Elife. 2024 Oct 14;12:RP89701. doi: 10.7554/eLife.89701.

ABSTRACT

Changes in chondrocyte gene expression can contribute to the development of osteoarthritis (OA), and so recognition of the regulative processes during chondrogenesis can lead to a better understanding of OA. microRNAs (miRNAs) are key regulators of gene expression in chondrocytes/OA, and we have used a combined experimental, bioinformatic, and systems biology approach to explore the multiple miRNA-mRNA interactions that regulate chondrogenesis. A longitudinal chondrogenesis bioinformatic analysis identified paralogues miR-199a-5p and miR-199b-5p as pro-chondrogenic regulators. Experimental work in human cells demonstrated alteration of miR-199a-5p or miR-199b-5p expression led to significant inverse modulation of key chondrogenic genes and extracellular matrix production. miR-199a/b-5p targets FZD6, ITGA3 and CAV1 were identified by inhibition experiments and verified as direct targets by luciferase assay. The experimental work was used to generate and parameterise a multi-miRNA 14-day chondrogenesis kinetic model to be used as a repository for the experimental work and as a resource for further investigation of this system. This is the first multi-miRNA model of a chondrogenesis-based system, and highlights the complex relationships between regulatory miRNAs, and their target mRNAs.

PMID:39401064 | PMC:PMC11473111 | DOI:10.7554/eLife.89701

Plant J. 2024 Oct 14. doi: 10.1111/tpj.17041. Online ahead of print.

ABSTRACT

Genome stability is significantly influenced by the precise coordination of chromatin complexes that facilitate the loading and eviction of histones from chromatin during replication, transcription, and DNA repair processes. In this study, we investigate the role of the Arabidopsis H3 histone chaperones ANTI-SILENCING FUNCTION 1 (ASF1) and HISTONE REGULATOR A (HIRA) in the maintenance of telomeres and 45S rDNA loci, genomic sites that are particularly susceptible to changes in the chromatin structure. We find that both ASF1 and HIRA are essential for telomere length regulation, as telomeres are significantly shorter in asf1a1b and hira mutants. However, these shorter telomeres remain localized around the nucleolus and exhibit a comparable relative H3 occupancy to the wild type. In addition to regulating telomere length, ASF1 and HIRA contribute to silencing 45S rRNA genes and affect their copy number. Besides, ASF1 supports global heterochromatin maintenance. Our findings also indicate that ASF1 transiently binds to the TELOMERE REPEAT BINDING 1 protein and the N terminus of telomerase in vivo, suggesting a physical link between the ASF1 histone chaperone and the telomere maintenance machinery.

PMID:39400911 | DOI:10.1111/tpj.17041

Tissue Eng Regen Med. 2024 Oct 14. doi: 10.1007/s13770-024-00665-x. Online ahead of print.

ABSTRACT

OBJECTIVE: Surgical wounds that can't complete primary healing three weeks after surgery are called postoperative refractory wounds. Postoperative refractory wounds would bring great physical and life burdens to the patients and seriously affect their quality of life. To investigate the effect of platelet fibrin plasma (PFP) on postoperative refractory wound healing.

APPROACH: The composition of PFP was analyzed using blood routine and blood biochemicals. Clinical data were collected that met the inclusion criteria after treatment with PFP, and the efficacy of PFP was evaluated by wound healing rate and days to healing. Next, growth factor content in PFP, PRP, and PPP was analyzed using ELISA, and PFP-treated cells were applied to investigate the effect of PFP on fibroblast and endothelial cell function.

RESULTS: PFP component analysis revealed no statistical difference between platelet concentration in PFP and physiological concentration. Clinical statistics showed that PFP treatment was effective in the postoperative refractory wound (four-week wound healing rate > 90%), significantly better than continuous wound dressing. Meanwhile, our result also proved that PFP treatment significantly enhanced vascularization by upregulated the expression level of CD31 and improved granulation tissue thickness. Activated PFP, PRP, and PPP could continuously release growth factors in vitro and the amount of growth factors released by PRP and PFP was significantly higher than PPP. In vitro studies demonstrated that active PFP could improve cell proliferation, migration, adhesion, and angiogenesis in fibroblasts and endothelial cells.

