and found that NSC59984 synergized with PARPi to reduce cell viability, inhibit colony formation, and increase cell death. The combination treatment enhanced DNA damage and correlated with reduction of BRCA1 at the protein level. These results, taken together, suggest that the induction of BRCAness causes a synthetical lethality with PARPi in BRCA1 wild-type cancer cells. Cell cycle profiling showed that the cells were arrested at the G2/M phase in response to combinational treatment. At the G2 phase arrest, the high doses of the combinational drugs led to cell death via mitotic catastrophe, and the intermediate doses induced cellular senescence defined by senescence phenotypic hallmarks including senescence-associated beta-gal staining and a secretome consistent with senescence-associated secretory phenotype (SASP). Therapy-induced senescence (TIS) in cancer cells is considered as one of the mechanisms of tumor recurrence and drug resistance. To reduce the risk of TIS in treatment, we applied senolytic treatment to target senescent cells in the combinational treatment. The senolytic drug ABT263 treatment eliminated the senescent cancer cells from the combinational treatment. ABT263, NSC59984 + PARPi combinational treatment further reduced cell viability. Our study provides a rationale for small molecular compounds targeting HR deficiency in combination with PARPi to treat BRCA1wild-type ovarian cancer cells, and additional senolytic treatment may be required to limit resistance by removal of the TIS.

Citation Format: Shengliang Zhang, Lanlan Zhou, Leiqing Zhang, Maximilian Pinho-Schwermann, Benedito Carneiro, John Sedivy, Wafik S. El-Deiry. Small molecule NSC59984 synergizes with PARP inhibitors in BRCA1 wild type 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 5941.
Abstract 5955: In vivo precision therapy for glioblastoma using a nanodrug targeting microRNA-10b
Authors: Kim Bryan Doyun , Kenyon Elizabeth , Chen Ming , Mondal Sujan , Carvalho Ana de , Moore Anna
Published: March 2024

Glioblastoma multiforme (GBM) is the most common and aggressive primary brain malignancy, which accounts for about half of all brain tumors. Notably, GBM has been shown to express high levels of microRNA-10b (miR-10b) compared to normal brain tissue, which expresses virtually no miR-10b. Importantly, the mounting body of evidence suggests that suppressing miR-10b in glioblastoma cells disrupts various pathways involved in tumor formation, ultimately leading to the suppression of tumor growth and an increase in apoptosis. We have recently reported that our experimental nanodrug targeting miR-10b (MN-anti-miR10b) effectively suppresses miR-10b expression, inhibits tumor cell migration and invasion, and decreases GBM cell viability in vitro. MN-anti-miR10b consists of an iron oxide core with cross-linked dextran, which acts as the delivery vehicle, and is further conjugated with Cy5.5 fluorophores and therapeutic anti-miR-10b locked-nucleic acid antagomirs. The iron oxide core provides MR imaging contrast while Cy5.5 enables optical imaging modalities in vivo. In this study, U251, human GBM cells, were orthotopically implanted in nude, athymic mice and injected via tail vein with PBS, scrambled antagomir vehicle control (MN-Scr), or MN-anti-miR10b (10 and 20 mg Fe/kg), beginning on day 7 post-implantation. Mice were injected with respective treatments once a week for 6 weeks before assessing changes in survival and expression of miR-10b. In one trial, we assessed the differences in survival between treatment groups after completion of the injection regimen and found that MN-anti-miR10b can increase survival compared to control groups. In another trial, mice were euthanized one week after the last injection and GBM tissues were assessed for miR-10b expression by qRT-PCR. RNA samples extracted from this trial have been submitted for RNA sequencing and differential gene expression analysis will be performed. Here, we demonstrated in vivo that MN-anti-miR10b can efficiently decrease miR-10b expression (57%) and increase median survival (MN-anti-miR10b: 54.5 days vs MN-Scr: 44 days vs PBS: 44 days) compared to PBS and MN-Scr treatment groups. These studies suggest the use of MN-anti-miR10b can be effective in the treatment of GBM in vivo.

