J Res Med Sci. 2023 May 29;28:43. doi: 10.4103/jrms.jrms_702_22. eCollection 2023.

ABSTRACT

BACKGROUND: Diabetic kidney disease has substantial burden and limited therapeutic options. An inadequate understanding of the complex gene regulatory circuits underlying this disorder contributes to the insufficiency of current treatment strategies. MicroRNAs (miRNAs) play a crucial role as regulators of functionally related gene networks. Previously, mmu-mir-802-5p was identified as the sole dysregulated miRNA in both the kidney cortex and medulla of diabetic mice. This study aims to investigate the role of miR-802-5p in diabetic kidney disease.

MATERIALS AND METHODS: The validated and predicted targets of miR-802-5p were identified using miRTarBase and TargetScan databases, respectively. The functional role of this miRNA was inferred using gene ontology enrichment analysis. The expression of miR-802-5p and its selected targets were assessed by qPCR. The expression of the angiotensin receptor (Agtr1a) was measured by ELISA.

RESULTS: miR-802-5p exhibited dysregulation in both the kidney cortex and medulla of diabetic mice, with two- and four-fold over-expressions, respectively. Functional enrichment analysis of the validated and predicted targets of miR-802-5p revealed its involvement in the renin-angiotensin pathway, inflammation, and kidney development. Differential expression was observed in the Pten transcript and Agtr1a protein among the examined gene targets.

CONCLUSION: These findings suggest that miR-802-5p is a critical regulator of diabetic nephropathy in the cortex and medulla compartments, contributing to disease pathogenesis through the renin-angiotensin axis and inflammatory pathways.

PMID:37405075 | PMC:PMC10315408 | DOI:10.4103/jrms.jrms_702_22

Front Bioeng Biotechnol. 2023 Jun 19;11:1202836. doi: 10.3389/fbioe.2023.1202836. eCollection 2023.

ABSTRACT

The optimization of genetically engineered biological constructs is a key step to deliver high-impact biotechnological applications. The use of high-throughput DNA assembly methods allows the construction of enough genotypic variants to successfully cover the target design space. This, however, entails extra workload for researchers during the screening stage of candidate variants. Despite the existence of commercial colony pickers, their high price excludes small research laboratories and budget-adjusted institutions from accessing such extensive screening capability. In this work we present COPICK, a technical solution to automatize colony picking in an open-source liquid handler Opentrons OT-2. COPICK relies on a mounted camera to capture images of regular Petri dishes and detect microbial colonies for automated screening. COPICK's software can then automatically select the best colonies according to different criteria (size, color and fluorescence) and execute a protocol to pick them for further analysis. Benchmark tests performed for E. coli and P. putida colonies delivers a raw picking performance over pickable colonies of 82% with an accuracy of 73.4% at an estimated rate of 240 colonies/h. These results validate the utility of COPICK, and highlight the importance of ongoing technical improvements in open-source laboratory equipment to support smaller research teams.

PMID:37404684 | PMC:PMC10315574 | DOI:10.3389/fbioe.2023.1202836

Front Neurosci. 2023 Jun 19;17:1198243. doi: 10.3389/fnins.2023.1198243. eCollection 2023.

ABSTRACT

INTRODUCTION: The human brain comprises heterogeneous cell types whose composition can be altered with physiological and pathological conditions. New approaches to discern the diversity and distribution of brain cells associated with neurological conditions would significantly advance the study of brain-related pathophysiology and neuroscience. Unlike single-nuclei approaches, DNA methylation-based deconvolution does not require special sample handling or processing, is cost-effective, and easily scales to large study designs. Existing DNA methylation-based methods for brain cell deconvolution are limited in the number of cell types deconvolved.

METHODS: Using DNA methylation profiles of the top cell-type-specific differentially methylated CpGs, we employed a hierarchical modeling approach to deconvolve GABAergic neurons, glutamatergic neurons, astrocytes, microglial cells, oligodendrocytes, endothelial cells, and stromal cells.

