Publications by authors named "Seohyun Kim"

27 Publications

  • Page 1 of 1

CRISPR as a Diagnostic Tool.

Biomolecules 2021 08 6;11(8). Epub 2021 Aug 6.

Department of Chemistry, Chung-Ang University, Seoul 06974, Korea.

Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system has recently gained growing attention as a diagnostic tool due to its capability of specific gene targeting. It consists of Cas enzymes and a guide RNA (gRNA) that can cleave the target DNA or RNA based on the sequence of the gRNA, making it an attractive genetic engineering technique. In addition to the target-specific binding and cleavage, the trans-cleavage activity was reported for some Cas proteins, including Cas12a and Cas13a, which is to cleave the surrounding single-stranded DNA or RNA upon the target binding of Cas-gRNA complex. All these activities of the CRISPR-Cas system are based on its target-specific binding, making it applied to develop diagnostic methods by detecting the disease-related gene as well as microRNAs and the genetic variations such as single nucleotide polymorphism and DNA methylation. Moreover, it can be applied to detect the non-nucleic acids target such as proteins. In this review, we cover the various CRISPR-based diagnostic methods by focusing on the activity of the CRISPR-Cas system and the form of the target. The CRISPR-based diagnostic methods without target amplification are also introduced briefly.
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http://dx.doi.org/10.3390/biom11081162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8391464PMC
August 2021

Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis.

Angew Chem Int Ed Engl 2021 Aug 24. Epub 2021 Aug 24.

Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.

The template-directed synthesis of RNA played an important role in the transition from prebiotic chemistry to the beginnings of RNA based life, but the mechanism of RNA copying chemistry is incompletely understood. We measured the kinetics of template copying with a set of primers with modified 3'-nucleotides and determined the crystal structures of these modified nucleotides in the context of a primer/template/substrate-analog complex. pH-rate profiles and solvent isotope effects show that deprotonation of the primer 3'-hydroxyl occurs prior to the rate limiting step, the attack of the alkoxide on the activated phosphate of the incoming nucleotide. The analogs with a E ribose conformation show the fastest formation of 3'-5' phosphodiester bonds. Among those derivatives, the reaction rate is strongly correlated with the electronegativity of the 2'-substituent. We interpret our results in terms of differences in steric bulk and charge distribution in the ground vs. transition states.
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http://dx.doi.org/10.1002/anie.202109714DOI Listing
August 2021

Down-regulation of photosynthesis and its relationship with changes in leaf N allocation and N availability after long-term exposure to elevated CO concentration.

J Plant Physiol 2021 Oct 12;265:153489. Epub 2021 Aug 12.

Department of Agriculture, Forestry and Bioresources, Seoul National University College of Agriculture and Life Sciences, Seoul, 08826, Republic of Korea; Interdisciplinary Program in Agricultural and Forest Meteorology, Seoul National University College of Agriculture and Life Sciences, Seoul, 08826, Republic of Korea; National Center for Agro Meteorology, Seoul, 08826, Republic of Korea; Research Institute of Agriculture and Life Sciences, Seoul National University College of Agriculture and Life Sciences, Seoul, 08826, Republic of Korea. Electronic address:

Down-regulation of photosynthesis under elevated CO (eCO) concentrations could be attributed to the depletion of nitrogen (N) availability after long-term exposure to eCO (progressive nitrogen limitation, PNL) or leaf N dilutions due to excessive accumulation of nonstructural carbohydrates. To determine the mechanism underlying this down-regulation, we investigated N availability, photosynthetic characteristics, and N allocation in leaves of Pinus densiflora (shade-intolerant species, evergreen tree), Fraxinus rhynchophylla (intermediate shade-tolerant species, deciduous tree), and Sorbus alnifolia (shade-tolerant species, deciduous tree). The three species were grown under three different CO concentrations in open-top chambers, i.e., ambient 400 ppm (aCO); ambient × 1.4, 560 ppm (eCO1.4); and ambient × 1.8, 720 ppm (eCO1.8), for 11 years. Unlike previous studies that addressed PNL, after 11 years of eCO exposure, N availability remained higher under eCO1.8, and chlorophyll and photosynthetic N use efficiency increased under eCO. In the case of nonstructural carbohydrates, starch and soluble sugar showed significant increases under eCO. The maximum carboxylation rate, leaf N per mass (N), and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) were low under eCO1.8. The ratio of RuBP regeneration to the carboxylation rate as well as that of chlorophyll N to Rubisco N increased with CO concentrations. Based on the reduction in N (not in N) that was diluted by increase in nonstructural carbohydrate, down-regulation of photosynthesis was found to be caused by the dilution rather than PNL. The greatest increases in chlorophyll under eCO were observed in S. alnifolia, which was the most shade-tolerant species. This study could help provide more detailed, mechanistically based processes to explain the down-regulation of photosynthesis by considering two hypotheses together and showed N allocation seems to be flexible against changes in CO concentration.
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http://dx.doi.org/10.1016/j.jplph.2021.153489DOI Listing
October 2021

Nanocages displaying SIRP gamma clusters combined with prophagocytic stimulus of phagocytes potentiate anti-tumor immunity.