Citation Format: Bryan Doyun Kim, Elizabeth Kenyon, Ming Chen, Sujan Mondal, Ana de Carvalho, Anna Moore. In vivo precision therapy for glioblastoma using a nanodrug targeting microRNA-10b [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 5955.
Abstract 5963: VGLL1-derived peptides demonstrated anticancer effect by inhibiting VGLL1-TEAD4 interaction
Authors: Ock Sangmi , Lee Changsub , Jung Wongi , Whang Ina , Kim Kyung-Soo , Han Jongmin , Yim Sujin , Kim Bo-Kyung , Lee Hong-Sub , Chang Kwan-Young , Won Misun
Published: March 2024

YAP/TAZ, cofactors of TEA domain-containing transcription factor TEADs (TEAD1-4), play a key role in the HIPPO pathway, which is involved in various function including embryonic development, organ size, cell proliferation, tissue regeneration, and the development and progression of several cancers. YAP/TAZ is therefore considered as master regulators of various cancers. However, we are interested in VGLL1, a cofactor of TEAD4, because it is mainly involved in the proliferation and metastasis of various cancers, including gastric, breast, pancreatic, and ovarian cancers. In gastric cancer, VGLL1 expression is regulated by the PI3K/AKT/β-catenin pathway. VGLL1 is then phosphorylated at S84 by TGF-β/ribosomal S6 kinase 2 (RSK2) and interacts with TEAD4 to express target genes such as MMP9, cyclin D1, IGFBP3, IGFBP5 and ITGαV. which are involved in cancer malignancy. We designed S84-containing VGLL1-derived peptides (VGLL1S84 peptides, SCVP), which consist of 7 to 15 amino acids linked to CPP, a cell-penetration peptide. We evaluated SCVP to inhibit the VGLL1-TEAD4 interaction and their therapeutic potential as anticancer agents. SCVP suppressed the growth of gastric and breast cancer cells expressing high levels of VGLL1, EGFR, and/or HER2. In the RNA-seq analysis of NUGC3 to elucidate the molecular mechanisms of SCVP induced cell death, SCVP-treated cells showed gene expression changes in metabolic pathway, RAS signaling, PI3K-AKT signaling, Wnt signaling, TNF signaling, and mTOR signaling. However, RNA-seq analysis of breast cancer cells treated with SCVP showed changes in the expression of genes involved in cell cycle, DNA replication, DNA repair, and apoptosis. Then, we performed CRISPR/Cas9 screening using SCVP and sgRNA library to explore companion biomarkers and genetic interactors of VGLL1 for targeted cancer therapy. As a result, we identified several candidate genes, including ZNF292 and PLK1, as synthetic lethal genes of VGLL1. As expected, HCC70 cells with ZNF292 mutation showed increased sensitivity to SCVP. We also found that SCVP in combination and the PLK inhibitor volasertib resulted in a synergistic effect on the growth inhibition of breast cancer cells. In conclusion, we demonstrated VGLL1 as a novel target for anticancer drug development, and elucidated the molecular mechanism and therapeutic potential of the SCVP in gastric and breast cancers.

Citation Format: Sangmi Ock, Changsub Lee, Wongi Jung, Ina Whang, Kyung-Soo Kim, Jongmin Han, Sujin Yim, Bo-Kyung Kim, Hong-Sub Lee, Kwan-Young Chang, Misun Won. VGLL1-derived peptides demonstrated anticancer effect by inhibiting VGLL1-TEAD4 interaction [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 5963.
Abstract 6029: 225Ac/89Zr labeled anti nectin 4 radioimmunoconjugates as theranostics against nectin 4 positive triple negative breast cancer
Authors: Babeker Hanan , Njotu Fabrice , Ketchmen Jessica , Tikum Florence , Doroudi Alireza , Nwangele Emmanuel , Uppalapati Maruti , Fonge Humphrey
Published: March 2024

