Application of plasma circulating KRAS mutations as a predictive biomarker for targeted treatment of pancreatic cancer

Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations in circulating tumor deoxyribonucleic acid (ctDNA) have been reported as representative noninvasive prognostic markers for pancreatic ductal adenocarcinoma (PDAC). Here, we aimed to evaluate single KRAS mutations as prognostic and predictive biomarkers, with an emphasis on potential therapeutic approaches to PDAC. A total of 128 patients were analyzed for multiple or single KRAS mutations (G12A, G12C, G12D, G12R, G12S, G12V, and G13D) in their tumors and plasma using droplet digital polymerase chain reaction (ddPCR). Overall, KRAS mutations were detected by multiplex ddPCR in 119 (93%) of tumor DNA and 68 (53.1%) of ctDNA, with a concordance rate of 80% between plasma ctDNA and tumor DNA in the metastatic stage, which was higher than the 44% in the resectable stage. Moreover, the prognostic prediction of both overall survival (OS) and progression-free survival (PFS) was more relevant using plasma ctDNA than tumor DNA. Further, we evaluated the selective tumor-suppressive efficacy of the KRAS G12C inhibitor sotorasib in a patient-derived organoid (PDO) from a KRAS G12C-mutated patient using a patient-derived xenograft (PDX) model. Sotorasib showed selective inhibition in vitro and in vivo with altered tumor microenvironment, including fibroblasts and macrophages. Collectively, screening for KRAS single mutations in plasma ctDNA and the use of preclinical models of PDO and PDX with genetic mutations would impact precision medicine in the context of PDAC.

Functional ultrasound imaging of the human spinal cord

Utilizing the first in-human functional ultrasound imaging (fUSI) of the spinal cord, we demonstrate the integration of spinal functional responses to electrical stimulation. We record and characterize the hemodynamic responses of the spinal cord to a neuromodulatory intervention commonly used for treating pain and increasingly used for the restoration of sensorimotor and autonomic function. We found that the hemodynamic response to stimulation reflects a spatiotemporal modulation of the spinal cord circuitry not previously recognized. Our analytical capability offers a mechanism to assess blood flow changes with a new level of spatial and temporal precision in vivo and demonstrates that fUSI can decode the functional state of spinal networks in a single trial, which is of fundamental importance for developing real-time closed-loop neuromodulation systems. This work is a critical step toward developing a vital technique to study spinal cord function and effects of clinical neuromodulation.

RFX4 is an intrinsic factor for neuronal differentiation through induction of proneural genes POU3F2 and NEUROD1

Proneural genes play a crucial role in neuronal differentiation. However, our understanding of the regulatory mechanisms governing proneural genes during neuronal differentiation remains limited. RFX4, identified as a candidate regulator of proneural genes, has been reported to be associated with the development of neuropsychiatric disorders. To uncover the regulatory relationship, we utilized a combination of multi-omics data, including ATAC-seq, ChIP-seq, Hi-C, and RNA-seq, to identify RFX4 as an upstream regulator of proneural genes. We further validated the role of RFX4 using an in vitro model of neuronal differentiation with RFX4 knock-in and a CRISPR-Cas9 knock-out system. As a result, we found that RFX4 directly interacts with the promoters of POU3F2 and NEUROD1. Transcriptomic analysis revealed a set of genes associated with neuronal development, which are highly implicated in the development of neuropsychiatric disorders, including schizophrenia. Notably, ectopic expression of RFX4 can drive human embryonic stem cells toward a neuronal fate. Our results strongly indicate that RFX4 serves as a direct upstream regulator of proneural genes, a role that is essential for normal neuronal development. Impairments in RFX4 function could potentially be related to the development of various neuropsychiatric disorders. However, understanding the precise mechanisms by which the RFX4 gene influences the onset of neuropsychiatric disorders requires further investigation through human genetic studies.

Mock-up performance evaluation study for crack reduction of blast furnace slag powder concrete mixed with expansive and swelling admixtures

In this study, the drying shrinkage and crack reduction characteristics of blast furnace slag concrete mixed with expansive and swelling admixtures were investigated. Basic performance experiments were conducted using different mixtures of ground granulated blast-furnace slag (GGBS), with calcium sulfoaluminate as the expansive admixture and bentonite and hydroxypropyl methyl cellulose (HPMC) as swelling admixtures. Bentonite outperformed HPMC as a swelling admixture. Specimens were then prepared for mock-up tests to evaluate the drying shrinkage of blast furnace slag concrete with different combinations of bentonite, a hardening accelerator, and a self-healing agent. The addition of bentonite and calcium phosphate as a self-healing agent in small quantities reduced the drying shrinkage of the specimens, thereby reducing cracks. The cement mixture composed of 30% GGBS, 1% bentonite, and 1% calcium phosphate (30-E1-I1) showed the optimal performance among the specimens. Further, crack monitoring was performed in concrete made with ordinary Portland cement and optimal mixture 30-E1-I1. No cracks were observed for the optimal mixture. This shows that GGBS concrete can be used in practical and field applications, subject to mid- and long-term tests for cracking.

Association of Molecular Subtypes with Pathologic Response, PFS, and OS in a Phase II Study of COXEN with Neoadjuvant Chemotherapy for Muscle-invasive Bladder Cancer

PURPOSE

The Coexpression Extrapolation (COXEN) gene expression model with chemotherapy-specific scores [for methotrexate, vinblastine, adriamycin, cisplatin (ddMVAC) and gemcitabine/cisplatin (GC)] was developed to identify responders to neoadjuvant chemotherapy (NAC). We investigated RNA-based molecular subtypes as additional predictive biomarkers for NAC response, progression-free survival (PFS), and overall survival (OS) in patients treated in S1314.

EXPERIMENTAL DESIGN

A total of 237 patients were randomized between four cycles of ddMVAC (51%) and GC (49%). On the basis of Affymetrix transcriptomic data, we determined subtypes using three classifiers: TCGA (k = 5), Consensus (k = 6), and MD Anderson (MDA; k = 3) and assessed subtype association with path response to NAC and determined associations with COXEN. We also tested whether each classifier contributed additional predictive power when added to a model based on predefined stratification (strat) factors (PS 0 vs. 1; T2 vs. T3, T4a).

RESULTS

A total of 155 patients had gene expression results, received at least three of four cycles of NAC, and had pT-N response based on radical cystectomy. TCGA three-group classifier basal-squamous (BS)/neuronal, luminal (Lum), Lum infiltrated, and GC COXEN score yielded the largest AUCs for pT0 (0.59, P = 0.28; 0.60, P = 0.18, respectively). For downstaging (

CONCLUSIONS

The Consensus classifier, based in part on the TCGA and MDA classifiers, modestly improved prediction for pathologic downstaging but subtypes were not associated with PFS or OS.

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Key Words Collapse

MESH Headings

• Humans
• Cisplatin/therapeutic use
• Cystectomy/methods
• Deoxycytidine/therapeutic use
• Muscles/pathology
• Neoadjuvant Therapy/methods
• Neoplasm Invasiveness
• Progression-Free Survival
• Retrospective Studies
• Urinary Bladder Neoplasms/drug therapy
• Urinary Bladder Neoplasms/genetics
• Urinary Bladder Neoplasms/pathology

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Grants

• UG1 CA233320 NCI NIH HHS
• UG1 CA233324 NCI NIH HHS
• UG1 CA180830 NCI NIH HHS
• UG1 CA233160 NCI NIH HHS
• U10 CA032102 NCI NIH HHS
• UG1 CA233196 NCI NIH HHS
• U10 CA180888 NCI NIH HHS
• U24 CA114748 NCI NIH HHS
• U10 CA180819 NCI NIH HHS
• UG1 CA233328 NCI NIH HHS

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Affiliation(s)

Seth P. Lerner Baylor College of Medicine, Houston, TX
David J. McConkey Johns Hopkins School of Medicine, Baltimore, MD
Catherine M. Tangen Fred Hutchinson Cancer Research Center, Seattle, WA
Joshua J Meeks Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL
Thomas W. Flaig University of Colorado, School of Medicine, University of Colorado, Aurora, CO
X Hua Fred Hutchinson Cancer Research Center, Seattle, WA
Siamak Daneshmand Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA
Ajjai Shivaram Alva University of Michigan, Ann Arbor, MI
M. Scott Lucia University of Colorado, School of Medicine, University of Colorado, Aurora, CO
Dan Theodorescu Cedars-Sinai CANCER, Los Angeles, CA
Amir Goldkorn University of Southern California, Los Angeles, CA
Matthew I. Milowsky University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC
W. Choi Johns Hopkins School of Medicine, Baltimore, MD
Rick Bangs SWOG Cancer Research Network, Portland, OR
Daniel L. Gustafson Colorado State University, Fort Collins, CO
Melissa Plets Fred Hutchinson Cancer Research Center, Seattle, WA
Ian M. Thompson CHRISTUS Medical Center Hospital, University of Texas Health Science Center at San Antonio, San Antonio, TX

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Clinical Features of Li-Fraumeni Syndrome in Korea

PURPOSE

Li-Fraumeni syndrome (LFS) is a hereditary disorder caused by germline mutation in TP53. Owing to the rarity of LFS, data on its clinical features are limited. This study aimed to evaluate the clinical characteristics and prognosis of Korean patients with LFS.