RESULTS: We demonstrate the utility of our method by applying it to data on normal tissues from various brain regions and in aging and diseased tissues, including Alzheimer's disease, autism, Huntington's disease, epilepsy, and schizophrenia.

DISCUSSION: We expect that the ability to determine the cellular composition in the brain using only DNA from bulk samples will accelerate understanding brain cell type composition and cell-type-specific epigenetic states in normal and diseased brain tissues.

PMID:37404460 | PMC:PMC10315586 | DOI:10.3389/fnins.2023.1198243

iScience. 2023 Jun 20;26(7):107187. doi: 10.1016/j.isci.2023.107187. eCollection 2023 Jul 21.

ABSTRACT

Tissue-residential natural killer (trNK) cells act as pioneering responders during infectious challenges. However, their discrimination with conventional NK (cNK) cells is still an issue. Through an integrative transcriptome comparison of the two NK subgroups from different tissues, we have defined two genesets capable of efficiently distinguishing them. Based on the two genesets, a fundamental difference between the activation of trNK and cNK is identified and further confirmed. Mechanistically, we have discovered a particular role of chromatin landscape in regulating the trNK activation. In addition, IL-21R and IL-18R are respectively highly expressed by trNK and cNK, indicating a role of cytokine milieu in determining their differential activation. Indeed, IL-21 is particularly critical in accessorily promoting trNK activation using a bunch of bifunctional transcription factors. Together, this study sheds light on the bona fide difference between trNK and cNK, which will further expand our knowledge about their distinct functionalities during immune responses.

PMID:37404378 | PMC:PMC10316664 | DOI:10.1016/j.isci.2023.107187

iScience. 2023 Jun 12;26(7):107101. doi: 10.1016/j.isci.2023.107101. eCollection 2023 Jul 21.

ABSTRACT

Cancer is a leading cause of mortality and morbidity globally. Sex differences in cancer are evident in death rates and treatment responses in several cancers. Asian patients have unique cancer epidemiology influenced by their genetic ancestry and sociocultural factors in the region. In this review, we show molecular associations that potentially mediate sex disparities observed in cancer in Asian populations. Differences in sex characteristics are evident at the cytogenetic, genetic, and epigenetic levels mediating processes that include cell cycle, oncogenesis, and metastasis. Larger clinical and in vitro studies that explore mechanisms can confirm the associations of these molecular markers. In-depth studies of these markers can reveal their importance as diagnostics, prognostics, and therapeutic efficacy markers. Sex differences should be considered in designing novel cancer therapeutics in this era of precision medicine.

PMID:37404373 | PMC:PMC10316661 | DOI:10.1016/j.isci.2023.107101

Appl Environ Microbiol. 2023 Jul 5:e0017723. doi: 10.1128/aem.00177-23. Online ahead of print.

ABSTRACT

Bacteriophages (phages), which are viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. However, the study of phage-host interactions is hindered by a paucity of model systems from natural environments. Here, we investigate phage-host interactions in the "pink berry" consortia, which are naturally occurring, low-diversity, macroscopic bacterial aggregates that are found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPRs), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect known pink berry symbionts, namely, Desulfofustis sp. PB-SRB1, Thiohalocapsa sp. PB-PSB1, and Rhodobacteraceae sp. A2, and they are largely divergent from known viruses. In contrast to the conserved bacterial community structure of pink berries, the distribution of these phages across aggregates is highly variable. Two phages persisted over a period of seven years with high sequence conservation, allowing us to identify gene gain and loss. Increased nucleotide variation in a conserved phage capsid gene that is commonly targeted by host CRISPR systems suggests that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages as well as provide evidence for phage-host coevolution via multiple mechanisms in a natural microbial system. IMPORTANCE Phages, which are viruses that infect bacteria, are important components of all microbial systems, in which they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and coevolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms is CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate the bacteria and phage populations from a simple marine microbial community, known as "pink berries", found in salt marshes of Falmouth, Massachusetts, as a model of phage-host coevolution. We identify eight novel phages and characterize a case of putative CRISPR-driven phage evolution as well as an instance of HGT between a phage and its host, together suggesting that phages have large evolutionary impacts in a naturally occurring microbial community.

