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1.
Pediatr Int ; 66(1): e15769, 2024.
Article in English | MEDLINE | ID: mdl-38742693

ABSTRACT

BACKGROUND: Spinal muscular atrophy (SMA) is an autosomal recessive disorder characterized by degeneration of lower motor neurons, resulting in progressive muscle weakness and atrophy. However, little is known regarding the cardiac function of children with SMA. METHODS: We recruited SMA patients younger than 18 years of age from January 1, 2022, to April 1, 2022, in the First Affiliated Hospital of Sun Yat-sen University. All patients underwent a comprehensive cardiac evaluation before treatment, including history taking, physical examination, blood tests of cardiac biomarkers, assessment of echocardiography and electrocardiogram. Age/gender-matched healthy volunteers were recruited as controls. RESULTS: A total of 36 SMA patients (26 with SMA type 2 and 10 with SMA type 3) and 40 controls were enrolled in the study. No patient was clinically diagnosed with heart failure. Blood tests showed elevated values of creatine kinase isoenzyme M and isoenzyme B (CK-MB) mass and high-sensitivity cardiac troponin T (hs-cTnT) in spinal muscular atrophy (SMA) patients. Regarding echocardiographic parameters, SMA children were detected with lower global left and right ventricular longitudinal strain, abnormal diastolic filling velocities of trans-mitral and trans-tricuspid flow. The results revealed no clinical heart dysfunction in SMA patients, but subclinical ventricular dysfunction was seen in SMA children including the diastolic function and myocardial performance. Some patients presented with elevated heart rate and abnormal echogenicity of aortic valve or wall. Among these SMA patients, seven patients (19.4%) had scoliosis. The Cobb's angles showed a significant negative correlation with LVEDd/BSA, but no correlation with other parameters, suggesting that mild scoliosis did not lead to significant cardiac dysfunction. CONCLUSIONS: Our findings warrant increased attention to the cardiac status and highlight the need to investigate cardiac interventions in SMA children.


Subject(s)
Echocardiography , Humans , Male , Female , Case-Control Studies , Child , Child, Preschool , Adolescent , Electrocardiography , Infant , Muscular Atrophy, Spinal/diagnosis , Muscular Atrophy, Spinal/physiopathology , Muscular Atrophy, Spinal/blood , Biomarkers/blood , Spinal Muscular Atrophies of Childhood/diagnosis , Spinal Muscular Atrophies of Childhood/physiopathology , Spinal Muscular Atrophies of Childhood/blood , Spinal Muscular Atrophies of Childhood/complications , Heart Function Tests/methods
2.
BMC Genomics ; 25(1): 406, 2024 May 09.
Article in English | MEDLINE | ID: mdl-38724906

ABSTRACT

Most proteins exert their functions by interacting with other proteins, making the identification of protein-protein interactions (PPI) crucial for understanding biological activities, pathological mechanisms, and clinical therapies. Developing effective and reliable computational methods for predicting PPI can significantly reduce the time-consuming and labor-intensive associated traditional biological experiments. However, accurately identifying the specific categories of protein-protein interactions and improving the prediction accuracy of the computational methods remain dual challenges. To tackle these challenges, we proposed a novel graph neural network method called GNNGL-PPI for multi-category prediction of PPI based on global graphs and local subgraphs. GNNGL-PPI consisted of two main components: using Graph Isomorphism Network (GIN) to extract global graph features from PPI network graph, and employing GIN As Kernel (GIN-AK) to extract local subgraph features from the subgraphs of protein vertices. Additionally, considering the imbalanced distribution of samples in each category within the benchmark datasets, we introduced an Asymmetric Loss (ASL) function to further enhance the predictive performance of the method. Through evaluations on six benchmark test sets formed by three different dataset partitioning algorithms (Random, BFS, DFS), GNNGL-PPI outperformed the state-of-the-art multi-category prediction methods of PPI, as measured by the comprehensive performance evaluation metric F1-measure. Furthermore, interpretability analysis confirmed the effectiveness of GNNGL-PPI as a reliable multi-category prediction method for predicting protein-protein interactions.


