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Article ; Online: Contrasting views on the role of AMPK in autophagy.

Kim, Do-Hyung

BioEssays : news and reviews in molecular, cellular and developmental biology

2024 Volume 46, Issue 3, Page(s) e2300211

Abstract: Efficient management of low energy states is vital for cells to maintain basic functions and metabolism and avoid cell death. While autophagy has long been considered a critical mechanism for ensuring survival during energy depletion, recent research has ...

Abstract	Efficient management of low energy states is vital for cells to maintain basic functions and metabolism and avoid cell death. While autophagy has long been considered a critical mechanism for ensuring survival during energy depletion, recent research has presented conflicting evidence, challenging the long-standing concept. This recent development suggests that cells prioritize preserving essential cellular components while restraining autophagy induction when cellular energy is limited. This essay explores the conceptual discourse on autophagy regulation during energy stress, navigating through the studies that established the current paradigm and the recent research that has challenged its validity while proposing an alternative model. This exploration highlights the far-reaching implications of the alternative model, which represents a conceptual departure from the established paradigm, offering new perspectives on how cells respond to energy stress.
MeSH term(s)	AMP-Activated Protein Kinases/metabolism ; Autophagy/physiology
Chemical Substances	AMP-Activated Protein Kinases (EC 2.7.11.31)
Language	English
Publishing date	2024-01-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.202300211
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Article: Technical Aspects of Lung Transplantation: Adverse Events and Circumstances.

Kim, Do Hyung

Journal of chest surgery

2022 Volume 55, Issue 4, Page(s) 307–312

Abstract: Adverse events or emergency situations that are unacceptable in the context of lung transplantation may occur during the procedure. These adverse events and circumstances are not problems that are caused by insufficient experience or can be solved by ... ...

Abstract	Adverse events or emergency situations that are unacceptable in the context of lung transplantation may occur during the procedure. These adverse events and circumstances are not problems that are caused by insufficient experience or can be solved by increasing surgical experience. The purpose of this review is to describe the adverse events and circumstances that occur during lung transplantation and to identify an appropriate surgical approach through an analysis of case reports in the global literature.
Language	English
Publishing date	2022-08-03
Publishing country	Korea (South)
Document type	Journal Article
ISSN	2765-1606
ISSN	2765-1606
DOI	10.5090/jcs.22.054
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Article: A Novel Acute Discogenic Myelopathy Model Using Merocel

Kim, Do-Hyung / Sim, Ki-Bum

Korean journal of neurotrauma

2023 Volume 19, Issue 2, Page(s) 204–217

Abstract: Objective: Animal models of spinal cord injuries (SCIs) use rats to simulate human SCIs. Among the various techniques, clips have been used to reproduce the compression-contusion model. However, the mechanism of injury in discogenic incomplete SCI may ... ...

Abstract	Objective: Animal models of spinal cord injuries (SCIs) use rats to simulate human SCIs. Among the various techniques, clips have been used to reproduce the compression-contusion model. However, the mechanism of injury in discogenic incomplete SCI may differ from that in clip injury; however, a model has yet to be established. Previously, we issued a patent (No. 10-2053770) for a rat SCI model using Merocel Methods: This study included 4 groups of rats: MC (n=30), MC-sham (n=5), clip (n=30), and clip-sham (n=5). Locomotor function was evaluated in all groups using the Basso, Beattie, and Bresnahan (BBB) scoring system, 4 weeks after injury. Histopathological analyses included morphology, presence of inflammatory cells, microglial activation, and extent of neuronal damage, which were compared among the groups. Results: The BBB scores in the MC group were significantly higher than those in the clip group throughout the 4 weeks ( Conclusion: The novel MC group can help elucidate the pathophysiology of acute discogenic incomplete SCIs and may be applied in various SCI therapeutic strategies.
Language	English
Publishing date	2023-06-23
Publishing country	Korea (South)
Document type	Journal Article
ZDB-ID	3028579-3
ISSN	2288-2243 ; 2234-8999
ISSN (online)	2288-2243
ISSN	2234-8999
DOI	10.13004/kjnt.2023.19.e28
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Article: Erratum: A Novel Acute Discogenic Myelopathy Model Using Merocel

Kim, Do-Hyung / Sim, Ki-Bum

Korean journal of neurotrauma

2023 Volume 19, Issue 3, Page(s) 405

Abstract: This corrects the article on p. 204 in vol. 19, PMID: 37431382.]. ...

Abstract	[This corrects the article on p. 204 in vol. 19, PMID: 37431382.].
Language	English
Publishing date	2023-08-24
Publishing country	Korea (South)
Document type	Published Erratum
ZDB-ID	3028579-3
ISSN	2288-2243 ; 2234-8999
ISSN (online)	2288-2243
ISSN	2234-8999
DOI	10.13004/kjnt.2023.19.e38
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Article ; Online: A paradigm shift: AMPK negatively regulates ULK1 activity.

Park, Ji-Man / Kim, Do-Hyung

Autophagy

2023 Volume 20, Issue 4, Page(s) 960–962

Abstract: In glucose-starved cells, macroautophagy (hereafter referred to as autophagy) is considered to serve as an energy-generating process contributing to cell survival. AMPK (adenosine monophosphate-activated protein kinase) is the primary cellular energy ... ...

