J Med Virol. 2023 Jun;95(6):e28857. doi: 10.1002/jmv.28857.

ABSTRACT

Cervical squamous cell carcinoma (SCC) and adenocarcinoma (AD) are the main histological types of human papillomavirus-related cervical cancer. However, there are few reports on cell type-specific molecular differences between SCC and AD. Here, we used unbiased droplet-based single-cell RNA sequencing to elucidate the cellular differences between SCC and AD in tumor heterogeneity, and tumor microenvironment (TME). A total of 61 723 cells from three SCC and three AD patients, were collected and divided into nine cell types. Epithelial cells exhibited high intra- and interpatient heterogeneity and functional diversity. Signaling pathways, such as epithelial-to-mesenchymal-transition (EMT), hypoxia and inflammatory response were upregulated in SCC, while cell cycle-related signaling pathways were highly enriched in AD. SCC was associated with high infiltration of cytotoxicity CD8 T, effector memory CD8 T, proliferative natural killer (NK), and CD160+ NK cells as well as tumor-associated macrophages (TAMs) with high major histocompatibility complex-II genes. AD exhibited a high proportion of naive CD8 T, naive CD4 T, Treg CD4, central memory CD8, and TAMs with immunomodulatory functions. Additionally, we also observed that the majority of cancer-associated fibroblasts (CAFs) were from AD, and participated in inflammation regulation, while SCC-derived CAFs exhibited similar functions to tumor cells, such as EMT and hypoxia. This study revealed the widespread reprogramming of multiple cell populations in SCC and AD, dissected the cellular heterogeneity and characteristics in TME, and proposed potential therapeutic strategies for CC, such as targeted therapy and immunotherapy.

PMID:37287196 | DOI:10.1002/jmv.28857

Commun Biol. 2023 Jun 7;6(1):612. doi: 10.1038/s42003-023-04971-3.

ABSTRACT

Beside the oral cavity, bitter taste receptors are expressed in several non-gustatory tissues. Whether extra-oral bitter taste receptors function as sensors for endogenous agonists is unknown. To address this question, we devised functional experiments combined with molecular modeling approaches to investigate human and mouse receptors using a variety of bile acids as candidate agonists. We show that five human and six mouse receptors are responsive to an array of bile acids. Moreover, their activation threshold concentrations match published data of bile acid concentrations in human body fluids, suggesting a putative physiological activation of non-gustatory bitter receptors. We conclude that these receptors could serve as sensors for endogenous bile acid levels. These results also indicate that bitter receptor evolution may not be driven solely by foodstuff or xenobiotic stimuli, but also depend on endogenous ligands. The determined bitter receptor activation profiles of bile acids now enable detailed physiological model studies.

PMID:37286811 | DOI:10.1038/s42003-023-04971-3

Nat Rev Genet. 2023 Jun 7. doi: 10.1038/s41576-023-00609-6. Online ahead of print.

ABSTRACT

Transposable elements (TEs) are mobile DNA elements that comprise almost 50% of mammalian genomic sequence. TEs are capable of making additional copies of themselves that integrate into new positions in host genomes. This unique property has had an important impact on mammalian genome evolution and on the regulation of gene expression because TE-derived sequences can function as cis-regulatory elements such as enhancers, promoters and silencers. Now, advances in our ability to identify and characterize TEs have revealed that TE-derived sequences also regulate gene expression by both maintaining and shaping 3D genome architecture. Studies are revealing how TEs contribute raw sequence that can give rise to the structures that shape chromatin organization, and thus gene expression, allowing for species-specific genome innovation and evolutionary novelty.

PMID:37286742 | DOI:10.1038/s41576-023-00609-6

Sci Rep. 2023 Jun 7;13(1):9264. doi: 10.1038/s41598-023-36429-1.