PMID:37404190 | DOI:10.1128/aem.00177-23

Rev Med Suisse. 2023 Jul 5;19(834):1322-1326. doi: 10.53738/REVMED.2023.19.834.1322.

ABSTRACT

Agent-Based Modelling (ABM) is a computer modelling technique that simulates the behaviour and interactions of autonomous agents within a virtual environment. Applied to health equity, this technique allows for a better understanding of the complex social and economic determinants that contribute to health inequities and enables the evaluation of the potential effects of public policies on the latter. Despite some limitations related to the accessibility and quality of health data and the complexity of the models, ABM appears to be a promising tool in the field of health equity, both for researchers in public or community health and for policy makers.

PMID:37403955 | DOI:10.53738/REVMED.2023.19.834.1322

Mol Omics. 2023 Jul 5. doi: 10.1039/d3mo00049d. Online ahead of print.

ABSTRACT

Molecular crosstalk, the dialogue between different cell types, is attracting more attention in cancer research. On the one hand, the communication between tumor and non-tumor cells in the microenvironment or between different tumor clones has influential consequences for the progression and spread of tumors and response to treatment. On the other hand, novel techniques such as single-cell sequencing or spatial transcriptomics provide detailed information that needs to be interpreted. TALKIEN: crossTALK IntEraction Network is a simple and intuitive online R/shiny application to visualize molecular crosstalk information through the construction and analysis of a protein-protein interaction network. Taking two or more lists of genes or proteins as input, which are representative of cell lineages, TALKIEN extracts information about ligand-receptor interactions, builds a network and analyzes it using systems biology techniques such as centrality measures and component analysis, among others. Moreover, it expands the network displaying pathways downstream receptors. The application allows users to select different graphical layouts, performs functional analysis and gives information about drugs targeting receptors. In conclusion, TALKIEN allows users to detect ligand-receptor interactions generating new in silico predictions of cell-cell communication thus providing a translational rationale for future experiments. It is freely available at https://www.odap-ico.org/talkien.

PMID:37403821 | DOI:10.1039/d3mo00049d

Nucleic Acids Res. 2023 Jul 5:gkad562. doi: 10.1093/nar/gkad562. Online ahead of print.

ABSTRACT

Cis-regulatory elements (CREs) can be classified by the shapes of their transcription start site (TSS) profiles, which are indicative of distinct regulatory mechanisms. Massively parallel reporter assays (MPRAs) are increasingly being used to study CRE regulatory mechanisms, yet the degree to which MPRAs replicate individual endogenous TSS profiles has not been determined. Here, we present a new low-input MPRA protocol (TSS-MPRA) that enables measuring TSS profiles of episomal reporters as well as after lentiviral reporter chromatinization. To sensitively compare MPRA and endogenous TSS profiles, we developed a novel dissimilarity scoring algorithm (WIP score) that outperforms the frequently used earth mover's distance on experimental data. Using TSS-MPRA and WIP scoring on 500 unique reporter inserts, we found that short (153 bp) MPRA promoter inserts replicate the endogenous TSS patterns of ∼60% of promoters. Lentiviral reporter chromatinization did not improve fidelity of TSS-MPRA initiation patterns, and increasing insert size frequently led to activation of extraneous TSS in the MPRA that are not active in vivo. We discuss the implications of our findings, which highlight important caveats when using MPRAs to study transcription mechanisms. Finally, we illustrate how TSS-MPRA and WIP scoring can provide novel insights into the impact of transcription factor motif mutations and genetic variants on TSS patterns and transcription levels.

PMID:37403796 | DOI:10.1093/nar/gkad562

J Sci Food Agric. 2023 Jul 5. doi: 10.1002/jsfa.12827. Online ahead of print.

