bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 5799: Landscape of TSC1 and TSC2 mutations in patients with advanced solid cancers
Authors: Gulati Gunsagar S. , Cacheris William , Dutta Ritika , Ahnert Jordi Rodon
Published: June 2022

Tuberous sclerosis proteins 1 and 2 (TSC1 and TSC2) are tumor suppressor genes and inhibitors of the mammalian target of rapamycin (mTOR) pathway. Mutations in these genes are candidates for novel mTOR inhibitors, such as nanoparticle albumin-bound (nab)-sirolimus, which have already demonstrated clinical efficacy in isolated case studies of patients with mutations in the mTOR pathway. However, the incidence of TSC1 and TSC2 mutations in the US and its distribution across tumors has not yet been systematically reported. Moreover, existing models for calculating incidence of targetable mutations do not account for cross-eligibility for other clinically approved targets. Therefore, here, we describe the landscape of TSC1 and TSC2 mutations across 16 solid tumors from The Cancer Genome Atlas (TCGA; n = 9,808 patients) and AACR GENIE database (MSK: n = 14,340 patients, DFCI: n = 5,271 patients) and estimate the annual incidence of eligible patients using the Surveillance, Epidemiology, and End Results Program (SEER) database. We then refined these estimates by excluding patients eligible for immunotherapy (tumor mutational burden (TMB) > 10 mutations/Mb) and other targeted therapies (n = 23 FDA-approved drug-targetable mutations). We find that the combined US incidence of patients with truncations (e.g. frameshift, nonsense, splice-site) or deep copy number deletions in TSC1 and TSC2 is ~11,000 ± 1,000 (mean Spearman ρ across datasets: 0.92). About 40% of these patients have mutations in at least one of 23 other drug-targetable genes. TSC1 and TSC2 mutations were most frequent in bladder and hepatobiliary cancers, respectively, with the absolute prevalence of mutations being highest in bladder and non-small-cell lung cancer. Among the patients with TSC1 and TSC2 mutations with other targetable mutations, we identified the most common co-occurring targetable mutations with TSC1 and TSC2, suggesting that combination or sequential treatment with immunotherapy and BRAF and FGFR3 inhibitors are possible options for clinical trials. Finally, we show that the combined annual US incidence of patients with TSC1 and TSC2 mutations is on average (n = 3 clinical genomic cohorts) higher than 17 of 23 other common targetable mutations. Our approach is now being used to estimate the population size of other medically relevant mutations and identify associated genomic targets for improved clinical trial design.

Citation Format: Gunsagar S. Gulati, William Cacheris, Ritika Dutta, Jordi Rodon Ahnert. Landscape of TSC1 and TSC2 mutations in patients with advanced solid cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5799.
Abstract 583: Improving anti-tumor response by increasing mitochondrial respiration of T-cell
Authors: Wu Meng-Han , Giddlings Emily , Danis Catherine , McCalab Megan , Kohler Mark Eric , Rincon Mercedes
Published: June 2022

Chimeric antigen receptor (CAR)-T cell therapy is revolutionary as a promising approach of cancer immunotherapy against lymphoblastic leukemia and lymphoma. While initially effective in up to 90% of patients with B-cell lymphoblastic leukemia, over 40% of patients will relapse, with sub-optimal persistence of functional CAR-T cells underlying many of these relapses. The major challenges of CAR-T cell to effectively eliminate cancer cells are extending persistence of CAR-T cells and retaining the effector function of CAR-T cells in vivo after prolonged in vitro expansion. To overcome such limitations, enhancing mitochondrial metabolism is emerging as an appealing approach to regulate CAR-T cell function, however, increasing mitochondrial respiration and ATP production is a challenging strategy. We have previously identified MCJ/DnaJC15 as an endogenous negative regulator of Complex I of electron transport chain. The absence of MCJ in CD8 cells (MCJ KO CD8 cells) increases Complex I activity, mitochondrial membrane potential, and mitochondrial respiration without affecting glycolysis. Lack of MCJ enhances cytokine secretion and cytotoxicity (two processes dependent on mitochondrial ATP) in CD8 cells in vitro and in vivo. Using the B16 melanoma cell model, we have shown that antigen-specific MCJ KO CD8 cells are superior in killing melanoma cells in vitro and in vivo. We have generated WT and MCJ KO CD19-41BB CAR-T cells and tested their anti-tumor activity against B-cell leukemia. The results reveal that MCJ-deficient CAR-T cells exhibit superior killing capacity against leukemia B cells and prolong survival of the leukemia-bearing mice. Together, these data demonstrate MCJ as an attractive target to enhance CAR-T cell therapy efficacy.

