Publications by authors named "J Keith Joung"

446 Publications

Ligand-Assisted Direct Photolithography of Perovskite Nanocrystals Encapsulated with Multifunctional Polymer Ligands for Stable, Full-Colored, High-Resolution Displays.

Nano Lett 2021 Mar 1;21(5):2288-2295. Epub 2021 Mar 1.

Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.

Micropatterns with a high stability, definition, and resolution are an absolute requirement in advanced display technology. Herein, patternable perovskite nanocrystals (PNCs) with excellent stability were prepared by exchanging pristine ligands with multifunctional polymer ligands, poly(2-cinnamoyloxyethyl methacrylate). The polymer backbone contains a cinnamoyl group that has been widely employed as a photo-cross-linker under 365 nm UV irradiation. Also, the terminal group is readily adjustable among NHCl, NHBr, and NHI, allowing us to obtain multicolored PNCs via instant anion exchange. Furthermore, the resulting ligand exchanged PNCs exhibited enhanced stability toward polar solvents without any undesirable influence on the structural or optical properties of the PNCs. Using anion exchanged PNCs, RGB microarrays with a subpixel size of 10 μm × 40 μm were successfully demonstrated. Our results highlight the versatility and feasibility of a simplified patterning strategy for nanomaterials, which can be generally applied in the fabrication of various optoelectronic devices.
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http://dx.doi.org/10.1021/acs.nanolett.1c00134DOI Listing
March 2021

PrimeDesign software for rapid and simplified design of prime editing guide RNAs.

Nat Commun 2021 02 15;12(1):1034. Epub 2021 Feb 15.

Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.

Prime editing (PE) is a versatile genome editing technology, but design of the required guide RNAs is more complex than for standard CRISPR-based nucleases or base editors. Here we describe PrimeDesign, a user-friendly, end-to-end web application and command-line tool for the design of PE experiments. PrimeDesign can be used for single and combination editing applications, as well as genome-wide and saturation mutagenesis screens. Using PrimeDesign, we construct PrimeVar, a comprehensive and searchable database that includes candidate prime editing guide RNA (pegRNA) and nicking sgRNA (ngRNA) combinations for installing or correcting >68,500 pathogenic human genetic variants from the ClinVar database. Finally, we use PrimeDesign to design pegRNAs/ngRNAs to install a variety of human pathogenic variants in human cells.
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http://dx.doi.org/10.1038/s41467-021-21337-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7884779PMC
February 2021

Validation of the European association of urology biochemical recurrence risk groups after radical prostatectomy in an Asian cohort and suggestions for refinement.

Urol Oncol 2021 Feb 9. Epub 2021 Feb 9.

Department of Urology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea. Electronic address:

Background: To validate the prognostic utility of the novel European Urology Association (EAU) biochemical recurrence (BCR) risk groups in an Asian cohort and to determine whether refinement is necessary.

Methods: Two cohorts of men who experienced BCR after radical prostatectomy between 1998 and 2014 were employed. The Cox model was used to validate and model the probability of metastasis and death after BCR. Data from 817 men from the first cohort were used to develop a modified model and external validation was performed on 344 men from the second cohort.

Results: Distant metastasis-free survival and cancer-specific survival from the time of BCR were significantly higher in patients with a low EAU BCR risk (prostate-specific antigen doubling time [PSADT] >1 year and pathologic Gleason score [pGS] ≤7) than in high EAU BCR risk patients (PSADT ≤1 year or pGS 8-10). In the high EAU BCR risk group, survival outcomes and efficacy of early salvage radiotherapy in patients with PSADT 6-12 months and pGS ≤7 were similar to those in the low EAU BCR risk group. The C-index, which predicts metastatic progression and cancer-specific death, improved after PSADT cutoff point was modified to 6 months, and was validated externally.

Conclusion: EAU BCR risk stratification reliably identified patients at increased risk of metastasis and cancer-specific mortality in the present cohort. Modification of the PSADT cutoff point may help to optimize the predictive performance and utility of the EAU BCR risk groups in clinical practice.
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http://dx.doi.org/10.1016/j.urolonc.2020.12.023DOI Listing
February 2021

A Code of Ethics for Gene Drive Research.

CRISPR J 2021 Feb 10;4(1):19-24. Epub 2021 Feb 10.

Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA.