ABSTRACT

BACKGROUND: Aroma is an important agronomic trait for strawberries, and the improvement of fruit flavor is a key goal in current strawberry breeding programs. Fragaria vesca (also known as woodland strawberry) has become an excellent model plant with exquisite flavor, a small genome size, and a short life cycle. Thus, the comprehensive identification of fruit volatiles and their accumulation pattern of F. vesca strawberries are very important and necessary to the fruit aroma study. This study examined the volatile profile changes from the fruits of three F. vesca genotypes during maturation using the headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME GC-MS) with multivariate analysis.

RESULTS: A total of 191 putative volatile compounds were identified, while 152, 159, and 175 volatiles were detected in 20-30 dap fruits of Hawaii 4 (HW), Reugen (RG), and Yellow Wonder (YW), respectively. Aldehydes and alcohols predominated in the early time point while esters were predominant during the late time point. Ketones were the dominant compounds from F. vesca strawberries fruits at the ripe stage. Certain genotype-characteristic volatiles were identified, including eugenol, γ-octalactone, and δ-decalactone were only detected in YW, and mesifurane was found in HW.

CONCLUSIONS: RG and YW showed very similar volatile compositions, but YW presented a greater number of volatiles and RG yielded a higher content. Differences in the volatile composition may be primarily due to genetic relationships. The metabolic changes that occurred during fruit ripening and characteristic volatiles will be a useful reference for future strawberry volatile studies. This article is protected by copyright. All rights reserved.

PMID:37403783 | DOI:10.1002/jsfa.12827

J Med Virol. 2023 Jul;95(7):e28900. doi: 10.1002/jmv.28900.

ABSTRACT

Antibodies triggering Fc-mediated NK cell activity may contribute to protection against disease caused by SARS-CoV-2 infection in humans. However, how these Fc-mediated humoral responses compare between individuals displaying hybrid immunity (Vac-ex) and those fully vaccinated with no history of SARS-CoV-2 infection (Vac-n) and whether they correlate with neutralizing antibody (NtAb) responses remains largely undetermined. In this retrospective study serum samples from 50 individuals (median age, 44.5 years; range, 11-85; 25 males), 25 Vac-ex and 25 Vac-n were studied. A flow-cytometry-based antibody-mediated NK-cell activation assay was used to quantitate effector NK-cells stimulated to express LAMP1 (lysosomal associated membrane protein 1), MIP1 (Macrophage inflammatory protein 1), and interferon-γ (IFNγ); NK cells isolated from two donors (D1 and D2) were used. NtAb levels targeting the Spike protein of Wuhan-Hu-1 and Omicron BA.1 SARS-CoV-2 variants were quantitated using a SARS-CoV-2 S pseudotyped neutralization assay. Regardless of the SARS-CoV-2 variant S antigen used in the NK-cell activation assay, the frequency of NK cells stimulated to express LAMP-1, MIP1β, and IFNγ was higher in Vac-ex compared with Vac-n (p values ranging from 0.07 to 0.006) for D1; this was only seen for BA.1 when NK cells from D2 were employed. The frequency of functional NK cells activated by antibody binding to either Wuhan-Hu-1 or Omicron BA.1 S protein was not significantly different for both VAC-ex and VAC-n. In contrast, NtAb titers against BA.1 were around 10-fold lower than that against Wuhan-Hu-1. Vac-ex displayed higher NtAb titers against both (sub)variants than Vac-n. NK-cell responses correlated poorly with NtAb titers (ρ ≤ 0.30). The data demonstrate higher cross-reactivity across variants of concern for antibodies triggering Fc-mediated NK cell than for NtAb. Moreover, Vac-Ex seemed to display more robust functional antibody responses as compared with Vac-n.

PMID:37403730 | DOI:10.1002/jmv.28900

Cancer Prev Res (Phila). 2023 Jul 5;16(7):365-367. doi: 10.1158/1940-6207.CAPR-23-0081.

