Microbiol Resour Announc. 2023 Dec 14;12(12):e0086823. doi: 10.1128/MRA.00868-23. Epub 2023 Nov 9.

ABSTRACT

Marinobacter nanhaiticus D15-8W is known for its ability to metabolize polycyclic aromatic hydrocarbons. Here, we report the complete circular genome sequence of this strain to be 5,336,660 bp (G + C content, 58.6%; 4,869 protein-coding sequences) with one plasmid (69,655 bp).

PMID:38095478 | DOI:10.1128/MRA.00868-23

J Am Coll Surg. 2023 Dec 14. doi: 10.1097/XCS.0000000000000922. Online ahead of print.

ABSTRACT

BACKGROUND: Major surgery triggers trauma-like stress responses linked to age, surgery duration, and blood loss, resembling polytrauma. This similarity suggests elective surgery as a surrogate model for studying polytrauma immune responses. We investigated stress responses across age groups and compared them to those of polytrauma patients.

STUDY DESIGN: Patients undergoing major spinal reconstruction surgery were divided into older (age > 65, n=5) and young (age=18-39, n=6) groups. A comparison group consisted of matched trauma patients (n=8). Blood samples were collected before, during, and after surgery. Bone marrow and peripheral blood mononuclear cells (BMMC and PBMC) were analyzed using CITEseq/scRNAseq. Plasma was subjected to dual-platform proteomic analysis (Somalogic and O-link).

RESULTS: Response to polytrauma was highest within 4 hrs. By comparison, the response to surgery was highest at 24 hrs. Both insults triggered significant changes in CD14+ monocytes, with increased inflammation and lower MHC-II expression. Older patient's CD14+ monocytes displayed higher inflammation and less MHC-II suppression; a trend also seen in BMMCs. While NK cells were markedly activated after polytrauma; NK cells were suppressed after surgery, especially in older patients. In plasma, innate immunity proteins dominated at 24 hours, shifting to adaptive immunity proteins by 6 weeks with heightened inflammation in older patients. SASP proteins were higher in older patients at baseline and further elevated during and after surgery.

CONCLUSION: While both major surgery and polytrauma initiate immune and stress responses, substantial differences exist in timing and cellular profiles, suggesting major elective surgery is not a suitable surrogate for the polytrauma response. Nonetheless, distinct responses in young vs. older patients highlight the utility of elective spinal in studying patient-specific factors affecting outcomes following major elective surgery.

PMID:38095316 | DOI:10.1097/XCS.0000000000000922

New Phytol. 2023 Dec 14. doi: 10.1111/nph.19472. Online ahead of print.

ABSTRACT

In angiosperms, basic leucine-zipper (bZIP) TGACG-motif-binding (TGA) transcription factors (TFs) regulate developmental and stress-related processes, the latter often involving NON EXPRESSOR OF PATHOGENESIS-RELATED GENES (NPR) coregulator interactions. To gain insight into their functions in an early diverging land-plant lineage, the single MpTGA and sole MpNPR genes were investigated in the liverwort Marchantia polymorpha. We generated Marchantia MpTGA and MpNPR knockout and overexpression mutants and conducted morphological, transcriptomic and expression studies. Furthermore, we investigated MpTGA interactions with wild-type and mutagenized MpNPR and expanded our analyses including TGA TFs from two streptophyte algae. Mptga mutants fail to induce the switch from vegetative to reproductive development and lack gametangiophore formation. MpTGA and MpNPR proteins interact and Mpnpr mutant analysis reveals a novel coregulatory NPR role in sexual reproduction. Additionally, MpTGA acts independently of MpNPR as a repressor of oil body (OB) formation and can thereby affect herbivory. The single MpTGA TF exerts a dual role in sexual reproduction and OB formation in Marchantia. Common activities of MpTGA/MpNPR in sexual development suggest that coregulatory interactions were established after emergence of land-plant-specific NPR genes and contributed to the diversification of TGA TF functions during land-plant evolution.

PMID:38095258 | DOI:10.1111/nph.19472

Anal Chem. 2023 Dec 14. doi: 10.1021/acs.analchem.3c03785. Online ahead of print.

