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1.
Ther Adv Med Oncol ; 16: 17588359241242972, 2024.
Article in English | MEDLINE | ID: mdl-38736554

ABSTRACT

Background: Afatinib is indicated for advanced-stage non-small-cell lung cancer (NSCLC) with Epidermal Growth Factor Receptor (EGFR) and uncommon mutations. However, real-world studies on this topic are limited. This study aimed to evaluate afatinib as first-line therapy for locally advanced and metastatic NSCLC with uncommon EGFR mutations. Patients and methods: A retrospective study included 92 patients with advanced NSCLC with uncommon and compound EGFR mutations, treated with afatinib as first-line therapy. Patients were followed up and evaluated every 3 months or when symptoms of progressive disease arose. The endpoints were objective response rate (ORR), time-to-treatment failure (TTF), and adverse events. Results: The G719X EGFR mutation had the highest occurrence rate (53.3% for both monotherapy and the compound). By contrast, the compound mutation G719X-S768I was observed at a rate of 22.8%. The ORR was 75%, with 15.2% of patients achieving complete response. The overall median TTF was 13.8 months. Patients with the G719X EGFR mutation (single and compound) had a median TTF of 19.3 months, longer than that of patients with other mutations, who had a median TTF of 11.2 months. Patients with compound EGFR mutations (G719X and S768I) demonstrated a median TTF of 23.2 months compared to that of 12.3 months for other mutations. Tolerated doses of 20 or 30 mg achieved a longer median TTF of 17.1 months compared to 11.2 months with 40 mg. Median TTF differed between patients with and without brain metastasis, at 11.2 and 16.9 months, respectively. Rash (55.4%) and diarrhea (53.3%) were the most common adverse events, primarily grades 1 and 2. Other side effects occurred at a low rate. Conclusion: Afatinib is effective for locally advanced metastatic NSCLC with uncommon EGFR mutations. Patients with G719X, compound G719X-S768I mutations, and tolerated doses of 20 or 30 mg had a longer median TTF than those with other mutations.

2.
Cell Stem Cell ; 31(5): 754-771.e6, 2024 May 02.
Article in English | MEDLINE | ID: mdl-38701759

ABSTRACT

Development of embryonic stem cells (ESCs) into neurons requires intricate regulation of transcription, splicing, and translation, but how these processes interconnect is not understood. We found that polypyrimidine tract binding protein 1 (PTBP1) controls splicing of DPF2, a subunit of BRG1/BRM-associated factor (BAF) chromatin remodeling complexes. Dpf2 exon 7 splicing is inhibited by PTBP1 to produce the DPF2-S isoform early in development. During neuronal differentiation, loss of PTBP1 allows exon 7 inclusion and DPF2-L expression. Different cellular phenotypes and gene expression programs were induced by these alternative DPF2 isoforms. We identified chromatin binding sites enriched for each DPF2 isoform, as well as sites bound by both. In ESC, DPF2-S preferential sites were bound by pluripotency factors. In neuronal progenitors, DPF2-S sites were bound by nuclear factor I (NFI), while DPF2-L sites were bound by CCCTC-binding factor (CTCF). DPF2-S sites exhibited enhancer modifications, while DPF2-L sites showed promoter modifications. Thus, alternative splicing redirects BAF complex targeting to impact chromatin organization during neuronal development.


Subject(s)
Alternative Splicing , Cell Differentiation , Chromatin , Heterogeneous-Nuclear Ribonucleoproteins , Neurons , Polypyrimidine Tract-Binding Protein , Transcription Factors , Alternative Splicing/genetics , Polypyrimidine Tract-Binding Protein/metabolism , Polypyrimidine Tract-Binding Protein/genetics , Animals , Cell Differentiation/genetics , Chromatin/metabolism , Mice , Neurons/metabolism , Neurons/cytology , Transcription Factors/metabolism , Transcription Factors/genetics , Heterogeneous-Nuclear Ribonucleoproteins/metabolism , Heterogeneous-Nuclear Ribonucleoproteins/genetics , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Transcription, Genetic , Embryonic Stem Cells/metabolism , Embryonic Stem Cells/cytology , Exons/genetics , Humans , Cell Self Renewal/genetics
3.
Asia Pac J Clin Nutr ; 33(2): 176-183, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38794977