ABSTRACT

The objective of this study was to clarify the impact of adverse reactions on immune dynamics. We investigated the pattern of systemic adverse reactions after the second and third coronavirus disease 2019 (COVID-19) vaccinations and their relationship with immunoglobulin G against severe acute respiratory syndrome coronavirus 2 spike 1 protein titers, neutralizing antibody levels, peak cellular responses, and the rate of decrease after the third vaccination in a large-scale community-based cohort in Japan. Participants who received a third vaccination with BNT162b2 (Pfizer/BioNTech) or mRNA-1273 (Moderna), had two blood samples, had not had COVID-19, and had information on adverse reactions after the second and third vaccinations (n = 2198) were enrolled. We collected data on sex, age, adverse reactions, comorbidities, and daily medicine using a questionnaire survey. Participants with many systemic adverse reactions after the second and third vaccinations had significantly higher humoral and cellular immunity in the peak phase. Participants with multiple systemic adverse reactions after the third vaccination had small changes in the geometric values of humoral immunity and had the largest geometric mean of cellar immunity in the decay phase. Systemic adverse reactions after the third vaccination helped achieve high peak values and maintain humoral and cellular immunity. This information may help promote uptake of a third vaccination, even among those who hesitate due to adverse reactions.

PMID:37286720 | DOI:10.1038/s41598-023-36429-1

NPJ Syst Biol Appl. 2023 Jun 7;9(1):24. doi: 10.1038/s41540-023-00282-9.

ABSTRACT

Adipocyte signaling, normally and in type 2 diabetes, is far from fully understood. We have earlier developed detailed dynamic mathematical models for several well-studied, partially overlapping, signaling pathways in adipocytes. Still, these models only cover a fraction of the total cellular response. For a broader coverage of the response, large-scale phosphoproteomic data and systems level knowledge on protein interactions are key. However, methods to combine detailed dynamic models with large-scale data, using information about the confidence of included interactions, are lacking. We have developed a method to first establish a core model by connecting existing models of adipocyte cellular signaling for: (1) lipolysis and fatty acid release, (2) glucose uptake, and (3) the release of adiponectin. Next, we use publicly available phosphoproteome data for the insulin response in adipocytes together with prior knowledge on protein interactions, to identify phosphosites downstream of the core model. In a parallel pairwise approach with low computation time, we test whether identified phosphosites can be added to the model. We iteratively collect accepted additions into layers and continue the search for phosphosites downstream of these added layers. For the first 30 layers with the highest confidence (311 added phosphosites), the model predicts independent data well (70-90% correct), and the predictive capability gradually decreases when we add layers of decreasing confidence. In total, 57 layers (3059 phosphosites) can be added to the model with predictive ability kept. Finally, our large-scale, layered model enables dynamic simulations of systems-wide alterations in adipocytes in type 2 diabetes.

PMID:37286693 | DOI:10.1038/s41540-023-00282-9

Nature. 2023 Jun;618(7964):E1-E7. doi: 10.1038/s41586-023-06066-9. Epub 2023 Jun 7.

NO ABSTRACT

PMID:37286658 | DOI:10.1038/s41586-023-06066-9

QJM. 2023 Jun 7:hcad122. doi: 10.1093/qjmed/hcad122. Online ahead of print.

ABSTRACT

OBJECTIVE: COVID-19 might cause neuroinflammation in the brain, which could decrease neurocognitive function. We aimed to evaluate the causal associations and genetic overlap between COVID-19 and intelligence.

METHODS: We performed Mendelian randomization (MR) analyses to assess potential associations between three COVID-19 outcomes and intelligence (N = 269,867). The COVID phenotypes included SARS-CoV-2 infection (N = 2,501,486), hospitalized COVID-19 (N = 1,965,329), and critical COVID-19 (N = 743,167). Genome-wide risk genes were compared between the genome-wide association study (GWAS) datasets on hospitalized COVID-19 and intelligence. In addition, functional pathways were constructed to explore molecular connections between COVID-19 and intelligence.

RESULTS: The MR analyses indicated that genetic liabilities to SARS-CoV-2 infection (OR: 0.965, 95% CI: 0.939-0.993) and critical COVID-19 (OR: 0.989, 95% CI: 0.979-0.999) confer causal effects on intelligence. There was suggestive evidence supporting the causal effect of hospitalized COVID-19 on intelligence (OR: 0.988, 95% CI: 0.972-1.003). Hospitalized COVID-19 and intelligence share ten risk genes within two genomic loci, including MAPT and WNT3. Enrichment analysis showed that these genes are functionally connected within distinct subnetworks of 30 phenotypes linked to cognitive decline. The functional pathway revealed that COVID-19-driven pathological changes within the brain and multiple peripheral systems may lead to cognitive impairment.