Cancer Gene Ther 2021 Sep 4;28(9):960-970. Epub 2021 Aug 4.

KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea.

Antigen-presenting cells (APCs), including macrophages and dendritic cells (DCs), play a crucial role in bridging innate and adaptive immunity; thereby, innate immune checkpoint blockade-based therapy is an attractive approach for the induction of sustainable tumor-specific immunity. The interaction between the cluster of differentiation 47 (CD47) on tumor and signal-regulatory protein alpha (SIRPα) on phagocytic cells inhibits the phagocytic function of APCs, acting as a "don't eat me" signal. Accordingly, CD47 blockade is known to increase tumor cell phagocytosis, eliciting tumor-specific CD8 T-cell immunity. Here, we introduced a nature-derived nanocage to deliver SIRPγ for blocking of antiphagocytic signaling through binding to CD47 and combined it with prophagocytic stimuli using a metabolic reprogramming reagent for APCs (CpG-oligodeoxynucleotides). Upon delivering the clustered SIRPγ variant, the nanocage showed enhanced CD47 binding profiles on tumor cells, thereby promoting active engulfment by phagocytes. Moreover, combination with CpG potentiated the prophagocytic ability, leading to the establishment of antitumorigenic surroundings. This combination treatment could competently inhibit tumor growth by invigorating APCs and CD8 T-cells in TMEs in B16F10 orthotopic tumor models, known to be resistant to CD47-targeting therapeutics. Collectively, enhanced delivery of an innate immune checkpoint antagonist with metabolic modulation stimuli of immune cells could be a promising strategy for arousing immune responses against cancer.
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http://dx.doi.org/10.1038/s41417-021-00372-yDOI Listing
September 2021

Statin-mediated inhibition of RAS prenylation activates ER stress to enhance the immunogenicity of KRAS mutant cancer.

J Immunother Cancer 2021 Jul;9(7)

Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea

Background: Statins preferentially promote tumor-specific apoptosis by depleting isoprenoid such as farnesyl pyrophosphate and geranylgeranyl pyrophosphate. However, statins have not yet been approved for clinical cancer treatment due, in part, to poor understanding of molecular determinants on statin sensitivity. Here, we investigated the potential of statins to elicit enhanced immunogenicity of -mutant ( ) tumors.

Methods: The immunogenicity of treated cancer cells was determined by western blot, flow cytometry and confocal microscopy. The immunotherapeutic efficacy of mono or combination therapy using statin was assessed in tumor models, including syngeneic colorectal cancer and genetically engineered lung and pancreatic tumors. Using NanoString analysis, we analyzed how statin influenced the gene signatures associated with the antigen presentation of dendritic cells in vivo and evaluated whether statin could induce CD8+ T-cell immunity. Multiplex immunohistochemistry was performed to better understand the complicated tumor-immune microenvironment.

Results: Statin-mediated inhibition of prenylation provoked severe endoplasmic reticulum (ER) stress by attenuating the anti-ER stress effect of mutation, thereby resulting in the immunogenic cell death (ICD) of cancer cells. Moreover, statin-mediated ICD enhanced the cross-priming ability of dendritic cells, thereby provoking CD8+ T-cell immune responses against tumors. Combination therapy using statin and oxaliplatin, an ICD inducer, significantly enhanced the immunogenicity of tumors and promoted tumor-specific immunity in syngeneic and genetically engineered tumor models. Along with immune-checkpoint inhibitors, the abovementioned combination therapy overcame resistance to PD-1 blockade therapies, improving the survival rate of tumor models.

Conclusions: Our findings suggest that mutation could be a molecular target for statins to elicit potent tumor-specific immunity.
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http://dx.doi.org/10.1136/jitc-2021-002474DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8327837PMC
July 2021

The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection.

Proc Natl Acad Sci U S A 2021 Jul;118(29)

Department of Biological Sciences, Seoul National University, Seoul 08826, Korea;

The flowering plant life cycle consists of alternating haploid (gametophyte) and diploid (sporophyte) generations, where the sporophytic generation begins with fertilization of haploid gametes. In , genome-wide DNA demethylation is required for normal development, catalyzed by the DEMETER (DME) DNA demethylase in the gamete companion cells of male and female gametophytes. In the sporophyte, postembryonic growth and development are largely dependent on the activity of numerous stem cell niches, or meristems. Analyzing plants homozygous for a loss-of-function allele, we show that DME influences many aspects of sporophytic growth and development. mutants exhibited delayed seed germination, variable root hair growth, aberrant cellular proliferation and differentiation followed by enhanced de novo shoot formation, dysregulation of root quiescence and stomatal precursor cells, and inflorescence meristem (IM) resurrection. We also show that sporophytic DME activity exerts a profound effect on the transcriptome of developing plants, including discrete groups of regulatory genes that are misregulated in mutant tissues, allowing us to potentially link phenotypes to changes in specific gene expression pathways. These results show that DME plays a key role in sporophytic development and suggest that DME-mediated active DNA demethylation may be involved in the maintenance of stem cell activities during the sporophytic life cycle in .
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http://dx.doi.org/10.1073/pnas.2026806118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8307533PMC
July 2021

Ribose Alters the Photochemical Properties of the Nucleobase in Thionated Nucleosides.

