bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 338: Unraveling layers of proteogenomic complexity in cancer through multiomic exploration of archived FFPE tissue
Authors: O'Hara Andrea J. , Han Yang , DeVito Ilaria , Turner Laure , Latif Haythem
Published: March 2024

Formalin Fixed Paraffin Embedded (FFPE) tissues are a staple in clinical diagnostics associated with solid tumor. The preserved tumor tissue can be interrogated using classical histopathology and complemented with molecular approaches to elucidate cancerous SNPs, indels, structural variants, repeat expansion, copy number expansions, and mutational burden. Increasingly, approaches are being deployed to interrogate tissue not only through individual datasets but through integrated approaches that provide spatial information that defines the tumor microenvironment. Here, we illustrate using FFPE blocks from various tissues a multiomic workflow that allows for deep exploration of the molecular underpinnings of cancerous tissue. FFPE blocks were serially sliced into various FFPE slides with a single slide H&E stained. Individual slides were then utilized to explore the genome, epigenome, single cell RNA-seq, and digital spatial profiling. Genome information was captured using hybrid capture based approaches (whole exome sequencing and targeted cancer panel) followed by deep NGS on an Illumina platform and analyzed for a variety of variants and tumor mutational burden. DNA methylation was detailed using target capture probes targeting DNA methylation sites. Single cell approaches were applied to explore the transcriptome using 10X Genomics scRNAseq Flex kit. Digital spatial profiling was done using the NanoString for both transcriptomics and proteomics, with the GeoMx Whole Transcriptome Atlas and Human Core and Pan-Tumor protein panels. Aggregating these data illustrates the expanding landscape of information that can be extracted from FFPE derived tissue and the potential for novel discovery and diagnostic power integrating these complex data types holds.

Citation Format: Andrea J. O'Hara, Yang Han, Ilaria DeVito, Laure Turner, Haythem Latif. Unraveling layers of proteogenomic complexity in cancer through multiomic exploration of archived FFPE tissue [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 338.
Abstract 3383: Growth suppression and selective disruption of actin by alpha-santalol in human melanoma SK-MEL2 cells
Authors: Bommareddy Ajay , Chandrasekaran Ritesh , Lu Michael , Penate Delilah
Published: March 2024

Alpha-santalol, a major component of sandalwood oil has been shown to have chemopreventive and anti-tumor effects in different pre-clinical cancer models. The present study was undertaken to determine the in vitro efficacy of alpha-santalol on SK-MEL2 human melanoma cells and an immortalized human keratinocyte cell line (HACaT). In this study, we employed MTT assay, Trypan blue assay, wound healing assay, and confocal microscopy for imaging phalloidin/DAPI stained cells to investigate the cytotoxicity, cell viability, migratory potential respectively of the cells treated with different concentrations of alpha-santalol and DMSO for given time periods. Results showed that alpha-santalol treatment significantly decreased SK-MEL2 cell viability, wound healing, while only affecting HACaT cells at higher concentrations. Alpha-santalol treatment also disrupted actin cytoskeleton in SK-MEL2 cells, whereas HACaT cells were more resistant to this effect. In conclusion, the present study reveals selective growth inhibitory and anti-migratory effects of alpha-santalol in human melanoma cells and warrants future studies to systemically explore the mechanistic details involved in its growth inhibitory and antimigratory effects.

Citation Format: Ajay Bommareddy, Ritesh Chandrasekaran, Michael Lu, Delilah Penate. Growth suppression and selective disruption of actin by alpha-santalol in human melanoma SK-MEL2 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 3383.
Abstract 3388: Targeting liver specific βII-Spectrin to prevent the development of metabolic dysfunction associated steatohepatitis (MASH) through CEACAM1 axis
Authors: Bhowmick Krishanu , Ohshiro Kazufumi , Xiang Xiyan , John Sahara , Yang Xiaochun , Beauchemin Nicole , Hassan Mohammad I. , Mohammad Taj , Mishra Lopa
Published: March 2024

Background: Obesity and pro-inflammatory alteration of the gut microbiome are risk factors for gastrointestinal (GI) cancers, including liver cancer (HCC). Dysregulated TGF-β signaling and loss of CEACAM1 activity are implicated in fatty liver disease. Clinically, 40% of human liver and GI cancers have genetic alterations in the TGF-β pathway members. CEACAM1 expression is significantly decreased in the liver of patients with Metabolic dysfunction-associated steatohepatitis (MASH). In contrast, in hepatocellular carcinoma (HCC), high CEACAM1 is associated with invasion, metastasis and poor prognosis. We hypothesized that TGF-β signaling and βII-Spectrin modulate MASH and HCC through CEACAM1.

Methods: Wild type and the liver-specific βII-Spectrin (Sptbn1) knockout (LSKO) mice fed a high-fat diet (HFD) or Western diet (WD) and analyzed for Ceacam1 expression, changes in immune cell population, liver inflammation, and cancer. We used Alphafold and molecular modeling to identify the CEACAM1 and SPTBN1 interaction sites.

