Single-cell transcriptome analysis reveals subtype-specific clonal evolution and microenvironmental changes in liver metastasis of pancreatic adenocarcinoma and their clinical implications

BACKGROUND

Intratumoral heterogeneity (ITH) and tumor microenvironment (TME) of pancreatic ductal adenocarcinoma (PDAC) play important roles in tumor evolution and patient outcomes. However, the precise characterization of diverse cell populations and their crosstalk associated with PDAC progression and metastasis is still challenging.

METHODS

We performed single-cell RNA sequencing (scRNA-seq) of treatment-naïve primary PDAC samples with and without paired liver metastasis samples to understand the interplay between ITH and TME in the PDAC evolution and its clinical associations.

RESULTS

scRNA-seq analysis revealed that even a small proportion (22%) of basal-like malignant ductal cells could lead to poor chemotherapy response and patient survival and that epithelial-mesenchymal transition programs were largely subtype-specific. The clonal homogeneity significantly increased with more prevalent and pronounced copy number gains of oncogenes, such as KRAS and ETV1, and losses of tumor suppressor genes, such as SMAD2 and MAP2K4, along PDAC progression and metastasis. Moreover, diverse immune cell populations, including naïve SELLhi regulatory T cells (Tregs) and activated TIGIThi Tregs, contributed to shaping immunosuppressive TMEs of PDAC through cellular interactions with malignant ductal cells in PDAC evolution. Importantly, the proportion of basal-like ductal cells negatively correlated with that of immunoreactive cell populations, such as cytotoxic T cells, but positively correlated with that of immunosuppressive cell populations, such as Tregs.

CONCLUSION

We uncover that the proportion of basal-like subtype is a key determinant for chemotherapy response and patient outcome, and that PDAC clonally evolves with subtype-specific dosage changes of cancer-associated genes by forming immunosuppressive microenvironments in its progression and metastasis.

Establishment of a patient-specific avatar organoid model derived from endoscopic ultrasonography-guided fine needle biopsy for timely clinical application in pancreatic ductal adenocarcinoma

BACKGROUND AND AIMS

Pancreatic ductal adenocarcinoma (PDAC) has the worst survival rate among tumors. At the time of diagnosis, over 80 percent of PDACs are considered surgically unresectable, and there is an unmet need for treatment options in these inoperable PDACs. The study aimed to establish a patient-derived organoid (PDO) platform from endoscopic ultrasound-guided fine needle biopsy (EUS-FNB) collected at diagnosis and to determine its clinical applicability for the timely treatment of unresectable PDAC.

METHODS

Patients with suspected PDAC were prospectively enrolled at the Samsung Medical Center from 2015 to 2019. PDAC tissues were acquired by EUS-FNB to establish PDAC PDOs, which were comprehensively analyzed for histology, genomic sequencing, and high-throughput screening (HTS) drug sensitivity test.

RESULTS

PDAC PDOs were established with a success rate of 83.2% (94/113). It took approximately 3 weeks from acquiring minimal EUS-FNB specimens to generating sufficient PDAC PDOs for the simultaneous analysis of HTS drug sensitivity test and genomic analysis. The high concordance between PDAC tissues and matched PDOs was confirmed, and whole-exome sequencing revealed the increased detection of genetic alterations in PDOs, compared with in EUS-FNB tissues. The HTS drug sensitivity test showed the clinical correlation between the ex vivo PDO response and the actual chemotherapeutic response of the study patients in the real world (13 out of 15 cases). In addition, whole-transcriptome sequencing identified candidate genes associated with nab-paclitaxel resistance, such as ITGB7, ANPEP, and ST3GAL1.

CONCLUSIONS

This PDAC PDO platform allows several therapeutic drugs to be tested within a short time window and opens the possibility for timely personalized medicine as a "Patient Avatar Model" in clinical practice.

Best method to determine DNA G-quadruplex folding: The 1H-13C HSQC NMR experiment

NMR spectroscopy is the major method for G-quadruplex structure determination under physiologically relevant solution conditions. Unlike duplex B-DNA, in which all nucleotides adopt an anti glycosidic conformation, the core tetrad-guanines in a G-quadruplex can adopt anti or syn glycosidic conformation depending on the folding structure. An experimental method that can clearly and unambiguously determine syn and anti tetrad-Gs in a G-quadruplex is highly desirable and necessary. In the present study, we exploit the advantages of the 1H-13C HSQC experiment to determine tetrad-G's glycosidic conformation and thus folding topology of G-quadruplexes. We use several examples to demonstrate the clear and straightforward determination of the guanine glycosidic conformations and G-quadruplex folding structures. Moreover, 1H-13C HSQC data can readily identify adenine H2 resonances as well as determine unusual syn conformation in loop and flanking sequences, a challenging task by standard 2D NOESY.

Single-cell RNA Sequencing Reveals Novel Cellular Factors for Response to Immunosuppressive Therapy in Aplastic Anemia

Aplastic anemia (AA) is a lethal hematological disorder; however, its pathogenesis is not fully understood. Although immunosuppressive therapy (IST) is a major treatment option for AA, one-third of patients do not respond to IST and its resistance mechanism remains elusive. To understand AA pathogenesis and IST resistance, we performed single-cell RNA sequencing (scRNA-seq) of bone marrow (BM) from healthy controls and patients with AA at diagnosis. We found that CD34+ early-stage erythroid precursor cells and PROM1+ hematopoietic stem cells were significantly depleted in AA, which suggests that the depletion of CD34+ early-stage erythroid precursor cells and PROM1+ hematopoietic stem cells might be one of the major mechanisms for AA pathogenesis related with BM-cell hypoplasia. More importantly, we observed the significant enrichment of CD8+ T cells and T cell-activating intercellular interactions in IST responders, indicating the association between the expansion and activation of T cells and the positive response of IST in AA. Taken together, our findings represent a valuable resource offering novel insights into the cellular heterogeneity in the BM of AA and reveal potential biomarkers for IST, building the foundation for future precision therapies in AA.

