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1.
BMC Genomics ; 25(1): 464, 2024 May 13.
Article En | MEDLINE | ID: mdl-38741085

Gonad development includes sex determination and divergent maturation of the testes and ovaries. Recent advances in measuring gene expression in single cells are providing new insights into this complex process. However, the underlying epigenetic regulatory mechanisms remain unclear. Here, we profiled chromatin accessibility in mouse gonadal cells of both sexes from embryonic day 11.5 to 14.5 using single-cell assay for transposase accessible chromatin by sequencing (scATAC-seq). Our results showed that individual cell types can be inferred by the chromatin landscape, and that cells can be temporally ordered along developmental trajectories. Integrative analysis of transcriptomic and chromatin-accessibility maps identified multiple putative regulatory elements proximal to key gonadal genes Nr5a1, Sox9 and Wt1. We also uncover cell type-specific regulatory factors underlying cell type specification. Overall, our results provide a better understanding of the epigenetic landscape associated with the progressive restriction of cell fates in the gonad.


Cell Lineage , Chromatin , Gonads , SOX9 Transcription Factor , Single-Cell Analysis , Animals , Chromatin/metabolism , Chromatin/genetics , Mice , Cell Lineage/genetics , Female , Male , SOX9 Transcription Factor/genetics , SOX9 Transcription Factor/metabolism , Gonads/metabolism , Gonads/cytology , Gonads/embryology , Steroidogenic Factor 1/genetics , Steroidogenic Factor 1/metabolism , WT1 Proteins/genetics , WT1 Proteins/metabolism , Testis/metabolism , Testis/cytology , Epigenesis, Genetic , Gene Expression Regulation, Developmental , Ovary/metabolism , Ovary/cytology
2.
Cell Metab ; 2024 Apr 29.
Article En | MEDLINE | ID: mdl-38703762

The mitochondrial genome transcribes 13 mRNAs coding for well-known proteins essential for oxidative phosphorylation. We demonstrate here that cytochrome b (CYTB), the only mitochondrial-DNA-encoded transcript among complex III, also encodes an unrecognized 187-amino-acid-long protein, CYTB-187AA, using the standard genetic code of cytosolic ribosomes rather than the mitochondrial genetic code. After validating the existence of this mtDNA-encoded protein arising from cytosolic translation (mPACT) using mass spectrometry and antibodies, we show that CYTB-187AA is mainly localized in the mitochondrial matrix and promotes the pluripotent state in primed-to-naive transition by interacting with solute carrier family 25 member 3 (SLC25A3) to modulate ATP production. We further generated a transgenic knockin mouse model of CYTB-187AA silencing and found that reduction of CYTB-187AA impairs females' fertility by decreasing the number of ovarian follicles. For the first time, we uncovered the novel mPACT pattern of a mitochondrial mRNA and demonstrated the physiological function of this 14th protein encoded by mtDNA.

3.
Nat Commun ; 15(1): 546, 2024 Jan 16.
Article En | MEDLINE | ID: mdl-38228611

Aging in mammals is accompanied by an imbalance of intestinal homeostasis and accumulation of mitochondrial DNA (mtDNA) mutations. However, little is known about how accumulated mtDNA mutations modulate intestinal homeostasis. We observe the accumulation of mtDNA mutations in the small intestine of aged male mice, suggesting an association with physiological intestinal aging. Using polymerase gamma (POLG) mutator mice and wild-type mice, we generate male mice with progressive mtDNA mutation burdens. Investigation utilizing organoid technology and in vivo intestinal stem cell labeling reveals decreased colony formation efficiency of intestinal crypts and LGR5-expressing intestinal stem cells in response to a threshold mtDNA mutation burden. Mechanistically, increased mtDNA mutation burden exacerbates the aging phenotype of the small intestine through ATF5 dependent mitochondrial unfolded protein response (UPRmt) activation. This aging phenotype is reversed by supplementation with the NAD+ precursor, NMN. Thus, we uncover a NAD+ dependent UPRmt triggered by mtDNA mutations that regulates the intestinal aging.