Gene drives hold promise for use in controlling insect vectors of diseases, agricultural pests, and for conservation of ecosystems against invasive species. At the same time, this technology comes with potential risks that include unknown downstream effects on entire ecosystems as well as the accidental or nefarious spread of organisms that carry the gene drive machinery. A code of ethics can be a useful tool for all parties involved in the development and regulation of gene drives and can be used to help ensure that a balanced analysis of risks, benefits, and values is taken into consideration in the interest of society and humanity. We have developed a code of ethics for gene drive research with the hope that this code will encourage the development of an international framework that includes ethical guidance of gene drive research and is incorporated into scientific practice by gaining broad agreement and adherence.
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http://dx.doi.org/10.1089/crispr.2020.0096DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7898401PMC
February 2021

2020 Korean guidelines for the management of metastatic prostate cancer.

Korean J Intern Med 2021 Feb 10. Epub 2021 Feb 10.

Department of Internal Medicine, Chungnam National University College of Medicine, Daejeon, Korea.

In 2017, Korean Society of Medical Oncology (KSMO) published the Korean management guideline of metastatic prostate cancer. This paper is the 2nd edition of the Korean management guideline of metastatic prostate cancer. We updated recent many changes of management in metastatic prostate cancer in this 2nd edition guideline. The present guideline consists of the three categories: management of metastatic hormone sensitive prostate cancer; management of metastatic castration resistant prostate cancer; and clinical consideration for treating patients with metastatic prostate cancer. In category 1 and 2, levels of evidence (LEs) have been mentioned according to the general principles of evidence-based medicine. And grades of recommendation (GR) was taken into account the quality of evidence, the balance between desirable and undesirable effects, the values and preferences, and the use of resources and GR were divided into strong recommendations (SR) and weak recommendations (WR). A total of 16 key questions are selected. And we proposed recommendations and described key evidence for each recommendation. The treatment landscape of metastatic prostate cancer is changing very rapid and many trials are ongoing. To verify the results of the future trials is necessary and should be applied to the treatment for metastatic prostate cancer patients in the clinical practice. Especially, many prostate cancer patients are old age, have multiple underlying medical comorbidities, clinicians should be aware of the significance of medical management as well as clinical efficacy of systemic treatment.
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http://dx.doi.org/10.3904/kjim.2020.213DOI Listing
February 2021

Scalable characterization of the PAM requirements of CRISPR-Cas enzymes using HT-PAMDA.

Nat Protoc 2021 03 5;16(3):1511-1547. Epub 2021 Feb 5.

Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.

The continued expansion of the genome-editing toolbox necessitates methods to characterize important properties of CRISPR-Cas enzymes. One such property is the requirement for Cas proteins to recognize a protospacer-adjacent motif (PAM) in DNA target sites. The high-throughput PAM determination assay (HT-PAMDA) is a method that enables scalable characterization of the PAM preferences of different Cas proteins. Here, we provide a step-by-step protocol for the method, discuss experimental design considerations, and highlight how the method can be used to profile naturally occurring CRISPR-Cas9 enzymes, engineered derivatives with improved properties, orthologs of different classes (e.g., Cas12a), and even different platforms (e.g., base editors). A distinguishing feature of HT-PAMDA is that the enzymes are expressed in a cell type or organism of interest (e.g., mammalian cells), permitting scalable characterization and comparison of hundreds of enzymes in a relevant setting. HT-PAMDA does not require specialized equipment or expertise and is cost effective for multiplexed characterization of many enzymes. The protocol enables comprehensive PAM characterization of dozens or hundreds of Cas enzymes in parallel in <2 weeks.
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http://dx.doi.org/10.1038/s41596-020-00465-2DOI Listing
March 2021

Protective Effects of Milk Casein on the Brain Function and Behavior in a Mouse Model of Chronic Stress.

J Agric Food Chem 2021 Feb 26;69(6):1936-1941. Epub 2021 Jan 26.

Department of Food and Biotechnology, Korea University, Sejong 30019, Korea.

Chronic stress is a major cause of mental health problems and primary medical issues. Milk has been studied for its stress-reducing effects. Tryptophan, which is abundant in milk, is a precursor of the neuroactive compounds serotonin and melatonin. This study investigated the preventive effects of milk casein on brain dysfunction and anxiety-like behavior induced by chronic stress. Mice were exposed to unpredictable chronic mild stress (UCMS) and milk casein was administered for 10 weeks. Milk casein significantly reduced stress-induced changes in serum corticosterone and serotonin levels. The negative effects of UCMS on the expression of proteins associated with neuroendocrine function, neurodegeneration, neuronal inflammation, and barrier function of the blood-brain barrier were statistically normalized by casein treatment. Pretreatment with casein significantly prevented anxiety-like behavior induced by UCMS. These results suggest that milk casein has the potential to prevent stress-induced brain dysfunction and anxiety-like behavior.
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http://dx.doi.org/10.1021/acs.jafc.0c07292DOI Listing
February 2021

Enhancing Happiness for Nursing Students through Positive Psychology Activities: A Mixed Methods Study.

Int J Environ Res Public Health 2020 12 11;17(24). Epub 2020 Dec 11.