ABSTRACT

BACKGROUND AND OBJECTIVES: A comprehensive nutritional management is necessary for favourable outcomes in patients with chronic kidney disease (CKD). We aimed to assess the changes in nutritional status and disease progression with nutritional management where renal replacement therapy (RRT) was not in place. METHODS AND STUDY DESIGN: A quasi-experiment intervention was conducted on 70 CKD patients at stages 3-5 from July to December 2022. Participants were excluded if they underwent RRT, including dialy-sis (hemodialysis or peritoneal dialysis), or kidney transplantation. The nutritional regimen covered nutrition-al counseling, samples of the dietary menu, and supplement products. We evaluated nutritional status using Subjective Global Assessment (SGA) scale and sub-clinical blood test at T0 (hospital admission) and T1 (two weeks after the admission or 24 hours before the discharge). RESULTS: After the intervention, the number of patients classified as malnutrition or at risk of malnourished reduced significantly (65.7% to 54.3% and 25.7% and 5.7%, respectively). The serum concentration of urea, creatinine and parathyroid hormone decreased remarkably, especially in patients receiving nutritional management. In the intervention group, the dietary pattern provided increased intakes of calcium and iron at T1, while phosphorus, sodium and potassium decreased after follow-up. Nausea/vomiting, loss of appetite, tiredness and sleep disorders were improved in the intervention compared to the control group. CONCLUSIONS: Nutritional therapy enhanced the nutritional sta-tus, and quality of dietary and renal function in CKD patients without RRT. Applying nutrition education and treatment at an early stage can slow CKD progression, which should be applicable elsewhere in Vietnam.


Subject(s)
Nutritional Status , Renal Insufficiency, Chronic , Humans , Renal Insufficiency, Chronic/diet therapy , Renal Insufficiency, Chronic/therapy , Male , Female , Vietnam , Middle Aged , Malnutrition/diet therapy , Aged , Adult , Nutrition Therapy/methods
4.
Eur J Case Rep Intern Med ; 11(3): 004335, 2024.
Article in English | MEDLINE | ID: mdl-38455702

ABSTRACT

Infection caused by Candida auris ha C. auris s rapidly become a global health threat. C. auris created a significant healthcare burden due to various complicating factors, including misidentification by commercial identification methods, potent antifungal resistance, high mortality rates and the possibility of nosocomial outbreaks through direct contact. In Vietnam, there are currently no clinical reports on C. auris infections. Here, we present four clinical cases of C. auris infections in the Department of Pulmonary Medicine of Cho Ray Hospital in southern Vietnam. Through this report, we aim to highlight the attention to the emergence of C. auris in Vietnam. Further research on C. auris infections is warranted, focusing on newly observed clinical characteristics present in all cases in this report, including hypoalbuminaemia and corticosteroid usage. Moreover, one case of resistance to amphotericin B has been identified, possibly due to prior exposure to this antifungal agent. LEARNING POINTS: Further research on Candida auris infections is warranted, focusing on newly observed clinical features present in all cases in this report, including hypoalbuminaemia and corticosteroid use during hospitalisation.While Candida auris remains susceptible to commonly used antifungal drugs, one case of resistance to amphotericin B has been documented, possibly due to prior exposure to this antifungal agent.