INNOVATION: Physiologically concentrated platelet plasma promoted wound healing and improved related cellular functions. The modified PFP (responsible for accelerating wound healing and enhancing the migration and proliferation of fibroblasts and endothelial cells) was prepared and analyzed for its clinical effectiveness in postoperative refractory wounds.

CONCLUSION: Physiologically concentrated platelet plasma promoted wound healing and improved related cellular functions. The preparation of PFP could significantly reduce the amount of prepared blood, with a good application value for postoperative wounds. PFP can be considered a treatment option, especially for postoperative refractory wounds.

PMID:39400879 | DOI:10.1007/s13770-024-00665-x

Microbiol Resour Announc. 2024 Oct 14:e0081424. doi: 10.1128/mra.00814-24. Online ahead of print.

ABSTRACT

Rhodopseudomonas palustris R1 is a phototrophic, purple, non-sulfur Gram-negative bacterium first isolated from the soils of rice fields, known for its polylactic acid degradability. Here, we present the complete circular genome sequence of this bacterium, spanning 5.32 Mbp and 4,949 protein-coding sequences.

PMID:39400143 | DOI:10.1128/mra.00814-24

Microbiol Resour Announc. 2024 Oct 14:e0081524. doi: 10.1128/mra.00815-24. Online ahead of print.

ABSTRACT

Serratia plymuthica strain SWSY-3.47 is a Gram-negative, rod-shaped bacteria isolated for its high chitinolytic activity. Here, we report the complete genome of this strain comprised of a single circular chromosome of 5,636,345 bp with a G + C content of 56.0%.

PMID:39400136 | DOI:10.1128/mra.00815-24

Curr Med Chem. 2024 Oct 11. doi: 10.2174/0109298673346264241008110105. Online ahead of print.

ABSTRACT

Tuberculosis (TB) is a leading cause of death from a single infectious disease worldwide. Early and accurate diagnosis is advantageous for timely detection and prompt treatment, thereby reducing the risk of disease transmission, which is essential for effective TB control. Biomarkers provide a valuable resource for TB diagnosis. Proteomic technologies have emerged as a powerful tool in biomarker discovery. In this perspective, we explore how proteomic technologies contribute to the discovery of TB diagnostic biomarkers. We also address the challenges and discuss prospective methods to augment the performance of biomarkers in diagnosing TB.

PMID:39400017 | DOI:10.2174/0109298673346264241008110105

Gigascience. 2024 Jan 2;13:giae071. doi: 10.1093/gigascience/giae071.

ABSTRACT

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields-isotope, isotopolog, isotopolog label, labeling approach, and gradient position-and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

PMID:39399973 | DOI:10.1093/gigascience/giae071

Bioact Mater. 2024 Sep 26;43:305-318. doi: 10.1016/j.bioactmat.2024.09.021. eCollection 2025 Jan.

ABSTRACT

Mitochondrial dysfunction increases ROS production and is closely related to many degenerative cellular organelle diseases. The NOX4-p22phox axis is a major contributor to ROS production and its dysregulation is expected to disrupt mitochondrial function. However, the field lacks a competitive inhibitor of the NOX4-p22phox interaction. Here, we created a povidone micelle-based Prussian blue nanozyme that we named "Mitocelle" to target the NOX4-p22phox axis, and characterized its impact on the major degenerative cellular organelle disease, osteoarthritis (OA). Mitocelle is composed of FDA-approved and biocompatible materials, has a regular spherical shape, and is approximately 88 nm in diameter. Mitocelle competitively inhibits the NOX4-p22phox interaction, and its uptake by chondrocytes can protect against mitochondrial malfunction. Upon intra-articular injection to an OA mouse model, Mitocelle shows long-term stability, effective uptake into the cartilage matrix, and the ability to attenuate joint degradation. Collectively, our findings suggest that Mitocelle, which functions as a competitive inhibitor of NOX4-p22phox, may be suitable for translational research as a therapeutic for OA and cellular organelle diseases related to dysfunctional mitochondria.

