Nat Commun. 2025 Jan 2;16(1):129. doi: 10.1038/s41467-024-55586-z.

ABSTRACT

The bacterium Bacillus subtilis undergoes asymmetric cell division during sporulation, producing a mother cell and a smaller forespore connected by the SpoIIQ-SpoIIIA (or Q-A) channel. The two cells differentiate metabolically, and the forespore becomes dependent on the mother cell for essential building blocks. Here, we investigate the metabolic interactions between mother cell and forespore using genome-scale metabolic and expression models as well as experiments. Our results indicate that nucleotides are synthesized in the mother cell and transported in the form of nucleoside di- or tri-phosphates to the forespore via the Q-A channel. However, if the Q-A channel is inactivated later in sporulation, then glycolytic enzymes can form an ATP and NADH shuttle, providing the forespore with energy and reducing power. Our integrated in silico and in vivo approach sheds light into the intricate metabolic interactions underlying cell differentiation in B. subtilis, and provides a foundation for future studies of metabolic differentiation.

PMID:39747067 | DOI:10.1038/s41467-024-55586-z

Nat Commun. 2025 Jan 2;16(1):317. doi: 10.1038/s41467-024-55447-9.

ABSTRACT

Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the raw accessibility data, without peak-calling or windows, to link regions to gene expression and determine differentially accessible chromatin. We show how ChromatinHD consistently outperforms existing peak and window-based approaches and find that this is due to a large number of uniquely captured, functional accessibility changes within and outside of putative cis-regulatory regions. Furthermore, ChromatinHD can delineate collaborating regulatory regions, including their preferential genomic conformations, that drive gene expression. Finally, our models also use changes in ATAC-seq fragment lengths to identify dense binding of transcription factors, a feature not captured by footprinting methods. Altogether, ChromatinHD, available at https://chromatinhd.org , is a suite of computational tools that enables a data-driven understanding of chromatin accessibility at various scales and how it relates to gene expression.

PMID:39747019 | DOI:10.1038/s41467-024-55447-9

Nat Commun. 2025 Jan 2;16(1):305. doi: 10.1038/s41467-024-54965-w.

ABSTRACT

Parasitic helminths are a major global health threat, infecting nearly one-fifth of the human population and causing significant losses in livestock and crops. Resistance to the few anthelmintic drugs is increasing. Here, we report a set of avocado fatty alcohols/acetates (AFAs) that exhibit nematocidal activity against four veterinary parasitic nematode species: Brugia pahangi, Teladorsagia circumcincta and Heligmosomoides polygyrus, as well as a multidrug resistant strain (UGA) of Haemonchus contortus. AFA shows significant efficacy in H. polygyrus infected mice. In C. elegans, AFA exposure affects all developmental stages, causing paralysis, impaired mitochondrial respiration, increased reactive oxygen species production and mitochondrial damage. In embryos, AFAs penetrate the eggshell and induce rapid developmental arrest. Genetic and biochemical tests reveal that AFAs inhibit POD-2, encoding an acetyl CoA carboxylase, the rate-limiting enzyme in lipid biosynthesis. These results uncover a new anthelmintic class affecting lipid metabolism.

PMID:39746976 | DOI:10.1038/s41467-024-54965-w

Nat Commun. 2025 Jan 2;16(1):138. doi: 10.1038/s41467-024-55227-5.

ABSTRACT

The role of the immune system in regulating tissue stem cells remains poorly understood, as does the relationship between immune-mediated tissue damage and regeneration. Graft vs. host disease (GVHD) occurring after allogeneic bone marrow transplantation (allo-BMT) involves immune-mediated damage to the intestinal epithelium and its stem cell compartment. To assess impacts of T-cell-driven injury on distinct epithelial constituents, we have performed single cell RNA sequencing on intestinal crypts following experimental BMT. Intestinal stem cells (ISCs) from GVHD mice have exhibited global transcriptomic changes associated with a substantial Interferon-γ response and upregulation of STAT1. To determine its role in crypt function, STAT1 has been deleted within murine intestinal epithelium. Following allo-BMT, STAT1 deficiency has resulted in reduced epithelial proliferation and impaired ISC recovery. Similarly, epithelial Interferon-γ receptor deletion has also attenuated proliferation and ISC recovery post-transplant. Investigating the mechanistic basis underlying this epithelial response, ISC STAT1 expression in GVHD has been found to correlate with upregulation of ISC c-Myc. Furthermore, activated T cells have stimulated Interferon-γ-dependent epithelial regeneration in co-cultured organoids, and Interferon-γ has directly induced STAT1-dependent c-Myc expression and ISC proliferation. These findings illustrate immunologic regulation of a core tissue stem cell program after damage and support a role for Interferon-γ as a direct contributor to epithelial regeneration.