Results: Single cell sequencing analysis of MASH mice liver revealed that Ceacam1 expression is significantly decreased in hepatocytes. Interestingly, we found that CEACAM1 levels are restored to normal in tissues from liver-specific βII-Spectrin knockout (LSKO) mice. Transcriptomic and multiplex imaging analysis suggest that proinflammatory TGF-β signaling is activated and infiltration of CD11b+ cells is increased in MASH liver. These phenotypes are blocked in LSKO mice. Furthermore, siRNA-knockdown of βII-Spectrin blocks diet-induced obesity, fibrosis, lipid accumulation, tissue damage, and cancer susceptibility. We have also found that CEACAM1 interacts with the Smad3 adaptor, βII-Spectrin. Furthermore, structural analysis of CECAM1 and βII-Spectrin revealed critical residues involved in the interaction.

Conclusion: These data suggest that βII-Spectrin regulates CEACAM1 expression in the liver and is a potential target for therapeutic intervention to treat MASH and prevent progression to HCC.

Citation Format: Krishanu Bhowmick, Kazufumi Ohshiro, Xiyan Xiang, Sahara John, Xiaochun Yang, Nicole Beauchemin, Mohammad I. Hassan, Taj Mohammad, Lopa Mishra. Targeting liver specific βII-Spectrin to prevent the development of metabolic dysfunction associated steatohepatitis (MASH) through CEACAM1 axis [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 3388.
Abstract 3426: Real-world biomarker testing rates and trends among patients with advanced non-small cell lung cancer in the US
Authors: Chen Yiyu , Carlson Angeline
Published: March 2024

Background: Broad biomarker profiling before treatment initiation for non-small cell lung cancer (NSCLC) is recommended. Patients may not receive or receive inadequate biomarker testing before treatment initiation. This study assesses rates and trends of biomarker testing in community and academic oncology practices in the US.

Methods: A descriptive cohort study was conducted using electronic health records from an NSCLC registry. Patients who initiated NSCLC treatment following diagnosis of advanced NSCLC (stage IIIB/IIIC/IV) from 01/01/2015-12/31/2021 were identified. Patient demographics (age, gender, race, region) along with histology type (squamous/non-squamous) and hospital type (academic/community) were included. The percentage of patients receiving tests for any of the nine biomarkers before and during therapy was calculated and compared.

Results: 8,769 patients were identified with advanced NSCLC; 65.9% having non-squamous cell carcinoma; 22.4% having squamous cell carcinoma; 11.7% unknown. 13.4% of patients were from academic centers, 78.7% from community hospitals, 8.0% unknown. The majority (59%) were 65+ years; 47.3% were female. Overall, 83.2% had biomarker testing at some point in treatment; only 66.3% before treatment initiation. Over time, biomarker testing rates prior to treatment initiation increased (46.9% in 2015 to 73.8% in 2021). The use of biomarker testing in non-squamous cell carcinoma was greater than in squamous cell carcinoma. The most frequent biomarker testing before treatment initiation were PD-L1 (52.2%), EGFR (51.6%), and ALK (50.7%), followed by ROS1 (46.9%), BRAF (39.5%), and KRAS (34.1%). Testing rates for the newest biomarkers NTRK, MET, and RET were 20.4%, 28.4%, and 28.0%, respectively. Testing rates were similar between academic centers and community-based hospitals, except for the newest biomarkers, where use in academic settings was greater. Biomarker testing rates were higher among female patients (χ2 P-value<0.001); rates by race were similar (χ2 P-value=0.83).

Conclusion: While the use of biomarker testing in advanced NSCLC is growing, 26% of patients remained untested before treatment initiation. Biomarker testing in non-squamous cell carcinoma is higher than in squamous cell carcinoma, in keeping with the guideline emphasis on biomarker testing for that histology type. Results suggest that further dissemination of guideline recommendations to obtain biomarker test results prior to treatment initiation is important to optimize treatment decisions in the NSCLC landscape.

Citation Format: Yiyu Chen, Angeline Carlson. Real-world biomarker testing rates and trends among patients with advanced non-small cell lung cancer in the US [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 3426.
Abstract 346: Trop-2 induces apoptosis via transcriptional activation of TRAIL, FAS-FASL, CD40-TNFRSF5
Authors: Alberti Saverio , Guerra Emanuela , Moschella Antonino , Ceci Martina , Pantalone Ludovica , Di Pietro Roberta , Trerotola Marco
Published: March 2024