PMID:39399840 | PMC:PMC11467566 | DOI:10.1016/j.bioactmat.2024.09.021

Mol Ther Oncol. 2024 Sep 10;32(4):200874. doi: 10.1016/j.omton.2024.200874. eCollection 2024 Dec 19.

ABSTRACT

Kidney cancer, particularly clear cell renal cell carcinoma (KIRC), presents significant challenges in disease-specific survival. This study investigates the prognostic potential of microRNAs (miRNAs) in kidney cancers, including KIRC and kidney papillary cell carcinoma (KIRP), focusing on their interplay with telomere maintenance genes. Utilizing data from The Cancer Genome Atlas, miRNA expression profiles of 166 KIRC and 168 KIRP patients were analyzed. An evolutionary learning-based kidney survival estimator identified robust miRNA signatures predictive of 5-year survival for both cancer types. For KIRC, a 37-miRNA signature showed a correlation coefficient (R) of 0.82 and mean absolute error (MAE) of 0.65 years. Similarly, for KIRP, a 23-miRNA signature exhibited an R of 0.82 and MAE of 0.64 years, demonstrating comparable predictive accuracy. These signatures also displayed diagnostic potential with receiver operating characteristic curve values between 0.70 and 0.94. Bioinformatics analysis revealed targeting of key telomere-associated genes such as TERT, DKC1, CTC1, and RTEL1 by these miRNAs, implicating crucial pathways such as cellular senescence and proteoglycans in cancer. This study highlights the significant link between miRNAs and telomere genes in kidney cancer survival, offering insights for therapeutic targets and improved prognostic markers.

PMID:39399813 | PMC:PMC11467672 | DOI:10.1016/j.omton.2024.200874

Front Immunol. 2024 Sep 27;15:1452214. doi: 10.3389/fimmu.2024.1452214. eCollection 2024.

ABSTRACT

INTRODUCTION: The complex and unresolved pathogenesis of schizophrenia has posed significant challenges to its diagnosis and treatment. While recent research has established a clear association between immune function and schizophrenia, the causal relationship between the two remains elusive.

METHODS: We employed a bidirectional two-sample Mendelian randomization approach to investigate the causal relationship between schizophrenia and 731 immune cell traits by utilizing public GWAS data. We further validated the causal relationship between schizophrenia and six types of white cell measures.

RESULTS: We found the overall causal effects of schizophrenia on immune cell traits were significantly higher than the reverse ones (0.011 ± 0.049 vs 0.001 ± 0.016, p < 0.001), implying that disease may lead to an increase in immune cells by itself. We also identified four immune cell traits that may increase the risk of schizophrenia: CD11c+ monocyte %monocyte (odds ratio (OR): 1.06, 95% confidence interval (CI): 1.03~1.09, FDR = 0.027), CD11c+ CD62L- monocyte %monocyte (OR:1.06, 95% CI: 1.03~1.09, FDR = 0.027), CD25 on IgD+ CD38- naive B cell (OR:1.03, 95% CI:1.01~1.06, FDR = 0.042), and CD86 on monocyte (OR = 1.04, 95% CI:1.01~1.06, FDR = 0.042). However, we did not detect any significant causal effects of schizophrenia on immune cell traits. Using the white blood cell traits data, we identified that schizophrenia increases the lymphocyte counts (OR:1.03, 95%CI: 1.01-1.04, FDR = 0.007), total white blood cell counts (OR:1.02, 95%CI: 1.01-1.04, FDR = 0.021) and monocyte counts (OR:1.02, 95%CI: 1.00-1.03, FDR = 0.034). The lymphocyte counts were nominally associated with the risk of schizophrenia (OR:1.08,95%CI:1.01-1.16, P=0.019).

DISCUSSION: Our study found that the causal relationship between schizophrenia and the immune system is complex, enhancing our understanding of the role of immune regulation in the development of this disorder. These findings offer new insights for exploring diagnostic and therapeutic options for schizophrenia.

