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Cells Dec 2023Alternative splicing changes are closely linked to aging, though it remains unclear if they are drivers or effects. As organisms age, splicing patterns change, varying... (Review)
Review
Alternative splicing changes are closely linked to aging, though it remains unclear if they are drivers or effects. As organisms age, splicing patterns change, varying gene isoform levels and functions. These changes may contribute to aging alterations rather than just reflect declining RNA quality control. Three main splicing types-intron retention, cassette exons, and cryptic exons-play key roles in age-related complexity. These events modify protein domains and increase nonsense-mediated decay, shifting protein isoform levels and functions. This may potentially drive aging or serve as a biomarker. Fluctuations in splicing factor expression also occur with aging. Somatic mutations in splicing genes can also promote aging and age-related disease. The interplay between splicing and aging has major implications for aging biology, though differentiating correlation and causation remains challenging. Declaring a splicing factor or event as a driver requires comprehensive evaluation of the associated molecular and physiological changes. A greater understanding of how RNA splicing machinery and downstream targets are impacted by aging is essential to conclusively establish the role of splicing in driving aging, representing a promising area with key implications for understanding aging, developing novel therapeutical options, and ultimately leading to an increase in the healthy human lifespan.
Topics: Humans; Alternative Splicing; RNA, Messenger; Protein Isoforms; RNA Splicing Factors; Aging; Nonsense Mediated mRNA Decay
PubMed: 38132139
DOI: 10.3390/cells12242819 -
EMBO Reports Dec 2021All living organisms have developed processes to sense and address environmental changes to maintain a stable internal state (homeostasis). When activated, the p53... (Review)
Review
All living organisms have developed processes to sense and address environmental changes to maintain a stable internal state (homeostasis). When activated, the p53 tumour suppressor maintains cell and organ integrity and functions in response to homeostasis disruptors (stresses) such as infection, metabolic alterations and cellular damage. Thus, p53 plays a fundamental physiological role in maintaining organismal homeostasis. The TP53 gene encodes a network of proteins (p53 isoforms) with similar and distinct biochemical functions. The p53 network carries out multiple biological activities enabling cooperation between individual cells required for long-term survival of multicellular organisms (animals) in response to an ever-changing environment caused by mutation, infection, metabolic alteration or damage. In this review, we suggest that the p53 network has evolved as an adaptive response to pathogen infections and other environmental selection pressures.
Topics: Animals; Genes, p53; Homeostasis; Infections; Mutation; Protein Isoforms; Stress, Physiological; Tumor Suppressor Protein p53
PubMed: 34779563
DOI: 10.15252/embr.202153085 -
Nucleic Acids Research May 2023Adenosine deaminase acting on RNA ADAR1 promotes A-to-I conversion in double-stranded and structured RNAs. ADAR1 has two isoforms transcribed from different promoters:...
Adenosine deaminase acting on RNA ADAR1 promotes A-to-I conversion in double-stranded and structured RNAs. ADAR1 has two isoforms transcribed from different promoters: cytoplasmic ADAR1p150 is interferon-inducible while ADAR1p110 is constitutively expressed and primarily localized in the nucleus. Mutations in ADAR1 cause Aicardi - Goutières syndrome (AGS), a severe autoinflammatory disease associated with aberrant IFN production. In mice, deletion of ADAR1 or the p150 isoform leads to embryonic lethality driven by overexpression of interferon-stimulated genes. This phenotype is rescued by deletion of the cytoplasmic dsRNA-sensor MDA5 indicating that the p150 isoform is indispensable and cannot be rescued by ADAR1p110. Nevertheless, editing sites uniquely targeted by ADAR1p150 remain elusive. Here, by transfection of ADAR1 isoforms into ADAR-less mouse cells we detect isoform-specific editing patterns. Using mutated ADAR variants, we test how intracellular localization and the presence of a Z-DNA binding domain-α affect editing preferences. These data show that ZBDα only minimally contributes to p150 editing-specificity while isoform-specific editing is primarily directed by the intracellular localization of ADAR1 isoforms. Our study is complemented by RIP-seq on human cells ectopically expressing tagged-ADAR1 isoforms. Both datasets reveal enrichment of intronic editing and binding by ADAR1p110 while ADAR1p150 preferentially binds and edits 3'UTRs.