Department of Nursing, Semyung University, 65 Semyung-ro, Jecheon-si, Chungbuk 27136, Korea.

This study aims to evaluate a program promoting character strengths, positive psychological capital, learning flow, and sense of calling for nursing students. We conducted a concurrent embedded mixed methods study with 51 nursing students randomly classified into an intervention or a control group. The intervention group exhibited significantly higher scores than the control group for positive psychological capital, learning flow, and sense of calling. Program participation experiences were categorized as "change of views about oneself", "change of views about the world", "stress relief", and "practice of positivity". Among nursing students, this program demonstrated change toward a positive, committed, and meaningful life.
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http://dx.doi.org/10.3390/ijerph17249274DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7762976PMC
December 2020

Light-directed trapping of metastable intermediates in a self-assembly process.

Nat Commun 2020 Dec 7;11(1):6260. Epub 2020 Dec 7.

Department of Chemical Engineering, Hanyang University, Seoul, 04763, Korea.

Self-assembly is a dynamic process that often takes place through a stepwise pathway involving formation of kinetically favored metastable intermediates prior to generation of a thermodynamically preferred supramolecular framework. Although trapping intermediates in these pathways can provide significant information about both their nature and the overall self-assembly process, it is a challenging venture without altering temperature, concentrations, chemical compositions and morphologies. Herein, we report a highly efficient and potentially general method for "trapping" metastable intermediates in self-assembly processes that is based on a photopolymerization strategy. By employing a chiral perylene-diimide possessing a diacetylene containing an alkyl chain, we demonstrated that the metastable intermediates, including nanoribbons, nanocoils and nanohelices, can be effectively trapped by using UV promoted polymerization before they form thermodynamic tubular structures. The strategy developed in this study should be applicable to naturally and synthetically abundant alkyl chain containing self-assembling systems.
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http://dx.doi.org/10.1038/s41467-020-20172-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7721704PMC
December 2020

Fermented Maillard reaction products attenuate stress-induced testicular dysfunction in mice.

J Dairy Sci 2021 Feb 30;104(2):1384-1393. Epub 2020 Nov 30.

Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Korea. Electronic address:

Chronic stress can cause psychological diseases and affect male fertility and the reproductive system. Maillard reaction of milk proteins improves their functional and nutritional properties through modification of proteins. Previously, we determined that Maillard reaction product (MRP) from milk casein and MRP fermented (FMRP) with Lactobacillus rhamnosus 4B15 (4B15) had anti-anxiolytic effects in mice under chronic stress. Therefore, we aimed to investigate the effects of MRP and FMRP on chronic stress-induced testicular dysfunction in mice through quantitative real-time PCR (qRT-PCR) and in situ hybridization analysis. Mice were pretreated with MRP and FMRP for 10 wk; simultaneously, from the third week of the experimental period, they were exposed to unpredictable chronic mild stress (UCMS) for 7 wk. The expression levels of the luteinizing hormone subunit β (Lhb) and follicle-stimulating hormone subunit β (Fshb) were remarkably reduced after exposure to UCMS. However, treatment with MRP and FMRP inhibited the UCMS-induced reduction, with FMRP showing especially significant inhibition. Moreover, the expression of steroidogenesis-related genes [luteinizing hormone receptor (Lhr), follicle-stimulating hormone (Fshr), 3-β hydroxysteroid dehydrogenase 2 (Hsd3b2), and steroidogenic acute regulatory protein (StAR)] were significantly reduced in response to UCMS. In contrast, the transcript levels of these genes were highest in the MRP-treated mice. Mice pretreated with FMRP also exhibited higher levels of gene expression compared with the nonstressed mice. Moreover, UCMS significantly downregulated the expression of genes associated with testicular function [i.e., a disintegrin and metallopeptidase domain 5 (Adam5), Adam29, bone morphogenetic protein 2 (Bmp2), tektin 3 (Tekt3), and sperm adhesion molecule 1 (Spam1)]. However, the administration of MRP and FMRP prevented the UCMS-induced reduction in the expressions of above genes. The localization of Lhr, Srd5a2, Adam29, and Spam1 was confirmed by in situ hybridization analysis and the results were consistent with those of qRT-PCR. Consequently, these results indicated that MRP and FMRP, manufactured by the heat treatment of milk casein and fermentation with probiotic 4B15, have the potential to prevent chronic stress-induced testicular dysfunction.
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http://dx.doi.org/10.3168/jds.2020-18996DOI Listing
February 2021

Revisiting Information Detection and Energy Harvesting: A Power Splitting-Based Approach.

Entropy (Basel) 2020 Nov 26;22(12). Epub 2020 Nov 26.

School of Electrical and Electronics Engineering, Chung-Ang University, Seoul 06974, Korea.

