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Scientific Reports Jun 2022Sepsis is caused by an uncontrolled inflammatory response, whose underlying mechanisms are not fully understood. It is well known that the majority of human genes can be...
Sepsis is caused by an uncontrolled inflammatory response, whose underlying mechanisms are not fully understood. It is well known that the majority of human genes can be expressed as alternative isoforms. While isoform switching is implicated in many diseases and is particularly prominent in cancer, it has never been reported in the context of sepsis. Patients presented to the emergency department of three tertiary care hospitals from January 2020 to December 2020 were enrolled. Clinical variables and genome-wide transcriptome of peripheral blood mononuclear cells (PBMC) were obtained. Isoform switching analysis were performed to identify significant isoform switches and relevant biological consequences. A total of 48 subjects with sepsis, involving 42 survivors and 6 non-survivors, admitted to the emergency department of three tertiary care hospitals were enrolled in this study. PBMCs were extracted for RNA sequencing (RNA-seq). Patients (n = 4) with mild stroke or acute coronary syndrome without infection were enrolled in this study as controls. The most frequent functional changes resulting from isoform switching were changes affecting the open reading frame, protein domains and intron retention. Many genes without differences in gene expression showed significant isoform switching. Many genes with significant isoform switches ([Formula: see text]> 0.1) were associated with higher mortality risk, including PIGS, CASP3, LITAF, HBB and RUVBL2. The study for the first time described the landscape of isoform switching in sepsis, including differentially expressed isoform fractions between patients with and without sepsis and survivors and nonsurvivors. The biological consequences of isoform switching, including protein domain loss, signal peptide gain, and intron retention, were identified.
Topics: ATPases Associated with Diverse Cellular Activities; Carrier Proteins; Cohort Studies; DNA Helicases; Gene Expression Profiling; Humans; Leukocytes, Mononuclear; Protein Isoforms; Sepsis
PubMed: 35715539
DOI: 10.1038/s41598-022-14231-9 -
Protein and Peptide Letters 2018Bromelain inhibitor, "bromein", is a proteinase-inhibitor specific to the cysteine proteinase bromelain from pineapple stem. In the stem, eight bromein isoforms are... (Review)
Review
Bromelain inhibitor, "bromein", is a proteinase-inhibitor specific to the cysteine proteinase bromelain from pineapple stem. In the stem, eight bromein isoforms are known to exist, and each isoform has a short peptide (light chain) and a long one (heavy chain) with five disulfide bonds. The three-dimensional structure of the sixth isoform (bromein-6) is composed of inhibitory and stabilizing domains, and each domain contains a three-stranded antiparallel β-sheet. The genomic sequence of a bromein precursor encodes three homologous bromein isoform domains, and each isoform domain has a signal peptide, three interchain peptides between the light chain and heavy chain, two interdomain peptides and a propeptide. Interestingly, at the protein level, bromein- 6 appears to share a similar folding and disulfide-bonding connectivity with Bowman-Birk serine proteinase inhibitors and shows weak inhibition toward chymotrypsin and trypsin. However, no significant similarity was found between them at the genomic level. This indicates that they have evolved convergently to possess such a structural similarity. To identify the essential reactive site(s) with bromelain, we investigated the inhibitory activity of 44 kinds of the single/double and insertion/ deletion mutants of bromein-6 towards stem bromelain. As a result, it was shown that both the appropriate positioning and the complete side-chain structure of Leu10 in the light chain are absolutely crucial for the inhibition, with an additional measure of importance for the preceding Pro9. Bromein and stem bromelain coexist in the acidic vacuoles of the stem tissue, and one of the key role of bromein appears to be the regulation of the bromelain activity.
