bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract LB239: Downregulation of spliceosomal proteins hnRNPH1 and H2 in WM266-4 melanoma cells induces immune signaling
Authors: Sultan Maab , Diez Juan , Smalley Keiran S.M. , Beljanski Vladimir , Nathonson Lubov , Minond Dmitriy 
Published: April 2023

Abstract
This study aims to determine the effect of hnRNPH1/H2 (H1/H2) downregulation on immune-related genes in vitro. Due to the molecular heterogeneity of melanoma, it is difficult to treat it, which necessitates new approaches. We discovered compounds that selectively kill melanoma cells by binding to spliceosomal proteins hnRNPH1/H2. RNAseq of melanoma cells treated with H1/H2 siRNA showed upregulation of immune pathways. To validate this effect of genomic modulation of H1/H2 on immune gene expression, we used NanoString method. We treated both WM266-4 cell line and melanocytes with H1/H2 siRNA and scrambled siRNA to knockdown our target gene. Then, RNA was extracted and analyzed by NanoString. Analysis data of melanoma cell line showed a significant difference between RNA samples treated with scrambled and the one treated with siRNA in upregulating immune-related genes. In contrast, data of melanocytes revealed no significant difference between scrambled and siRNA samples and did not show upregulation of these genes. This implies the specificity of this response to melanoma cells. In conclusion, we hypothesize that downregulation of spliceosomal proteins H1/H2 can upregulate immune-related genes, which in turn can improve melanoma patients’ survival. Consequently, H1/H2 can be targeted as a novel therapeutic approach.
Citation Format: Maab Sultan, Juan Diez, Keiran S.M. Smalley, Vladimir Beljanski, Lubov Nathonson, Dmitriy Minond. Downregulation of spliceosomal proteins hnRNPH1 and H2 in WM266-4 melanoma cells induces immune signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB239.
Abstract LB258: Therapeutic advantage of targeting lysosome as signaling hub for metabolic conditions in malignant gliomas
Authors: Jing Yongwei , Kobayashi Masahiko , Hirao Atsushi 
Published: April 2023

Abstract
Lysosome, as the digestive system of the cell, participated in numerous cell biological processes, such as macromolecular degradation, cell adhesion/migration, and apoptosis by regulating metabolic status and pro-growth signaling. Therefore, lysosome could be a promising therapeutic target for cancer therapy, but it remains unclear how lysosome is involved in cancer malignancy. In this study, to investigate the roles of function lysosomes in the regulation of malignant status, we evaluated the proteolytic activity of lysosomes using BODIPY-dye conjugated BSA (DQ-BSA) in malignant gliomas characterized by high aggressivity, destructivity, and invasiveness, glioblastoma multiforme (GBM). While most GBM patient-derived cells showed higher lysosomal proteolytic activity than an immortalized human neural progenitor cell line derived from the embryonic brain, levels of lysosome activity positively co-related with sphere formation. Multi-omics analysis demonstrated that the level of lysosomal proteolytic activity was co-related with metabolic status, including activated mitochondria biogenesis and amino acid transport. The orthotopic xenograft model revealed that lysosome activity in vitro is a critical biomarker representing malignant phenotypes of GBM. We found that the MiT/TFE family, a master regulator of lysosomal biogenesis, controlled the malignant progression of GBM, including therapy resistance, indicating that quality control of lysosomes is a critical determinant for the malignant properties of gliomas. To develop a novel therapeutic approach for targeting lysosomal function, we performed screening of FDA-approved compounds and found that lysosomotropic agents, which induced galectin-3 punctation as an indicator of lysosomal membrane damage, efficiently suppressed tumor growth. Ifenprodil, a clinically available drug that acts as a lysosomotropic agent, increased intracellular Ca2+ levels, resulting in mitochondrial reactive oxygen species-mediated cytotoxicity. Furthermore, we found that the efficacy of ifenprodil was remarkably enhanced by metabolic modifications, such as amino acid restriction, in vitro and in vivo. Collectively, these data indicate that lysosomes as signaling hubs for metabolic conditions play critical roles in the regulation of the malignant status of GBM patients. Our findings propose that lysosomal biogenesis is a promising target to develop a novel therapeutic approach for GBM.
Citation Format: Yongwei Jing, Masahiko Kobayashi, Atsushi Hirao. Therapeutic advantage of targeting lysosome as signaling hub for metabolic conditions in malignant gliomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB258.
Abstract LB263: An in vivo unbiased screen identifies clathrin adaptor protein complex-2 as a novel tumor suppressor
Authors: Zimmerman Seth Parker , Counter Christopher M. 
Published: April 2023