CONCLUSIONS: Our study suggests that COVID-19 may exert a detrimental effect on intelligence. The tau protein and Wnt signaling may mediate the influence of COVID-19 on intelligence.

PMID:37286376 | DOI:10.1093/qjmed/hcad122

Cells Dev. 2023 Jun 5:203861. doi: 10.1016/j.cdev.2023.203861. Online ahead of print.

ABSTRACT

Hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs) generate the immune system in development, and contribute to its maintenance under steady state conditions. How stem and progenitor cells respond to increased demand for mature cells upon injury is a fundamental question of stem cell biology. Several studies of murine hematopoiesis have reported increased proliferation of HSCs in situ when exposed to inflammatory stimuli, which has been taken as a proxy for increased HSC differentiation. Such surplus generation of HSC may fuel enhanced HSC differentiation or, alternatively, maintain HSC cellularity in the face of increased cell death without enhanced HSC differentiation. This key question calls for direct measurements of HSC differentiation in their natural niches in vivo. Here, we review work that quantifies native HSC differentiation by fate mapping and mathematical inference. Recent differentiation tracing studies show that HSC do not increase their differentiation rate upon a wide range of challenges, including systemic bacterial infection (sepsis), blood loss, and transient or persistent ablation of specific mature immune cells. By contrast, MPPs differentiate more rapidly in response to systemic infection to accelerate the production of myeloid cells. These new in vivo data identify MPPs as a major source of hematopoietic regeneration while HSCs might not contribute to regeneration while remaining protected.

PMID:37286105 | DOI:10.1016/j.cdev.2023.203861

Plant J. 2023 Jun 7. doi: 10.1111/tpj.16329. Online ahead of print.

ABSTRACT

Legumes represent an important component of human and livestock diets; they are rich in macro- and micronutrients such as proteins, dietary fibers and polyunsaturated fatty acids. Whilst, several health-promoting and anti-nutritious properties have been associated with grain content, in-depth metabolomics characterization of major legume species remains elusive. In this article, we used both gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) to assess the metabolic diversity in the five legume species commonly grown in Europe, including common bean, chickpea, lentil, white and pearl lupin at the tissue-specific level. We were able to detect and quantify over 3,430 metabolites covering major nutritional and anti-nutritional compounds. Specifically, the metabolomics atlas includes 224 derivatized metabolites, 2283 specialized metabolites, and 923 lipids. The data generated here will serve the community as a basis for future integration to metabolomics-assisted crop breeding and facilitate the metabolite-based genome-wide association study (mGWAS) to dissect the genetic and biochemical bases of metabolism in legume species.

PMID:37285370 | DOI:10.1111/tpj.16329

Bioinformatics. 2023 Jun 7:btad370. doi: 10.1093/bioinformatics/btad370. Online ahead of print.

ABSTRACT

MOTIVATION: While the search for associations between genetic markers and complex traits has led to the discovery of tens of thousands of trait-related genetic variants, the vast majority of these only explain a small fraction of the observed phenotypic variation. One possible strategy to overcome this while leveraging biological prior is to aggregate the effects of several genetic markers and to test entire genes, pathways or (sub)networks of genes for association to a phenotype. The latter, network-based genome-wide association studies, in particular suffers from a vast search space and an inherent multiple testing problem. As a consequence, current approaches are either based on greedy feature selection, thereby risking that they miss relevant associations, or neglect doing a multiple testing correction, which can lead to an abundance of false positive findings.

RESULTS: To address the shortcomings of current approaches of network-based genome-wide association studies, we propose networkGWAS, a computationally efficient and statistically sound approach to network-based genome-wide association studies using mixed models and neighborhood aggregation. It allows for population structure correction and for well-calibrated p-values, which are obtained through circular and degree-preserving network permutations. networkGWAS successfully detects known associations on diverse synthetic phenotypes, as well as known and novel genes in phenotypes from S. cerevisiae and H. sapiens. It thereby enables the systematic combination of gene-based genome-wide association studies with biological network information.

