Nat Commun. 2023 Nov 23;14(1):7674. doi: 10.1038/s41467-023-42862-7.

ABSTRACT

Sporadic Parkinson's Disease (sPD) is a progressive neurodegenerative disorder caused by multiple genetic and environmental factors. Mitochondrial dysfunction is one contributing factor, but its role at different stages of disease progression is not fully understood. Here, we showed that neural precursor cells and dopaminergic neurons derived from induced pluripotent stem cells (hiPSCs) from sPD patients exhibited a hypometabolism. Further analysis based on transcriptomics, proteomics, and metabolomics identified the citric acid cycle, specifically the α-ketoglutarate dehydrogenase complex (OGDHC), as bottleneck in sPD metabolism. A follow-up study of the patients approximately 10 years after initial biopsy demonstrated a correlation between OGDHC activity in our cellular model and the disease progression. In addition, the alterations in cellular metabolism observed in our cellular model were restored by interfering with the enhanced SHH signal transduction in sPD. Thus, inhibiting overactive SHH signaling may have potential as neuroprotective therapy during early stages of sPD.

PMID:37996418 | DOI:10.1038/s41467-023-42862-7

Int J Biol Macromol. 2023 Nov 21:128309. doi: 10.1016/j.ijbiomac.2023.128309. Online ahead of print.

ABSTRACT

PhoSL (Pholiota squarrosa Lectin) has an exceptional binding affinity for biomolecules with core-fucosylated N-glycans. This modification involves the addition of fucose to the inner N-acetylglucosamine within the N-glycan structure and is known to influence many physiological processes. Nevertheless, the molecular interactions underlying high-affinity binding of native PhoSL to core-fucosylated N-glycans remain largely unknown. In this study, we devised a strategy to produce PhoSL with the essential structural characteristics of the native protein (n-PhoSL). To do so, a fusion protein was expressed in E. coli and purified. Then, enzymatic cleavage and incubation with glutathione were utilized to recapitulate the native primary structure and disulfide bonding pattern. Subsequently, we identified the residues crucial for n-PhoSL binding to core-fucosylated chitobiose (N2F) via NMR spectroscopy. Additionally, crystal structures were solved for both apo n-PhoSL and its N2F complex. These analyses suggested a pivotal role of the N-terminal amine in maintaining the integrity of the binding pocket and actively contributing to core-fucose recognition. In support of this idea, the inclusion of additional residues at the N-terminus considerably reduced binding affinity and PhoSL cytotoxicity toward breast cancer cells. Taken together, these findings can facilitate the utilization of PhoSL in basic research, diagnostics and therapeutic strategies.

PMID:37995778 | DOI:10.1016/j.ijbiomac.2023.128309

Am J Hum Genet. 2023 Nov 14:S0002-9297(23)00365-8. doi: 10.1016/j.ajhg.2023.10.012. Online ahead of print.

ABSTRACT

In this perspective we discuss the current lack of genetic and environmental diversity in functional genomics datasets. There is a well-described Eurocentric bias in genetic and functional genomic research that has a clear impact on the benefit this research can bring to underrepresented populations. Current research focused on genetic variant-to-function experiments aims to identify molecular QTLs, but the lack of data from genetically diverse individuals has limited analyses to mostly populations of European ancestry. Although some efforts have been established to increase diversity in functional genomic studies, much remains to be done to consistently generate data for underrepresented populations from now on. We discuss the major barriers for this continuity and suggest actionable insights, aiming to empower research and researchers from underserved populations.

PMID:37995684 | DOI:10.1016/j.ajhg.2023.10.012

Cell Syst. 2023 Nov 20:S2405-4712(23)00302-2. doi: 10.1016/j.cels.2023.10.010. Online ahead of print.

