Nat Food. 2020 Oct;1(10):599-604. doi: 10.1038/s43016-020-00155-y. Epub 2020 Oct 14.

ABSTRACT

The recent emergence of the fungus Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), the deadly strain that causes Fusarium wilt of banana, has put the banana production chain for export under threat. Here, we propose research priorities and complementary strategies and challenges for effective and efficient mitigation management of Fusarium wilt. Our strategies include diversifying the agrosystems to increase crop resilience, as well as using precision breeding approaches to rapidly assess and introduce disease-resistance genes to develop stable and complete Foc resistance in commercial banana cultivars.

PMID:37128105 | DOI:10.1038/s43016-020-00155-y

Annu Rev Immunol. 2023 Apr 26;41:317-342. doi: 10.1146/annurev-immunol-101220-031513.

ABSTRACT

Over the last decade, immunometabolism has emerged as a novel interdisciplinary field of research and yielded significant fundamental insights into the regulation of immune responses. Multiple classical approaches to interrogate immunometabolism, including bulk metabolic profiling and analysis of metabolic regulator expression, paved the way to appreciating the physiological complexity of immunometabolic regulation in vivo. Studying immunometabolism at the systems level raised the need to transition towards the next-generation technology for metabolic profiling and analysis. Spatially resolved metabolic imaging and computational algorithms for multi-modal data integration are new approaches to connecting metabolism and immunity. In this review, we discuss recent studies that highlight the complex physiological interplay between immune responses and metabolism and give an overview of technological developments that bear the promise of capturing this complexity most directly and comprehensively.

PMID:37126419 | DOI:10.1146/annurev-immunol-101220-031513

Curr Opin Struct Biol. 2023 Apr 29;80:102600. doi: 10.1016/j.sbi.2023.102600. Online ahead of print.

ABSTRACT

We provide an overview of the methods that can be used for protein structure-based evaluation of missense variants. The algorithms can be broadly divided into those that calculate the difference in free energy (ΔΔG) between the wild type and variant structures and those that use structural features to predict the damaging effect of a variant without providing a ΔΔG. A wide range of machine learning approaches have been employed to develop those algorithms. We also discuss challenges and opportunities for variant interpretation in view of the recent breakthrough in three-dimensional structural modelling using deep learning.

PMID:37126977 | DOI:10.1016/j.sbi.2023.102600

Nat Immunol. 2023 May 1. doi: 10.1038/s41590-023-01504-2. Online ahead of print.

ABSTRACT

While regulatory T (Treg) cells are traditionally viewed as professional suppressors of antigen presenting cells and effector T cells in both autoimmunity and cancer, recent findings of distinct Treg cell functions in tissue maintenance suggest that their regulatory purview extends to a wider range of cells and is broader than previously assumed. To elucidate tumoral Treg cell 'connectivity' to diverse tumor-supporting accessory cell types, we explored immediate early changes in their single-cell transcriptomes upon punctual Treg cell depletion in experimental lung cancer and injury-induced inflammation. Before any notable T cell activation and inflammation, fibroblasts, endothelial and myeloid cells exhibited pronounced changes in their gene expression in both cancer and injury settings. Factor analysis revealed shared Treg cell-dependent gene programs, foremost, prominent upregulation of VEGF and CCR2 signaling-related genes upon Treg cell deprivation in either setting, as well as in Treg cell-poor versus Treg cell-rich human lung adenocarcinomas. Accordingly, punctual Treg cell depletion combined with short-term VEGF blockade showed markedly improved control of PD-1 blockade-resistant lung adenocarcinoma progression in mice compared to the corresponding monotherapies, highlighting a promising factor-based querying approach to elucidating new rational combination treatments of solid organ cancers.

PMID:37127830 | DOI:10.1038/s41590-023-01504-2

Nat Biomed Eng. 2023 May 1. doi: 10.1038/s41551-023-01034-0. Online ahead of print.