MATERIALS AND METHODS

Patients who underwent genetic counseling and confirmed with germline TP53 mutation in the National Cancer Center in Korea between 2011 and 2022 were retrospectively reviewed. Data on family history with pedigree, types of mutation, clinical features, and prognosis were collected.

RESULTS

Fourteen patients with LFS were included in this study. The median age at diagnosis of the first tumor was 32 years. Missense and nonsense mutations were observed in 13 and one patients, respectively. The repeated mutations were p.Arg273His, p.Ala138Val, and pPro190Leu. The sister with breast cancer harbored the same mutation of p.Ala138Val. Seven patients had multiple primary cancers. Breast cancer was most frequently observed, and other types of tumor included sarcoma, thyroid cancer, pancreatic cancer, brain tumor, adrenocortical carcinoma, ovarian cancer, endometrial cancer, colon cancer, vaginal cancer, skin cancer, and leukemia. The median follow-up period was 51.5 months. Two and four patients showed local recurrence and distant metastasis, respectively. Two patients died of leukemia and pancreatic cancer 3 and 23 months after diagnosis, respectively.

CONCLUSION

This study provides information on different characteristics of patients with LFS, including types of mutation, types of cancer, and prognostic outcomes. For more appropriate management of these patients, proper genetic screening and multidisciplinary discussion are required.

Regional disparities in the availability of cancer clinical trials in Korea

OBJECTIVES

Unequal access to cancer clinical trials is an important issue, given the potential benefits of participation for cancer patients. We evaluated regional disparities in access to cancer clinical trials in Korea.

METHODS

From the Ministry of Food and Drug Safety database, we extracted 2,465 records of all cancer clinical trials approved between January 2012 and April 2023. To measure disparities in cancer clinical trial access, we calculated the ratio of clinical trials open to non-capital areas relative to those open to capital areas. We then analyzed temporal trends in this ratio, which we termed the trial geographical equity index (TGEI).

RESULTS

Disparities in access to cancer clinical trials, as indicated by the TGEI, did not significantly improve during the study period (regression coefficient, 0.002; p=0.59). However, for phase II/III trials sponsored by global pharmaceutical companies, the TGEI improved significantly (regression coefficient, 0.021; p<0.01). In contrast, the TGEI deteriorated for trials initiated by investigators or those testing domestically developed therapeutics (regression coefficient, -0.015; p=0.05). Furthermore, the increasing trend of TGEI for phase II/III trials sponsored by global companies began to reverse after 2019, coinciding with the outbreak of coronavirus disease 2019 (COVID-19).

CONCLUSIONS

Over the past decade, access to cancer clinical trials has improved in Korea, particularly for phase II/III trials evaluating therapeutics from global companies. However, this increase in accessibility has not extended to trials initiated by investigators or those assessing domestically developed therapeutics. Additionally, the impact of COVID-19 on disparities in clinical trial access should be closely monitored.

Phase 1 trial of 4-1BB-based adoptive T-cell therapy targeting human telomerase reverse transcriptase in patients with advanced refractory solid tumors

BACKGROUND AIMS

Human telomerase reverse transcriptase (hTERT) is an attractive target for anti-cancer therapies. We developed an effective method for generating hTERT-specific CD8+ T cells (hTERT-induced natural T cells [TERTiNTs]) using peripheral blood mononuclear cells (PBMCs) from patients with solid cancers and investigated their feasibility and safety.

METHODS

This was a single-center phase 1 trial using a 3 + 3 dose escalation design to evaluate six dose levels of TERTiNTs. PBMCs from each patient were screened using an hTERT peptide panel to select those that stimulated CD8+ T cells. The four most stimulatory peptides were used to produce autologous CD8+ T cells from patients refractory or intolerant to standard therapies. Eligible patients received a single intravenous infusion of TERTiNTs at different dose levels (4 × 108 cells/m2, 8 × 108 cells/m2 and 16 × 108 cells/m2). Pre-conditioning chemotherapy, including cyclophosphamide alone or in combination with fludarabine, was administered to induce lymphodepletion.

RESULTS

From January 2014 to October 2019, a total of 24 patients with a median of three prior lines of therapy were enrolled. The most common adverse events were lymphopenia (79.2%), nausea (58.3%) and neutropenia (54.2%), mostly caused by pre-conditioning chemotherapy. The TERTiNT infusion was well tolerated, and dose-limiting toxicities were not observed. None of the patients showed objective responses. Seven patients (30.4%) achieved stable disease with a median progression-free survival of 3.9 months (range, 3.2-11.3). At the highest dose level (16 × 108 cells/m2), four of five patients showed disease stabilization.

CONCLUSIONS

The generation of TERTiNTs was feasible and safe and provided an interesting disease control rate in heavily pre-treated cancer patients.

Novel Deep Learning Segmentation Models for Accurate GTV and OAR Segmentation in MR-Guided Adaptive Radiotherapy for Pancreatic Cancer Patients

PURPOSE/OBJECTIVE(S)

MR-guided adaptive radiotherapy (MRgART) improves target coverage and organ-at-risk (OAR) sparing in pancreatic cancer radiation therapy (RT). Inter-fractional changes in patients undergoing RT require time intensive re-delineation of gross tumor volume (GTV) and OARs prior to adaptive optimization. Accurate automatic segmentation has the potential to significantly improve efficiency of the adaptive workflow. We hypothesized that state-of-the-art deep learning (DL) segmentation models could adequately segment GTV and OARs in both planning and daily fractional MR scans.

MATERIALS/METHODS

The study included 21 patients with pancreatic cancer treated with MRgART (10 Gy x 5 fractions). The planning MR as well as all daily MR images and registrations were collected (6 image sets per patient and a total of 126 image sets). The planning MR and fraction 1-4 image sets were used as the training set (N = 105), while the test set (N = 21) comprised images for fraction 5, to simulate the last step of incremental learning from planning to final fraction. Evaluated contours included the GTV, Small Bowel, Large Bowel, Duodenum, Left and Right Kidney, Liver, Spinal Cord, and Stomach. To mimic clinical conditions, contour accuracy was evaluated within the ring structure surrounding the PTV, inside of which daily adaptive re-contouring is applied (2 cm expansion in the cradio-caudal direction, 3 cm expansion otherwise). We evaluated three DL model architectures: SegResNet, SegResNet 2D, and SwinUNETR to autosegment GTV and OARs. The segmentation models were trained on the training set using 5-fold cross-validation (CV) and quantitatively analyzed by comparing against clinically used contours with DICE scores. Qualitative analysis was performed by a radiation oncologist using a scoring scale: 1 = perfect, 2 = minor discrepancy, 3 = moderate discrepancy, and 4 = rejected.

RESULTS

Overall, the DL segmentations were in acceptable agreement with clinical contours. The best performing model was the SwinUNETR model with overall training DICE = 0.88±0.06, test DICE = 0.78±0.11, and qualitative score of 1.6±0.8. The agreement between the DL model and clinical segmentation for the GTV was 0.79±0.08, with a qualitative score of 2.2±0.9. The highest and lowest OAR DICE scores were for the Left Kidney (DICE = 0.93) and Small Bowel (DICE = 0.68), respectively. The highest qualitative OAR scores were for the Kidney, Liver, and Spinal Cord (score = 1.0) and the lowest qualitative score was for the Duodenum (score = 2.3) CONCLUSION: We report here the most comprehensive work on DL segmentation for pancreatic cancer MRgART, including quantitative and clinically-pertinent qualitative evaluations of 126 image sets and 3 DL architectures. Our data show good quantitative agreement between DL and clinical contours, and acceptable clinician evaluations for the majority of GTVs and OARs. The current work has great potential to significantly reduce a major bottleneck in the MRgART workflow for pancreatic cancer patients.

Novel Functional Radiomics for Prediction of Cardiac PET Avidity in Lung Cancer Radiotherapy

PURPOSE/OBJECTIVE(S)

Traditional methods of evaluating cardiotoxicity focus solely on radiation doses to the heart and do not incorporate functional imaging information. Functional imaging has great potential to improve the ability to provide early prediction for cardiotoxicity for lung cancer patients undergoing radiotherapy. FDG-based PET/CT imaging is routinely obtained as part of standard staging work up for lung cancer patients. Although FDG PET/CT scans are typically used to evaluate the tumor, imaging guidelines note that FDG PET/CT scans are an FDA-approved method to image for cardiac inflammation, and studies have noted that the PET cardiac signal can be predictive of clinical outcomes. The purpose of this work was to develop a radiomics model to predict clinical cardiac assessment of standard of care FDG PET/CT scans.