Topics: Animals; Humans; Mice; Adenosine Deaminase; Cell Nucleus; Cytoplasm; Interferons; Protein Isoforms; RNA, Double-Stranded; RNA Editing
PubMed: 37026479
DOI: 10.1093/nar/gkad265 -
Viruses Jan 2020The human OAS1 (hOAS1) gene produces multiple possible isoforms due to alternative splicing events and sequence variation among individuals, some of which affect...
The human OAS1 (hOAS1) gene produces multiple possible isoforms due to alternative splicing events and sequence variation among individuals, some of which affect splicing. The unique C-terminal sequences of the hOAS1 isoforms could differentially affect synthetase activity, protein stability, protein partner interactions and/or cellular localization. Recombinant p41, p42, p44, p46, p48, p49 and p52 hOAS1 isoform proteins expressed in bacteria were each able to synthesize trimer and higher order 2'-5' linked oligoadenylates in vitro in response to poly(I:C). The p42, p44, p46, p48 and p52 isoform proteins were each able to induce RNase-mediated rRNA cleavage in response to poly(I:C) when overexpressed in HEK293 cells. The expressed levels of the p42 and p46 isoform proteins were higher than those of the other isoforms, suggesting increased stability in mammalian cells. In a yeast two-hybrid screen, Fibrillin1 (FBN1) was identified as a binding partner for hOAS1 p42 isoform, and Supervillin (SVIL) as a binding partner for the p44 isoform. The p44-SVIL interaction was supported by co-immunoprecipitation data from mammalian cells. The data suggest that the unique C-terminal regions of hOAS1 isoforms may mediate the recruitment of different partners, alternative functional capacities and/or different cellular localization.
Topics: 2',5'-Oligoadenylate Synthetase; Alternative Splicing; Cloning, Molecular; Escherichia coli; Fibrillin-1; Gene Expression; HEK293 Cells; Humans; Membrane Proteins; Microfilament Proteins; Poly I-C; Polylysine; Protein Isoforms; Recombinant Proteins
PubMed: 32013110
DOI: 10.3390/v12020152 -
Molecular Neurobiology Sep 2023Tau is a microtubule-associated binding protein in the nervous system that is known for its role in stabilizing microtubules throughout the nerve cell. It accumulates as... (Review)
Review
Tau is a microtubule-associated binding protein in the nervous system that is known for its role in stabilizing microtubules throughout the nerve cell. It accumulates as β-sheet-rich aggregates and neurofibrillary tangles, leading to an array of different pathologies. Six splice variants of this protein, generated from the microtubule-associated protein tau (MAPT) gene, are expressed in the brain. Amongst these variants, 0N3R, is prominent during fetal development, while the rest, 0N4R, 1N3R, 1N4R, 2N3R, and 2N4R, are expressed in postnatal stages. Tau isoforms play their role separately or in combination with others to contribute to one or multiple neurodegenerative disorders and clinical syndromes. For instance, in Alzheimer's disease and a subset of frontotemporal lobar degeneration (FTLD)-MAPT (i.e., R406W and V337M), both 3R and 4R isoforms are involved; therefore, they are called 3R/4R mix tauopathies. On the other hand, 4R isoforms are aggregated in progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), and a majority of FTLD-MAPT and these diseases are called 4R tauopathies. Similarly, Pick's disease has an association with 3R tau isoforms and is thereby referred to as 3R tauopathy. Unlike 3R isoforms, the 4R variants have a faster rate of aggregation that accelerates the associated neurodegenerative mechanisms. Moreover, post-translational modifications of each isoform occur at a different rate and dictate their physiological and pathological attributes. The smallest tau isoform (0N3R) is highly phosphorylated in the fetal brain but does not lead to the generation of aggregates. On the other hand, proteoforms in the adult human brain undergo aggregation upon their phosphorylation and glycation. Expanding on this knowledge, this article aims to review the physiological and pathological roles of tau isoforms and their underlying mechanisms that result in neurological deficits. Physiological and pathological relevance of microtubule-associated protein tau (MAPT): Tau exists as six splice variants in the brain, each differing with respect to expression, post-translational modifications (PTMs), and aggregation kinetics. Physiologically, they are involved in the stabilization of microtubules that form the molecular highways for axonal transport. However, an imbalance in their expression and the associated PTMs leads to a disruption in their physiological function through the formation of neurofibrillary tangles that accumulate in various regions of the brain and contribute to several types of tauopathies.