Trop-2 is a transmembrane signal transducer that activates cancer growth and metastatic diffusion (1). However, this does not occur in all tumor types, as Trop-2 is associated to better disease outcome in some cancers, e.g. breast and lung tumors. A prototypic pattern of Trop-2 expression in normal multistratified epithelia, e.g. epidermis, esophagus, is that of preferential expression in non-proliferating, terminally differentiated cells. The corresponding expression gradient parallels that of induction of programmed cell death, e.g. in the corneum layer of skin keratinocytes. This led us to explore Trop-2 function as a trigger of apoptosis. We thus assessed NS-0 myeloma Trop-2 transfectants for apoptosis induction by dynamic cell morphometry and quantification of membrane blebbing and cell fragmentation. This was shown to be preceded by phosphatidyl-serine membrane exposure, and was followed by nuclear pyknosis and karyorrhexis. DNA fragmentation was shown by TUNEL and DNA laddering, and was accompanied by a dramatic increase of apoptotic death of Trop-2-expressing cells. Transcriptomic analysis at early time points of apoptosis induction indicated overexpression of TRAIL, FAS/FASL and CD40/TNFRSF5 transmembrane death receptors. This paralleled upregulation of downstream death-inducing signaling complex components and of executioner Caspases 8 and 3, suggesting Trop-2 as a trigger of extrinsic apoptosis pathways. Apoptosis induction translated into diminished tumor growth in vivo, which was shown to be proportional to Trop-2 expression levels. However, apoptosis induction was found to parallel stimulation of NS-0 cell growth and of defence mechanisms from apoptosis, as increased levels of inhibitory transcription factors, Rb-binding protein, survivin, Myd-118. These findings suggest a previously unappreciated balance between stimulation of cell growth and triggering of cell death by Trop-2, and may pave the way for selective anticancer therapy approaches in Trop-2-expressing cancers.(1) Trerotola M. et al., Neoplasia 23: 415-428 (2021).

Citation Format: Saverio Alberti, Emanuela Guerra, Antonino Moschella, Martina Ceci, Ludovica Pantalone, Roberta Di Pietro, Marco Trerotola. Trop-2 induces apoptosis via transcriptional activation of TRAIL, FAS-FASL, CD40-TNFRSF5 [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 346.
Abstract 3475: Prediction of nausea or vomiting, and fatigue or malaise in cancer care
Authors: Vienne Raphael , Filori Quentin , Susplugas Vincent , Crochet Hugo , Verlingue Loic
Published: March 2024

Introduction: Natural language processing has recently achieved unprecedented performances for several medical tasks, but requires additional improvements in oncology. Moreover, very few projects have assessed the potential of language models to help prevent the most frequent serious or severe medical events in medical oncology. We aim at predicting nausea or vomiting (ICD10 code R11), and fatigue or malaise (ICD10 code R53) from patients' medical reports.

Material and methods: The study included all the patients of Centre Léon Bérard between 2000 and 2023 that have not refused to share their data for this analysis. We have retrieved all the clinical notes and manual coding of hospitalization stays in ICD10, in French. We have pretrained a BERT language model with a masking strategy on this data and then fine-tuned it and compared it to several medical pretrained open source models (DrBert and K-memBERT). The labels were medical events leading to or associated with a hospitalization in the 90 days after every patients’ notes. For OncoBERT, we included sequential reports from the patients’ history, along with a time-encoding layer, and integrated it in a final transformer layer.

Results: We analyzed 140,523 patients, representing 2,515,957 pseudo-anonymized text reports and 6.6M hospitalizations codes in total. The medical texts were consultations reports (56%), end-of-stay reports (17%) and hospitalization summaries (9%). The most frequent types of oncology treatments received by the patients at each time point were 18.8% for chemotherapy, 10.8% for targeted therapies and 1.3% for immunotherapies. The most frequent medical events were nausea or vomiting (20% of patients with 1 or more events), and fatigue or malaise (18% of patients with 1 or more events). In the final dataset, nausea and vomiting (R11) accounted for 16% of the labels while malaise and fatigue (R53) accounted for 24.7% of the labels. We performed random undersampling of reports without any event to balance the label dataset. The fine-tuning on R11 and R53 achieved the performances of 0.58 macro-aucpr (OncoBERT) and 0.50 macro-aucpr (best open-source model) on the validation set.

Conclusion: The language models achieved high performance on the prediction of the most frequent serious medical events in our hospital dedicated to cancer care. We plan to validate the external performances of these models on collaborating hospitals and prospectively and improve the interpretations that we will present at the congress.

Citation Format: Raphael Vienne, Quentin Filori, Vincent Susplugas, Hugo Crochet, Loic Verlingue. Prediction of nausea or vomiting, and fatigue or malaise in cancer care [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 3475.
Abstract 3479: Evaluation of subclonal deconvolution pipelines using reference cell-lines and patient plasma samples
Authors: Dong Xiaoxi , Huang Yong , Zhang Tom , Jia Shidong , Du Pan
Published: March 2024

Background: Intratumor heterogeneity plays a pivotal role in treatment resistance, emphasizing the need for a comprehensive understanding of tumor clonal architecture. While various methods exist for extracting this information from bulk tumor sequencing data, few studies have evaluated the entire workflow, from sample processing to subclone calls.

Methods: To address this gap, we utilized cell lines with known copy number changes and somatic mutations, constructing 12 ground truth sample sets with varying cellular proportions and tumor purities. These cell lines underwent NGS pipeline using PredicineWES+ with increased sequencing depth across ~600 cancer-related genes. Subclonal analysis workflows, including FACETS, PyClone, and ECLIPSE, were implemented to to assess variant assignment and cellular fractions. The subclone analysis was extended to 91 plasma samples from cancer patients.

Results: Our findings indicate that subclonal decomposition effectively segregates mutations from distinct cell lines. Notably, analyzing multiple samples with different proportions of the same subclones outperformed deconvolution from single mixture samples. In plasma samples from cancer patients, nearly one-third exhibited subclonal clinically actionable variants.