ABSTRACT

Nearly all cancers have identifiable histologically defined precursors known as precancers. These precancers offer a window of opportunity to intercept the neoplastic process to prevent its development into invasive cancer. However, lack of knowledge regarding the evolution of precancers and the microenvironmental pressures shaping them precludes efforts to intercept them. Technological developments over the past decade have facilitated the study of precancers at a previously unattainable resolution. Calls for a national PreCancer Atlas effort incorporating these technologies were heeded in 2018, with the launch of the Human Tumor Atlas Network (HTAN) as part of the Beau Biden National Cancer Moonshot. Since then, five funded HTAN groups have focused their efforts on profiling precancers from breast, colon, skin, and lung. In this time, what progress has been made? What is next for HTAN and the field of premalignant biology? And are there lessons that individual investigators and the larger prevention field can learn from this initial effort to accelerate the development of novel early detection methods, risk prediction biomarkers, and interception agents? A special collection of invited reviews by experts in cancer evolution, systems biology, immunology, cancer genetics, preventive agent development, among other areas, attempts to answer these questions.

PMID:37403656 | DOI:10.1158/1940-6207.CAPR-23-0081

BJPsych Open. 2023 Jul 5;9(4):e120. doi: 10.1192/bjo.2023.507.

ABSTRACT

BACKGROUND: Poor air quality is associated with poor health. Little attention is given to the complex array of environmental exposures and air pollutants that affect mental health during the life course.

AIMS: We gather interdisciplinary expertise and knowledge across the air pollution and mental health fields. We seek to propose future research priorities and how to address them.

METHOD: Through a rapid narrative review, we summarise the key scientific findings, knowledge gaps and methodological challenges.

RESULTS: There is emerging evidence of associations between poor air quality, both indoors and outdoors, and poor mental health more generally, as well as specific mental disorders. Furthermore, pre-existing long-term conditions appear to deteriorate, requiring more healthcare. Evidence of critical periods for exposure among children and adolescents highlights the need for more longitudinal data as the basis of early preventive actions and policies. Particulate matter, including bioaerosols, are implicated, but form part of a complex exposome influenced by geography, deprivation, socioeconomic conditions and biological and individual vulnerabilities. Critical knowledge gaps need to be addressed to design interventions for mitigation and prevention, reflecting ever-changing sources of air pollution. The evidence base can inform and motivate multi-sector and interdisciplinary efforts of researchers, practitioners, policy makers, industry, community groups and campaigners to take informed action.

CONCLUSIONS: There are knowledge gaps and a need for more research, for example, around bioaerosols exposure, indoor and outdoor pollution, urban design and impact on mental health over the life course.

PMID:37403494 | DOI:10.1192/bjo.2023.507

Curr Neurovasc Res. 2023 Jul 3. doi: 10.2174/1567202620666230703122140. Online ahead of print.

ABSTRACT

BACKGROUND: Autoimmune diseases are associated with cardiovascular and cerebrovascular diseases. However, whether myasthenia gravis (MG) and ischemic stroke (IS) are causally related remains unclear.

OBJECTIVE: This study aimed to evaluate potential causal links between MG and IS using bidirectional Mendelian randomization (MR).

METHODS: We conducted a two-sample MR analysis to assess the potential associations between MG and IS. Genetic variants associated with MG and IS as well as their subtypes were extracted from genome-wide association studies by meta-analysis. The inverse-variance weighted method was used for the main MR analysis. Sensitivity analyses, including the MREgger, simple mode, simple median, weighted mode, and weighted median approaches were applied to test the robustness of the results.

RESULTS: The MR analyses indicated no causal effects of general MG on IS of all causes (odds ratio [OR] = 0.990, 95% confidence interval [CI]: 0.953-1.029, P = 0.615), large vessel atherosclerosis stroke (OR = 0.943, 95% CI: 0.856-1.039, P = 0.233), cardioembolic stroke (OR = 0.975, 95% CI: 0.867-1.096, P = 0.670), and small vessel occlusion stroke (OR = 1.059, 95% CI 0.974-1.150, P = 0.178). Subgroup analyses indicated no causal effects of early- or late-onset MG on IS and its subtypes (all P > 0.05). The reverse MR analysis showed no significant causal associations of IS on MG (all P > 0.05).