Topics: Adult; Humans; tau Proteins; Tauopathies; Alzheimer Disease; Neurofibrillary Tangles; Frontotemporal Lobar Degeneration; Protein Isoforms; Frontotemporal Dementia
PubMed: 37266762
DOI: 10.1007/s12035-023-03387-8 -
European Journal of Medicinal Chemistry Aug 2022In the past few decades, the development of heat shock protein 90 (Hsp90) inhibitors for cancer treatment has not stopped. About twenty compounds have been evaluated in... (Review)
Review
In the past few decades, the development of heat shock protein 90 (Hsp90) inhibitors for cancer treatment has not stopped. About twenty compounds have been evaluated in the clinical trials, but the FDA approved none of them because of toxic effects and/or not enough efficacies. Insufficient isoform selectivity has been considered as one of the reasons for these failures recently. Therefore, developing isoform-selective Hsp90 inhibitors could probably make great progress in searching for therapeutic agents for cancer as well as many other diseases. Here, we summarized classic pan-inhibitors of Hsp90 based on the classification of binding sites and illustrated design strategies applied in the drug discovery. We summed up current isoform-specific Hsp90 inhibitors including their discovery processes and potential indications.
Topics: Antineoplastic Agents; Binding Sites; HSP90 Heat-Shock Proteins; Humans; Neoplasms; Protein Isoforms
PubMed: 35691175
DOI: 10.1016/j.ejmech.2022.114516 -
Current Topics in Microbiology and... 2022Improving the anti-tumour T cell response as a consequence of immunotherapy can result in eradication of tumour burden, however, the majority of patients fail with... (Review)
Review
Improving the anti-tumour T cell response as a consequence of immunotherapy can result in eradication of tumour burden, however, the majority of patients fail with current treatment regimens and so novel immunotherapies with greater efficacy and improved tolerability are needed. The phosphoinositide-3-kinase (PI3K) family members that are directly involved in cell signalling comprise PI3Kα, PI3Kβ, PI3Kδ and PI3Kγ, with the latter two isoforms expressed primarily by leukocytes. The survival and optimal function of regulatory T cells (Treg) and myeloid-derived suppressor cells (MDSCs) is dependent on PI3Kδ, whereas tumour-associated macrophages (TAMs), use PI3Kγ. Blocking these signalling isoforms can boost development of effective anti-cancer immune responses and result in control of tumour burden. The dependence on different PI3K isoforms in immune cells makes targeting this pathway an attractive approach for tumour immunotherapy. Herein, we discuss how inhibiting specific PI3K isoforms in pro-tumoural Tregs, MDSCS and TAMs can unleash a powerful anti-tumour immune response, driven by CD8 T cells, capable of controlling tumour burden and consider how the immune response to therapy needs careful investigation, to identify both the correlates of successful treatment and those that impede the generation of robust anti-tumour responses. Furthermore, we review how combination immunotherapy approaches with both PI3K inhibitors and subsequent immune checkpoint blockade can potentiate the efficacy of monotherapy. Finally, we discuss the recent advances in the use of PI3K isoform-specific inhibitors as an immunotherapy for solid tumours in clinical trials.
Topics: CD8-Positive T-Lymphocytes; Humans; Immune Checkpoint Inhibitors; Immunotherapy; Neoplasms; Phosphatidylinositol 3-Kinase; Phosphatidylinositol 3-Kinases; Phosphatidylinositols; Phosphoinositide-3 Kinase Inhibitors; Protein Isoforms
PubMed: 36243853
DOI: 10.1007/978-3-031-06566-8_16 -
Nature Communications Oct 2022Although accumulating evidence indicates that alternative splicing is aberrantly altered in many cancers, the functional mechanism remains to be elucidated. Here, we...