Conclusions: The established subclonal deconvolution pipeline enhances biomarker analysis from assays utilizing WES with boosted sequencing depth for selected genes.

Citation Format: Xiaoxi Dong, Yong Huang, Tom Zhang, Shidong Jia, Pan Du. Evaluation of subclonal deconvolution pipelines using reference cell-lines and patient plasma samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3479.
Abstract 3484: Mechanism of BRAF V600E resistance revealed by cell panel screening and bioinformatics
Authors: Hu Kaiqiang , Yang Qiuyuan , Pan Pengwei , He Fang
Published: March 2024

The BRAF V600E mutation is pivotal target in the treatment of melanoma. Dabrafenib, one of the most potent inhibitors approved by the FDA, exhibits differential sensitivity across different cancer types. To explore the underlying mechanisms responsible for the resistance of certain cancers to Dabrafenib, we tested a panel of 20 BRAF V600E positive cancer cell lines. Our results showed that 15 of these cell lines demonstrated sensitivity to Dabrafenib, whereas the remaining 5 exhibited resistance. We then investigated the correlation between Dabrafenib potency and gene expression patterns based on public high throughput sequencing data via bioinformatics methods. The results uncovered that the cell lines resistant to Dabrafenib showed low expression of MAP3K1, alongside with elevated expression of G0S2 and PIK3CG. These alterations are known to promote tumor cell proliferation, migration, and invasion, thereby contributing to a reduced sensitivity to BRAF inhibitors. Subsequent in vitro experiments validated the findings derived from our analysis. This unbiased, bioinformatics-driven approach provides valuable insight into the reasons behind treatment resistance and aids in the development of next-generation treatment approaches for inhibitor-resistant cancers.

Citation Format: Kaiqiang Hu, Qiuyuan Yang, Pengwei Pan, Fang He. Mechanism of BRAF V600E resistance revealed by cell panel screening and bioinformatics [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 3484.
Abstract 3503: New generation drug development from in-silico identification to preclinical evaluation in glioblastoma
Authors: Arunachalam Mahesh , Gaikwad Shreyas , Ramachandran Sharavan , Srivastava Sanjay K.
Published: March 2024

Glioblastoma(GBM) is the most common malignancy of the central nervous system in adults. Despite medical advancements, stagnant survival rate improvements (<13%) and failure of conventional treatments such as temozolomide, have warranted the need for novel drug discovery methodologies. Considering the enormous potential of drug repurposing, we developed a method to identify a safe, active, and effective treatment for GBM. This method comprises two key stages, drug-target prediction and preclinical functional evaluation. Stage 1 fabricated a novel five phase in-silico pipeline for drug-target prediction against Ephrin-Type-A Receptor 2, chosen through preliminary literature and genomic analysis. Around 1562 FDA approved drugs were screened against the developed criterion and analyzed for bond type, location, repulsion, Gibbs free energy, stability, interactions over time, blood brain barrier permeability, and possible false positives (PAINS). Our results provided five plausible hits: Empagliflozin, Mycophenolate mofetil, Canagliflozin, Rivaroxaban, and Carvedilol. We subsequently evaluated the anti-proliferative effects of these hits using Sulforhodamine-B cytotoxicity assay on glioblastoma cell lines U251 and SF295. Our results demonstrated that Canaglifozin and Empagliflozin reduced the proliferation of GBM cell lines with IC50 value ranging from 30-40 μM. On the other hand, Mycophenolate mofetil (IC50: 5μM) and Carvedilol (IC50:16μM) also exhibited significant cytotoxic effects. Effects of Mycophenolate mofetil and Carvedilol were further evaluated in pancreatic cell line SUIT-2 where results exhibited cytotoxic responses similar to those observed in GBM. Furthermore, Annexin V/FITC analysis showed apoptosis in SUIT-2 cells by Carvedilol. Taken together, our results show the anti-cancer repurposing candidates extracted from our in-silico pipeline show significant cytotoxic effects of compounds identified through in-silico screening. Further studies are currently underway in our laboratory to delineate the anti-cancer mechanism, toxicity and off-target effects of these compounds.

Citation Format: Mahesh Arunachalam, Shreyas Gaikwad, Sharavan Ramachandran, Sanjay K. Srivastava. New generation drug development from in-silico identification to preclinical evaluation in glioblastoma [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 3503.
Abstract 353: Investigate the role of homoharringtonine in treating B-cell acute lymphoblastic leukemia
Authors: Jiao Emilie An An , Yuen Kei Ching , Li Bai Lin , Sin Chun Fung
Published: March 2024