Nectin4 (N4) is a biomarker that is overexpressed in ~62% of triple negative breast cancer (TNBC) and its lack of expression in normal tissues makes it an ideal target for the therapy and PET imaging of TNBC. Methods: We developed a fully human antibody against nectin 4 (anti N4) using phage display. Anti N4 was radiolabeled with 89Zr & 225Ac, respectively, for imaging & radiotherapy using TNBC xenograft & syngeneic mouse models. TNBC murine 4T1 cells were transduced with human N4 and N4 expression was confirmed by FACS. Biodistribution & PET imaging of 89Zr anti N4 radioimmunoconjugate (RIC) was studied in mice bearing N4 positive xenografts. Dosimetry of 225Ac anti N4 was studied in healthy mice & the therapeutic efficacy was evaluated for 90 days in mice bearing MDA MB 468 xenograft & transduced 4T1 syngeneic models. Mice were treated with 2 doses of 350 nCi administered at 10 days apart. Tumor growth was monitored by a digital caliper. Results: The pharmacokinetic profile of 89Zr-anti-N4 RIC showed biphasic distribution with a moderate elimination of 63 h. PET imaging & biodistribution of 89Zr anti N4 in mice bearing MDA MB 468 xenograft showed high tumor uptake of 13.2 ± 1.12 %IA/g at 120 h. 225Ac anti N4 was effectively internalized in MDA MB 468 and was cytotoxic to the cells with IC50 of 1.2 kBq/mL. Treatment with 225Ac anti N4 led to complete tumor remission in all mice bearing MDA MB 468 xenografts and 4T1 syngeneic model by day 20 and 28, respectively. Conclusions: 89Zr anti N4 was an effective PET imaging probe with specific uptake in tumor. 225Ac anti N4 was effective as a therapeutic agent resulting in complete remission of tumors in both mouse xenograft & syngeneic models. These results are promising for the development of anti-N4 RICs as theranostics for TNBC.

Citation Format: Hanan Babeker, Fabrice Njotu, Jessica Ketchmen, Florence Tikum, Alireza Doroudi, Emmanuel Nwangele, Maruti Uppalapati, Humphrey Fonge. 225Ac/89Zr labeled anti nectin 4 radioimmunoconjugates as theranostics against nectin 4 positive 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 6029.
Abstract 6091: Multi-cancer early cancer detection and cancer-type identification with high sensitivity non-invasive using urine: Pancreatic lung cancer early detection
Authors: Luccio Eric Di , Hirotsu Takaaki
Published: March 2024

N-NOSE, a breakthrough cancer detection test from HIROTSU BIO SCIENCE, utilizes the unique chemotactic behavior of the nematode C. elegans. This nematode is drawn to the urine of individuals with 15 different types of cancers (including stomach, colon-rectum, lung, breast, pancreas, liver, prostate, uterus, esophagus, gallbladder, bile duct, kidney, urinary bladder, ovary, oropharynx) while avoiding urine from healthy persons, making N-NOSE a comprehensive primary screening tool. It has a high accuracy rate, with 87.5% sensitivity and 90.2% specificity for early-stage cancers. Being non-invasive and reasonably priced, N-NOSE has been a significant success in Japan since its 2020 launch, with over 500,000 screenings.This presentation delves into the technology aspect of N-NOSE in Japan, comparing its clinical research and key findings with competitors to underscore its effectiveness in early cancer detection. Furthermore, N-NOSE now advances to not only detect cancer but also identify its type in a noninvasive way, using urine and with high PPV.With pancreatic cancer being particularly lethal, we outline “N-NOSE plus pancreas,” the world’s first pancreatic cancer detection test at an early stage. This involves genetically modifying C. elegans to react specifically to early-stage pancreatic cancer urine samples, a development centered on the newly identified cr-4 GPCR in AWC neurons. Next, we profile our newest liver-cancer-specific test, “N-NOSE plus liver,” which offers early liver cancer detection with high sensitivity and specificity using urine.Finally, we highlight how N-NOSE bridges the gap in cancer screening and type identification, offering a complete, non-invasive solution.