AVAILABILITY: https://github.com/BorgwardtLab/networkGWAS.git.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:37285313 | DOI:10.1093/bioinformatics/btad370

Cell Rep. 2023 Jun 6;42(6):112619. doi: 10.1016/j.celrep.2023.112619. Online ahead of print.

ABSTRACT

Vibrio natriegens regulates natural competence through the TfoX and QstR transcription factors, which are involved in external DNA capture and transport. However, the extensive genetic and transcriptional regulatory basis for competency remains unknown. We used a machine-learning approach to decompose Vibrio natriegens's transcriptome into 45 groups of independently modulated sets of genes (iModulons). Our findings show that competency is associated with the repression of two housekeeping iModulons (iron metabolism and translation) and the activation of six iModulons; including TfoX and QstR, a novel iModulon of unknown function, and three housekeeping iModulons (representing motility, polycations, and reactive oxygen species [ROS] responses). Phenotypic screening of 83 gene deletion strains demonstrates that loss of iModulon function reduces or eliminates competency. This database-iModulon-discovery cycle unveils the transcriptomic basis for competency and its relationship to housekeeping functions. These results provide the genetic basis for systems biology of competency in this organism.

PMID:37285268 | DOI:10.1016/j.celrep.2023.112619

iScience. 2023 May 19;26(6):106908. doi: 10.1016/j.isci.2023.106908. eCollection 2023 Jun 16.

ABSTRACT

Chromatin organization, whose malfunction causes various diseases including cancer, is fundamentally controlled by cohesin. While cancer cells have been found with mutated or misexpressed cohesin genes, there is no comprehensive survey about the presence and role of abnormal cohesin binding in cancer cells. Here, we systematically identified ∼1% of cohesin-binding sites (701-2,633) as cancer-aberrant binding sites of cohesin (CASs). We integrated CASs with large-scale transcriptomics, epigenomics, 3D genomics, and clinical information. CASs represent tissue-specific epigenomic signatures enriched for cancer-dysregulated genes with functional and clinical significance. CASs exhibited alterations in chromatin compartments, loops within topologically associated domains, and cis-regulatory elements, indicating that CASs induce dysregulated genes through misguided chromatin structure. Cohesin depletion data suggested that cohesin binding at CASs actively regulates cancer-dysregulated genes. Overall, our comprehensive investigation suggests that aberrant cohesin binding is an essential epigenomic signature responsible for dysregulated chromatin structure and transcription in cancer cells.

PMID:37283809 | PMC:PMC10239702 | DOI:10.1016/j.isci.2023.106908

Front Immunol. 2023 May 22;14:1211704. doi: 10.3389/fimmu.2023.1211704. eCollection 2023.

NO ABSTRACT

PMID:37283746 | PMC:PMC10240098 | DOI:10.3389/fimmu.2023.1211704

Front Immunol. 2023 May 22;14:1150890. doi: 10.3389/fimmu.2023.1150890. eCollection 2023.

ABSTRACT

The balance between pro- and anti-inflammatory immune system responses is crucial to preventing complex diseases like cancer. Macrophages are essential immune cells that contribute to this balance constrained by the local signaling profile of the tumor microenvironment. To understand how pro- and anti-inflammatory unbalance emerges in cancer, we developed a theoretical analysis of macrophage differentiation that is derived from activated monocytes circulating in the blood. Once recruited to the site of inflammation, monocytes can be polarized based on the specific interleukins and chemokines in the microenvironment. To quantify this process, we used a previous regulatory network reconstructed by our group and transformed Boolean Network attractors of macrophage polarization to an ODE scheme, it enables us to quantify the activation of their genes in a continuous fashion. The transformation was developed using the interaction rules with a fuzzy logic approach. By implementing this approach, we analyzed different aspects that cannot be visualized in the Boolean setting. For example, this approach allows us to explore the dynamic behavior at different concentrations of cytokines and transcription factors in the microenvironment. One important aspect to assess is the evaluation of the transitions between phenotypes, some of them characterized by an abrupt or a gradual transition depending on specific concentrations of exogenous cytokines in the tumor microenvironment. For instance, IL-10 can induce a hybrid state that transits between an M2c and an M2b macrophage. Interferon- γ can induce a hybrid between M1 and M1a macrophage. We further demonstrated the plasticity of macrophages based on a combination of cytokines and the existence of hybrid phenotypes or partial polarization. This mathematical model allows us to unravel the patterns of macrophage differentiation based on the competition of expression of transcriptional factors. Finally, we survey how macrophages may respond to a continuously changing immunological response in a tumor microenvironment.

