-
Cell Oct 2020Determining protein levels in each tissue and how they compare with RNA levels is important for understanding human biology and disease as well as regulatory processes...
Determining protein levels in each tissue and how they compare with RNA levels is important for understanding human biology and disease as well as regulatory processes that control protein levels. We quantified the relative protein levels from over 12,000 genes across 32 normal human tissues. Tissue-specific or tissue-enriched proteins were identified and compared to transcriptome data. Many ubiquitous transcripts are found to encode tissue-specific proteins. Discordance of RNA and protein enrichment revealed potential sites of synthesis and action of secreted proteins. The tissue-specific distribution of proteins also provides an in-depth view of complex biological events that require the interplay of multiple tissues. Most importantly, our study demonstrated that protein tissue-enrichment information can explain phenotypes of genetic diseases, which cannot be obtained by transcript information alone. Overall, our results demonstrate how understanding protein levels can provide insights into regulation, secretome, metabolism, and human diseases.
Topics: Gene Expression; Gene Expression Profiling; Humans; Proteome; Proteomics; RNA; RNA, Messenger; Transcriptome
PubMed: 32916130
DOI: 10.1016/j.cell.2020.08.036 -
Cancer Cell Apr 2021Mutant p53 (mtp53) proteins can exert cancer-promoting gain-of-function activities. We report a mechanism by which mtp53 suppresses both cell-autonomous and...
Mutant p53 (mtp53) proteins can exert cancer-promoting gain-of-function activities. We report a mechanism by which mtp53 suppresses both cell-autonomous and non-cell-autonomous signaling to promote cancer cell survival and evasion of tumor immune surveillance. Mtp53 interferes with the function of the cytoplasmic DNA sensing machinery, cGAS-STING-TBK1-IRF3, that activates the innate immune response. Mtp53, but not wild-type p53, binds to TANK-binding protein kinase 1 (TBK1) and prevents the formation of a trimeric complex between TBK1, STING, and IRF3, which is required for activation, nuclear translocation, and transcriptional activity of IRF3. Inactivation of innate immune signaling by mtp53 alters cytokine production, resulting in immune evasion. Restoring TBK1 signaling is sufficient to bypass mtp53 and lead to restored immune cell function and cancer cell eradication. This work is of translational interest because therapeutic approaches that restore TBK1 function could potentially reactivate immune surveillance and eliminate mtp53 tumors.
Topics: Animals; Carcinogenesis; Cell Transformation, Neoplastic; Cytosol; Gene Expression; Immunity, Innate; Membrane Proteins; Mice; Nucleotidyltransferases; Signal Transduction; Tumor Suppressor Protein p53
PubMed: 33545063
DOI: 10.1016/j.ccell.2021.01.003 -
Nucleic Acids Research May 2023In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems....
In situ capturing technologies add tissue context to gene expression data, with the potential of providing a greater understanding of complex biological systems. However, splicing variants and full-length sequence heterogeneity cannot be characterized at spatial resolution with current transcriptome profiling methods. To that end, we introduce spatial isoform transcriptomics (SiT), an explorative method for characterizing spatial isoform variation and sequence heterogeneity using long-read sequencing. We show in mouse brain how SiT can be used to profile isoform expression and sequence heterogeneity in different areas of the tissue. SiT reveals regional isoform switching of Plp1 gene between different layers of the olfactory bulb, and the use of external single-cell data allows the nomination of cell types expressing each isoform. Furthermore, SiT identifies differential isoform usage for several major genes implicated in brain function (Snap25, Bin1, Gnas) that are independently validated by in situ sequencing. SiT also provides for the first time an in-depth A-to-I RNA editing map of the adult mouse brain. Data exploration can be performed through an online resource (https://www.isomics.eu), where isoform expression and RNA editing can be visualized in a spatial context.
Topics: Animals; Mice; Alternative Splicing; Sequence Analysis, RNA; Protein Isoforms; Gene Expression Profiling; Gene Expression; Transcriptome
PubMed: 36928528
DOI: 10.1093/nar/gkad169 -
STAR Protocols Dec 2023This overview guides both novices and experienced researchers facing challenging targets to select the most appropriate gene expression system for producing a particular... (Review)
Review
This overview guides both novices and experienced researchers facing challenging targets to select the most appropriate gene expression system for producing a particular protein. By answering four key questions, readers can determine the most suitable gene expression system following a decision scheme. This guide addresses the most commonly used and accessible systems and provides brief descriptions of the main gene expression systems' key characteristics to assist decision making. Additionally, information has been included for selected less frequently used "exotic" gene expression systems.
