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We investigated the anticancer effect of the aptamer-conjugated gemcitabine-loaded atelocollagen patch in a pancreatic cancer patient-derived xenograft (PDX) model to propose a future potential adjuvant surgical strategy during curative pancreatic resection for pancreatic cancer. A pancreatic cancer PDX model was established. Animals were grouped randomly into a no-treatment control group; treatment group treated with intraperitoneal gemcitabine injection (IP-GEM) or aptamer-conjugated gemcitabine (APT:GEM); and transplant with three kinds of patches: atelocollagen-aptamer-gemcitabine (patch I), atelocollagen-inactive aptamer-gemcitabine (patch II), and atelocollagen-gemcitabine (patch III). Tumor volumes and response were evaluated based on histological analysis by HE staining and Immunohistochemistry (IHC) was performed. Anticancer therapy-related toxicity was evaluated by hematologic findings. The patch I group showed the most significant reduction of tumor growth rate, compared with the no-treatment group (p 0.05). However, other treatment groups were not found to show significant reduction in tumor growth rate (0.05 p 0.1). There was no microscopic evidence suggesting potential toxicity, such as inflammation, nor necrotic changes in liver, lung, kidney, and spleen tissue. In addition, no leukopenia, anemia, or neutropenia was observed in the patch I group. This implantable aptamer-drug conjugate system is thought to be a new surgical strategy to augment the oncologic significance of margin-negative resection in treating pancreatic cancer in near future.

Introduction Pancreatic cancer is a devastating disease with a high relapse rate, even in resectable pancreatic cancer. This study aimed to identify the prognostic significance and therapeutic chance of the metabolic subtypes for resectable pancreatic cancer. Methods We obtained transcriptomic data from the TCGA-PAAD cohort via the The Cancer Genome Atlas (TCGA) data portal (n = 182). After integrative analysis of transcriptomic data in the discovery cohort, immunohistochemical (IHC) staining was performed in the independent cohort to validate the molecule of interest. Experimental testing for the molecule of interest was performed using pancreatic cancer cell lines, including AsPC1, BxPC3, MIA PaCa-2, and PANC-1 in vitro. Results Two subtypes showing distinct gene expression patterns in the TCGA-PAAD dataset were identified. The active glucose metabolism subtype showed significantly lower survival regarding cancer relapse after surgical resection. The genes SLC2A1 (GLUT1) and SLC16A3 (MCT4) were highly enriched in the active metabolism subtype. The validation cohort showed high IHC staining intensity for MCT4 and a significantly high relapse rate (p = 0.01). Several molecular pathways associated with aggressive tumor biology regarding cell cycle, Myc, and mTOR downstream signaling were highly enriched in the high glucose uptake subtype as well as distinct response for immunotherapy. MCT4 inhibition suppressed pancreatic cancer cell lines in vitro and showed a synergetic effect with gemcitabine treatment. Conclusions MCT4 was identified from integrative analysis as a potential therapeutic target in resectable pancreatic cancer. The precision strategy for resectable pancreatic cancer should be validated in a clinical setting with a prospective study design.

Introduction: Pancreatic cancer is lethal, showing dismal prognosis and therapeutic resistance. Previous molecular subtypes from genome or transcriptome did not show clinical relevance regarding precision strategy for optimal therapeutic options followed by precise patient classification. This study aims to uncover consensus molecular subtypes from cancer-specific multi-omics data showing clinically relevant therapeutic opportunities. Methods: We performed comprehensive analyses using the dataset from the cancer dependency map (DepMap) project, including cancer-specific molecular characterization with multi-omics data, genome-wide loss-of-function screening using the CRISPR-Cas9 system, and cancer drug sensitivity. The subtype-specific molecular signatures were validated in independent translational cohorts (TCGA-PAAD; n=150, ICGC-PACA-AU; n=461, ICGC-PACA-CA; n=317). Results: Integrative profiling of multi-omics molecular layers (Mutational signature, Copy number alteration, Transcriptome, MicroRNA, Chromatic profile, Proteome, and Metabolome) from pancreatic cancer cell lines (n=59) from the Cancer Cell Line Encyclopedia (CCLE) revealed a total of three cancer-specific molecular subtypes showing distinct tumor biology through all omics layer as well as clinical relevance with unique molecular dependency. Major molecular features of each subtype were reproducible in the validation cohorts. Subtype-specific molecular biomarkers, including mutational signatures and metabolites, were identified. Finally, the target drug with subtype-specific genetic dependency was analyzed to provide a precision strategy according to distinct subtypes’ molecular characterization. Conclusions: Integrative profiling from multi-omics molecular layers revealed precision strategies based on cancer-specific molecular subtypes of pancreatic cancer in terms of tumor classification and discriminative therapeutic opportunities. Prospective translational studies companion with clinical trials based on cancer-specific molecular subtypes is mandatory to establish the precision strategy for managing pancreatic cancer. Citation Format: Sung Hwan Lee, Jiyeon Park, Sunyoung Lee, Ju-Seog Lee. Cancer-specific molecular subtypes of pancreatic cancer reveal clinically relevant molecular dependency [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1064.