Citation Format: Eric Di Luccio, Takaaki Hirotsu. Multi-cancer early cancer detection and cancer-type identification with high sensitivity non-invasive using urine: Pancreatic lung cancer early detection [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 6091.
Abstract 6099: Identification of intrinsic precursors of Barrett's and gastric intestinal metaplasia
Authors: Xian Wa , McKeon Frank , Yamamoto Yusuke , Khorrami Melika , Khorrami Melina , Mory Zaal , Siegelman Jeremy , Su Amber , Montes Raul Caballero , Hoffman Ashley , Ajani Jaffer , Crum Christopher , Bachovchin William , Wang Shan , Vincent Matthew , Nguyen Crystal
Published: March 2024

The origin of Barrett's esophagus (BE) and gastric intestinal metaplasia (GIM), obligate precursors of esophageal adenocarcinoma (EAC) and intestinal gastric cancer (iGC), has intrigued investigators for decades and would likely guide preemptive strategies. From endoscopic biopsies of clinically confirmed BE and GIM, we have cloned stem cells committed to intestinal metaplasia in vitro. Remarkably, the gene expression profiles of BE and GIM stem cells are highly related down to broad arrays of transcription factors compared with stem cells of the normal gastric mucosa. Using cell surface markers in common between BE and GIM stem cells, we have identified clusters of cells at the squamocolumnar junction and the distal stomach in mice and have used Fluorescence-activated cell sorting (FACS) to clone these cells from both sites. These murine clones can be differentiated in air-liquid interface cultures, and both are committed to intestinal metaplasia marked by goblet cells and Alcian blue staining. To ask whether similar cells exist in humans, we generated stem cell libraries from endoscopic biopsies taken from the gastroesophageal junction (GEJ) and the antrum-body junction (ABJ) in patients without BE or GIM. FACS sorting of these stem cell libraries using the same cell surface markers common to BE and GIM stem cells and the murine precursors, we have identified stem cells from the GEJ and ABJ that show similar gene expression profiles and share a commitment to intestinal metaplasia upon in vitro differentiation. Using identical transformation protocols involving retrovirally transduced protooncogenes, we find that these transformed intrinsic cells give rise to tumors with expression profiles similar to EAC and iGC in TCGA datasets, whereas transformed gastric mucosal stem cells yield tumors marked by signet ring cells typical of diffuse gastric cancer. Lastly, we find that drugs we have developed that target the stem cells of BE and GIM also eliminate the putative precursor cells of BE and GIM, suggesting the potential of therapeutics that might eliminate the emergence of intestinal metaplasia and the cancers derived from them.

Citation Format: Wa Xian, Frank McKeon, Yusuke Yamamoto, Melika Khorrami, Melina Khorrami, Zaal Mory, Jeremy Siegelman, Amber Su, Raul Caballero Montes, Ashley Hoffman, Jaffer Ajani, Christopher Crum, William Bachovchin, Shan Wang, Matthew Vincent, Crystal Nguyen. Identification of intrinsic precursors of Barrett's and gastric intestinal metaplasia [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 6099.
Abstract 6145: A trans-ethnic meta-analysis identified additional novel genomic loci associated with cervical cancer
Authors: Kamiza Abram Bunya , Brandenburg Jean-Tristan , Ramsay Michele , Mathew Christopher
Published: March 2024

Introduction: Cervical cancer is the second most common cause of cancer-related deaths among women worldwide. Genome-wide association studies (GWAS) have identified genetic variants associated with cervical cancer. However, these discoveries have been limited by the small sample sizes of the individual cohorts. To identify additional novel loci associated with cervical cancer, we performed a trans-ethnic meta-analysis.

Methods: GWAS summary data for trans-ethic meta-analysis were identified in women of European ancestry from the UK Biobank, East Asian ancestry from Biobank Japan, and African ancestries from the pan-UK Biobank and Johannesburg cancer study. Meta-analyses were performed using fixed effect inverse variance weighted method implemented in GWAMA. To localize putative genomic loci associated with cervical cancer, we performed fine mapping using the Bayesian approach by calculating the marginal posterior probability of causality for each single nucleotide polymorphisms (SNPs) and 99% credible set size.