5.
BMC Cancer ; 24(1): 176, 2024 Feb 05.
Article in English | MEDLINE | ID: mdl-38317094

ABSTRACT

BACKGROUND: This study aimed to evaluate the efficacy and side effects of first-line afatinib treatment in a real-world setting in Vietnam. METHODS: This retrospective study was conducted across nine hospitals in Vietnam. Advanced epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer (NSCLC) patients who received afatinib as first-line therapy between April 2018 and June 2022 were included, and patient medical records were reviewed. Key outcomes were overall response rate (ORR), time-to-treatment failure (TTF), and tolerability. RESULTS: A total of 343 patients on first-line afatinib were eligible for the study. EGFR exon 19 deletion (Del19) alone was detected in 46.9% of patients, L858R mutation alone in 26.3%, and other uncommon EGFR mutations, including compound mutations, in 26.8%. Patients with brain metastases at baseline were 25.4%. Patients who received 40 mg, 30 mg, and 20 mg as starting doses of afatinib were 58.6%, 39.9%, and 1.5%, respectively. The ORR was 78.1% in the overall population, 82.6% in the Del19 mutation subgroup, 73.3% in the L858R mutation subgroup, and 75.0% in the uncommon mutation subgroup (p > 0.05). The univariate and multivariate analyses indicate that the ORR increased when the starting dose was 40 mg compared to starting doses below 40 mg (83.9% vs. 74.3%, p = 0.034). The median TTF (mTTF) was 16.7 months (CI 95%: 14.8-18.5) in all patients, with a median follow-up time of 26.2 months. The mTTF was longer in patients in the common EGFR mutation subgroup (Del19/L858R) than in those in the uncommon mutation subgroup (17.5 vs. 13.8 months, p = 0.045) and in those without versus with brain metastases at baseline (17.5 vs. 15.1 months, p = 0.049). There were no significant differences in the mTTF between subgroups based on the starting dose of 40 mg and < 40 mg (16.7 vs. 16.9 months, p > 0.05). The most common treatment-related adverse events (any grade/grade ≥ 3) were diarrhea (55.4%/3.5%), rash (51.9%/3.2%), paronychia (35.3%/5.0%), and stomatitis (22.2%/1.2%). CONCLUSIONS: Afatinib demonstrated clinical effectiveness and good tolerability in Vietnamese EGFR-mutant NSCLC patients. In our real-world setting, administering a starting dose below 40 mg might result in a reduction in ORR; however, it might not have a significant impact on TTF.


Subject(s)
Afatinib , Brain Neoplasms , Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Humans , Afatinib/therapeutic use , Brain Neoplasms/drug therapy , Brain Neoplasms/secondary , Carcinoma, Non-Small-Cell Lung/drug therapy , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Cohort Studies , ErbB Receptors/genetics , Lung Neoplasms/drug therapy , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Mutation , Protein Kinase Inhibitors/therapeutic use , Retrospective Studies , Vietnam/epidemiology
6.
Development ; 151(2)2024 Jan 15.
Article in English | MEDLINE | ID: mdl-38112206

ABSTRACT

Placental development involves coordinated expansion and differentiation of trophoblast cell lineages possessing specialized functions. Among the differentiated trophoblast cell lineages are invasive trophoblast cells, which exit the placenta and invade the uterus, where they restructure the uterine parenchyma and facilitate remodeling of uterine spiral arteries. The rat exhibits deep intrauterine trophoblast cell invasion, a feature shared with human placentation, and is also amenable to gene manipulation using genome-editing techniques. In this investigation, we generated a conditional rat model targeting the invasive trophoblast cell lineage. Prolactin family 7, subfamily b, member 1 (Prl7b1) is uniquely and abundantly expressed in the rat invasive trophoblast cell lineage. Disruption of Prl7b1 did not adversely affect placental development. We demonstrated that the Prl7b1 locus could be effectively used to drive the expression of Cre recombinase in invasive trophoblast cells. Our rat model represents a new tool for investigating candidate genes contributing to the regulation of invasive trophoblast cells and their roles in trophoblast-guided uterine spiral artery remodeling.


Subject(s)
Placenta , Placentation , Pregnancy , Rats , Female , Animals , Humans , Placenta/metabolism , Placentation/genetics , Trophoblasts , Uterus , Cell Lineage/genetics , Models, Animal
7.
bioRxiv ; 2023 Aug 05.
Article in English | MEDLINE | ID: mdl-37577576

ABSTRACT

Placental development involves coordinated expansion and differentiation of trophoblast cell lineages possessing specialized functions. Among the differentiated trophoblast cell lineages are invasive trophoblast cells, which exit the placenta and invade into the uterus where they restructure the uterine parenchyma and facilitate remodeling of uterine spiral arteries. The rat exhibits deep intrauterine trophoblast cell invasion, a feature shared with human placentation, and is also amenable to gene manipulation using genome editing techniques. In this investigation, we generated a conditional rat model targeting the invasive trophoblast cell lineage. Prolactin family 7, subfamily b, member 1 ( Prl7b1 ) is uniquely and abundantly expressed in the rat invasive trophoblast cell lineage. Disruption of Prl7b1 did not adversely affect placental development. We demonstrated that the Prl7b1 locus could be effectively used to drive the expression of Cre recombinase in invasive trophoblast cells. Our rat model represents a new tool for investigating candidate genes contributing to the regulation of invasive trophoblast cells and their contributions to trophoblast-guided uterine spiral artery remodeling.