CONCLUSION: Bidirectional MR analysis did not provide evidence to support a causal relationship between genetically predicted MG and IS, although observational studies have found such a potential link.

PMID:37403387 | DOI:10.2174/1567202620666230703122140

Biophys J. 2023 Jul 4:S0006-3495(23)00411-3. doi: 10.1016/j.bpj.2023.06.023. Online ahead of print.

ABSTRACT

Bacterial cells that stop growing but maintain viability and the capability to regrow are termed dormant and have been shown to transiently tolerate high concentrations of antimicrobials. Links between tolerance and cellular energetics as a possible explanation for the tolerance, have been investigated and have produced mixed and seemingly contradictory results. Because dormancy merely indicates growth arrest, which can be induced by various stimuli, we hypothesise that dormant cells may exist in a range of energetic states that depend on the environment. To energetically characterise different dormancies, we first induce them in a way that results in dormant populations and subsequently measured both of their main energy sources, the PMF magnitude and the concentration of ATP. We find that different types of dormancy exhibit characteristic energetic profiles that vary in level and dynamics. The energetic makeup was associated with survival to some antibiotics, but not others. Our findings portray dormancy as a state that is rich in phenotypes with various stress survival capabilities. Because environmental conditions outside of the lab often halt or limit microbial growth, a typologisation of dormant states may yield relevant insights on the survival and evolutionary strategies of these organisms.

PMID:37403359 | DOI:10.1016/j.bpj.2023.06.023

Plant Commun. 2023 Jul 4:100645. doi: 10.1016/j.xplc.2023.100645. Online ahead of print.

ABSTRACT

Understanding plant immune responses is complex due to the high interdependence among biological processes in homeostatic networks. Hence, the integration of environmental cues causes network rewiring that interferes with defence responses. Similarly, plants retain molecular signatures configured under abiotic stress periods to rapidly respond to recurrent stress that can alter immunity. Metabolome changes imposed by abiotic stressors are persistent, although the impact on defence is elusive. In this study, we profiled metabolomes of Arabidopsis plants under several abiotic stress treatments applied individually or simultaneously to capture temporal trajectories in metabolite composition during adverse conditions and recovery. Further systemic analysis was conducted to address the relevance of metabolome changes and extract central features to be tested in planta. Our results demonstrate irreversibility in major fractions of metabolome changes as a general pattern in response to abiotic stress periods. Functional analysis of metabolomes and co-abundance networks points to convergences in the reconfiguration of the metabolism of organic acids and secondary metabolites. Arabidopsis mutant lines for components related to these metabolic pathways displayed altered defence capacities against different pathogens. Collectively, our data support that sustained metabolome changes configured during adverse environments can act as modulators of immune responses and provide evidence for a new layer of regulation in plant defence.

PMID:37403356 | DOI:10.1016/j.xplc.2023.100645

Traffic. 2023 Jul 4. doi: 10.1111/tra.12908. Online ahead of print.

ABSTRACT

Each cell in a multicellular organism permanently adjusts the concentration of its cell surface proteins. In particular, epithelial cells tightly control the number of carriers, transporters and cell adhesion proteins at their plasma membrane. However, sensitively measuring the cell surface concentration of a particular protein of interest in live cells and in real time represents a considerable challenge. Here, we introduce a novel approach based on split luciferases, which uses one luciferase fragment as a tag on the protein of interest and the second fragment as a supplement to the extracellular medium. Once the protein of interest arrives at the cell surface, the luciferase fragments complement and generate luminescence. We compared the performance of split Gaussia luciferase and split Nanoluciferase by using a system to synchronize biosynthetic trafficking with conditional aggregation domains. The best results were achieved with split Nanoluciferase, for which luminescence increased more than 6000-fold upon recombination. Furthermore, we showed that our approach can separately detect and quantify the arrival of membrane proteins at the apical and basolateral plasma membrane in single polarized epithelial cells by detecting the luminescence signals with a microscope, thus opening novel avenues for characterizing the variations in trafficking in individual epithelial cells.