PMID:39746933 | DOI:10.1038/s41467-024-55227-5

Ocul Surf. 2024 Dec 31:S1542-0124(24)00145-9. doi: 10.1016/j.jtos.2024.12.010. Online ahead of print.

ABSTRACT

Dry eye disease (DED) is a multifactorial condition with complex and incompletely understood molecular mechanisms. Advances in multi-omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and microbiomics, have provided new insights into the pathophysiology of DED. Genomic analyses have identified key genetic variants linked to immune regulation and lacrimal gland function. Transcriptomic studies reveal upregulated inflammatory pathways in ocular surface tissues, implicating these as core drivers of chronic inflammation. Proteomic research highlights significant alterations in tear protein composition, especially proteins involved in inflammation and tissue repair. Metabolomics studies focus on disrupted lipid metabolism and oxidative stress, which are crucial in maintaining tear film stability. Furthermore, microbiome research has demonstrated reduced microbial diversity and increased pathogenic bacteria, exacerbating inflammatory responses. The integration of multi-omics data allows for the identification of novel biomarkers and therapeutic targets, enabling precision diagnostics and personalized treatments. Therefore, this review highlights the critical importance of multi-omics approaches in deepening our understanding of DED's complex molecular mechanisms and their potential to transform clinical management and therapeutic innovations in this challenging field.

PMID:39746576 | DOI:10.1016/j.jtos.2024.12.010

J Allergy Clin Immunol. 2024 Dec 31:S0091-6749(24)02473-4. doi: 10.1016/j.jaci.2024.12.1083. Online ahead of print.

NO ABSTRACT

PMID:39746555 | DOI:10.1016/j.jaci.2024.12.1083

Science. 2025 Jan 3;387(6729):eadr0510. doi: 10.1126/science.adr0510. Epub 2025 Jan 3.

ABSTRACT

The most advanced monoclonal antibodies (mAbs) and vaccines against malaria target the central repeat region or closely related sequences within the Plasmodium falciparum circumsporozoite protein (PfCSP). Here, using an antigen-agnostic strategy to investigate human antibody responses to whole sporozoites, we identified a class of mAbs that target a cryptic PfCSP epitope that is only exposed after cleavage and subsequent pyroglutamylation (pGlu) of the newly formed N terminus. This pGlu-CSP epitope is not targeted by current anti-PfCSP mAbs and is not included in the licensed malaria vaccines. MAD21-101, the most potent mAb in this class, confers sterile protection against Pf infection in a human liver-chimeric mouse model. These findings reveal a site of vulnerability on the sporozoite surface that can be targeted by next-generation antimalarial interventions.

PMID:39745947 | DOI:10.1126/science.adr0510

Environ Sci Technol. 2025 Jan 2. doi: 10.1021/acs.est.4c11832. Online ahead of print.

NO ABSTRACT

PMID:39745662 | DOI:10.1021/acs.est.4c11832

Methods Mol Biol. 2025;2886:243-263. doi: 10.1007/978-1-0716-4310-5_12.

ABSTRACT

A key goal of biology is to understand the origin of the many cell types that can be observed during diverse processes such as development, regeneration, and disease. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ. However, organizing the resulting taxonomy of cell types into lineage trees to understand the origins of cell states and relationships between cells remains challenging. Here we present LINNAEUS (Spanjaard et al, Nat Biotechnol 36:469-473. https://doi.org/10.1038/nbt.4124 , 2018; Hu et al, Nat Genet 54:1227-1237. https://doi.org/10.1038/s41588-022-01129-5 , 2022) (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences)-a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, LINNAEUS can be used to reconstruct organism-wide single-cell lineage trees. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.