Aging , NAD , Mice , Male , Animals , NAD/metabolism , Aging/genetics , Aging/metabolism , Mutation , Mitochondria/genetics , Mitochondria/metabolism , DNA, Mitochondrial/genetics , DNA, Mitochondrial/metabolism , DNA Polymerase gamma/genetics , DNA Polymerase gamma/metabolism , Mammals/genetics
4.
Cell Biosci ; 14(1): 7, 2024 Jan 06.
Article En | MEDLINE | ID: mdl-38184705

BACKGROUND: Metabolic dysfunction is one of the main symptoms of Werner syndrome (WS); however, the underlying mechanisms remain unclear. Here, we report that loss of WRN accelerates adipogenesis at an early stage both in vitro (stem cells) and in vivo (zebrafish). Moreover, WRN depletion causes a transient upregulation of late-stage of adipocyte-specific genes at an early stage. METHODS: In an in vivo study, we generated wrn-/- mutant zebrafish and performed histological stain and Oil Red O staining to assess the fat metabolism. In an in vitro study, we used RNA-seq and ATAC-seq to profile the transcriptional features and chromatin accessibility in WRN depleted adipocytes. Moreover, we performed ChIP-seq to further study the regulatory mechanisms of metabolic dysfunction in WS. RESULTS: Our findings show that mechanistically WRN deficiency causes SMARCA5 upregulation. SMARCA5 is crucial in chromatin remodeling and gene regulation. Additionally, rescuing WRN could normalize SMARCA5 expression and adipocyte differentiation. Moreover, we find that nicotinamide riboside (NR) supplementation restores adipocyte metabolism in both stem cells and zebrafish models. CONCLUSIONS: Our findings unravel a new mechanism for the influence of WRN in the early stage of adipogenesis and provide a possible treatment for metabolic dysfunction in WS. These data provide promising insights into potential therapeutics for ageing and ageing-related diseases.

5.
EMBO Rep ; 25(2): 646-671, 2024 Feb.
Article En | MEDLINE | ID: mdl-38177922

The dorsoventral gradient of BMP signaling plays an essential role in embryonic patterning. Zinc Finger SWIM-Type Containing 4 (zswim4) is expressed in the Spemann-Mangold organizer at the onset of Xenopus gastrulation and is then enriched in the developing neuroectoderm at the mid-gastrula stages. Knockdown or knockout of zswim4 causes ventralization. Overexpression of zswim4 decreases, whereas knockdown of zswim4 increases the expression levels of ventrolateral mesoderm marker genes. Mechanistically, ZSWIM4 attenuates the BMP signal by reducing the protein stability of SMAD1 in the nucleus. Stable isotope labeling by amino acids in cell culture (SILAC) identifies Elongin B (ELOB) and Elongin C (ELOC) as the interaction partners of ZSWIM4. Accordingly, ZSWIM4 forms a complex with the Cul2-RING ubiquitin ligase and ELOB and ELOC, promoting the ubiquitination and degradation of SMAD1 in the nucleus. Our study identifies a novel mechanism that restricts BMP signaling in the nucleus.


Bone Morphogenetic Proteins , Carrier Proteins , Animals , Bone Morphogenetic Proteins/genetics , Bone Morphogenetic Proteins/metabolism , Carrier Proteins/genetics , Carrier Proteins/metabolism , Organizers, Embryonic/metabolism , Xenopus laevis/metabolism , Body Patterning/physiology , Xenopus Proteins/genetics , Xenopus Proteins/metabolism , Gene Expression Regulation, Developmental
6.
Can Assoc Radiol J ; 75(1): 92-97, 2024 Feb.
Article En | MEDLINE | ID: mdl-37075322

The past two decades have seen a significant increase in the use of CT, with a corresponding rise in the mean population radiation dose. This rise in CT use has caused improved diagnostic certainty in conditions that were not previously routinely evaluated using CT, such as headaches, back pain, and chest pain. Unused data, unrelated to the primary diagnosis, embedded within these scans have the potential to provide organ-specific measurements that can be used to prognosticate or risk-profile patients for a wide variety of conditions. The recent increased availability of computing power, expertise and software for automated segmentation and measurements, assisted by artificial intelligence, provides a conducive environment for the deployment of these analyses into routine use. Data gathering from CT has the potential to add value to examinations and help offset the public perception of harm from radiation exposure. We review the potential for the collection of these data and propose the incorporation of this strategy into routine clinical practice.