Subject(s)
Algorithms , Computational Biology , Neural Networks, Computer , Protein Interaction Mapping , Protein Interaction Mapping/methods , Computational Biology/methods , Protein Interaction Maps , Humans , Proteins/metabolism
3.
Circulation ; 2024 May 06.
Article in English | MEDLINE | ID: mdl-38708635

ABSTRACT

BACKGROUND: Recent interest in understanding cardiomyocyte cell cycle has been driven by potential therapeutic applications in cardiomyopathy. However, despite recent advances, cardiomyocyte mitosis remains a poorly understood process. For example, it is unclear how sarcomeres are disassembled during mitosis to allow the abscission of daughter cardiomyocytes. METHODS: Here, we use a proteomics screen to identify adducin, an actin capping protein previously not studied in cardiomyocytes, as a regulator of sarcomere disassembly. We generated many adeno-associated viruses and cardiomyocyte-specific genetic gain-of-function models to examine the role of adducin in neonatal and adult cardiomyocytes in vitro and in vivo. RESULTS: We identify adducin as a regulator of sarcomere disassembly during mammalian cardiomyocyte mitosis. α/γ-adducins are selectively expressed in neonatal mitotic cardiomyocytes, and their levels decline precipitously thereafter. Cardiomyocyte-specific overexpression of various splice isoforms and phospho-isoforms of α-adducin in identified Thr445/Thr480 phosphorylation of a short isoform of α-adducin as a potent inducer of neonatal cardiomyocyte sarcomere disassembly. Concomitant overexpression of this α-adducin variant along with γ-adducin resulted in stabilization of the adducin complex and persistent sarcomere disassembly in adult mice, which is mediated by interaction with α-actinin. CONCLUSIONS: These results highlight an important mechanism for coordinating cytoskeletal morphological changes during cardiomyocyte mitosis.

4.
Exp Cell Res ; 439(1): 114068, 2024 May 13.
Article in English | MEDLINE | ID: mdl-38750717

ABSTRACT

Acetylation, a critical regulator of diverse cellular processes, holds significant implications in various cancer contexts. Further understanding of the acetylation patterns of key cancer-driven proteins is crucial for advancing therapeutic strategies in cancer treatment. This study aimed to unravel the acetylation patterns of Engulfment and Cell Motility Protein 1 (ELMO1) and its relevance to the pathogenesis of colorectal cancer (CRC). Immunoprecipitation and mass spectrometry precisely identified lysine residue 505 (K505) as a central acetylation site in ELMO1. P300 emerged as the acetyltransferase for ELMO1 K505 acetylation, while SIRT2 was recognized as the deacetylase. Although K505 acetylation minimally affected ELMO1's localization and stability, it played a crucial role in mediating ELMO1-Dock180 interaction, thereby influencing Rac1 activation. Functionally, ELMO1 K505 acetylation proved to be a pivotal factor in CRC progression, exerting its influence on key cellular processes. Clinical analysis of CRC samples unveiled elevated ELMO1 acetylation in primary tumors, indicating a potential association with CRC pathologies. This work provides insights into ELMO1 acetylation and its significance in advancing potentially therapeutic interventions in CRC treatment.

5.
Article in Chinese | MEDLINE | ID: mdl-38686486

ABSTRACT

Trichoblastoma(TB) is a rare germ cell skin adnexal tumor of the hair, and it is a rare follicular tumor of the skin that differentiates from the hair germ epithelium and is often regarded as a benign skin tumorHowever, it is poorly confined and has a local infiltrative growth pattern. tb occurs in the head and neck region, especially in the face, and presents clinically as a slow growing, well-defined and elevated nodule. TB is routinely treated surgically. Due to the lack of universally accepted treatment guidelines or protocols, the recurrence rate after surgery is high, which makes clinical cure more difficult. In this study, a 65-year-old female patient was found to have a swelling with recurrent rupture and pus flow from the right external auditory canal opening and the auricular cavity. After initial misdiagnosis as otitis externa, she was treated with conventional anti-infective therapy, but her symptoms did not resolve and gradually worsened before coming to our hospital. The condition presented in this case is relativelyrare,therepre,timely and accurate diagnosis and treatment are crucial for prognosis improvement of such diseases.