Abstract
Pancreatic ductal adenocarcinoma (PDAC) is almost uniformly lethal. It is thus imperative to find new therapeutic approaches to treat this disease. While whole genome CRISPR/Cas9 screens have successfully identified new vulnerabilities in PDAC cell lines, it is becoming increasingly clear that cell culture do not faithfully recapitulate the complex nature of tumorigenesis in vivo, and hence may fail to identify the full spectrum of potential therapeutic targets to be explored in this devastating disease. As previous screens we performed identified phosphatidylinositol (Ptdlns) metabolism as important for pancreatic cell growth, I generated a custom sgRNA library targeting this entire form of metabolism. To identify vulnerabilities specific to tumor growth, I screened this library in five different human PDAC cell lines grown in culture versus as xenograft tumors. I found that sgRNAs targeting two genes encoding separate subunits of the Adaptor Protein complex-2 (AP2), a regulator of clathrin mediated endocytosis, were negatively enriched in all five PDAC cell lines when grown in culture. In agreement, AP2 subunit genes are considered common essential by DepMap. Paradoxically however, the same sgRNAs were positively enriched in three of these five cell lines when grown as xenograft tumors. This begs the question how the loss of a supposably essential complex behaves like a tumor suppressor and instead enhances tumor growth when disrupted. Here, I will present data that loss of AP2 results in a substantial restructuring the plasma membrane proteome, which in cultured cells results in the loss of iron transport, one of the main functions of this complex, and cell death. Conversely, this restructuring in vivo retains receptors and adhesion proteins on the cell surface, where transcriptome and proteomic analysis indicate enhances proliferative signaling. These data support AP2 promoting cell viability of cultured cells through active iron transport, but suppresses tumor growth in vivo by endocytosing the very receptors needed for tumor growth.
Citation Format: Seth Parker Zimmerman, Christopher M. Counter. An in vivo unbiased screen identifies clathrin adaptor protein complex-2 as a novel tumor suppressor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB263.
Abstract LB272: Spatial cellular architecture predicts prognosis in glioblastoma
Authors: Zheng Yuanning , Carrillo-Perez Francisco , Pizurica Marija , Gevaert Olivier 
Published: April 2023

Abstract
Intra-tumoral heterogeneity and cell-state plasticity are key drivers for the therapeutic resistance of glioblastoma (GBM). Studies based on single-cell RNA-seq and spatial transcriptomics have classified GBM cells into distinct transcriptional phenotypes. However, how the transcriptional diversity and spatial cellular organization are associated with patient prognosis remains incompletely resolved. Here, we developed a deep learning model to predict spatially resolved transcriptional programs from histology images. The model was trained on spatial transcriptomics data and validated in external testing cohorts. Applying the model to two separate patient cohorts led to the discovery of conserved relationships between tumor architecture and prognosis. Patient with poor prognosis had higher proportions of GBM cells expressing a hypoxia-induced transcriptional program. In addition, high clustering patterns of reactive astrocytes were associated with a poor prognosis. Conversely, when the reactive astrocytes were dispersed and connected to other cell types, the risk was decreased. To validate our results, we developed a separate deep learning model that used histology images to predict prognosis. Applying the model to spatial transcriptomics data discovered survival-associated regional gene expression programs. Genes related to glycoprotein metabolism and injury response were significantly upregulated in tumor cells with high aggressiveness. Our studies established a scalable approach to resolve the transcriptional heterogeneity of GBM and linked the spatial cellular architecture to clinical outcomes.
Citation Format: Yuanning Zheng, Francisco Carrillo-Perez, Marija Pizurica, Olivier Gevaert. Spatial cellular architecture predicts prognosis in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB272.
Abstract LB284: CLAUDIN-1 targeting antibody ALE.C04 drives single activity and restores anti-PD1 efficacy in solid tumors
Authors: Toso Alberto , Teixeira Geoffrey , Zimmermann Tina , Gill Stefanie Gill , Schmitter Daniela , Meyer Markus , Muller Marion , Mailly Laurent , Baumert Thomas , Manenti Luigi , Iacone Roberto 
Published: April 2023