Background & Aims: High metabolic activity is a hallmark of cancers including hepatocellular carcinoma (HCC), a major form of liver cancer. However, the molecular features of HCC with high metabolic activity contributing to the clinical outcomes and their therapeutic implications are poorly understood. We aimed to uncover the metabolic characteristics of HCC that are associated with clinical relevance such as overall survival and response to immunotherapy. Methods: By applying cross-species comparison of genomic data, we integrated gene expression profile data from well-defined mouse models and human HCC tumor tissues to stratify HCC tumors according to their intrinsic metabolic activity. For stratification of HCC tumors, we developed a robust genomic predictor and validated it in 5 HCC cohorts (n=1038). Statistics and informatics approaches were performed to assess clinical significance such as overall survival and response to immunotherapy in metabolic subtypes. Genomic data from patient derived xenograft (PDX) models were integrated to the analysis. Results: Analysis of systematically integrated genomic data revealed three distinct metabolic subtypes of HCC (high, moderate and low metabolic subtypes). The high metabolic subtype is characterized by poor survival, the strongest stem cell features, high genomic instability, high expression of alpha-fetoprotein and KRT19, and activation of EPCAM and SALL4, and poor response to immunotherapy. Importantly, analysis of immune cell population in HCC tumors showed that immune-suppressive regulatory T-cells (Treg) are highly enriched in high metabolic HCC tumors, suggesting that high metabolic activity of HCC cells may trigger activation or infiltration of Treg cells, leading to evasion of HCC cells from anti-cancer immune cells. Interestingly, recent study showed that Treg cells can effectively utilize lactic acid as metabolic fuel for its proliferation. Because high metabolic activity of HCC tumors eventually leads to accumulation of glycolysis by-product lactic acid in tumor microenvironment, we postulate that accumulated lactic acid in tumor microenvironment might account for aggregation of Treg cells in high metabolic HCC tumors, leading to resistance to immunotherapy. In agreement with this, 18F-FDG PET/CT imaging data showed that high metabolic activity of tumors reflected in SUVmax is significantly associated with poorer survival of cancer patients after immunotherapy. Conclusions: We identified clinically and metabolically distinct subtypes of HCC tumors, potential biomarkers associated with these subtypes, and potential mechanism of metabolism-mediated evasion of HCC cells to anti-cancer immunotherapy. Moreover, the metabolic subtypes are well conserved in PDX models, offering a tool for selecting the best preclinical models for future study. Citation Format: Sowon Grace Park, Joann Jung, Yeonwoo Grace Jang, Sung Hwan Lee, Yun-Seong Jeong, Sun Young Yim, Ju-Seog Lee. Clinical significance of glycolytic metabolic activity in liver cancer and its implication to immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 296.

Background: Gastric adenocarcinoma (GAC) is heterogeneous lethal disease in genomic and clinical level. Although the clinical relevance of genomic and molecular subtypes of GAC has been demonstrated, their translation to the clinic has been hindered by discrepancies in classification methods. We aim to examine a consensus of genomic subtypes and correlate them with clinical outcomes. Method: We collected genomic data from 2527 GAC tumors and divided the data into discovery (n = 1427) and validation sets (n = 1100). By integrating 8 previously established genomic subtype algorithms, we identified 6 clinically and molecularly distinct genomic consensus subtypes (CGSs) in discovery set. For validation of clinical significance of new subtypes, we constructed GAC predictor of integrated consensus subtype with 120 genes (GPICS120) and applied it to validation data set. In systematic analysis of genomic and proteomic data, we estimated potential response rate of each subtype to standard and experimental treatments such as radiation therapy, target therapy, and immunotherapy and further validated their functional significance in cell line models. Results: Among identified 6 subtypes. CGS1 is characterized by poorest prognosis, very high stem cell characteristics, and high IGF1 expression, but low genomic alterations. CGS2 showed canonical epithelial gene expression patterns. CGS3 and CGS4 are characterized by high copy number alterations and low immune activity. However, CGS3 and CGS4 are different in high HER2 activation (CGS3) and SALL4 and KRAS activation (CSG4). CGS5 has highest mutation burden and moderately high immune activity that is characteristics of MSI-high tumors. Most of CGS6 tumors are EBV-positive and shows extremely high methylation and high immune activity. Most interestingly, CSG1 is most responsive to immunotherapy while CGS3 is significantly associated with benefit of chemoradiation therapy due to high basal level ferroptosis. In addition, we also identified potential therapeutic targets for each subtype. Conclusion: Consensus subtype is robust classification system and can be the basis for pre-clinical investigation of subtype-based targeted interventions and future clinical trials. Citation Format: Yun Seong Jeong, Young-Gyu Eun, Sung Hwan Lee, Sang-Hee Kang, Sun Young Yim, Eui Hyun Kim, Joo Kyung Noh, Bo Hwa Sohn, Ju-Seog Lee. Consensus genomic subtypes of gastric adenocarcinoma and their therapeutic implication. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4344.