J Phys Chem Lett 2021 Jul 14;12(28):6707-6713. Epub 2021 Jul 14.

EaStCHEM, School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K.

Substitution of exocyclic oxygen with sulfur was shown to substantially influence the properties of RNA/DNA bases, which are crucial for prebiotic chemistry and photodynamic therapies. Upon UV irradiation, thionucleobases were shown to efficiently populate triplet excited states and can be involved in characteristic photochemistry or generation of singlet oxygen. Here, we show that the photochemistry of a thionucleobase can be considerably modified in a nucleoside, that is, by the presence of ribose. Our transient absorption spectroscopy experiments demonstrate that thiocytosine exhibits 5 times longer excited-state lifetime and different excited-state absorption features than thiocytidine. On the basis of accurate quantum chemical simulations, we assign these differences to the dominant population of a shorter-lived triplet nπ* state in the nucleoside and longer-lived triplet ππ* states in the nucleobase. This explains the distinctive photoanomerziation of thiocytidine and indicates that the nucleoside will be a less efficient phototherapeutic agent with regard to singlet oxygen generation.
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http://dx.doi.org/10.1021/acs.jpclett.1c01384DOI Listing
July 2021

Conceptualizing "Family" and the Role of "Chosen Family" within the LGBTQ+ Refugee Community: A Text Network Graph Analysis.

Healthcare (Basel) 2021 Mar 25;9(4). Epub 2021 Mar 25.

Department of Social Welfare, Jeonbuk National University, Jeonju 54888, Korea.

This study analyzed meaning attributions regarding "family" and "chosen family" by Lesbian, Gay, Bisexual, Pansexual, Transgender, Gender Queer, Queer, Intersex, Agender, Asexual, and other Queer-identifying community (LGBTQ+) refugees. The meaning and significance of a chosen family in the newly established life of the refugees was also pin-pointed for its value of safekeeping the wellbeing and settlement process. We analyzed narrative statements given by 67 LGBTQ+ refugees from 82 YouTube videos. Using InfraNodus, a text graph analysis tool, we identified pathways for meaning circulation within the narrative data, and generated a contextualized meaning for family and chosen family. The conceptualization process produced a deduction within family relationships, exploring why people, other than in biological relationships, appear to be vital in their overall wellbeing and settlement, as well as the process through which this occurs. Biological family is sometimes associated with words that instigate fear, danger, and insecurity, while the concept of chosen family is associated with words like trusting, like-minded, understanding, welcoming, loving, committed, etc. The results of the study are intended to add knowledge to the gap by showing the types and characteristics of family relationships in LGBTQ+ refugee settings. It is also a call for the relevant research community to produce more evidence in such settings, as this is essential for obtaining a better understanding of these issues.
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http://dx.doi.org/10.3390/healthcare9040369DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8066340PMC
March 2021

Design of PD-1-decorated nanocages targeting tumor-draining lymph node for promoting T cell activation.

J Control Release 2021 05 29;333:328-338. Epub 2021 Mar 29.

KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea; Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea. Electronic address:

Targeted delivery of immunomodulatory molecules to the lymph nodes is an attractive means of improving the efficacy of anti-cancer immunotherapy. In this study, to improve the efficacy of PD-1 blockade-based therapy, nanocages were designed by surface engineering to decorate a programmed cell death protein 1 (PD-1) that is capable of binding against programmed death-ligand 1 (PD-L1) and -ligand 2 (PD-L2). This nanocage-mediated multivalent interaction remarkably increases the binding affinity and improves the antagonistic activity compared to free soluble PD-1. In addition, with the desirable nanocage size for optimal tumor-draining lymph node (TDLN) targeting (approximately 20 nm), rapid draining and increased accumulation into the TDLNs were observed. Moreover, the interference of the PD-1/PD-L axis with ultra-high affinity in the tumor microenvironment (effector phase) and the TDLNs (cognitive phase) significantly enhances the dendritic cell-mediated tumor-specific T cell activation. This characteristic successfully inhibited tumor growth and induced complete tumor eradication in some mice. Thus, the delivery of immunomodulatory molecules with nanocages can be a highly efficient strategy to achieve stronger anti-tumor immunity.
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http://dx.doi.org/10.1016/j.jconrel.2021.03.038DOI Listing
May 2021

The Emergence of RNA from the Heterogeneous Products of Prebiotic Nucleotide Synthesis.

J Am Chem Soc 2021 03 26;143(9):3267-3279. Epub 2021 Feb 26.

Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.