Abstract
Claudin 1 (CLDN1) is a protein confined within the normal epithelial tight junctions of different tissues. Upon malignant transformation, CLDN1 is overxpressed and epitopes become exposed outside the tight junctions (non-Junctional CLDN1). ALE.C04 is a highly specific humanized monoclonal antibody that recognizes a unique CLDN1 exposed epitope in different solid tumors. Herein we show that non-Junctional CLDN1 (NJ-CLDN1) is frequently overexpressed in solid tumors. Pre-clinically, ALE.C04 drives tumor growth inhibition in different CDXs and PDX in vivo tumor models. Notably, CLDN1 expression on tumor cells positively correlates with T cell exclusion, a mechanism described to hinder the efficacy of Checkpoint inhibitors (CPIs). On this line, the overexpression of Cldn1 in mouse tumor cells promoted T-cell exclusion and resistance to anti-PD1 treatment. Importantly, ALE.C04 restored both T-cell infiltration and anti-PD1 efficacy in tumors. Mechanistically, NJ-CLDN1 interacts with different components involved in extracellular matrix remodeling, thus establishing a physical barrier that exclude immune cells from the tumor nest. ALE.C04 perturbs the interface between CLDN1+ tumor cells and the stroma, thus restoring immune cell infiltration. Our pre-clinical data showed that: i) NJ-CLDN1 is a novel and druggable target in solid tumors ii) ALE.C04 is a selective anti-CLDN1 antibody capable of driving anti-tumor activity as both single agent and in combination with anti-PD1.
Citation Format: Alberto Toso, Geoffrey Teixeira, Tina Zimmermann, Stefanie Gill Gill, Daniela Schmitter, Markus Meyer, Marion Muller, Laurent Mailly, Thomas Baumert, Luigi Manenti, Roberto Iacone. CLAUDIN-1 targeting antibody ALE.C04 drives single activity and restores anti-PD1 efficacy in solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB284.
Abstract LB293: The evolution of MRD assays: Moving beyond the tumor-Informed bespoke NGS panel
Authors: Labrousse Paul , Stetson Daniel , Hadfield James , Abbosh Chris , Zehir Ahmet , Barrett Carl , Dougherty Brian , Hodgson Darren 
Published: April 2023

Abstract
The non-invasive detection of circulating tumor DNA (ctDNA) from plasma has been shown to have clinical value for detection of minimal residual disease (MRD), identification of emerging resistance to treatment, and predicting treatment response. The ability to detect MRD following curative treatment allows for the stratification of patients with higher risk of disease recurrence. Multiple studies, across hundreds of patients in different indications, including lung and colon cancer, have shown that tumor-informed personalized assays have high sensitivity to detect recurrence. The tumor-informed bespoke panels utilize sequencing of the tumor tissue to identify clonal somatic variants, which are then used to generate a personalized panel to track the variants in patient plasma. Next-generation MRD technologies are aiming to provide greater sensitivity by expanding methods beyond the small, personalized panels. Utilization of increased numbers of somatic variants is predicted to achieve a greater level of sensitivity for detection of MRD.
Here we describe, C2I Genomics which provides a novel platform that exploits whole genome sequencing of the tumor tissue and plasma to define a somatic variant signature. An important difference of this method is that it develops a personalized bioinformatic signature rather than a personalized NGS panel. To understand the potential of this novel methodology, we utilized a set of 54 contrived clinical sample dilutions from three indications, with an expected (or engineered) VAF range of 0.2-0.002%, that have commutability to the intended use population.
We found that C2I Genomics technology is highly sensitive, where for all returned samples, the assay routinely achieved detection down to the lowest dilution of 0.002% allelic frequency. Overall, the assay resulted in an average detection rate of 93% across all dilutions (n = 54). The aggregate detection rate of several tumor-informed assays, examining the same dilutions, yielded a detection rate of 68%.
In summary, the C2I Genomics assay showed robust detection from contrived samples which are representative of clinical trial samples in both cfDNA yields and allele frequency.
Citation Format: Paul Labrousse, Daniel Stetson, James Hadfield, Chris Abbosh, Ahmet Zehir, Carl Barrett, Brian Dougherty, Darren Hodgson. The evolution of MRD assays: Moving beyond the tumor-Informed bespoke NGS panel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB293.
Abstract LB322: Antitumor activity of 1st-in-class pan-RAS inhibitor ADT-1004 in mouse models of pancreatic ductal adenocarcinoma
Authors: Maxuitenko Yulia Y. , Foote Jeremy B. , Keeton Adam B. , Chen Xi , Berry Kristy , Fadlalla Khalda , Valiyaveettil Jacob , Huang Chung-Hui , Moore Austin M. , Graff Emily C. , Nagaraju Ganji P. , Carstens Julienne L. , El-Rayes Bassel F. , Buchsbaum Donald J. , Piazza Gary A. 
Published: April 2023