ABSTRACT

Machine learning may aid the choice of optimal combinations of anticancer drugs by explaining the molecular basis of their synergy. By combining accurate models with interpretable insights, explainable machine learning promises to accelerate data-driven cancer pharmacology. However, owing to the highly correlated and high-dimensional nature of transcriptomic data, naively applying current explainable machine-learning strategies to large transcriptomic datasets leads to suboptimal outcomes. Here by using feature attribution methods, we show that the quality of the explanations can be increased by leveraging ensembles of explainable machine-learning models. We applied the approach to a dataset of 133 combinations of 46 anticancer drugs tested in ex vivo tumour samples from 285 patients with acute myeloid leukaemia and uncovered a haematopoietic-differentiation signature underlying drug combinations with therapeutic synergy. Ensembles of machine-learning models trained to predict drug combination synergies on the basis of gene-expression data may improve the feature attribution quality of complex machine-learning models.

PMID:37127711 | DOI:10.1038/s41551-023-01034-0

Nat Methods. 2023 May 1. doi: 10.1038/s41592-023-01868-1. Online ahead of print.

ABSTRACT

Efficient methods for the generation of specific mutations enable the study of functional variations in natural populations and lead to advances in genetic engineering applications. Here, we present a new approach, mutagenesis by template-guided amplicon assembly (MEGAA), for the rapid construction of kilobase-sized DNA variants. With this method, many mutations can be generated at a time to a DNA template at more than 90% efficiency per target in a predictable manner. We devised a robust and iterative protocol for an open-source laboratory automation robot that enables desktop production and long-read sequencing validation of variants. Using this system, we demonstrated the construction of 31 natural SARS-CoV2 spike gene variants and 10 recoded Escherichia coli genome fragments, with each 4 kb region containing up to 150 mutations. Furthermore, 125 defined combinatorial adeno-associated virus-2 cap gene variants were easily built using the system, which exhibited viral packaging enhancements of up to 10-fold compared with wild type. Thus, the MEGAA platform enables generation of multi-site sequence variants quickly, cheaply, and in a scalable manner for diverse applications in biotechnology.

PMID:37127666 | DOI:10.1038/s41592-023-01868-1

BMC Genomics. 2023 May 1;24(1):226. doi: 10.1186/s12864-023-09311-7.

ABSTRACT

Open reading frames (ORFs) with fewer than 100 codons are generally not annotated in genomes, although bona fide genes of that size are known. Newer biochemical studies have suggested that thousands of small protein-coding ORFs (smORFs) may exist in the human genome, but the true number and the biological significance of the micropeptides they encode remain uncertain. Here, we used a comparative genomics approach to identify high-confidence smORFs that are likely protein-coding. We identified 3,326 high-confidence smORFs using constraint within human populations and evolutionary conservation as additional lines of evidence. Next, we validated that, as a group, our high-confidence smORFs are conserved at the amino-acid level rather than merely residing in highly conserved non-coding regions. Finally, we found that high-confidence smORFs are enriched among disease-associated variants from GWAS. Overall, our results highlight that smORF-encoded peptides likely have important functional roles in human disease.

PMID:37127568 | DOI:10.1186/s12864-023-09311-7

Atherosclerosis. 2023 Apr 14:S0021-9150(23)00160-0. doi: 10.1016/j.atherosclerosis.2023.04.005. Online ahead of print.

ABSTRACT

BACKGROUND AND AIMS: This study aims to identify sex-specific transcriptional differences and signaling pathways in circulating monocytes contributing to cardiovascular disease.

METHODS AND RESULTS: We generated sex-biased gene expression signatures by comparing male versus female monocytes of coronary artery disease (CAD) patients (n = 450) from the Center for Translational Molecular Medicine-Circulating Cells Cohort. Gene set enrichment analysis demonstrated that monocytes from female CAD patients carry stronger chemotaxis and migratory signature than those from males. We then inferred cytokine signaling activities based on CytoSig database of 51 cytokine and growth factor regulation profiles. Monocytes from females feature a higher activation level of EGF, IFN1, VEGF, GM-CSF, and CD40L pathways, whereas IL-4, INS, and HMGB1 signaling was seen to be more activated in males. These sex differences were not observed in healthy subjects, as shown for an independent monocyte cohort of healthy subjects (GSE56034, n = 485). More pronounced GM-CSF signaling in monocytes of female CAD patients was confirmed by the significant enrichment of GM-CSF-activated monocyte signature in females. As we show these effects were not due to increased plasma levels of the corresponding ligands, sex-intrinsic differences in monocyte signaling regulation are suggested. Consistently, regulatory network analysis revealed jun-B as a shared transcription factor activated in all female-specific pathways except IFN1 but suppressed in male-activated IL-4.