Citation Format: Meng-Han Wu, Emily Giddlings, Catherine Danis, Megan McCalab, Mark Eric Kohler, Mercedes Rincon. Improving anti-tumor response by increasing mitochondrial respiration of T-cell [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 583.
Abstract 5835: Functional and mechanistic characterization of ΔNp63α in esophageal squamous cell carcinoma
Authors: So Shan Shan , Yu Valen Z. , Law Simon Y. , Lung Maria L.
Published: June 2022

Esophageal squamous cell carcinoma (ESCC) is highly prevalent in Asia with a poor prognosis and a high mortality rate [1, 2]. The p63 protein, encoded by TP63, is a master regulator involved in many cell events including cell cycle, DNA damage, cell proliferation, stem cell maintenance, and cell death in different cancer types. ΔNp63α is the dominantly expressed isoform of p63 in squamous cell carcinomas, playing a critical role in tumorigenesis [3, 4]. However, the functional roles of ΔNp63α in ESCC have not been fully elucidated. Our results have revealed that ΔNp63α is highly expressed and up-regulated in ESCC. We have shown that ΔNp63α protein expression plays an oncogenic role in ESCC cells, depletion of which inhibits in vitro cell proliferation and colony formation and greatly suppresses in vivo tumor growth, in a panel of ESCC cell lines and our latest patient-derived organoid cultures, potentially in a differentiation-dependent manner. Glycolysis pathway and two novel downstream signaling pathways of ΔNp63α, MYC/4EBP1 and AKT/NDRG1, are significantly suppressed upon ΔNp63α depletion in ESCC cell lines. Notably, xenografts of ΔNp63α-depleted human ESCC cells show elevated infiltrating cancer-associated fibroblasts (CAFs), which may contribute to tumor suppression by ΔNp63α depletion. These data not only shed light on the ΔNp63α functions and how they contribute to the ESCC tumorigenesis, but also unravel potential therapeutic benefits for ESCC patients in the future. Acknowledgements: We acknowledge DSMZ (German Collection of Microorganisms and Cell Culture) for the KYSE cell lines. We acknowledge the Research Grants Council Theme-Based Research Scheme grant T12-701/17-R to MLL. References [1] Chen, W., et al., Cancer statistics in China, 2015. CA Cancer J Clin, 2016. 66(2): p. 115-32. [2] Peng, L., et al., CCGD-ESCC: A Comprehensive Database for Genetic Variants Associated with Esophageal Squamous Cell Carcinoma in Chinese Population. Genomics Proteomics Bioinformatics, 2018. 16(4): p. 262-268. [3] Fukunishi, N., et al., Induction of DeltaNp63 by the newly identified keratinocyte-specific transforming growth factor beta Signaling Pathway with Smad2 and IkappaB Kinase alpha in squamous cell carcinoma. Neoplasia, 2010. 12(12): p. 969-79. [4] Moses, M.A., et al., Molecular Mechanisms of p63-Mediated Squamous Cancer Pathogenesis. Int J Mol Sci, 2019. 20(14).

Citation Format: Shan Shan So, Valen Z. Yu, Simon Y. Law, Maria L. Lung. Functional and mechanistic characterization of ΔNp63α in esophageal squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5835.
Abstract 5873: Distinct prevalence and spectrum of germline cancer susceptibility gene mutations between early-onset and late-onset colorectal caner
Authors: Gao Zhidong , Zhou Jing , Xin Ying , Liang Bin , Shen Kai , Guo Peng , Jiang Kewei , Yin Mujun , Yang Xiaodong , Shen Zhanlong , Zhang Hui , Huang Depei , Ye Yingjiang
Published: June 2022

Background: In the past few decades, the incidence of early-onset CRC (<50 years of age) has increased globally. Previous studies with small sample sizes have shown that early-onset CRC appears to have a distinct clinical, pathologic, and molecular features compared to late-onset CRC (≥ 50 years of age). However, few studies in a large population have focused on the differences in germline gene mutation spectrums of these two groups of patients.

Methods: Hybrid capture-based next-generation sequencing (NGS) were performed in 5080 colorectal patients in a CAP/CLIA-approved laboratory (3DMed). NGS testing for germline mutations and MSI was implemented.

Results: Of 5080 colorectal patients, early-onset CRC was observed in 1305 (25.7%) patients. The incidence of germline mutation was higher in early-onset CRCs than late-onset CRCs (8.97% vs. 4.15%,OR=2.27, P<0.0001). Consistently, the frequency of MSI-H was higher in early-onset CRCs (13.0% vs. 5.7%, OR=2.48, P<0.0001). The most frequently mutated gene was MLH1 (3.07%) in early-onset CRCs, followed by MSH2 (1.69%), APC (1.0%), MSH6 (0.84%), PMS2 (0.38%), RAD50 (0.31%), CHEK2 (0.31%), MUTYH (0.23%), BRCA1 (0.23%), and BRCA2 (0.23%). The frequency of MMR gene mutations among early- and late-onset patients was 5.98% and 1.27%, respectively (OR=4.95, P<0.0001). MMR gene mutations accounted for 60% of germline mutations of early-onset patients, while this percentage was lower for late-onset CRC (30%). Higher frequencies of APC, RAD50 and CHEK2 gene mutations were associated with early-onset CRCs (all P<0.05). The mutation frequencies of other DDR genes, MUTYH, BRCA1, BRCA2, ATM, ATR, FANCD2, TP53, were not statistically different between the two groups. The late-onset CRC tended to harbor a wider spectrum of germline cancer gene mutations, including an additional 14 cancer-related gene that were not found in early-onset CRC.

Conclusions: Our findings revealed different prevalence and spectrum of germline cancer gene mutations between early-onset and late-onset CRC, suggesting that young patients should be specially considered.