ABSTRACT

Metabolomics and proteomics offer significant advantages in understanding biological mechanisms at two hierarchical levels. However, conventional single omics analysis faces challenges due to the high demand for specimens and the complexity of intrinsic associations. To obtain comprehensive and accurate system biological information, we developed a multiomics analytical method called Windows Scanning Multiomics (WSM). In this method, we performed simultaneous extraction of metabolites and proteins from the same sample, resulting in a 10% increase in the coverage of the identified biomolecules. Both metabolomics and proteomics analyses were conducted by using ultrahigh-performance liquid chromatography mass spectrometry (UPLC-MS), eliminating the need for instrument conversions. Additionally, we designed an R-based program (WSM.R) to integrate mathematical and biological correlations between metabolites and proteins into a correlation network. The network created from simultaneously extracted biomolecules was more focused and comprehensive compared to those from separate extractions. Notably, we excluded six pairs of false-positive relationships between metabolites and proteins in the network established using simultaneously extracted biomolecules. In conclusion, this study introduces a novel approach for multiomics analysis and data processing that greatly aids in bioinformation mining from multiomics results. This method is poised to play an indispensable role in systems biology research.

PMID:38095040 | DOI:10.1021/acs.analchem.3c03785

ACS ES T Water. 2023 Nov 8;3(12):3730-3735. doi: 10.1021/acsestwater.3c00012. eCollection 2023 Dec 8.

ABSTRACT

In the context of the European Union (EU) Drinking Water Directive, freshwater mussels (Order Unionoida: Bivalvia) can help us face the challenges of safe drinking water provisions for all citizens in the EU. Specifically, the implementation of high frequency noninvasive (HFNI) valvometers allows the early detection of eventual pollution events in drinking water treatment plants. Currently real-time behavioral analysis is deployed in a number of EU countries, and we foresee a bright future as new technological advances are developed concerning HFNI valvometers.

PMID:38094916 | PMC:PMC10714398 | DOI:10.1021/acsestwater.3c00012

Hortic Res. 2023 Nov 8;10(12):uhad224. doi: 10.1093/hr/uhad224. eCollection 2023 Dec.

ABSTRACT

In recent years, multiple advances have been made in understanding the photosynthetic machinery in model organisms. Knowledge transfer to horticultural important fruit crops is challenging and time-consuming due to restrictions in gene editing tools and prolonged life cycles. Here, we characterize a gene encoding a PetM domain-containing protein in tomato. The CRISPR/Cas9 knockout lines of the PetM showed impairment in the chloroplastic electron transport rate (ETR), reduced CO2 assimilation, and reduction of carotenoids and chlorophylls (Chl) under several light conditions. Further, growth-condition-dependent elevation or repression of Chl a/b ratios and de-epoxidation states were identified, underlining possible impairment compensation mechanisms. However, under low light and glasshouse conditions, there were basal levels in CO2 assimilation and ETR, indicating a potential role of the PetM domain in stabilizing the cytochrome b6f complex (Cb6f) under higher light irradiance and increasing its quantum efficiency. This suggests a potential evolutionary role in which this domain might stabilize the site of the Cb6f regulating ratios of cyclic and linear electron transport and its potential importance during the conquest of terrestrial ecosystems during which plants were exposed to higher irradiance. Finally, the results are discussed with regard to metabolism and their implication to photosynthesis from an agronomic perspective.

PMID:38094587 | PMC:PMC10716634 | DOI:10.1093/hr/uhad224

J Med Chem. 2023 Dec 14;66(23):16330-16341. doi: 10.1021/acs.jmedchem.3c01660. Epub 2023 Nov 21.

ABSTRACT

Biosynthetic engineering of bicyclic darobactins, selectively sealing the lateral gate of the outer membrane protein BamA, leads to active analogues, which are up to 128-fold more potent against Gram-negative pathogens compared to native counterparts. Because of their excellent antibacterial activity, darobactins represent one of the most promising new antibiotic classes of the past decades. Here, we present a series of structure-driven biosynthetic modifications of our current frontrunner, darobactin 22 (D22), to investigate modifications at the understudied positions 2, 4, and 5 for their impact on bioactivity. Novel darobactins were found to be highly active against critical pathogens from the WHO priority list. Antibacterial activity data were corroborated by dissociation constants with BamA. The most active derivatives D22 and D69 were subjected to ADMET profiling, showing promising features. We further evaluated D22 and D69 for bioactivity against multidrug-resistant clinical isolates and found them to have strong activity.

PMID:38093695 | DOI:10.1021/acs.jmedchem.3c01660

Adv Sci (Weinh). 2023 Dec 13:e2306576. doi: 10.1002/advs.202306576. Online ahead of print.