Topics: Ananas; Catalytic Domain; Cysteine Proteinase Inhibitors; INDEL Mutation; Models, Molecular; Plant Proteins; Protein Domains; Protein Isoforms; Protein Structure, Secondary; Protein Structure, Tertiary; Structure-Activity Relationship
PubMed: 30129400
DOI: 10.2174/0929866525666180821115432 -
Current Protein & Peptide Science 2019TOYOPEARL particles are cross-linked hydroxylated methacrylic polymers available in different pore and particle sizes. They are conjugated with different ligands to... (Review)
Review
TOYOPEARL particles are cross-linked hydroxylated methacrylic polymers available in different pore and particle sizes. They are conjugated with different ligands to generate ion-exchange, hydrophobic interaction and affinity resins. They have excellent physical and chemical properties. A mixed-mode resin, TOYOPEARL MX-Trp-650M, is made of this particle with tryptophan conjugated via N-terminal amino group and hence has both hydrophobic/aromatic side chain and carboxyl group. In this review, I will summarize the properties of the TOYOPEARL particles and MX-Trp-650M resin and application of this resin for purification of proteins and in some detail the separation of disulfide (SS)- scrambled oligomers of insulin-like growth factor-1 (IGF-1). For this particular application, the intact IGF-1 was used to examine binding and elution conditions of TOYOSCREEN MX-Trp-650M column. Strong binding was obtained at pH 4.0, at which arginine, but not NaCl, resulted in elution. Both NaCl and arginine resulted in elution at pH 6.5. In addition, a pH gradient from 4.0 to 8.5 was effective. When applied to SS-scrambled IGF-1 oligomers, both pH and arginine gradient exhibited an efficient separation of the oligomers.
Topics: Arginine; Chromatography; Humans; Hydrogen Bonding; Hydrogen-Ion Concentration; Hydrophobic and Hydrophilic Interactions; Insulin-Like Growth Factor I; Ligands; Polymers; Protein Binding; Protein Isoforms; Resins, Synthetic; Sodium Chloride; Solvents; Static Electricity; Tryptophan
PubMed: 28990530
DOI: 10.2174/1389203718666171009111355 -
Integrative and Comparative Biology Dec 2022Hibernation in brown bears is an annual process involving multiple physiologically distinct seasons-hibernation, active, and hyperphagia. While recent studies have...
Hibernation in brown bears is an annual process involving multiple physiologically distinct seasons-hibernation, active, and hyperphagia. While recent studies have characterized broad patterns of differential gene regulation and isoform usage between hibernation and active seasons, patterns of gene and isoform expression during hyperphagia remain relatively poorly understood. The hyperphagia stage occurs between active and hibernation seasons and involves the accumulation of large fat reserves in preparation for hibernation. Here, we use time-series analyses of gene expression and isoform usage to interrogate transcriptomic regulation associated with all three seasons. We identify a large number of genes with significant differential isoform usage (DIU) across seasons and show that these patterns of isoform usage are largely tissue-specific. We also show that DIU and differential gene-level expression responses are generally non-overlapping, with only a small subset of multi-isoform genes showing evidence of both gene-level expression changes and changes in isoform usage across seasons. Additionally, we investigate nuanced regulation of candidate genes involved in the insulin signaling pathway and find evidence of hyperphagia-specific gene expression and isoform regulation that may enhance fat accumulation during hyperphagia. Our findings highlight the value of using temporal analyses of both gene- and isoform-level gene expression when interrogating complex physiological phenotypes and provide new insight into the mechanisms underlying seasonal changes in bear physiology.
Topics: Animals; Ursidae; Hibernation; Hyperphagia; Protein Isoforms; Transcriptome; Seasons
PubMed: 35709393
DOI: 10.1093/icb/icac093 -
Biochemistry. Biokhimiia Jun 2019Actin plays an important role in cellular adhesion, muscle and non-muscle contractility, migration, polarization, mitosis, and meiosis. Investigation of specific... (Review)
Review
Actin plays an important role in cellular adhesion, muscle and non-muscle contractility, migration, polarization, mitosis, and meiosis. Investigation of specific mechanisms underlying these processes is essential not only for fundamental research but also for clinical applications, since modulations of actin isoforms are directly or indirectly correlate with severe pathologies. In this review we summarize the isoform-specific functions of actin associated with adhesion structures, motility and division of normal and tumor cells; alterations of the expression and structural organization of actin isoforms in normal and tumor cells. Selective regulation of cytoplasmic β- or γ-actin expression determines functional diversity between isoforms: β-actin plays the predominant role in contraction and intercellular adhesion, and γ-actin is responsible for the cellular plasticity and motility. Similar data were obtained in different epithelial and mesenchymal neoplastic cell cultures, as well as in immunomorphological comparison of normal human tissues with tumor analogues. Reorganization of the actin cytoskeleton and cell-cell contacts is essential for proliferation control and acquisition of invasiveness in epithelial tumors.