Second Data Release from the European Pulsar Timing Array: Challenging the Ultralight Dark Matter Paradigm

Pulsar Timing Array experiments probe the presence of possible scalar or pseudoscalar ultralight dark matter particles through decade-long timing of an ensemble of galactic millisecond radio pulsars. With the second data release of the European Pulsar Timing Array, we focus on the most robust scenario, in which dark matter interacts only gravitationally with ordinary baryonic matter. Our results show that ultralight particles with masses 10^{-24.0}  eV≲m≲10^{-23.3}  eV cannot constitute 100% of the measured local dark matter density, but can have at most local density ρ≲0.3  GeV/cm^{3}.

Spectral noise and data reduction using a long short-term memory network for nonlinear ultrasonic modulation-based fatigue crack detection

This paper presents a spectral noise and data reduction technique based on long short-term memory (LSTM) network for nonlinear ultrasonic modulation-based fatigue crack detection. The amplitudes of the nonlinear modulation components created by a micro fatigue crack are often very small and masked by noise. In addition, the collection of large amounts of data is often undesirable owing to the limited power, data storage, and data transmission bandwidth of monitoring systems. To tackle the issues, an LSTM network was applied to ultrasonic signals to reduce the noise level and the amount of data. The proposed technique offers the following benefits: (1) spectral noise reduction using the LSTM network for ultrasonic signals and (2) data reduction without compromising the spectral density amplitude of the existing nonlinear modulation components. Finally, the performance evaluation was conducted using the data obtained from complex geometry and real structure under external noises, indicating that the proposed method can be applied to various structures.

RAMP: response-aware multi-task learning with contrastive regularization for cancer drug response prediction

The accurate prediction of cancer drug sensitivity according to the multiomics profiles of individual patients is crucial for precision cancer medicine. However, the development of prediction models has been challenged by the complex crosstalk of input features and the resistance-dominant drug response information contained in public databases. In this study, we propose a novel multidrug response prediction framework, response-aware multitask prediction (RAMP), via a Bayesian neural network and restrict it by soft-supervised contrastive regularization. To utilize network embedding vectors as representation learning features for heterogeneous networks, we harness response-aware negative sampling, which applies cell line-drug response information to the training of network embeddings. RAMP overcomes the prediction accuracy limitation induced by the imbalance of trained response data based on the comprehensive selection and utilization of drug response features. When trained on the Genomics of Drug Sensitivity in Cancer dataset, RAMP achieved an area under the receiver operating characteristic curve > 89%, an area under the precision-recall curve > 59% and an $\textrm{F}_1$ score > 52% and outperformed previously developed methods on both balanced and imbalanced datasets. Furthermore, RAMP predicted many missing drug responses that were not included in the public databases. Our results showed that RAMP will be suitable for the high-throughput prediction of cancer drug sensitivity and will be useful for guiding cancer drug selection processes. The Python implementation for RAMP is available at https://github.com/hvcl/RAMP.

Cellular plasticity and immune microenvironment of malignant pleural effusion are associated with EGFR-TKI resistance in non–small-cell lung carcinoma

Malignant pleural effusion (MPE) is a complication of lung cancer that can be used as an alternative method for tissue sampling because it is generally simple and minimally invasive. Our study evaluated the diagnostic potential of non–small-cell lung carcinoma (NSCLC)-associated MPE in terms of understanding tumor heterogeneity and identifying response factors for EGFR tyrosine kinase inhibitor (TKI) therapy. We performed a single-cell RNA sequencing analysis of 31,743 cells isolated from the MPEs of 9 patients with NSCLC (5 resistant and 4 sensitive to EGFR TKI) with EGFR mutations. Interestingly, lung epithelial precursor-like cells with upregulated GNB2L1 and CAV1 expression were enriched in the EGFR TKI-resistant group. Moreover, GZMK upregulated transitional effector T cells, and plasmacytoid dendritic cells were significantly enriched in the EGFR TKI-resistant patients. Our results suggest that cellular plasticity and immunosuppressive microenvironment in MPEs are potentially associated with the TKI response of patients with EGFR-mutated NSCLC.

•

ScRNA-seq reveals associations between cellular plasticity and EGFR-TKI response

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Lung epithelial progenitor-like cells are abundant in the TKI-resistant group

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HLA-II gene expression are upregulated in the epithelial cells of TKI-sensitive group

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Immunosuppressive TME was associated with the TKI resistance in NSCLC

Anticoagulant treatment patterns and thromboembolic events by tumor type among patients with VTE and cancer

Background

Patients with venous thromboembolism (VTE) and cancer are at higher risk of adverse outcomes (mortality, recurrent VTE etc.) versus patients with cancer alone; as such, clinical guidelines recommend anticoagulant treatment for patients with VTE and cancer. There is limited real world data about how anticoagulant treatment and thromboembolic outcomes differ by tumor type in patients with VTE and cancer. Understanding such differences may help identify appropriate anticoagulant treatment for specific tumor types.

Purpose

To describe anticoagulant treatment patterns and thromboembolic outcomes by tumor type among patients with VTE and cancer.