Background & Aim: Aberrant upregulation of EZH2 is frequently observed in hepatocellular carcinoma (HCC) and significantly associated with poor prognosis of HCC patients. While EZH2 inhibitors (EZH2i) are recently approved for treatment of lymphoma and sarcoma, their antitumor effect alone is not optimally efficacious against solid tumors like HCC. Ferroptosis is a newly discovered nonapoptotic type of cell death characterized by the iron-dependent accumulation of lipid hydroperoxides in cell membrane to lethal levels. Owing to anti-cancer effects of ferroptosis, many oncogenes are known to suppress ferroptosis. However, their mechanisms in HCC are currently unknown. We aim to uncover a novel mechanism for EZH2-mediated resistance to ferroptosis in HCC. Methods: Multi-step analyses were performed with genomic data from mouse models (Ezh1/2 KO), cancer cell lines treated with EZH2i GSK126, and primary tumors including HCC to identify genetic networks or signaling/metabolic pathways associated with EZH2 in cancer cells. Functional connection of identified networks or pathways from the prediction analyses was tested in cell line models with various molecular biology approaches including western blots, colony forming assay, overexpression and/or depletion of genes of interest. Results: Gene network analysis predicted that ferroptosis pathway is inhibited by EZH2. Interestingly, lipid biosynthesis is also identified as an inhibited metabolic pathway by EZH2. Since polyunsaturated fatty acid (PUFA) is essential for executing ferroptosis, we hypothesize that EZH2 suppresses ferroptosis by inhibiting synthesis of PUFA. HCC cells with high EZH2 expression have higher IC50 values to erastin, a ferroptosis inducer, than those with low EZH2 expression. Moreover, inhibition or depletion of EZH2 sensitize HCC cells to erastin-induced ferroptotic cell death, strongly suggesting that EZH2 accounts for resistance to ferroptosis. Mechanistically, EZH2 increases H3K27me3 methylation near PUFA gene promoters, leading to suppression of PUFA gene expression and subsequently low cellular PUFA level. Most interestingly, treatment of EZH2i significantly sensitized HCC cells with high EZH2 expression to erastin-induced ferroptosis, suggesting potential therapeutic opportunity for treatment of HCC patients with high EZH2 expression. Conclusion: EZH2 is a novel suppressor of ferroptosis by negatively regulating lipid metabolism. Thus, our study provides scientific evidence for developing a novel therapeutic strategy for treatment of HCC patients with co-treatment of ferroptosis inducers and EZH2 inhibitors. Citation Format: Bo Hwa Sohn, Sung Hwan Lee, Yun Seong Jeong, Ju-Seog Lee. Clinical implication of EZH2 inhibitors in hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6139.

Introduction: Cholangiocarcinoma is a heterogeneous tumor entity harboring distinct tumor biology and clinical phenotype according to their unique tumor microenvironment (TME), especially anatomic location in terms of intrahepatic, peri-hilar, and distal extrahepatic portion. Therefore, there is a clear unmet need for the precision strategy based on cancer-specific genomic features rather than previous molecular subtypes from bulk RNA sequencing. Methods: Comprehensive analyses were performed using the dataset from the cancer dependency map (DepMap) project, including cancer-specific molecular characterization with multi-omics data, genome-wide loss-of-function screening with CRISPR-Cas9 system, and drug sensitivity with compound screening to uncover cancer-specific molecular subtypes showing clinical relevance. The cancer-specific molecular signatures were validated in independent translational cohorts (TCGA-CHOL; n=45, ICGC-BTC; n=181, GSE132305; n=220). Results: Integrative profiling of transcriptome from bile duct cancer cell lines (n=39) from the Cancer Cell Line Encyclopedia (CCLE) revealed a total of three cancer-specific molecular subtypes showing distinct tumor biology through all omics layer as well as clinical relevance with prognostic significance. Major molecular features of each subtype were reproducible in the validation cohorts. Subtype-specific molecular biomarkers, including mutational signature and metabolites, were identified. Finally, the target drug with subtype-specific genetic dependency was analyzed to provide precision strategy according to distinct subtypes’ molecular characterization. Conclusions: Comprehensive analysis using a multi-omics dataset revealed precision strategies based on cancer-specific molecular subtypes of cholangiocarcinoma in terms of tumor classification and discriminative therapeutic chances. Prospective translational studies companion with clinical trials based on cancer-specific molecular subtypes is mandatory to establish the precision strategy for managing cholangiocarcinoma. Citation Format: Woo Young Kwon, Sung Hwan LEE. Cancer-specific molecular subtypes of cholangiocarcinoma reveal unique molecular dependency with clinical relevance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1065.

Purpose This study sought to investigate associations among Yonsei criteria (tumor confined to the pancreas, intact fascia layer between the distal pancreas and the left adrenal gland and kidney, and tumor located more than 1-2 cm from the celiac axis) and tumor infiltrating lymphocytes in pancreatic cancer. Materials and methods Patients who underwent curative distal pancreatectomy due to left-sided pancreatic cancer from January 2000 to December 2011 were enrolled. Follow-up was completed September 30, 2015. Results Fifty patients were enrolled. Having ≥ two metastatic lymph nodes (LNs, p=0.002), intraoperative transfusion (p=0.011), low levels of tumor infiltrating CD8⁺ T-cells (p=0.001), and a high Foxp3⁺/CD8⁺ ratio (p=0.009) were independent risk factors for disease-free survival. Not satisfying the Yonsei criteria (p=0.021), having ≥ two metastatic LNs (p=0.032), low levels of tumor infiltrating CD8⁺ T-cells (p=0.040) and a high Foxp3⁺/CD8⁺ ratio (p=0.032) were associated with unfavorable overall survival. High levels of CA19-9 and not satisfying the Yonsei criteria were significantly associated with a high Foxp3⁺/CD8⁺ ratio [Exp(β)=3.558; 95% confidence inverval: 1.000-12.658; p=0.050]. Conclusion Yonsei criteria may be clinically detectable biologic marker with which to predict immunologic status and survival in pancreatic cancer patients.

High metabolic activity is a hallmark of cancers, including hepatocellular carcinoma (HCC). However, the molecular features of HCC with high metabolic activity contributing to clinical outcomes and the therapeutic implications of these characteristics are poorly understood. We aimed to define the features of HCC with high metabolic activity and uncover its association with response to current therapies. By integrating gene expression data from mouse liver tissues and tumor tissues from HCC patients (n = 1038), we uncovered three metabolically distinct HCC subtypes that differ in clinical outcomes and underlying molecular biology. The high metabolic subtype is characterized by poor survival, the strongest stem cell signature, high genomic instability, activation of EPCAM and SALL4, and low potential for benefitting from immunotherapy. Interestingly, immune cell analysis showed that regulatory T cells (Tregs) are highly enriched in high metabolic HCC tumors, suggesting that high metabolic activity of cancer cells may trigger activation or infiltration of Tregs, leading to cancer cells’ evasion of anti-cancer immune cells. In summary, we identified clinically and metabolically distinct subtypes of HCC, potential biomarkers associated with these subtypes, and a potential mechanism of metabolism-mediated immune evasion by HCC cells.