8.
Development ; 150(15)2023 08 01.
Article in English | MEDLINE | ID: mdl-37417811

ABSTRACT

The invasive trophoblast cell lineages in rat and human share crucial responsibilities in establishing the uterine-placental interface of the hemochorial placenta. These observations have led to the rat becoming an especially useful animal model for studying hemochorial placentation. However, our understanding of similarities or differences between regulatory mechanisms governing rat and human invasive trophoblast cell populations is limited. In this study, we generated single-nucleus ATAC-seq data from gestation day 15.5 and 19.5 rat uterine-placental interface tissues, and integrated the data with single-cell RNA-seq data generated at the same stages. We determined the chromatin accessibility profiles of invasive trophoblast, natural killer, macrophage, endothelial and smooth muscle cells, and compared invasive trophoblast chromatin accessibility with extravillous trophoblast cell accessibility. In comparing chromatin accessibility profiles between species, we found similarities in patterns of gene regulation and groups of motifs enriched in accessible regions. Finally, we identified a conserved gene regulatory network in invasive trophoblast cells. Our data, findings and analysis will facilitate future studies investigating regulatory mechanisms essential for the invasive trophoblast cell lineage.


Subject(s)
Gene Regulatory Networks , Trophoblasts , Animals , Pregnancy , Rats , Cell Nucleus , Chromatin , Placenta/cytology , Single-Cell Gene Expression Analysis , Transcription Factors/metabolism , Trophoblasts/cytology , Trophoblasts/metabolism , Uterus/cytology , Female
9.
Genome Biol ; 24(1): 153, 2023 06 27.
Article in English | MEDLINE | ID: mdl-37370147

ABSTRACT

A large-scale application of the "stacked modeling" approach for chromatin state discovery previously provides a single "universal" chromatin state annotation of the human genome based jointly on data from many cell and tissue types. Here, we produce an analogous chromatin state annotation for mouse based on 901 datasets assaying 14 chromatin marks in 26 cell or tissue types. To characterize each chromatin state, we relate the states to external annotations and compare them to analogously defined human states. We expect the universal chromatin state annotation for mouse to be a useful resource for studying this key model organism's genome.


Subject(s)
Chromatin , Genome, Human , Animals , Mice , Chromatin/genetics , Molecular Sequence Annotation
10.
Genome Res ; 33(7): 1133-1144, 2023 07.
Article in English | MEDLINE | ID: mdl-37217250

ABSTRACT

The assay for transposase-accessible chromatin with sequencing (ATAC-seq) is a common assay to identify chromatin accessible regions by using a Tn5 transposase that can access, cut, and ligate adapters to DNA fragments for subsequent amplification and sequencing. These sequenced regions are quantified and tested for enrichment in a process referred to as "peak calling." Most unsupervised peak calling methods are based on simple statistical models and suffer from elevated false positive rates. Newly developed supervised deep learning methods can be successful, but they rely on high quality labeled data for training, which can be difficult to obtain. Moreover, though biological replicates are recognized to be important, there are no established approaches for using replicates in the deep learning tools, and the approaches available for traditional methods either cannot be applied to ATAC-seq, where control samples may be unavailable, or are post hoc and do not capitalize on potentially complex, but reproducible signal in the read enrichment data. Here, we propose a novel peak caller that uses unsupervised contrastive learning to extract shared signals from multiple replicates. Raw coverage data are encoded to obtain low-dimensional embeddings and optimized to minimize a contrastive loss over biological replicates. These embeddings are passed to another contrastive loss for learning and predicting peaks and decoded to denoised data under an autoencoder loss. We compared our replicative contrastive learner (RCL) method with other existing methods on ATAC-seq data, using annotations from ChromHMM genomic labels and transcription factor ChIP-seq as noisy truth. RCL consistently achieved the best performance.