Methods

Patients with VTE and cancer age ≥65 were identified from the Surveillance, Epidemiology and End Results (SEER) Medicare database from 1/1/2014–12/31/2019. Patients were required to be enrolled for ≥6-months prior to their first VTE diagnosis (index) and without evidence of other conditions requiring anticoagulant (i.e., atrial fibrillation) prior to index. Cancer status and tumor type were identified from SEER or Medicare database in the 6-months prior through 30-days post VTE. This analysis focused on the following specific tumor types: high risk (brain, pancreas, and stomach) and common tumor types (breast, and prostate). Patients treated with an anticoagulant within 30-days after index were included in the final population. Major bleeding (MB) and recurrent VTE events were measured during follow-up (index date through earliest of disenrollment, death or 12/31/2019).

Results

A total of 3,546 anticoagulated patients with VTE and cancer of interest met all study criteria (breast [n=1,197], prostate [n=849], pancreatic [n=995], brain [n=248] and stomach [n=257] cancer). Patient mean age ranged from 73 (brain) to 76 (stomach) at index. Anticoagulant treatment patterns varied by tumor type (Figure 1). LMWH was more likely to be used in the 3 high risk tumor types whereas apixaban and rivaroxaban were more likely to be used in the 2 common tumor types. The incidence rate of recurrent VTE and major bleeding events also varied among different tumor types: ranging from 1.4 (breast) to 6.4 (pancreatic) per 100 person-years for recurrent VTE and from 4.3 (prostate) to 15.1 (pancreatic) per 100 person-years for major bleeding (Figure 2).

Conclusion

There are notable variations in anticoagulant treatment patters and the risks of major bleeding and recurrent VTE events by tumor type among patients with VTE and cancer. Further research is needed to understand which anticoagulant treatment option is more appropriate for VTE patients with specific tumor type.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): Pfizer Inc. and Bristol Myers Squibb Company

Volumetric Measurement of Relative CBV Using T1-Perfusion-Weighted MRI with High Temporal Resolution Compared with Traditional T2*-Perfusion-Weighted MRI in Postoperative Patients with High-Grade Gliomas

BACKGROUND AND PURPOSE

T1-PWI with high temporal resolution may provide a reliable relative CBV value as a valid alternative to T2*-PWI under increased susceptibility. The purpose of this study was to assess the technical and clinical performance of T1-relative CBV in patients with postoperative high-grade gliomas.

MATERIALS AND METHODS

Forty-five MRIs of 34 patients with proved high-grade gliomas were included. In all MRIs, T1- and T2*-PWIs were both acquired and processed semiautomatically to generate relative CBV maps using a released commercial software. Lesion masks were overlaid on the relative CBV maps, followed by a histogram of the whole VOI. The intraclass correlation coefficient and Bland-Altman plots were used for quantitative and qualitative comparisons. Signal loss from both methods was compared using the Wilcoxon signed-rank test of zero voxel percentage. The MRIs were divided into a progression group (n = 20) and a nonprogression group (n = 14) for receiver operating characteristic curve analysis.

RESULTS

Fair intertechnique consistency was observed between the 90th percentiles of the T1- and T2*-relative CBV values (intraclass correlation coefficient = 0.558, P < .001). T2*-PWI revealed a significantly higher percentage of near-zero voxels than T1-PWI (17.7% versus 3.1%, P < .001). There was no statistically significant difference between the area under the curve of T1- and T2*-relative CBV (0.811 versus 0.793, P = .835). T1-relative CBV showed 100% sensitivity and 57.1% specificity for the detection of progressive lesions.

CONCLUSIONS

T1-relative CBV demonstrated exquisite diagnostic performance for detecting progressive lesions in postoperative patients with high-grade gliomas, suggesting the potential role of T1-PWI as a valid alternative to the traditional T2*-PWI.

Attenuation of intrinsic aging of the skin via elimination of senescent dermal fibroblasts with senolytic drugs

BACKGROUND

Skin aging is caused by numerous factors that result in structural and functional changes in cutaneous components. Research has shown that senescent cells are known to accumulate in skin aging, however, the role of senescent cells in skin aging has not been defined.

OBJECTIVES

To elucidate the role of senescent cell in skin aging, we evaluated the effect of known senolytic drugs on senescent dermal fibroblasts.

METHODS

Primary human dermal fibroblasts (HDFs) were induced to senescence by long-term passaging, UV irradiation, and H2O2 treatment. Cell viability was measured after treatment of ABT-263 and ABT-737 on HDFs. Young and aged hairless mice were intradermally injected with drugs or vehicle on the dorsal skin for 10 days. Skin specimens were obtained and reverse-transcription quantitative PCR, western blotting, and histological analysis were performed.

RESULTS

We found that ABT-263 and ABT-737 induced selective clearance of senescent dermal fibroblasts, regardless of the method of senescence induction. Aged mouse skin treated with ABT-263 or ABT-737 showed increased collagen density, epidermal thickness, and proliferation of keratinocytes, as well as decreased senescence-associated secretory phenotypes, such as MMP-1 and IL-6.

CONCLUSIONS

Taken together, our results indicate that selective clearance of senescent skin cells can attenuate and improve skin aging phenotypes and that senolytic drugs may be of potential use as new therapeutic agents for treating aging of the skin.

Drug-likeness scoring based on unsupervised learning

Drug-likeness prediction is important for the virtual screening of drug candidates. It is challenging because the drug-likeness is presumably associated with the whole set of necessary properties to pass through clinical trials, and thus no definite data for regression is available. Recently, binary classification models based on graph neural networks have been proposed but with strong dependency of their performances on the choice of the negative set for training. Here we propose a novel unsupervised learning model that requires only known drugs for training. We adopted a language model based on a recurrent neural network for unsupervised learning. It showed relatively consistent performance across different datasets, unlike such classification models. In addition, the unsupervised learning model provides drug-likeness scores that well separate distributions with increasing mean values in the order of datasets composed of molecules at a later step in a drug development process, whereas the classification model predicted a polarized distribution with two extreme values for all datasets presumably due to the overconfident prediction for unseen data. Thus, this new concept offers a pragmatic tool for drug-likeness scoring and further can be applied to other biochemical applications.