A ketogenic diet is a potential adjuvant cancer therapy that limits glucose availability to tumours while fuelling normal tissues with ketone bodies. We examined the effect of a low carbohydrate ketogenic diet (LCKD) (80% kcal from fat, ketogenic ratio 1.75:1, w/w) compared to a general hospital diet (GD) on serum metabolic profiles in patients (n = 18, ≥ 19 years old) who underwent pancreatectomy for pancreatobiliary cancer. Serum samples collected preoperatively (week 0) and after the dietary intervention (week 2) were analysed with a nontargeted metabolomics approach using liquid chromatography–tandem mass spectrometry. Serum β-hydroxybutyrate and total ketone levels significantly increased after 2 weeks of LCKD compared to GD (p

This article proposes an external capacitor-less low-dropout (LDO) regulator with undershoot and settling time reduction technique for fast transient response. In the proposed LDO, a feedback capacitor is applied instead of a complicated voltage-spike detection circuit to reduce undershoot voltage and settling time without consuming additional quiescent current. When an undershoot or overshoot voltage occurs in the load transient response, the undershoot voltage and settling time are reduced by increasing the gate discharging current or gate charging current of the pass transistor by the current flowing through the feedback capacitor. An adaptively biased single-stage error amplifier with a cross-coupled pair is used to improve stability without external capacitors at low quiescent current consumption. The proposed LDO regulator is implemented with a 0.18 μm CMOS process and consumes a quiescent current of 3.0 μA at a minimum load current of 0.1 mA. Compared with the conventional LDO regulator, the proposed LDO regulator reduces the undershoot voltage by 53.3% and the settling time by 55.5% without consuming additional quiescent current.

Background/Aims 18F-fluorodeoxyglucose-positron emission tomography (18F-FDG-PET) reflects biological aggressiveness and predicts prognoses in various tumors. Evaluating the oncologic significance of the preoperative metabolic phenotype might be necessary for planning the surgical strategy in resectable pancreatic cancers. Methods From January 2010 to December 2015, a total of 93 patients with pathologic T3 (pT3) pancreatic cancer were included in this study. Clinicopathological parameters and PET parameters were evaluated, and transcriptome-wide analysis was performed to identify the oncologic impact and molecular landscape of the metabolic phenotype of resectable pancreatic cancers. Results Preoperative metabolic tumor volume (MTV)2.5 was significantly higher in the pN1 group compared to the pN0 group (11.1±11.2 vs 6.5±7.8, p=0.031). Higher MTV2.5 values (MTV2.5 ≥4.5) were associated with multiple lymph node metastasis (p=0.003), and the lymph node ratio was also significantly higher in resected pT3 pancreatic cancer with MTV2.5 ≥4.5 compared to those with MTV2.5

Non-volatile memory (NVM) is a cutting-edge storage technology that promises the performance of DRAM with the durability of SSD. Recent work has proposed several persistency models for mainstream architectures such as Intel-x86 and Armv8, describing the order in which writes are propagated to NVM. However, these models have several limitations; most notably, they either lack operational models or do not support persistent synchronization patterns. We close this gap by revamping the existing persistency models. First, inspired by the recent work on promising semantics, we propose a unified operational style for describing persistency using views, and develop view-based operational persistency models for Intel-x86 and Armv8, thus presenting the first operational model for Armv8 persistency. Next, we propose a unified axiomatic style for describing hardware persistency, allowing us to recast and repair the existing axiomatic models of Intel-x86 and Armv8 persistency. We prove that our axiomatic models are equivalent to the authoritative semantics reviewed by Intel and Arm engineers. We further prove that each axiomatic hardware persistency model is equivalent to its operational counterpart. Finally, we develop a persistent model checking algorithm and tool, and use it to verify several representative examples.

Single-incision cholecystectomy is a surgical method that offers comparable results to conventional laparoscopic cholecystectomy. However, a high risk of postoperative incisional hernia is an issue in single-incision cholecystectomy. This study evaluated the risk factors and incidences of incisional hernia after single-incision cholecystectomy and the advantage issue of using barbed suture material during wound closures.A total of 1,111 patients underwent laparoscopic or robotic single-incision cholecystectomy between March 2014 and February 2020 at our institution at CHA Bundang Medical Center. During this period, there were 693 patients who underwent wound closure with monofilament suture material (Monosyn 2-0; B. Braun) and the other 418 patients used barbed suture material (Stratafix 2-0; Ethicon).The two patient groups were comparable in age, body mass index, and diagnosis. The total incidence of incisional hernia after single-incision cholecystectomy was 0.5% (five cases). All patients who developed incisional hernia were in the monofilament suture material group (0.7% vs. 0%,Our study showed a low incidence of incisional hernia, all of which occurred in the monofilament suture material group. If technically appropriate, single-incision cholecystectomy does not appear to present a high incidence of hernia. Barbed suture material can be safely applied in wound closure showing comparable incisional hernia incidence to monofilament suture material.

