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Frontiers in Immunology 2020C-reactive protein (CRP) is a widely known, hepatically synthesized protein whose blood levels change rapidly and pronouncedly in response to any tissue damaging event... (Review)
Review
C-reactive protein (CRP) is a widely known, hepatically synthesized protein whose blood levels change rapidly and pronouncedly in response to any tissue damaging event associated with an inflammatory response. The synthesis and secretion of CRP is stimulated by interleukin-6, an early pleiotropic cytokine released by macrophages, endothelial, and other cells that are activated when localized normal tissue structures are compromised by trauma or disease. Serum CRP levels can change rapidly and robustly from 10-100-fold within 6-72 h of any tissue damaging event. Elevated blood levels correlate with the onset and extent of both activated inflammation and the acute phase biochemical response to the tissue insult. Because its functional bioactivity as the prototypic acute phase reactant has eluded clear definition for decades, diagnosticians of various conditions and diseases use CRP blood levels as a simple index for ongoing inflammation. In many pathologies, which involves many different tissues, stages of disease, treatments, and responses to treatments, its interpretive diagnostic value requires a deeper understanding of the localized tissue processes and events that contribute signals which regulate protective or pathological host defense bioactivities. This report presents concepts that describe how local tissue activation events can lead to a non-proteolytic, conformational rearrangement of CRP into a unique isoform with distinctive solubility, antigenicity, binding reactivities and bioactivities from that protein widely known and measured in serum. By describing factors that control the expression, tissue localization, half-life and pro-inflammatory amplification activity of this CRP isoform, a unifying explanation for the diagnostic significance of CRP measurement in disease is advanced.
Topics: C-Reactive Protein; Disease Progression; Humans; Inflammation; Protein Conformation; Protein Isoforms
PubMed: 33013897
DOI: 10.3389/fimmu.2020.02126 -
Seminars in Cell & Developmental Biology Jun 2020Actin is one of the most abundant and essential intracellular proteins that mediates nearly every form of cellular movement and underlies such key processes as... (Review)
Review
Actin is one of the most abundant and essential intracellular proteins that mediates nearly every form of cellular movement and underlies such key processes as embryogenesis, tissue integrity, cell division and contractility of all types of muscle and non-muscle cells. In mammals, actin is represented by six isoforms, which are encoded by different genes but produce proteins that are 95-99 % identical to each other. The six actin genes have vastly different functions in vivo, and the small amino acid differences between the proteins they encode are rigorously maintained through evolution, but the underlying differences behind this distinction, as well as the importance of specific amino acid sequences for each actin isoform, are not well understood. This review summarizes different levels of actin isoform-specific regulation in cellular and developmental processes, starting with the nuclear actin's role in transcription, and covering the gene-level, mRNA-level, and protein-level regulation, with a special focus on mammalian actins in non-muscle cells.
Topics: Actins; Animals; Cells; Growth and Development; Humans; Protein Isoforms
PubMed: 32001148
DOI: 10.1016/j.semcdb.2019.12.003 -
Genome Biology Feb 2022High-throughput single-cell analysis today is facilitated by protocols like the 10X Genomics platform or Drop-Seq which generate cDNA pools in which the origin of a...
High-throughput single-cell analysis today is facilitated by protocols like the 10X Genomics platform or Drop-Seq which generate cDNA pools in which the origin of a transcript is encoded at its 5' or 3' end. Here, we used R2C2 to sequence and demultiplex 12 million full-length cDNA molecules generated by the 10X Genomics platform from ~3000 peripheral blood mononuclear cells. We use these reads, independent from Illumina data, to identify B cell, T cell, and monocyte clusters and generate isoform-level transcriptomes for cells and cell types. Finally, we extract paired adaptive immune receptor sequences unique to each T and B cell.
Topics: Gene Expression Profiling; High-Throughput Nucleotide Sequencing; Humans; Leukocytes, Mononuclear; Protein Isoforms; Sequence Analysis, RNA; Single-Cell Analysis
PubMed: 35130954
DOI: 10.1186/s13059-022-02615-z -
Angewandte Chemie (International Ed. in... May 2021The 90 kDa heat shock protein (Hsp90) is a molecular chaperone that processes nascent polypeptides into their biologically active conformations. Many of these proteins...
The 90 kDa heat shock protein (Hsp90) is a molecular chaperone that processes nascent polypeptides into their biologically active conformations. Many of these proteins contribute to the progression of cancer, and consequently, inhibition of the Hsp90 protein folding machinery represents an innovative approach toward cancer chemotherapy. However, clinical trials with Hsp90 N-terminal inhibitors have encountered deleterious side effects and toxicities, which appear to result from the pan-inhibition of all four Hsp90 isoforms. Therefore, the development of isoform-selective Hsp90 inhibitors is sought to delineate the pathological role played by each isoform. Herein, we describe a structure-based approach that was used to design the first Hsp90α-selective inhibitors, which exhibit >50-fold selectivity versus other Hsp90 isoforms.