Subject(s)
Chromatin Immunoprecipitation Sequencing , High-Throughput Nucleotide Sequencing , Sequence Analysis, DNA/methods , High-Throughput Nucleotide Sequencing/methods , Chromatin/genetics , DNA/genetics
11.
bioRxiv ; 2023 Apr 03.
Article in English | MEDLINE | ID: mdl-37066272

ABSTRACT

The invasive trophoblast cell lineage in rat and human share crucial responsibilities in establishing the uterine-placental interface of the hemochorial placenta. These observations have led to the rat becoming an especially useful animal model to study hemochorial placentation. However, our understanding of similarities or differences between regulatory mechanisms governing rat and human invasive trophoblast cell populations is limited. In this study, we generated single-nucleus (sn) ATAC-seq data from gestation day (gd) 15.5 and 19.5 rat uterine-placental interface tissues and integrated the data with single-cell RNA-seq data generated at the same stages. We determined the chromatin accessibility profiles of invasive trophoblast, natural killer, macrophage, endothelial, and smooth muscle cells, and compared invasive trophoblast chromatin accessibility to extravillous trophoblast (EVT) cell accessibility. In comparing chromatin accessibility profiles between species, we found similarities in patterns of gene regulation and groups of motifs enriched in accessible regions. Finally, we identified a conserved gene regulatory network in invasive trophoblast cells. Our data, findings and analysis will facilitate future studies investigating regulatory mechanisms essential for the invasive trophoblast cell lineage.

12.
Biotechnol Lett ; 45(5-6): 689-702, 2023 Jun.
Article in English | MEDLINE | ID: mdl-37071381

ABSTRACT

OBJECTIVES: This work aimed to construct a versatile, effective, and food-grade Agrobacterium tumefaciens-mediated transformation (ATMT) system for recombinant expression in the filamentous fungus Penicillium rubens (also known as Pencillium chrysogenum). RESULTS: In this study, the wild-type P. chrysogenum VTCC 31172 strain was re-classified as P. rubens by a multilocus sequencing analysis. Further, the pyrG gene required for uridine/uracil biosynthesis was successfully deleted in the VTCC 31172 strain by homologous recombination to generate a stable uridine/uracil auxotrophic mutant (ΔpyrG). The growth of the P. rubens ΔpyrG strain could be restored by uridine/uracil supplementation, and a new ATMT system based on the uridine/uracil auxotrophic mechanism was established for this strain. The optimal ATMT efficiency could reach 1750 transformants for 106 spores (equivalent to 0.18%). In addition, supplementation of uridine/uracil at the concentrations of 0.005-0.02% during the co-cultivation process significantly promoted transformation efficiency. Especially, we demonstrated that the pyrG marker and the amyB promoter from the koji mold Aspergillus oryzae were fully functional in P. rubens ΔpyrG. Expression of the DsRed reporter gene under the regulation of the A. oryzae amyB promoter lighted up the mycelium of P. rubens with a robust red signal under fluorescence microscopy. Furthermore, genomic integration of multiple copies of the Aspergillus fumigatus phyA gene under the control of the amyB promoter significantly enhanced phytase activity in P. rubens. CONCLUSIONS: The ATMT system developed in our work provides a safe genetic platform for producing recombinant products in P. rubens without using drug resistance markers.


Subject(s)
Penicillium , Penicillium/genetics , Penicillium/metabolism , Agrobacterium tumefaciens/genetics , Uracil/metabolism , Uridine , Transformation, Genetic
13.
Comput Methods Programs Biomed ; 233: 107453, 2023 May.
Article in English | MEDLINE | ID: mdl-36921463