BackgroundNeoadjuvant chemoradiation therapy (CRT) is a widely used preoperative treatment strategy for locally advanced rectal cancer (LARC). However, a few studies have evaluated the molecular changes caused by neoadjuvant CRT in these cancer tissues. Here, we aimed to investigate changes in immunotherapy-related immunogenic effects in response to preoperative CRT in LARC.MethodsWe analyzed 60 pairs of human LARC tissues before and after irradiation from three independent LARC cohorts, including a LARC patient RNA sequencing (RNA-seq) dataset from our cohort and GSE15781 and GSE94104 datasets.ResultsGene ontology analysis showed that preoperative CRT significantly enriched the immune response in LARC tissues. Moreover, gene set enrichment analysis revealed six significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways associated with downregulated genes, including mismatch repair (MMR) genes, in LARC tissues after CRT in all three cohorts. Radiation also induced apoptosis and downregulated various MMR system-related genes in three colorectal cancer cells. One patient with LARC showed a change in microsatellite instability (MSI) status after CRT, as demonstrated by the loss of MMR protein and PCR for MSI. Moreover, CRT significantly increased tumor mutational burden in LARC tissues. CIBERSORT analysis revealed that the proportions of M2 macrophages and CD8 T cells were significantly increased after CRT in both the RNA-seq dataset and GSE94104. Notably, preoperative CRT increased various immune biomarker scores, such as the interferon-γ signature, the cytolytic activity and the immune signature.ConclusionsTaken together, our findings demonstrated that neoadjuvant CRT modulated the immune-related characteristics of LARC, suggesting that neoadjuvant CRT may enhance the responsiveness of LARC to immunotherapy.

Background & Aims: While many studies revealed transcriptomic subtypes of hepatocellular carcinoma (HCC), they are not translated to the clinic yet due to lack of consensus. We aim to examine consensus of transcriptomic subtypes and uncover their clinical significance. Methods: We integrated 15 previously established transcriptomic signatures for HCC to uncover consensus subtypes. We also developed and validated a robust predictor of consensus subtype with 100 genes (PICS100). Informatics and statistics approaches were applied to find clinical relevant association of genomic features. Patient derived xenograft (PDX) models were used for testing hypothesis from analysis of transcriptomic data. Results: We identified 5 clinically and molecularly distinct consensus subtypes. STM (STeM) is characterized by high stem cell features, vascular invasion, and poor prognosis. CIN (Chromosomal INstability) has moderate stem cell features but high genomic instability and low immune activity. IMH (IMmune High) is characterized by high immune activity. BCM (Beta-Catenin with high Male predominance) is characterized by prominent β-catenin activation, low miRNA expression, hypomethylation, and high sensitivity to sorafenib. DLP (Differentiated and Low Proliferation) is differentiated with high HNF4A activity. We also identified potential serum biomarkers that can stratify patients into 5 subtypes. Conclusions: Five HCC subtypes are associated with potential response to treatments and highly conserved in pre-clinical models, providing a framework for selecting the most appropriate models for preclinical studies of new drugs and potentially for future clinical trials. Citation Format: Ju-Seog Lee, Sun Young Yim, Sung Hwan Lee, Yun Seong Jeong. Consensus subtypes of hepatocellular carcinoma associated with clinical outcomes [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 768.

Introduction: Pancreatic cancer is a lethal disease showing dismal prognosis and therapeutic resistance. Previous molecular subtypes from genome or transcriptome did not show clinical relevance regarding precision strategy for optimal therapeutic options followed by precise patient classification. This study aims to uncover consensus molecular subtypes from cancer-specific multi-omics data showing clinically relevant therapeutic opportunities. Methods: We performed comprehensive analyses using the dataset from the cancer dependency map (DepMap) project, including cancer-specific molecular characterization with multi-omics data, genome-wide loss-of-function screening using the CRISPR-Cas9 system, and cancer drug sensitivity. The subtype-specific molecular signatures were validated in independent translational cohorts (TCGA-PAAD; n=150, ICGC-PACA-AU; n=461, ICGC-PACA-CA; n=317). Results: Integrative profiling of multi-omics molecular layers (Mutational signature, Copy number alteration, Transcriptome, MicroRNA, Chromatic profile, Proteome, and Metabolome) from pancreatic cancer cell lines (n=59) from the Cancer Cell Line Encyclopedia (CCLE) revealed a total of three cancer-specific molecular subtypes showing distinct tumor biology through all omics layer as well as clinical relevance with unique molecular dependency. Major molecular features of each subtype were reproducible in the validation cohorts. Subtype-specific molecular biomarkers, including mutational signature and metabolites, were identified. Finally, the target drug with subtype-specific genetic dependency was analyzed to provide precision strategy according to distinct subtypes’ molecular characterization. Conclusions: Integrative profiling from multi-omics molecular layers revealed precision strategies based on cancer-specific molecular subtypes of pancreatic cancer in terms of tumor classification and discriminative therapeutic opportunities. Prospective translational studies companion with clinical trials based on cancer-specific molecular subtypes is mandatory to establish the precision strategy for managing pancreatic cancer. Citation Format: Sung Hwan Lee, Jiyeon Park. Unsupervised clustering of multi-omics molecular layers reveals consensus molecular subtypes showing potential therapeutic opportunities for 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 2273.