MATERIALS/METHODS

The study included 100 consecutive lung cancer patients treated with radiotherapy who underwent standard pre-treatment FDG-PET/CT staging scans. A clinician reviewed the PET/CT scans per clinical cardiac assessment guidelines and classified the cardiac uptake as: 0 = uniform diffuse, 1 = absent, 2 = heterogeneous, with event rates of 20%, 44%, and 35%, respectively. The heart was delineated and 200 novel functional radiomics features were selected to classify cardiac FDG uptake patterns. We divided the data into an 80% training set and a 20% test set to train and evaluate the classification models. Feature reduction was carried out using the Wilcoxon test (with Bonferroni adjusted p<0.05), hierarchical clustering, and Recursive Feature Elimination. Two automatic machine learning (AutoML) frameworks were used to determine classification models: a Random Forest Classifier (Tree-based Pipeline Optimization Tool, TPOT) and Linear Discriminant Analysis (AutoSklearn). 10-fold cross validation was carried out for training and the accuracy of the ability of the models to predict for clinical cardiac assessment is reported.

RESULTS

Fifty-one independent radiomics features were reduced to 3 clinically pertinent features (PET 2D Skewness, PET Grey Level Co-occurrence Matrix Correlation, and PET Median) using feature reduction techniques. The model selected by TPOT showed 89.8% predictive accuracy in the cross validation of the training set and 85% predictive accuracy on the test set. The model selected by AutoSklearn showed 89.7% predictive accuracy in the cross validation of the training set and 80% predictive accuracy on the test set.

CONCLUSION

The novelty of this work is that it is the first study to develop and evaluate functional cardiac radiomic features from standard of care FDG PET/CT scans with the data showing good predictive accuracy with clinical imaging evaluation. If validated, the current work provides automated methods to provide functional cardiac information using standard of care imaging that can be used as an imaging biomarker for early clinical toxicity prediction for lung cancer patients.

Deep-Learning Based Auto-Segmentation for Liver Yttrium-90 Selective Internal Radiation Therapy

PURPOSE/OBJECTIVE(S)

In resin Yttrium-90 (Y-90) selective internal radiation therapy (SIRT), liver volume sizes are needed for Y-90 activity calculations using the body-surface-area method, which are obtained from contours that are manually delineated in 3D images. The aim was to apply a deep-learning based auto-segmentation method for liver delineation for Y-90 SIRT.

MATERIALS/METHODS

A deep-learning-based liver segmentation method was applied using the U-Net3D architecture, which is a 3D convolutional neural network (CNN) extended from the original 2D U-Net architecture for 3D objects in medical imaging. The segmentation model was trained on the Liver Tumor Segmentation (LiTS) dataset. The training data set contained 130 CT scans, and the test data set contained 70 CT scans. The model was deployed in the clinic using DICOM communication. Auto-segmentation of liver in the CT images of 18 SIRT patients was studied. The CT images were exported from clinical database to the segmentation model's DICOM location, where a monitoring software detected the incoming data and automatically ran the liver segmentation. The results were then returned to the original DICOM location where the CT images were stored. Auto-segmented liver contours were compared with physician manually-delineated contours. Dice similarity coefficient (DSC), mean distance to agreement (MDA), ratio of volume (RV), and ratio of activity (RA, ratio of activity calculated using an auto-segmented liver contour to the accurate activity calculated using a manually-delineated contour), were assessed.

RESULTS

DSC, MDA, and RV are 0.942±0.014 (range: 0.908-0.959), 1.902±0.503 mm (range: 1.043-2.956 mm), and 0.988±0.039 (range: 0.901-1.045), respectively. RA is 1.001±0.003 (range: 0.993-1.007), which indicates that the activities calculated using the auto-segmented liver contours are close to the accurate activities.

CONCLUSION

The segmentation model was able to successfully identify and segment livers in the CT images, and provide accurate and reliable results. The proposed method is beneficial for clinical use as it can process large amounts of data quickly and efficiently, and can be easily deployed in a clinical environment using DICOM communication.

Establishment of Patient-Derived Organoids Using Ascitic or Pleural Fluid from Cancer Patients

PURPOSE

Patient-derived tumor cells can be a powerful resource for studying pathophysiological mechanisms and developing robust strategies for precision medicine. However, establishing organoids from patient-derived cells is challenging because of limited access to tissue specimens. Therefore, we aimed to establish organoids from malignant ascites and pleural effusions.

MATERIALS AND METHODS

Ascitic or pleural fluid from pancreatic, gastric, and breast cancer patients was collected and concentrated to culture tumor cells ex vivo. Organoids were considered to be successfully cultured when maintained for five or more passages. Immunohistochemical staining was performed to compare the molecular features, and drug sensitivity was assayed to analyze the clinical responses of original patients.

RESULTS

We collected 70 fluid samples from 58 patients (pancreatic cancer, n=39; gastric cancer, n=21; and breast cancer, n=10). The overall success rate was 40%; however, it differed with types of malignancy, with pancreatic, gastric, and breast cancers showing 48.7%, 33.3%, and 20%, respectively. Cytopathological results significantly differed between successful and failed cases (p=0.014). Immunohistochemical staining of breast cancer organoids showed molecular features identical to those of tumor tissues. In drug sensitivity assays, pancreatic cancer organoids recapitulated the clinical responses of the original patients.

CONCLUSION

Tumor organoids established from malignant ascites or pleural effusion of pancreatic, gastric, and breast cancers reflect the molecular characteristics and drug sensitivity profiles. Our organoid platform could be used as a testbed for patients with pleural and peritoneal metastases to guide precision oncology and drug discovery.

Exploring Connections between Oral Microbiota, Short-Chain Fatty Acids, and Specific Cancer Types: A Study of Oral Cancer, Head and Neck Cancer, Pancreatic Cancer, and Gastric Cancer

The association between oral microbiota and cancer development has been a topic of intense research in recent years, with compelling evidence suggesting that the oral microbiome may play a significant role in cancer initiation and progression. However, the causal connections between the two remain a subject of debate, and the underlying mechanisms are not fully understood. In this case-control study, we aimed to identify common oral microbiota associated with several cancer types and investigate the potential mechanisms that may trigger immune responses and initiate cancer upon cytokine secretion. Saliva and blood samples were collected from 309 adult cancer patients and 745 healthy controls to analyze the oral microbiome and the mechanisms involved in cancer initiation. Machine learning techniques revealed that six bacterial genera were associated with cancer. The abundance of Leuconostoc, Streptococcus, Abiotrophia, and Prevotella was reduced in the cancer group, while abundance of Haemophilus and Neisseria enhanced. G protein-coupled receptor kinase, H+-transporting ATPase, and futalosine hydrolase were found significantly enriched in the cancer group. Total short-chain fatty acid (SCFAs) concentrations and free fatty acid receptor 2 (FFAR2) expression levels were greater in the control group when compared with the cancer group, while serum tumor necrosis factor alpha induced protein 8 (TNFAIP8), interleukin-6 (IL6), and signal transducer and activator of transcription 3 (STAT3) levels were higher in the cancer group when compared with the control group. These results suggested that the alterations in the composition of oral microbiota can contribute to a reduction in SCFAs and FFAR2 expression that may initiate an inflammatory response through the upregulation of TNFAIP8 and the IL-6/STAT3 pathway, which could ultimately increase the risk of cancer onset.

Abstract 4297: OFFONOME: a new notion of genes’ on/off

Background: RNA-seq is now the most widely used technique for gene expression profiling, which generates nucleotide level genome coverage as well as summary gene expression values. In general, low-expressed genes are excluded in the data processing due to their low signal-to-noise ratio. Nonetheless, it has been shown that low-expressed genes can provide crucial information such as presence of rare cells in bulk tissue samples. To optimize signal to noise in low-expressed genes, we applied a novel approach in which we transform low-expressed genes to a robust dichotomized state of being either “on” or “off”.

Methods: To determine the status of genes, we use the shape of base-level read coverage which is expected to be homogeneous across the samples if they are “on”, whereas appear to be random noise if they are “off”. We model base-resolution RNA-seq data as vectors in high dimensional data space and measure their level of shape similarity (LSS) using angles between samples with lower angles indicating higher similarity which is more likely to be “on” status. Applying this approach to 3 human cancer samples (head and neck squamous cell carcinoma (HNSC), lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC)) from the Cancer Genome Atlas (TCGA), we identified lists of genes, the OFFONOME, that were either always or sometimes “off”. Differential OFFONOME genes were queried to address supervised and unsupervised analyses.