Abstract	In glucose-starved cells, macroautophagy (hereafter referred to as autophagy) is considered to serve as an energy-generating process contributing to cell survival. AMPK (adenosine monophosphate-activated protein kinase) is the primary cellular energy sensor that is activated during glucose starvation. According to the current paradigm in the field, AMPK promotes autophagy in response to energy deprivation by binding and phosphorylating ULK1 (UNC-51 like kinase 1), the protein kinase responsible for autophagy initiation. However, conflicting findings have been reported casting doubts about the current established model. In our recent study, we have thoroughly reevaluated the role of AMPK in autophagy. Contrary to the current paradigm, our study revealed that AMPK functions as a negative regulator of ULK1 activity. The study has elucidated the underlying mechanism and demonstrated the significance of the negative role in controlling autophagy and maintaining cellular resilience during energy depletion.
MeSH term(s)	Autophagy-Related Protein-1 Homolog/metabolism ; Humans ; AMP-Activated Protein Kinases/metabolism ; Autophagy/physiology ; Animals ; Models, Biological ; Intracellular Signaling Peptides and Proteins
Chemical Substances	Autophagy-Related Protein-1 Homolog (EC 2.7.11.1) ; AMP-Activated Protein Kinases (EC 2.7.11.31) ; ULK1 protein, human (EC 2.7.11.1) ; Intracellular Signaling Peptides and Proteins
Language	English
Publishing date	2023-06-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.1080/15548627.2023.2223465
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Article ; Online: Automated CT quantification of interstitial lung abnormality in patients with resectable stage I non-small cell lung cancer: Prognostic significance.

Chung, Jae Ho / Park, Jong Myung / Kim, Do Hyung

Thoracic cancer

2024

Abstract: Background: In patients with non-small cell lung cancer (NSCLC), interstitial lung abnormalities (ILA) have been linked to mortality and can be identified on computed tomography (CT) scans. In the present study we aimed to evaluate the predictive value ... ...

Abstract	Background: In patients with non-small cell lung cancer (NSCLC), interstitial lung abnormalities (ILA) have been linked to mortality and can be identified on computed tomography (CT) scans. In the present study we aimed to evaluate the predictive value of automatically quantified ILA based on the Fleischner Society definition in patients with stage I NSCLC. Methods: We retrospectively reviewed 948 patients with pathological stage I NSCLC who underwent pulmonary resection between April 2009 and October 2022. A commercially available deep learning-based automated quantification program for ILA was used to evaluate the preoperative CT data. The Fleischner Society definition, quantitative results, and interdisciplinary discussion led to the division of patients into normal and ILA groups. The sum of the fibrotic and nonfibrotic ILA components constituted the total ILA component and more than 5%. Results: Of the 948 patients with stage I NSCLC, 99 (10.4%) patients had ILA. Shorter overall survival and recurrence-free survival was associated with the presence of ILA. After controlling for confounding variables, the presence of ILA remained significant for increased risk of death (hazard ratio [HR] = 3.09; 95% confidence interval [CI]: 1.91-5.00; p < 0.001) and the presence of ILA remained significant for increased recurrence (HR = 1.96; 95% CI: 1.16-3.30; p = 0.012). Conclusions: The automated CT quantification of ILA, based on the Fleischner Society definition, was significantly linked to poorer survival and recurrence in patients with stage I NSCLC.
Language	English
Publishing date	2024-04-29
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2625856-0
ISSN	1759-7714 ; 1759-7706
ISSN (online)	1759-7714
ISSN	1759-7706
DOI	10.1111/1759-7714.15306
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Article ; Online: Identification, classification and functional characterization of HSP70s in rainbow trout (Oncorhynchus mykiss) through multi-omics approaches.

Roh, HyeongJin / Kim, Do-Hyung

Fish & shellfish immunology

2022 Volume 121, Page(s) 205–214

Abstract: Heat shock protein 70s (HSP70s) are known to play vital biological processes in rainbow trout. However, information on the numerous roles and classification of many different HSP70s is insufficient. The purpose of this study was to investigate the ... ...