Background & aims: While many studies revealed genomic subtypes of hepatocellular carcinoma (HCC), they are not translated to the clinic yet due to lack of consensus. We aim to examine consensus of genomic subtypes and uncover their clinical significance. Methods: We integrated 15 previously established genomic signatures for HCC to uncover consensus genomic subtypes. We also developed and validated a robust predictor of consensus subtype with 100 genes (PICS100). Informatics and statistics approaches were applied to find clinical relevant association of genomic features. Patient derived xenograft (PDX) models were used for testing hypothesis from analysis of genomic data. Results: We identified 5 clinically and molecularly distinct consensus subtypes. STM (STeM) is characterized by high stem cell features, vascular invasion, and poor prognosis. CIN (Chromosomal INstability) has moderate stem cell features but high genomic instability and low immune activity. IMH (IMmune High) is characterized by high immune activity. BCM (Beta-Catenin with high Male predominance) is characterized by prominent β-catenin activation, low miRNA expression, hypomethylation, and high sensitivity to sorafenib. DLP (Differentiated and Low Proliferation) is differentiated with high HNF4A activity. We also identified potential serum biomarkers that can stratify patients into 5 subtypes. Because these subtypes are highly associated with currently available treatments, our findings may provide the foundation for rationalized biomarker-based clinical trials. Conclusions: Five HCC subtypes are highly associated with response to standard and experimental treatments and highly conserved in pre-clinical models, providing a framework for selecting the most appropriate models for preclinical studies and rationalized clinical trials of new drugs. Citation Format: Sung Hwan Lee, Ju-Seog Lee. Consensus subtypes of hepatocellular carcinoma associated with clinical outcomes, response to therapies, and multiple biomarkers [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 480.

In multifocal intrahepatic cholangiocarcinoma (IHC), intrahepatic metastases (IM) represent a contraindication to surgical resection, whereas satellite nodules (SN) do not. However, no consensus criteria exist to distinguish IM from SN. The purpose of this study was to determine genetic alterations and clonal relationships in surgically resected multifocal IHC. Next-generation sequencing of 34 spatially separated IHC tumors was performed using a targeted panel of 201 cancer-associated genes. Proposed definitions in the literature were applied of SN located in the same liver segment and ≤2 cm from the primary tumor; and IM located in a different liver segment and/or >2 cm from the primary tumor. Somatic point mutations concordant across tumors from individual patients included BAP1, SMARCA4 and IDH1. Small insertions and deletions (indels) present at the same genome positions among all tumors from individuals included indels in DNA repair genes, CHEK1, ERCC5, ATR and MSH6. Copy number alterations were also similar between all tumors in each patient. In this cohort of multifocal IHC, genomic profiles were concordant across all tumors in each patient, suggesting a common progenitor cell origin, regardless of the location of tumors in the liver. The decision to perform surgery should not be based upon a perceived distinction between IM and SN.

Hepatocellular carcinoma (HCC) is the most common liver cancer with a higher incidence in males. Here, we report that the spontaneous HCC development subsequent to the deletion of both Farnesoid X Receptor and Small Heterodimer Partner (DKO) mimics the sex-specific incidence seen clinically. In female DKO mice, we find lower levels of circulating bile acids (BA) and show that BAs can co-opt the estrogen axis to auto-regulate their homeostasis and amino acid metabolism. These regulations are lost when female mice are ovariectomized. Conversely, increasing serum BA levels is sufficient to promote tumorigenesis in female livers. To examine the translational relevance, we mined the transcriptomic signatures corresponding to that of female mice and found that it correlated well with those of low-grade tumors and associated with better outcomes for HCC patients. We demonstrate that decreasing enterohepatic recirculation of BAs using a resin dramatically reduced the liver cancer burden in male mice. These results uncover that sexual dimorphism in liver cancer incidence is linked to sex-differences in the handling of circulating BA concentrations and that lowering it might alleviate liver cancer.SignificanceWe demonstrate that serum BA concentration facilitates sex-differences in tumor burden, with reduced BA levels resulting in lower HCC risk in female mice. Increasing or decreasing circulating BA levels, promotes or alleviates HCC risk, respectively. We show that the sex-specific gene profiles identified in the DKO mice model of HCC correlate directly with patient outcomes.

For more than fifteen years, researchers have tried to support global optimizations in a usable semantics for a concurrent programming language, yet this task has been proven to be very difficult because of (1) the infamous “out of thin air” problem, and (2) the subtle interaction between global and thread-local optimizations. In this paper, we present a solution to this problem by redesigning a key component of the promising semantics (PS) of Kang et al. Our updated PS 2.0 model supports all the results known about the original PS model (i.e., thread-local optimizations, hardware mappings, DRF theorems), but additionally enables transformations based on global value-range analysis as well as register promotion (i.e., making accesses to a shared location local if the location is accessed by only one thread). PS 2.0 also resolves a problem with the compilation of relaxed RMWs to ARMv8, which required an unintended extra fence.

Dehydration, electrolyte disturbance, and acid-base imbalance are the most significant consequences of diarrhea in calves. We aimed to determine blood gas, hematological, electrolyte, and biochemical values and investigate the relationship between the physical status and blood parameters in Korean native calves (KNCs) with diarrhea. One hundred eighty KNCs with diarrhea (age < 75 days) were investigated. Blood samples were collected from the external jugular vein and analyzed using a portable clinical blood gas analyzer. The measured parameters were statistically compared according to the status of physical activity, dehydration, or prognosis. The mean values of parameters in the Calves with diarrhea showed metabolic acidosis, hyponatremia, and azotemia. The mean values of potassium, chloride, hematocrit, and hemoglobin were in the upper limit of their reference ranges. More than 75% of the calves had metabolic acidosis caused by bicarbonate loss, and 63.6% had high blood urea nitrogen (BUN) values. Moreover, BUN showed the highest correlation with the physical activity status and dehydration. pH, base excess of the extracellular fluid (BE), anion gap, potassium, hematocrit, bicarbonate, and hemoglobin were closely correlated with physical deterioration and dehydration (p < 0.001). BUN, pH, BE, and anion gap were closely correlated with physical deterioration and dehydration. These correlations between clinical symptoms and blood gas parameters can be clinically relevant in predicting the status of parameters according to clinical symptoms.