PMID:39399496 | PMC:PMC11466782 | DOI:10.3389/fimmu.2024.1452214

Front Pharmacol. 2024 Sep 27;15:1442752. doi: 10.3389/fphar.2024.1442752. eCollection 2024.

ABSTRACT

An in silico target discovery pipeline was developed by including a directional and weighted molecular disease network for metabolic dysfunction-associated steatohepatitis (MASH)-induced liver fibrosis. This approach integrates text mining, network biology, and artificial intelligence/machine learning with clinical transcriptome data for optimal translational power. At the mechanistic level, the critical components influencing disease progression were identified from the disease network using in silico knockouts. The top-ranked genes were then subjected to a target efficacy analysis, following which the top-5 candidate targets were validated in vitro. Three targets, including EP300, were confirmed for their roles in liver fibrosis. EP300 gene-silencing was found to significantly reduce collagen by 37%; compound intervention studies performed in human primary hepatic stellate cells and the hepatic stellate cell line LX-2 showed significant inhibition of collagen to the extent of 81% compared to the TGFβ-stimulated control (1 μM inobrodib in LX-2 cells). The validated in silico pipeline presents a unique approach for the identification of human-disease-mechanism-relevant drug targets. The directionality of the network ensures adherence to physiologically relevant signaling cascades, while the inclusion of clinical data boosts its translational power and ensures identification of the most relevant disease pathways. In silico knockouts thus provide crucial molecular insights for successful target identification.

PMID:39399467 | PMC:PMC11466758 | DOI:10.3389/fphar.2024.1442752

Front Genet. 2024 Sep 27;15:1432378. doi: 10.3389/fgene.2024.1432378. eCollection 2024.

ABSTRACT

INTRODUCTION: Multiple linked single nucleotide polymorphisms (SNPs) have shown potential in personal identification and mixture detection. However, the limited number of marker and sequencing errors have obstructed accurate DNA typing.

METHODS: To develop more candidate loci, the diversity value (D-value) was introduced as a new parameter for screening the novel polymorphic multiple linked-SNP markers, referred to as multi-SNP. In this study, a "FD Multi-SNP Mixture Kit" comprising 567 multi-SNPs was developed for mixture detection. Additionally, a new computational error correction method was applied as a quality control approach for sequencing data.

RESULTS: The results demonstrated higher typing success rates than the conventional CE typing method. For single-source DNA, approximately 70-80 loci were detected with a DNA input of 0.009765625 ng. More than 65% of the minor alleles were distinguishable at 1 ng DNA with a frequency of 0.5% in 2- to 4-person mixtures.

CONCLUSION: This study offers a polymorphic and high-resolution detection method for DNA genotyping and complex mixture detection, providing an alternative strategy for addressing challenging mixed DNA traces.

PMID:39399220 | PMC:PMC11466842 | DOI:10.3389/fgene.2024.1432378

medRxiv [Preprint]. 2024 Sep 27:2024.09.26.24314381. doi: 10.1101/2024.09.26.24314381.

ABSTRACT

Somatic mitochondrial DNA (mtDNA) mutations are prevalent in tumors, yet defining their biological significance remains challenging due to the intricate interplay between selective pressure, heteroplasmy, and cell state. Utilizing bulk whole-genome sequencing data from matched tumor and normal samples from two cohorts of pediatric cancer patients, we uncover differences in the accumulation of synonymous and nonsynonymous mtDNA mutations in pediatric leukemias, indicating distinct selective pressures. By integrating single-cell sequencing (SCS) with mathematical modeling and network-based systems biology approaches, we identify a correlation between the extent of cell-state changes associated with tumor-enriched mtDNA mutations and the selective pressures shaping their distribution among individual leukemic cells. Our findings also reveal an association between specific heteroplasmic mtDNA mutations and cellular responses that may contribute to functional heterogeneity among leukemic cells and influence their fitness. This study highlights the potential of SCS strategies for distinguishing between pathogenic and passenger somatic mtDNA mutations in cancer.

PMID:39398996 | PMC:PMC11469342 | DOI:10.1101/2024.09.26.24314381

iScience. 2024 Sep 17;27(10):110975. doi: 10.1016/j.isci.2024.110975. eCollection 2024 Oct 18.