CONCLUSIONS: We observed overt CAD-specific sex differences in monocyte transcriptional profiles and cytokine- or growth factor-induced responses, which provide insights into underlying mechanisms of sex differences in CVD.

PMID:37127497 | DOI:10.1016/j.atherosclerosis.2023.04.005

Proc Natl Acad Sci U S A. 2023 May 9;120(19):e2212118120. doi: 10.1073/pnas.2212118120. Epub 2023 May 1.

ABSTRACT

The prognosis and treatment outcomes of heart failure (HF) patients rely heavily on disease etiology, yet the majority of underlying signaling mechanisms are complex and not fully elucidated. Phosphorylation is a major point of protein regulation with rapid and profound effects on the function and activity of protein networks. Currently, there is a lack of comprehensive proteomic and phosphoproteomic studies examining cardiac tissue from HF patients with either dilated dilated cardiomyopathy (DCM) or ischemic cardiomyopathy (ICM). Here, we used a combined proteomic and phosphoproteomic approach to identify and quantify more than 5,000 total proteins with greater than 13,000 corresponding phosphorylation sites across explanted left ventricle (LV) tissue samples, including HF patients with DCM vs. nonfailing controls (NFC), and left ventricular infarct vs. noninfarct, and periinfarct vs. noninfarct regions of HF patients with ICM. Each pair-wise comparison revealed unique global proteomic and phosphoproteomic profiles with both shared and etiology-specific perturbations. With this approach, we identified a DCM-associated hyperphosphorylation cluster in the cardiomyocyte intercalated disc (ICD) protein, αT-catenin (CTNNA3). We demonstrate using both ex vivo isolated cardiomyocytes and in vivo using an AAV9-mediated overexpression mouse model, that CTNNA3 phosphorylation at these residues plays a key role in maintaining protein localization at the cardiomyocyte ICD to regulate conductance and cell-cell adhesion. Collectively, this integrative proteomic/phosphoproteomic approach identifies region- and etiology-associated signaling pathways in human HF and describes a role for CTNNA3 phosphorylation in the pathophysiology of DCM.

PMID:37126683 | DOI:10.1073/pnas.2212118120

PLoS Biol. 2023 May 1;21(5):e3002098. doi: 10.1371/journal.pbio.3002098. Online ahead of print.

ABSTRACT

Adult stem cells undergo asymmetric cell divisions to produce 2 daughter cells with distinct cell fates: one capable of self-renewal and the other committed for differentiation. Misregulation of this delicate balance can lead to cancer and tissue degeneration. During asymmetric division of Drosophila male germline stem cells (GSCs), preexisting (old) and newly synthesized histone H3 are differentially segregated, whereas old and new histone variant H3.3 are more equally inherited. However, what underlies these distinct inheritance patterns remains unknown. Here, we report that the N-terminal tails of H3 and H3.3 are critical for their inheritance patterns, as well as GSC maintenance and proper differentiation. H3 and H3.3 differ at the 31st position in their N-termini with Alanine for H3 and Serine for H3.3. By swapping these 2 amino acids, we generated 2 mutant histones (i.e., H3A31S and H3.3S31A). Upon expressing them in the early-stage germline, we identified opposing phenotypes: overpopulation of early-stage germ cells in the H3A31S-expressing testes and significant germ cell loss in testes expressing the H3.3S31A. Asymmetric H3 inheritance is disrupted in the H3A31S-expressing GSCs, due to misincorporation of old histones between sister chromatids during DNA replication. Furthermore, H3.3S31A mutation accelerates old histone turnover in the GSCs. Finally, using a modified Chromatin Immunocleavage assay on early-stage germ cells, we found that H3A31S has enhanced occupancy at promoters and transcription starting sites compared with H3, while H3.3S31A is more enriched at transcriptionally silent intergenic regions compared to H3.3. Overall, these results suggest that the 31st amino acids for both H3 and H3.3 are critical for their proper genomic occupancy and function. Together, our findings indicate a critical role for the different amino acid composition of the N-terminal tails between H3 and H3.3 in an endogenous stem cell lineage and provide insights into the importance of proper histone inheritance in specifying cell fates and regulating cellular differentiation.