Citation Format: Zhidong Gao, Jing Zhou, Ying Xin, Bin Liang, Kai Shen, Peng Guo, Kewei Jiang, Mujun Yin, Xiaodong Yang, Zhanlong Shen, Hui Zhang, Depei Huang, Yingjiang Ye. Distinct prevalence and spectrum of germline cancer susceptibility gene mutations between early-onset and late-onset colorectal caner [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5873.
Abstract 5878: The prognostic model of colorectal liver metastases contribute extended molecular profiling
Authors: Cui Chunhui , Wang Xintong
Published: June 2022

Background: Over half of colorectal cancer (CRC) patients will metastasize at the same/different times, Only 15-20% of patients are considered resectable at the time of diagnosis. The clinical situation attributed to the clinical heterogeneity of metastatic colorectal cancer(mCRC), the prognosis of patients with mCRC at different metastatic sites is different. The proportion of higher is colorectal liver metastasis (CRLM) and the mechanism of CRLM is complicated,studies have found cancer-related genes expand the predictive molecular profile of survival, The aim of this analysis was to verify and further develop the genetic risk scores.

Methods: In this study, bioinformatics methods were used to comprehensively analyze the CRLM cohort (n=270) in the database. The cohort patients were divided into high-risk group and low-risk group. Independent data (n=105) verified the prognostic validity of the model.

Results: The models established by commonly genes(APC, BRAF, ERBB2, KRAS, NRAS, PIK3CA, TP53, SMAD2-4) of CRLM were confirmed by prognostic markers. Differences between high-risk prognostic groups compared to low-risk were significant (HR = 1.9023, 95% CI: 1.61-2.23, P_value <0.001), risk score can be used as biomarkers for constructing prognosis. we found significantly higher proportion of low-risk group diagnosed in stage I (82% vs 18%, P_value = 0.035), This model can distinguish in diagnosed stage I CRLM patients with poor prognosis, the model also has a good prognostic effect in validating data and clinical staging.

Conclusions: We found that the survival OS of the model risk-high cohort was significant, and is helpful for subsequent treatment.The model risk score was established to be superior to common biomarkers for CRLM, and the discovery of the model is helpful for find metastatic progression the treatment of patients with CRLM.

Citation Format: Chunhui Cui, Xintong Wang. The prognostic model of colorectal liver metastases contribute extended molecular profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5878.
Abstract 59: Optimization of high-throughput, high-depth, targeted single-cell DNA sequencing to pancreatic ductal adenocarcinoma
Authors: Zhang Haochen , Karnoub Elias-Ramzey , Chaligné Ronan , Masilionis Ignas , Makohon-Moore Alvin , Hong Jungeui , Iacobuzio-Donahue Christine
Published: June 2022

Purpose of study: Despite insights gained by bulk DNA sequencing of cancer it remains challenging to resolve “mixed signals”, i.e. the admixture of normal and tumor cells, and/or of distinct tumor subclones. Bulk sequencing of pancreatic ductal adenocarcinoma (PDAC) has been particularly problematic due to the high stromal content and resulting low tumor cellularity. Strategies to account for this have included laser capture microdissection yet this is a laborious process not amenable to high-throughput pipelines. We sought to develop and apply a high-throughput, high-depth, targeted single-cell DNA sequencing (scDNA-seq) method to account for these issues, including the ability to extract high quality genomic information from low purity and archival samples.

Experimental procedures: Bulk whole exome sequencing (WES) was performed on 29 biologically distinct samples. For single cell sequencing, we developed a custom panel containing 186 amplicons covering 93 genes that represent the most common germline and somatic targets reported in PDAC. Based on a commercially available system that enables automatic enzymatic and mechanical tissue disruption with integrated fluidic processes, we optimized a nuclei extraction workflow from frozen tissues that is highly compatible with downstream microdroplet-based single-cell encapsulation and library preparation. With it we generated scDNA-seq data from archival tissues of 15 PDAC patients at varying stages of the disease. Results were compared to that found in matched bulk sequencing data.

Summary of new, unpublished data and conclusions: 42 samples were analyzed by single cell sequencing. Our nuclei extraction workflow generated on average 2867 single cell libraries per sample at >80X read depth. The single-cell results aligned well with matched bulk data in terms of the detection of key genetic variants and their variant allele frequency (VAF). We also identified additional driver variants not seen by WES, some with direct clinical evidence. Benefits of this workflow over preexisting methods are its speed of sample preparation, efficiency of sample use (particularly for small samples), flexibility by allowing for storage of excess extracted nuclei, and economy of scale. Together, these features support preparation of large numbers of cancer samples in a relatively short period of time.

Citation Format: Haochen Zhang, Elias-Ramzey Karnoub, Ronan Chaligné, Ignas Masilionis, Alvin Makohon-Moore, Jungeui Hong, Christine Iacobuzio-Donahue. Optimization of high-throughput, high-depth, targeted single-cell DNA sequencing to pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 59.
Abstract 5903: Polygenic risk scores for prediction of breast cancer in Korean women
Authors: Jee Yon Ho , Ho Weang-Kee , Park Sohee , Easton Douglas , Teo Soo-Hwang , Jung Keum Ji , Kraft Peter
Published: June 2022

Background: Polygenic risk scores (PRS) developed in large European GWAS have been shown to perform well in Asian women relative to PRS developed in smaller Asian studies. However, prospective validation of absolute risk prediction models combining lifestyle and PRS in Asian women is limited. We evaluate the calibration of four PRS developed using Asian or European training samples; two PRS were restricted to genome-wide significant SNPs (GRS-11ASN, GRS-136EUR) and two included sub-genome-wide significant SNPs (PRS-42ASN, PRS-209EUR).