Subject(s)
Skin Neoplasms , Humans , Female , Aged , Skin Neoplasms/pathology , Skin Neoplasms/diagnosis , Ear Neoplasms/pathology , Neoplasms, Adnexal and Skin Appendage/pathology , Neoplasms, Adnexal and Skin Appendage/diagnosis , Ear Canal/pathology
6.
BMC Geriatr ; 24(1): 331, 2024 Apr 11.
Article in English | MEDLINE | ID: mdl-38605326

ABSTRACT

BACKGROUND: Motor cognitive risk syndrome (MCR) represents a critical pre-dementia and disability state characterized by a combination of objectively measured slow walking speed and subjective memory complaints (SMCs). This study aims to identify risk factors for MCR and investigate the relationship between plasma levels of 8-hydroxy-2'-deoxyguanosine (8-OHdG) and MCR among Chinese community-dwelling elderly populations. METHODS: A total of 1312 participants were involved in this study based on the data of the Rugao Longevity and Aging Study (RuLAS). The MCR was characterized by SMCs and slow walking speed. The SCCs were defined as a positive answer to the question 'Do you feel you have more problems with memory than most?' in a 15-item Geriatric Depression Scale. Slow walking speed was determined by one standard deviation or more below the mean value of the patient's age and gender group. The plasma of 8-OHdG were measured by a technician in the biochemistry laboratory of the Rugao People's Hospital during the morning of the survey. RESULTS: The prevalence of MCR was found to be 7.9%. After adjusting for covariates, significant associations with MCR were observed in older age (OR 1.057; p = 0.018), history of cerebrovascular disease (OR 2.155; p = 0.010), and elevated 8-OHdG levels (OR 1.007; p = 0.003). CONCLUSIONS: This study indicated the elevated plasma 8-OHdG is significantly associated with increased MCR risk in the elderly, suggesting its potential as a biomarker for early detection and intervention in MCR. This finding underscores the importance of monitoring oxidative DNA damage markers in predicting cognitive and motor function declines, offering new avenues for research and preventive strategies in aging populations.


Subject(s)
Cognition Disorders , Cognitive Dysfunction , East Asian People , Humans , Aged , Cognition Disorders/diagnosis , Cross-Sectional Studies , 8-Hydroxy-2'-Deoxyguanosine , Longevity , Aging/psychology , Risk Factors , Cognition , Cognitive Dysfunction/epidemiology
7.
Article in English | MEDLINE | ID: mdl-38648138

ABSTRACT

Surface reconstruction for point clouds is an important task in 3D computer vision. Most of the latest methods resolve this problem by learning signed distance functions from point clouds, which are limited to reconstructing closed surfaces. Some other methods tried to represent open surfaces using unsigned distance functions (UDF) which are learned from ground truth distances. However, the learned UDF is hard to provide smooth distance fields due to the discontinuous character of point clouds. In this paper, we propose CAP-UDF, a novel method to learn consistency-aware UDF from raw point clouds. We achieve this by learning to move queries onto the surface with a field consistency constraint, where we also enable to progressively estimate a more accurate surface. Specifically, we train a neural network to gradually infer the relationship between queries and the approximated surface by searching for the moving target of queries in a dynamic way. Meanwhile, we introduce a polygonization algorithm to extract surfaces using the gradients of the learned UDF. We conduct comprehensive experiments in surface reconstruction for point clouds, real scans or depth maps, and further explore our performance in unsupervised point normal estimation, which demonstrate non-trivial improvements of CAP-UDF over the state-of-the-art methods.