PMID:39745644 | DOI:10.1007/978-1-0716-4310-5_12

mSphere. 2024 Dec 31:e0053224. doi: 10.1128/msphere.00532-24. Online ahead of print.

ABSTRACT

Thousands of complete genome sequences for strains of a species that are now available enable the advancement of pangenome analytics to a new level of sophistication. We collected 2,377 publicly available complete genomes of Escherichia coli for detailed pangenome analysis. The core genome and accessory genomes consisted of 2,398 and 5,182 genes, respectively. We developed a machine learning approach to define the accessory genes characterizing the major phylogroups of E. coli plus Shigella: A, B1, B2, C, D, E, F, G, and Shigella. The analysis resulted in a detailed structure of the genetic basis of the phylogroups' differential traits. This pangenome structure was largely consistent with a housekeeping-gene-based MLST distribution, sequence-based Mash distance, and the Clermont quadruplex classification. The rare genome (consisting of genes found in <6.8% of all strains) consisted of 163,619 genes, about 79% of which represented variations of 315 underlying transposon elements. This analysis generated a mathematical definition of the genetic basis for a species.

IMPORTANCE: The comprehensive analysis of the pangenome of Escherichia coli presented in this study marks a significant advancement in understanding bacterial genetic diversity. By employing machine learning techniques to analyze 2,377 complete E. coli genomes, the study provides a detailed mapping of core, accessory, and rare genes. This approach reveals the genetic basis for differential traits across phylogroups, offering insights into pathogenicity, antibiotic resistance, and evolutionary adaptations. The findings enhance the potential for genome-based diagnostics and pave the way for future studies aimed at achieving a global genetic definition of bacterial phylogeny.

PMID:39745367 | DOI:10.1128/msphere.00532-24

J Chem Phys. 2025 Jan 7;162(1):014903. doi: 10.1063/5.0243454.

ABSTRACT

In the last years, it has been proved that some viruses are able to re-structure chromatin organization and alter the epigenomic landscape of the host genome. In addition, they are able to affect the physical mechanisms shaping chromatin 3D structure, with a consequent impact on gene activity. Here, we investigate with polymer physics genome re-organization of the host genome upon SARS-CoV-2 viral infection and how it can impact structural variability within the population of single-cell chromatin configurations. Using published Hi-C data and molecular dynamics simulations, we build ensembles of 3D configurations representing single-cell chromatin conformations in control and SARS-CoV-2 infected conditions. We focus on genomic length scales of TADs and consider, as a case study, models of real loci containing DDX58 and IL6 genes, belonging, respectively, to the antiviral interferon response and pro-inflammatory genes. Clustering analysis applied to the ensemble of polymer configurations reveals a generally increased variability and a more heterogeneous population of 3D structures in infected conditions. This points toward a scenario in which viral infection leads to a loss of chromatin structural specificity with, likely, a consequent impact on the correct regulation of host cell genes.

PMID:39745153 | DOI:10.1063/5.0243454

Aliment Pharmacol Ther. 2025 Jan 2. doi: 10.1111/apt.18468. Online ahead of print.

ABSTRACT

BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is the leading chronic liver disease worldwide, with alarming prevalence reaching epidemic proportions.

AIMS AND METHODS: The objective of this study is to provide a comprehensive review of the latest blood proteomics studies on MASLD and metabolic dysfunction-associated steatohepatitis (MASH), with emphasis on fibrosis. Furthermore, our objective is to conduct an analysis of protein pathways and interactions by integrating proteomics data using functional enrichment analysis of the deregulated proteins.

RESULTS: Notwithstanding the considerable discrepancies in the methodology and the number of proteins examined in the circulation, the analysis reveals a consistent pattern among the list of proteins that are decreased or increased in the blood of the affected patients. The relevant biological processes (BP) associated with down- and upregulated proteins are high-density lipoprotein remodelling and complement activation, respectively. The protein families identified include not only those expected to be involved in the immune system and cell adhesion and migration but also ligands of glycoproteins expressed in cells that have been subjected to stress and proteins containing the Sushi domain.