Methods: For each PRS, we compared discrimination (area under the curve [AUC]) and calibration (expected-to-observed ratio [E/O]) of three absolute risk models among 41,031 women from the Korean Cancer Prevention Study-II Biobank: (i) a model using incidence, mortality, and risk factor distributions (reference inputs) among U.S. women and European relative risks; (ii) a recalibrated model, using Korean reference but European relative risks; and (iii) a fully Korean-based model using Korean reference and relative risk estimates from KCPS.

Results: All Asian and European PRS improved risk prediction for breast cancer in Korean women (Qx: AUC=0.65, Qx+PRS-42ASN: AUC=0.68, Qx+PRS-209EUR: AUC=0.69 in Korean-based model for age less than 50). We found that the U.S.-based absolute risk models overestimated the risks for women age ≥50 years (PRS-42ASN: E/O=1.93, 95% CI=1.69, 2.19, PRS-209EUR: E/O = 1.92, 95% CI=1.69, 2.19). Our absolute risk projections suggest that risk-reducing lifestyle changes would lead to larger absolute risk reductions among women at higher PRS.

Conclusions: Incorporation of PRS previously developed in Asian and European-ancestry populations can improve discrimination in Korean women. Our finding suggests that PRS may be useful for prioritizing individuals for targeted intervention on their lifestyle such as alcohol intake and obesity. Larger Asian training samples should improve PRS discrimination among Korean women. Further studies are needed to evaluate the value of incorporating additional information on factors into a model in ancestrally diverse populations.

Citation Format: Yon Ho Jee, Weang-Kee Ho, Sohee Park, Douglas Easton, Soo-Hwang Teo, Keum Ji Jung, Peter Kraft. Polygenic risk scores for prediction of breast cancer in Korean women [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5903.
Abstract 5910: Exploration of genetic ancestry and socioeconomic status in the incidence of neuroblastoma: An ecological study
Authors: Jung Eun Mi , Johnson Rebecca A. , Hubbard Aubrey , Spector Logan G.
Published: June 2022

Although global differences in the incidence of neuroblastoma have been examined, the underlying mechanism has yet to be elucidated. Previous studies have suggested genetic ancestry and human development index (HDI) as contributing factors, but few studies have been conducted at the international level. Here, we aimed to examine whether the frequency of common genomic variation associated with neuroblastoma can affect its risk at the ecological level with consideration of the socioeconomic status of a population. Minor allele frequencies (MAFs) for 22 single nucleotide polymorphisms (SNPs) were abstracted from the Geography of Genetic Variants Browser. The number of incident neuroblastomas for each population was obtained from the Cancer Incidence in Five Continents series. Further, population pseudo-polygenic risk scores (pp-PRSs) were calculated as a sum of MAFs at the population level, each of which was weighted by effect sizes from prior studies. Negative binomial regression was used to estimate the incidence rate ratios (IRRs) and the 95% confidence intervals (CIs) to examine whether differences in MAFs across the population influence the risk of neuroblastoma, with and without adjustment for HDI and whether pp-PRSs can be a predictor of the risk of neuroblastoma. Overall, our results indicated that the neuroblastoma risk associated with variation in SNP frequency could not be differentiated from that of HDI at the ecological level. Additionally, pp-PRSs were not significantly associated with the risk of neuroblastoma (IRR: 0.99, 95% CI: 0.62—1.60). Further study using individual-level data is warranted to minimize the ecological fallacy in this study.

Citation Format: Eun Mi Jung, Rebecca A. Johnson, Aubrey Hubbard, Logan G. Spector. Exploration of genetic ancestry and socioeconomic status in the incidence of neuroblastoma: An ecological study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5910.
Abstract 5943: Association between the consumption of meat and carbonated drinks and early onset gastric cancer in Chilean patients
Authors: Parra Carol , Molina Graciela , Coo Carla , López Jessica , Martín María San , Siche Javiera , Carvajal-Carmona Luis
Published: June 2022

Gastric cancer (GC) is the 5th most frequent neoplasm and the 3rd cancer with the highest mortality according to GLOBOCAN. GC is often diagnosed in middle aged and elderly people, with a peak in incidence between 60 and 70 years old. In contrast, early-onset GC is the GC had a strong hereditary component. Associations of sporadic late onset-GC and dietary factors have been published but the role of nutritional factors in early onset GC is unknown. The aim of this study is to investigate the association between the intake of red meat, pork, processed meats and carbonated drinks in a group of early-onset GC. Our study was carried out in 19 Chilean early-onset GC patients, aged between 32 and 60 years, and 32 healthy age matched individuals from the same population. Through a survey of nutritional habits carried out retrospectively considering the stage prior to the diagnosis of GC, we determined the amount, type and frequency of ingestion of red meat, pork, processed meat and carbonated beverages. To measure the association an odds ratio and non-parametric association statistic tests were used. For the association of meat intake, we used the WHO recommendation (less than 70 g of meat per day) to classify the meat consumption levels in both groups. An odds ratio of 25.5 (4.8-135.4, p=8.3x105) was determined between the consumption of more than 70 g of meat per day in the early onset GC group vs the control group. Even though there are no international recommendations for carbonated drinks consumption levels, we found a higher carbonated drink consumption among cases (cases: Ave.= 180,7, SD= ±108,5 vs controls: Ave.=43,3, SD=±38,3. P=0033). In conclusion, our results shows significant associations between the consumption of red meat, pork, processed meats, and carbonated drinks in the risk of early-onset GC patients compared with the control group. Our findings, suggest that nutritional factors could play a role in the early GC presentation, acting in conjunction with low penetrance gene mutations. We will incorporate more early onset patients to the study group and do a sex matching for the control group to evaluate this possible confounding factor. We will also incorporate a late onset GC group. We think that nutritional factors could be an important factor to modulate genetic risk, even in early-onset patients. Beca Chile Postdoctorado 74190063 to GM.