B lymphoblastic leukemia (B-ALL) is an aggressive and highly lethal hematolymphoid malignancy and it is the most common cancer in children. Although the incidence of B-ALL in adult is lower than that in children, adult patients with B-ALL have a poor prognosis. Relapse/refractory disease is still the main cause of death in B-ALL patients. Homoharringtonine (HHT) is a plant alkaloid that was approved to treat chronic myeloid leukemia (CML) by FDA. Herein, we aimed to investigate the anti-leukemic activity of HHT in B-ALL. Cell viability was reduced in a time and dose-dependent manner upon treatment with HHT. Moreover, HHT was able to induce apoptosis in B-ALL cell lines by downregulating the MCL-1 protein level after 24 hours of treatment. Cell cycle analysis indicated G1 phase arrest, and western blot analysis demonstrated downregulation of CDK-4 and CDK-6. A proteomics study using label-free protein quantitation revealed enrichment of proteins involved in fatty acid oxidation, and further analysis showed downregulation of acyl-CoA desaturase after HHT treatment. Additionally, HHT significantly reduced the leukemic burden and prolonged survival in NSG mice injected with the PALL-2 cell line. Overall, the findings suggest that HHT is effective in treating B-ALL by inducing cell cycle arrest, with a potential inhibitory effect on fatty acid oxidation. Further studies will be conducted to evaluate the mechanism of modulation of fatty acid oxidation.

Citation Format: Emilie An An Jiao, Kei Ching Yuen, Bai Lin Li, Chun Fung Sin. Investigate the role of homoharringtonine in treating B-cell acute lymphoblastic leukemia [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 353.
Abstract 3546: Putting genes in context by linking gene signatures to established cancer hallmarks
Authors: Menyhart Otília , Kothalawala William , Győrffy Balázs
Published: March 2024

The concept of the "Hallmarks of Cancer" provides a valuable framework for understanding fundamental organizing principles common to various types of cancers. However, the absence of a consensus gene set for cancer hallmarks poses data comparison and integration challenges, resulting in diverse biological interpretations across studies.

Here, we first established a consensus cancer hallmark-gene set by merging data from available mapping resources. We searched the scientific literature for relevant publications from which a list of hallmark genes could be reconstructed. By consolidating data from seven publications, we identified 6,763 candidate cancer hallmark genes associated with ten cancer hallmarks. Of these, 1574 genes were part of at least two resources, forming a "core" hallmark gene set.

Then, we compared the enrichment of cancer hallmarks by analyzing the prognostic genes associated with overall survival across twelve solid tumor types. Notably, the hallmark "tissue invasion and metastasis" was most prominent in the stomach (p=1.2E-11), pancreatic (p=1.5E-09), bladder (p=1.8E-08), and ovarian cancers (p=0.0002), aligning with their heightened potential to spread. "Sustained angiogenesis" predominated in lung squamous carcinomas (p=4.5E-08), while "genome instability" showed strong enrichment in lung adenocarcinomas (p=1.3E-09), liver (p=1.4E-10), pancreatic (p=1E-5) and kidney cancers (p=0.0025). Compelling evidence links lifestyle choices like alcohol consumption and smoking to genomic instability across tumors, suggesting a potential common underlying mechanism of tumorigenesis.

Pancreatic cancers displayed the highest enrichment of hallmarks (8 out of 10), emphasizing the disease's complexity, while in melanomas, liver, and kidney cancer, a single hallmark (,,genomic instability”) was enriched among the prognostic markers of survival. These findings underscore the utility of the hallmark concept as an effective organizational tool, particularly when establishing a clear connection between genes and biological functions.

Finally, we integrated the data into a publicly accessible and user-friendly online tool (available at www.cancerhallmarks.com) that allows users to identify the most relevant cancer-associated "candidate hallmark genes" in their datasets.

In summary, we have established a consensus list of genes associated with cancer hallmarks. The analysis of survival-associated genes revealed a unique pattern of hallmark enrichment for each tumor type.

Citation Format: Otília Menyhart, William Kothalawala, Balázs Győrffy. Putting genes in context by linking gene signatures to established cancer hallmarks [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 3546.
Abstract 3550: PerturbDB: A resource for revealing gene functions and cancer-associated phenotypes
Authors: Yang Bing , Zhang Man , Shi Yanmei , Dong Yi-Ming , Ma Xingyu , Zhang Jingyuan , Lu Daning , Liao Jian-You , Yin Dong
Published: March 2024

Perturb-seq is a high-throughput technique that combines clustered regularly interspaced short palindromic repeats (CRISPR)-based screens with single-cell RNA sequencing (scRNA-seq) readouts for high-content phenotypic screens to comprehensively map the transcriptional effects of genetic perturbations, showing great advantages in revealing disease-associated gene functions and mechanisms in high volumes. Despite the rapid accumulation of Perturb-seq datasets, no dedicated database exists for reusing these valuable information. In this study, we developed a platform called PerturbDB (http://research.gzsys.org.cn/perturbdb) to facilitate users to unveil genotype-phenotype relations, especially gene functions and regulatory networks involved in several classical cancer associated phenotypes using 37 Perturb-seq datasets from 15 studies. By reanalyzing 3,429,829 single-cell transcriptomes from the knockdown of 3214 genes across 10 different cell lines, we identified 749 classical cancer phenotype-related genes and 373 functional gene clusters annotating potential novel functions. Utilizing Marker genes scoring and the InferCNV algorithm, we identified genes involved in 9 malignant phenotypes, which consists of sustaining proliferative signaling (362 genes), resisting cell death (120 genes), inducing angiogenesis (145 genes), tissue invasion and metastasis (321 genes), enabling replicative immortality (160 genes), deregulating cellular metabolism (247 genes), avoiding immune destruction (95 genes), unlocking phenotypic plasticity (231 genes), and chromosome instability (231 genes). Additionally, functional clusters were calculated utilizing Principal Component Analysis (PCAs) and the HDBSCAN package to introduce unknown gene functions related to the cancer associated phenotypes. Perturbation clusters (PCs) were identified by comparing similarities in the transcriptomes of perturbed cells, suggesting individual genes in the same functional cluster perform similar gene functions, and therefore novel functions of 735 genes can be inferred from the known functions of neighboring genes. The PGSEA tool was developed to facilitate functional analysis of genes not yet included, which helps users to predict gene functions through a combination of PerturbDB datasets and personalized RNA-seq datasets. This study will greatly expand our understanding of genes involved in emblematic cancer associated phenotypes and their coordinated functions and regulatory networks.