Recent advances in prebiotic chemistry are beginning to outline plausible pathways for the synthesis of the canonical ribonucleotides and their assembly into oligoribonucleotides. However, these reaction pathways suggest that many noncanonical nucleotides are likely to have been generated alongside the standard ribonucleotides. Thus, the oligomerization of prebiotically synthesized nucleotides is likely to have led to a highly heterogeneous collection of oligonucleotides comprised of a wide range of types of nucleotides connected by a variety of backbone linkages. How then did relatively homogeneous RNA emerge from this primordial heterogeneity? Here we focus on nonenzymatic template-directed primer extension as a process that would have strongly enriched for homogeneous RNA over the course of multiple cycles of replication. We review the effects on copying the kinetics of nucleotides with altered nucleobase and sugar moieties, when they are present as activated monomers and when they are incorporated into primer and template oligonucleotides. We also discuss three variations in backbone connectivity, all of which are nonheritable and regenerate native RNA upon being copied. The kinetic superiority of RNA synthesis suggests that nonenzymatic copying served as a chemical selection mechanism that allowed relatively homogeneous RNA to emerge from a complex mixture of prebiotically synthesized nucleotides and oligonucleotides.
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http://dx.doi.org/10.1021/jacs.0c12955DOI Listing
March 2021

Integrating a Statistical Topic Model and a Diagnostic Classification Model for Analyzing Items in a Mixed Format Assessment.

Front Psychol 2020 9;11:579199. Epub 2021 Feb 9.

Rossier School of Education, University of Southern California, Los Angeles, CA, United States.

Selected response items and constructed response (CR) items are often found in the same test. Conventional psychometric models for these two types of items typically focus on using the scores for correctness of the responses. Recent research suggests, however, that more information may be available from the CR items than just scores for correctness. In this study, we describe an approach in which a statistical topic model along with a diagnostic classification model (DCM) was applied to a mixed item format formative test of English and Language Arts. The DCM was used to estimate students' mastery status of reading skills. These mastery statuses were then included in a topic model as covariates to predict students' use of each of the latent topics in their written answers to a CR item. This approach enabled investigation of the effects of mastery status of reading skills on writing patterns. Results indicated that one of the skills, Integration of Knowledge and Ideas, helped detect and explain students' writing patterns with respect to students' use of individual topics.
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http://dx.doi.org/10.3389/fpsyg.2020.579199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7899971PMC
February 2021

In situ immunogenic clearance induced by a combination of photodynamic therapy and rho-kinase inhibition sensitizes immune checkpoint blockade response to elicit systemic antitumor immunity against intraocular melanoma and its metastasis.

J Immunother Cancer 2021 01;9(1)

KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, South Korea

Background: Uveal melanoma (UM) is the most frequent intraocular malignancy and is resistant to immunotherapy. Nearly 50% of patients with UM develop metastatic disease, and the overall survival outcome remains very poor. Therefore, a treatment regimen that simultaneously targets primary UM and prevents metastasis is needed. Here, we suggest an immunotherapeutic strategy for UM involving a combination of local photodynamic therapy (PDT), rho-kinase (ROCK) inhibitor, and PD-1/PD-L1 immune checkpoint blockade.

Methods: The antitumor efficacy and immune response of monotreatment or combinational treatment were evaluated in B16F10-bearing syngeneic mouse models. Abscopal antitumor immune responses induced by triple-combinational treatment were validated in syngeneic bilateral B16F10 models. After each treatment, the immune profiles and functional examinations were assessed in tumors and tumor draining lymph nodes by flow cytometry, ELISA, and immunofluorescence assays. In orthotopic intraocular melanoma models, the location of the immune infiltrate in the tumor microenvironment (TME) was evaluated after each treatment by multiplex immunohistochemistry and metastatic nodules were monitored.

Results: PDT with Ce6-embedded nanophotosensitizer (FIC-PDT) elicited immunogenic cell death and stimulated antigen-presenting cells. In situ immunogenic clearance induced by a combination of FIC-PDT with ripasudil, a clinically approved ROCK inhibitor, stimulated antigen-presenting cells, which in turn primed tumor-specific cytotoxic T cells. Moreover, local immunogenic clearance sensitized PD-1/PD-L1 immune checkpoint blockade responses to reconstruct the TME immune phenotypes of cold tumors into hot tumors, resulting in recruitment of robust cytotoxic CD8 T cells in the TME, propagation of systemic antitumor immunity to mediate abscopal effects, and prolonged survival. In an immune-privileged orthotopic intraocular melanoma model, even low-dose FIC-PDT and ripasudil combined with anti-PD-L1 antibody reduced the primary tumor burden and prevented metastasis.

Conclusions: A combination of localized FIC-PDT and a ROCK inhibitor exerted a cancer vaccine-like function. Immunogenic clearance led to the trafficking of CD8 T cells into the primary tumor site and sensitized the immune checkpoint blockade response to evoke systemic antitumor immunity to inhibit metastasis, one of the major challenges in UM therapy. Thus, immunogenic clearance induced by FIC-PDT and ROCK inhibitor combined with anti-PD-L1 antibody could be a potent immunotherapeutic strategy for UM.
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http://dx.doi.org/10.1136/jitc-2020-001481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7825261PMC
January 2021

The Association between Dynamic Changes in Serum Presepsin Levels and Mortality in Immunocompromised Patients with Sepsis: A Prospective Cohort Study.

Diagnostics (Basel) 2021 Jan 2;11(1). Epub 2021 Jan 2.

Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.