Abstract
Pancreatic ductal adenocarcinoma (PDA) is the 4th leading cause of cancer death in the U.S. with only about a 10% five-year survival rate and an estimated 60,000 deaths/year by 2030. Poor survival is frequently due to advanced disease at the time of diagnosis, as well as the high prevalence of KRAS driver mutations. Currently, approved KRAS-targeted therapeutics are designed to covalently inactivate only KRAS-G12C mutants, whereas the most common mutations in PDA are KRAS-G12D, KRAS-G12V, and KRAS-G12R. Thus, the need for novel RAS-targeted therapeutics with efficacy in tumors with these more common mutations is of utmost urgency to reduce PDA disease burden. We have synthesized a novel chemical class of pan-RAS inhibitors with unique biological properties and attractive drug-like properties. As a prodrug, ADT-1004, generates an active metabolite, ADT-007, that potently inhibits the growth of human and murine PDA cell lines in vitro with single-digit nM IC50 irrespective of specific RAS mutational codon or isozyme by inhibiting activated RAS and signaling downstream of KRAS (ERK1/2 and AKT phosphorylation). ADT-1004 is well tolerated with no discernable toxicity at oral dosages of up to 175 mg/kg bid. Pharmacokinetic studies demonstrated that ADT-1004 produces sustained plasma concentrations of ADT-007 ~50-fold above IC50 values, with even higher concentrations in both subcutaneous and orthotopic pancreatic tumors. Once daily oral administration of ADT-1004 significantly inhibited the growth of orthotopically implanted PDA tumors with a corresponding reduction in RAS/MAPK signaling. ADT-1004 represents a 1st-in-class pan-RAS inhibitor with potential advantages over mutant-specific KRAS inhibitors for greater efficacy and ability to avert mechanisms of resistance. These data support future clinical trials of ADT-1004 as a monotherapy for the treatment of patients with PDA regardless of the underlying mutation.
Citation Format: Yulia Y. Maxuitenko, Jeremy B. Foote, Adam B. Keeton, Xi Chen, Kristy Berry, Khalda Fadlalla, Jacob Valiyaveettil, Chung-Hui Huang, Austin M. Moore, Emily C. Graff, Ganji P. Nagaraju, Julienne L. Carstens, Bassel F. El-Rayes, Donald J. Buchsbaum, Gary A. Piazza. Antitumor activity of 1st-in-class pan-RAS inhibitor ADT-1004 in mouse models of pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB322.
Abstract LB354: 9p arm loss is an important predictor of immune evasion in several human cancers
Authors: Bianchi Joy 
Published: April 2023