Citation Format: Bing Yang, Man Zhang, Yanmei Shi, Yi-Ming Dong, Xingyu Ma, Jingyuan Zhang, Daning Lu, Jian-You Liao, Dong Yin. PerturbDB: A resource for revealing gene functions and cancer-associated phenotypes [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 3550.
Abstract 3556: A pan-cancer ex vivo drug screen database for next-generation pharmacogenomics and functional precision oncology
Authors: Markus Anneliese , Pichotta Karl , Quinn Jeffrey , White Jessica , Tosh Christopher , Liu Jinrui , Coyne Erin , Tansey Wesley
Published: March 2024

Large-scale drug screens across thousands of drugs and biological models enable pan-cancer analyses that can reveal novel insights into therapeutic response and resistance. Existing databases, such as the Cancer Dependency Map only screen established 2D cell lines, which are known to poorly translate to patients. Ex vivo models such as patient-derived cells, spheroids, and organoids, have consistently demonstrated superior translatability from drug screening responses as they better replicate the original tumor. However, the cost, complexity, and difficulty of developing and screening ex vivo models has thus far prevented the establishment of any large-scale database comparable to existing cell line databases. We present the pan-preclinical (PPC) project, a large pan-cancer database of ex vivo drug responses comprising 2.1M raw dose-response measurements with curve-level summary statistics and metadata. The PPC database is assembled from over 30 previously published ex vivo studies and contains 2,880 ex vivo models spanning 106 cancer subtypes tested against subsets of 3,023 drugs. Compounds are harmonized across studies and paired with detailed chemoinformatics derived from PubChem. Each ex vivo sample is matched to an underlying patient and paired, where available, with genomics, transcriptomics, and clinical information such as sex, treatment history, and overall survival. Two thirds of the underlying studies did not originally make the underlying drug screening data available at publication time, making the PPC database a novel resource beyond data integration. Results: To investigate the power of the PPC database, we developed a preliminary computational modeling and statistical analysis pipeline. A hierarchical Bayesian factor model was developed to estimate dose-response curves, remove batch effects across studies, and impute missing drugs. Low-dimensional projections of ex vivo drug responses show biologically meaningful clustering. Statistical analyses of both observed and imputed drug responses recapitulate standard of care drugs as significantly effective across several cancer types. Overall, we envision the PPC project laying the foundation for the next generation of large-scale pharmacogenomic analyses and aiding in the coming era of functional precision oncology.

Citation Format: Anneliese Markus, Karl Pichotta, Jeffrey Quinn, Jessica White, Christopher Tosh, Jinrui Liu, Erin Coyne, Wesley Tansey. A pan-cancer ex vivo drug screen database for next-generation pharmacogenomics and functional precision oncology [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 3556.
Abstract 356: Developing a multiplex assay to monitor apoptosis and necrosis using the Cellaca® PLX Image Cytometer
Authors: Mukherjee Joydeep , Pierce Mackenzie , Huang Yongyang , Lin Allen , Chan Leo Li-Ying
Published: March 2024

Apoptosis is a critical pathway for programmed cell death that cancer cells can evade to ensure survival. For pharmaceutical drug discovery, it is important to characterize and compare cancer therapeutics (i.e., small molecules, antibody drugs, cell therapies) that can initiate the process of apoptosis, allowing for the identification of potential therapeutic candidates. In this work, we developed and demonstrated a multiplex detection method for monitoring apoptosis and necrosis with Annexin V, Caspase 3/7, and Propidium Iodide (PI) using the Cellaca® PLX Image Cytometer. First, apoptosis was induced in Jurkat and K562 cell lines with staurosporine over the course of 24 h, and were monitored at 0, 1, 1.5, 2, 4, 20, and 24 h timepoints. Samples were stained with Hoechst 33342 (total dye), Annexin V-APC (early-stage apoptosis), Caspase-3 488 (late-stage apoptosis), and PI (necrosis) at each timepoint and evaluated using the Cellaca® PLX. Results showed that apoptotic factors and cascades were successfully detected along the pathway from early to late-stage apoptosis, and ultimately necrosis. A clear trend was observed during the first 2 h showing differences of up to 25% between the single Annexin V+ and Caspase-3+ populations in treated Jurkat cells, however, a significant increase in double positive apoptotic/necrotic cells for Annexin V+PI+ and Capase-3+PI+ was not observed until 20 h. Upon further analysis amongst apoptotic populations, Annexin V+ only populations were higher than Caspase-3+ only populations by up to 30% between 0-2 hours. Conversely, K562 cells did not exhibit a notable change in apoptotic and necrotic populations due to low sensitivity to staurosporine. The proposed image-based detection method using the Cellaca® PLX may provide an effective and efficient tool for rapid and reliable simultaneous detection of early, late-stage apoptosis, and necrosis. This may allow researchers to better characterize and screen potential cancer therapeutic drug candidates in a high-throughput manner to determine their treatment efficacy.