Intraindividual Comparison between the Contrast-Enhanced Golden-Angle Radial Sparse Parallel Sequence and the Conventional Fat-Suppressed Contrast-Enhanced T1-Weighted Spin-Echo Sequence for Head and Neck MRI

BACKGROUND AND PURPOSE

The golden-angle radial sparse parallel-volumetric interpolated breath-hold (GRASP-VIBE) sequence is a recently introduced imaging technique with high resolution. This study compared the image quality between conventional fat-suppressed T1-weighted TSE and GRASP-VIBE after gadolinium enhancement in the head and neck region.

MATERIALS AND METHODS

Data from 65 patients with clinical indications for head and neck MR imaging between September 2020 and January 2021 were retrospectively reviewed. Two radiologists assessed the overall image quality, overall artifacts, and image conspicuities in the oropharynx, hypopharynx, and cervical lymph nodes according to 5-point scores (best score: 5). Interobserver agreement was assessed using weighted κ statistics. The SNR and contrast-to-noise ratio were calculated and compared between the 2 sequences using a paired Wilcoxon signed rank test.

RESULTS

The analysis included 52 patients (mean age, 60 [SD, 14 ] years; male, 71.2% [37/52]) who were mostly diagnosed with head and neck malignancies (94.3% [50/52]). κ statistics ranged from slight agreement in cervical lymph node conspicuity (κ = 0.18) to substantial agreement in oropharyngeal mucosal conspicuity (κ = 0.80) (κ range, 0.18-0.80). Moreover, GRASP-VIBE demonstrated significantly higher mean scores in overall image quality (4.68 [SD, 0.41] versus 3.66 [SD, 0.73]), artifacts (4.47 [SD, 0.48] versus 3.58 [SD, 0.71]), oropharyngeal mucosal conspicuity (4.85 [SD, 0.41] versus 4.11 [SD, 0.79]), hypopharyngeal mucosal conspicuity (4.84 [SD, 0.34] versus 3.58 [SD, 0.81]), and cervical lymph node conspicuity (4.79 [SD, 0.32] versus 4.08 [SD, 0.64]) than fat-suppressed T1-weighted TSE (all, P < .001). Furthermore, GRASP-VIBE demonstrated a higher SNR (22.8 [SD, 11.5] versus 11.3 [SD, 5.6], P < .001) and contrast-to-noise ratio (4.7 [SD, 5.4] versus 2.3 [SD, 2.7], P = .059) than fat-suppressed T1-weighted TSE.

CONCLUSIONS

GRASP-VIBE provided better image quality with fewer artifacts than conventional fat-suppressed T1-weighted TSE for the head and neck regions.

Microbiome of Saliva and Plaque in Children According to Age and Dental Caries Experience

Dental caries are one of the chronic diseases caused by organic acids made from oral microbes. However, there was a lack of knowledge about the oral microbiome of Korean children. The aim of this study was to analyze the metagenome data of the oral microbiome obtained from Korean children and to discover bacteria highly related to dental caries with machine learning models. Saliva and plaque samples from 120 Korean children aged below 12 years were collected. Bacterial composition was identified using Illumina HiSeq sequencing based on the V3–V4 hypervariable region of the 16S rRNA gene. Ten major genera accounted for approximately 70% of the samples on average, including Streptococcus, Neisseria, Corynebacterium, and Fusobacterium. Differential abundant analyses revealed that Scardovia wiggsiae and Leptotrichia wadei were enriched in the caries samples, while Neisseria oralis was abundant in the non-caries samples of children aged below 6 years. The caries and non-caries samples of children aged 6–12 years were enriched in Streptococcus mutans and Corynebacterium durum, respectively. The machine learning models based on these differentially enriched taxa showed accuracies of up to 83%. These results confirmed significant alterations in the oral microbiome according to dental caries and age, and these differences can be used as diagnostic biomarkers.

Single-cell RNA sequencing reveals distinct cellular factors for response to immunotherapy targeting CD73 and PD-1 in colorectal cancer

BACKGROUND

Although cancer immunotherapy is one of the most effective advanced-stage cancer therapies, no clinically approved cancer immunotherapies currently exist for colorectal cancer (CRC). Recently, programmed cell death protein 1 (PD-1) blockade has exhibited clinical benefits according to ongoing clinical trials. However, ongoing clinical trials for cancer immunotherapies are focused on PD-1 signaling inhibitors such as pembrolizumab, nivolumab, and atezolizumab. In this study, we focused on revealing the distinct response mechanism for the potent CD73 ectoenzyme selective inhibitor AB680 as a promising drug candidate that functions by blocking tumorigenic ATP/adenosine signaling in comparison to current therapeutics that block PD-1 to assess the value of this drug as a novel immunotherapy for CRC.

METHODS

To understand the distinct mechanism of AB680 in comparison to that of a neutralizing antibody against murine PD-1 used as a PD-1 blocker, we performed single-cell RNA sequencing of CD45⁺ tumor-infiltrating lymphocytes from untreated controls (n=3) and from AB680-treated (n=3) and PD-1-blockade-treated murine CRC in vivo models. We also used flow cytometry, Azoxymethane (AOM)/Dextran Sulfate Sodium (DSS) models, and in vitro functional assays to validate our new findings.

RESULTS

We initially observed that the expressions of Nt5e (a gene for CD73) and Entpd1 (a gene for CD39) affect T cell receptor (TCR) diversity and transcriptional profiles of T cells, thus suggesting their critical roles in T cell exhaustion within tumor. Importantly, PD-1 blockade significantly increased the TCR diversity of Entpd1-negative T cells and Pdcd1-positive T cells. Additionally, we determined that AB680 improved the anticancer functions of immunosuppressed cells such as Treg and exhausted T cells, while the PD-1 blocker quantitatively reduced Malat1^high Treg and M2 macrophages. We also verified that PD-1 blockade induced Treg depletion in AOM/DSS CRC in vivo models, and we confirmed that AB680 treatment caused increased activation of CD8⁺ T cells using an in vitro T cell assay.