PMID:37403269 | DOI:10.1111/tra.12908

Mol Cell. 2023 Jun 28:S1097-2765(23)00461-6. doi: 10.1016/j.molcel.2023.06.016. Online ahead of print.

ABSTRACT

Insertions and deletions (indels) are common sources of structural variation, and insertions originating from spontaneous DNA lesions are frequent in cancer. We developed a highly sensitive assay called insertion and deletion sequencing (Indel-seq) to monitor rearrangements in human cells at the TRIM37 acceptor locus that reports indels stemming from experimentally induced and spontaneous genome instability. Templated insertions, which derive from sequences genome wide, require contact between donor and acceptor loci, require homologous recombination, and are stimulated by DNA end-processing. Insertions are facilitated by transcription and involve a DNA/RNA hybrid intermediate. Indel-seq reveals that insertions are generated via multiple pathways. The broken acceptor site anneals with a resected DNA break or invades the displaced strand of a transcription bubble or R-loop, followed by DNA synthesis, displacement, and then ligation by non-homologous end joining. Our studies identify transcription-coupled insertions as a critical source of spontaneous genome instability that is distinct from cut-and-paste events.

PMID:37402370 | DOI:10.1016/j.molcel.2023.06.016

Mol Cell. 2023 Jun 27:S1097-2765(23)00434-3. doi: 10.1016/j.molcel.2023.06.012. Online ahead of print.

ABSTRACT

Transcription factors (TFs) orchestrate the gene expression programs that define each cell's identity. The canonical TF accomplishes this with two domains, one that binds specific DNA sequences and the other that binds protein coactivators or corepressors. We find that at least half of TFs also bind RNA, doing so through a previously unrecognized domain with sequence and functional features analogous to the arginine-rich motif of the HIV transcriptional activator Tat. RNA binding contributes to TF function by promoting the dynamic association between DNA, RNA, and TF on chromatin. TF-RNA interactions are a conserved feature important for vertebrate development and disrupted in disease. We propose that the ability to bind DNA, RNA, and protein is a general property of many TFs and is fundamental to their gene regulatory function.

PMID:37402367 | DOI:10.1016/j.molcel.2023.06.012

J Leukoc Biol. 2023 Jul 4:qiad076. doi: 10.1093/jleuko/qiad076. Online ahead of print.

ABSTRACT

The differentiation and activation of macrophages are critical regulatory programs that are central to host inflammation and defense against pathogens. However, the transcriptional regulatory pathways involved in these programs are not well understood. Herein, we demonstrate that the activity and expression of Activating Transcription Factor 2 (ATF2) is precisely regulated during primary human monocyte to macrophage differentiation, and that its activation is linked to M1 polarization and antibacterial responses. Genetic perturbation experiments demonstrated that deletion of ATF2 (THP-ΔATF2) resulted in irregular and abnormal macrophage morphology, whereas macrophages overexpressing ATF2 (THP-ATF2) developed round and pancake-like morphology, resembling classically activated (M1) macrophages. Mechanistically, we show that ATF2 binds to the core promoter of PPM1A, a phosphatase that regulates monocyte-to-macrophage differentiation, to regulate its expression. Functionally, overexpression of ATF2 sensitized macrophages to M1 polarization, resulting in increased production of MHC Class II, IL-1β and IP-10, improved phagocytic capacity, and enhanced control of the intracellular pathogen Mycobacterium tuberculosis. Gene expression profiling revealed that overexpression of ATF2 reprogramed macrophages to promote antibacterial pathways enriched in chemokine signaling, metabolism and antigen presentation. Consistent with pathways analysis, metabolic profiling revealed that genetic overexpression or stimuli-induced activation of ATF2 alters the metabolic capacity of macrophages and primes these cells for glycolytic metabolism during M1 polarization or bacterial infection. Our findings reveal that ATF2 plays a central role during macrophage differentiation and M1 polarization to enhance the functional capacities of macrophages.

PMID:37403209 | DOI:10.1093/jleuko/qiad076