ABSTRACT

Sex disparities in serum bile acid (BA) levels and Alzheimer's disease (AD) prevalence have been established. However, the precise link between changes in serum BAs and AD development remains elusive. Here, authors quantitatively determined 33 serum BAs and 58 BA features in 4 219 samples collected from 1 180 participants from the Alzheimer's Disease Neuroimaging Initiative. The findings revealed that these BA features exhibited significant correlations with clinical stages, encompassing cognitively normal (CN), early and late mild cognitive impairment, and AD, as well as cognitive performance. Importantly, these associations are more pronounced in men than women. Among participants with progressive disease stages (n = 660), BAs underwent early changes in men, occurring before AD. By incorporating BA features into diagnostic and predictive models, positive enhancements are achieved for all models. The area under the receiver operating characteristic curve improved from 0.78 to 0.91 for men and from 0.76 to 0.83 for women for the differentiation of CN and AD. Additionally, the key findings are validated in a subset of participants (n = 578) with cerebrospinal fluid amyloid-beta and tau levels. These findings underscore the role of BAs in AD progression, offering potential improvements in the accuracy of AD prediction.

PMID:38093507 | DOI:10.1002/advs.202306576

Clin Epigenetics. 2023 Dec 13;15(1):191. doi: 10.1186/s13148-023-01612-8.

ABSTRACT

BACKGROUND: In 1990, David Barker proposed that prenatal nutrition is directly linked to adult cardiovascular disease. Since then, the relationship between adult cardiovascular risk, metabolic syndrome and birth weight has been widely documented. Here, we used the TruSeq Methyl Capture EPIC platform to compare the methylation patterns in cord blood from large for gestational age (LGA) vs adequate for gestational age (AGA) newborns from the LARGAN cohort.

RESULTS: We found 1672 differentially methylated CpGs (DMCs) with a nominal p < 0.05 and 48 differentially methylated regions (DMRs) with a corrected p < 0.05 between the LGA and AGA groups. A systems biology approach identified several biological processes significantly enriched with genes in association with DMCs with FDR < 0.05, including regulation of transcription, regulation of epinephrine secretion, norepinephrine biosynthesis, receptor transactivation, forebrain regionalization and several terms related to kidney and cardiovascular development. Gene ontology analysis of the genes in association with the 48 DMRs identified several significantly enriched biological processes related to kidney development, including mesonephric duct development and nephron tubule development. Furthermore, our dataset identified several DNA methylation markers enriched in gene networks involved in biological pathways and rare diseases of the cardiovascular system, kidneys, and metabolism.

CONCLUSIONS: Our study identified several DMCs/DMRs in association with fetal overgrowth. The use of cord blood as a material for the identification of DNA methylation biomarkers gives us the possibility to perform follow-up studies on the same patients as they grow. These studies will not only help us understand how the methylome responds to continuum postnatal growth but also link early alterations of the DNA methylome with later clinical markers of growth and metabolic fitness.

PMID:38093359 | DOI:10.1186/s13148-023-01612-8

Plant Cell. 2023 Dec 13:koad310. doi: 10.1093/plcell/koad310. Online ahead of print.

ABSTRACT

Selective partitioning of amino acids among organelles, cells, tissues, and organs is essential for cellular metabolism and plant growth. Nitrogen assimilation into glutamine and glutamate and de novo biosynthesis of most protein amino acids occurs in chloroplasts; therefore, various transport mechanisms must exist to accommodate their directional efflux from the stroma to the cytosol and feed the amino acids into the extraplastidial metabolic and long-distance transport pathways. Yet, Arabidopsis (Arabidopsis thaliana) transporters functioning in plastidial export of amino acids remained undiscovered. Here, USUALLY MULTIPLE ACIDS MOVE IN AND OUT TRANSPORTER 44 (UMAMIT44) was identified and shown to function in glutamate export from Arabidopsis chloroplasts. UMAMIT44 controls glutamate homeostasis within and outside of chloroplasts and influences nitrogen partitioning from leaves to sinks. Glutamate imbalances in chloroplasts and leaves of umamit44 mutants impact cellular redox state, nitrogen and carbon metabolism, and amino acid and sucrose supply of growing sinks, leading to negative effects on plant growth. Nonetheless, the mutant lines adjust to some extent by upregulating alternative pathways for glutamate synthesis outside the plastids and by mitigating oxidative stress through the production of other amino acids and antioxidants. Overall, this study establishes that the role of UMAMIT44 in glutamate export from chloroplasts is vital for controlling nitrogen availability within source leaf cells and for sink nutrition, with impact on growth and seed yield.