Citation Format: Joydeep Mukherjee, Mackenzie Pierce, Yongyang Huang, Allen Lin, Leo Li-Ying Chan. Developing a multiplex assay to monitor apoptosis and necrosis using the Cellaca® PLX Image Cytometer [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 356.
Abstract 3581: IGFR1 and MEK inhibition synergize to mediate anti-tumor activity in adrenocortical carcinoma
Authors: Kumar Suresh , Sun Nai-Yun , Arakawa Yasuhiro , Varghese Diana , Hoang Chuong D. , Hernandez Jonathan M. , Pommier Yves , Thomas Craig , Rivero Jaydira Del , Roper Nitin
Published: March 2024

Adrenocortical carcinoma (ACC) is an aggressive and rare endocrine malignancy with limited treatment options and poor prognosis. IGF2, the ligand for IGFR1, is highly expressed in ACC. However, linsitinib, an IGFR1 inhibitor, failed to improve overall survival over placebo in a randomized, phase 3 clinical trial of metastatic ACC. We hypothesized that combination therapy with IGFR1 inhibition may have greater anti-tumor efficacy in ACC than IGFR1 inhibition alone. To test this hypothesis, we performed high-throughput cell toxicity screening of 2803 clinical-stage compounds with linsitinib in an ACC cell line. MAPK inhibitors were among the top screening hits. MEK inhibitors were chosen for further evaluation given the safety, tolerability, and broad clinical activity of these FDA-approved agents. IGFR1 and MEK inhibitors were strongly synergistic in cytotoxicity across ACC cell lines, ACC organoid short-term cultures derived from surgical tissue resections (PDOs), and PDX-derived organoids (PDXOs). Genetic depletion of IGF2 significantly inhibited growth with cobimetinib and genetic depletion of MEK1 inhibited growth with linsitinib in ACC cell lines. Combination IGFR1 and MEK inhibition downregulated ERK phosphorylation and increased apoptosis compared to either IGFR1 or MEK inhibition alone. Linsitinib combined with cobimetinib significantly reduced tumor growth compared to either linsitinib or cobimetinib alone in an ACC xenograft model. Our study provides preclinical support for testing the combination of IGFR1 and MEK inhibition in patients with ACC.

Citation Format: Suresh Kumar, Nai-Yun Sun, Yasuhiro Arakawa, Diana Varghese, Chuong D. Hoang, Jonathan M. Hernandez, Yves Pommier, Craig Thomas, Jaydira Del Rivero, Nitin Roper. IGFR1 and MEK inhibition synergize to mediate anti-tumor activity in adrenocortical 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 3581.
Abstract 36: The discovery of a novel CD19xCD22 dual-targeting CAR for the development of an IPSC-derived cell therapy
Authors: Carton Jill M. , Wheeler John , Dower Chris , Campion Liam , Millar Hillary J. , Beqiri Marilda , Morse Barry , Gurung Buddha , Genovese Rebecca , DeLuca Steven , Dominick Charles , Naso Michael , Levitsky Hy
Published: March 2024

Dual-targeting cell therapies to address CD19 antigen loss in heme malignancies are being explored by Century Therapeutics and others for unmet clinical need in hematological malignancies. CD22 chimeric antigen receptor (CAR) T-cell therapies have shown promising efficacy in relapsed or refractory B-lineage acute lymphoblastic leukemia (B-ALL) alone and in combination with CD19 CAR-T cell therapies (1,2). CD22 is a multi-domain glycoprotein expressed on B-cells. Natural splice variants of CD22 can exclude domains near the N-terminus, allowing for therapeutic resistance when these domains are targeted. We identified novel single domain antibodies (VHH) to CD22 that bind to multiple epitopes on different domains of CD22, including membrane proximal binders. The VHHs were affinity matured to enhance cell-based binding and formatted as CARs in monovalent and tandem, bivalent formats. Our data demonstrates the best efficacy against CD22+ tumor cells with a biparatopic, tandem VHH CAR format. Through additional engineering, bispecific CARs that combined three CD22-binding VHH and the anti-CD19 scFv, FMC63, in a loop CAR configuration were designed and tested. This CD19xCD22 bispecific, CD22 biparatopic CAR was engineered into primary T-cells and demonstrated cytotoxicity activity against CD19 and CD22 positive tumor cells as well as CD19 knockout and CD22 knockout cell lines. CD19xCD22 bispecific primary CAR-T cells were efficacious in controlling tumors in mouse xenograft models. This novel CAR is being tested in IPSC-derived iT and iNK cells for off-the-shelf allogeneic cell therapy to expand patient access beyond CD19 CAR-T cell therapies. Ref: 1. Nat Med. 2018;24(1):20-28. doi: 10.1038/nm.4441. 2. Blood. 2018;132(suppl 1). Abstract 27