Although accumulating evidence indicates that alternative splicing is aberrantly altered in many cancers, the functional mechanism remains to be elucidated. Here, we show that epithelial and mesenchymal isoform switches of leucine-rich repeat Fli-I-interacting protein 2 (LRRFIP2) regulated by epithelial splicing regulatory protein 1 (ESRP1) correlate with metastatic potential of gastric cancer cells. We found that expression of the splicing variants of LRRFIP2 was closely correlated with that of ESRP1. Surprisingly, ectopic expression of the mesenchymal isoform of LRRFIP2 (variant 3) dramatically increased liver metastasis of gastric cancer cells, whereas deletion of exon 7 of LRRFIP2 by the CRISPR/Cas9 system caused an isoform switch, leading to marked suppression of liver metastasis. Mechanistically, the epithelial LRRFIP2 isoform (variant 2) inhibited the oncogenic function of coactivator-associated arginine methyltransferase 1 (CARM1) through interaction. Taken together, our data reveals a mechanism of LRRFIP2 isoform switches in gastric cancer with important implication for cancer metastasis.
Topics: Humans; Adaptor Proteins, Signal Transducing; Alternative Splicing; Cell Line, Tumor; Epithelial-Mesenchymal Transition; Liver Neoplasms; Protein Isoforms; RNA-Binding Proteins; Stomach Neoplasms; Transcription Factors; Neoplasm Metastasis
PubMed: 36307405
DOI: 10.1038/s41467-022-33786-9 -
IEEE/ACM Transactions on Computational... 2022Alternative splicing enables a gene spliced into different isoforms and hence protein variants. Identifying individual functions of these isoforms help deciphering the...
Alternative splicing enables a gene spliced into different isoforms and hence protein variants. Identifying individual functions of these isoforms help deciphering the functional diversity of proteins. Although much efforts have been made for automatic gene function prediction, few efforts have been moved toward computational isoform function prediction, mainly due to the unavailable (or scanty) functional annotations of isoforms. Existing efforts directly combine multiple RNA-seq datasets without account of the important tissue specificity of alternative splicing. To bridge this gap, we introduce a novel approach called TS-Isofun to predict the functions of isoforms by integrating multiple functional association networks with respect to tissue specificity. TS-Isofun first constructs tissue-specific isoform functional association networks using multiple RNA-seq datasets from tissue-wise. Next, TS-Isofun assigns weights to these networks and models the tissue specificity by selectively integrating them with adaptive weights. It then introduces a joint matrix factorization-based data fusion model to leverage the integrated network, gene-level data and functional annotations of genes to infer the functions of isoforms. To achieve coherent weight assignment and isoform function prediction, TS-Isofun jointly optimizes the weights of individual networks and the isoform function prediction in a unified objective function. Experimental results show that TS-Isofun significantly outperforms state-of-the-art methods and the account of tissue specificity contributes to more accurate isoform function prediction.
Topics: Alternative Splicing; Organ Specificity; Protein Isoforms
PubMed: 34185647
DOI: 10.1109/TCBB.2021.3093167 -
Trends in Cell Biology Apr 2023Our understanding of cancer and the key pathways that drive cancer survival has expanded rapidly over the past several decades. However, there are still important... (Review)
Review
Our understanding of cancer and the key pathways that drive cancer survival has expanded rapidly over the past several decades. However, there are still important challenges that continue to impair patient survival, including our inability to target cancer stem cells (CSCs), metastasis, and drug resistance. The transcription factor p63 is a p53 family member with multiple isoforms that carry out a wide array of functions. Here, we discuss the critical importance of the ΔNp63α isoform in cancer and potential therapeutic strategies to target ΔNp63α expression to impair the CSC population, as well as to prevent metastasis and drug resistance to improve patient survival.
Topics: Humans; Tumor Suppressor Proteins; Neoplasms; Transcription Factors; Protein Isoforms; Gene Expression Regulation, Neoplastic; Cell Line, Tumor
PubMed: 36115734
DOI: 10.1016/j.tcb.2022.08.003