Results: Using our technique, we characterized the OFFONOME of HNSC (5851 genes), a set which would typically have been filtering for removal because of low expression. In the HNSC OFFONOME, we observed five gene clusters, each of which was strongly associated with specific gene ontology. One of the clusters identified a rare population of normal myocytes infiltrating otherwise invasive tumors. For the OFFONOME of LUAD (5435 genes) and LUSC (5292 genes), we found clusters enriched with cilia and keratinization-related genes. In the result of integrated analysis, we observed that squamous cell carcinoma (SCC) tumor types shared “on” status for keratinization-related genes known for the cause of SCC. By comparison, LUAD had “on” status genes related to microtubule-based movement related with cilia structure. Strikingly, clustering the OFFONOME with the LSS distinguished 3 tumor types with almost perfect separation, outperforming several competing gene expression measures.

Conclusion: In this study, we applied a new notion of gene expression. This approach enables a robust characterization of “on” and “off” status which can be especially effective for the genes expressed at low level. The OFFONOME from 3 cancer types revealed not only the tissue-specific genes but also the genes shared in similar tumor types. Collectively, OFFONOME can provide new insights into genes expressed at vanishingly low levels, such as from minor cell populations within bulk tumor analysis.

Citation Format: Wonyoung Choi, Hyo Young Choi, Daivd Neil Hayes. OFFONOME: a new notion of genes’ on/off. [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 4297.

Abstract 2404: Patient-derived organoid platform for the prediction of radiation response and modeling radiation resistance in oral cancer

Oral cancer is rare cancer that accounts for roughly 1.5% of all cancers in Korea. The standard treatment for the patient with oral cancer is surgery followed by radiotherapy. However, 30-50% of patients had local recurrence and metastasis to lymph nodes within 2 years. Numerous radiation-resistant cell lines have been created and utilized for research due to the significance of biomarkers for predicting response to radiation therapy; however, the homogenous 2D cell lines limit the practical use of the identified molecules. Patient-derived organoid (PDO) systems, as opposed to 2D cell lines, have significant advantages for the preclinical model in that they are similar to the genetic heterogeneity seen in patient tumors and reflect the clinical characteristics of patients. In this study, we generated organoid models that mimic radiation therapy from the oral PDO library in order to identify molecular profiles associated with radiation resistance. From January 2021 to August 2022, we prospectively collected 164 normal tissues and 179 tumor tissues from enrolled patients with oral cancer. 60 tumor organoids and 66 normal organoids were maintained over 4 passages and cryopreserved, which is the largest PDO repository with normal and malignant ever published for oral cancer to date. Each organoid was identified through long-term clinical information follow-up in their respective patients, notably recurrence after radiation therapy. In the oral PDO library, organoids were categorized as derived from tumor tissues of non-recurred patients (nPDOs), derived from primary tumor tissues of patients who recurred after radiotherapy (pPDOs), and derived from recurrent tumor tissues (rPDOs). There was also one pair of pPDO and rPDO for the same patient. A total of 60 Gy of radiation was irradiated to the organoids for the construction of a radiation-resistant PDO model, and finally, four cases of radiotherapy mimic organoid models were successfully established. Survival analysis for radiation dose-response and post-irradiation calcein-AM staining were used to validate these models. The pPDO and rPDO models of radiation resistance are well-established, whereas nPDO was not. Given the rarity of oral cancer, this platform is the first preclinical model to closely resemble the clinical radiation pipeline for patients with oral cancer. It would help make a more accurate prediction of radiation response in patients with oral cancer, as well as the development of treatment guidelines. (This research was supported by National Cancer Center, Korea (No. 2210980) and National Research Foundation of Korea (NRF) grant, funded by the Korean government (MSIT) (No. 2020M3A9A5036362))

Citation Format: Sumin Kang, Mi Rim Lee, Sun-Young Kong, Jong-Ho Lee, Dohyun Kwon, Ikjae Kwon, Soung-Min Kim, Youngwook Kim, Wonyoung Choi, Hye Won Shon, Yu-Sun Lee, Joo Yong Park, Sung Weon Choi, Yun-Hee Kim. Patient-derived organoid platform for the prediction of radiation response and modeling radiation resistance in oral cancer [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 2404.

Abstract 161: Patient-derived organoids (PDOs) hub of National Cancer Center, Korea: pre-clinical model for drug screening

Purpose Cancer is one of the leading causes of death worldwide. Patient-derived tumor cells can serve as a powerful resource for studying pathophysiologic mechanisms and developing robust strategies for precision medicine. To address this problem, we launched the patient-derived organoids (PDOs) Hub to establish a comprehensive model of various tumor organoids from pancreatic, biliary tract, liver, colorectal, breast, gastric, ovarian, and oral cancers, with matching clinical data and molecular characteristics.

Methods All specimens were collected from histologically confirmed cancer patients at the National Cancer Center. Samples obtained from surgery, biopsy, or body fluid (malignant ascites or pleural effusion) were collected for ex vivo culture of tumor cells. PDOs were managed according to our standard operating procedure (SOP), which included specimen delivery process, separation of cells from tissues, criteria for subculture, quality control (QC), production of genomic and histologic data, and the 384-well-based drug response evaluation system. Organoids were considered to be successfully cultured when they were maintained for five or more passages.

Results A total of 263 PDOs were established from various cancer types, including oral cancer (N = 89), pancreatic cancer (N = 48), ovarian cancer (N = 32), breast cancer (N = 30), biliary tract cancer (N = 29), hepatocellular carcinoma (N = 17), gallbladder cancer (N = 8), gastric cancer (N = 7) and colorectal cancer (N = 3). PDOs broadly recapitulated the histologic and genetic characteristics of the patient’s tumor. These organoids available for long-term culture were cryopreserved, and a total of 2986 stocks have been accumulated. Drug screening tests were performed with 60 PDOs (pancreatic cancer, N = 36; breast cancer, N = 15; ovarian cancer, N = 6; gastric cancer, N = 3) using selected agents among the 47 drugs for each type of cancer. Profiles of cytotoxic agents were well correlated with the patient’s clinical responses to the matched drugs and tested investigational agents also showed promising antitumor activity.

Conclusions We have established a model of several human cancer organoids. This will serve as the platform that can recapitulate the physiology and drug response profiles of human cancer and pave the way for screening innovative drugs, identifying novel targets, and stratifying patients for pertinent therapeutic options.

(This work was supported by National Research Foundation of Korea grant, funded by the Korean government (MSIT) (No. 2020M3A9A5036362))

Citation Format: Yebeen Yu, Mi Rim Lee, Wonyoung Choi, Sumin Kang, Jeong Eun Gong, Soobeen Heo, Hye Ju Park, Sang Myung Woo, So-Youn Jung, Sung Weon Choi, Jong-Ho Lee, Myong Cheol Lim, Ji Yeon Baek, Bo Hyun Kim, Ji Hoon Kim, Yuri Cho, Sang-Jae Park, Yun-Hee Kim, Sun-Young Kong. Patient-derived organoids (PDOs) hub of National Cancer Center, Korea: pre-clinical model for drug screening [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 161.

Abstract 4929: ICX-101, a novel MYC inhibitor, shows antitumor activity in patient-derived cells of advanced lung cancer with high MYC expression

Background: MYC is an attractive therapeutic target in lung cancer. ICX-101 is a novel potent, selective small molecule that directly inhibits the binding of MYC/MAX dimers to the DNA binding sequence E-box. Here, we show that ICX-101 shows antitumor activity in patient-derived cells (PDC) of advanced lung cancer and that the drug responses are correlated with the MYC expression levels.

Methods: PDCs of lung cancer were treated with ICX-101, and the area under the dose-response curve (AUC) was measured as the readout for antitumor efficacy. MYC expression level of each PDC was measured with the fold expression of mRNA compared to the normal lung tissue. The patient’s clinical data and survival outcomes were analyzed to correlate with the drug responses of PDCs.

Results: We collected 100 PDCs from 82 lung cancer patients. The histologic types included adenocarcinoma (N = 82), squamous cell carcinoma (N = 10), non-small cell lung cancer (NSCLC) not otherwise specified (NOS) (N = 4), and small cell lung cancer (SCLC, N = 4). PDCs derived from SCLC showed higher MYC expression levels than NSCLC (P = 0.004). MYC was a prognostic factor, as the patient groups with the top and bottom 25 percentiles of MYC mRNA expression had an overall survival of 932.5 and 256 days, respectively (P = 0.029). However, MYC expression was predictive for the response to ICX-101, as the PDCs with the top 25 percentiles of MYC levels showed markedly lower AUC values than those with the bottom 25 percentile (P &lt; 0.001). Additionally, the MYC mRNA levels and AUC values were inversely correlated with statistical significance (R = -0.46, P &lt; 0.001).