Wireless sensors are becoming essential in machine-type communications and Internet of Things. As the key performance metrics, the spectral efficiency as well as the energy efficiency have been considered while determining the effectiveness of sensor networks. In this paper, we present several power-splitting solutions to maximize the average harvested energy under a rate constraint when both the information and power are transmitted through the same wireless channel to a sensor (i.e., a receiver). More specifically, we first designed the optimal dynamic power-splitting policy, which decides the optimal fractional power of the received signal used for energy harvesting at the receiver. As effective solutions, we proposed two types of single-threshold-based power-splitting policies, namely, Policies I and II, which decide to switch between energy harvesting and information decoding by comparing the received signal power with some given thresholds. Additionally, we performed asymptotic analysis for a large number of packets along with practical statistics-based policies. Consequently, we demonstrated the effectiveness of the proposed power-splitting solutions in terms of the rate-energy trade-off.
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http://dx.doi.org/10.3390/e22121341DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7761457PMC
November 2020

Epithelial Splicing Regulatory Protein (ESPR1) Expression in an Unfavorable Prognostic Factor in Prostate Cancer Patients.

Front Oncol 2020 26;10:556650. Epub 2020 Oct 26.

Department of Urology, Center for Prostate Cancer, National Cancer Center, Goyangsi, South Korea.

Background: To evaluate the role of epithelial splicing regulatory protein 1 (ESRP1) expression in survival prognoses and disease progression for prostate cancer (PC) using The Cancer Genome Atlas (TCGA) dataset and to validate it using patients' prostatectomy specimens.

Methods: A preliminary investigation into the clinical significance of ESRP1 in PC was conducted using TCGA PC PRAD dataset and then using immunohistochemistry in 514 PC patients' tissue microarrays of radical prostatectomy specimens. The interpretation of immunohistochemistry was done using its intensity (high vs. low) or the semi-quantitative expression value (H-score, 0-300). The prognostic significance of ESRP1 expression was analyzed for biochemical recurrence (BCR), recurrence-free survival (RFS), overall survival (OS) and cancer-specific survival (CSS) using the Cox proportional-hazards model (p < 0.05).

Results: In the publicly available prostate adenocarcinoma dataset, ESRP1 expression was significantly higher in the tumor samples compared to the normal samples (p < 0.001). Survival analysis showed that the tumor samples in the ESRP1-high group had significantly worse BCR-free survival and RFS compared to the ESRP1-low group (p < 0.05), whereas OS was not (p=0.08). These results were largely consistent with the 514 patients' clinical data during a median 91.2 months of follow-up. After adjusting for significant prognostic clinicopathological factors, the multivariable models showed that the ESRP1 was a significantly risk factor for CSS (Hazard ratio 3.37, p = 0.034) and for BCR (HR 1.34, p=0.049) without any significance for OS (p=0.464).

Conclusions: The higher ESRP1 expression appeared increased risk of disease progression and cancer-specific death in PC.
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http://dx.doi.org/10.3389/fonc.2020.556650DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7649424PMC
October 2020

Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay.

PLoS One 2020 2;15(11):e0238612. Epub 2020 Nov 2.

Department II of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.

Background: Rapid and extensive testing of large parts of the population and specific subgroups is crucial for proper management of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and decision-making in times of a pandemic outbreak. However, point-of-care (POC) testing in places such as emergency units, outpatient clinics, airport security points or the entrance of any public building is a major challenge. The need for thermal cycling and nucleic acid isolation hampers the use of standard PCR-based methods for this purpose.

Methods: To avoid these obstacles, we tested PCR-independent methods for the detection of SARS-CoV-2 RNA from primary material (nasopharyngeal swabs) including reverse transcription loop-mediated isothermal amplification (RT-LAMP) and specific high-sensitivity enzymatic reporter unlocking (SHERLOCK).

Results: Whilst specificity of standard RT-LAMP assays appears to be satisfactory, sensitivity does not reach the current gold-standard quantitative real-time polymerase chain reaction (qPCR) assays yet. We describe a novel multiplexed RT-LAMP approach and validate its sensitivity on primary samples. This approach allows for fast and reliable identification of infected individuals. Primer optimization and multiplexing helps to increase sensitivity significantly. In addition, we directly compare and combine our novel RT-LAMP assays with SHERLOCK.

Conclusion: In summary, this approach reveals one-step multiplexed RT-LAMP assays as a prime-option for the development of easy and cheap POC test kits.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0238612PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605681PMC
November 2020

Outcomes of Consumer Involvement in Mental Health Nursing Education: An Integrative Review.

Int J Environ Res Public Health 2020 09 16;17(18). Epub 2020 Sep 16.

Department of Nursing, Semyung University, Jecheon, 27136, Korea.