Artificial Intelligence , Tomography, X-Ray Computed , Humans , Prognosis , Biomarkers
7.
Gene Expr Patterns ; 50: 119345, 2023 Dec.
Article En | MEDLINE | ID: mdl-37844856

Peroxidase genes (Prdx) encode a family of antioxidant proteins, which can protect cells from oxidative damage by reducing various cellular peroxides. This study investigated the spatiotemporal expression patterns of gene members in this family during the early development of Xenopus tropicalis. Real-time quantitative PCR showed that all members of this gene family have a distinct temporal expression pattern during the early development of X. tropicalis embryos. Additionally, whole mount in situ hybridization revealed that individual prdx genes display differential expression patterns, with overlapping expression in lymphatic vessels, pronephros, proximal tubule, and branchial arches. This study provides a basis for further study of the function of the prdx gene family.


Embryonic Development , Xenopus Proteins , Animals , Xenopus , Xenopus Proteins/genetics , Xenopus Proteins/metabolism , Real-Time Polymerase Chain Reaction , Embryonic Development/genetics , Gene Expression Regulation, Developmental , Xenopus laevis/genetics
9.
Nucleic Acids Res ; 51(21): 11652-11667, 2023 Nov 27.
Article En | MEDLINE | ID: mdl-37889087

Fully grown oocytes remain transcriptionally quiescent, yet many maternal mRNAs are synthesized and retained in growing oocytes. We now know that maternal mRNAs are stored in a structure called the mitochondria-associated ribonucleoprotein domain (MARDO). However, the components and functions of MARDO remain elusive. Here, we found that LSM14B knockout prevents the proper storage and timely clearance of mRNAs (including Cyclin B1, Btg4 and other mRNAs that are translationally activated during meiotic maturation), specifically by disrupting MARDO assembly during oocyte growth and meiotic maturation. With decreased levels of storage and clearance, the LSM14B knockout oocytes failed to enter meiosis II, ultimately resulting in female infertility. Our results demonstrate the function of LSM14B in MARDO assembly, and couple the MARDO with mRNA clearance and oocyte meiotic maturation.


Oogenesis , RNA, Messenger, Stored , Female , Humans , Meiosis/genetics , Oocytes/physiology , Oogenesis/genetics , RNA, Messenger/genetics , RNA, Messenger, Stored/genetics , Mice, Inbred C57BL , Male , Animals , Mice
10.
Biomedicines ; 11(9)2023 Sep 17.
Article En | MEDLINE | ID: mdl-37760991

BACKGROUND: Stroke represents the second leading cause of death and the primary cause of long-term disability in humans. The transplantation of mesenchymal stem cells (MSC) reportedly improves functional outcomes in animal models of cerebral ischemia. Here, we evaluate the neuroprotective potential of extracellular vesicles secreted from human-induced pluripotent stem cell-derived mesenchymal stem cells (hiPS-MSC-EV) using preclinical cell-based and animal-based models of ischemic strokes. METHODS: hiPS-MSC-EV were isolated using an ultrafiltration method. HT22 cells were subjected to oxygen-glucose deprivation/reoxygenation (OGD/R) injury for 2 h, followed by treatment with hiPS-MSC-EV (100 µg/mL). Male C57BL/6 mice were subjected to middle cerebral artery occlusion (MCAO) followed by an intravenous injection of hiPS-MSC-EV (100 µg) at three distinct time points. RESULTS: Our experimental approach revealed hiPS-MSC-EV promoted HT22 cell proliferation, reduced apoptosis, and altered cellular morphology following OGD/R. In addition, hiPS-MSC-EV reduced the volume of infarcts, improved spontaneous movement abilities, and enhanced angiogenesis by expressing the VEGF and CXCR4 proteins in the infarcted hemisphere of the MCAO-treated mouse model. CONCLUSION: Our findings provide evidence of the potential neuroprotective effects of hiPS-MSC-derived extracellular vesicles (hiPS-MSC-EVs) in both in vitro and in vivo mouse models of ischemic stroke. These results suggest that hiPS-MSC-EVs may play a role in neurorestoration and offer insights into potential cell-free strategies for addressing cerebral ischemia.