8.
Front Pharmacol ; 15: 1375522, 2024.
Article in English | MEDLINE | ID: mdl-38628639

ABSTRACT

Accurate calculation of drug-target affinity (DTA) is crucial for various applications in the pharmaceutical industry, including drug screening, design, and repurposing. However, traditional machine learning methods for calculating DTA often lack accuracy, posing a significant challenge in accurately predicting DTA. Fortunately, deep learning has emerged as a promising approach in computational biology, leading to the development of various deep learning-based methods for DTA prediction. To support researchers in developing novel and highly precision methods, we have provided a comprehensive review of recent advances in predicting DTA using deep learning. We firstly conducted a statistical analysis of commonly used public datasets, providing essential information and introducing the used fields of these datasets. We further explored the common representations of sequences and structures of drugs and targets. These analyses served as the foundation for constructing DTA prediction methods based on deep learning. Next, we focused on explaining how deep learning models, such as Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs), Transformer, and Graph Neural Networks (GNNs), were effectively employed in specific DTA prediction methods. We highlighted the unique advantages and applications of these models in the context of DTA prediction. Finally, we conducted a performance analysis of multiple state-of-the-art methods for predicting DTA based on deep learning. The comprehensive review aimed to help researchers understand the shortcomings and advantages of existing methods, and further develop high-precision DTA prediction tool to promote the development of drug discovery.

9.
Zhongguo Dang Dai Er Ke Za Zhi ; 26(3): 321-324, 2024 Mar 15.
Article in Chinese | MEDLINE | ID: mdl-38557387

ABSTRACT

The male patient, one day old, was admitted to the hospital due to hypoglycemia accompanied by apnea appearing six hours after birth. The patient had transient hypoglycemia early after birth, and acute heart failure suddenly occurred on the eighth day after birth. Laboratory tests showed significantly reduced levels of adrenocorticotropic hormone and cortisol, and pituitary magnetic resonance imaging was normal. Genetic testing results showed that the patient had probably pathogenic compound heterozygous mutations of the TBX19 gene (c.917-2A>G+c.608C>T), inherited respectively from the parents. The patient was conclusively diagnosed with congenital isolated adrenocorticotropic hormone deficiency caused by mutation of the TBX19 gene. Upon initiating hydrocortisone replacement therapy, cardiac function rapidly returned to normal. After being discharged, the patient continued with the hydrocortisone replacement therapy. By the 18-month follow-up, the patient was growing and developing well. In neonates, unexplained acute heart failure requires caution for possible endocrine hereditary metabolic diseases, and timely cortisol testing and genetic testing should be conducted.


Subject(s)
Adrenal Insufficiency , Heart Failure , Hypoglycemia , Infant, Newborn , Humans , Male , Hydrocortisone/therapeutic use , Hypoglycemia/etiology , Adrenal Insufficiency/congenital , Adrenal Insufficiency/diagnosis , Adrenal Insufficiency/genetics , Heart Failure/etiology , Heart Failure/genetics , Adrenocorticotropic Hormone
10.
Gut Microbes ; 16(1): 2333413, 2024.
Article in English | MEDLINE | ID: mdl-38561312

ABSTRACT

Urinary tract infections (UTIs) are among the most common late-onset infections in preterm infants, characterized by nonspecific symptoms and a pathogenic spectrum that diverges from that of term infants and older children, which present unique diagnostic and therapeutic challenges. Existing data on the role of gut microbiota in UTI pathogenesis in this demographic are limited. This study aims to investigate alterations in gut microbiota and fecal calprotectin levels and their association with the development of UTIs in hospitalized preterm infants. A longitudinal case-control study was conducted involving preterm infants admitted between January 2018 and October 2020. Fecal samples were collected weekly and analyzed for microbial profiles and calprotectin levels. Propensity score matching, accounting for key perinatal factors including age and antibiotic use, was utilized to match samples from UTI-diagnosed infants to those from non-UTI counterparts. Among the 151 preterm infants studied, 53 were diagnosed with a UTI, predominantly caused by Enterobacteriaceae (79.3%) and Enterococcaceae (19.0%). Infants with UTIs showed a significantly higher abundance of these families compared to non-UTI infants, for both Gram-negative and positive pathogens, respectively. Notably, there was a significant pre-UTI increase in the abundance of pathogen-specific taxa in infants later diagnosed with UTIs, offering high predictive value for early detection. Shotgun metagenomic sequencing further confirmed the dominance of specific pathogenic species pre-UTI and revealed altered virulence factor profiles associated with Klebsiella aerogenes and Escherichia coli infections. Additionally, a decline in fecal calprotectin levels was observed preceding UTI onset, particularly in cases involving Enterobacteriaceae. The observed pathogen-specific alterations in the gut microbiota preceding UTI onset offer novel insight into the UTI pathogenesis and promising early biomarkers for UTIs in preterm infants, potentially enhancing the timely management of this common infection. However, further validation in larger cohorts is essential to confirm these findings.