PMID:37126497 | DOI:10.1371/journal.pbio.3002098

J Agric Food Chem. 2023 Apr 26. doi: 10.1021/acs.jafc.3c01002. Online ahead of print.

ABSTRACT

Fresh kernels of the walnut tree (Juglans regia L.) show a characteristic and pleasant aroma, the molecular basis of which was unknown. The application of an aroma extract dilution analysis resulted in 50 odor-active compounds. Among them, 37 had not been reported as fresh walnut kernel volatiles before, including the two odorants with the highest flavor dilution factors, namely, fenugreek-like smelling 3-hydroxy-4,5-dimethylfuran-2(5H)-one (sotolon) and oatmeal-like smelling (2E,4E,6Z)-nona-2,4,6-trienal. Quantitations revealed 17 odorants with concentrations in the walnuts that exceeded their odor threshold concentrations. Aroma reconstitution and omission experiments finally showed that the characteristic aroma of fresh walnuts is best represented by a binary mixture of sotolon and (2E,4E,6Z)-nona-2,4,6-trienal. Of both, the natural concentration was ∼10 μg/kg. Further sensory studies showed that the walnut character is intensified when their concentrations are in parallel increased to ∼100 μg/kg. This finding may guide the future breeding of new walnut cultivars with improved aroma.

PMID:37126476 | DOI:10.1021/acs.jafc.3c01002

Biotechnol Genet Eng Rev. 2023 Apr 26:1-10. doi: 10.1080/02648725.2023.2205197. Online ahead of print.

ABSTRACT

Tuberculous uveitis can be a manifestation of extrapulmonary tuberculosis or an allergic reaction to tuberculosis infection. The clinical signs and symptoms of other uveitis causes are generic, making a false diagnosis simple. We present a brief introduction to theoretical modelling and simulation in systems biology and explore the consequences of TB uveitis if left untreated. Patients were admitted to our hospital with recurrent fever. They had a previous definitive diagnosis of binocular uveitis and a positive interferon gamma release assay (IGRA) test result. At the time, there was no antituberculosis medicine available, and immunosuppressive and glucocorticoid therapy did not work. After the admission, their pleural fluid tested positive for Mycobacterium tuberculosis. No other causes to explain the fever were found. A diagnosis of tuberculosis was made, and their body temperature normalized after antituberculosis treatment and closed chest drainage. Vigilance should be exercised to rule out tuberculous uveitis in cases of unexplained uveitis; this calls for IGRA screening, tuberculin skin testing, and cyst imaging. For patients with latent tuberculosis infections, it is recommended to administer antituberculosis treatment, after excluding other possible causes, and to avoid using glucocorticoids in isolation.

PMID:37125900 | DOI:10.1080/02648725.2023.2205197

J Chem Phys. 2023 May 7;158(17):174502. doi: 10.1063/5.0142648.

ABSTRACT

The vibrational density of states of glasses is considerably different from that of crystals. In particular, there exist spatially localized vibrational modes in glasses. The density of states of these non-phononic modes has been observed to follow g(ω) ∝ ω4, where ω is the frequency. However, in two-dimensional systems, the abundance of phonons makes it difficult to accurately determine this non-phononic density of states because they are strongly coupled to non-phononic modes and yield strong system-size and preparation-protocol dependencies. In this article, we utilize the random pinning method to suppress phonons and disentangle their coupling with non-phononic modes and successfully calculate their density of states as g(ω) ∝ ω4. We also study their localization properties and confirm that low-frequency non-phononic modes in pinned systems are truly localized without far-field contributions. We finally discuss the excess density of states over the Debye value that results from the hybridization of phonons and non-phononic modes.