CONCLUSIONS

The intratumoral immunomodulation of CD73 inhibition is distinct from PD-1 inhibition and exhibits potential as a novel anticancer immunotherapy for CRC, possibly through a synergistic effect when combined with PD-1 blocker treatments. This study may contribute to the ongoing development of anticancer immunotherapies targeting refractory CRC.

Loss of BubR1 acetylation provokes replication stress and leads to complex chromosomal rearrangements

Accurate chromosomal segregation during mitosis is regulated by the spindle assembly checkpoint (SAC). SAC failure results in aneuploidy, a hallmark of cancer. However, many studies have suggested that aneuploidy alone is not oncogenic. We have reported that BubR1 acetylation deficiency in mice (K243R/+) caused spontaneous tumorigenesis via weakened SAC signaling and unstable chromosome-spindle attachment, resulting in massive chromosomal mis-segregation. In addition to aneuploidy, cells derived from K243R/+ mice exhibited moderate genetic instability and chromosomal translocation. Here, we investigated how the loss of BubR1 acetylation led to genetic instability and chromosomal rearrangement. To rescue all chromosomal abnormalities generated by the loss of BubR1 acetylation during development, K243R/+ mice were crossed with p53-deficient mice. Genome-wide sequencing and spectral karyotyping of tumors derived from these double-mutant mice revealed that BubR1 acetylation deficiency was associated with complex chromosomal rearrangements, including Robertsonian-like whole-arm translocations. By analyzing the telomeres and centromeres in metaphase chromosome spreads, we found that BubR1 acetylation deficiency increased the collapse of stalled replication forks, commonly referred to as replication stress, and led to DNA damage and chromosomal rearrangements. BubR1 mutations that are critical in interacting with PCAF acetyltransferase and acetylating K250, L249F and A251P, were found from human cancers. Furthermore, a subset of human cancer cells exhibiting whole-arm translocation also displayed defects in BubR1 acetylation, supporting that defects in BubR1 acetylation in mitosis contributes to tumorigenesis. Collectively, loss of BubR1 acetylation provokes replication stress, particularly at the telomeres, leading to genetic instability and chromosomal rearrangement.

Determination of in vitro dry matter, protein, and fiber digestibility and fermentability of novel corn coproducts for swine and ruminants

New processes are being used in some dry-grind ethanol plants in the United States and Brazil to improve ethanol yield and efficiency of production while also providing nutritionally enhanced corn coproducts compared with conventional corn distillers dried grains with solubles (DDGS). The objectives of this study were to determine the chemical composition and in vitro digestibility of 5 conventional corn DDGS sources and 10 emerging novel corn coproducts for swine and ruminants, and compare coproducts produced using similar processes in the United States and Brazil. Chemical composition, on a dry matter (DM) basis, among the 15 coproducts ranged from 18.5% to 54.7% for crude protein (CP), 12.3% to 51.4% for neutral detergent fiber (NDF), 1.6% to 8.6% for acid detergent fiber, 4.7% to 12.3% for ether extract, and 1.6% to 8.6% for ash. For swine, in vitro hydrolysis of DM and CP were greater (P < 0.01) for the three U.S. corn DDGS sources compared with the two Brazilian corn DDGS sources, but in vitro fermentability of DM was comparable (P > 0.05) among all sources except one U.S. DDGS source that had less fermentable DM. High-protein and yeast dried distillers grains (Ultramax, UM; StillPro, SP) coproducts also had comparable (P > 0.05) DM fermentability for swine, but UM coproducts had greater (P < 0.01) DM and CP hydrolysis compared with SP. High-protein distillers dried grains (HP-DDG) from Brazil had greater (P < 0.01) DM and CP hydrolysis, but less (P < 0.01) DM fermentability for swine than HP-DDG produced in the United States, using the same process. For ruminants, total DM digestibility was greater (P < 0.01) in conventional DDGS sources from the United States compared with the two DDGS sources from Brazil. Total protein digestibility for ruminants was comparable and above 81% for all coproducts except for a DDGS source from Brazil, a HP-DDG source from the United States, and a UM sample. Interestingly, the corn fiber + solubles coproduct had not only relatively high digestibility of NDF (67.9%), DM (91.6%), and total CP (81.9%) for ruminants, but it also had relatively high total tract digestibility of DM (86.2%) and CP (69.9%) for swine. These results suggest that nutrient digestibility of conventional DDGS sources produced in the United States appear to be greater than corn Brazilian DDGS sources, but new process technologies being implemented in ethanol and coproduct production in both countries can enhance the nutritional value of corn coproducts for both swine and ruminants.