Presepsin is a subtype of soluble CD14 that is increased in the blood of septic patients. We investigated the role of dynamic changes in serum presepsin levels in critically ill, immunocompromised patients with sepsis. This is a prospective cohort study that included 119 adult patients admitted to the intensive care unit (ICU). Presepsin level was measured on day 1 and day 3 after ICU admission. The primary outcome was in-hospital mortality. In immunocompromised patients, presepsin levels on day 1 were higher in patients with sepsis than those in patients without sepsis. The area under the curve (AUC) of presepsin for diagnosing sepsis in immunocompromised patients was 0.87, which was comparable with that of procalcitonin (AUC, 0.892). Presepsin levels on day 3 were higher in patients who died in the hospital than in those who survived. In immunocompromised patients who died in the hospital, presepsin levels on day 3 were significantly higher than those on day 1. In the multivariate analysis, ΔPresepsin+ alone was independently correlated with in-hospital mortality in immunocompromised patients. These findings suggest that dynamic changes in presepsin levels between day 1 and day 3 are associated with in-hospital mortality in patients with sepsis, especially in immunocompromised patients.
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http://dx.doi.org/10.3390/diagnostics11010060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7823693PMC
January 2021

Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization.

Nucleic Acids Res 2021 01;49(2):646-656

Howard Hughes Medical Institute and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA.

The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here, we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequential threo-nucleotide monomers is strongly disfavored relative to ribo-nucleotides. Kinetic, NMR and crystallographic studies suggest that this is due in part to the slow formation of the imidazolium-bridged TNA dinucleotide intermediate in primer extension, and in part because of the greater distance between the attacking RNA primer 3'-hydroxyl and the phosphate of the incoming threo-nucleotide intermediate. Even a single activated threo-nucleotide in the presence of an activated downstream RNA oligonucleotide is added to the primer 10-fold more slowly than an activated ribonucleotide. In contrast, a single activated threo-nucleotide at the end of an RNA primer or in an RNA template results in only a modest decrease in the rate of primer extension, consistent with the minor and local structural distortions revealed by crystal structures. Our results are consistent with a model in which heterogeneous primordial oligonucleotides would, through cycles of replication, have given rise to increasingly homogeneous RNA strands.
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http://dx.doi.org/10.1093/nar/gkaa1215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7826252PMC
January 2021

Emerging Prospects of Exosomes for Cancer Treatment: From Conventional Therapy to Immunotherapy.

Adv Mater 2020 Dec 5;32(51):e2002440. Epub 2020 Oct 5.

Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea.

Exosomes are a class of extracellular vesicles of around 100 nm in diameter that are secreted by most cells and contain various bioactive molecules reflecting their cellular origin and mediate intercellular communication. Studies of these exosomal features in tumor pathogenesis have led to the development of therapeutic and diagnostic approaches using exosomes for cancer therapy. Exosomes have many advantages for conveying therapeutic agents such as small interfering RNAs, microRNAs, membrane-associated proteins, and chemotherapeutic compounds; thus, they are considered a prime candidate as a delivery tool for cancer treatment. Since exosomes also provide an optimal microenvironment for the effective function of immunomodulatory factors, exosomes harboring bioactive molecules have been bioengineered as cancer immunotherapies that can effectively activate each stage of the cancer immunity cycle to successfully elicit cancer-specific immunity. This review discusses the advantages of exosomes for treating cancer and the challenges that must be overcome for their successful clinical development.
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http://dx.doi.org/10.1002/adma.202002440DOI Listing
December 2020

Reliability for Tests With Items Having Different Numbers of Ordered Categories.

Appl Psychol Meas 2020 Mar 20;44(2):137-149. Epub 2019 Mar 20.

University of Georgia, Athens, USA.

This study describes a structural equation modeling (SEM) approach to reliability for tests with items having different numbers of ordered categories. A simulation study is provided to compare the performance of this reliability coefficient, coefficient alpha and population reliability for tests having items with different numbers of ordered categories, a one-factor and a bifactor structures, and different skewness distributions of test scores. Results indicated that the proposed reliability coefficient was close to the population reliability in most conditions. An empirical example was used to illustrate the performance of the different coefficients for a test of items with two or three ordered categories.
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http://dx.doi.org/10.1177/0146621619835498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7003185PMC
March 2020

A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2'-Deoxynucleotides.

J Am Chem Soc 2020 02 22;142(5):2317-2326. Epub 2020 Jan 22.

Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology , Massachusetts General Hospital , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.

The abiotic synthesis of ribonucleotides is thought to have been an essential step toward the emergence of the RNA world. However, it is likely that the prebiotic synthesis of ribonucleotides was accompanied by the simultaneous synthesis of arabinonucleotides, 2'-deoxyribonucleotides, and other variations on the canonical nucleotides. In order to understand how relatively homogeneous RNA could have emerged from such complex mixtures, we have examined the properties of arabinonucleotides and 2'-deoxyribonucleotides in nonenzymatic template-directed primer extension reactions. We show that nonenzymatic primer extension with activated arabinonucleotides is much less efficient than with activated ribonucleotides, and furthermore that once an arabinonucleotide is incorporated, continued primer extension is strongly inhibited. As previously shown, 2'-deoxyribonucleotides are also less efficiently incorporated in primer extension reactions, but the difference is more modest. Experiments with mixtures of nucleotides suggest that the coexistence of ribo- and arabinonucleotides does not impede the copying of RNA templates. Moreover, chimeric oligoribonucleotides containing 2'-deoxy- or arabinonucleotides are effective templates for RNA synthesis. We propose that the initial genetic polymers were random sequence chimeric oligonucleotides formed by untemplated polymerization, but that template copying chemistry favored RNA synthesis; multiple rounds of replication may have led to pools of oligomers composed mainly of RNA.
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http://dx.doi.org/10.1021/jacs.9b11239DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7577264PMC
February 2020

Dendritic cell activation by an E. coli-derived monophosphoryl lipid A enhances the efficacy of PD-1 blockade.