Topics: Antineoplastic Agents; HSP90 Heat-Shock Proteins; Humans; Neoplasms; Protein Isoforms
PubMed: 33621416
DOI: 10.1002/anie.202015422 -
International Journal of Molecular... Jun 2023Over the past 8 years, multiple studies examined the phenomenon of isoform switching in human cancers and discovered that isoform switching is widespread, with hundreds...
Over the past 8 years, multiple studies examined the phenomenon of isoform switching in human cancers and discovered that isoform switching is widespread, with hundreds to thousands of such events per cancer type. Although all of these studies used slightly different definitions of isoform switching, which in part led to a rather poor overlap of their results, they all leveraged transcript usage, a proportion of the transcript's expression in the total expression level of the parent gene, to detect isoform switching. However, how changes in transcript usage correlate with changes in transcript expression is not sufficiently explored. In this article, we adopt the most common definition of isoform switching and use a state-of-the-art tool for the analysis of differential transcript usage, SatuRn, to detect isoform switching events in 12 cancer types. We analyze the detected events in terms of changes in transcript usage and the relationship between transcript usage and transcript expression on a global scale. The results of our analysis suggest that the relationship between changes in transcript usage and changes in transcript expression is far from straightforward, and that such quantitative information can be effectively used for prioritizing isoform switching events for downstream analyses.
Topics: Humans; Alternative Splicing; Gene Expression Profiling; Protein Isoforms; Neoplasms
PubMed: 37373214
DOI: 10.3390/ijms241210065 -
BMB Reports Jul 2021Cancer stem cells (CSCs) are a subpopulation of cancer that can self-renew and differentiate into large tumor masses. Evidence accumulated to date shows that CSCs affect... (Review)
Review
Cancer stem cells (CSCs) are a subpopulation of cancer that can self-renew and differentiate into large tumor masses. Evidence accumulated to date shows that CSCs affect tumor proliferation, recurrence, and resistance to chemotherapy. Recent studies have shown that, like stem cells, CSCs maintain cells with self-renewal capacity by means of asymmetric division and promote cell proliferation by means of symmetric division. This cell division is regulated by fate determinants, such as the NUMB protein, which recently has also been confirmed as a tumor suppressor. Loss of NUMB expression leads to uncontrolled proliferation and amplification of the CSC pool, which promotes the Notch signaling pathway and reduces the expression of the p53 protein. NUMB genes are alternatively spliced to produce six functionally distinct isoforms. An interesting recent discovery is that the protein NUMB isoform produced by alternative splicing of NUMB plays an important role in promoting carcinogenesis. In this review, we summarize the known functions of NUMB and NUMB isoforms related to the proliferation and generation of CSCs. [BMB Reports 2021; 54(7): 335-343].
Topics: Alternative Splicing; Asymmetric Cell Division; Carcinogenesis; Cell Division; Cell Line, Tumor; Cell Lineage; Cell Proliferation; Humans; Membrane Proteins; Neoplastic Stem Cells; Nerve Tissue Proteins; Protein Isoforms; Receptors, Notch; Tumor Suppressor Protein p53
PubMed: 34078527
DOI: 10.5483/BMBRep.2021.54.7.048 -
Bioinformatics (Oxford, England) Dec 2021Alternative splicing creates the considerable proteomic diversity and complexity on relatively limited genome. Proteoforms translated from alternatively spliced isoforms...
MOTIVATION
Alternative splicing creates the considerable proteomic diversity and complexity on relatively limited genome. Proteoforms translated from alternatively spliced isoforms of a gene actually execute the biological functions of this gene, which reflect the functional knowledge of genes at a finer granular level. Recently, some computational approaches have been proposed to differentiate isoform functions using sequence and expression data. However, their performance is far from being desirable, mainly due to the imbalance and lack of annotations at isoform-level, and the difficulty of modeling gene-isoform relations.
RESULT
We propose a deep multi-instance learning-based framework (DMIL-IsoFun) to differentiate the functions of isoforms. DMIL-IsoFun firstly introduces a multi-instance learning convolution neural network trained with isoform sequences and gene-level annotations to extract the feature vectors and initialize the annotations of isoforms, and then uses a class-imbalance Graph Convolution Network to refine the annotations of individual isoforms based on the isoform co-expression network and extracted features. Extensive experimental results show that DMIL-IsoFun improves the Smin and Fmax of state-of-the-art solutions by at least 29.6% and 40.8%. The effectiveness of DMIL-IsoFun is further confirmed on a testbed of human multiple-isoform genes, and maize isoforms related with photosynthesis.
AVAILABILITY AND IMPLEMENTATION
The code and data are available at http://www.sdu-idea.cn/codes.php?name=DMIL-Isofun.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Humans; Proteomics; Protein Isoforms; Alternative Splicing; Neural Networks, Computer; Molecular Sequence Annotation
PubMed: 34282449
DOI: 10.1093/bioinformatics/btab532 -
Journal of Cellular Physiology May 2023Voltage-dependent potassium channel Kv1.3 plays a key role on T-cell activation; however, lack of reliable antibodies has prevented its accurate detection under...