Subject(s)
Gastrointestinal Microbiome , Urinary Tract Infections , Infant , Child , Humans , Infant, Newborn , Adolescent , Case-Control Studies , Escherichia coli , Infant, Premature , Anti-Bacterial Agents/therapeutic use , Enterobacteriaceae , Leukocyte L1 Antigen Complex
11.
Micromachines (Basel) ; 15(4)2024 Mar 29.
Article in English | MEDLINE | ID: mdl-38675284

ABSTRACT

Fixed-diamond abrasive wire saw cutting is one of the most common methods for cutting hard and brittle materials. This process has unique advantages including a narrow kerf and the ability to use a relatively small cutting force. In the cutting process, controlling the main process parameters can improve the processing efficiency, obtaining a better processing surface roughness. This work designs the PI controller (Proportional-Integral controller) based on the reciprocating wire saw cutting process. The control objects are the workpiece feed rate and wire saw velocity, and the control objective is the normal cutting force. For the control trials, several reference values of various normal cutting forces were chosen. The effects of feed rate and saw velocity on the cutting surface finish and cutting time were investigated in this work using wire saw cutting analysis on a square monocrystalline silicon specimen. The results of this study showed that under a constant applied force of 2.5 N, the optimal feed rate of the diamond wire through the specimen could reduce cutting time by 42% while achieving a 60% improvement in the measured surface finish. Likewise, optimal control of the wire saw velocity could reduce cycle time by 18% with a 45% improvement in the surface finish. Consequently, the feed speed control is more effective than the wire saw velocity.

12.
BMC Bioinformatics ; 25(1): 156, 2024 Apr 20.
Article in English | MEDLINE | ID: mdl-38641811

ABSTRACT

BACKGROUND: Accurately identifying drug-target interaction (DTI), affinity (DTA), and binding sites (DTS) is crucial for drug screening, repositioning, and design, as well as for understanding the functions of target. Although there are a few online platforms based on deep learning for drug-target interaction, affinity, and binding sites identification, there is currently no integrated online platforms for all three aspects. RESULTS: Our solution, the novel integrated online platform Drug-Online, has been developed to facilitate drug screening, target identification, and understanding the functions of target in a progressive manner of "interaction-affinity-binding sites". Drug-Online platform consists of three parts: the first part uses the drug-target interaction identification method MGraphDTA, based on graph neural networks (GNN) and convolutional neural networks (CNN), to identify whether there is a drug-target interaction. If an interaction is identified, the second part employs the drug-target affinity identification method MMDTA, also based on GNN and CNN, to calculate the strength of drug-target interaction, i.e., affinity. Finally, the third part identifies drug-target binding sites, i.e., pockets. The method pt-lm-gnn used in this part is also based on GNN. CONCLUSIONS: Drug-Online is a reliable online platform that integrates drug-target interaction, affinity, and binding sites identification. It is freely available via the Internet at http://39.106.7.26:8000/Drug-Online/ .


Subject(s)
Deep Learning , Drug Interactions , Binding Sites , Drug Delivery Systems , Drug Evaluation, Preclinical
13.
Adv Sci (Weinh) ; 11(20): e2306703, 2024 May.
Article in English | MEDLINE | ID: mdl-38561967

ABSTRACT

The dermis and epidermis, crucial structural layers of the skin, encompass appendages, hair follicles (HFs), and intricate cellular heterogeneity. However, an integrated spatiotemporal transcriptomic atlas of embryonic skin has not yet been described and would be invaluable for studying skin-related diseases in humans. Here, single-cell and spatial transcriptomic analyses are performed on skin samples of normal and hairless fetal pigs across four developmental periods. The cross-species comparison of skin cells illustrated that the pig epidermis is more representative of the human epidermis than mice epidermis. Moreover, Phenome-wide association study analysis revealed that the conserved genes between pigs and humans are strongly associated with human skin-related diseases. In the epidermis, two lineage differentiation trajectories describe hair follicle (HF) morphogenesis and epidermal development. By comparing normal and hairless fetal pigs, it is found that the hair placode (Pc), the most characteristic initial structure in HFs, arises from progenitor-like OGN+/UCHL1+ cells. These progenitors appear earlier in development than the previously described early Pc cells and exhibit abnormal proliferation and migration during differentiation in hairless pigs. The study provides a valuable resource for in-depth insights into HF development, which may serve as a key reference atlas for studying human skin disease etiology using porcine models.