Citation Format: Carol Parra, Graciela Molina, Carla Coo, Jessica López, María San Martín, Javiera Siche, Luis Carvajal-Carmona. Association between the consumption of meat and carbonated drinks and early onset gastric cancer in Chilean patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5943.
Abstract 5960: Blood-based extracellular vesicle biomarker test for detection of early-stage pancreatic cancer
Authors: Hinestrosa Juan P. , Lewis Jean M. , Balcer Heath I. , Kurzrock Razelle , Lippman Scott , Krishnan Rajaram
Published: June 2022

Pancreatic cancer is an almost uniformly lethal malignancy, in large part because is it rarely detected in its early, curable stages. We recently conducted a study to evaluate the use of proteins associated with extracellular vesicles (EVs) isolated using an alternating current electrokinetic (ACE) system for the early detection of pancreatic ductal adenocarcinoma. Because earlier detection of pancreatic cancer greatly improves outcomes, we sought to devise a blood-based test with high specificity for detecting early-stage PDAC based on identification of EV-bound biomarkers. EVs were purified from control or stage I-II pancreatic ductal adenocarcinoma (PDAC) patient plasma using an ACE microelectrode array. Following collection of EVs onto the electrodes, contaminating plasma elements were washed away, and the electric field was turned off to release EVs into buffer. The isolated EV/exosome samples were then tested using bead-based multiplex immunoassay kits to determine relative concentrations of biomarkers of interest. Sample cohorts were divided into a training set (controls, N=146; PDAC cases, N=33) to develop a logistic regression-based classification model, and a validation set (controls, N=139; PDAC cases, N=35) to generate a probability-based score for predicting the presence of PDAC. For the training set, the algorithm identified six protein biomarkers associated with the presence of stages I-II cancer in PDAC patient plasma, with a receiver-operating characteristic (AUC) of 0.997 (95% CI: 0.978-1.000) compared to control plasma samples. For the validation set, the algorithm had a sensitivity of 82.9% (95% CI: 67.3% - 91.9%) at a specificity of 99.3% (95% CI: 96.0% - 99.9%), generating an AUC = 0.978 (95% CI=0.954-0.995). The exosomal PDAC assay shows feasibility for developing minimally invasive liquid biopsies that allow low-risk, routine screening of high-risk patients. Those patients identified by the test would be able to undergo additional testing to determine if there is PDAC present. The additional screening and testing of these patients may increase the likelihood of curative treatment. Further work in large datasets is warranted.

Citation Format: Juan P. Hinestrosa, Jean M. Lewis, Heath I. Balcer, Razelle Kurzrock, Scott Lippman, Rajaram Krishnan. Blood-based extracellular vesicle biomarker test for detection of early-stage pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5960.
Abstract 5981: Single cell RNA sequencing uncovers high-plasticity cell state during tumor metastasis
Authors: Zhang Yu , Wong Ching Ngar , Gong Lanqi , Guan Xin-yuan , Ru Beibei , Liu Beilei
Published: June 2022

Cancer metastasis remains the key barrier for patient’s cure. Tumor metastasis initiating from a single disseminated cell into the invasive nodule in the foreign microenvironment is poorly understand. In this study, we established the intravenous injection pulmonary metastatic model followed by single-cell RNA sequencing of disseminating cells from mice lungs at different timepoints, we identified a cluster of SLPI-high esophageal squamous cell carcinoma (ESCC) cells that mediates the lung metastasis evolution and predicts worse overall survival of ESCC patients. GSEA analysis reveals that the SLPI-high subset is functionally associated with epithelial-to-mesenchymal transition and neutrophil activation during lung metastasis. Immune infiltration prediction from TIMER also confirmed that high SLPI is tightly correlated with more abundance of neutrophils in the ESCC tumor microenvironment. SLPI is reported to drive the metastasis progression through regulating the vascular mimicry. In the next step, further in-vitro and in-vivo studies is required to explore the role of SLPI in ESCC cells in promoting lung metastasis evolution. We identified a SLPI+ ESCC cells with high pluripotency that particularly initiates the metastasis process.