ABSTRACT

Hypoxia-induced upregulation of HIF1α triggers adipose tissue dysfunction and insulin resistance in obese patients. HIF1α closely interacts with PPARγ, the master regulator of adipocyte differentiation and lipid accumulation, but there are conflicting results regarding how this interaction controls the excessive lipid accumulation that drives adipocyte dysfunction. To directly address these conflicts, we established a differentiation system that recapitulated prior seemingly opposing observations made across different experimental settings. Using single-cell imaging and coarse-grained mathematical modeling, we show how HIF1α can both promote and repress lipid accumulation during adipogenesis. Our model predicted and our experiments confirmed that the opposing roles of HIF1α are isolated from each other by the positive-feedback-mediated upregulation of PPARγ that drives adipocyte differentiation. Finally, we identify three factors: strength of the differentiation cue, timing of hypoxic perturbation, and strength of HIF1α expression changes that, when considered together, provide an explanation for many of the previous conflicting reports.

PMID:37995680 | DOI:10.1016/j.cels.2023.10.010

Cell. 2023 Nov 22;186(24):5269-5289.e22. doi: 10.1016/j.cell.2023.10.023.

ABSTRACT

A generic level of chromatin organization generated by the interplay between cohesin and CTCF suffices to limit promiscuous interactions between regulatory elements, but a lineage-specific chromatin assembly that supersedes these constraints is required to configure the genome to guide gene expression changes that drive faithful lineage progression. Loss-of-function approaches in B cell precursors show that IKAROS assembles interactions across megabase distances in preparation for lymphoid development. Interactions emanating from IKAROS-bound enhancers override CTCF-imposed boundaries to assemble lineage-specific regulatory units built on a backbone of smaller invariant topological domains. Gain of function in epithelial cells confirms IKAROS' ability to reconfigure chromatin architecture at multiple scales. Although the compaction of the Igκ locus required for genome editing represents a function of IKAROS unique to lymphocytes, the more general function to preconfigure the genome to support lineage-specific gene expression and suppress activation of extra-lineage genes provides a paradigm for lineage restriction.

PMID:37995656 | DOI:10.1016/j.cell.2023.10.023

Bioinformatics. 2023 Nov 23:btad711. doi: 10.1093/bioinformatics/btad711. Online ahead of print.

ABSTRACT

SUMMARY: Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. pyPESTO is a modular framework for systematic parameter estimation, with scalable algorithms for optimization and uncertainty quantification. While tailored to ordinary differential equation problems, pyPESTO is broadly applicable to black-box parameter estimation problems. Besides own implementations, it provides a unified interface to various popular simulation and inference methods.

AVAILABILITY: pyPESTO is implemented in Python, open-source under a 3-Clause BSD license. Code and documentation are available on GitHub (https://github.com/icb-dcm/pypesto).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:37995297 | DOI:10.1093/bioinformatics/btad711

J Phycol. 2023 Nov 23. doi: 10.1111/jpy.13390. Online ahead of print.

ABSTRACT

Diatoms are a crucial component in the study of aquatic ecosystems and ancient environmental records. However, traditional methods for identifying diatoms, such as morphological taxonomy and molecular detection, are costly, are time consuming, and have limitations. To address these issues, we developed an extensive collection of diatom images, consisting of 7983 images from 160 genera and 1042 species, which we expanded to 49,843 through preprocessing, segmentation, and data augmentation. Our study compared the performance of different algorithms, including backbones, batch sizes, dynamic data augmentation, and static data augmentation on experimental results. We determined that the ResNet152 network outperformed other networks, producing the most accurate results with top-1 and top-5 accuracies of 85.97% and 95.26%, respectively, in identifying 1042 diatom species. Additionally, we propose a method that combines model prediction and cosine similarity to enhance the model's performance in low-probability predictions, achieving an 86.07% accuracy rate in diatom identification. Our research contributes significantly to the recognition and classification of diatom images and has potential applications in water quality assessment, ecological monitoring, and detecting changes in aquatic biodiversity.

PMID:37994558 | DOI:10.1111/jpy.13390

Proteins. 2023 Dec;91(12):1935-1951. doi: 10.1002/prot.26644.