ABSTRACT

Cisplatin is a chemotherapy drug that causes permanent hearing loss by injuring cochlear hair cells. Hair cell mitochondria have emerged as potential mediators of hair cell cytotoxicity. Using in vivo live imaging of hair cells in the zebrafish lateral-line organ expressing a genetically encoded indicator of cumulative mitochondrial activity, we first demonstrate that greater redox history increases susceptibility to cisplatin. Next, we conducted time-lapse imaging to understand dynamic changes in mitochondrial homeostasis and observe elevated mitochondrial and cytosolic calcium that surge prior to hair cell death. Furthermore, using a localized probe that fluoresces in the presence of cisplatin, we show that cisplatin directly accumulates in hair cell mitochondria, and this accumulation occurs before mitochondrial dysregulation and apoptosis. Our findings provide evidence that cisplatin directly targets hair cell mitochondria and support that the mitochondria are integral to cisplatin cytotoxicity in hair cells.

PMID:39398243 | PMC:PMC11466657 | DOI:10.1016/j.isci.2024.110975

ArXiv [Preprint]. 2024 Sep 25:arXiv:2407.04865v2.

ABSTRACT

The Gillespie algorithm is commonly used to simulate and analyze complex chemical reaction networks. Here, we leverage recent breakthroughs in deep learning to develop a fully differentiable variant of the Gillespie algorithm. The differentiable Gillespie algorithm (DGA) approximates discontinuous operations in the exact Gillespie algorithm using smooth functions, allowing for the calculation of gradients using backpropagation. The DGA can be used to quickly and accurately learn kinetic parameters using gradient descent and design biochemical networks with desired properties. As an illustration, we apply the DGA to study stochastic models of gene promoters. We show that the DGA can be used to: (i) successfully learn kinetic parameters from experimental measurements of mRNA expression levels from two distinct $\textit{E. coli}$ promoters and (ii) design nonequilibrium promoter architectures with desired input-output relationships. These examples illustrate the utility of the DGA for analyzing stochastic chemical kinetics, including a wide variety of problems of interest to synthetic and systems biology.

PMID:39398212 | PMC:PMC11469443

Genes Dis. 2024 Feb 2;12(1):101232. doi: 10.1016/j.gendis.2024.101232. eCollection 2025 Jan.

NO ABSTRACT

PMID:39397867 | PMC:PMC11471209 | DOI:10.1016/j.gendis.2024.101232

Plant Pathol J. 2024 Oct;40(5):537-550. doi: 10.5423/PPJ.OA.08.2024.0126. Epub 2024 Oct 1.

ABSTRACT

Pectobacterium is a major bacterial causal agent leading to soft rot disease in host plants. With the Arabidopsis-Pectobacterium pathosystem, we investigated the function of an Arabidopsis thaliana WRKY55 during defense responses to Pectobacterium carotovorum ssp. carotovorum (Pcc). Pcc-infection specifically induced WRKY55 gene expression. The overexpression of WRKY55 was resistant to the Pcc infection, while wrky55 knockout plants compromised the defense responses against Pcc. WRKY55 expression was mediated via Arabidopsis COI1-dependent signaling pathway showing that WRKY55 can contribute to the gene expression of jasmonic acid-mediated defense marker genes such as PDF1.2 and LOX2. WRKY55 physically interacts with Arabidopsis ORA59 facilitating the expression of PDF1.2&lt;/i. Our results suggest that WRKY55 can function as a positive regulator for resistance against Pcc in Arabidopsis.

PMID:39397307 | DOI:10.5423/PPJ.OA.08.2024.0126

Biotechnol Appl Biochem. 2024 Oct 13. doi: 10.1002/bab.2678. Online ahead of print.