ABSTRACT

PURPOSE: Selective internal radiation therapy (SIRT) has been proven to be an effective treatment for hepatocellular carcinoma (HCC) patients. In clinical practice, the treatment planning for SIRT using 90Y microspheres requires estimation of the liver-lung shunt fraction (LSF) to avoid radiation pneumonitis. Currently, the manual segmentation method to draw a region of interest (ROI) of the liver and lung in 2D planar imaging of 99mTc-MAA and 3D SPECT/CT images is inconvenient, time-consuming and observer-dependent. In this study, we propose and evaluate a nearly automatic method for LSF quantification using 3D SPECT/CT images, offering improved performance compared with the current manual segmentation method. METHODS: We retrospectively acquired 3D SPECT with non-contrast-enhanced CT images (nCECT) of 60 HCC patients from a SPECT/CT scanning machine, along with the corresponding diagnostic contrast-enhanced CT images (CECT). Our approach for LSF quantification is to use CNN-based methods for liver and lung segmentations in the nCECT image. We first apply 3D ResUnet to coarsely segment the liver. If the liver segmentation contains a large error, we dilate the coarse liver segmentation into the liver mask as a ROI in the nCECT image. Subsequently, non-rigid registration is applied to deform the liver in the CECT image to fit that obtained in the nCECT image. The final liver segmentation is obtained by segmenting the liver in the deformed CECT image using nnU-Net. In addition, the lung segmentations are obtained using 2D ResUnet. Finally, LSF quantitation is performed based on the number of counts in the SPECT image inside the segmentations. Evaluations and Results: To evaluate the liver segmentation accuracy, we used Dice similarity coefficient (DSC), asymmetric surface distance (ASSD), and max surface distance (MSD) and compared the proposed method to five well-known CNN-based methods for liver segmentation. Furthermore, the LSF error obtained by the proposed method was compared to a state-of-the-art method, modified Deepmedic, and the LSF quantifications obtained by manual segmentation. The results show that the proposed method achieved a DSC score for the liver segmentation that is comparable to other state-of-the-art methods, with an average of 0.93, and the highest consistency in segmentation accuracy, yielding a standard deviation of the DSC score of 0.01. The proposed method also obtains the lowest ASSD and MSD scores on average (2.6 mm and 31.5 mm, respectively). Moreover, for the proposed method, a median LSF error of 0.14% is obtained, which is a statically significant improvement to the state-of-the-art-method (p=0.004), and is much smaller than the median error in LSF manual determination by the medical experts using 2D planar image (1.74% and p<0.001). CONCLUSIONS: A method for LSF quantification using 3D SPECT/CT images based on CNNs and non-rigid registration was proposed, evaluated and compared to state-of-the-art techniques. The proposed method can quantitatively determine the LSF with high accuracy and has the potential to be applied in clinical practice.


Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , Humans , Liver Neoplasms/diagnostic imaging , Liver Neoplasms/radiotherapy , Carcinoma, Hepatocellular/diagnostic imaging , Carcinoma, Hepatocellular/radiotherapy , Retrospective Studies , Single Photon Emission Computed Tomography Computed Tomography , Lung/diagnostic imaging , Image Processing, Computer-Assisted/methods
14.
bioRxiv ; 2023 Jan 08.
Article in English | MEDLINE | ID: mdl-36712015

ABSTRACT

The assay for transposase-accessible chromatin with sequencing (ATAC-seq) is a common assay to identify chromatin accessible regions by using a Tn5 transposase that can access, cut, and ligate adapters to DNA fragments for subsequent amplification and sequencing. These sequenced regions are quantified and tested for enrichment in a process referred to as "peak calling". Most unsupervised peak calling methods are based on simple statistical models and suffer from elevated false positive rates. Newly developed supervised deep learning methods can be successful, but they rely on high quality labeled data for training, which can be difficult to obtain. Moreover, though biological replicates are recognized to be important, there are no established approaches for using replicates in the deep learning tools, and the approaches available for traditional methods either cannot be applied to ATAC-seq, where control samples may be unavailable, or are post-hoc and do not capitalize on potentially complex, but reproducible signal in the read enrichment data. Here, we propose a novel peak caller that uses unsupervised contrastive learning to extract shared signals from multiple replicates. Raw coverage data are encoded to obtain low-dimensional embeddings and optimized to minimize a contrastive loss over biological replicates. These embeddings are passed to another contrastive loss for learning and predicting peaks and decoded to denoised data under an autoencoder loss. We compared our Replicative Contrastive Learner (RCL) method with other existing methods on ATAC-seq data, using annotations from ChromHMM genome and transcription factor ChIP-seq as noisy truth. RCL consistently achieved the best performance.

15.
Life Sci Alliance ; 6(2)2023 02.
Article in English | MEDLINE | ID: mdl-36622342

ABSTRACT

The placenta serves as a connection between the mother and the fetus during pregnancy, providing the fetus with oxygen, nutrients, and growth hormones. However, the regulatory mechanisms and dynamic gene interaction networks underlying early placental development are understudied. Here, we generated RNA-sequencing data from mouse fetal placenta at embryonic days 7.5, 8.5, and 9.5 to identify genes with timepoint-specific expression, then inferred gene interaction networks to analyze highly connected network modules. We determined that timepoint-specific gene network modules were associated with distinct developmental processes, and with similar expression profiles to specific human placental cell populations. From each module, we identified hub genes and their direct neighboring genes, which were predicted to govern placental functions. We confirmed that four novel candidate regulators identified through our analyses regulate cell migration in the HTR-8/SVneo cell line. Overall, we predicted several novel regulators of placental development expressed in specific placental cell types using network analysis of bulk RNA-sequencing data. Our findings and analysis approaches will be valuable for future studies investigating the transcriptional landscape of early development.