Abstract
The identification of biomarkers that predict patient response to immune checkpoint blockade (ICB) is a key focus of current cancer research. We and others have found that high levels of Somatic Copy Number Alterations (SCNAs) in tumors are associated with decreased infiltration by cytotoxic immune cells and predict patient’s response to ICB. Recently, we predicted that the strongest SCNA driver of cytotoxic T cell depletion in HPV-negative oral cancer, was the loss of the entire 9p arm and that it was a marker of poor survival in recurrent oral cancers treated by anti-PD1 therapy. 9p arm loss is among the most common SCNAs in solid tumors and we revealed its importance beyond 9p21.3 deletion (i.e., CDKN2A and the IFNA cluster).To systematically investigate the immune-related role of 9p deletion and other SCNAs in cancer, we have developed a computational pipeline to identify the genes altered by SCNAs predicting the strongest risk of cancer immune evasion. We analyzed 7 solid tumor types and identified thousands of tumor-specific SCNAs predicting an immune cold phenotype but only ~100 SCNAs were conserved across all tumor types. Strikingly, 60% of the conserved deletions were localized on the 9p arm and the strongest 9p candidates included some known cancer drivers but also new candidates such as RANBP6 and TOPORS, that have been suggested to decrease proinflammatory and pro-immunogenic molecules. We have identified a 17-gene cluster deletion in 9p13 composed mostly of genes involved in proteasomal degradation or membrane trafficking, suggesting that its deletion might disturb MHC-mediated antigen presentation. We are now engineering human and mouse oral cancer cell lines to recapitulate 9p deletion and decipher its role in immune evasion through in vitro and in vivo immunological assays. We are also using the parameters we determined in our computational pipeline to develop a machine learning method improving our prediction of SCNAs driving immune evasion. Our findings identified 9p deletion as a novel biomarker for predicting clinical benefit of ICB and will allow a better understanding of the SCNA-mediated mechanisms suppressing tumor immune response.
Citation Format: Joy Bianchi. 9p arm loss is an important predictor of immune evasion in several human cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB354.
Abstract LB357: CRISPR-Cas9 targeting of somatic mutations selectively kills cancer cells
Authors: Bowland Kirsten , Teh Selina Shiqing K. , Skaist Alyza , Hruban Ralph H. , Roberts Nicholas J. , Iacobuzio-Donahue Chrisine , Eshleman James R. 
Published: April 2023

Abstract
Pancreatic ductal adenocarcinoma (PDAC) accounts for 3% of all cancers but is the 3rd leading cause of cancer death in the United States. This staggering discrepancy is partly because most pancreatic cancers evade early detection and patients most commonly present with metastatic disease. As cancer initiates from a single transformed cell, passenger mutations that accumulate over the course of the patient’s lifetime in that cell are then clonally propagated to the growing tumor and metastases, providing a targetable molecular signature throughout the cancer. Here we propose a CRISPR-Cas9 gene therapy aimed at these tumor-specific somatic mutations. Using whole genome sequencing of rapid autopsy tumor and normal samples from five patient cases, we identified single base substitutions present in tumor tissues and absent in patient-matched normal tissue. A subset (6.6% on average) of these mutations lead to novel protospacer adjacent motif (PAM) sites. These tumor specific PAM sites are necessary for Cas9 binding and DNA scission and are therefore selectively targetable by CRISPR-Cas9 systems. Using a hybrid capture/NGS approach, we demonstrate in patients with multiple metastases that the majority of these novel PAM sites, ~70%, are maintained among the different metastases. Using multitarget sgRNA which cut at a known number of sites in the human genome, we determined a relationship between number of CRISPR-Cas9 cuts and growth inhibition in PDAC cells. We found that 8-10 cut sites in non-coding regions are sufficient to induce &gt;95% cancer cell death. Finally, using cocultures of fluorescently labeled PDAC cells and a multiplexed sgRNA array targeting multiple tumor specific PAMs, we demonstrate selective cell killing of the targeted cell line. Importantly, deep sequencing of patient-matched normal lymphocytes lacking the tumor-specific PAMs treated with the same sgRNA array exhibited no editing at the targeted loci. This work establishes a bioinformatic platform for the discovery of tumor-specific CRISPR targets in the context of metastatic disease and demonstrates selective killing to cancer cells while sparing the patient’s normal cells. These data establish the proof of principle for a gene therapy approach targeting metastatic disease.
Citation Format: Kirsten Bowland, Selina Shiqing K. Teh, Alyza Skaist, Ralph H. Hruban, Nicholas J. Roberts, Chrisine Iacobuzio-Donahue, James R. Eshleman. CRISPR-Cas9 targeting of somatic mutations selectively kills cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB357.