Prediction of Chronic Periodontitis Severity Using Machine Learning Models Based On Salivary Bacterial Copy Number

Periodontitis is a widespread chronic inflammatory disease caused by interactions between periodontal bacteria and homeostasis in the host. We aimed to investigate the performance and reliability of machine learning models in predicting the severity of chronic periodontitis. Mouthwash samples from 692 subjects (144 healthy controls and 548 generalized chronic periodontitis patients) were collected, the genomic DNA was isolated, and the copy numbers of nine pathogens were measured using multiplex qPCR. The nine pathogens are as follows: Porphyromonas gingivalis (Pg), Tannerella forsythia (Tf), Treponema denticola (Td), Prevotella intermedia (Pi), Fusobacterium nucleatum (Fn), Campylobacter rectus (Cr), Aggregatibacter actinomycetemcomitans (Aa), Peptostreptococcus anaerobius (Pa), and Eikenella corrodens (Ec). By adding the species one by one in order of high accuracy to find the optimal combination of input features, we developed an algorithm that predicts the severity of periodontitis using four machine learning techniques. The accuracy was the highest when the models classified “healthy” and “moderate or severe” periodontitis (H vs. M-S, average accuracy of four models: 0.93, AUC = 0.96, sensitivity of 0.96, specificity of 0.81, and diagnostic odds ratio = 112.75). One or two red complex pathogens were used in three models to distinguish slight chronic periodontitis patients from healthy controls (average accuracy of 0.78, AUC = 0.82, sensitivity of 0.71, and specificity of 0.84, diagnostic odds ratio = 12.85). Although the overall accuracy was slightly reduced, the models showed reliability in predicting the severity of chronic periodontitis from 45 newly obtained samples. Our results suggest that a well-designed combination of salivary bacteria can be used as a biomarker for classifying between a periodontally healthy group and a chronic periodontitis group.

Treatment strategy for papillary renal cell carcinoma type 2: a case series of seven patients treated based on next generation sequencing data

Background

Papillary renal cell carcinoma type 2 (PRCC2) is refractory to systemic treatment and has a dismal prognosis. Previous studies showed that genetic alterations in PRCC2 were heterogeneous regardless of germline or somatic mutations. In this study, we aimed to perform precision treatment of PRCC2 based on genetic information.

Methods

We performed exome and genome sequencing of tumor tissues and matched normal samples. Based on sequencing data, we treated patients with metastatic PRCC2 using precision oncology.

Results

Four patients underwent curative surgery of PRCC2 and three patients had metastatic PRCC2. All PRCC2 heterogeneously harbored own driver mutations. Two out of the three patients with metastatic disease had fumarate hydratase (FH) germline mutations. One patient with a germline FH mutation was diagnosed with hereditary leiomyomatosis RCC. He was treated with bevacizumab and erlotinib combination and showed a durable response. The other metastatic PRCC2 patient harboring a germline FH mutation had an additional somatic FH mutation and was durably controlled with pazopanib. Other metastatic PRCC2 patient with somatic PBRM1 and SETD2 mutations had over 5 years of overall survival with axitinib treatment.

Conclusions

We performed precision systemic treatment based on genetic information. Genome sequencing could help identify candidates for targeted therapy in PRCC2, a genetically heterogeneous disease.

Prediction of Human Papillomavirus Status and Overall Survival in Patients with Untreated Oropharyngeal Squamous Cell Carcinoma: Development and Validation of CT-Based Radiomics

BACKGROUND AND PURPOSE

Human papillomavirus is a prognostic marker for oropharyngeal squamous cell carcinoma. We aimed to determine the value of CT-based radiomics for predicting the human papillomavirus status and overall survival in patients with oropharyngeal squamous cell carcinoma.

MATERIALS AND METHODS

Eighty-six patients with oropharyngeal squamous cell carcinoma were retrospectively collected and grouped into training (n = 61) and test (n = 25) sets. For human papillomavirus status and overall survival prediction, radiomics features were selected via a random forest-based algorithm and Cox regression analysis, respectively. Relevant features were used to build multivariate Cox regression models and calculate the radiomics score. Human papillomavirus status and overall survival prediction were assessed via the area under the curve and concordance index, respectively. The models were validated in the test and The Cancer Imaging Archive cohorts (n = 78).

RESULTS

For prediction of human papillomavirus status, radiomics features yielded areas under the curve of 0.865, 0.747, and 0.834 in the training, test, and validation sets, respectively. In the univariate Cox regression, the human papillomavirus status (positive: hazard ratio, 0.257; 95% CI, 0.09-0.7; P = .008), T-stage (≥III: hazard ratio, 3.66; 95% CI, 1.34-9.99; P = .011), and radiomics score (high-risk: hazard ratio, 3.72; 95% CI, 1.21-11.46; P = .022) were associated with overall survival. The addition of the radiomics score to the clinical Cox model increased the concordance index from 0.702 to 0.733 (P = .01). Validation yielded concordance indices of 0.866 and 0.720.

CONCLUSIONS

CT-based radiomics may be useful in predicting human papillomavirus status and overall survival in patients with oropharyngeal squamous cell carcinoma.

0047 The Change in Melatonin Rhythm Depending on Dementia Severity in Alzheimer’s Disease (AD) Patients

Introduction

In Alzheimer’s disease (AD), both sleep and circadian dysfunctions are commonly reported and these are associated with neurodegenerative change. Actually, it has been reported that changes in circadian rhythms in AD were apparently discrete from those seen in normal aging. Previous studies reported the delayed phase in the activity or core body temperature rhythms in severe AD patients compared to normal controls. However, it is unknown whether similar changes in melatonin rhythms occur in AD patients who were not severely demented. We aimed to compare melatonin rhythms depending on dementia severity in mild and moderate AD patients.

Methods

We recruited AD patients of mild or moderate degree who had the Pittsburgh Sleep Quality Index (PSQI) score of 5 or greater and/or complained insomnia symptoms more than 3 times a week for a month. The patients were classified according to their Clinical Dementia Rating (CDR) score into 3 groups (CDR=0.5, 1, 2). The dim light melatonin onset (DLMO) was determined from seven hourly saliva samples obtained in the laboratory prior to sleep onset measured by actigraphy. The phase angle between the DLMO and sleep onset (PA-SO), and that between the DLMO and midsleep time (PA-MST) were calculated. Each group included 13, 13 and 6 AD patients with the CDR score of 0.5, 1 and 2, respectively. The DLMO and PA were compared among the 3 groups, and correlation analyses of the DLMO and PA with the MMSE in the Korean version of CERAD Packet (MMSE-KC) scores were done in total patients.