ABSTRACT

CASP assessments primarily rely on comparing predicted coordinates with experimental reference structures. However, experimental structures by their nature are only models themselves-their construction involves a certain degree of subjectivity in interpreting density maps and translating them to atomic coordinates. Here, we directly utilized density maps to evaluate the predictions by employing a method for ranking the quality of protein chain predictions based on their fit into the experimental density. The fit-based ranking was found to correlate well with the CASP assessment scores. Overall, the evaluation against the density map indicated that the models are of high accuracy, and occasionally even better than the reference structure in some regions of the model. Local assessment of predicted side chains in a 1.52 Å resolution map showed that side-chains are sometimes poorly positioned. Additionally, the top 118 predictions associated with 9 protein target reference structures were selected for automated refinement, in addition to the top 40 predictions for 11 RNA targets. For both proteins and RNA, the refinement of CASP15 predictions resulted in structures that are close to the reference target structure. This refinement was successful despite large conformational changes often being required, showing that predictions from CASP-assessed methods could serve as a good starting point for building atomic models in cryo-EM maps for both proteins and RNA. Loop modeling continued to pose a challenge for predictors, and together with the lack of consensus amongst models in these regions suggests that modeling, in combination with model-fit to the density, holds the potential for identifying more flexible regions within the structure.

PMID:37994556 | DOI:10.1002/prot.26644

BMC Chem. 2023 Nov 22;17(1):161. doi: 10.1186/s13065-023-01082-2.

ABSTRACT

Melanoma presents increasing prevalence and poor outcomes. Progression to aggressive stages is characterized by overexpression of the transcription factor E2F1 and activation of downstream prometastatic gene regulatory networks (GRNs). Appropriate therapeutic manipulation of the E2F1-governed GRNs holds the potential to prevent metastasis however, these networks entail complex feedback and feedforward regulatory motifs among various regulatory layers, which make it difficult to identify druggable components. To this end, computational approaches such as mathematical modeling and virtual screening are important tools to unveil the dynamics of these signaling networks and identify critical components that could be further explored as therapeutic targets. Herein, we integrated a well-established E2F1-mediated epithelial-mesenchymal transition (EMT) map with transcriptomics data from E2F1-expressing melanoma cells to reconstruct a core regulatory network underlying aggressive melanoma. Using logic-based in silico perturbation experiments of a core regulatory network, we identified that simultaneous perturbation of Protein kinase B (AKT1) and oncoprotein murine double minute 2 (MDM2) drastically reduces EMT in melanoma. Using the structures of the two protein signatures, virtual screening strategies were performed with the FDA-approved drug library. Furthermore, by combining drug repurposing and computer-aided drug design techniques, followed by molecular dynamics simulation analysis, we identified two potent drugs (Tadalafil and Finasteride) that can efficiently inhibit AKT1 and MDM2 proteins. We propose that these two drugs could be considered for the development of therapeutic strategies for the management of aggressive melanoma.

PMID:37993971 | DOI:10.1186/s13065-023-01082-2

Plant Methods. 2023 Nov 22;19(1):131. doi: 10.1186/s13007-023-01108-9.

ABSTRACT

BACKGROUND: In the past few years, there has been an explosion in single-cell transcriptomics datasets, yet in vivo confirmation of these datasets is hampered in plants due to lack of robust validation methods. Likewise, modeling of plant development is hampered by paucity of spatial gene expression data. RNA fluorescence in situ hybridization (FISH) enables investigation of gene expression in the context of tissue type. Despite development of FISH methods for plants, easy and reliable whole mount FISH protocols have not yet been reported.

RESULTS: We adapt a 3-day whole mount RNA-FISH method for plant species based on a combination of prior protocols that employs hybridization chain reaction (HCR), which amplifies the probe signal in an antibody-free manner. Our whole mount HCR RNA-FISH method shows expected spatial signals with low background for gene transcripts with known spatial expression patterns in Arabidopsis inflorescences and monocot roots. It allows simultaneous detection of three transcripts in 3D. We also show that HCR RNA-FISH can be combined with endogenous fluorescent protein detection and with our improved immunohistochemistry (IHC) protocol.

CONCLUSIONS: The whole mount HCR RNA-FISH and IHC methods allow easy investigation of 3D spatial gene expression patterns in entire plant tissues.

PMID:37993896 | DOI:10.1186/s13007-023-01108-9

Virol J. 2023 Nov 22;20(1):273. doi: 10.1186/s12985-023-02235-4.

ABSTRACT

BACKGROUND: Coronavirus disease 19 (COVID-19) is a major public health problem that cannot be ignored. As a widely used drug in the treatment of COVID-19, whether glucocorticoids may accelerate the clearance of COVID-19 is still not clear, and the glucocorticoids may improve the prognosis of patients is also controversial. Therefore, to explore the relationship between COVID-19 viral load and the use of glucocorticoids we designed this study.