Topics: Ligands; Databases, Pharmaceutical; Recombinant Proteins; Gene Expression
PubMed: 37917580
DOI: 10.1016/j.xpro.2023.102572 -
Current Opinion in Chemical Biology Aug 2019Visualization of transcription in living cells has taught us that genes are often transcribed in bursts, with periods of gene activity interspersed by periods of... (Review)
Review
Visualization of transcription in living cells has taught us that genes are often transcribed in bursts, with periods of gene activity interspersed by periods of inactivity. Recently, technological advances in live-cell imaging have provided a more detailed picture of the characteristics of transcriptional bursts, and have allowed direct visualization of the upstream regulatory steps of bursting at single-molecule resolution. In this review, we highlight the latest insights into transcription dynamics and we discuss recent developments in understanding the regulation of transcriptional bursting through the binding kinetics of transcription factors, enhancer-promoter interactions and clustering/phase separation of the transcriptional machinery.
Topics: Gene Expression; Transcription Factors; Transcription, Genetic
PubMed: 31284216
DOI: 10.1016/j.cbpa.2019.05.031 -
Biological Psychiatry Mar 2021Major depression (MD) is determined by a multitude of factors including genetic risk variants that regulate gene expression. We examined the genetic component of gene...
BACKGROUND
Major depression (MD) is determined by a multitude of factors including genetic risk variants that regulate gene expression. We examined the genetic component of gene expression in MD by performing a transcriptome-wide association study (TWAS), inferring gene expression-trait relationships from genetic, transcriptomic, and phenotypic information.
METHODS
Genes differentially expressed in depression were identified with the TWAS FUSION method, based on summary statistics from the largest genome-wide association analysis of MD (n = 135,458 cases, n = 344,901 controls) and gene expression levels from 21 tissue datasets (brain; blood; thyroid, adrenal, and pituitary glands). Follow-up analyses were performed to extensively characterize the identified associations: colocalization, conditional, and fine-mapping analyses together with TWAS-based pathway investigations.
RESULTS
Transcriptome-wide significant differences between cases and controls were found at 94 genes, approximately half of which were novel. Of the 94 significant genes, 6 represented strong, colocalized, and potentially causal associations with depression. Such high-confidence associations include NEGR1, CTC-467M3.3, TMEM106B, LRFN5, ESR2, and PROX2. Lastly, TWAS-based enrichment analysis highlighted dysregulation of gene sets for, among others, neuronal and synaptic processes.
CONCLUSIONS
This study sheds further light on the genetic component of gene expression in depression by characterizing the identified associations, unraveling novel risk genes, and determining which associations are congruent with a causal model. These findings can be used as a resource for prioritizing and designing subsequent functional studies of MD.
Topics: Depression; Depressive Disorder, Major; Gene Expression Profiling; Genetic Predisposition to Disease; Genome-Wide Association Study; Humans; Membrane Proteins; Nerve Tissue Proteins; Transcriptome
PubMed: 33279206
DOI: 10.1016/j.biopsych.2020.09.010 -
Clinical and Translational Medicine Jan 2022Chemoradiotherapy-induced PD-L1 upregulation leads to therapeutic resistance and treatment failure. The PD-1/PD-L1 blocking antibodies sensitize cancers to...
BACKGROUND
Chemoradiotherapy-induced PD-L1 upregulation leads to therapeutic resistance and treatment failure. The PD-1/PD-L1 blocking antibodies sensitize cancers to chemoradiotherapy by blocking extracellular PD-1 and PD-L1 binding without affecting the oncogenic function of intracellular PD-L1. Reversing the chemoradiation-induced PD-L1 expression could provide a new strategy to achieve a greater anti-tumour effect of chemoradiotherapy. Here, we aimed to identify candidate small molecular inhibitors that might boost the anti-tumour immunity of chemoradiotherapy by decreasing treatment-induced PD-L1 expression in non-small cell lung cancer (NSCLC).
METHODS
A drug array was used to recognize compounds that can suppress the cisplatin-induced and radiation-induced PD-L1 expression in NSCLC via the flow cytometry-based assay. We examined whether and how targeting bromodomain containing 4 (BRD4) inhibits chemoradiation-induced PD-L1 expression and evaluated the effect of BRD4 inhibition and chemoradiation combination in vivo.
RESULTS
BRD4 inhibitors JQ1 and ARV-771 were identified as the most promising drugs both in the cisplatin and radiation screening projects in two NSCLC cell lines. Targeting BRD4 was supposed to block chemoradiotherapy inducible PD-L1 expression by disrupting the recruitment of BRD4-IRF1 complex to PD-L1 promoter. A positive correlation between BRD4 and PD-L1 expression was observed in human NSCLC tissues. Moreover, BRD4 inhibition synergized with chemoradiotherapy and PD-1 blockade to show a robust anti-tumour immunity dependent on CD8+ T cell through limiting chemoradiation-induced tumour cell surface PD-L1 upregulation in vivo. Notably, the BRD4-targeted combinatory treatments did not show increased toxicities.