PMID:38092462 | DOI:10.1093/plcell/koad310

Reprod Toxicol. 2023 Dec 11:108523. doi: 10.1016/j.reprotox.2023.108523. Online ahead of print.

ABSTRACT

Understanding drug transport across the placental barrier is important for assessing the potential fetal drug toxicity and birth defect risks. Current in vivo and in vitro models have structural and functional limitations in evaluating placental drug transfer and toxicity. Microphysiological systems (MPSs) offer more accurate and relevant physiological models of human tissues and organs on a miniature scale for drug development and toxicology testing. MPSs for the placental barrier have been recently explored to study placental drug transfer. We utilized a multilayered hydrogel membrane-based microphysiological model composed of human placental epithelial and endothelial cells to replicate the key structure and function of the human placental barrier. A macroscale human placental barrier model was created using a transwell to compare the results with the microphysiological model. Placental barrier models were characterized by assessing monolayer formation, intercellular junctions, barrier permeability, and their structural integrity. Three small molecule drugs (glyburide, rifaximin, and caffeine) that are prescribed or taken during pregnancy were studied for their placental transfer. The results showed that all three drugs crossed the placental barrier, with transfer rates in the order: glyburide (molecular weight, MW = 494Da) < rifaximin (MW = 785.9Da) < caffeine (MW = 194.19Da). Using non-compartmental analysis, we estimated human pharmacokinetic characteristics based on in vitro data from both MPS and transwell models. While further research is needed, our findings suggest that MPS holds potential as an in vitro tool for studying placental drug transfer and predicting fetal exposure, offering insights into pharmacokinetics.

PMID:38092131 | DOI:10.1016/j.reprotox.2023.108523

Bioinformatics. 2023 Dec 13:btad750. doi: 10.1093/bioinformatics/btad750. Online ahead of print.

ABSTRACT

MOTIVATION: Cell type identification plays an important role in the analysis and interpretation of single-cell data and can be carried out via supervised or unsupervised clustering approaches. Supervised methods are best suited where we can list all cell types and their respective marker genes a priori. While unsupervised clustering algorithms look for groups of cells with similar expression properties. This property permits the identification of both known and unknown cell populations, making unsupervised methods suitable for discovery. Success is dependent on the relative strength of the expression signature of each group as well as the number of cells. Rare cell types therefore present a particular challenge that are magnified when they are defined by differentially expressing a small number of genes.

RESULTS: Typical unsupervised approaches fail to identify such rare sub-populations, and these cells tend to be absorbed into more prevalent cell types. In order to balance these competing demands, we have developed a novel statistical framework for unsupervised clustering, named Rarity, that enables the discovery process for rare cell types to be more robust, consistent and interpretable. We achieve this by devising a novel clustering method based on a Bayesian latent variable model in which we assign cells to inferred latent binary on/off expression profiles. This lets us achieve increased sensitivity to rare cell populations while also allowing us to control and interpret potential false positive discoveries. We systematically study the challenges associated with rare cell type identification and demonstrate the utility of Rarity on various IMC data sets.

AVAILABILITY: Implementation of Rarity together with examples are available from the Github repository (https://github.com/kasparmartens/rarity).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:38092048 | DOI:10.1093/bioinformatics/btad750

Dev Cell. 2023 Dec 5:S1534-5807(23)00612-3. doi: 10.1016/j.devcel.2023.11.014. Online ahead of print.

ABSTRACT

Morphogenetic movements during animal development involve repeated making and breaking of cell-cell contacts. Recent biophysical models of cell-cell adhesion integrate adhesion molecule interactions and cortical cytoskeletal tension modulation, describing equilibrium states for established contacts. We extend this emerging unified concept of adhesion to contact formation kinetics, showing that aggregating Xenopus embryonic cells rapidly achieve Ca2+-independent low-contact states. Subsequent transitions to cadherin-dependent high-contact states show rapid decreases in contact cortical F-actin levels but slow contact area growth. We developed a biophysical model that predicted contact growth quantitatively from known cellular and cytoskeletal parameters, revealing that elastic resistance to deformation and cytoskeletal network turnover are essential determinants of adhesion kinetics. Characteristic time scales of contact growth to low and high states differ by an order of magnitude, being at a few minutes and tens of minutes, respectively, thus providing insight into the timescales of cell-rearrangement-dependent tissue movements.

PMID:38091998 | DOI:10.1016/j.devcel.2023.11.014

Cell Host Microbe. 2023 Dec 8:S1931-3128(23)00461-4. doi: 10.1016/j.chom.2023.11.011. Online ahead of print.