Conclusion: ICX-101 is a potent MYC inhibitor that shows antitumor activity in lung cancer PDCs. Our results suggest the potential of ICX-101 as a possible therapeutic option in advanced lung cancer with high MYC expressions.

Citation Format: Wonyoung Choi, Kyung-Chae Jeong, Seog-Yun Park, Sunshin Kim, Eun Hye Kang, Mihwa Hwang, Ji-Youn Han. ICX-101, a novel MYC inhibitor, shows antitumor activity in patient-derived cells of advanced lung cancer with high MYC expression. [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 4929.

Optimal injection rate and catheter size for brain perfusion computed tomography using non-ionic contrast medium in clinically normal Beagles

OBJECTIVE

To evaluate the effects of contrast medium injection rates and intravenous injection catheter sizes on the time-density curve (TDC) of brain perfusion computed tomography (PCT) images in clinically normal Beagles and provide a reference range for the perfusion parameters for clinical application of PCT in veterinary medicine.

ANIMALS

5 healthy, sexually intact male Beagles.

PROCEDURES

All dogs underwent general anesthesia for PCT. Contrast medium (350 mg I/kg) was injected at 3 different injection rates (2, 3, and 4 mL/second) and with 2 sizes of an intravenous catheter (20-gauge and 24-gauge). The rostral cerebral artery and dorsal sagittal sinus were selected as the regions of interest of the TDC. Initiation time of arterial inflow (ta), venous outflow (tv), peak time of arterial enhancement (Tap), and the peak time of venous enhancement (Tvp), were measured, and the difference between Tap and tv (Tap-tv) and between Tap and ta (Tap-ta) was calculated.

RESULTS

Both Tap-tv and Tap-ta were significantly (P < .05) shorter at the rate of 3 mL/second than at 2 mL/second with the 24-gauge catheter. However, there was no significant difference according to catheter sizes. Particularly, a 4 mL/second injection rate using a 24-gauge catheter mostly resulted in contrast medium leakage and catheter rupture.

CLINICAL RELEVANCE: CONTRAST MEDIUM INJECTION

At a rate of 3 mL/second and with a 24-gauge catheter ensures optimal image acquisition and stable contrast medium injection in brain PCT for small dogs. PCT may be useful for diagnosing cerebrovascular events and hemodynamic changes in small dogs.

A prospective phase II trial of pembrolizumab plus lenvatinib in advanced adrenal cortical carcinoma after failure of platinum- and mitotane-based chemotherapy (ACCOMPLISH)

TPS3

Background: Adrenal cortical carcinoma (ACC) is a very rare cancer with poor prognosis. For advanced ACC, systemic treatment options are limited. There has been only one randomized phase III clinical trial in which etoposide, doxorubicin, cisplatin, and mitotane (EDP-M) achieved statistically significant improvement in terms of objective response rate (ORR) and progression-free survival (PFS). However, after failure of EDP-M regimen, no universally accepted treatment option exists. In human ACC sample, vascular endothelial growth factor (VEGF) and VEGF receptor-2 (VEGFR-2) expression were higher than adrenal adenoma, and 10-20% of tumor cells and 70% of tumor infiltrating monocyte are PD-L1 positive. In retrospective review of cabozantinib in advanced ACC, cabozantinib demonstrated 19% of ORR and 16.2 weeks of median PFS. Also, in phase II clinical trial of pembrolizumab in advanced ACC, ORR of 14-23% were shown. Considering synergism of VEGFR tyrosine kinase inhibitors (TKIs) and immune check point inhibitors (ICIs) in other cancers, combination of VEGFR TKI and ICI is an attractive approach in advanced ACC. Methods: This is an open-label,single-arm,multi-center,investigator-initiated phase II trial of lenvatinib plus pembrolizumab in patients with advanced ACC who failed previous platinum and mitotane therapy (NCT 05036434). Using Simon’s optimal two-stage design, 10 patients will be enrolled initially in the first stage. If at least 2 or more patients achieve complete response or partial response, the trial will continue until enrollment of a total of 30 patients. Patients will receive 200 mg of pembrolizumab every 3 weeks intravenously and 20 mg of daily lenvatinib orally until disease progression, intolerable toxicity, or patients’ withdrawal of consent. Key eligibility criteria are age ≥ 19 years, ECOG PS 0-1, biopsy-proven ACC, disease progression despite cisplatin- and mitotane-based chemotherapy, measurable disease according to RECIST v1.1, no uncontrolled hypertension, adequate kidney, liver, and bone marrow function. Primary endpoint is ORR, and secondary endpoints include PFS, safety profile, overall survival, duration of response. Exploratory evaluation of tumor genomics and immune microenvironment by whole exome sequencing, single-cell RNA sequencing, and T cell receptor sequencing in correlation with response will be performed. Enrollment began in June 2022 and projected enrollment goal is 3 years. Clinical trial information: NCT05036434 .

Highly Stable Iron- and Carbon-Based Electrodes for Li-Ion Batteries: Negative Fading and Fast Charging within 12 Min

Lithium-ion batteries (LIBs) with high energy density and safety under fast-charging conditions are highly desirable for electric vehicles. However, owing to the growth of Li dendrites, increased temperature at high charging rates, and low specific capacity in commercially available anodes, they cannot meet the market demand. In this study, a facile one-pot electrochemical self-assembly approach has been developed for constructing hybrid electrodes composed of ultrafine Fe₃ O₄ particles on reduced graphene oxide (Fe₃ O₄ @rGO) as anodes for LIBs. The rationally designed Fe₃ O₄ @rGO electrode containing 36 wt % rGO exhibits an increase in specific capacity as cycling progresses, owing to improvements in the active sites, electrochemical kinetics, and catalytic behavior, leading to a high specific capacity of 833 mAh g^-1 and outstanding cycling stability over 2000 cycles with a capacity loss of only 0.127 % per cycle at 5 A g^-1 , enabling the full charging of batteries within 12 min. Furthermore, the origin of this abnormal improvement in the specific capacity (called negative fading), which exceeds the theoretical capacity, is investigated. This study opens up new possibilities for the commercial feasibility of Fe₃ O₄ @rGO anodes in fast-charging LIBs.

MYC amplification-conferred primary resistance to capmatinib in a MET-amplified NSCLC patient: a case report

Background

Capmatinib, a potent and selective mesenchymalepithelial transition factor (MET) inhibitor, is an effective treatment option for non-small cell lung cancer (NSCLC) patients with MET exon 14 skipping mutations or gene amplification. However, the mechanisms that confer resistance to capmatinib remain elusive. Here, we present a case of primary resistance to capmatinib in a MET-amplified NSCLC patient which was conferred by concurrent MYC amplification.

Case Description

Capmatinib was administered as first-line treatment in an 82-year-old MET-amplified [gene copy number (GCN) 13.5] and MET overexpressed (immunohistochemical staining 3+/3, >50%) NSCLC patient. However, the tumor rapidly progressed and showed primary resistance to capmatinib. Next-generation target sequencing using rebiopsy tumor samples revealed MYC amplification. We also performed functional drug susceptibility testing using patient-derived cells (PDCs), which showed overexpression of MYC mRNA and resistance to capmatinib. Meanwhile, ICX-101, an investigational MYC inhibitor, successfully inhibited the growth of PDCs at a relatively low IC50 value. Also, a synergistic effect was shown when capmatinib treatment was followed by ICX-101.

Conclusions

Concurrent MYC amplification could potentially confer primary resistance to capmatinib in highly MET amplified NSCLC patients. Further clinical studies are warranted to corroborate these findings, and treatment with MYC inhibitors could be suggested as an alternative therapeutic strategy for this subset of patients.

New Constraint on the Local Relic Neutrino Background Overdensity with the First KATRIN Data Runs

We report on the direct search for cosmic relic neutrinos using data acquired during the first two science campaigns of the KATRIN experiment in 2019. Beta-decay electrons from a high-purity molecular tritium gas source are analyzed by a high-resolution MAC-E filter around the end point at 18.57 keV. The analysis is sensitive to a local relic neutrino overdensity ratio of η<9.7×10^{10}/α (1.1×10^{11}/α) at a 90% (95%) confidence level with α=1 (0.5) for Majorana (Dirac) neutrinos. A fit of the integrated electron spectrum over a narrow interval around the end point accounting for relic neutrino captures in the tritium source reveals no significant overdensity. This work improves the results obtained by the previous neutrino mass experiments at Los Alamos and Troitsk. We furthermore update the projected final sensitivity of the KATRIN experiment to η<1×10^{10}/α at 90% confidence level, by relying on updated operational conditions.