PMID:37283734 | PMC:PMC10240616 | DOI:10.3389/fimmu.2023.1150890

Front Bioinform. 2023 May 22;3:1215141. doi: 10.3389/fbinf.2023.1215141. eCollection 2023.

NO ABSTRACT

PMID:37283696 | PMC:PMC10240056 | DOI:10.3389/fbinf.2023.1215141

JBMR Plus. 2023 Apr 24;7(6):e10746. doi: 10.1002/jbm4.10746. eCollection 2023 Jun.

ABSTRACT

The L-enantiomer of β-aminoisobutyric acid (BAIBA) is secreted by contracted muscle in mice, and exercise increases serum levels in humans. In mice, L-BAIBA reduces bone loss with unloading, but whether it can have a positive effect with loading is unknown. Since synergism can be more easily observed with sub-optimal amounts of factors/stimulation, we sought to determine whether L-BAIBA could potentiate the effects of sub-optimal loading to enhance bone formation. L-BAIBA was provided in drinking water to C57Bl/6 male mice subjected to either 7 N or 8.25 N of sub-optimal unilateral tibial loading for 2 weeks. The combination of 8.25 N and L-BAIBA significantly increased the periosteal mineral apposition rate and bone formation rate compared to loading alone or BAIBA alone. Though L-BAIBA alone had no effect on bone formation, grip strength was increased, suggesting a positive effect on muscle function. Gene expression analysis of the osteocyte-enriched bone showed that the combination of L-BAIBA and 8.25 N induced the expression of loading-responsive genes such as Wnt1, Wnt10b, and the TGFb and BMP signaling pathways. One dramatic change was the downregulation of histone genes in response to sub-optimal loading and/or L-BAIBA. To determine early gene expression, the osteocyte fraction was harvested within 24 hours of loading. A dramatic effect was observed with L-BAIBA and 8.25 N loading as genes were enriched for pathways regulating the extracellular matrix (Chad, Acan, Col9a2), ion channel activity (Scn4b, Scn7a, Cacna1i), and lipid metabolism (Plin1, Plin4, Cidec). Few changes in gene expression were observed with sub-optimal loading or L-BAIBA alone after 24 hours. These results suggest that these signaling pathways are responsible for the synergistic effects between L-BAIBA and sub-optimal loading. Showing that a small muscle factor can enhance the effects of sub-optimal loading of bone may be of relevance for individuals unable to benefit from optimal exercise. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.

PMID:37283651 | PMC:PMC10241089 | DOI:10.1002/jbm4.10746

Zhongguo Zhong Yao Za Zhi. 2023 May;48(9):2316-2324. doi: 10.19540/j.cnki.cjcmm.20230213.104.

ABSTRACT

Patchoulol is an important sesquiterpenoid in the volatile oil of Pogostemon cablin, and is also considered to be the main contributing component to the pharmacological efficacy and fragrance of P. cablin oil, which has antibacterial, antitumor, antioxidant, and other biological activities. Currently, patchoulol and its essential oil blends are in high demand worldwide, but the traditional plant extraction method has many problems such as wasting land and polluting the environment. Therefore, there is an urgent need for a new method to produce patchoulol efficiently and at low cost. To broaden the production method of patchouli and achieve the heterologous production of patchoulol in Saccharomyces cerevisiae, the patchoulol synthase(PS) gene from P. cablin was codon optimized and placed under the inducible strong promoter GAL1 to transfer into the yeast platform strain YTT-T5, thereby obtaining strain PS00 with the production of(4.0±0.3) mg·L~(-1) patchoulol. To improve the conversion rate, this study used protein fusion method to fuse SmFPS gene from Salvia miltiorrhiza with PS gene, leading to increase the yield of patchoulol to(100.9±7.4) mg·L~(-1) by 25-folds. By further optimizing the copy number of the fusion gene, the yield of patchoulol was increased by 90% to(191.1±32.7) mg·L~(-1). By optimizing the fermentation process, the strain was able to achieve a patchouli yield of 2.1 g·L~(-1) in a high-density fermentation system, which was the highest yield so far. This study provides an important basis for the green production of patchoulol.