Results: Our meta-analysis identified four additional novel genomic loci associated with cervical cancer. These loci include: rs147778467 (odds ratio [OR] = 1.12, 95% confidence interval [CI] = 1.08-1.16, P-value = 3.12 x 10-08) in RGS21, rs53150478 (OR =1.03, 95%CI = 1.01-1.05, P-value = 4.48 x 10-08) in MAN1C1, rs113842373 (OR = 0.68, 95%CI = 0.56-0.81, P-value = 2.31 x 10-09) in LINCO1850 and rs75372437 (OR = 0.80, 95%CI = 0.72-0.88, P-value = 3.32 x 10-08) in RNU6-356P. These loci are implicated in carcinogenic pathways. Moreover, our Bayesian fine mapping identified five loci with a marginal posterior probability of causality > 1 and reduced the 99% credible set sizes.

Conclusion: We identified additional novel loci associated with cervical cancer and our fine mapping identified loci with a high posterior probability of being causal.

Citation Format: Abram Bunya Kamiza, Jean-Tristan Brandenburg, Michele Ramsay, Christopher Mathew. A trans-ethnic meta-analysis identified additional novel genomic loci associated with cervical 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 6145.
Abstract 6216: Single cell DNA sequencing of BRAF treatment resistant anaplastic thyroid cancer
Authors: Thennavan Aatish , Tarabichi Maxime , Wu Per , Martin Meghan , Dadu Ramona , Cabanillas Maria , Busaidy Nafia , Henderson Ying C. , Zafereo Mark , Williams Michelle D. , Lai Stephen , Navin Nicholas , Wang Jennifer R.
Published: March 2024

Anaplastic thyroid cancer (ATC) is one of the most lethal cancers. Although dramatic responses to BRAFV600E-mutated ATC are seen with BRAF/MEK inhibition, treatment resistance inevitably develops, limiting survival. In this study we sequentially profiled BRAFV600E-mutated ATC at diagnosis, after BRAF/MEK targeted therapy and at the time of disease recurrence using both bulk and single-cell DNA/RNA sequencing. We profiled (~400-800 single cells) for each patient - Patient 1 (n = 704 cells); Patient 2 (n = 817 cells) and Patient 3 (n = 407 cells). At diagnosis, we show that tumor cell populations were characterized by a predominance of arm-level aneuploidies. Across all patients, there is a sharp decline in tumor cells post BRAF-targeted treatment. Interestingly, we observe at least 2 distinct tumor subclones present in the pre-treatment tumor and subsequently there was an expansion event that occurred in each patient after BRAF treatment. This was associated with acquiring unique copy number aberrations (CNA)events and the dominance of these subclones in the recurrent disease. For Patient 2, we also performed single-cell RNA sequencing and show that the recurrent tumor cells have high proliferation and stem-cell like cell states even though they had higher differentiation scores. Importantly, correlating the scDNAseq identified CNA with the inferred CNA from scRNAseq, we show proof of concept that copy number aberrations can be directly correlated with gene expression changes and gene dosage effects. Collectively our data reveal an early polyclonal dissemination model of clones in BRAF-mutated ATCs and suggests that treatment resistance to BRAF inhibition develops as a results of incomplete elimination of viable tumor cell reservoirs in ATC.

Citation Format: Aatish Thennavan, Maxime Tarabichi, Per Wu, Meghan Martin, Ramona Dadu, Maria Cabanillas, Nafia Busaidy, Ying C. Henderson, Mark Zafereo, Michelle D. Williams, Stephen Lai, Nicholas Navin, Jennifer R. Wang. Single cell DNA sequencing of BRAF treatment resistant anaplastic thyroid 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 6216.
Abstract 6239: Human computer interface guided approach to accelerate anticancer drug discovery: Application to human estrogen receptor interactome
Authors: Rajnarayanan Rajendram V. , Alsabagh Aya
Published: March 2024