ABSTRACT

Cancer is a global health problem despite the most developed therapeutic modalities. The delivery of specific therapeutic agents to a target increases the effectiveness of cancer treatment by reducing side effects and post-treatment issues. Our aim in this study was to design a recombinant protein consisting of nanobody molecules and exotoxin that targets the surface GRP78 receptor on tumor cells. Bioinformatics methods make drug design and recombinant protein evaluation much easier before the laboratory steps. Two constructs were designed from a single-variable domain on heavy chain nanobody domains and PE toxin domains II, Ib, and III. The physicochemical properties, secondary structure, and solubility of the chimeric protein were analyzed using different software. Prostate cancer DU-145 and breast cancer MDA-MB-468 cell lines were used as GRP78-positive and negative controls, respectively. Accordingly, the cytotoxicity, binding affinity, cell internalization, and apoptosis were evaluated using MTT, enzyme-linked immunosorbent assay, and western blot. The results showed that in the DU-145 cell line, the cytotoxicity of two recombinant immunotoxins is dose and time-dependent. In MDA-MB-468 and HEK-293 cells, such an event does not occur. It is possible that two constructs designed for immunotoxins can attach to GRP78-positive cancer cells and then eradicate cancer cells by internalization and apoptosis. As our in vitro results were in line with in silico data confirming the Bioinformatics predictions, it can be concluded that the designed recombinant immunotoxins may exhibit therapeutic potential against GRP78-positive tumor cells.

PMID:39397264 | DOI:10.1002/bab.2678

Commun Biol. 2024 Oct 14;7(1):1317. doi: 10.1038/s42003-024-07006-7.

ABSTRACT

Preclinical and clinical studies suggest that lipid-induced hepatic insulin resistance is a primary defect that predisposes to dysfunction in islets, implicating a perturbed liver-pancreas axis underlying the comorbidity of T2DM and MASLD. To investigate this hypothesis, we developed a human biomimetic microphysiological system (MPS) coupling our vascularized liver acinus MPS (vLAMPS) with pancreatic islet MPS (PANIS) enabling MASLD progression and islet dysfunction to be assessed. The modular design of this system (vLAMPS-PANIS) allows intra-organ and inter-organ dysregulation to be deconvoluted. When compared to normal fasting (NF) conditions, under early metabolic syndrome (EMS) conditions, the standalone vLAMPS exhibited characteristics of early stage MASLD, while no significant differences were observed in the standalone PANIS. In contrast, with EMS, the coupled vLAMPS-PANIS exhibited a perturbed islet-specific secretome and a significantly dysregulated glucose stimulated insulin secretion response implicating direct signaling from the dysregulated liver acinus to the islets. Correlations between several pairs of a vLAMPS-derived and a PANIS-derived factors were significantly altered under EMS, as compared to NF conditions, mechanistically connecting MASLD and T2DM associated hepatic-factors with islet-derived GLP-1 synthesis and regulation. Since vLAMPS-PANIS is compatible with patient-specific iPSCs, this platform represents an important step towards addressing patient heterogeneity, identifying disease mechanisms, and advancing precision medicine.

PMID:39397070 | PMC:PMC11471816 | DOI:10.1038/s42003-024-07006-7

Nat Commun. 2024 Oct 14;15(1):8848. doi: 10.1038/s41467-024-53108-5.

ABSTRACT

The nematode Caenorhabditis elegans is widely employed as a model organism to study basic biological mechanisms. However, transgenic C. elegans are generated by manual injection, which remains low-throughput and labor-intensive, limiting the scope of approaches benefitting from large-scale transgenesis. Here, we report a robotic microinjection system, integrating a microfluidic device capable of reliable worm immobilization, transfer, and rotation, for high-speed injection of C. elegans. The robotic system provides an injection speed 2-3 times faster than that of experts with 7-22 years of experience while maintaining comparable injection quality and only limited trials needed by users to become proficient. We further employ our system in a large-scale reverse genetic screen using multiplexed alternative splicing reporters, and find that the TDP-1 RNA-binding protein regulates alternative splicing of zoo-1 mRNA, which encodes variants of the zonula occludens tight junction proteins. With its high speed, high accuracy, and high efficiency in worm injection, this robotic system shows great potential for high-throughput transgenic studies of C. elegans.

PMID:39397017 | PMC:PMC11471809 | DOI:10.1038/s41467-024-53108-5