Therapeutic Targeting of DNA Damage Response in Cancer

DNA damage response (DDR) is critical to ensure genome stability, and defects in this signaling pathway are highly associated with carcinogenesis and tumor progression. Nevertheless, this also provides therapeutic opportunities, as cells with defective DDR signaling are directed to rely on compensatory survival pathways, and these vulnerabilities have been exploited for anticancer treatments. Following the impressive success of PARP inhibitors in the treatment of BRCA-mutated breast and ovarian cancers, extensive research has been conducted toward the development of pharmacologic inhibitors of the key components of the DDR signaling pathway. In this review, we discuss the key elements of the DDR pathway and how these molecular components may serve as anticancer treatment targets. We also summarize the recent promising developments in the field of DDR pathway inhibitors, focusing on novel agents beyond PARP inhibitors. Furthermore, we discuss biomarker studies to identify target patients expected to derive maximal clinical benefits as well as combination strategies with other classes of anticancer agents to synergize and optimize the clinical benefits.

A Comprehensive and Comparative Review of Global Gastric Cancer Treatment Guidelines

Countries differ in their treatment expertise and research results regarding gastric cancer; hence, treatment guidelines are diverse based on evidence and medical situations. A comprehensive and comparative review of each country’s guidelines is imperative to understand the similarities and differences among countries. We reviewed and compared five gastric cancer treatment guidelines in terms of endoscopic, surgical, perioperative, and palliative systemic treatment based on evidence levels and recommendation grades, as well as the postoperative follow-up strategies for each guideline. The Korean, Chinese, and European guidelines provided evidence and grading of the recommendations. The United States guidelines suggested categories for evidence and consensus. The Japanese guidelines suggested evidence and recommendations only for systemic treatment. The Korean and Japanese guidelines described endoscopic treatment, surgery, and lymphadenectomy in detail. The Chinese, United States, and European guidelines more intensively considered perioperative chemotherapy. In particular, the indications for chemotherapy and the regimens recommended by each guideline differed slightly. Considering their medical situations, each guideline had some diversity in terms of adopting evidence, which resulted in heterogeneous recommendations. This review will help medical personnel to comprehensively understand the diversity in gastric cancer treatment guidelines for each country in terms of evidence and recommendations.

Plasma complement C7 as a target in non-small cell lung cancer patients to implement 3P medicine strategies

Background

Programmed cell death-1 (PD-1)/programmed cell death ligand-1 (PD-L1) immune checkpoint inhibitors (ICIs) significantly affect outcomes in non-small cell lung cancer (NSCLC) patients. However, differences in reactions toward PD-1/PD-L1 ICI among patients impose inefficient treatment. Therefore, developing a reliable biomarker to predict PD-1/PD-L1 ICI reaction is highly necessary for predictive, preventive, and personalized (3P) medicine.

Materials and methods

We recruited 63 patients from the National Cancer Center (NCC) and classified them into the training and validation sets. Next, 99 patients were recruited for inclusion into the external validation set at the Samsung Medical Center (SMC). Proteomic analysis enabled us to identify plasma C7 levels, which were significantly different among groups classified by their overall response to the RECIST V 1.1-based assessment. Analytical performance was evaluated to predict the PD-1/PD-L1 ICI response for each type of immunotherapy, and NSCLC histology was evaluated by determining the C7 levels via ELISA.

Results

Plasma C7 levels were significantly different between patients with and without clinical benefits (PFS ≥ 6 months). Among the groups sorted by histology and PD-1/PD-L1 immunotherapy type, only the predicted accuracy for pembrolizumab-treated patients from both NCC and SMC was greater than 73%. In patients treated with pembrolizumab, C7 levels were superior to those of the companion diagnostics 22C3 (70.3%) and SP263 (62.1%). Moreover, for pembrolizumab-treated patients for whom the PD-L1 tumor proportion score (TPS) was < 50%, the predictive accuracy of C7 was nearly 20% higher than that of 22C3 and SP263.

Conclusion

Evaluation of plasma C7 levels shows an accurate prediction of NSCLC patient reactions on pembrolizumab. It demonstrates plasma C7 is an alternative and supportive biomarker to overcome the predictive limitation of previous 22C3 and SP263. Thus, it is clear that clinical use of plasma C7 allows predictive diagnosis on lung cancer patients who have not been successfully treated with current CDx and targeted prevention on metastatic diseases in secondary care caused by a misdiagnosis of current CDx. Reduction of patients' financial burden and increased efficacy of cancer treatment would also enable prediction, prevention, and personalization of medical service on NSCLC patients. In other words, plasma C7 provides efficient medical service and an optimized medical economy followed which finally promotes the prosperity of 3P medicine.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13167-021-00266-x.

Components of the endocytic and recycling trafficking pathways interfere with the integrity of the Legionella-containing vacuole

Legionella pneumophila requires the Dot/Icm translocation system to replicate in a vacuolar compartment within host cells. Strains lacking the translocated substrate SdhA form a permeable vacuole during residence in the host cell, exposing bacteria to the host cytoplasm. In primary macrophages, mutants are defective for intracellular growth, with a pyroptotic cell death response mounted due to bacterial exposure to the cytosol. To understand how SdhA maintains vacuole integrity during intracellular growth, we performed high-throughput RNAi screens against host membrane trafficking genes to identify factors that antagonise vacuole integrity in the absence of SdhA. Depletion of host proteins involved in endocytic uptake and recycling resulted in enhanced intracellular growth and lower levels of permeable vacuoles surrounding the ΔsdhA mutant. Of interest were three different Rab GTPases involved in these processes: Rab11b, Rab8b and Rab5 isoforms, that when depleted resulted in enhanced vacuole integrity surrounding the sdhA mutant. Proteins regulated by these Rabs are responsible for interfering with proper vacuole membrane maintenance, as depletion of the downstream effectors EEA1, Rab11FIP1, or VAMP3 rescued vacuole integrity and intracellular growth of the sdhA mutant. To test the model that specific vesicular components associated with these effectors could act to destabilise the replication vacuole, EEA1 and Rab11FIP1 showed increased density about the sdhA mutant vacuole compared with the wild type (WT) vacuole. Depletion of Rab5 isoforms or Rab11b reduced this aberrant redistribution. These findings are consistent with SdhA interfering with both endocytic and recycling membrane trafficking events that act to destabilise vacuole integrity during infection.

Bound on 3+1 Active-Sterile Neutrino Mixing from the First Four-Week Science Run of KATRIN

We report on the light sterile neutrino search from the first four-week science run of the KATRIN experiment in 2019. Beta-decay electrons from a high-purity gaseous molecular tritium source are analyzed by a high-resolution MAC-E filter down to 40 eV below the endpoint at 18.57 keV. We consider the framework with three active neutrinos and one sterile neutrino. The analysis is sensitive to the mass, m_{4}, of the fourth mass state for m_{4}^{2}≲1000  eV^{2} and to active-to-sterile neutrino mixing down to |U_{e4}|^{2}≳2×10^{-2}. No significant spectral distortion is observed and exclusion bounds on the sterile mass and mixing are reported. These new limits supersede the Mainz results for m_{4}^{2}≲1000  eV^{2} and improve the Troitsk bound for m_{4}^{2}<30  eV^{2}. The reactor and gallium anomalies are constrained for 100<Δm_{41}^{2}<1000  eV^{2}.

Three-dimensional myocardial strain for the prediction of clinical events in patients with successfully reperfused ST-segment elevation myocardial infarction

Funding Acknowledgements

Type of funding sources: None.

Background/Introduction

Two-dimensional (2D) myocardial strain analysis can be used to evaluate the prognosis of patients with acute myocardial infarction and has comparable predictive power as conventional echocardiographic parameters such as left ventricular ejection fraction (LV EF). Three-dimensional (3D) myocardial strain analysis is also expected to have similar clinical usefulness and overcome several inherent limitations of 2D strain analysis. However, no large-scale studies have been reported to date.

Purpose

We aimed to clarify the prognostic significance of 3D strain analysis in patients with ST-segment elevation myocardial infarction (STEMI) who are most likely to benefit from 3D strain analysis.

Methods

 Patients who underwent successful revascularization for STEMI from June 2011 to April 2017 were retrospectively recruited. In addition to conventional echocardiographic parameters, 3D global area strain (GAS), 3D global longitudinal strain (GLS), as well as 2D GLS were obtained.

 To evaluate the clinical outcomes, we constructed a composite outcome consisting of all-cause death or re-hospitalisation due to acute decompensation of heart failure.