This integrative review analyzed the research on consumer involvement in mental health nursing education in the last decade. We aimed to derive the main contents, methods, and outcomes of education using consumer involvement for mental health nursing students. We searched six electronic databases using English and Korean search terms; two authors independently reviewed the 14 studies that met the selection criteria. Studies on the topic were concentrated in Australia and some European countries; most of them used a qualitative design. The main education subject was recovery, and consumers tended to actively participate in education planning. Moreover, students' perceptions about education using consumer involvement and people with mental health problems changed positively, as well as their experiences of participating in mental health nursing education. There is a lack of interest in the topic in Asian countries, including Korea. Thus, future studies in Asian countries are needed to conduct qualitative and in-depth explorations of students' experiences regarding an educational intervention that uses consumer involvement as a tool rigorously designed for mental health nursing education. Consumer involvement can be an innovative strategy to produce high-quality mental health nurses by minimizing the gap between theory and practice in the undergraduate program.
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http://dx.doi.org/10.3390/ijerph17186756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7559165PMC
September 2020

Peer mentoring experiences of nursing students based on the caring perspective: A qualitative study.

Nurse Educ Today 2020 Nov 29;94:104586. Epub 2020 Aug 29.

Department of Nursing, Semyung University, Jecheon, Republic of Korea.

Background: Care competency is a critical aspect required of nursing students who want to become nurses. Peer mentoring is a useful way to experience the natural care process.

Objectives: This study aimed to explore from the caring perspective the experiences of nursing students who have participated in peer mentoring as mentors and mentees.

Design: This was a qualitative study; individual interviews were conducted and content analysis was performed to explore and describe peer mentoring experiences.

Settings: This study was conducted in the department of nursing at a university in the Republic of Korea.

Participants: The participants were nine students in their second to fourth year who participated as mentors and mentees in the peer mentoring program organized by the department of nursing.

Methods: Data on participants' experiences of mentoring were collected through individual interviews. The transcribed content was analyzed using content analysis, and the categorized content was reorganized through the framework of the theory of caring.

Results: The results of the content analysis revealed five categories that formed a sequential process of caring, which became the cycle of another process of care.

Conclusions: This study's findings regarding peer mentoring experiences of nursing college students indicate that the program can be effective in improving care competencies related to nursing. Peer mentoring in nursing education could be a useful method to develop students' professional competencies.
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http://dx.doi.org/10.1016/j.nedt.2020.104586DOI Listing
November 2020

Experimental database of optical properties of organic compounds.

Sci Data 2020 09 8;7(1):295. Epub 2020 Sep 8.

Department of Chemistry and Research Institute for Natural Science, Korea University, Seoul, 02841, Korea.

Experimental databases on the optical properties of organic chromophores are important for the implementation of data-driven chemistry using machine learning. Herein, we present a series of experimental data including various optical properties such as the first absorption and emission maximum wavelengths and their bandwidths (full width at half maximum), extinction coefficient, photoluminescence quantum yield, and fluorescence lifetime. A database of 20,236 data points was developed by collecting the optical properties of organic compounds already reported in the literature. A dataset of 7,016 unique organic chromophores in 365 solvents or in solid state is available in CSV format.
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http://dx.doi.org/10.1038/s41597-020-00634-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7478979PMC
September 2020

Cell-based artificial APC resistant to lentiviral transduction for efficient generation of CAR-T cells from various cell sources.

J Immunother Cancer 2020 09;8(2)

Cellular Immunotherapy Program, Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA

Background: Adoptive cell therapy with chimeric antigen receptor T cells (CAR-T) has become a standard treatment for patients with certain aggressive B cell malignancies and holds promise to improve the care of patients suffering from numerous other cancers in the future. However, the high manufacturing cost of CAR-T cell therapies poses a major barrier to their broader clinical application. Among the key cost drivers of CAR-T production are single-use reagents for T cell activation and clinical-grade viral vector. The presence of variable amounts of contaminating monocytes in the starting material poses an additional challenge to CAR-T manufacturing, since they can impede T cell stimulation and transduction, resulting in manufacturing failure.

Methods: We created K562-based artificial antigen-presenting cells (aAPC) with genetically encoded T cell stimulation and costimulation that represent an inexhaustible source for T cell activation. We additionally disrupted endogenous expression of the low-density lipoprotein receptor (LDLR) on these aAPC (aAPC-ΔLDLR) using CRISPR-Cas9 gene editing nucleases to prevent inadvertent lentiviral transduction and avoid the sink effect on viral vector during transduction. Using various T cell sources, we produced CD19-directed CAR-T cells via aAPC-ΔLDLR-based activation and tested their in vitro and in vivo antitumor potency against B cell malignancies.