11.
J Digit Imaging ; 36(6): 2441-2460, 2023 12.
Article En | MEDLINE | ID: mdl-37537514

Detecting neurological abnormalities such as brain tumors and Alzheimer's disease (AD) using magnetic resonance imaging (MRI) images is an important research topic in the literature. Numerous machine learning models have been used to detect brain abnormalities accurately. This study addresses the problem of detecting neurological abnormalities in MRI. The motivation behind this problem lies in the need for accurate and efficient methods to assist neurologists in the diagnosis of these disorders. In addition, many deep learning techniques have been applied to MRI to develop accurate brain abnormality detection models, but these networks have high time complexity. Hence, a novel hand-modeled feature-based learning network is presented to reduce the time complexity and obtain high classification performance. The model proposed in this work uses a new feature generation architecture named pyramid and fixed-size patch (PFP). The main aim of the proposed PFP structure is to attain high classification performance using essential feature extractors with both multilevel and local features. Furthermore, the PFP feature extractor generates low- and high-level features using a handcrafted extractor. To obtain the high discriminative feature extraction ability of the PFP, we have used histogram-oriented gradients (HOG); hence, it is named PFP-HOG. Furthermore, the iterative Chi2 (IChi2) is utilized to choose the clinically significant features. Finally, the k-nearest neighbors (kNN) with tenfold cross-validation is used for automated classification. Four MRI neurological databases (AD dataset, brain tumor dataset 1, brain tumor dataset 2, and merged dataset) have been utilized to develop our model. PFP-HOG and IChi2-based models attained 100%, 94.98%, 98.19%, and 97.80% using the AD dataset, brain tumor dataset1, brain tumor dataset 2, and merged brain MRI dataset, respectively. These findings not only provide an accurate and robust classification of various neurological disorders using MRI but also hold the potential to assist neurologists in validating manual MRI brain abnormality screening.


Alzheimer Disease , Brain Neoplasms , Humans , Magnetic Resonance Imaging/methods , Neuroimaging , Brain/diagnostic imaging , Brain Neoplasms/diagnostic imaging , Brain Neoplasms/pathology , Machine Learning , Alzheimer Disease/diagnostic imaging
12.
Curr Med Imaging ; 2023 Aug 29.
Article En | MEDLINE | ID: mdl-37649292

BACKGROUND: The use of breast MRI for screening has increased over the past decade, mostly in women with a high risk of breast cancer. Abbreviated breast MRI (AB-MR) is introduced to make MRI a more accessible screening modality. AB-MR decreases scanning and reporting time and the overall cost of MRI. OBJECTIVE: This study aims to evaluate the diagnostic efficacy of abbreviated MRI protocol in detecting breast cancer in screening and diagnostic populations, using histopathology as the reference standard. MATERIALS AND METHODS: This is a single-centre retrospective cross-sectional study of 134 patients with 198 histologically proven breast lesions who underwent full diagnostic protocol contrast-enhanced breast MRI (FDP-MR) at the University Malaya Medical Centre (UMMC) from 1st January 2018 to 31st December 2019. AB-MR was pre-determined and evaluated with regard to the potential to detect and exclude malignancy from 3 readers of varying radiological experiences. The sensitivity of both AB-MR and FDP-MR were compared using the McNemar test, where both protocols' diagnostic performances were assessed via the receiver operating characteristic (ROC) curve. Inter-observer agreement was analysed using Fleiss Kappa. RESULT: There were 134 patients with 198 lesions. The average age was 50.9 years old (range 27 - 80). A total of 121 (90%) MRIs were performed for diagnostic purposes. Screening accounted for 9.4% of the cases, 55.6% (n=110) lesions were benign, and 44.4% (n=88) were malignant. The commonest benign and malignant lesions were fibrocystic change (27.3%) and invasive ductal carcinoma (78.4%). The mean sensitivity, specificity, positive predictive value, and negative predictive value for AB-MR were 0.96, 0.57, 0.68 and 0.94, respectively. Both AB-MR and FDP-MR showed excellent diagnostic performance with AUC of 0.88 and 0.96, respectively. The general inter-observer agreement of all three readers for AB-MR was substantial (k=0.69), with fair agreement demonstrated between AB-MR and FDP-MR (k=0.36). CONCLUSION: The study shows no evidence that the diagnostic efficacy of AB-MR is inferior to FDP-MR. AB-MR, with high sensitivity, has proven its capability in cancer detection and exclusion, especially for biologically aggressive cancers.