Citation Format: Yu Zhang, Ching Ngar Wong, Lanqi Gong, Xin-yuan Guan, Beibei Ru, Beilei Liu. Single cell RNA sequencing uncovers high-plasticity cell state during tumor metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5981.
Abstract 5984: MT1-MMP cooperates with TGF-beta receptor-mediated signaling to trigger SNAIL and induce epithelial-to-mesenchymal-like transition in U87 glioblastoma cells
Authors: Djediai Souad , Suarez Narjara Gonzalez , Joly-Lopez Zoé , Annabi Borhane
Published: June 2022

Transforming growth factor (TGF)-β triggers metastasis through epithelial-to-mesenchymal transition (EMT) to which a role for a membrane type-1 matrix metalloproteinase (MT1-MMP) has been associated. While EMT cooperates with MMP activity in glioblastoma multiforme, the molecular crosstalk between TGF-β signaling and MT1-MMP however remains poorly understood. Here, the existence of common EMT biomarkers, induced through TGF-β and MT1-MMP inducer Concanavalin A (ConA), was explored using RNA-seq analysis and differential gene arrays in human U87 glioblastoma cells. TGF-β and ConA triggered SNAIL and Fibronectin expressions in a dose-dependent manner. Those inductions were antagonized by the TGF-β receptor kinase inhibitor Galunisertib, the JAK/STAT inhibitors AG490 and Tofacitinib, and by the diet-derived epigallocatechin gallate (EGCG). Transient gene silencing of MT1-MMP prevented the induction of SNAIL by ConA and abrogated TGF-β-induced cell chemotaxis. Moreover, ConA induced STAT3 and Src phosphorylation suggesting these pathways to be involved in the MT1-MMP-mediated signaling axis that led to SNAIL induction. Our findings highlight a new signaling axis linking MT1-MMP to TGF-β-mediated EMT-like induction in glioblastoma cells, which process can be prevented by the diet-derived EGCG

Citation Format: Souad Djediai, Narjara Gonzalez Suarez, Zoé Joly-Lopez, Borhane Annabi. MT1-MMP cooperates with TGF-beta receptor-mediated signaling to trigger SNAIL and induce epithelial-to-mesenchymal-like transition in U87 glioblastoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5984.
Abstract 599: Identification of lymphocyte activation gene 3 binding peptides using phage displayed peptide libraries for cancer immunotherapy
Authors: Lee Seok-Min , Lee Byungheon
Published: June 2022

Treatment with immune checkpoint blockades against cytotoxic T lymphocyte associated protein-4, programmed cell death-1, and programmed death-ligand 1 is currently giving improved results to many cancer patients. Nevertheless, a significant proportion of cancer patients treated with immune checkpoint blockades are still largely unsatisfied with the benefits of these drugs. One of the reasons is that cancer cells also use other immune checkpoints such as lymphocyte activation gene-3 (LAG-3), T cell immunoreceptor with Ig and ITIM domains, and T-cell immunoglobulin and mucin-domain containing-3. LAG-3 negatively regulates activated T cells. In this study, we screened phage displayed-peptide libraries for peptides that selectively bind to LAG-3. After five rounds of screening, we selected a candidate peptide and named it LAG3Pep. LAG3Pep preferentially bound to human LAG-3-transfected HEK 293T cells over mock-transfected cells and phorbol myristate acetate/ionomycin/chloroquine-stimulated Jurkat T cells over unstimulated cells. LAG3Pep also bound to splenocytes isolated from tumor-bearing mice, suggesting the reactivity across human and mouse LAG-3. Pull-down of Jurkat T cell lysates using biotin-labeled LAG3Pep yielded a protein band of LAG-3. A competition by the pre-treatment of Jurkat T cells with a LAG-3-blocking antibody inhibited the cell binding of LAG3Pep. In addition, LAG3Pep inhibited the binding of LAG-3 protein to THP-1 cells expressing HLA-DR, a well-known LAG-3 ligand. Moreover, LAG3Pep recovered IL2 production by stimulated Jurkat T cells, which were suppressed by fibrinogen-like protein 1, another ligand of LAG-3, in the culture medium of HepG2 tumor cells. These results show that LAG3Pep selectively binds to LAG-3 and has a potential as a LAG-3 blocker for cancer immunotherapy.

Citation Format: Seok-Min Lee, Byungheon Lee. Identification of lymphocyte activation gene 3 binding peptides using phage displayed peptide libraries for cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 599.
Abstract 5998: Peroxiredoxin IV promotes progression of colorectal cancer
Authors: Thapa Pratik , Jiang Hong , Hao Yanning , Ding Na , Alshahrani Aziza , Zaytseva Yekaterina , Wei Qiou
Published: June 2022

Peroxiredoxin IV (Prx4) is a multifunction enzyme with a primary antioxidant role of reducing free radicals such as hydrogen peroxide and peroxynitrite. Literature review suggests that Prx4 upregulation in colorectal cancer is associated with higher tumor metastasis and shorter survival of patients. However, the function and mechanisms of Prx4 in cancer development are not well understood. The goal of this study is to validate the oncogenic role of Prx4 and to identify potential mechanisms of invasion and metastasis. Western Blot was performed to compare the expression of Prx4 protein in a normal colon cell line and seven colorectal cancer cell lines. shRNA mediated knockdown of Prx4 was performed in cancer cell lines with higher expression of Prx4. Stable vector control and Prx4 knockdown cells were used to perform Scratch Wound healing assay to compare the rate of migration. Transwell Matrigel invasion assay was performed using the same cell lines with 10% FBS containing-medium as chemoattractant. Vector control and Prx4 knockdown HCT116 cells were orthotopically implanted into the cecum wall of immunodeficient mice and humanely euthanized four weeks later. Prx4 expression is upregulated in colorectal cancer cell lines compared to normal colon cell line NCM356. Stable knockdown of Prx4 in HCT116 and RKO cell lines resulted in a significant decrease in migration and invasion rates of cancer cell lines in vitro compared to vector control. Orthotopic implantation of HCT116 vector control and Prx4 knockdown cells into cecum wall resulted in a lower metastasis rate to the liver and the lungs. We are currently conducting mechanistic studies to determine how the loss of Prx4 leads to a decrease in malignancy of colorectal cancer cell lines. Prx4 promotes colorectal cancer cell invasion and metastasis. Our study suggests Prx4 is a critical oncogenic protein that can be used as a therapeutic target for patients. This work was partially supported by the National Institutes of Health R01CA222596, Molecular Mechanisms of Toxicity Training Grant in Toxicology (T32ES07266), and American Cancer Society RSG-16-213-01-TBE.