Abstract	Heat shock protein 70s (HSP70s) are known to play vital biological processes in rainbow trout. However, information on the numerous roles and classification of many different HSP70s is insufficient. The purpose of this study was to investigate the characteristics of all HSP70s in rainbow trout using multi-dimensional genomic and transcriptomic analyses for inspecting HSP70 homologs, phylogenetic characteristics, DNA motifs, and transcription factor binding sites (TFBSs). Also, the transcriptomic results in conditions of acute thermal stress and Ichthyophthirius multifiliis infection were used to characterize the expression of all HSP70 homologs, and the isoforms of the most sensitive HSP70 were predicted in silico. A total of 23 HSP70s were identified, and they were divided into seven evolutionary groups (groups 1-7). Groups 1 and 2 had relatively longer phylogenetic distances compared to the other groups, which can speculate origin of groups 1 and 2 HSP70s would be different compared to others. With transcriptomic profiling, most HSPs belonging to group 3 showed highly sensitive responses to I. multifiliis infection, not thermal stress, but the group 6 HSP70s had the opposite expression tendencies. Likewise, the composition of the TFBS in each HSP70 was consistent with its group classification. Since TFBSs are widely known to influence transcriptomic expression, they could be one of the major reasons for the different patterns of expression within the HSP70 groups. Moreover, this study demonstrated several isoforms of HSP70a, by far the most sensitive HSP70s, under several stress environments such as hypoxia, thermal, and overcrowding stress. This is an important fundamental study to expand the understanding of HSP70s in rainbow trout as well as for selecting the most sensitive biomarkers for types of stress.
MeSH term(s)	Animals ; Fish Proteins/genetics ; Gene Expression Profiling ; Genomics ; HSP70 Heat-Shock Proteins/genetics ; Oncorhynchus mykiss/genetics ; Phylogeny ; Stress, Physiological
Chemical Substances	Fish Proteins ; HSP70 Heat-Shock Proteins
Language	English
Publishing date	2022-01-03
Publishing country	England
Document type	Journal Article
ZDB-ID	1067738-0
ISSN	1095-9947 ; 1050-4648
ISSN (online)	1095-9947
ISSN	1050-4648
DOI	10.1016/j.fsi.2021.12.059
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Article ; Online: Intraoperative Handheld Digital X-ray for Assessment of Intracochlear Positioning of Electrode Arrays in Recipients of Cochlear Implants.

Shin, Bong-Jin / Kim, Hong Chan / Kim, Do Hyung / Cho, Hyong-Ho

Ear, nose, & throat journal

2024 , Page(s) 1455613231223954

Abstract: Objectives: ...

Abstract	Objectives:
Language	English
Publishing date	2024-02-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	750153-5
ISSN	1942-7522 ; 0145-5613
ISSN (online)	1942-7522
ISSN	0145-5613
DOI	10.1177/01455613231223954
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Article: Wide-genome selection of lactic acid bacteria harboring genes that promote the elimination of antinutritional factors.

Pham, Hai-Ha-Thi / Kim, Do-Hyung / Nguyen, Thanh Luan

Frontiers in plant science

2023 Volume 14, Page(s) 1145041

Abstract: Anti-nutritional factors (ANFs) substances in plant products, such as indigestible non-starchy polysaccharides (α-galactooligosaccharides, α-GOS), phytate, tannins, and alkaloids can impede the absorption of many critical nutrients and cause major ... ...

Abstract	Anti-nutritional factors (ANFs) substances in plant products, such as indigestible non-starchy polysaccharides (α-galactooligosaccharides, α-GOS), phytate, tannins, and alkaloids can impede the absorption of many critical nutrients and cause major physiological disorders. To enhance silage quality and its tolerance threshold for humans as well as other animals, ANFs must be reduced. This study aims to identify and compare the bacterial species/strains that are potential use for industrial fermentation and ANFs reduction. A pan-genome study of 351 bacterial genomes was performed, and binary data was processed to quantify the number of genes involved in the removal of ANFs. Among four pan-genomes analysis, all 37 tested
Language	English
Publishing date	2023-04-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2023.1145041
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Article ; Online: Redefining the role of AMPK in autophagy and the energy stress response.

Park, Ji-Man / Lee, Da-Hye / Kim, Do-Hyung

Nature communications

2023 Volume 14, Issue 1, Page(s) 2994

Abstract: Autophagy maintains cellular homeostasis during low energy states. According to the current understanding, glucose-depleted cells induce autophagy through AMPK, the primary energy-sensing kinase, to acquire energy for survival. However, contrary to the ... ...

Abstract	Autophagy maintains cellular homeostasis during low energy states. According to the current understanding, glucose-depleted cells induce autophagy through AMPK, the primary energy-sensing kinase, to acquire energy for survival. However, contrary to the prevailing concept, our study demonstrates that AMPK inhibits ULK1, the kinase responsible for autophagy initiation, thereby suppressing autophagy. We found that glucose starvation suppresses amino acid starvation-induced stimulation of ULK1-Atg14-Vps34 signaling via AMPK activation. During an energy crisis caused by mitochondrial dysfunction, the LKB1-AMPK axis inhibits ULK1 activation and autophagy induction, even under amino acid starvation. Despite its inhibitory effect, AMPK protects the ULK1-associated autophagy machinery from caspase-mediated degradation during energy deficiency, preserving the cellular ability to initiate autophagy and restore homeostasis once the stress subsides. Our findings reveal that dual functions of AMPK, restraining abrupt induction of autophagy upon energy shortage while preserving essential autophagy components, are crucial to maintain cellular homeostasis and survival during energy stress.
MeSH term(s)	Humans ; Amino Acids ; AMP-Activated Protein Kinases ; Autophagy ; Caspases ; Glucose ; Cells, Cultured
Chemical Substances	Amino Acids ; AMP-Activated Protein Kinases (EC 2.7.11.31) ; Caspases (EC 3.4.22.-) ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2023-05-24
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-38401-z
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