Subject(s)
Placenta , Transcriptome , Animals , Female , Mice , Pregnancy , Gene Regulatory Networks/genetics , Placenta/metabolism , Placentation/genetics , RNA/metabolism , Transcriptome/genetics
16.
Bioinformatics ; 39(1)2023 01 01.
Article in English | MEDLINE | ID: mdl-36342196

ABSTRACT

MOTIVATION: Genome-wide maps of epigenetic modifications are powerful resources for non-coding genome annotation. Maps of multiple epigenetics marks have been integrated into cell or tissue type-specific chromatin state annotations for many cell or tissue types. With the increasing availability of multiple chromatin state maps for biologically similar samples, there is a need for methods that can effectively summarize the information about chromatin state annotations within groups of samples and identify differences across groups of samples at a high resolution. RESULTS: We developed CSREP, which takes as input chromatin state annotations for a group of samples. CSREP then probabilistically estimates the state at each genomic position and derives a representative chromatin state map for the group. CSREP uses an ensemble of multi-class logistic regression classifiers that predict the chromatin state assignment of each sample given the state maps from all other samples. The difference in CSREP's probability assignments for the two groups can be used to identify genomic locations with differential chromatin state assignments. Using groups of chromatin state maps of a diverse set of cell and tissue types, we demonstrate the advantages of using CSREP to summarize chromatin state maps and identify biologically relevant differences between groups at a high resolution. AVAILABILITY AND IMPLEMENTATION: The CSREP source code and generated data are available at http://github.com/ernstlab/csrep. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Chromatin , Genomics , Chromatin/genetics , Genomics/methods , Genome , Software , Chromosome Mapping
17.
Proc Natl Acad Sci U S A ; 119(41): e2210633119, 2022 10 11.
Article in English | MEDLINE | ID: mdl-36191208

ABSTRACT

The hemochorial placentation site is characterized by a dynamic interplay between trophoblast cells and maternal cells. These cells cooperate to establish an interface required for nutrient delivery to promote fetal growth. In the human, trophoblast cells penetrate deep into the uterus. This is not a consistent feature of hemochorial placentation and has hindered the establishment of suitable animal models. The rat represents an intriguing model for investigating hemochorial placentation with deep trophoblast cell invasion. In this study, we used single-cell RNA sequencing to characterize the transcriptome of the invasive trophoblast cell lineage, as well as other cell populations within the rat uterine-placental interface during early (gestation day [gd] 15.5) and late (gd 19.5) stages of intrauterine trophoblast cell invasion. We identified a robust set of transcripts that define invasive trophoblast cells, as well as transcripts that distinguished endothelial, smooth muscle, natural killer, and macrophage cells. Invasive trophoblast, immune, and endothelial cell populations exhibited distinct spatial relationships within the uterine-placental interface. Furthermore, the maturation stage of invasive trophoblast cell development could be determined by assessing gestation stage-dependent changes in transcript expression. Finally, and most importantly, expression of a prominent subset of rat invasive trophoblast cell transcripts is conserved in the invasive extravillous trophoblast cell lineage of the human placenta. These findings provide foundational data to identify and interrogate key conserved regulatory mechanisms essential for the development and function of an important compartment within the hemochorial placentation site that is essential for a healthy pregnancy.


Subject(s)
Placenta , Placentation , Animals , Cell Lineage , Female , Humans , Placenta/metabolism , Pregnancy , Rats , Trophoblasts/metabolism , Uterus
18.
J Mater Sci Mater Med ; 33(10): 72, 2022 Oct 04.
Article in English | MEDLINE | ID: mdl-36195780