PMID:37125708 | DOI:10.1063/5.0142648

Nucleic Acids Res. 2023 May 1:gkad320. doi: 10.1093/nar/gkad320. Online ahead of print.

ABSTRACT

Gene expression changes are orchestrated by transcription factors (TFs), which bind to DNA to regulate gene expression. It remains surprisingly difficult to predict basic features of the transcriptional process, including in vivo TF occupancy. Existing thermodynamic models of TF function are often not concordant with experimental measurements, suggesting undiscovered biology. Here, we analyzed one of the most well-studied TFs, the yeast zinc cluster Gal4, constructed a Shea-Ackers thermodynamic model to describe its binding, and compared the results of this model to experimentally measured Gal4p binding in vivo. We found that at many promoters, the model predicted no Gal4p binding, yet substantial binding was observed. These outlier promoters lacked canonical binding motifs, and subsequent investigation revealed Gal4p binds unexpectedly to DNA sequences with high densities of its half site (CGG). We confirmed this novel mode of binding through multiple experimental and computational paradigms; we also found most other zinc cluster TFs we tested frequently utilize this binding mode, at 27% of their targets on average. Together, these results demonstrate a novel mode of binding where zinc clusters, the largest class of TFs in yeast, bind DNA sequences with high densities of half sites.

PMID:37125648 | DOI:10.1093/nar/gkad320

Nucleic Acids Res. 2023 May 1:gkad300. doi: 10.1093/nar/gkad300. Online ahead of print.

ABSTRACT

Cell identity genes are distinct from other genes with respect to the epigenetic mechanisms to activate their transcription, e.g. by super-enhancers and broad H3K4me3 domains. However, it remains unclear whether their post-transcriptional regulation is also unique. We performed a systematic analysis of transcriptome-wide RNA stability in nine cell types and found that unstable transcripts were enriched in cell identity-related pathways while stable transcripts were enriched in housekeeping pathways. Joint analyses of RNA stability and chromatin state revealed significant enrichment of super-enhancers and broad H3K4me3 domains at the gene loci of unstable transcripts. Intriguingly, the RNA m6A methyltransferase, METTL3, preferentially binds to chromatin at super-enhancers, broad H3K4me3 domains and their associated genes. METTL3 binding intensity is positively correlated with RNA m6A methylation and negatively correlated with RNA stability of cell identity genes, probably due to co-transcriptional m6A modifications promoting RNA decay. Nanopore direct RNA-sequencing showed that METTL3 knockdown has a stronger effect on RNA m6A and mRNA stability for cell identity genes. Our data suggest a run-and-brake model, where cell identity genes undergo both frequent transcription and fast RNA decay to achieve precise regulation of RNA expression.

PMID:37125636 | DOI:10.1093/nar/gkad300

J Am Chem Soc. 2023 Apr 26;145(16):9176-9181. doi: 10.1021/jacs.3c01214. Epub 2023 Apr 17.

ABSTRACT

Homologous recombination, an evolutionarily conserved DNA double-strand break repair pathway to protect genome stability, has long been exploited for the in vivo and in vitro assembly of multiple DNA duplex fragments in molecular cloning. Whether such methods can also be applied in the self-assembly of DNA nanostructures remains underexplored. Here, we report an enzymatic approach for the self-assembly of high-order DNA constructs with overlapping segments. In our system, a DNA polymerase with exonuclease activity was introduced to produce ssDNA overhangs for specific sticky end cohesion, and as many as 25 DNA structural units were designed to be hierarchically assembled. Using this approach, we successfully constructed a variety of high-order DNA nanostructures, including tubes and extended oligomers, from homogeneous assembly and custom multimers from heterogeneous assembly. Our strategy expands the construction toolbox of complex DNA nanostructures and highlights the potential to enhance the assembly of duplex fragments in molecular cloning.