Results

There was no significant difference in the DLMO and PA between the 3 groups. The MMSE-KC score was positively correlated with the DLMO and negatively correlated with the PA-MST.

Conclusion

There were no changes in melatonin rhythms according to dementia severity in mild and moderate AD patients with sleep complaints. However, our study showed that earlier melatonin phase was associated with more impaired cognitive function.

Support

Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning (2017R1A2B4003493)

Korean Genome Project: 1094 Korean personal genomes with clinical information

We present the initial phase of the Korean Genome Project (Korea1K), including 1094 whole genomes (sequenced at an average depth of 31×), along with data of 79 quantitative clinical traits. We identified 39 million single-nucleotide variants and indels of which half were singleton or doubleton and detected Korean-specific patterns based on several types of genomic variations. A genome-wide association study illustrated the power of whole-genome sequences for analyzing clinical traits, identifying nine more significant candidate alleles than previously reported from the same linkage disequilibrium blocks. Also, Korea1K, as a reference, showed better imputation accuracy for Koreans than the 1KGP panel. As proof of utility, germline variants in cancer samples could be filtered out more effectively when the Korea1K variome was used as a panel of normals compared to non-Korean variome sets. Overall, this study shows that Korea1K can be a useful genotypic and phenotypic resource for clinical and ethnogenetic studies.

Abstract A13: Implication of immune cell composition in biopsy specimens of triple-negative breast cancer for responsiveness to neoadjuvant chemotherapy

Triple-negative breast cancer (TNBC) is a subtype of breast carcinoma that has little or no expression of hormone receptors and human epidermal growth factor receptor 2 (HER2). Most patients with TNBC receive chemotherapy, since TNBC is an aggressive type of cancer and lacks targeted therapy. Recently, possible effectiveness of immunotherapy for TNBC has been identified. Here, we aim to elucidate predictive power of immune cell composition and immune-related gene expression in neoadjuvant chemotherapy (NAC) setting of TNBC. Expression profiles of 579 immune-related genes were examined in biopsy tissues obtained from 55 patients with primary TNBC treated with NAC (anthracycline, cyclophosphamide, and docetaxel) using NanoString nCounter GX Human Immunology Panel. Then, the composition of 22 subtypes of immune cells was estimated from the gene expression profiles using CIBERSORT. The optimal combination of immune cell subsets as well as immune-related genes to predict pathologic complete response (pCR) and clinical outcome (death) was inferred by univariate receiver operating characteristic (ROC) curve and subsequent multivariate ROC curve analyses. Among the 55 patients, 17 cases showed pCR whereas the others showed non-pCR. P values were provided by CIBERSORT for all the specimens but two were less than 0.05. Immune cell composition varied by patients, and only the proportion of resting dendritic cells was significantly different between the two groups, pCR vs. non-pCR (p=0.038). In our univariate ROC curve analysis, follicular helper T cell (area under the curve, AUC 0.646) and monocyte (AUC 0.625) were the most relevant immune cell subtypes to patients’ clinical outcome and pCR, respectively. Multivariate ROC curve-based exploratory analysis identified the highest AUC (0.647) for the prediction of clinical outcome from the combination of follicular helper T cell and naive B cell proportions. The combination of 18 out of 22 immune cell subsets showed highest AUC (0.745) for pCR. In terms of immune-related genes, univariate ROC curve analysis identified TNFSF13B (AUC 0.756) and MAPK1 (AUC 0.718) as the most relevant genes to patients’ survival and pCR, respectively. From our multivariate ROC curve analysis, the combination of 113 genes including RUNX1 had highest AUC (0.915) for survival outcome prediction. For the prediction of pCR, the combination of 107 genes including MAPK1, NFKB1, and TRAF1 showed highest AUC (0.946). Forty-one genes were overlapped between the two sets of genes. Our study showed not only immune-related gene expression but also composition of immune cell subtypes could predict responsiveness to neoadjuvant chemotherapy in biopsy specimens of TNBC, though its predictive power seemed to be lower than that of combination of gene expression. Further analysis of immune-related gene expression in each immune cell type might improve our understanding of immune microenvironment and provide higher predictive values in clinical response to chemotherapy in TNBC patients.

Citation Format: In Ah Park, Jinho Jang, Hyoung-oh Jeong, Gyungyub Gong, Semin Lee, Hee Jin Lee. Implication of immune cell composition in biopsy specimens of triple-negative breast cancer for responsiveness to neoadjuvant chemotherapy [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr A13.

Androgen-induced expression of DRP1 regulates mitochondrial metabolic reprogramming in prostate cancer

Androgen receptor (AR) signaling plays a central role in metabolic reprogramming for prostate cancer (PCa) growth and progression. Mitochondria are metabolic powerhouses of the cell and support several hallmarks of cancer. However, the molecular links between AR signaling and the mitochondria that support the metabolic demands of PCa cells are poorly understood. Here, we demonstrate increased levels of dynamin-related protein 1 (DRP1), a mitochondrial fission mediator, in androgen-sensitive and castration-resistant AR-driven PCa. AR signaling upregulates DRP1 to form the VDAC-MPC2 complex, increases pyruvate transport into mitochondria, and supports mitochondrial metabolism, including oxidative phosphorylation and lipogenesis. DRP1 inhibition activates the cellular metabolic stress response, which involves AMPK phosphorylation, induction of autophagy, and the ER unfolded protein response, and attenuates androgen-induced proliferation. Additionally, DRP1 expression facilitates PCa cell survival under diverse metabolic stress conditions, including hypoxia and oxidative stress. Moreover, we found that increased DRP1 expression was indicative of poor prognosis in patients with castration-resistant PCa. Collectively, our findings link androgen signaling-mediated mitochondrial dynamics to metabolic reprogramming; moreover, they have important implications for understanding PCa progression.