Structure-based drug discovery of target specific drugs greatly rely on the existence of high resolution X-ray crystal structure of the target proteins. Flexible and dynamic regions including hinges and loops which constitute major protein-protein interaction sites as well as allosteric sites are often beyond the scope of current tools and techniques available for protein folding and modeling. Human ability in recognizing patterns and to solve complex puzzles are far superior to any existing computer program at folding these atypical regions of proteins. We have utilized an unconventional combination of using dynamic three-dimensional protein models as physical human computer interface (HCI) devices and integrated proteomics data to predict flexible and dynamic protein-protein interfaces and allosteric pockets of key regulatory proteins to accelerate compound discovery. To this end, we have successfully utilized 1) Flexible HCI devices to generate an ensemble of dynamic three dimensional structures which includes a subset of biologically active conformations among others (thereby exploring the viable chemical space) and 2) Structure refinement and efficient filtering of biologically active conformations can be accomplished by integrating protein-protein interface and fold proteomics data. Here we present AI ready, HCI guided exploration of human estrogen receptor interactome and early in vitro confirmatory analyses. AI approachs to predict 3D protein structures from amino acid sequences like AlphaFold are often on par with experimentally generated structures and AI-guided structure prediction or docking approaches have been reported to significantly reduce computer time utilization. Streamlining of HCIguided tools to enable access to dynamic druggable pockets in protein targets will accelerate drug discovery.

Citation Format: Rajendram V. Rajnarayanan, Aya Alsabagh. Human computer interface guided approach to accelerate anticancer drug discovery: Application to human estrogen receptor interactome [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 6239.
Abstract 6242: A workflow execution system in a data fabric for integrative cancer analyses
Authors: Venkat Aarti , Ribeyre Pauline , Qureshi Jawad , Narumanchi Sai Shanmukha , Maxwell J Montgomery , Winslow Bill , Garcia Sara Volk , Meyer Chris , Garcia Tzintzuni , Vassilatos Peter , Malson Clinton , Zhang Zhenyu , Grossman Robert
Published: March 2024

Cancer researchers are increasingly conducting multi-omic research and performing integrative analyses on combinations of genomic, proteomic, transcriptomic, imaging, single cell and other data modalities. However, it is quite challenging for a researcher to effectively access, aggregate and analyze data and metadata from different data sources in a scalable and reproducible manner, as the individual datasets may be disconnected from each other, and have separate authentication and authorization requirements. We developed a workflow execution system in a data fabric called the Biomedical Research Hub (BRH) to overcome these challenges for academic researchers. The BRH is powered by the Gen3 technology, an open-source Kubernetes based software stack that allows cancer researchers to create their own data fabric and interoperate with data from multiple data sources. The workflow execution system utilizes nextflow and allows researchers to run containerized applications in the cloud in a secure and isolated environment. Data from multiple resources can be combined for analysis using convenient pay models including NIH STRIDES. We plan to demonstrate the application of our system on a scientific use case involving Clonal Hematopoiesis of Indeterminate potential (CHIP), a phenomenon that has been associated with aging, cancer, cardiovascular diseases, infection and all-cause mortality. We run containerized CHIP workflows on the cloud, utilizing two datasets accessible through BRH: i) The Genomic Data Commons, the world’s largest source of harmonized cancer data and ii) BioDataCatalyst, an NHLBI ecosystem that drives discovery and innovation for heart, lung, blood and sleep disorders. Our system is ideally suited for machine learning on large aggregated cancer datasets and federated learning tasks.