Subject(s)
Hair Follicle , Transcriptome , Animals , Swine/genetics , Swine/embryology , Hair Follicle/metabolism , Hair Follicle/embryology , Hair Follicle/growth & development , Transcriptome/genetics , Single-Cell Analysis/methods , Skin/metabolism , Skin/embryology , Cell Differentiation/genetics , Gene Expression Profiling/methods , Humans , Mice
14.
Breastfeed Med ; 2024 Mar 19.
Article in English | MEDLINE | ID: mdl-38501370

ABSTRACT

Objectives: This study aimed to explore the associations of growth and body composition with gut microbiome and metabolome in preterm infants. Materials and Methods: A prospective cohort study including 73 human milk-fed very preterm infants was conducted. During hospitalization, fecal samples were collected to detect microbes and metabolites using 16S rRNA gene sequencing and liquid chromatography-mass spectrometry. Growth and body composition indices were measured at term equivalent age (TEA) and 6 months of corrected age (CA). Associations of the fecal microbiome and metabolome profiles with growth and body composition indices, as well as their changes, were analyzed. Results: A higher abundance of Streptococcus was associated with a lower fat-free mass (FFM) z-score at 6 months of CA (p = 0.002) and a smaller increase in FFM z-score from TEA to 6 months of CA (p = 0.018). Higher levels of 3'-sialyllactose and 6'-sialyllactose (6'-SL) in feces were correlated with a lower z-score of percentage body fat (PBF) (p = 0.018 and 0.020, respectively) and a lower z-score of fat mass (p = 0.044 and 0.043, respectively) at 6 months of CA. A higher level of 6'-SL in feces was correlated with a greater increase in FFM z-score from TEA to 6 months of CA (p = 0.021). Conclusions: This study sheds light on the role of specific microbial-host interactions in metabolic changes in preterm infants, indicating the potential role of sialylated human milk oligosaccharides in optimizing body composition.

15.
Biomimetics (Basel) ; 9(3)2024 Mar 01.
Article in English | MEDLINE | ID: mdl-38534834

ABSTRACT

The gecko can achieve flexible climbing on various vertical walls and even ceilings, which is closely related to its unique foot adhesion system. In the past two decades, the mechanism of the gecko adhesion system has been studied in-depth, and a verity of gecko-inspired adhesives have been proposed. In addition to its strong adhesion, its easy detachment is also the key to achieving efficient climbing locomotion for geckos. A similar controllable adhesion characteristic is also key to the research into artificial gecko-inspired adhesives. In this paper, the structures, fabrication methods, and applications of gecko-inspired controllable adhesives are summarized for future reference in adhesive development. Firstly, the controllable adhesion mechanism of geckos is introduced. Then, the control mechanism, adhesion performance, and preparation methods of gecko-inspired controllable adhesives are described. Subsequently, various successful applications of gecko-inspired controllable adhesives are presented. Finally, future challenges and opportunities to develop gecko-inspired controllable adhesive are presented.

16.
Int Heart J ; 65(2): 173-179, 2024.
Article in English | MEDLINE | ID: mdl-38556328

ABSTRACT

Keshan disease (KD) is a type of endemic cardiomyopathy with an unknown cause. It is primarily found in areas in China with low selenium levels, from northeast to southwest. The nutritional biogeochemical etiology hypothesis suggests that selenium deficiency is a major factor in KD development. Selenium is important in removing free radicals and protecting cells and tissues from peroxide-induced damage. Thus, low environmental selenium may affect the selenium level within the human body, and selenium level differences are commonly observed between healthy people in KD and nonKD areas. From the 1970s to the 1990s, China successfully reduced KD incidence in endemic KD areas through a selenium supplementation program. After years of implementing prevention and control measures, the selenium level of the population in the KD areas has gradually increased, and the prevalence of KD in China has remained low and stable in recent years. Currently, the pathogenesis of KD remains vague, and the effect of selenium supplementation on the prognosis of KD still needs further study. This paper comprehensively reviews selenium deficiency and its connection to KD. Thus, this study aims to offer novel ideas and directions to effectively prevent and treat KD in light of the current situation.