CONCLUSIONS: The application of cutting-edge methodologies to investigate the blood proteome in MASH is yielding insights that facilitate the elucidation of disease mechanisms and the identification of optimal noninvasive biomarkers. However, several challenges remain to be addressed in future research, including the generalisation of results on a global scale, the optimisation of analytical technologies and the implementation of large longitudinal studies to gain insights into the molecular mechanisms that underpin the development of advanced disease.

PMID:39744897 | DOI:10.1111/apt.18468

Mol Omics. 2025 Jan 2. doi: 10.1039/d4mo00156g. Online ahead of print.

ABSTRACT

Lung cancer remains the leading cause of cancer-related deaths worldwide due to its poor prognosis. Despite significant advancements in the understanding of cancer development, improvements in diagnostic methods, and multimodal therapeutic regimens, the prognosis of lung cancer has still not improved. Therefore, it is reasonable to look for newer and alternative medicines for treatment. Bhallataka nut extract, derived from the seeds of Semecarpus anacardium, is known for its anti-inflammatory and antioxidant properties, suggesting potential as a treatment for cancer. In this study, we investigated the molecular networks associated with the Bhallataka taila-mediated inhibition of lung adenocarcinoma. Treating lung cancer cell lines with Bhallataka taila resulted in decreased colony formation, proliferation, and migration, and increased apoptosis. Using a tandem mass tag (TMT)-based temporal quantitative proteomic analysis, we identified 173 overexpressed and 249 downregulated proteins among a total of 2879 proteins. Significantly altered proteins are associated with lung cancer progression, metastasis, invasion, migration, and epithelial-mesenchymal transition (EMT). The analysis of these altered proteins revealed molecular networks underlying the anticancer mechanisms of Bhallataka taila. Validation of these proteins and pathways affected by Bhallataka taila confirmed its utility in cancer treatment.

PMID:39744844 | DOI:10.1039/d4mo00156g

Histol Histopathol. 2024 Dec 13:18861. doi: 10.14670/HH-18-861. Online ahead of print.

ABSTRACT

Recent advancements in single-cell spatial proteomics have revolutionized our ability to elucidate cellular signaling networks and their implications in health and disease. This review examines these cutting-edge technologies, focusing on mass spectrometry (MS) imaging and multiplexed immunofluorescence (mIF). Such approaches allow high-resolution protein profiling at the single-cell level, revealing intricate cellular heterogeneity, spatial organization, and protein functions within their native cellular contexts. MS imaging techniques offer unprecedented high-dimensional resolution and provide detailed insights into their subcellular protein localization and abundance. mIF enables rapid and high-throughput protein profiling, enhancing its accessibility for diverse research and clinical applications. This review assesses the current challenges associated with these methodologies and also discusses the potential solutions to overcome these obstacles. The integration of spatial proteomics with other systems biology approaches holds great promise for enhancing our understanding of complex biological systems. It could also lead to significant advancements in molecular diagnostics and personalized treatment strategies.

PMID:39744823 | DOI:10.14670/HH-18-861

Theranostics. 2025 Jan 1;15(1):103-121. doi: 10.7150/thno.99588. eCollection 2025.

ABSTRACT

Rationale: Osteosarcoma (OS) is the most common bone malignancy. c-MET is recognized as a therapeutic target. However, traditional c-MET inhibitors show compromised efficacy due to the acquired resistance and side effects. PROTACs targeting c-MET have displayed improved antitumor efficacy by overcoming drug resistance, whereas safety concern caused by lack of tumor-targeting ability is still a pending issue. AS1411 is an aptamer that recognizes and penetrates tumors by targeting nucleolin (NCL) overexpressed on the surface of tumor cells. Since NCL interacts with an E3 ligase MDM2 intracellularly, we repurposed AS1411 as an MDM2 recruiter by employing NCL as a bridge. Methods: We select the ssDNA c-MET aptamer SL1 as the c-MET ligand to design dual aptamer-functionalized PROTACs, as SL1 can be easily conjugated to AS1411 through base-pair complementarity using a nucleic acid linker. Four AS1411-SL1 chimeras are generated by linking AS1411 to either the 5' or 3' terminus of SL1 via two different lengths of nucleic acid linkers. The therapeutic efficacy of these PROTACs is evaluated through both in vitro and in vivo experiments. Results: The PROTACs enable the ubiquitination and degradation of c-MET. The PROTACs effectively inhibit growth, enhance apoptosis, and overcome drug resistance of OS cells in vitro. The PROTACs demonstrate in vivo tumor-targeting ability and facilitate the OS treatment with no detectable toxicity. Conclusion: This study suggests that the AS1411-SL1 chimeras could be promising c-MET degraders for targeted therapy of OS.