Introduction: Even though the 8th edition AJCC cancer staging system for pancreatic cancer has validated major clinicopathologic factors in multiple clinical cohorts, there is still an unmet need for integrative consideration using multi-omics data to stratify the patients with pancreatic cancer elaborately. Methods: We performed a comprehensive analysis and profiling using genomic, transcriptomic, and proteomic data from TCGA-PAAD and other translational cohorts (4 cohorts, n=340). Molecular features and major subtypes were analyzed mutually with clinical and pathologic factors, especially the 8th AJCC staging system. Results: Aggressive molecular subtypes, basal-like and squamous subtype, were significantly associated with a higher nodal stage, but tumor size didn't show a clear association with molecular features. The activated stroma of the pancreatic cancer microenvironment was significantly correlated with poor differentiation and large tumor size. The mutational pattern of KRAS and several transcriptomic pathways, such as epithelial-mesenchymal transition and DNA repair, were differently presented in each clinical stage from the 8th AJCC TNM staging system. The optimal algorithm was identified to show significantly higher performance for the prediction for cancer relapse and cancer-specific survival in discovery and validation cohorts. The in-silico prediction for molecular target agents and immunotherapy was performed for final clusters from the optimal stratification system revealed from the integrative analysis. Conclusions: Our comprehensive multi-omics analysis reveals clear needs for the combination of clinical staging and molecular profiling and provides crucial evidence for precision strategy in patients with resectable pancreatic cancer. Citation Format: Sung Hwan Lee, Sunyoung Lee, Ju-Seog Lee. Molecular validation of the 8th edition AJCC cancer staging system for resectable pancreatic cancer: Proposal of integrative translational staging system [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 627.

We investigated the potential application of preoperative serum metabolomes in predicting recurrence in patients with resected pancreatic cancer. From November 2012 to June 2014, patients who underwent potentially curative pancreatectomy for pancreatic ductal adenocarcinoma were examined. Among 57 patients, 32 were men; 42 had pancreatic head cancers. The 57 patients could be clearly categorized into two main clusters using 178 preoperative serum metabolomes. Patients within cluster 2 showed earlier tumor recurrence, compared with those within cluster 1 (p = 0.034). A nomogram was developed for predicting the probability of early disease-free survival in patients with resected pancreatic cancer. Preoperative cancer antigen (CA) 19–9 levels and serum metabolomes PC.aa.C38_4, PC.ae.C42_5, and PC.ae.C38_6 were the most powerful preoperative clinical variables with which to predict 6-month and 1-year cancer recurrence-free survival after radical pancreatectomy, with a Harrell’s concordance index of 0.823 (95% CI: 0.750–0.891) and integrated area under the curve of 0.816 (95% CI: 0.736–0.893). Patients with resected pancreatic cancer could be categorized according to their different metabolomes to predict early cancer recurrence. Preoperative detectable parameters, serum CA 19–9, PC.aa.C38_4, PC.ae.C42_5, and PC.ae.C38_6 were the most powerful predictors of early recurrence of pancreatic cancer.

Calf diarrhea caused by infectious agents is associated with economic losses in the cattle industry. The purpose of this study was to identify the causative agents and epidemiological characteristics of diarrhea in Korean native calves (KNC). In total, 207 diarrheal KNC aged less than 7 months were investigated. Fecal samples collected from the rectum were examined for causative agents using polymerase chain reaction (PCR) or real-time PCR and the number of oocysts were counted. Fourteen causative agents were detected from 164 of the 207 diarrheal KNC. Rotavirus was the most common agent (34.8%), followed by Eimeria spp. (31.7%), Escherichia coli (22.0%), Giardia spp. (14.0%), Clostridium difficile (9.8%), bovine viral diarrhea virus (8.5%), coronavirus (7.9%), Cryptosporidium spp. (7.3%), torovirus (6.7%), parvovirus (5.5%), norovirus (4.9%), kobuvirus (1.8%), adenovirus (1.2%), and Salmonella spp. (0.6%). About 95 (57.9%) of 164 calves were infected with a single causative agent and 42.1% were infected by multiple agents. No significant difference was observed in mortality between calves infected with a single agent and multiple agents. The occurrence of diarrhea caused by rotavirus, Eimeria spp., kobuvirus, and Giardia spp. was significantly different based on onset age, and the prevalence of diarrhea caused by rotavirus or C. difficile was significantly different between seasons. This study help the understanding of KNC diarrhea for the development of an effective strategy for disease prevention and control, especially in Eastern provinces of South Korea.

For ARMv8 and RISC-V, there are concurrency models in two styles, extensionally equivalent: axiomatic models, expressing the concurrency semantics in terms of global properties of complete executions; and operational models, that compute incrementally. The latter are in an abstract microarchitectural style: they execute each instruction in multiple steps, out-of-order and with explicit branch speculation. This similarity to hardware implementations has been important in developing the models and in establishing confidence, but involves complexity that, for programming and model-checking, one would prefer to avoid. We present new more abstract operational models for ARMv8 and RISC-V, and an exploration tool based on them. The models compute the allowed concurrency behaviours incrementally based on thread-local conditions and are significantly simpler than the existing operational models: executing instructions in a single step and (with the exception of early writes) in program order, and without branch speculation. We prove the models equivalent to the existing ARMv8 and RISC-V axiomatic models in Coq. The exploration tool is the first such tool for ARMv8 and RISC-V fast enough for exhaustively checking the concurrency behaviour of a number of interesting examples. We demonstrate using the tool for checking several standard concurrent datastructure and lock implementations, and for interactively stepping through model-allowed executions for debugging.