Subject(s)
Cardiomyopathies , Enterovirus Infections , Malnutrition , Selenium , Humans , Selenium/analysis , Cardiomyopathies/epidemiology , Cardiomyopathies/etiology , Cardiomyopathies/prevention & control , Enterovirus Infections/complications , Enterovirus Infections/epidemiology , Enterovirus Infections/prevention & control , China/epidemiology
17.
Epigenomics ; 2024 Mar 21.
Article in English | MEDLINE | ID: mdl-38511238

ABSTRACT

Aim: The present study was designed to investigate the coregulatory effects of multiple histone modifications (HMs) on gene expression in lung adenocarcinoma (LUAD). Materials & methods: Ten histones for LUAD were analyzed using ChIP-seq and RNA-seq data. An innovative computational method is proposed to quantify the coregulatory effects of multiple HMs on gene expression to identify strong coregulatory genes and regions. This method was applied to explore the coregulatory mechanisms of key ferroptosis-related genes in LUAD. Results: Nine strong coregulatory regions were identified for six ferroptosis-related genes with diverse coregulatory patterns (CA9, PGD, CDKN2A, PML, OTUB1 and NFE2L2). Conclusion: This quantitative method could be used to identify important HM coregulatory genes and regions that may be epigenetic regulatory targets in cancers.

18.
J Cardiovasc Aging ; 4(1)2024 Jan.
Article in English | MEDLINE | ID: mdl-38455514

ABSTRACT

Introduction: Gradual exposure to a chronic hypoxic environment leads to cardiomyocyte proliferation and improved cardiac function in mouse models through a reduction in oxidative DNA damage. However, the upstream transcriptional events that link chronic hypoxia to DNA damage have remained obscure. Aim: We sought to determine whether hypoxia signaling mediated by the hypoxia-inducible factor 1 or 2 (HIF1A or HIF2A) underlies the proliferation phenotype that is induced by chronic hypoxia. Methods and Results: We used genetic loss-of-function models using cardiomyocyte-specific HIF1A and HIF2A gene deletions in chronic hypoxia. We additionally characterized a cardiomyocyte-specific HIF2A overexpression mouse model in normoxia during aging and upon injury. We performed transcriptional profiling with RNA-sequencing on cardiac tissue, from which we verified candidates at the protein level. We find that HIF2A - rather than HIF1A - mediates hypoxia-induced cardiomyocyte proliferation. Ectopic, oxygen-insensitive HIF2A expression in cardiomyocytes reveals the cell-autonomous role of HIF2A in cardiomyocyte proliferation. HIF2A overexpression in cardiomyocytes elicits cardiac regeneration and improvement in systolic function after myocardial infarction in adult mice. RNA-sequencing reveals that ectopic HIF2A expression attenuates DNA damage pathways, which was confirmed with immunoblot and immunofluorescence. Conclusion: Our study provides mechanistic insights about a new approach to induce cardiomyocyte renewal and mitigate cardiac injury in the adult mammalian heart. In light of evidence that DNA damage accrues in cardiomyocytes with aging, these findings may help to usher in a new therapeutic approach to overcome such age-related changes and achieve regeneration.