13.
Int J Med Sci ; 20(8): 1009-1023, 2023.
Article En | MEDLINE | ID: mdl-37484808

Ischemic stroke (IS) is the majority of strokes which remain the second leading cause of deaths in the last two decades. Circulating microRNAs (miRNAs) have been suggested as potential diagnostic and therapeutic tools for IS by previous studies analyzing their differential expression. However, inconclusive and controversial conclusions of these results have to be addressed. In this study, comprehensive analysis and real-world validation were performed to assess the associations between circulating miRNAs and IS. 29 studies with 112 miRNAs were extracted after manual selection and filtering, 12 differentially expressed miRNAs were obtained from our results of meta-analysis. These miRNAs were evaluated in 20 IS patients, compared to 20 healthy subjects. 4 miRNAs (hsa-let-7e-5p, hsa-miR-124-3p, hsa-miR-17-5p, hsa-miR-185-5p) exhibited the significant expression level in IS patient plasma samples. Pathway and biological process enrichment analysis for the target genes of the 4 validated miRNAs identified cellular senescence and neuroinflammation as key post-IS response pathways. The results of our analyses closely correlated with the pathogenesis and implicated pathways observed in IS subjects suggested by the literature, which may provide aid in the development of circulating diagnostic or therapeutic targets for IS patients.


Circulating MicroRNA , Ischemic Stroke , MicroRNAs , Stroke , Humans , MicroRNAs/metabolism , Biomarkers
14.
NPJ Biofilms Microbiomes ; 9(1): 47, 2023 Jul 08.
Article En | MEDLINE | ID: mdl-37422471

Knowledge gaps that limit the development of therapies for polycystic ovary syndrome (PCOS) concern various environmental factors that impact clinical characteristics. Circadian dysrhythmia contributes to glycometabolic and reproductive hallmarks of PCOS. Here, we illustrated the amelioration of Limosilactobacillus reuteri (L. reuteri) on biorhythm disorder-ignited dyslipidemia of PCOS via a microbiota-metabolite-liver axis. A rat model of long-term (8 weeks) darkness treatment was used to mimic circadian dysrhythmia-induced PCOS. Hepatic transcriptomics certified by in vitro experiments demonstrated that increased hepatic galanin receptor 1 (GALR1) due to darkness exposure functioned as a critical upstream factor in the phosphoinositide 3-kinase (PI3K)/protein kinase B pathway to suppress nuclear receptors subfamily 1, group D, member 1 (NR1D1) and promoted sterol regulatory element binding protein 1 (SREBP1), inducing lipid accumulation in the liver. Further investigations figured out a restructured microbiome-metabolome network following L. reuteri administration to protect darkness rats against dyslipidemia. Notably, L. reuteri intervention resulted in the decrease of Clostridium sensu stricto 1 and Ruminococcaceae UCG-010 as well as gut microbiota-derived metabolite capric acid, which could further inhibit GALR1-NR1D1-SREBP1 pathway in the liver. In addition, GALR antagonist M40 reproduced similar ameliorative effects as L. reuteri to protect against dyslipidemia. While exogenous treatment of capric acid restrained the protective effects of L. reuteri in circadian disruption-induced PCOS through inhibiting GALR1-dependent hepatic lipid metabolism. These findings purport that L. reuteri could serve for circadian disruption-associated dyslipidemia. Manipulation of L. reuteri-capric acid-GALR1 axis paves way for clinical therapeutic strategies to prevent biorhythm disorder-ignited dyslipidemia in PCOS women.


Dyslipidemias , Limosilactobacillus reuteri , Polycystic Ovary Syndrome , Humans , Rats , Female , Animals , Receptor, Galanin, Type 1 , Phosphatidylinositol 3-Kinases , Dyslipidemias/etiology , Dyslipidemias/prevention & control
15.
Obes Rev ; 24(10): e13603, 2023 10.
Article En | MEDLINE | ID: mdl-37452501

Currently, obesity has achieved epidemic levels in reproductive-aged women with a myriad of consequences. Obesity is susceptible to several reproductive complications that eventually affect fertility rates. These complications originate from the deteriorated quality of oocytes from mothers with obesity, which increases the probability of chromosomal aneuploidy, elevated reactive oxygen species production, compromised embryonic developmental competency, and eventually reduced fertility. Maternal obesity is linked to pregnancy complications such as implantation error, abortion, miscarriage, and early pregnancy loss. This review highlights the adverse effects of maternal obesity on female fertility, with a focus on the mechanistic link between maternal obesity and oocyte quality and discusses possible measures to reduce its associated risks.