PMID:39744222 | PMC:PMC11667235 | DOI:10.7150/thno.99588

NPJ Syst Biol Appl. 2025 Jan 2;11(1):2. doi: 10.1038/s41540-024-00483-w.

ABSTRACT

Interconnected feedback loops are prevalent across biological mechanisms, including cell fate transitions enabled by epigenetic mechanisms in carcinomas. However, the operating principles of these networks remain largely unexplored. Here, we identify numerous interconnected feedback loops implicated in cell lineage decisions, which we discover to be the hallmarks of lower- and higher-dimensional state space. We demonstrate that networks having higher centrality nodes have restricted state space while those with lower centrality nodes have higher dimensional state space. The topologically distinct networks with identical node or loop counts have different steady-state distributions, highlighting the crucial influence of network structure on emergent dynamics. Further, regardless of topology, networks with autoregulated nodes exhibit multiple steady states, thereby "liberating" network dynamics from absolute topological control. These findings unravel the design principles of multistable networks implicated in fate decisions and can have crucial implications in engineering or comprehending multi-fate decision circuits.

PMID:39743534 | DOI:10.1038/s41540-024-00483-w

J Biomed Sci. 2025 Jan 2;32(1):2. doi: 10.1186/s12929-024-01094-7.

ABSTRACT

BACKGROUND: In regions with a high prevalence of chronic hepatitis B virus (HBV) and hepatitis C virus (HCV) infections, coinfected patients face a heightened risk of developing hepatocellular carcinoma (HCC), termed HBV/HCV-related HCC (HBCV-HCC). We aimed to investigate the contribution of preexisting chronic hepatitis B (CHB) and subsequent chronic hepatitis C (CHC) to the development of HBCV-HCC.

METHODS: We examined HBV's involvement in 93 HBCV-HCC cases by analyzing HBV DNA integration as an indicator of HCC originating from HBV-infected hepatocytes, compared with 164 HBV-HCCs and 56 HCV-HCCs as controls.

RESULTS: Next generation sequencing revealed that 55% of HBCV-HCCs exhibited clonal HBV integration, which falls between the rates observed in HBV-HCCs (88%) and HCV-HCCs (7%), with similar integration patterns to HBV-HCCs. Common HCC somatic mutation analysis indicated HCV superinfection in HBCV-HCCs correlated with increased mutation rates in the telomerase reverse transcriptase (TERT) promoter and beta-catenin genes. Transcriptome analysis showed a prevalence of replicating HCV over HBV in HBCV-HCCs, with preexisting HBV exerting a proliferative role. The comparison of clinical characteristics revealed similarities between HBCV-HCC and HCV-HCC patients, including later onset for HBCV-HCC, possibly due to HCV superinfection slowing carcinogenesis. Notably, HBCV-HCCs with the same driver mutation, HBV integration at the TERT promoter, tended to develop later and showed a better prognosis post-tumor resection than HBV-HCCs.

CONCLUSIONS: Our findings shed light on the interplay between preexisting CHB and subsequent CHC in elevating the risk of HBCV-HCC. These insights are crucial for understanding viral etiology-specific carcinogenesis and guiding surveillance policies for HBCV-HCC post-antiviral therapy.

PMID:39743539 | DOI:10.1186/s12929-024-01094-7

J Infect. 2024 Dec 30:106396. doi: 10.1016/j.jinf.2024.106396. Online ahead of print.