Citation Format: Pratik Thapa, Hong Jiang, Yanning Hao, Na Ding, Aziza Alshahrani, Yekaterina Zaytseva, Qiou Wei. Peroxiredoxin IV promotes progression of colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5998.
Abstract 600: Discovery of a single-domain antibody fragment targeting PD-L1 for cancer immunotherapy
Authors: Liu Yanli , Liu Hao , Cheng Kun
Published: June 2022

Immunotherapy has shown enormous promise for cancer treatment. The use of Antibodies to target immune checkpoints, particularly PD-1/PD-L1, has made a profound impact in cancer immunotherapy. Single-domain antibody fragment (sdAb) is an antibody fragment composed of a single variable domain of the heavy chain. sdAb is the smallest antibody fragment (15 kDa) that maintains the similar antigen-binding affinity. sdAbs show many advantages over monoclonal antibodies such as small size, low immunogenicity, ease of production, and ease of modification, making sdAbs promising candidates for cancer immunotherapy. Here, we use a phage display library to identify an anti-PD-L1 sdAb (CLV3) which effectively blocks the PD-1/PD-L1 interaction. The CLV3 sdAb demonstrates high binding affinity and specificity to PD-L1 protein and PD-L1 overexpression DU145 tumor cells. Moreover, the CLV3 sdAb exhibits efficient tumor penetration in a 3D tumor spheroid model, suggesting its good penetration capability in the tumor microenvironment in vivo. CLV3 restores T cell proliferation and reduces T cell apoptosis in the co-culture experiment of peripheral blood mononuclear cells (PBMC) with tumor cells. These data suggest that the CLV3 sdAb can be potentially used as an anti-PD-L1 inhibitor for cancer immunotherapy.

Citation Format: Yanli Liu, Hao Liu, Kun Cheng. Discovery of a single-domain antibody fragment targeting PD-L1 for cancer immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 600.
Abstract 6007: Identification of drivers of soft tissue sarcoma metastasis
Authors: Carr-Ascher Janai R. , Munoz Maria
Published: June 2022

Soft tissue sarcomas are a rare and heterogeneous group of tumors with a 65% five-year survival rate despite aggressive treatment with surgery, radiation, and chemotherapy. Even with intensive multimodality treatment, many patients will develop incurable metastatic disease, providing evidence that our current therapies are ineffective and new treatments are desperately needed. Pre-clinical models to study metastasis of human soft tissue sarcomas are limited. We have developed a system that allows for the formation of distinct soft tissue sarcoma subtypes from mesenchymal stem cells that have been depleted of p53 and Rb1 using CRISPR. Injection of these cells intramuscularly results in metastasis to the lung. Using this novel model system, we have performed a genetic screen to identify pathways and specific drivers of sarcoma metastasis. This pre-clinical in vivo model system will allow for the identification of putative therapeutic targets to prevent the development of lethal metastatic growth.

Citation Format: Janai R. Carr-Ascher, Maria Munoz. Identification of drivers of soft tissue sarcoma metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6007.
Abstract 6011: RNA-seq analysis of liver from NASH derived HCC model mouse treated with streptozotocin-high fat diet
Authors: Hashiguchi Taishi , Linh Bui Phuong , Sakakibara Yuki , Tanaka Ryuto , Pigney Elizabeth H
Published: June 2022

Introduction; Non-alcoholic steatohepatitis (NASH) is a chronic liver disease often associated with type 2 diabetes. It sometimes progresses to more serious conditions such as liver fibrosis and hepatocellular carcinoma (HCC). Therapeutic agents for NASH have not yet been developed, and an animal model with high clinical correlation is required. The STAM mouse is a NASH model mouse with a background of type 2 diabetes. This mouse model shows the same pathological progression as human NASH patients, and has been used for the evaluation of many drug candidates, as well as basic research. However the gene profile, including mutations, has not been elucidated in this model. In this study, we analyzed the RNA-seq data of STAM mice at each pathological stage and examined the clinical correlation at the gene level.

Methods;NASH was induced in male mice by a single subcutaneous injection of 200 ug streptozotocin solution 2 days after birth and feeding with high fat diet after 4 weeks of age. The mice were sacrificed and livers collected at 6, 8, 10, 12, 16 and 20 weeks of age. For liver samples, the left lateral lobe was snap frozen in liquid nitrogen and stored at -80°C for RNA-seq analysis. Total RNA of the cells was isolated using RNeasy mini kit.