PMID:37125454 | DOI:10.1021/jacs.3c01214

Front Endocrinol (Lausanne). 2023 Apr 12;14:1128767. doi: 10.3389/fendo.2023.1128767. eCollection 2023.

ABSTRACT

INTRODUCTION: The human gut microbiota (GM) is a dynamic system which ecological interactions among the community members affect the host metabolism. Understanding the principles that rule the bidirectional communication between GM and its host, is one of the most valuable enterprise for uncovering how bacterial ecology influences the clinical variables in the host.

METHODS: Here, we used SparCC to infer association networks in 16S rRNA gene amplicon data from the GM of a cohort of Mexican patients with type 2 diabetes (T2D) in different stages: NG (normoglycemic), IFG (impaired fasting glucose), IGT (impaired glucose tolerance), IFG + IGT (impaired fasting glucose plus impaired glucose tolerance), T2D and T2D treated (T2D with a 5-year ongoing treatment).

RESULTS: By exploring the network topology from the different stages of T2D, we observed that, as the disease progress, the networks lose the association between bacteria. It suggests that the microbial community becomes highly sensitive to perturbations in individuals with T2D. With the purpose to identify those genera that guide this transition, we computationally found keystone taxa (driver nodes) and core genera for a Mexican T2D cohort. Altogether, we suggest a set of genera driving the progress of the T2D in a Mexican cohort, among them Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-010, Ruminococcaceae UCG-002, Ruminococcaceae UCG-005, Alistipes, Anaerostipes, and Terrisporobacter.

DISCUSSION: Based on a network approach, this study suggests a set of genera that can serve as a potential biomarker to distinguish the distinct degree of advances in T2D for a Mexican cohort of patients. Beyond limiting our conclusion to one population, we present a computational pipeline to link ecological networks and clinical stages in T2D, and desirable aim to advance in the field of precision medicine.

PMID:37124757 | PMC:PMC10130651 | DOI:10.3389/fendo.2023.1128767

Front Endocrinol (Lausanne). 2023 Apr 13;14:1179413. doi: 10.3389/fendo.2023.1179413. eCollection 2023.

NO ABSTRACT

PMID:37124729 | PMC:PMC10133721 | DOI:10.3389/fendo.2023.1179413

HGG Adv. 2023 Apr 3;4(3):100190. doi: 10.1016/j.xhgg.2023.100190. eCollection 2023 Jul 13.

ABSTRACT

The ability to detect cancer at an early stage in patients who would benefit from effective therapy is a key factor in increasing survivability. This work proposes an evolutionary supervised learning method called CancerSig to identify cancer stage-specific microRNA (miRNA) signatures for early cancer predictions. CancerSig established a compact panel of miRNA signatures as potential markers from 4,667 patients with 15 different types of cancers for the cancer stage prediction, and achieved a mean performance: 10-fold cross-validation accuracy, sensitivity, specificity, and area under the receiver operating characteristic curve of 84.27% ± 6.31%, 0.81 ± 0.12, 0.80 ± 0.10, and 0.80 ± 0.06, respectively. The pan-cancer analysis of miRNA signatures suggested that three miRNAs, hsa-let-7i-3p, hsa-miR-362-3p, and hsa-miR-3651, contributed significantly toward stage prediction across 8 cancers, and each of the 67 miRNAs of the panel was a biomarker of stage prediction in more than one cancer. CancerSig may serve as the basis for cancer screening and therapeutic selection..

PMID:37124139 | PMC:PMC10130501 | DOI:10.1016/j.xhgg.2023.100190

Front Cell Infect Microbiol. 2023 Apr 12;13:1192732. doi: 10.3389/fcimb.2023.1192732. eCollection 2023.

NO ABSTRACT

PMID:37124048 | PMC:PMC10130575 | DOI:10.3389/fcimb.2023.1192732