Cancer Lett 2020 03 17;472:19-28. Epub 2019 Dec 17.

KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Republic of Korea; Biomedical Research Institute, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea. Electronic address:

Cancer immunotherapy is a powerful approach for cancer treatment, but its clinical effects rely on the tumor's immune conditions. In particular, low response rates to PD-1 blockades are highly correlated with impaired T cell priming. Here, we demonstrate that E. coli-derived monophosphoryl lipid A (EcML) activates dendritic cells in a toll-like receptor-4 (TLR-4)-dependent manner and increases the sensitivity of cancer cells to anti-PD-1 immunotherapy. EcML is a mixture of 4'-monophosphoryl lipids A (MPLAs) produced directly by an engineered Escherichia coli strain; it has a unique congener composition that differentiates it from the well-established MPLA adjuvants, 3-O-desacyl-4'-monophosphoryl lipid A and glucopyranosyl lipid A. Given that active dendritic cells initiate adaptive immune responses, we investigated the anti-tumor activity of an aqueous formulation of EcML. Upon sensing EcML via TLR-4, dendritic cells matured into powerful antigen-presenting cells that could stimulate naïve T cells. EcML reduced tumor growth in the B16F10 mouse model via dendritic cell activation and potentiated PD-1 blockade therapy in the B16F10-OVA melanoma model. These data identify EcML as a promising TLR-4 agonist that can induce anti-tumor immune responses and potentiate PD-1 blockade therapy against tumors.
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http://dx.doi.org/10.1016/j.canlet.2019.12.012DOI Listing
March 2020

Non-enzymatic primer extension with strand displacement.

Elife 2019 11 8;8. Epub 2019 Nov 8.

Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.

Non-enzymatic RNA self-replication is integral to the emergence of the 'RNA World'. Despite considerable progress in non-enzymatic template copying, demonstrating a full replication cycle remains challenging due to the difficulty of separating the strands of the product duplex. Here, we report a prebiotically plausible approach to strand displacement synthesis in which short 'invader' oligonucleotides unwind an RNA duplex through a toehold/branch migration mechanism, allowing non-enzymatic primer extension on a template that was previously occupied by its complementary strand. Kinetic studies of single-step reactions suggest that following invader binding, branch migration results in a 2:3 partition of the template between open and closed states. Finally, we demonstrate continued primer extension with strand displacement by employing activated 3'-aminonucleotides, a more reactive proxy for ribonucleotides. Our study suggests that complete cycles of non-enzymatic replication of the primordial genetic material may have been facilitated by short RNA oligonucleotides.
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http://dx.doi.org/10.7554/eLife.51888DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6872209PMC
November 2019

Enantioselective Synthesis of α-Allyl Amino Esters via Hydrogen-Bond-Donor Catalysis.

J Am Chem Soc 2019 07 11;141(29):11414-11419. Epub 2019 Jul 11.

Department of Chemistry & Chemical Biology , Harvard University , Cambridge , Massachusetts 02138 , United States.

We report a chiral-squaramide-catalyzed enantio- and diastereoselective synthesis of α-allyl amino esters. The optimized protocol provides access to -carbamoyl-protected amino esters via nucleophilic allylation of readily accessible α-chloro glycinates. A variety of useful α-allyl amino esters were prepared, including crotylated products bearing vicinal stereocenters that are inaccessible through enolate alkylation, with high enantioselectivity (up to 97% ee) and diastereoselectivity (>10:1). The reactions display first-order kinetic dependence on both the α-chloro glycinate and the nucleophile, consistent with rate-limiting C-C bond formation. Computational analysis of the uncatalyzed reaction predicts an energetically inaccessible iminium intermediate, and a lower energy concerted S2 mechanism.
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http://dx.doi.org/10.1021/jacs.9b05556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293823PMC
July 2019

Ketalization of 2-heptanone to prolong its activity as mite repellant for the protection of honey bees.

J Sci Food Agric 2019 Nov 12;99(14):6267-6277. Epub 2019 Aug 12.

School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, NY, USA.

Background: 2-Heptanone is a volatile liquid known to be effective in protecting honey bees from parasitic mite infestations in hives. The present study aimed to show that chemical derivatives of 2-heptanone would release the ketone for a significantly longer time than it takes for the pure ketone to evaporate and preferably for as long as two brood cycles of a honey bee (42 days).