PMID:37282860 | DOI:10.19540/j.cnki.cjcmm.20230213.104

J Cell Sci. 2023 Jun 7:jcs.260910. doi: 10.1242/jcs.260910. Online ahead of print.

ABSTRACT

Tylosis with Oesophageal Cancer (TOC), is a rare familial disorder caused by cytoplasmic mutations in inactive rhomboid 2 (iR2). iR2 and the related iR1 are key regulators of the membrane-anchored metalloprotease ADAM17, which is required for activating EGFR ligands and for releasing pro-inflammatory cytokines such as TNFa. A cytoplasmic deletion in iR2, including the TOC site, leads to curly whiskers and bare skin (cub) in mice, whereas a knock-in TOC mutation causes less severe alopecia and wavy fur. The abnormal skin and hair phenotypes of iR2cub/cub and iR2toc/toc mice depend on amphiregulin and ADAM17, since loss of one allele of either gene rescues the fur phenotypes. Remarkably, iR1-/-iR2cub/cub mice survive, despite a lack of mature ADAM17, whereas iR2cub/cubAdam17-/-mice die perinatally, suggesting that the iR2cub gain-of-function mutation requires the presence of ADAM17, but not its catalytic activity. iR2toc does not substantially reduce the levels of mature ADAM17, but instead affects its function in a substrate selective manner. Our findings provide new insights into the role of the cytoplasmic domain of iR2 in vivo, with implications for the treatment of TOC patients.

PMID:37282854 | DOI:10.1242/jcs.260910

Adv Healthc Mater. 2023 Jun 6:e2301062. doi: 10.1002/adhm.202301062. Online ahead of print.

ABSTRACT

Drug delivery systems (DDS) are designed to temporally and spatially control drug availability and activity. They assist in improving the balance between on-target therapeutic efficacy and off-target toxic side effects. DDS aid in overcoming biological barriers encountered by drug molecules upon applying them via various routes of administration. They are furthermore increasingly explored for modulating the interface between implanted (bio)medical materials and host tissue. Here, an overview of the biological barriers and host-material interfaces encountered by DDS upon oral, intravenous, and local administration is provided, and material engineering advances at different time and space scales to exemplify how current and future DDS can contribute to improved disease treatment are highlighted.

PMID:37282805 | DOI:10.1002/adhm.202301062

Parasite Immunol. 2023 Jun 6:e12998. doi: 10.1111/pim.12998. Online ahead of print.

ABSTRACT

Intestinal tuft cells have been shown to induce type 2 immune responses during viable parasite infections, but whether oral supplementation with a parasitic exudate is able to promote type 2 immune responses that have been shown to positively regulate obesogenic metabolic processes is yet unresolved. High-fat fed mice were gavaged with pseudocoelomic fluid (PCF) derived from the helminth Ascaris suum or saline thrice a week during weeks 5-9, followed by examination of intestinal tuft cell activity, immune, and metabolic parameters. Helminth PCF upregulated expression of distinct genes in small intestinal tuft cells, including genes involved in regulation of RUNX1 and organic cation transporters. Helminth PCF also enhanced levels of innate lymphoid cells in the ileum, and eosinophils in epididymal white adipose tissue (eWAT). Network analyses revealed two distinct immunometabolic cues affected by oral helminth PCF in high-fat fed mice: one coupling the small intestinal tuft cell responses to the fat-to-lean mass ratio and a second coupling eosinophils in eWAT to general regulation of body fat mass. Our findings point to specific mechanisms by which oral supplementation with helminth PCF may translate into systems-wide effects linking to reduced body and fat mass gain in mice during high-fat feeding.

PMID:37282739 | DOI:10.1111/pim.12998