High metabolic activity, reflected in increased glucose uptake, is one of the hallmarks of many cancers including breast cancer. However, not all cancers avidly take up glucose, suggesting heterogeneity in their metabolic demand. Thus, we aim to generate a genomic signature of glucose hypermetabolism in breast cancer and examine its clinical relevance. To identify genes significantly associated with glucose uptake, gene expression data were analyzed together with the standardized uptake values (SUVmax) of (18)F-fluorodeoxy-glucose on positron emission tomography (PET) for 11 breast cancers. The resulting PET signature was evaluated for prognostic significance in four large independent patient cohorts (n = 5417). Potential upstream regulators accountable for the high glucose uptake were identified by gene network analysis. A PET signature of 242 genes was significantly correlated with SUVmax in breast cancer. In all four cohorts, high PET signature was significantly associated with poorer prognosis. The prognostic value of this PET signature was further supported by Cox regression analyses (hazard ratio 1.7, confidential interval 1.48–2.02; P

Introduction Even though the current clinical staging system for resectable pancreatic cancer has validated major clinicopathologic factors in multiple clinical cohorts, there is still an unmet need for integrative consideration using multi-omics data to stratify the patients with pancreatic cancer elaborately. Methods We performed a comprehensive analysis and profiling using genomic, transcriptomic, and proteomic data from TCGA-PAAD (n = 150) and other translational cohorts (4 cohorts, n = 340). Molecular features and major subtypes were analyzed mutually with clinical and pathologic factors to discover a clinically relevant translational staging system. Results The correlation analysis for each 50 cancer-specific molecular pathways with the clinical staging system revealed no remarkable pattern of the association. The mutational pattern of KRAS and several transcriptomic pathways, such as epithelial-mesenchymal transition and DNA repair, were differently presented in each clinical stage from the 8th AJCC TNM staging system. From the cluster of cluster analysis, we identified three consensus molecular subtypes, specifically subtype A was remarkably correlated with previously known aggressive subtypes, Basal, Mesenchymal, and Squamous subtypes, and subtype B and C were correlated with other subtypes regarding classical, exocrine, immunogenic, progenitor and ADEX subtypes. This consensus subtypes were validated at the independent pancreatic cancer genomics cohorts. Our in-silico prediction revealed subtype-specific biomarkers and potential therapeutics, including molecular target agents as well as immunotherapeutic options. Conclusions Our comprehensive multi-omics analysis reveals prognostically significant consensus subtypes showing distinct tumor biology with unique therapeutic opportunities including biomarkers with high performance. This study provides exact needs for clinical trials based on translational approaches to establish precision surgical oncology.

Introduction Microvascular invasion (MVI) is a well-known prognostic factor to predict cancer relapse after curative resection of resectable hepatocellular carcinoma (HCC). It is mandatory to uncover clinically available serum biomarkers to predict the MVI feature at the initial diagnosis of HCC. Methods Using gene expression profiling for resected human HCC (Discovery cohort, n = 240), we identified transcriptomic signature predicting the MVI feature. Repeated validation for the MVI signature performed using the Bayesian covariate compound predictor method at the multiple independent cohorts (Six Validation cohorts, n = 1,263). Serum biomarker dataset from the patients of TCGA-LIHC samples correlated with the MVI signature. Results The MVI signature with 1028 genes was identified from robust statistical testing from the discovery cohort, and robust validation for the prediction performance of the MVI signature showed significant accuracy in the validation cohort (AUC = 0.865, p < 0.01). Multi-omics analysis revealed aggressive tumor biology associated with the MVI signature regarding FOXM1, CD24, and MYC downstream pathways. A diagnostic panel from integrating significant serum biomarkers to predict MVI was identified from stepwise regression (p < 0.001). Comprehensive analysis of drug-sensitivity for the MVI signature was performed by integrative in-silico prediction methods using the dataset from Cancer Dependency Map project. Conclusions Integrative multi-omics profiling for resectable HCC uncovers clinically available serum biomarkers to predict MVI without a surgical specimen. A novel combination of serum biomarkers shows high performance in sorting out the tumor with aggressive tumor biology. Precision strategy to discover resectable tumors beneficial from surgical resection can be established from consecutive clinical trials based on this translational study.

Introduction Bile duct cancer is a heterogeneous tumor entity harboring distinct tumor biology and clinical phenotype according to their unique tumor microenvironment, especially anatomic location in terms of intrahepatic, peri-hilar, and distal extrahepatic portion. Therefore, there is a clear unmet need for the precision strategy based on cancer-specific genomic features rather than previous molecular subtypes from bulk RNA sequencing. Methods Comprehensive analyses were performed using the dataset from the cancer dependency map project, including cancer-specific molecular characterization with multi-omics data, genome-wide loss-of-function screening with CRISPR-Cas9 system, and drug sensitivity with compound screening to uncover cancer-specific molecular subtypes showing clinical relevance. The cancer-specific molecular signatures were validated in independent translational cohorts (TCGA-CHOL; n = 45, ICGC-BTC; n = 181, GSE132305; n = 220). Results Integrative profiling of transcriptome from bile duct cancer cell lines (n = 39) from the Cancer Cell Line Encyclopedia revealed a total of three cancer-specific molecular subtypes showing distinct tumor biology through all omics layer as well as clinical relevance with prognostic significance. Major molecular features of each subtype were reproducible in the validation cohorts. Subtype-specific molecular biomarkers, including mutational signature and metabolites, were identified. Finally, the target drug with subtype-specific genetic dependency was analyzed to provide precision strategy according to distinct subtypes' molecular characterization. Conclusions Comprehensive analysis using a multi-omics dataset revealed precision strategies based on cancer-specific molecular subtypes of bile duct cancer in terms of tumor classification and discriminative therapeutic chances. Prospective translational studies companion with clinical trials based on cancer-specific molecular subtypes is mandatory to establish the precision strategy for managing bile duct.