Results: A liquid ketal of 2-heptanone with glycerol (Glyc-Ket) and solid ketals of the ketone with polyvinyl alcohol (PVAl-Ket), containing different amounts of the ketone, were synthesized. The fully resolved H and C nuclear magenetic resonance (NMR) spectra of the ketals are discussed. In the case of the polymer, differential scanning calorimetry (DSC) of a ketal was also compared with the unketalized polyvinyl alcohol. The length of time for which 2-heptanone was released by the ketals was determined by gas chromatography-mass spectrometry of the headspace. In the case of Glyc-Ket, the concentration of the 2-heptanone in the liquid phase was also monitored by H NMR spectroscopy. The deketalization was pH dependent, ranging between 2.0 and 2.5 for Glyc-Ket and between 2.0 and 3.5 for PVAl-Ket.

Conclusion: Under bee hive conditions, the release of 55 mmol 2-heptanone from Glyc-Ket lasted for 42 days, whereas the release of the ketone from the PVAl-Ket with a similar amount of the ketone lasted for 23 days, versus a maximum of 17 days for an equivalent amount of the pure ketone. These ketals therefore have the potential to be effective mite repellants for the protection of honey bees. © 2019 Society of Chemical Industry.
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http://dx.doi.org/10.1002/jsfa.9900DOI Listing
November 2019

Inosine, but none of the 8-oxo-purines, is a plausible component of a primordial version of RNA.

Proc Natl Acad Sci U S A 2018 12 3;115(52):13318-13323. Epub 2018 Dec 3.

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138;

The emergence of primordial RNA-based life would have required the abiotic synthesis of nucleotides, and their participation in nonenzymatic RNA replication. Although considerable progress has been made toward potentially prebiotic syntheses of the pyrimidine nucleotides (C and U) and their 2-thio variants, efficient routes to the canonical purine nucleotides (A and G) remain elusive. Reported syntheses are low yielding and generate a large number of undesired side products. Recently, a potentially prebiotic pathway to 8-oxo-adenosine and 8-oxo-inosine has been demonstrated, raising the question of the suitability of the 8-oxo-purines as substrates for prebiotic RNA replication. Here we show that the 8-oxo-purine nucleotides are poor substrates for nonenzymatic RNA primer extension, both as activated monomers and when present in the template strand; their presence at the end of a primer also strongly reduces the rate and fidelity of primer extension. To provide a proper comparison with 8-oxo-inosine, we also examined primer extension reactions with inosine, and found that inosine exhibits surprisingly rapid and accurate nonenzymatic RNA copying. We propose that inosine, which can be derived from adenosine by deamination, could have acted as a surrogate for G in the earliest stages of the emergence of life.
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http://dx.doi.org/10.1073/pnas.1814367115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6310819PMC
December 2018

Diagnosing small bowel carcinoid tumor in a patient with oligometastatic prostate cancer imaged with PSMA-Targeted [F]DCFPyL PET/CT: Value of the PSMA-RADS-3D Designation.

Urol Case Rep 2018 Mar 19;17:22-25. Epub 2017 Dec 19.

The James Buchanan Brady Urological Institute and Department of Urology, United States.

Radiotracers targeting prostate-specific membrane antigen (PSMA), including [F]DCFPyL, have been extensively investigated as a means to image prostate cancer more accurately. We present the case of a man with oligometastatic prostate cancer who was also diagnosed with a metastatic small bowel carcinoid tumor following the detection of indeterminate findings on a [F]DCFPyL PET and discuss how this case highlights the utility of a newly proposed reporting system for PSMA-targeted PET (PSMA-RADS version 1.0).
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http://dx.doi.org/10.1016/j.eucr.2017.12.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5849869PMC
March 2018

Physicochemical study of ascorbic acid 2-glucoside loaded hyaluronic acid dissolving microneedles irradiated by electron beam and gamma ray.

Carbohydr Polym 2018 Jan 13;180:297-303. Epub 2017 Oct 13.

Department of Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Juvic Inc., Yonsei Engineering Research Park, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea. Electronic address:

A dissolving microneedle (DMN) patch encapsulated with ascorbic acid 2-glucoside (AA2G) in a needle-shaped hyaluronic acid (HA) backbone was fabricated and sterilized by electron beam (e-beam, 5-40kGy) and gamma ray (γ-ray, 5-30kGy). DMN structures maintained their morphologies and fracture force regardless of e-beam and γ-ray irradiation doses. Both e-beam (40kGy) and γ-ray (20 and 30kGy) met the product sterility requirements for cosmetics and vaccines; however, γ-ray irradiation significantly degraded the encapsulated AA2G, while e-beam maintained AA2G activity. Thus, an e-beam dose of 40kGy, which satisfied the sterility requirements without loss of AA2G, is suitable for terminal sterilization of DMNs. Moreover, we confirmed that the optimized irradiation (e-beam, 40kGy) did not affect dissolution rate and drug release profile of DMNs. Further, we confirmed that HA, the backbone polymer of DMNs, could be utilized as a stabilizer that inhibits degradation of encapsulated AA2G by irradiation. This detailed analysis can be developed further to optimize various biological drugs in transdermal drug delivery systems.
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http://dx.doi.org/10.1016/j.carbpol.2017.10.044DOI Listing
January 2018

Control of DEMETER DNA demethylase gene transcription in male and female gamete companion cells in .