Citation Format: Jill M. Carton, John Wheeler, Chris Dower, Liam Campion, Hillary J. Millar, Marilda Beqiri, Barry Morse, Buddha Gurung, Rebecca Genovese, Steven DeLuca, Charles Dominick, Michael Naso, Hy Levitsky. The discovery of a novel CD19xCD22 dual-targeting CAR for the development of an IPSC-derived cell therapy [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 36.
Abstract 3606: Tumor-specific CD8+ Tc9 cells activate host CD4+ T cells to control antigen-lost tumors
Authors: Xiao Liuling , Yi Qing
Published: March 2024

Cancer immunotherapies relying on targeted destruction of cancer cells by potent antitumor T cells have achieved unprecedented success in recent years. As a main form of cancer immunotherapies, adoptive T cell therapy (ACT) has shown a durable response in certain cancer patients. However, this response is often short-lived and tumor relapse occurs due to the outgrowth of antigen-lost-variant (ALV) tumors and poor antitumor immune response. Here, We reported that adoptively transfer of murine tumor-specific CD8+ Tc9 but not Tc1/CTL cells achieved long-term control of tumor growth in vivo. Here, we demonstrated that murine tumor-specific Tc9 cells not only killed antigen-expressing primary tumors but also controlled the outgrowth of antigen-lost relapsed tumors by recruiting and activating host effector CD4+ T cells that recognized relapsed tumors. Tc9 cells secreted IL-24 and recruited CCR7-expressing conventional type-2 dendritic cells (cDC2) into tumor-draining lymph nodes to prime host CD4+ T cell response against relapsed tumors. Depleting host CD4+ T cells or deficiency in CCR7 expression impaired Tc9 cell ability to control the outgrowth of relapsed tumor. We also observed that intratumoral IL24 expression was positively correlated with gene signatures of cDC2 and CD4+ T cells in human cancers and expression of IL24 and cDC2 and CD4+ T cell gene signatures were associated with patient’s overall survival. Thus, this study uncovers a novel mechanism underlying activation of tumor-specific CD4+ T cells in vivo.

Citation Format: Liuling Xiao, Qing Yi. Tumor-specific CD8+ Tc9 cells activate host CD4+ T cells to control antigen-lost 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 3606.
Abstract 3624: A low-cost kit for gentle, effective and timely extracellular vesicle (GET EVs) isolation: Accelerating development of RNA-based liquid biopsies for neuroendocrine neoplasms
Authors: Su Boyang , Jeyhani Morteza , Yang Xiaojing , Nanayakkara Jina , Wunsche Reese , Renwich Neil , Tsai Scott , Leong Hon
Published: March 2024

Extracellular vesicles (EVs) are cell fragments released by all cells, making them promising platforms for cancer biomarker development. Effective isolation of ultra-pure EVs for downstream analyses is key for EV-based liquid biopsy development. However, current EV isolation methods such as ultracentrifugation (UC) and other commercialized EV isolation kits are lackluster because of damage to EVs, length of time required, and low EV recovery rates. In response, we developed an “GET EV” kit which is based on the principles of lipid energy states, also known as the aqueous two-phase system (ATPS) to isolate EVs from any media. Nanoscale flow cytometry (nFC) analysis revealed that ATPS has greater EV enrichment capability (21.4 × vs. 10.9 × times fold enrichment) and higher EV recovery efficiency (97.6% vs. 69.3% recovery) than UC. Other EV isolation kits were tested and were inferior to ATPS in terms of EV recovery and EV-RNA recovery. EV subpopulations as determined by EV biomarkers (CD9, CD63, CD81, etc.) were confirmed by nFC. “Omics” studies (small RNA sequencing and proteomics) also confirmed the presence of expected EV markers. We developed an RNA-based liquid biopsy for Neuroendocrine Neoplasms (NENs) by quantitating the presence of EVs containing miR-375, an established biomarker for NENs. Using the GET EVs kit, we isolated EVs from healthy volunteer and patient plasma samples of NEN patients. RT-qPCR demonstrated enriched expression of miR-375 in EVs isolated from Lung and GI NEN patient plasma samples. Our study establishes the use of GET EV kits to efficiently, rapidly, and gently isolate EVs from small plasma samples (250 uL). This is a low-cost innovation that will finally enable the development of other RNA-based Liquid Biopsies for other disease sites with significant diagnostic and prognostic implications.

Citation Format: Boyang Su, Morteza Jeyhani, Xiaojing Yang, Jina Nanayakkara, Reese Wunsche, Neil Renwich, Scott Tsai, Hon Leong. A low-cost kit for gentle, effective and timely extracellular vesicle (GET EVs) isolation: Accelerating development of RNA-based liquid biopsies for neuroendocrine neoplasms [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 3624.