METHODS: Patients with COVID-19 infection who were admitted to the emergency department of Peking Union Medical College Hospital from the end of 2022 to early 2023 were enrolled in this study. Characteristics of baseline, clinical and laboratory evaluation especially immunological indicator and daily viral load were carefully collected. Kolmogorov-Smirnov test, Student's t test, Mann-Whitney U test and proportional-hazards model (Cox model) were chosen as appropriate for comparison of variables.

RESULTS: By comparing the daily COVID-19 viral load and prognosis of patients with and without glucocorticoid therapy, we found that glucocorticoids did not statistically enhance the clearance or replication of COVID-19, nor did it change the 28-days and in-hospital mortality. However, glucocorticoid therapy may be a favorable factor for COVID-19 negative conversion in Cox model. The inflammatory factors in patients with glucocorticoid therapy were significantly decreased.

CONCLUSIONS: We believe that the real effect of glucocorticoids may be to improve the destruction of host immune system caused by inflammatory storm through host immune regulation and then achieve the improvement of clinical symptoms.

PMID:37993863 | DOI:10.1186/s12985-023-02235-4

Nature. 2023 Nov 22. doi: 10.1038/s41586-023-06749-3. Online ahead of print.

ABSTRACT

Diet-derived nutrients are inextricably linked to human physiology by providing energy and biosynthetic building blocks and by functioning as regulatory molecules. However, the mechanisms by which circulating nutrients in the human body influence specific physiological processes remain largely unknown. Here we use a blood nutrient compound library-based screening approach to demonstrate that dietary trans-vaccenic acid (TVA) directly promotes effector CD8+ T cell function and anti-tumour immunity in vivo. TVA is the predominant form of trans-fatty acids enriched in human milk, but the human body cannot produce TVA endogenously1. Circulating TVA in humans is mainly from ruminant-derived foods including beef, lamb and dairy products such as milk and butter2,3, but only around 19% or 12% of dietary TVA is converted to rumenic acid by humans or mice, respectively4,5. Mechanistically, TVA inactivates the cell-surface receptor GPR43, an immunomodulatory G protein-coupled receptor activated by its short-chain fatty acid ligands6-8. TVA thus antagonizes the short-chain fatty acid agonists of GPR43, leading to activation of the cAMP-PKA-CREB axis for enhanced CD8+ T cell function. These findings reveal that diet-derived TVA represents a mechanism for host-extrinsic reprogramming of CD8+ T cells as opposed to the intrahost gut microbiota-derived short-chain fatty acids. TVA thus has translational potential for the treatment of tumours.

PMID:37993715 | DOI:10.1038/s41586-023-06749-3

Sci Rep. 2023 Nov 22;13(1):20517. doi: 10.1038/s41598-023-46844-z.

ABSTRACT

Diabetes mellitus (DM) represents a major health problem in Egypt and worldwide, with increasing numbers of patients with prediabetes every year. Numerous factors, such as obesity, hyperlipidemia, and hypertension, which have recently become serious concerns, affect the complex pathophysiology of diabetes. These metabolic syndrome diseases are highly linked to genetic variability that drives certain populations, such as Egypt, to be more susceptible to developing DM. Here we conduct a comprehensive analysis to pinpoint the similarities and uniqueness among the Egyptian genome reference and the 1000-genome subpopulations (Europeans, Ad-Mixed Americans, South Asians, East Asians, and Africans), aiming at defining the potential genetic risk of metabolic syndromes. Selected approaches incorporated the analysis of the allele frequency of the different populations' variations, supported by genotypes' principal component analysis. Results show that the Egyptian's reference metabolic genes were clustered together with the Europeans', Ad-Mixed Americans', and South-Asians'. Additionally, 8563 variants were uniquely identified in the Egyptian cohort, from those, two were predicted to cause structural damage, namely, CDKAL1: 6_21065070 (A > T) and PPARG: 3_12351660 (C > T) utilizing the Missense3D database. The former is a protein coding gene associated with Type 2 DM while the latter is a key regulator of adipocyte differentiation and glucose homeostasis. Both variants were detected heterozygous in two different Egyptian individuals from overall 110 sample. This analysis sheds light on the unique genetic traits of the Egyptian population that play a role in the DM high prevalence in Egypt. The proposed analysis pipeline -available through GitHub- could be used to conduct similar analysis for other diseases across populations.