Proc Natl Acad Sci U S A 2017 02 27;114(8):2078-2083. Epub 2017 Jan 27.

Department of Biological Sciences, Seoul National University, Seoul 151-747, Korea;

The DEMETER (DME) DNA glycosylase initiates active DNA demethylation via the base-excision repair pathway and is vital for reproduction in DME-mediated DNA demethylation is preferentially targeted to small, AT-rich, and nucleosome-depleted euchromatic transposable elements, influencing expression of adjacent genes and leading to imprinting in the endosperm. In the female gametophyte, expression and subsequent genome-wide DNA demethylation are confined to the companion cell of the egg, the central cell. Here, we show that, in the male gametophyte, expression is limited to the companion cell of sperm, the vegetative cell, and to a narrow window of time: immediately after separation of the companion cell lineage from the germline. We define transcriptional regulatory elements of using reporter genes, showing that a small region, which surprisingly lies within the gene, controls its expression in male and female companion cells. expression from this minimal promoter is sufficient to rescue seed abortion and the aberrant DNA methylome associated with the null mutation. Within this minimal promoter, we found short, conserved enhancer sequences necessary for the transcriptional activities of and combined predicted binding motifs with published transcription factor binding coordinates to produce a list of candidate upstream pathway members in the genetic circuitry controlling DNA demethylation in gamete companion cells. These data show how DNA demethylation is regulated to facilitate endosperm gene imprinting and potential transgenerational epigenetic regulation, without subjecting the germline to potentially deleterious transposable element demethylation.
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http://dx.doi.org/10.1073/pnas.1620592114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5338364PMC
February 2017

Prevalence of chronic disease and its controlled status according to income level.

Medicine (Baltimore) 2016 Nov;95(44):e5286

Department of Internal Medicine Department of General Surgery Department of Urology, Inje University Seoul Paik Hospital Department of Internal Medicine, Inje University Ilsan Paik Hospital, Inje University School of Medicine, Jung-gu, Seoul Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam-si, Kyeonggi-do, Republic of Korea.

The relationship between the prevalence of chronic diseases and income level has now become a main theme in poor national economic situations. We examined the prevalence of well-controlled chronic diseases according to income level. Data from the 2008 to 2014 Korea National Health and Nutrition Examination Survey, conducted by using a stratified, multistage, probability-cluster sampling method, were used. Systolic blood pressure (SBP) inversely correlated with income level (P < 0.001). Diastolic blood pressure (DBP) showed no relationship. In the low-income group, the prevalence rates of hypertension and diabetes mellitus (DM) were highest but the proportion of patients with well-controlled chronic disease and the SBPs of the patients with hypertension showed a decreasing trend. In the high-income group, the proportions of patients with well-controlled DM and chronic kidney disease were higher than those in other groups. After adjusting for age, body mass index, SBP, DBP, HbA1c level, and serum creatinine level, income level significantly affected the prevalence of chronic diseases (for income, β=0.184; 95% confidence interval, 1.105-1.042). The daily sodium intake estimated by using spot urine samples was higher in the low- and low-to-mid-income groups. The prevalence of not using essential medical service for chronic disease was highest in the low- and low-to-mid-income groups for economic reasons. In the low- and low-to-mid-income groups, the prevalence of chronic disease was higher and the proportion of patients with well-controlled chronic disease was lower than in the other groups.
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http://dx.doi.org/10.1097/MD.0000000000005286DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5591148PMC
November 2016

Chronic expression of interferon-gamma leads to murine autoimmune cholangitis with a female predominance.

Hepatology 2016 10 15;64(4):1189-201. Epub 2016 Jun 15.

Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, MD.

Unlabelled: In most autoimmune diseases the serologic hallmarks of disease precede clinical pathology by years. Therefore, the use of animal models in defining early disease events becomes critical. We took advantage of a "designer" mouse with dysregulation of interferon gamma (IFNγ) characterized by prolonged and chronic expression of IFNγ through deletion of the IFNγ 3'-untranslated region adenylate uridylate-rich element (ARE). The ARE-Del(-/-) mice develop primary biliary cholangitis (PBC) with a female predominance that mimics human PBC that is characterized by up-regulation of total bile acids, spontaneous production of anti-mitochondrial antibodies, and portal duct inflammation. Transfer of CD4 T cells from ARE-Del(-/-) to B6/Rag1(-/-) mice induced moderate portal inflammation and parenchymal inflammation, and RNA sequencing of liver gene expression revealed that up-regulated genes potentially define early stages of cholangitis. Interestingly, up-regulated genes specifically overlap with the gene expression signature of biliary epithelial cells in PBC, implying that IFNγ may play a pathogenic role in biliary epithelial cells in the initiation stage of PBC. Moreover, differentially expressed genes in female mice have stronger type 1 and type 2 IFN signaling and lymphocyte-mediated immune responses and thus may drive the female bias of the disease.

Conclusion: Changes in IFNγ expression are critical for the pathogenesis of PBC. (Hepatology 2016;64:1189-1201).
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http://dx.doi.org/10.1002/hep.28641DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5033675PMC
October 2016
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