Obesity, Maternal , Pregnancy Complications , Pregnancy , Female , Humans , Fertility , Obesity/complications , Pregnancy Complications/etiology , Oocytes
16.
J Thorac Oncol ; 18(10): 1303-1322, 2023 10.
Article En | MEDLINE | ID: mdl-37390982

INTRODUCTION: The incidence and mortality of lung cancer are highest in Asia compared with Europe and USA, with the incidence and mortality rates being 34.4 and 28.1 per 100,000 respectively in East Asia. Diagnosing lung cancer at early stages makes the disease amenable to curative treatment and reduces mortality. In some areas in Asia, limited availability of robust diagnostic tools and treatment modalities, along with variations in specific health care investment and policies, make it necessary to have a more specific approach for screening, early detection, diagnosis, and treatment of patients with lung cancer in Asia compared with the West. METHOD: A group of 19 advisors across different specialties from 11 Asian countries, met on a virtual Steering Committee meeting, to discuss and recommend the most affordable and accessible lung cancer screening modalities and their implementation, for the Asian population. RESULTS: Significant risk factors identified for lung cancer in smokers in Asia include age 50 to 75 years and smoking history of more than or equal to 20 pack-years. Family history is the most common risk factor for nonsmokers. Low-dose computed tomography screening is recommended once a year for patients with screening-detected abnormality and persistent exposure to risk factors. However, for high-risk heavy smokers and nonsmokers with risk factors, reassessment scans are recommended at an initial interval of 6 to 12 months with subsequent lengthening of reassessment intervals, and it should be stopped in patients more than 80 years of age or are unable or unwilling to undergo curative treatment. CONCLUSIONS: Asian countries face several challenges in implementing low-dose computed tomography screening, such as economic limitations, lack of efforts for early detection, and lack of specific government programs. Various strategies are suggested to overcome these challenges in Asia.


Lung Neoplasms , Humans , Middle Aged , Aged , Lung Neoplasms/diagnosis , Lung Neoplasms/epidemiology , Early Detection of Cancer/methods , Consensus , Tomography, X-Ray Computed/methods , Asia/epidemiology , Mass Screening
17.
Cells ; 12(12)2023 06 13.
Article En | MEDLINE | ID: mdl-37371084

The axoneme and accessory structures of flagella are critical for sperm motility and male fertilization. Sperm production needs precise and highly ordered gene expression to initiate and sustain the many cellular processes that result in mature spermatozoa. Here, we identified a testis enriched gene transmembrane protein 232 (Tmem232), which is essential for the structural integrity of the spermatozoa flagella axoneme. Tmem232 knockout mice were generated for in vivo analyses of its functions in spermatogenesis. Phenotypic analysis showed that deletion of Tmem232 in mice causes male-specific infertility. Transmission electron microscopy together with scanning electron microscopy were applied to analyze the spermatozoa flagella and it was observed that the lack of TMEM232 caused failure of the cytoplasm removal and the absence of the 7th outer microtubule doublet with its corresponding outer dense fiber (ODF). Co-IP assays further identified that TMEM232 interacts with ODF family protein ODF1, which is essential to maintain sperm motility. In conclusion, our findings indicate that TMEM232 is a critical protein for male fertility and sperm motility by regulating sperm cytoplasm removal and maintaining axoneme integrity.


Infertility, Male , Membrane Proteins , Sperm Motility , Sperm Tail , Animals , Male , Mice , Infertility, Male/genetics , Infertility, Male/metabolism , Mice, Knockout , Semen , Sperm Motility/genetics , Sperm Tail/metabolism , Membrane Proteins/deficiency , Membrane Proteins/genetics , Membrane Proteins/metabolism
18.
Zool Res ; 44(3): 559-576, 2023 May 18.
Article En | MEDLINE | ID: mdl-37161651

Parkinson's disease (PD) relates to defective mitochondrial quality control in the dopaminergic motor network. Genetic studies have revealed that PINK1 and Parkin mutations are indicative of a heightened propensity to PD onset, pinpointing mitophagy and inflammation as the culprit pathways involved in neuronal loss in the substantia nigra (SNpc). In a reciprocal manner, LRRK2 functions in the regulation of basal flux and inflammatory responses responsible for PINK1/Parkin-dependent mitophagy activation. Pharmacological intervention in these disease-modifying pathways may facilitate the development of novel PD therapeutics, despite the current lack of an established drug evaluation model. As such, we reviewed the feasibility of employing the versatile global Pink1 knockout (KO) rat model as a self-sufficient, spontaneous PD model for investigating both disease etiology and drug pharmacology. These rats retain clinical features encompassing basal mitophagic flux changes with PD progression. We demonstrate the versatility of this PD rat model based on the incorporation of additional experimental insults to recapitulate the proinflammatory responses observed in PD patients.