Results: We found that lack of LDLR expression on our aAPC-ΔLDLR conferred resistance to lentiviral transduction during CAR-T production. Using aAPC-ΔLDLR, we achieved efficient expansion of CAR-T cells even from unpurified starting material like peripheral blood mononuclear cells or unmanipulated leukapheresis product, containing substantial proportions of monocytes. CD19-directed CAR-T cells that we produced via aAPC-ΔLDLR-based expansion demonstrated potent antitumor responses in preclinical models of acute lymphoblastic leukemia and B-cell lymphoma.

Conclusions: Our aAPC-ΔLDLR represent an attractive approach for manufacturing of lentivirally transduced T cells that may be simpler and more cost efficient than currently available methods.
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http://dx.doi.org/10.1136/jitc-2020-000990DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7477986PMC
September 2020

Penta-fluorophenol: a Smiles rearrangement-inspired cysteine-selective fluorescent probe for imaging of human glioblastoma.

Chem Sci 2020 Jun 11;11(22):5658-5668. Epub 2020 May 11.

Department of Biomedical Science , Graduate School , Kyung Hee University , Seoul 02447 , Korea . Email:

Two of the most critical factors for the survival of glioblastoma (GBM) patients are precision diagnosis and the tracking of treatment progress. At the moment, various sophisticated and specific diagnostic procedures are being used, but there are relatively few simple diagnosis methods. This work introduces a sensing probe based on a turn-on type fluorescence response that can measure the cysteine (Cys) level, which is recognized as a new biomarker of GBM, in human-derived cells and within on-site human clinical biopsy samples. The Cys-initiated chemical reactions of the probe cause a significant fluorescence response with high selectivity, high sensitivity, a fast response time, and a two-photon excitable excitation pathway, which allows the imaging of GBM in both mouse models and human tissue samples. The probe can distinguish the GBM cells and disease sites in clinical samples from individual patients. Besides, the probe has no short or long-term toxicity and immune response. The present findings hold promise for application of the probe to a relatively simple and straightforward following of GBM at clinical sites.
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http://dx.doi.org/10.1039/d0sc01085eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7449700PMC
June 2020

Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA.

Nat Biomed Eng 2020 12 26;4(12):1140-1149. Epub 2020 Aug 26.

School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.

Nucleic acid detection by isothermal amplification and the collateral cleavage of reporter molecules by CRISPR-associated enzymes is a promising alternative to quantitative PCR. Here, we report the clinical validation of the specific high-sensitivity enzymatic reporter unlocking (SHERLOCK) assay using the enzyme Cas13a from Leptotrichia wadei for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-the virus that causes coronavirus disease 2019 (COVID-19)-in 154 nasopharyngeal and throat swab samples collected at Siriraj Hospital, Thailand. Within a detection limit of 42 RNA copies per reaction, SHERLOCK was 100% specific and 100% sensitive with a fluorescence readout, and 100% specific and 97% sensitive with a lateral-flow readout. For the full range of viral load in the clinical samples, the fluorescence readout was 100% specific and 96% sensitive. For 380 SARS-CoV-2-negative pre-operative samples from patients undergoing surgery, SHERLOCK was in 100% agreement with quantitative PCR with reverse transcription. The assay, which we show is amenable to multiplexed detection in a single lateral-flow strip incorporating an internal control for ribonuclease contamination, should facilitate SARS-CoV-2 detection in settings with limited resources.
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http://dx.doi.org/10.1038/s41551-020-00603-xDOI Listing
December 2020

Direct Photolithographic Patterning of Colloidal Quantum Dots Enabled by UV-Crosslinkable and Hole-Transporting Polymer Ligands.

ACS Appl Mater Interfaces 2020 Sep 2;12(37):42153-42160. Epub 2020 Sep 2.

Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea.

Quantum dot (QD)-based displays call for nondestructive, high-throughput, and high-resolution patterning techniques with micrometer precision. In particular, self-emissive QD-based displays demand fine patterns of conductive QD films with uniform thickness at the nanometer scale. To meet these requirements, we functionalized QDs with photopatternable and semiconducting poly(vinyltriphenylamine--azidostyrene) (PTPA-N-SH) ligands in which hole-transporting triphenylamine and UV-crosslinkable azide (-N) groups are integrated. The hybridized QD films undergo chemical crosslinking upon UV irradiation without loss in the luminescence efficiency, enabling micrometer-scale QD patterns (pitch size down to ∼10 μm) via direct photolithography. In addition, the conjugated moieties in the ligands allow the crosslinked QD films to be used in electrically driven light-emitting diodes (LED). As the ultimate achievement, a patterned QD-LED was prepared with a maximum luminance of 11 720 cd m and a maximum external quantum efficiency (EQE) of 6.25%. The present study offers a simple platform to fabricate conductive nanoparticle films with micrometer-scale patterns, and thus we anticipate that this system will expedite the realization of QD-based displays and will also be applicable to the manufacture of nanoparticles for other electronic devices.
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http://dx.doi.org/10.1021/acsami.0c11988DOI Listing
September 2020

Earlier-Phased Cancer Immunity Cycle Strongly Influences Cancer Immunity in Operable Never-Smoker Lung Adenocarcinoma.

iScience 2020 Aug 18;23(8):101386. Epub 2020 Jul 18.

Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Korea. Electronic address:

Exome and transcriptome analyses of clinically homogeneous early-stage never-smoker female patients with lung adenocarcinoma were performed to understand tumor-T cell interactions and immune escape points. Using our novel gene panels of eight functional categories in the cancer-immunity cycle, three distinct subgroups were identified in this immune checkpoint blockade-refractory cohort by defective gene expression in two major domains, i.e., type I interferon production/signaling pathway and antigen-presenting machinery. Our approach could play a critical role in understanding immune evasion mechanisms, developing a method for effective selection of rare immune checkpoint blockade responders, and finding new treatment strategies.
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http://dx.doi.org/10.1016/j.isci.2020.101386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426575PMC
August 2020

Pan-Cancer Analysis of Alternative Lengthening of Telomere Activity.

Cancers (Basel) 2020 Aug 7;12(8). Epub 2020 Aug 7.

Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea.

Alternative lengthening of telomeres (ALT) is a telomerase-independent mechanism that extends telomeres in cancer cells. It influences tumorigenesis and patient survival. Despite the clinical significance of ALT in tumors, the manner in which ALT is activated and influences prognostic outcomes in distinct cancer types is unclear. In this work, we profiled distinct telomere maintenance mechanisms (TMMs) using 8953 transcriptomes of 31 different cancer types from The Cancer Genome Atlas (TCGA). Our results demonstrated that approximately 29% of cancer types display high ALT activity with low telomerase activity in the telomere-lengthening group. Among the distinct ALT mechanisms, homologous recombination was frequently observed in sarcoma, adrenocortical carcinoma, and kidney chromophobe. Five cancer types showed a significant difference in survival in the presence of high ALT activity. Sarcoma patients with elevated ALT had unfavorable risks ( < 0.038) coupled with a high expression of , suggesting this as a potential drug target. On the contrary, glioblastoma patients had favorable risks ( < 0.02), and showed low levels of antigen-presenting cells. Together, our analyses highlight cancer type-dependent TMM activities and ALT-associated genes as potential therapeutic targets.
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http://dx.doi.org/10.3390/cancers12082207DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7465155PMC
August 2020

How Does Androgen Deprivation Therapy Affect Mental Health Including Cognitive Dysfunction In Patients with Prostate Cancer?

World J Mens Health 2020 Jul 21. Epub 2020 Jul 21.

Department Urology, Urological Cancer Center, Research Institute and Hospital of National Cancer Center, Goyang, Korea.

Androgen deprivation therapy (ADT) is used to block the release of androgen in prostate cancer to promote the regression of cancer cells, and hence, disease progression. Its indication has been widened from the metastatic setting to the localized setting in prostate cancer. Long-term ADT for suppressing androgen release leads to a rapid decrease in androgen, termed as andropause, resulting in several dose and duration dependent adverse effects, including cognitive dysfunction such as dementia. Many retrospective and prospective studies, as well as meta-analyses, have attempted to confirm the crucial relationship between ADT and cognitive dysfunction, but pro and contrary opinions regarding this issue are ongoing owing to the absence of randomized controlled trials. Additionally, several recent studies have suggested the negative effects of dose- and duration-dependent ADT on cognitive dysfunction, especially in 40-65-year-old patients with prostate cancer, who are currently active workers in the society. This review article discusses several studies examining the influence of ADT on mental health based on diverse significant perspectives, especially cognitive dysfunction.
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http://dx.doi.org/10.5534/wjmh.200092DOI Listing
July 2020

CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells.

Nat Biotechnol 2021 01 20;39(1):41-46. Epub 2020 Jul 20.

Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, MA, USA.