PMID:37993469 | DOI:10.1038/s41598-023-46844-z

Nat Commun. 2023 Nov 22;14(1):7608. doi: 10.1038/s41467-023-43435-4.

ABSTRACT

Many microorganisms are auxotrophic-unable to synthesize the compounds they require for growth. With this work, we quantify the prevalence of amino acid auxotrophies across a broad diversity of bacteria and habitats. We predicted the amino acid biosynthetic capabilities of 26,277 unique bacterial genomes spanning 12 phyla using a metabolic pathway model validated with empirical data. Amino acid auxotrophy is widespread across bacterial phyla, but we conservatively estimate that the majority of taxa (78.4%) are able to synthesize all amino acids. Our estimates indicate that amino acid auxotrophies are more prevalent among obligate intracellular parasites and in free-living taxa with genomic attributes characteristic of 'streamlined' life history strategies. We predicted the amino acid biosynthetic capabilities of bacterial communities found in 12 unique habitats to investigate environmental associations with auxotrophy, using data compiled from 3813 samples spanning major aquatic, terrestrial, and engineered environments. Auxotrophic taxa were more abundant in host-associated environments (including the human oral cavity and gut) and in fermented food products, with auxotrophic taxa being relatively rare in soil and aquatic systems. Overall, this work contributes to a more complete understanding of amino acid auxotrophy across the bacterial tree of life and the ecological contexts in which auxotrophy can be a successful strategy.

PMID:37993466 | DOI:10.1038/s41467-023-43435-4

Sci Data. 2023 Nov 22;10(1):820. doi: 10.1038/s41597-023-02703-0.

ABSTRACT

The Tibellus oblongus spider is an active hunter that does not spin webs and remains highly underinvestigated in terms of the venom composition. Here, we describe venom glands transcriptome and venom proteome analysis for unveiling the polypeptide composition of Tibellus oblongus spider venom. The resulting EST database includes 1733 records, including 1263 nucleotide sequences with ORFs, of these 942 have been identified as toxin-coding. The database of peptide sequences was built based on of the transcriptomics results. It contains 217 new toxins, 212 of them were detected in the T. oblongus venom by the proteomics.

PMID:37993463 | DOI:10.1038/s41597-023-02703-0

Sci Bull (Beijing). 2023 Nov 14:S2095-9273(23)00781-8. doi: 10.1016/j.scib.2023.11.027. Online ahead of print.

ABSTRACT

Nuclear factor kappa-B (NF-κB), a pivotal transcriptional regulator, plays a crucial role in modulating downstream genes implicated in tumor drug resistance. We establish a programmable system within bladder cancer cells to tailor drug responses by employing a synthetic clustered regularly interspaced short palindromic repeats (CRISPR)-based expression strategy that emulates natural transcriptional regulators. Our investigation uncovers the functional significance of Opa-interacting protein 5 (OIP5), upregulated upon NF-κB activation, as a key regulator governing drug-resistance to vincristine (VCR) treatment in bladder cancer. Through engineered guide RNAs (sgRNAs) targeting OIP5 to integrate NF-κB aptamers, we construct a modular scaffold RNA that encodes both the target locus and regulatory functionality. This engineered CRISPR scaffold RNA effectively responds to VCR stimulus by binding with activated NF-κB. Intriguingly, it redirects NF-κB to attenuate OIP5 expression-a reversal of its original role-while concurrently obstructing multiple NF-κB-mediated drug resistance pathways. This dual action thwarts drug resistance development. Further enhancing therapeutic potential, we develop a versatile nanoparticle system capable of co-delivering CRISPR scaffold RNAs and VCR. This synergistic approach demonstrates potent anti-tumor effects in both in vitro and in vivo settings. Our nanoparticle-mediated combination presents a compelling proof-of-concept, showcasing the utility of engineered CRISPR-based synthetic expression programs to reconfigure cellular drug responses and heighten tumor cell susceptibility to chemotherapy.