Results: The gene expression of the canonical pathway in NASH progression from steatosis to hepatocellular carcinoma was analyzed. Increased expression was observed in CCL2, TLR4, HSP47, alpha-SMA, c-Myc, and cyclin D1. Since it has been reported that genetic traits are involved in the development of NASH-HCC, we next analyzed the genetic mutations in the STAM mice. The number of individuals showing mutations in Mtorinvolved in Insulin signaling increases as the disease progresses, especially in the liver cancer phase.

Citation Format: Taishi Hashiguchi, Bui Phuong Linh, Yuki Sakakibara, Ryuto Tanaka, Elizabeth H Pigney. RNA-seq analysis of liver from NASH derived HCC model mouse treated with streptozotocin-high fat diet [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6011.
Abstract 6015: Comprehensive evaluation of three-dimensional (3D) culture systems as compound screening platforms with primary cancer cell lines
Authors: Zhang Chao , Wu Qinghua , Jin Lei , Chen Deyin , Tang Xuzhen , Qi Hui , Gao Wenjie , Ji Qunsheng
Published: June 2022

There are a number of challenges associated with personalized medicines. For example, many models revolve around the question of whether or not the in vitro models capture the relevant in vivo pathobiology and drug response information that may impact a patient's response to a therapy. Most in vitro oncology drug screening techniques are based on two-dimensional (2D) cell culture, which, to date, has failed to accurately imitate the physiological microenvironments due to the inherent limitations, such as the lack of interactions between intracellular and extracellular environments, or modifications in three-dimensional cell morphology, polarity, and division. These disadvantages prompted the development of models which would better simulate the microenvironment of tumor cells. Three-dimensional (3D) culture systems are becoming increasingly popular due to their ability to mimic natural cell characteristics and tissue-like structures compared with traditional 2D monolayer cell culture. Currently, multicellular spheroid and organoid cell culture are two popular 3D culture methods to evaluate drug activity. Spheroid cell culture utilizes ultra-low attachment plate to allow cells grow in spheroid format. Organoid cell culture is accomplished by growing cells in extracellular matrix scaffolds (such as Matrigel). In this study, we attempted to compare different drug screening platforms, including patient-derived xenograft (PDX) and two 3D cell cultures (spheroid and organoid). Compound sensitivity, genomics, pathology and expression of clinical marker were profiled. The purpose of this study is to identify an optimal model as a drug testing platform and a bridge between in vitro studies and animal experiments for identifying novel therapeutic targets.

Citation Format: Chao Zhang, Qinghua Wu, Lei Jin, Deyin Chen, Xuzhen Tang, Hui Qi, Wenjie Gao, Qunsheng Ji. Comprehensive evaluation of three-dimensional (3D) culture systems as compound screening platforms with primary cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6015.
Abstract 6028: Patient derived organoids demonstrate hallmark characteristics of small cell lung cancer
Authors: D'Rozario Joshua , George Julie , Thomas Roman
Published: June 2022

Small cell lung cancer (SCLC) accounts for approximately 15% of all lung cancers with an overall 5-year survival rate of 5-10%. Although transgenic mouse models and patient derived xenograft models have been shown to capture the heterogeneity and complexity of SCLC, the costs involved and timeframe of generating these models can be extensive. Furthermore, these models lack the ability to study the patients’ immune components and tumor microenvironment. Alternatively, in other cancer types in vitro methods to generate organoids have been successful in the hope to develop personalized patient derived organoids for screening and further downstream analyses. Here, we have generated and characterized small cell lung cancer patient-derived tumor organoids and confirmed that the organoids possess similar molecular characteristics, genetic profiles and morphological architectures to the corresponding patient tumor tissue. Organoids were shown to express hallmark features for SCLC, which included expression of neuroendocrine markers CD56, CHGA, INSM1 and SYP shown by immunohistochemistry. We suggest utilizing these organoids as SCLC patient models would be ideal for investigating the tumor microenvironment in SCLC, mechanisms between tumor immune cell interactions as well as assessing patients’ responses to therapy.

Citation Format: Joshua D'Rozario, Julie George, Roman Thomas. Patient derived organoids demonstrate hallmark characteristics of small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6028.
Abstract 6088: Reconstructing mutational lineages in breast cancer by multi-patient-targeted single cell DNA sequencing
Authors: Leighton Jake , Hu Min , Sei Emi , Meric-Bernstam Funda , Navin Nicholas
Published: June 2022

Single cell DNA sequencing (scDNA-seq) methods are powerful tools for profiling mutations in cancer cells, however most genomic regions characterized in single cells are non-informative. To overcome this issue, we developed a Multi-Patient-Targeted (MPT) scDNA-seq sequencing method. MPT involves first performing bulk exome sequencing across a cohort of cancer patients to identify somatic mutations, which are then pooled together to develop a single custom targeted panel for high-throughput scDNA-seq using a microfluidics platform. We applied MPT to profile 330 mutations across 23,500 cells from 5 TNBC patients, which showed that 3 tumors were monoclonal and 2 tumors were polyclonal. From this data, we reconstructed mutational lineages and identified early mutational and copy number events, including early TP53 mutations that occurred in all five patients. Collectively, our data suggests that MPT can overcome technical obstacles for studying tumor evolution using scDNA-seq by profiling information-rich mutation sites.

Citation Format: Jake Leighton, Min Hu, Emi Sei, Funda Meric-Bernstam, Nicholas Navin. Reconstructing mutational lineages in breast cancer by multi-patient-targeted single cell DNA sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6088.