ABSTRACT

Timely liver function recovery (LFR) is crucial for postoperative hepatocellular carcinoma (HCC) patients. Here, we established the significance of LFR on patient long-term survival through retrospective and prospective cohorts and identified a key gut microbe, Bifidobacterium longum, depleted in patients with delayed recovery. Fecal microbiota transfer from HCC patients with delayed recovery to mice similarly impacted recovery time post hepatectomy. However, oral gavage of B. longum improved liver function and repair in these mice. In a clinical trial of HCC patients, orally administering a probiotic bacteria cocktail containing B. longum reduced the rates of delayed recovery, shortened hospital stays, and improved overall 1-year survival. These benefits, attributed to diminished liver inflammation, reduced liver fibrosis, and hepatocyte proliferation, were associated with changes in key metabolic pathways, including 5-hydroxytryptamine, secondary bile acids, and short-chain fatty acids. Our findings propose that gut microbiota modulation can enhance LFR, thereby improving postoperative outcomes for HCC patients.

PMID:38091982 | DOI:10.1016/j.chom.2023.11.011

Biomech Model Mechanobiol. 2023 Dec 13. doi: 10.1007/s10237-023-01793-4. Online ahead of print.

ABSTRACT

Calcific aortic valve disease (CAVD) is a common cardiovascular disease that affects millions of people worldwide. The disease is characterized by the formation of calcium nodules on the aortic valve leaflets, which can lead to stenosis and heart failure if left untreated. The pathogenesis of CAVD is still not well understood, but involves several signaling pathways, including the transforming growth factor beta (TGF[Formula: see text]) pathway. In this study, we developed a multiscale computational model for TGF[Formula: see text]-stimulated CAVD. The model framework comprises cellular behavior dynamics, subcellular signaling pathways, and tissue-level diffusion fields of pertinent chemical species, where information is shared among different scales. Processes such as endothelial to mesenchymal transition (EndMT), fibrosis, and calcification are incorporated. The results indicate that the majority of myofibroblasts and osteoblast-like cells ultimately die due to lack of nutrients as they become trapped in areas with higher levels of fibrosis or calcification, and they subsequently act as sources for calcium nodules, which contribute to a polydispersed nodule size distribution. Additionally, fibrosis and calcification processes occur more frequently in regions closer to the endothelial layer where the cell activity is higher. Our results provide insights into the mechanisms of CAVD and TGF[Formula: see text] signaling and could aid in the development of novel therapeutic approaches for CAVD and other related diseases such as cancer. More broadly, this type of modeling framework can pave the way for unraveling the complexity of biological systems by incorporating several signaling pathways in subcellular models to simulate tissue remodeling in diseases involving cellular mechanobiology.

PMID:38093148 | DOI:10.1007/s10237-023-01793-4

Nat Rev Mol Cell Biol. 2023 Dec 13. doi: 10.1038/s41580-023-00688-7. Online ahead of print.

ABSTRACT

Tissue and organ development during embryogenesis relies on the collective and coordinated action of many cells. Recent studies have revealed that tissue material properties, including transitions between fluid and solid tissue states, are controlled in space and time to shape embryonic structures and regulate cell behaviours. Although the collective cellular flows that sculpt tissues are guided by tissue-level physical changes, these ultimately emerge from cellular-level and subcellular-level molecular mechanisms. Adherens junctions are key subcellular structures, built from clusters of classical cadherin receptors. They mediate physical interactions between cells and connect biochemical signalling to the physical characteristics of cell contacts, hence playing a fundamental role in tissue morphogenesis. In this Review, we take advantage of the results of recent, quantitative measurements of tissue mechanics to relate the molecular and cellular characteristics of adherens junctions, including adhesion strength, tension and dynamics, to the emergent physical state of embryonic tissues. We focus on systems in which cell-cell interactions are the primary contributor to morphogenesis, without significant contribution from cell-matrix interactions. We suggest that emergent tissue mechanics is an important direction for future research, bridging cell biology, developmental biology and mechanobiology to provide a holistic understanding of morphogenesis in health and disease.

PMID:38093099 | DOI:10.1038/s41580-023-00688-7

Nat Rev Genet. 2023 Dec 13. doi: 10.1038/s41576-023-00674-x. Online ahead of print.