ABSTRACT

Hepatocellular carcinoma is a common type of cancer associated with a high mortality rate. Among several bioactive compounds, Murrayafoline A (MuA) has been proved as a bio substance that exhibits great potentials in treating liver cancer. In order to overcome the high cytotoxicity and low solubility of MuA, a delivery system based on nanocarriers is necessary to deliver MuA towards the desired target. In the present study, 18ß-glycyrrhetinic acid (GA), which is known as a ligand for liver targeting, was used to construct the cholesterol-poly (ethylene glycol)-glycyrrhetinic acid (GA-PEG-Chol) conjugate and liposome for MuA administration. The compound was then examined for therapeutic efficacy and safety in HUVEC and HepG2 cells in 2D and 3D cell cultures. Results have shown that MuA-loaded liposomes had IC50 value of 2 µM in HepG2 and had the cytosolic absorption of 8.83 ± 0.97 ng/105 cells, while The IC50 value of MuA-loaded liposomes in HUVEC cell lines was 15 µM and the the cytosolic absorption was recorded as 3.62 ± 0.61 cells. The drug test on the 3D cancer sphere platform of the HepG2 cancer sphere showed that MuA-loaded GA liposomes had the highest efficacy at a concentration of 100 µg/mL. In short, these results suggest that MuA-loaded GA liposomes have the potential for maintenance drug delivery and liver targeting.


Subject(s)
Carcinoma, Hepatocellular , Glycyrrhetinic Acid , Liver Neoplasms , Alkaloids , Carbazoles , Carcinoma, Hepatocellular/drug therapy , Cholesterol , Glycyrrhetinic Acid/therapeutic use , Hep G2 Cells , Humans , Ligands , Liposomes , Liver Neoplasms/drug therapy
19.
Zootaxa ; 5129(1): 60-76, 2022 Apr 26.
Article in English | MEDLINE | ID: mdl-36101150

ABSTRACT

Otostigmus consonensis sp. nov. was described from Vietnam, and O. sulcipes Verhoeff, 1937 was recorded for the first time in this country. The new species can be recognized by having 18 antennomeres including 2.32.5 glabrous basal ones, three coxosternal teeth, tergites 520 with complete paramedia sutures, sternites with incomplete paramedian sutures, and the ultimate leg with 1115 prefemoral spines. The fragment of the COI gene was extracted for each species; thus, a new species and a record of O. sulcipes were supported by the COI genetic distances and the corresponding phylogenetic analysis.


Subject(s)
Arthropods , Chilopoda , Animals , Arthropods/genetics , Phylogeny , Vietnam
20.
PLoS One ; 17(9): e0273047, 2022.
Article in English | MEDLINE | ID: mdl-36155973

ABSTRACT

OBJECTIVE: This study aimed to measure the exposure of residents to health education messages about non-communicable diseases (NCD)-related risk factors, and activities of village health workers (VHWs) in NCDs prevention and control in the mountainous setting of Vietnam. METHOD: A cross-sectional study was performed in Dap Thanh commune (Ba Che, Quang Ninh province, Vietnam), a mountainous area. There were 151 residents aged 18 years or above recruited for this study. Information regarding exposure to messages about risk factors of NCDs, and activities of VHWs was collected via face-to-face interviews using a structured questionnaire. Multivariate logistic regression was employed to identify associated factors with exposing messages about NCD-related risk factors. RESULTS: The majority of participants heard about messages related to risk factors of NCDs in the last 30 days, from 56.3% (physical inactivity message), 59.6% (diet message), 75.5% (alcohol use message) to 79.5% (smoking message). Radio/television was the most common source of the messages (from 91.8% to 95.8%) and the majority of participants heard these messages from one source (from 77.1% to 80.9%). Most of sample reported the unavailability of VHWs in their locals (53.6%). Among locals having VHWs, health communication and education was the most common service provided (54.3%); however, only 30% received NCD management services. Participants who had other jobs were less likely to hear about diet-related messages (OR = 0.32; 95%CI = 0.11-0.92), and those ever smoking were more likely to hear these messages in the last 30 days (OR = 6.86; 95%CI = 1.06-44.51). People who had diabetes mellitus were more likely to hear physical activity-related messages in the last 30 days (OR = 2.55; 95%CI = 1.20-5.41). CONCLUSION: Our findings indicated that health communication regarding risk factors of NCDs in mountainous areas in Vietnam was insufficient, and the role of health workers as formal information source was not recognized. Efforts should be made to increase the capacity and involvement of VHWs in health education and NCD prevention in mountainous regions.


Subject(s)
Noncommunicable Diseases , Community Health Workers , Cross-Sectional Studies , Health Education , Humans , Noncommunicable Diseases/epidemiology , Noncommunicable Diseases/prevention & control , Vietnam/epidemiology
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