PMID:37993335 | DOI:10.1016/j.scib.2023.11.027

J Neurosci. 2023 Nov 22;43(47):7899-7901. doi: 10.1523/JNEUROSCI.1440-23.2023.

NO ABSTRACT

PMID:37993277 | DOI:10.1523/JNEUROSCI.1440-23.2023

Environ Res. 2023 Nov 20:117717. doi: 10.1016/j.envres.2023.117717. Online ahead of print.

ABSTRACT

Understanding the behavior and potential toxicity of copper nanoparticles (nano-Cu) in the aquatic environment is a primary way to assess their environmental risks. In this study, RNA-seq was performed on three different tissues (gills, intestines, and muscles) of zebrafish exposed to nano-Cu, to explore the potential toxic mechanism of nano-Cu on zebrafish. The results indicated that the toxic mechanism of nano-Cu on zebrafish was tissue-specific. Nano-Cu enables the CB1 receptor of the presynaptic membrane of gill cells to affect short-term synaptic plasticity or long-term synaptic changes (ECB-LTD) through DSI and DSE, causing dysfunction of intercellular signal transmission. Imbalance of de novo synthesis of UMP in intestinal cells and its transformation to UDP, UTP, uridine, and uracil, resulted in many functions involved in the pyrimidine metabolic pathway being blocked. Meanwhile, the toxicity of nano-Cu caused abnormal expression of RAD51 gene in muscle cells, which affects the repair of damaged DNA through Fanconi anemia and homologous recombination pathway, thus causing cell cycle disorder. These results provide insights for us to better understand the differences in toxicity of nano-Cu on zebrafish tissues and are helpful for a comprehensive assessment of nano-Cu's effects on aquatic organisms.

PMID:37993046 | DOI:10.1016/j.envres.2023.117717

Cell Rep Methods. 2023 Nov 14:100652. doi: 10.1016/j.crmeth.2023.100652. Online ahead of print.

ABSTRACT

Glycomics, the comprehensive profiling of all glycan structures in samples, is rapidly expanding to enable insights into physiology and disease mechanisms. However, glycan structure complexity and glycomics data interpretation present challenges, especially for differential expression analysis. Here, we present a framework for differential glycomics expression analysis. Our methodology encompasses specialized and domain-informed methods for data normalization and imputation, glycan motif extraction and quantification, differential expression analysis, motif enrichment analysis, time series analysis, and meta-analytic capabilities, synthesizing results across multiple studies. All methods are integrated into our open-source glycowork package, facilitating performant workflows and user-friendly access. We demonstrate these methods using dedicated simulations and glycomics datasets of N-, O-, lipid-linked, and free glycans. Differential expression tests here focus on human datasets and cancer vs. healthy tissue comparisons. Our rigorous approach allows for robust, reliable, and comprehensive differential expression analyses in glycomics, contributing to advancing glycomics research and its translation to clinical and diagnostic applications.

PMID:37992708 | DOI:10.1016/j.crmeth.2023.100652

Cell Rep Med. 2023 Nov 21;4(11):101281. doi: 10.1016/j.xcrm.2023.101281.

ABSTRACT

During cancer progression, tumorigenic and immune signals are spread through circulating molecules, such as cell-free DNA (cfDNA) and cell-free RNA (cfRNA) in the blood. So far, they have not been comprehensively investigated in gastrointestinal cancers. Here, we profile 4 categories of cell-free omics data from patients with colorectal cancer and patients with stomach adenocarcinoma and then assay 15 types of genomic, epigenomic, and transcriptomic variations. We find that multi-omics data are more appropriate for detection of cancer genes compared with single-omics data. In particular, cfRNAs are more sensitive and informative than cfDNAs in terms of detection rate, enriched functional pathways, etc. Moreover, we identify several peripheral immune signatures that are suppressed in patients with cancer. Specifically, we establish a γδ-T cell score and a cancer-associated-fibroblast (CAF) score, providing insights into clinical statuses like cancer stage and survival. Overall, we reveal a cell-free multi-molecular landscape that is useful for blood monitoring in personalized cancer treatment.

PMID:37992683 | DOI:10.1016/j.xcrm.2023.101281