Voltage-dependent potassium channel Kv1.3 plays a key role on T-cell activation; however, lack of reliable antibodies has prevented its accurate detection under endogenous circumstances. To overcome this limitation, we created a Jurkat T-cell line with endogenous Kv1.3 channel tagged, to determine the expression, location, and changes upon activation of the native Kv1.3 channels. CRISPR-Cas9 technique was used to insert a Flag-Myc peptide at the C terminus of the KCNA3 gene. Basal or activated channel expression was studied using western blot analysis and imaging techniques. We identified two isoforms of Kv1.3 other than the canonical channel (54 KDa) differing on their N terminus: a longer isoform (70 KDa) and a truncated isoform (43 KDa). All three isoforms were upregulated after T-cell activation. We focused on the functional characterization of the truncated isoform (short form, SF), because it has not been previously described and could be present in the available Kv1.3-/- mice models. Overexpression of SF in HEK cells elicited small amplitude Kv1.3-like currents, which, contrary to canonical Kv1.3, did not induce HEK proliferation. To explore the role of endogenous SF isoform in a native system, we generated both a knockout Jurkat clone and a clone expressing only the SF isoform. Although the canonical isoform (long form) localizes mainly at the plasma membrane, SF remains intracellular, accumulating perinuclearly. Accordingly, SF Jurkat cells did not show Kv1.3 currents and exhibited depolarized resting membrane potential (V ), decreased Ca influx, and a reduction in the [Ca ] increase upon stimulation. Functional characterization of these Kv1.3 channel isoforms showed their differential contribution to signaling pathways involved in formation of the immunological synapse. We conclude that alternative translation initiation generates at least three endogenous Kv1.3 channel isoforms in T cells that exhibit different functional roles. For some of these functions, Kv1.3 proteins do not need to form functional plasma membrane channels.
Topics: Animals; Humans; Mice; Cell Line; Cell Membrane; Jurkat Cells; Protein Isoforms; Kv1.3 Potassium Channel
PubMed: 36852591
DOI: 10.1002/jcp.30984 -
Experimental Eye Research Nov 2023Phosphoinositide 3-kinases (PI3Ks) generate lipids that control multitudinous intracellular cell signaling events which participate in cell survival and proliferation.... (Review)
Review
Phosphoinositide 3-kinases (PI3Ks) generate lipids that control multitudinous intracellular cell signaling events which participate in cell survival and proliferation. In addition, PI3K signaling also contributes to metabolism, immunity, angiogenesis and cardiovascular homeostasis, and many diseases. The diverse actions of PI3K stem from the existence of their various isoforms and a variety of protein effectors. Hence, PI3K isoform-specific inhibitors have already achieved a wonderful effect on treating cancer. Herein, we summarize the molecular mechanism of PI3K inhibitors in preventing the permeability of vessels and neovascularization. Additionally, we briefly illustrate how PI3K signaling modulates blood vessel growth and discuss the different roles that PI3K isoforms play in angiogenesis.
Topics: Phosphatidylinositol 3-Kinase; Phosphatidylinositol 3-Kinases; Signal Transduction; Phosphoinositide-3 Kinase Inhibitors; Protein Isoforms
PubMed: 37716399
DOI: 10.1016/j.exer.2023.109646 -
Molecular Psychiatry Feb 2021Mutations in AUTS2 are associated with autism, intellectual disability, and microcephaly. AUTS2 is expressed in the brain and interacts with polycomb proteins, yet it is...
Mutations in AUTS2 are associated with autism, intellectual disability, and microcephaly. AUTS2 is expressed in the brain and interacts with polycomb proteins, yet it is still unclear how mutations in AUTS2 lead to neurodevelopmental phenotypes. Here we report that when neuronal differentiation is initiated, there is a shift in expression from a long isoform to a short AUTS2 isoform. Yeast two-hybrid screen identified the splicing factor SF3B1 as an interactor of both isoforms, whereas the polycomb group proteins, PCGF3 and PCGF5, were found to interact exclusively with the long AUTS2 isoform. Reporter assays showed that the first exons of the long AUTS2 isoform function as a transcription repressor, but the part that consist of the short isoform acts as a transcriptional activator, both influenced by the cellular context. The expression levels of PCGF3 influenced the ability of the long AUTS2 isoform to activate or repress transcription. Mouse embryonic stem cells (mESCs) with heterozygote mutations in Auts2 had an increase in cell death during in vitro corticogenesis, which was significantly rescued by overexpressing the human AUTS2 transcripts. mESCs with a truncated AUTS2 protein (missing exons 12-20) showed premature neuronal differentiation, whereas cells overexpressing AUTS2, especially the long transcript, showed increase in expression of pluripotency markers and delayed differentiation. Taken together, our data suggest that the precise expression of AUTS2 isoforms is essential for regulating transcription and the timing of neuronal differentiation.
Topics: Animals; Cell Differentiation; Cytoskeletal Proteins; Exons; Mice; Neurons; Phenotype; Protein Isoforms; Transcription Factors
PubMed: 30953002
DOI: 10.1038/s41380-019-0409-1