Image Quality of Low-Dose Cerebral Angiography and Effectiveness of Clinical Implementation on Diagnostic and Neurointerventional Procedures for Intracranial Aneurysms

BACKGROUND AND PURPOSE

Awareness of the potential for exposure to high doses of radiation from interventional radiologic procedures has increased. The purpose of this study was to evaluate image quality and dose reduction of low-dose cerebral angiography during diagnostic and therapeutic procedures for intracranial aneurysms.

MATERIALS AND METHODS

A retrospective review of 1137 prospectively collected patients between January 2012 and June 2014 was performed. Beginning in April 2013, a dose-reduction strategy was implemented. Subjective image-quality assessment of 506 standard and 540 low-dose cerebral angiography images was performed by 2 neuroradiologists using a 5-point scale and was tested using noninferiority statistics. Radiation dose-area product and air kerma of 1046 diagnostic and 317 therapeutic procedures for intracranial aneurysms were analyzed and compared between groups before (group 1) and after (group 2) clinical implementation of a dose-reduction strategy.

RESULTS

The image quality of the low-dose cerebral angiography was not inferior on the basis of results from the 2 readers. For diagnostic cerebral angiography, the mean dose-area product and air kerma were 140.8 Gy×cm² and 1.0 Gy, respectively, in group 1 and 82.0 Gy×cm² and 0.6 Gy in group 2 (P < .001, P < .001). For the neurointerventional procedure, the mean dose-area product and air kerma were 246.0 Gy×cm² and 3.7 Gy, respectively, in group 1 and 169.8 Gy×cm² and 3.3 Gy in group 2 (P < .001, P = .291).

CONCLUSIONS

With low-dose cerebral angiography, image quality was maintained, and implementation of dose-reduction strategies reduced radiation doses in patients undergoing diagnostic and neurointerventional procedures for intracranial aneurysms.

Effect of experimental infections of various Tembusu virus strains isolated from geese, ducks and chickens on ducklings

In order to compare the pathogenicity of different Tembusu virus (TMUV) strains from geese, ducks and chickens, 56 5-day-old Cherry Valley ducklings which were divided into 7 groups and infected intramuscularly with 7´105 PFU/ml per duck of six challenge virus stocks. The clinical signs, weight gain, mortality, macroscopic and microscopic lesions, virus loads in sera of 1, 3, 5, 7, 11 and 14 dpi and serum antibody titers were examined. The results showed that these viruses could make the young ducks sick, but the clinical signs differed with the different species-original strains. All the experimental groups lose markedly in weight gain compared to the control, but there were no obvious distinctions in weight gains, as well as macroscopic and microscopic lesions of dead ducks between the infected groups. However, the groups of waterfowl-derived strains (from geese and ducks) showed more serious clinical signs and higher relative expressions of virus loads in sera than those from chicken-derived. The mortality of waterfowl groups was 37.5%, and the greatest mortality of chicken groups was 12.5%. The serum antibodies of the geese-species group JS804 appeared earlier and were higher in the titers than others. Taken toghter, the pathogenicity of waterfowl-derived TMUV was more serious than chicken-derived TMUV and JS804 could be chosen as one TMUV vaccine strain to protect from the infection.

Potential involvement of Drosophila flightless-1 in carbohydrate metabolism

A previous study of ours indicated that Drosophila flightless-1 controls lipid metabolism, and that there is an accumulation of triglycerides in flightless-1 (fliI)-mutant flies, where this mutation triggers metabolic stress and an obesity phenotype. Here, with the aim of characterizing the function of FliI in metabolism, we analyzed the levels of gene expression and metabolites in fliI-mutant flies. The levels of enzymes related to glycolysis, lipogenesis, and the pentose phosphate pathway increased in fliI mutants; this result is consistent with the levels of metabolites corresponding to a metabolic pathway. Moreover, high-throughput RNA sequencing revealed that Drosophila FliI regulates the expression of genes related to biological processes such as chromosome organization, carbohydrate metabolism, and immune reactions. These results showed that Drosophila FliI regulates the expression of metabolic genes, and that dysregulation of the transcription controlled by FliI gives rise to metabolic stress and problems in the development and physiology of Drosophila.

Comparative study of precise measurements of natural radionuclides and radiation dose using in-situ and laboratory γ-ray spectroscopy techniques

In this study, in-situ and laboratory γ-ray spectroscopy techniques were compared to evaluate the activity concentration of natural radionuclides in soil. The activity concentrations of 238U (226Ra), 232Th, and 40K in the soil in 11 sites were simultaneously measured with in-situ portable HPGe and the NaI(Tl) detectors. In parallel, 55 soil samples collected from these sites were analyzed with a laboratory γ-ray spectroscopy technique (HPGe). A strong correlation was observed between the in-situ and laboratory HPGe techniques with a linear correlation coefficient (R2) of 0.99 for 226Ra and 232Th and 0.975 for 40K, respectively. The in-situ HPGe technique shows a strong correlation with the NaI(Tl) detector. γ-Rays cps of 226Ra, 232Th, and 40K of the NaI (Tl) detector were then converted to specific activities (Bq kg-1 unit) in soil using the empirical formulas obtained in this study. The absorbed dose rate in air at 1 m height above ground due to these radionuclides was calculated using the Beck's formula and the results were compared with measured values obtained with an high pressure ionization chamber. The results of the calculated and measured dose rate show a strong correlation of R2 = 0.96. The reliability and precision of analytical spectroscopy techniques of radioactivity and radiation dose were confirmed in this work.