Citation Format: Aarti Venkat, Pauline Ribeyre, Jawad Qureshi, Sai Shanmukha Narumanchi, J Montgomery Maxwell, Bill Winslow, Sara Volk Garcia, Chris Meyer, Tzintzuni Garcia, Peter Vassilatos, Clinton Malson, Zhenyu Zhang, Robert Grossman. A workflow execution system in a data fabric for integrative cancer analyses [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 6242.
Abstract 6278: Effect of tumor size and BRAF mutational status in Middle Eastern differentiated thyroid cancer
Authors: Bu Rong , Siraj Abdul K. , Parvathareddy Sandeep K. , Iqbal Kaleem , Azam Saud , Qadri Zeeshan , Al-Rasheed Maha , Haqawi Wael , Benito Allianah D. , Al-Kuraya Khawla S.
Published: March 2024

Background: Risk stratified treatment strategies have become a focus in the treatment of Differentiated Thyroid Cancer (DTC). Tumor size at diagnosis has been widely used as a major mortality risk factor in risk stratification of DTC, but whether this is generally applicable, particularly in patient with different BRAF genetic backgrounds, is unclear. The current study was designed to analyze whether tumor size at diagnosis is a major prognostic factor in Middle Eastern DTC.

Methods: We conducted a comparative study of the relationship between tumor size at diagnosis and event free survival with respect to BRAF status in 1709 consecutive patients treated surgically for Middle Eastern DTC. Patients were divided into four groups according to the size of tumor (≤4 cm vs. >4 cm) and BRAF mutation status: Group 1 (≤4 cm without BRAF mutation, n = 587), Group 2 (≤4 cm with BRAF mutation, n = 765), Group 3 (>4 cm without BRAF mutation, n = 198) and Group 4 (>4 cm with BRAF mutation, n = 159). Predictors of event-free survival (EFS) were compared using the Log-rank test and Cox proportional hazards models.

Results: Following multivariate analysis, patients with tumors >4cm did worse than patients with tumors <4cm with respect to EFS (Group 3 vs Group1 HRadjusted=1.38, 95% CI=1.02-1.86, p = 0.0359; Group 4 vs Group 2 HRadjusted=1.61, 95% CI=1.20-2.16, p = 0.0017). However, patients did not differ according to EFS, regardless of the presence of BRAF mutation within each size category (Group 2 vs Group 1 HRadjusted=0.98 CI=.78-1.23, p=0.8415 ; Group 4 vs Group 3 HRadjusted=1.17, 95% CI=0.84-1.62, p=0.3523]

Conclusion: Tumor size is an independent predictor of EFS in Middle Eastern DTC patients, regardless of BRAF mutational status.

Citation Format: Rong Bu, Abdul K. Siraj, Sandeep K. Parvathareddy, Kaleem Iqbal, Saud Azam, Zeeshan Qadri, Maha Al-Rasheed, Wael Haqawi, Allianah D. Benito, Khawla S. Al-Kuraya. Effect of tumor size and BRAF mutational status in Middle Eastern differentiated thyroid 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 6278.
Abstract 6280: Vitamin D enhances luminal differentiation of prostate organoids more than androgens
Authors: Cerna Oscar Fernando , Nonn Larisa , Schlicht Mike , Krieger Kirty
Published: March 2024

Background: Prostate Cancer (PCa) is a prevalent disease affecting over two million men worldwide. Vitamin D is a fat-soluble hormone that is well-known for its role in the maintenance of strong bones and has anti-cancer effects in prostate cancer. Vitamin D is synthesized in the skin in response to sun exposure and may be supplemented with diet. However, since melanin hinders this synthesis many African Americans are deficient in vitamin D. Vitamin D circulates as 25-hydroxyvitamin D3 (25D) and 25-dihydroxyvitamin D3 (1,25D). Hydroxylation of 25D by the kidney or within tissues forms the active hormone 1,25D. 1,25D binds the vitamin D receptor (VDR), a steroid transcription factor. Androgens are the main regulatory hormones involved in prostate growth and differentiation. Epithelial differentiation is the process in which progenitor or stem cells become specialized cells, such as basal or luminal. In the prostate, luminal epithelial cells are the most differentiated and are the origin of PCa. We used mouse prostate organoids to replicate the differentiation process in vitro and to help identify the role of 1,25D on epithelial differentiation in the presence and absence of other androgens.