ABSTRACT

Modern health care faces several serious challenges, including an ageing population and its inherent burden of chronic diseases, rising costs and marginal quality metrics. By assessing and optimizing the health trajectory of each individual using a data-driven personalized approach that reflects their genetics, behaviour and environment, we can start to address these challenges. This assessment includes longitudinal phenome measures, such as the blood proteome and metabolome, gut microbiome composition and function, and lifestyle and behaviour through wearables and questionnaires. Here, we review ongoing large-scale genomics and longitudinal phenomics efforts and the powerful insights they provide into wellness. We describe our vision for the transformation of the current health care from disease-oriented to data-driven, wellness-oriented and personalized population health.

PMID:38093095 | DOI:10.1038/s41576-023-00674-x

Nature. 2023 Dec 13. doi: 10.1038/s41586-023-06838-3. Online ahead of print.

ABSTRACT

Evidence is accumulating that perturbed postnatal development of the gut microbiome contributes to childhood malnutrition1-4. Here we analyse biospecimens from a randomized, controlled trial of a microbiome-directed complementary food (MDCF-2) that produced superior rates of weight gain compared with a calorically more dense conventional ready-to-use supplementary food in 12-18-month-old Bangladeshi children with moderate acute malnutrition4. We reconstructed 1,000 bacterial genomes (metagenome-assembled genomes (MAGs)) from the faecal microbiomes of trial participants, identified 75 MAGs of which the abundances were positively associated with ponderal growth (change in weight-for-length Z score (WLZ)), characterized changes in MAG gene expression as a function of treatment type and WLZ response, and quantified carbohydrate structures in MDCF-2 and faeces. The results reveal that two Prevotella copri MAGs that are positively associated with WLZ are the principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilizing the component glycans of MDCF-2. The predicted specificities of carbohydrate-active enzymes expressed by their polysaccharide-utilization loci are correlated with (1) the in vitro growth of Bangladeshi P. copri strains, possessing varying degrees of polysaccharide-utilization loci and genomic conservation with these MAGs, in defined medium containing different purified glycans representative of those in MDCF-2, and (2) the levels of faecal carbohydrate structures in the trial participants. These associations suggest that identifying bioactive glycan structures in MDCFs metabolized by growth-associated bacterial taxa will help to guide recommendations about their use in children with acute malnutrition and enable the development of additional formulations.

PMID:38093016 | DOI:10.1038/s41586-023-06838-3

Nature. 2023 Dec;624(7991):355-365. doi: 10.1038/s41586-023-06823-w. Epub 2023 Dec 13.

ABSTRACT

Single-cell analyses parse the brain's billions of neurons into thousands of 'cell-type' clusters residing in different brain structures1. Many cell types mediate their functions through targeted long-distance projections allowing interactions between specific cell types. Here we used epi-retro-seq2 to link single-cell epigenomes and cell types to long-distance projections for 33,034 neurons dissected from 32 different regions projecting to 24 different targets (225 source-to-target combinations) across the whole mouse brain. We highlight uses of these data for interrogating principles relating projection types to transcriptomics and epigenomics, and for addressing hypotheses about cell types and connections related to genetics. We provide an overall synthesis with 926 statistical comparisons of discriminability of neurons projecting to each target for every source. We integrate this dataset into the larger BRAIN Initiative Cell Census Network atlas, composed of millions of neurons, to link projection cell types to consensus clusters. Integration with spatial transcriptomics further assigns projection-enriched clusters to smaller source regions than the original dissections. We exemplify this by presenting in-depth analyses of projection neurons from the hypothalamus, thalamus, hindbrain, amygdala and midbrain to provide insights into properties of those cell types, including differentially expressed genes, their associated cis-regulatory elements and transcription-factor-binding motifs, and neurotransmitter use.

PMID:38092919 | DOI:10.1038/s41586-023-06823-w

Nature. 2023 Dec;624(7991):390-402. doi: 10.1038/s41586-023-06819-6. Epub 2023 Dec 13.

ABSTRACT

Divergence of cis-regulatory elements drives species-specific traits1, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains unclear. Here we investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset and mouse using single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome and chromosomal conformation profiles from a total of over 200,000 cells. From these data, we show evidence that divergence of transcription factor expression corresponds to species-specific epigenome landscapes. We find that conserved and divergent gene regulatory features are reflected in the evolution of the three-dimensional genome. Transposable elements contribute to nearly 80% of the human-specific candidate cis-regulatory elements in cortical cells. Through machine learning, we develop sequence-based predictors of candidate cis-regulatory elements in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Finally, we show that epigenetic conservation combined with sequence similarity helps to uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.

PMID:38092918 | DOI:10.1038/s41586-023-06819-6