Results

From June 2011 to April 2017, 632 patients were retrospectively recruited in our hospital. Of these patients, 545 patients (86.2%) had a reliable 3D strain analysis. The clinical course of each patient was followed up for a maximum of 96 months (median 49.5 months). During follow-up periods, 55 (10.1%) among 545 patients experienced the composite outcome of all-cause death or re-hospitalisation due to acute decompensation of heart failure. Patients with adverse events were older, had more underlying diseases such as obesity, dyslipidemia, previous history of stroke, or chronic kidney disease. (all, p &lt; 0.05) LV EF was significantly lower, while 2D GLS, 3D GLS, and 3D GAS were significantly higher in patients with poor outcomes. (all, p &lt; 0.001) The area under the receiver operating characteristic curve (AUC) values of LV EF, 2D GLS, 3D GLS, and 3D GAS were 0.70, 0.71, 0.67, and 0.65, respectively. (all, p &lt; 0.05) Kaplan-Meier analysis of composite outcomes based on the best cut-off values of each parameter demonstrated similar results. (Figure 1) In the Cox proportional hazard model, the hazard ratios of LV EF, 2D GLS, and 3D GLS were 3.0, 5.5, and 2.0, respectively. (all, p &lt; 0.05) The maximum likelihood-ratio test was performed to evaluate the additional prognostic value of 2D GLS or 3D GLS over the basic prognostic model consisting of baseline clinical characteristics and LV EF, and the likelihood ratio was 15.9 for 2D GLS (p &lt; 0.001) and 1.49 for 3D GLS (p = 0.22).

Conclusion(s)

 3D strain could be reliably measured in the majority of the patients and had a significant prognostic value. However, the predictive power of the 3D strain was lower than that of the 2D strain. The clinical implications of 3D strain indices should be investigated further.

Abstract Figure.

The Clinical Impact of Capmatinib in the Treatment of Advanced Non-Small Cell Lung Cancer with MET Exon 14 Skipping Mutation or Gene Amplification

Purpose

Capmatinib, an oral MET kinase inhibitor, has demonstrated its efficacy against non–small cell lung cancer (NSCLC) with MET dysregulation. We investigated its clinical impact in advanced NSCLC with MET exon 14 skipping mutation (METex14) or gene amplification.

Materials and Methods

Patients who participated in the screening of a phase II study of capmatinib for advanced NSCLC were enrolled in this study. MET gene copy number (GCN), protein expression, and METex14 were analyzed and the patients’ clinical outcome were retrospectively reviewed.

Results

A total of 72 patients were included in this analysis (group A: GCN ≥ 10 or METex14, n=14; group B: others, n=58). Among them, 13 patients were treated with capmatinib (group A, n=8; group B, n=5), and the overall response rate was 50% for group A, and 0% for group B. In all patients, the median overall survival (OS) was 20.2 months (95% confidence interval [CI], 6.9 to not applicable [NA]) for group A, and 11.3 months (95% CI, 8.2 to 20.3) for group B (p=0.457). However, within group A, median OS was 21.5 months (95% CI, 20.8 to NA) for capmatinib-treated, and 7.5 months (95% CI, 3.2 to NA) for capmatinib-untreated patients (p=0.025). Among all capmatinib-untreated patients (n=59), group A showed a trend towards worse OS to group B (median OS, 7.5 months vs. 11.3 months; p=0.123).

Conclusion

Our data suggest that capmatinib is a new compelling treatment for NSCLC with MET GCN ≥ 10 or METex14 based on the improved survival within these patients.

3D wide-field multispectral photoacoustic imaging of human melanomas in vivo: a pilot study

BACKGROUND

The Breslow depth is an important parameter to determine the excision margin and prognosis of melanoma. However, it is difficult to accurately determine the actual Breslow depth before surgery using the existing ocular micrometer and biopsy technique.

OBJECTIVES

To evaluate the use of 3D wide-field multispectral photoacoustic imaging to non-invasively measure depth and outline the boundary of melanomas for optimal surgical margin selection.

METHODS

Six melanoma patients were examined in vivo using the 3D multispectral photoacoustic imaging system. For five cases of melanomas (one in situ, three nodular, and one acral lentiginous type melanoma), the spectrally unmixed photoacoustic depths were calculated and compared against histopathological depths.

RESULTS

Spectrally unmixed photoacoustic depths and histopathological depths match well within a mean absolute error of 0.36 mm. In particular, the measured minimum and maximum depths in the in situ and nodular type of melanoma were 0.6 and 9.1 mm, respectively. In the 3D photoacoustic image of one metastatic melanoma, feeding vessels were visualized in the melanoma, suggesting the neovascularization around the tumour.

CONCLUSIONS

The 3D multispectral photoacoustic imaging not only provides well-measured depth and sizes of various types of melanomas, it also visualizes the metastatic type of melanoma. Obtaining accurate depth and boundary information of melanoma before surgery would play a useful role in the complete excision of melanoma during surgery.

YAP and AP-1 Cooperate to Initiate Pancreatic Cancer Development from Ductal Cells in Mice

The development of pancreatic cancer is heavily dependent upon the aberrant activation of KRAS signaling. Among the downstream targets of KRAS, the effectors of the Hippo pathway YAP and TAZ (YAP/TAZ) are crucial during cancer initiation and progression. However, little is known about the cell type-specific effects of YAP/TAZ on the development of pancreatic cancer. Here we clarify the unique consequences of YAP/TAZ activation in the ductal cell population of the pancreas by generating mice with pancreatic duct cell-specific, inducible knockouts of Lats1 and Lats2, the main kinases upstream of YAP/TAZ. Oncogenic activation of YAP by deletion of Lats1/2 in ductal cells led to the rapid transformation of the pancreas, which was accompanied by a robust increase in the expression of YAP and AP-1 target genes. Pharmacologic inhibition of AP-1 activity induced death in Lats1/2 knockout organoids and attenuated YAP-dependent transformation of the pancreas in vivo. Both YAP and AP-1 were activated during the development of KRAS-dependent cancer in mice and human patients with pancreatic ductal adenocarcinoma, suggesting that this signaling hub represents an important mediator of pancreatic cancer development and progression. Collectively, these data define a YAP-dependent mechanism of pancreatic cancer cell development and suggest that inhibition of AP-1 can suppress this development. SIGNIFICANCE: A pancreatic ductal cell-specific knockout mouse model featuring constitutively active YAP allows for the study of YAP-dependent transformation of the pancreas and for screening pharmacologically active inhibitors.

Reproducibility of Histologic Assessment in Porto-sinusoidal Vascular Disease Liver Biopsies

Introduction/Objective

Variable histologic findings that may be seen in porto-sinusoidal vascular disease (PSVD) liver biopsies are subject to high interobserver variability, requiring correlation with clinical history of portal hypertension (traditionally interpreted as non-cirrhotic portal hypertension NCPH). We investigated which histologic features are reproducible in PSVD biopsies.

Methods

Archived liver biopsies (n=38) from patients with NCPH (n=14) and without NCPH (n=21) were reviewed. Static H&E images of lobules (L, x100, NCPH=27, non-NCPH=23) and portal tracts (P, x200, NCPH=23, non- NCPH=27) were distributed among 9 gastrointestinal pathologists blinded to clinical history. Each pathologist answered multiple choice questions based on the presence (Q2) or absence (Q1) of portal hypertension clinically. The choice selected by 6 pathologists or more was considered consensus answer for the image. The interpretation of the image was considered reproducible when consensus was reached on both Q1 and Q2.

Results

The interpretations of 27 (54%; 17L, 10P) images from NCPH and 21 (42%; 10L, 11P) from non-NCPH were reproducible. In NCPH, the interpretations of normal (n=10, 4L, 6P), sinusoidal dilatation (n=7), and increased parenchymal draining vessels (n=3) were reproducible, while there was no consensus on the diagnoses of nodular regeneration and increased number of portal vessels. In non-NCPH, the interpretations of normal (n=8, 2L, 6P), sinusoidal dilatation (n=6), and paraportal shunting vessel(s) (n=4) were reproducible, whereas no consensus was reached on the diagnoses of nodular regeneration, incomplete fibrous septa, and increased number of portal vessels.

Conclusion

Histologic assessment of normal L and P as well as sinusoidal dilatation appears to be reproducible independent of clinical history. The findings of increased parenchymal draining vessels in NCPH group and paraportal shunting vessels in non-NCPH group may be consistently diagnosed to a certain extent. The assessment for nodular regeneration without reticulin stain, incomplete fibrous septa, or increased number of portal vessels appears to be unreliable.

A nanowire-based liquid biopsy method using cerebrospinal fluid cell-free DNA for targeted management of leptomeningeal carcinomatosis

PURPOSE

This study aimed to evaluate whether genotyping cell free DNA (cfDNA) in the cerebrospinal fluid (CSF) may be helpful in managing leptomeningeal carcinomatosis (LMC) of EGFR-mutant non-small cell lung cancer (NSCLC).