CRISPR-guided DNA cytosine and adenine base editors are widely used for many applications but primarily create DNA base transitions (that is, pyrimidine-to-pyrimidine or purine-to-purine). Here we describe the engineering of two base editor architectures that can efficiently induce targeted C-to-G base transversions, with reduced levels of unwanted C-to-W (W = A or T) and indel mutations. One of these C-to-G base editors (CGBE1), consists of an RNA-guided Cas9 nickase, an Escherichia coli-derived uracil DNA N-glycosylase (eUNG) and a rat APOBEC1 cytidine deaminase variant (R33A) previously shown to have reduced off-target RNA and DNA editing activities. We show that CGBE1 can efficiently induce C-to-G edits, particularly in AT-rich sequence contexts in human cells. We also removed the eUNG domain to yield miniCGBE1, which reduced indel frequencies but only modestly decreased editing efficiency. CGBE1 and miniCGBE1 enable C-to-G edits and will serve as a basis for optimizing C-to-G base editors for research and therapeutic applications.
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http://dx.doi.org/10.1038/s41587-020-0609-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7854778PMC
January 2021

Optimization of AsCas12a for combinatorial genetic screens in human cells.

Nat Biotechnol 2021 01 13;39(1):94-104. Epub 2020 Jul 13.

Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Cas12a RNA-guided endonucleases are promising tools for multiplexed genetic perturbations because they can process multiple guide RNAs expressed as a single transcript, and subsequently cleave target DNA. However, their widespread adoption has lagged behind Cas9-based strategies due to low activity and the lack of a well-validated pooled screening toolkit. In the present study, we describe the optimization of enhanced Cas12a from Acidaminococcus (enAsCas12a) for pooled, combinatorial genetic screens in human cells. By assaying the activity of thousands of guides, we refine on-target design rules and develop a comprehensive set of off-target rules to predict and exclude promiscuous guides. We also identify 38 direct repeat variants that can substitute for the wild-type sequence. We validate our optimized AsCas12a toolkit by screening for synthetic lethalities in OVCAR8 and A375 cancer cells, discovering an interaction between MARCH5 and WSB2. Finally, we show that enAsCas12a delivers similar performance to Cas9 in genome-wide dropout screens but at greatly reduced library size, which will facilitate screens in challenging models.
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http://dx.doi.org/10.1038/s41587-020-0600-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7854777PMC
January 2021

Cause of Mortality after Radical Prostatectomy and the Impact of Comorbidity in Men with Prostate Cancer: A Multi-institutional Study in Korea.

Cancer Res Treat 2020 Oct 3;52(4):1242-1250. Epub 2020 Jul 3.

Department of Urology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.

Purpose: This study aimed to examine the causes of death in Korean patients who underwent radical prostatectomy for prostate cancer and investigate the relationship between comorbidity and mortality.

Materials And Methods: We conducted a retrospective multicenter cohort study including 4,064 consecutive patients who had prostate cancer and underwent radical prostatectomy between January 1998 and June 2013. The primary endpoint of this study was all-cause mortality, and the secondary endpoints were cancer-specific mortality (CSM) and other-cause mortality (OCM). Charlson comorbidity index (CCI) was calculated to assess the comorbidities of each patient.

Results: Of 4,064 patients, 446 (11.0%) died during follow-up. The cause of death was prostate cancer in 132 patients (29.6%), other cancers in 121 patients (27.1%), and vascular disease in 57 patients (12.8%) in our cohort. The overall 10-year CSM rate was lower than the OCM rate (4.6% vs. 10.5%). The 10-year CSM rate was lower than the OCM rate in low- to intermediate-risk group patients (1.2% vs. 10.6%), whereas they were similar in high-risk group patients (11.8% vs. 10.1%). In the multivariable analysis, CCI was independently associated with all-cause mortality after radical prostatectomy, regardless of age and pathologic features.

Conclusion: Death from prostate cancer was rare in Korean men who underwent radical prostatectomy. Clinicians should be aware of the possibility of overtreatment of low-risk prostate cancer in men with significant comorbidity. Our findings may help to facilitate counseling and plan management in this patient group.
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http://dx.doi.org/10.4143/crt.2020.286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7577814PMC
October 2020

Technologies and Computational Analysis Strategies for CRISPR Applications.

Mol Cell 2020 07;79(1):11-29

Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Department of Pathology, Harvard Medical School, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA. Electronic address:

The CRISPR-Cas system offers a programmable platform for eukaryotic genome and epigenome editing. The ability to perform targeted genetic and epigenetic perturbations enables researchers to perform a variety of tasks, ranging from investigating questions in basic biology to potentially developing novel therapeutics for the treatment of disease. While CRISPR systems have been engineered to target DNA and RNA with increased precision, efficiency, and flexibility, assays to identify off-target editing are becoming more comprehensive and sensitive. Furthermore, techniques to perform high-throughput genome and epigenome editing can be paired with a variety of readouts and are uncovering important cellular functions and mechanisms. These technological advances drive and are driven by accompanying computational approaches. Here, we briefly present available CRISPR technologies and review key computational advances and considerations for various CRISPR applications. In particular, we focus on the analysis of on- and off-target editing and CRISPR pooled screen data.
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http://dx.doi.org/10.1016/j.molcel.2020.06.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7497852PMC
July 2020