19.
J Biol Chem ; 300(5): 107235, 2024 May.
Article in English | MEDLINE | ID: mdl-38552739

ABSTRACT

Defects in mitochondrial RNA metabolism have been linked to sensorineural deafness that often occurs as a consequence of damaged or deficient inner ear hair cells. In this report, we investigated the molecular mechanism underlying a deafness-associated tRNAPhe 593T > C mutation that changed a highly conserved uracil to cytosine at position 17 of the DHU-loop. The m.593T > C mutation altered tRNAPhe structure and function, including increased melting temperature, resistance to S1 nuclease-mediated digestion, and conformational changes. The aberrant tRNA metabolism impaired mitochondrial translation, which was especially pronounced by decreases in levels of ND1, ND5, CYTB, CO1, and CO3 harboring higher numbers of phenylalanine. These alterations resulted in aberrant assembly, instability, and reduced activities of respiratory chain enzyme complexes I, III, IV, and intact supercomplexes overall. Furthermore, we found that the m.593T > C mutation caused markedly diminished membrane potential, and increased the production of reactive oxygen species in the mutant cell lines carrying the m.593T > C mutation. These mitochondrial dysfunctions led to the mitochondrial dynamic imbalance via increasing fission with abnormal mitochondrial morphology. Excessive fission impaired the process of autophagy including the initiation phase, formation, and maturation of the autophagosome. In particular, the m.593T > C mutation upregulated the PARKIN-dependent mitophagy pathway. These alterations promoted an intrinsic apoptotic process for the removal of damaged cells. Our findings provide critical insights into the pathophysiology of maternally inherited deafness arising from tRNA mutation-induced defects in mitochondrial and cellular integrity.


Subject(s)
Deafness , Mitochondria , Humans , Mitochondria/metabolism , Mitochondria/genetics , Mitochondria/pathology , Deafness/genetics , Deafness/metabolism , Deafness/pathology , Mutation , Reactive Oxygen Species/metabolism , Autophagy , Mitochondrial Dynamics , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/metabolism , Membrane Potential, Mitochondrial
20.
Sci Rep ; 14(1): 2676, 2024 02 01.
Article in English | MEDLINE | ID: mdl-38302630

ABSTRACT

To determine the dietary structure and its associated factors of tuberculosis (TB) patients in the community. This cross-sectional study analysed the dietary intake of 300 TB patients in two impoverished counties in China. Food intake was collected by using food frequency and two consecutive 24-h dietary review (24hdr) methods. The dietary composition and dietary structure of TB patients were compared with China's 2022 Dietary Reference Intake (DRIs) and the average reference value of dietary composition (ARC) in China in 2013. Binary logistic regression models were used to explore the factors associated with inadequate intake of animal food, insufficient protein and fat energy supply in patients with TB. The daily intake of various foods in TB patients was measured and the results were as follows: staple foods-median 372.12 g (interquartile range [IQR] 315.87 g); vegetables-median 200.00 g (IQR 205.55 g); fruits-median 20.22 g (IQR 36.82 g); animal foods-median 100.82 g (IQR 180.74 g); dairy products-median 0.00 g (IQR 0.00 g); nuts-median 17.10 g (IQR 29.75 g). The average daily intakes of vegetables, fruits, animal food, dairy products, soy and nuts were lower than those recommended by the DRIs (P < 0.01). Compared to women, men consumed more whole grains and mixed legumes, but less fruit. The dietary structures, including food and nutrient supply for energy, protein and fat, were significantly different in 300 patients compared with DRIs or ARC values. Inadequate rates of animal food intake were observed in 54.85% of men and 59.57% of women. Protein undersupply rates were 66.02% in men and 56.38% in women, while fat undersupply rates were 52.91% in men and 52.13% in women. The study revealed that being 18-49 years old, being the Han nationality, having less than 2 h of physical activity per day on average, and eating twice a day were risk factors for inadequate animal protein intake, protein energy deficiency and fat energy deficiency. TB patients from impoverished counties in China have inadequate intake of several food categories and insufficient protein and fat energy supply, correlating with multiple factors in socio-demographics, behavioral practices, and TB disease. To improve the nutritional status of TB patients, urgent public health actions, especially carrying out nutritional screening and evaluation once diagnosed, developing individualized nutritional support treatment plans, strengthening dietary nutritional health education and intervention, and advocating for enhanced nutritional support, should be taken.


Subject(s)
Nutritional Status , Tuberculosis , Male , Animals , Humans , Female , Adolescent , Young Adult , Adult , Middle Aged , Cross-Sectional Studies , Nutrition Assessment , Energy Intake , Diet , Fruit , Vegetables , China/epidemiology , Tuberculosis/epidemiology , Feeding Behavior
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