Methods: Primary mouse prostate cells were isolated from dorsal lateral lobes and grown as organoids. Over two weeks, we treated these organoids with concentrations of 1,25D and androgen (dihydrotestosterone, DHT). The four treatment groups were control, 1,25D only, DHT only and 1,25D+DHT. Organoids were imaged and analyzed for number, size and phenotype. Phenotypes were identified as luminal, acinar, or solid.

Results: Luminal phenotypes were more prevalent in 1,25D conditions compared to control or DHT alone. The number, size and percent of luminal organoids was highest in 1,25D + DHT compared to all other groups. Ongoing studies include examination of prostate organoids from mice with a vitamin D-deficient diet and staining of the organoids for differentiation markers.

Conclusions/Significance: We observed that 1,25D enhanced luminal epithelial differentiation in mouse prostate organoids. These findings suggest that chronic vitamin D deficiency may increase risk of aggressive prostate cancer, due to decreased epithelial differentiation. This has implications for the disparity of aggressive PCa observed in African American men who have lower vitamin D levels compared to their white counterparts.

Citation Format: Oscar Fernando Cerna, Larisa Nonn, Mike Schlicht, Kirty Krieger. Vitamin D enhances luminal differentiation of prostate organoids more than androgens [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 6280.
Abstract 6284: Multimoics reveal aberrant pathways and regulation of castration resistant and metastatic prostate cancer
Authors: Horning Aaron M. , Hung Chia-Nung , Liebermann Brandon , Chou Chih-Wei , Lin Che-Kuang , Wang Yao Vickie , Jin Victor X. , Liss Michael A. , Wang Chiou-Miin , Lin Chun- , Chen Meizhen , Huang Tim H-M , Chen Chun-Liang
Published: March 2024

Prostate cancer is a highly heterogeneous disease and in the end, 30% of patients will experience metastatic and fatal castration resistant prostate cancer (mCRPC). In spite of the vigorous efforts to search the causes of metastatic CRPC (mCRPC), the mechanisms are still largely unresolved. To understand the progression of mCRPC, we utilized scRNA-seq to profile global expression patterns in LNCaP, LNCaP-Abl and PC3 representing castration sensitive and resistant states. ScRNA-seq revealed 335 and 2393 differentially expressed (DE) genes in early and advanced castration resistant states enriched in 43 and 163 aberrant pathways. These included focal adhesion, adherens junction, leukocyte transendothelial migration, ECM-receptor interaction, regulation of actins, gap junction, TGFb, WNT, Hippo, Ephrin and other pathways. Upregulation of these pathways predicted worst disease free/overall survival of The Cancer Genomes Atlas (TCGA) PC cohort using Kaplan-Meir estimation. Further scRNA-seq also indicated most of the pathways were also enriched in ex vivo circulating tumor cells derived from biochemical recurrent or mCRPC patients. Small molecule perturbation verified function of 9 pathways involved in cell proliferation, migration, invasion, and organoid formation of mCRPC cell lines and CTCs. We then delved into how these genes are regulated by the global chromatin landscape through Assay for Transposase-Accessible Chromatin and high throughput DNA-seq (ATAC-seq). In castration sensitive LNCaP, active chromatins are associated with genes but most of them are located in distal intergenic regions. Conversely, the majority (51.9-57.6%) of open chromatins in castration resistant PC cells are situated in promoters that lie within 1kb of transcription start sites. KEGG pathway enrichment analysis uncovered Hippo, Wnt, tight junction, adherens junction, circadian and other pathways that corroborate the scRNA-seq findings. GRO-seq data indicated that nascent transcription supports gene body transcription in castration resistant cells but leads to massive pausing in castration sensitive cells.

Citation Format: Aaron M. Horning, Chia-Nung Hung, Brandon Liebermann, Chih-Wei Chou, Che-Kuang Lin, Yao Vickie Wang, Victor X. Jin, Michael A. Liss, Chiou-Miin Wang, Chun- Lin, Meizhen Chen, Tim H-M Huang, Chun-Liang Chen. Multimoics reveal aberrant pathways and regulation of castration resistant and metastatic prostate 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 6284.