CONCLUSION
The data showed that BRD4-targeted therapy synergized with chemoradiotherapy and anti-PD-1 antibody by boosting anti-tumour immunity in NSCLC.
Topics: Animals; Carcinoma, Non-Small-Cell Lung; Cell Cycle Proteins; Chemoradiotherapy; Disease Models, Animal; Gene Expression; Interferon Regulatory Factor-1; Mice; Signal Transduction; Transcription Factors
PubMed: 35083874
DOI: 10.1002/ctm2.718 -
Proceedings of the National Academy of... May 2021Gene expression signatures (GES) connect phenotypes to differential messenger RNA (mRNA) expression of genes, providing a powerful approach to define cellular identity,...
Gene expression signatures (GES) connect phenotypes to differential messenger RNA (mRNA) expression of genes, providing a powerful approach to define cellular identity, function, and the effects of perturbations. The use of GES has suffered from vague assessment criteria and limited reproducibility. Because the structure of proteins defines the functional capability of genes, we hypothesized that enrichment of structural features could be a generalizable representation of gene sets. We derive structural gene expression signatures (sGES) using features from multiple levels of protein structure (e.g., domain and fold) encoded by the mRNAs in GES. Comprehensive analyses of data from the Genotype-Tissue Expression Project (GTEx), the all RNA-seq and ChIP-seq sample and signature search (ARCHS4) database, and mRNA expression of drug effects on cardiomyocytes show that sGES are useful for characterizing biological phenomena. sGES enable phenotypic characterization across experimental platforms, facilitates interoperability of expression datasets, and describe drug action on cells.
Topics: Cell Line; Chromatin Immunoprecipitation Sequencing; Computational Biology; Gene Expression; Gene Expression Profiling; Humans; Myocytes, Cardiac; Protein Conformation; Proteins; RNA, Messenger; RNA-Seq; Reproducibility of Results; Transcriptome
PubMed: 33941686
DOI: 10.1073/pnas.2014866118 -
Current Genetics Dec 2021Cellular systems depend on multiprotein complexes whose functionalities require defined stoichiometries of subunit proteins. Proper stoichiometry is achieved by... (Review)
Review
Cellular systems depend on multiprotein complexes whose functionalities require defined stoichiometries of subunit proteins. Proper stoichiometry is achieved by controlling the amount of protein synthesis and degradation even in the presence of genetic perturbations caused by changes in gene dosage. As a consequence of increased gene copy number, excess subunits unassembled into the complex are synthesized and rapidly degraded by the ubiquitin-proteasome system. This mechanism, called protein-level dosage compensation, is widely observed not only under such perturbed conditions but also in unperturbed physiological cells. Recent studies have shown that recognition of unassembled subunits and their selective degradation are intricately regulated. This review summarizes the nature, strategies, and increasing complexity of protein-level dosage compensation and discusses possible mechanisms for controlling proteome stoichiometry in multiple layers of biological processes.
Topics: Fungal Proteins; Gene Expression Regulation, Fungal; Models, Biological; Multiprotein Complexes; Protein Binding; Protein Biosynthesis; Proteolysis; Proteome; Yeasts
PubMed: 34382105
DOI: 10.1007/s00294-021-01205-z -
Experimental Cell Research Oct 2022Skeletal muscle development and regeneration is governed by the combined action of Myf5, MyoD, Mrf4 and MyoG, also known as the myogenic regulatory factors (MRFs). These... (Review)
Review
Skeletal muscle development and regeneration is governed by the combined action of Myf5, MyoD, Mrf4 and MyoG, also known as the myogenic regulatory factors (MRFs). These transcription factors are expressed in a highly spatio-temporal restricted manner, ensuring the significant functional and metabolic diversity observed between the different muscle groups. In this review, we will discuss the multiple layers of regulation that contribute to the control of the exquisite expression patterns of the MRFs in particular, and of myogenic genes in general. We will highlight all major regulatory processes that play a role in myogenesis: from those that modulate chromatin status and transcription competence, such as DNA methylation, histone modification, chromatin remodeling, or non-coding RNAs, to those that control transcript and protein processing and modification, such as alternative splicing, polyadenylation, other mRNA modifications, or post-translational protein modifications. All these processes are exquisitely and tightly coordinated to ensure the proper activation, maintenance and termination of the myogenic process.
Topics: Chromatin Assembly and Disassembly; Gene Expression; Gene Expression Regulation; Muscle Development; Muscle, Skeletal; Myogenic Regulatory Factors; Transcription Factors
PubMed: 35926660
DOI: 10.1016/j.yexcr.2022.113299