Parkinson Disease , Animals , Rats , Dopamine , Inflammation , Parkinson Disease/genetics , Signal Transduction , Ubiquitin-Protein Ligases/genetics
19.
Comput Methods Programs Biomed ; 236: 107544, 2023 Jun.
Article En | MEDLINE | ID: mdl-37148668

OBJECTIVES: To elucidate a novel radiogenomics approach using three-dimensional (3D) topologically invariant Betti numbers (BNs) for topological characterization of epidermal growth factor receptor (EGFR) Del19 and L858R mutation subtypes. METHODS: In total, 154 patients (wild-type EGFR, 72 patients; Del19 mutation, 45 patients; and L858R mutation, 37 patients) were retrospectively enrolled and randomly divided into 92 training and 62 test cases. Two support vector machine (SVM) models to distinguish between wild-type and mutant EGFR (mutation [M] classification) as well as between the Del19 and L858R subtypes (subtype [S] classification) were trained using 3DBN features. These features were computed from 3DBN maps by using histogram and texture analyses. The 3DBN maps were generated using computed tomography (CT) images based on the Cech complex constructed on sets of points in the images. These points were defined by coordinates of voxels with CT values higher than several threshold values. The M classification model was built using image features and demographic parameters of sex and smoking status. The SVM models were evaluated by determining their classification accuracies. The feasibility of the 3DBN model was compared with those of conventional radiomic models based on pseudo-3D BN (p3DBN), two-dimensional BN (2DBN), and CT and wavelet-decomposition (WD) images. The validation of the model was repeated with 100 times random sampling. RESULTS: The mean test accuracies for M classification with 3DBN, p3DBN, 2DBN, CT, and WD images were 0.810, 0.733, 0.838, 0.782, and 0.799, respectively. The mean test accuracies for S classification with 3DBN, p3DBN, 2DBN, CT, and WD images were 0.773, 0.694, 0.657, 0.581, and 0.696, respectively. CONCLUSION: 3DBN features, which showed a radiogenomic association with the characteristics of the EGFR Del19/L858R mutation subtypes, yielded higher accuracy for subtype classifications in comparison with conventional features.


Lung Neoplasms , Humans , Retrospective Studies , Lung Neoplasms/diagnostic imaging , Lung Neoplasms/genetics , Mutation , Tomography, X-Ray Computed/methods , ErbB Receptors/genetics
20.
J Digit Imaging ; 36(4): 1533-1540, 2023 08.
Article En | MEDLINE | ID: mdl-37253893

This study investigates the feasibility of using texture radiomics features extracted from mammography images to distinguish between benign and malignant breast lesions and to classify benign lesions into different categories and determine the best machine learning (ML) model to perform the tasks. Six hundred and twenty-two breast lesions from 200 retrospective patient data were segmented and analysed. Three hundred fifty radiomics features were extracted using the Standardized Environment for Radiomics Analysis (SERA) library, one of the radiomics implementations endorsed by the Image Biomarker Standardisation Initiative (IBSI). The radiomics features and selected patient characteristics were used to train selected machine learning models to classify the breast lesions. A fivefold cross-validation was used to evaluate the performance of the ML models and the top 10 most important features were identified. The random forest (RF) ensemble gave the highest accuracy (89.3%) and positive predictive value (66%) and likelihood ratio of 13.5 in categorising benign and malignant lesions. For the classification of benign lesions, the RF model again gave the highest likelihood ratio of 3.4 compared to the other models. Morphological and textural radiomics features were identified as the top 10 most important features from the random forest models. Patient age was also identified as one of the significant features in the RF model. We concluded that machine learning models trained against texture-based radiomics features and patient features give reasonable performance in differentiating benign versus malignant breast lesions. Our study also demonstrated that the radiomics-based machine learning models were able to emulate the visual assessment of mammography lesions, typically used by radiologists, leading to a better understanding of how the machine learning model arrive at their decision.


Breast , Mammography , Humans , Retrospective Studies , Breast/diagnostic imaging , Mammography/methods , Machine Learning , Random Forest
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