ABSTRACT

BACKGROUND: Shifts in dietary patterns during lifestyle transitions are integral components of the dynamic interactions between humans and their environments. Investigating the link between dietary diversity, the composition of the human lipidome and infection is key to understanding the interplay between diet and susceptibility to pathogens.

METHODS: Here we address this question by performing a comparative study of two ethnic groups with divergent dietary patterns: Fulani, who are nomad pastoralists with a dairy-centric diet, and Mossi, who are farmers with a plant-based diet. We generate 196 paired global lipidomes (927 lipid molecules) from both groups before and during natural Plasmodium falciparum infection.

RESULTS: Our analysis revealed 211 significantly differentially abundant lipid molecules between the two ethnic groups in both infection states. We show that ethnicity has a greater impact on the lipidome of these children than do P. falciparum infection and report inter-ethnic differences that impact pathogenesis. We highlight elevated levels of pentadecanoic acid (C15:0)-containing phospholipids in Fulani and experimentally demonstrate the suppressive effects of lysophosphatidylcholine LysoPC (15:0) on P. falciparum gametocyte production.

CONCLUSION: These findings link the Fulani's dairy-centric diet and lower P. falciparum gametocyte densities reported in this group and underscore the intricate links between dietary lipids and the host response to infection.

PMID:39742977 | DOI:10.1016/j.jinf.2024.106396

J Genet Genomics. 2024 Dec 30:S1673-8527(24)00369-2. doi: 10.1016/j.jgg.2024.12.016. Online ahead of print.

ABSTRACT

Plant synthetic biology has emerged as a transformative field in agriculture, offering innovative solutions to enhance food security, provide resilience to climate change, and transition to sustainable farming practices. By integrating advanced genetic tools, computational modeling, and systems biology, researchers can precisely modify plant genomes to enhance traits such as yield, stress tolerance, and nutrient use efficiency. The ability to design plants with specific characteristics tailored to diverse environmental conditions and agricultural needs holds great potential to address global food security challenges. Here we highlight recent advancements and applications of plant synthetic biology in agriculture, focusing on key areas such as photosynthetic efficiency, nitrogen fixation, drought tolerance, pathogen resistance, nutrient use efficiency, biofortification, climate resilience, microbiology engineering, synthetic plant genomes, and the integration of artificial intelligence (AI) with synthetic biology. These innovations aim to maximize resource use efficiency, reduce reliance on external inputs, and mitigate environmental impacts associated with conventional agricultural practices. Despite challenges related to regulatory approval and public acceptance, the integration of synthetic biology in agriculture holds immense promise for creating more resilient and sustainable agricultural systems, contributing to global food security and environmental sustainability. Rigorous multi-field testing of these approaches will undoubtedly be required to ensure reproducibility.

PMID:39742963 | DOI:10.1016/j.jgg.2024.12.016

Metab Eng. 2024 Dec 30:S1096-7176(24)00182-4. doi: 10.1016/j.ymben.2024.12.011. Online ahead of print.

ABSTRACT

Precise and predictable genetic elements are required to address various issues, such as suboptimal metabolic flux or imbalanced protein assembly caused by the inadequate control of polycistronic gene expression in bacteria. Here, we devised a synthetic biopart based on the translational coupling to control polycistronic gene expression. This module links the translation of genes within a polycistronic mRNA, maintaining their expression ratios regardless of coding sequences, transcription rate, and upstream gene translation rate. By engineering the Shine-Dalgarno sequences within these synthetic bioparts, we adjusted the expression ratios of polycistronic genes. We created 41 bioparts with varied relative expression ratios, ranging from 0.03 to 0.92, enabling precise control of pathway enzyme gene expression in a polycistronic manner. This led to up to a 7.6-fold increase in the production of valuable biochemicals such as 3-hydroxypropionic acid, poly(3-hydroxybutyrate), and lycopene. Our work provides genetic regulatory modules for precise and predictable polycistronic gene expression, facilitating efficient protein assembly, biosynthetic gene cluster expression, and pathway optimization.

PMID:39742955 | DOI:10.1016/j.ymben.2024.12.011