METHODS

Patients with EGFR-mutant NSCLC who progressed as LMC after 3rd-generation tyrosine kinase inhibitors (EGFR-TKIs) were evaluated. A nanowire-based cfDNA assay was performed for genotyping cfDNA from the CSF and plasma. We focused on de novo EGFR C797S mutation and MET amplification, which are the most common mechanisms of resistance to 3rd-generation EGFR-TKIs.

RESULTS

Among 11 patients, five (45.5%) had progression only at the leptomeninges. The tumor-associated CSF-cfDNA was identified in eight (72.7%) patients, and plasma-cfDNA in six (54.5%) patients. In the CSF-cfDNA, EGFR C797S mutation and MET amplification were detected in four (36.3%) and two (18.2%) patients, respectively. Of four patients with the C797S-positive LMC, only one had concurrent CSF-T790M mutation. Three patients who had the C797S-positive LMC without CSF-T790M mutation, received 1st-2nd generation EGFR-TKIs and showed clinical benefits for 20.8, 17.8, and 8.8 weeks, respectively. Serial assessment with cfDNA in these patients demonstrated that the CSF levels of C797S mutation were decreased with radiological or neurological improvement but the plasma levels of T790M mutation were markedly increased before objective progression.

CONCLUSION

Genotyping CSF-cfDNA by the nanowire-based assay is feasible and effective in guiding the treatment of LMC in patients with EGFR-mutant NSCLC.

An Electrochemically Mediated Amine Regeneration Process with a Mixed Absorbent for Postcombustion CO2 Capture

Electrochemically mediated amine regeneration (EMAR) was recently developed to avoid the use of thermal means to release CO₂ captured from postcombustion flue gas in the benchmark amine process. To address concerns related to the high vapor pressure of ethylenediamine (EDA) as the primary amine used in EMAR, a mixture of EDA and aminoethylethanolamine (AEEA) was investigated. The properties of the mixed amine systems, including the absorption rates, electrolyte pH and conductivity, and CO₂ capacity, were evaluated in comparison with those of solely EDA. The mixed amine system had similar properties to that of EDA, indicating no significant changes would be necessary for the future implementation of the EMAR process with mixed amines as opposed to that with just EDA. The electrochemical performance of the mixed amines in terms of the cell voltage, gas desorption rate, electron utilization, and energetics was also investigated. A 50/50 mixture of EDA and AEEA displayed the lowest energetics: ∼10% lower than that of 100% EDA. With this mixture, a continuous EMAR process, in which the absorption column was connected to the electrochemical cell as the desorption stage, was tested over 100 h. The cell voltage was very stable and there was a steady gas output close to theoretical values. The desorbed gas was further analyzed and found to be 100% CO₂, confirming no evaporation of the amine. The mixed absorbent composition was also characterized using titration and nuclear magnetic resonance (NMR) spectroscopy, and the results showed no amine degradation. These findings that demonstrate a stable, low vapor pressure absorbent with improved energetics are promising and could be a guideline for the future development of EMAR for CO₂ capture from flue gas and other sources.

Ceritinib-Induced Organizing Pneumonia in Lung Cancer: A Retrospective Analysis

BACKGROUND

Ceritinib is a potent selective ALK inhibitor with a manageable safety profile. In anecdotal reports, ceritinib was associated with organizing pneumonia (OP), which could be confused with disease progression.

OBJECTIVE

We aimed to delineate the characteristics of OP that occurs during treatment with ceritinib, and evaluate its clinical implications.

PATIENTS AND METHODS

We retrospectively analyzed 44 lung cancer patients whose tumors harbored ALK or ROS1 fusions and who had received ceritinib. OP diagnosis was based on radiographic and clinical features. Four OP cases were pathologically confirmed.

RESULTS

Among 44 patients, 22 OP events occurred in 16 (36.4%) patients. The median time to the first event was 17.2 weeks (range 6.7-68.7 weeks). All events were grade 1 or 2. Radiographic features were categorized into four patterns: nodular (54.6%), consolidation (27.3%), parenchymal band (4.5%), and ground-glass opacity (GGO) (13.6%). OP improved in 20 events with drug interruption or corticosteroids. The median duration of OP was 11.3 weeks (range 2-24 weeks). Tumor response rate was 75% in OP-positive and 42.9% in OP-negative groups. The median progression-free survival was 16.7 months [95% confidence interval (CI) 10.1-not applicable (NA)] in OP-positive and 5.4 months (95% CI 3.6-8.4) in OP-negative patients (P = 0.004). The median overall survival was 46.2 months (95% CI 38.1-NA) in OP-positive and 10.5 months (95% CI 6.2-18.9) in OP-negative patients (P < 0.001).

CONCLUSION

OP occurs frequently during ceritinib treatment and must be distinguished from disease progression. OP could be reversible without fatal complications and its occurrence is associated with better survival outcomes.

Epigenetic profiling demarcates molecular subtypes of muscle-invasive bladder cancer

Muscle-invasive bladder cancer (MIBC) is a heterogeneous disease that often recurs despite aggressive treatment with neoadjuvant chemotherapy and (radical) cystectomy. Basal and luminal molecular subtypes have been identified that are linked to clinical characteristics and have differential sensitivities to chemotherapy. While it has been suggested that epigenetic mechanisms play a role in defining these subtypes, a thorough understanding of the biological mechanisms is lacking. This report details the first genome-wide analysis of histone methylation patterns of human primary bladder tumours by chromatin immunoprecipitations and next-generation sequencing (ChIP-seq). We profiled multiple histone marks: H3K27me3, a marker for repressed genes, and H3K4me1 and H3K4me3, which are indicators of active enhancers and active promoters. Integrated analysis of ChIP-seq data and RNA sequencing revealed that H3K4 mono-methylation demarcates MIBC subtypes, while no association was found for the other two histone modifications in relation to basal and luminal subtypes. Additionally, we identified differentially methylated H3K4me1 peaks in basal and luminal tumour samples, suggesting that active enhancers play a role in defining subtypes. Our study is the first analysis of histone modifications in primary bladder cancer tissue and provides an important resource for the bladder cancer community.

Improved Upper Limit on the Neutrino Mass from a Direct Kinematic Method by KATRIN

We report on the neutrino mass measurement result from the first four-week science run of the Karlsruhe Tritium Neutrino experiment KATRIN in spring 2019. Beta-decay electrons from a high-purity gaseous molecular tritium source are energy analyzed by a high-resolution MAC-E filter. A fit of the integrated electron spectrum over a narrow interval around the kinematic end point at 18.57 keV gives an effective neutrino mass square value of (-1.0_{-1.1}^{+0.9})  eV^{2}. From this, we derive an upper limit of 1.1 eV (90% confidence level) on the absolute mass scale of neutrinos. This value coincides with the KATRIN sensitivity. It improves upon previous mass limits from kinematic measurements by almost a factor of 2 and provides model-independent input to cosmological studies of structure formation.

P1740Clinical impact of symptom onset-to-balloon time and door-to-balloon time on 1-year adverse event in patients with ST-segment elevation myocardial infarction

Background and objectives

The impact of treatment delays to reperfusion on patient mortality after primary percutaneous coronary intervention (PCI) for ST elevation myocardial infarction (STEMI) is controversial. we evaluated the relation between the delay in the time to reperfusion during primary PCI and the 1-year clinical outcome of patients with STEMI treated by primary angioplasty.

Methods

The study enrolled 6,676 patients (age, 62.5±12.6 years; 26.5% female) with STEMI who underwent primary angioplasty onset between November 2005 and March 2012 from the KAMIR and KorMI Registry. The patients were divided into three groups according to the symptom onset-to-balloon (STB) time: group I, II, III (≤180 minutes, >180 ∼ ≤360 minutes, >360 minutes), and divided into three groups according to the door-to-balloon (DTB) time: group A, B, C (≤90 minutes, >90 ∼ ≤120 minutes, >120 minutes). The 1-year cardiac death and major adverse cardiac event (MACE) rates were compared among the three groups of time variables

Results

The cardiac death rate was 7.9% and MACE rate was 16.9% at one year follow-up. The 1-year cardiac death rate among STB time groups were significantly higher in group II (95% CI=1.05–2.60:p=0.030) and group III (95% CI=1.14–2.74:p=0.011), while that among DTB time groups were not significantly different based on a multivariate Cox proportional analysis, which was adjusted by age, sex, diabetes mellitus, hypertension, systolic blood pressure, left ventricular ejection fraction, peak level of CK-MB, anterior myocardial infarction. The 1-year MACE rate were not significantly different among STB time groups and DTB time group A, B, but was significantly higher in group C (95% CI=1.08–1.58:p=0.006).

Conclusions

These results suggest that, in patient with STEMI treated by primary angioplasty, STB time rather than DTB time was related 1-year clinical outcome especially cardiac death after adjustment for baseline characteristics. Therefore, all efforts should be made to shorten the total ischemic time in patients with acute myocardial infarction