Topics: Actins; Animals; Cell Adhesion; Cell Movement; Cell Transformation, Neoplastic; Cytoplasm; Cytosol; Humans; Mammals; Protein Isoforms; Structure-Activity Relationship
PubMed: 31238858
DOI: 10.1134/S0006297919060014 -
Biological Chemistry May 2017The partitioning of the lipidated signaling proteins N-Ras and K-Ras4B into various membrane systems, ranging from single-component fluid bilayers, binary fluid... (Review)
Review
The partitioning of the lipidated signaling proteins N-Ras and K-Ras4B into various membrane systems, ranging from single-component fluid bilayers, binary fluid mixtures, heterogeneous raft model membranes up to complex native-like lipid mixtures (GPMVs) in the absence and presence of integral membrane proteins have been explored in the last decade in a combined chemical-biological and biophysical approach. These studies have revealed pronounced isoform-specific differences regarding the lateral distribution in membranes and formation of protein-rich membrane domains. In this context, we will also discuss the effects of lipid head group structure and charge density on the partitioning behavior of the lipoproteins. Moreover, the dynamic properties of N-Ras and K-Ras4B have been studied in different model membrane systems and native-like crowded milieus. Addition of crowding agents such as Ficoll and its monomeric unit, sucrose, gradually favors clustering of Ras proteins in forming small oligomers in the bulk; only at very high crowder concentrations association is disfavored.
Topics: Amino Acid Motifs; Amino Acid Sequence; Animals; Cell Membrane; Humans; Lipid Metabolism; Membranes, Artificial; Protein Isoforms; ras Proteins
PubMed: 27977396
DOI: 10.1515/hsz-2016-0289 -
Expert Review of Vaccines Apr 2015The identification and characterization of cytokine isoforms is likely to provide critical important new insight into immunobiology. Cytokine isoforms can provide...
The identification and characterization of cytokine isoforms is likely to provide critical important new insight into immunobiology. Cytokine isoforms can provide additional diversity to their complex biological effects that participate in control and protection against different foreign pathogens. Recently, IL-33 has been identified as a proinflammatory cytokine having several different biologically active isoform products. Originally associated with Th2 immunity, new evidence now supports the role of two IL-33 isoforms to facilitate the generation of protective Th1 and CD8 T cell immunity against specific pathogens. Therefore, a better understanding of the IL-33 isoforms will inform us on how to utilize them to facilitate their development as tools as vaccine adjuvants for immune therapy.
Topics: Adjuvants, Immunologic; Biomedical Research; Humans; Interleukin-33; Interleukins; Protein Isoforms; Vaccines
PubMed: 25656504
DOI: 10.1586/14760584.2015.1011135 -
Molecules (Basel, Switzerland) Dec 2021After being rather neglected as a research field in the past, carbonic anhydrase activators (CAAs) were undoubtedly demonstrated to be useful in diverse pharmaceutical... (Review)
Review
After being rather neglected as a research field in the past, carbonic anhydrase activators (CAAs) were undoubtedly demonstrated to be useful in diverse pharmaceutical and industrial applications. They also improved the knowledge of the requirements to selectively interact with a CA isoform over the others and confirmed the catalytic mechanism of this class of compounds. Amino acid and amine derivatives were the most explored in in vitro, in vivo and crystallographic studies as CAAs. Most of them were able to activate human or non-human CA isoforms in the nanomolar range, being proposed as therapeutic and industrial tools. Some isoforms are better activated by amino acids than amines derivatives and the stereochemistry may exert a role. Finally, non-human CAs have been very recently tested for activation studies, paving the way to innovative industrial and environmental applications.
Topics: Amines; Amino Acids; Animals; Carbonic Anhydrases; Enzyme Activation; Enzyme Activators; Humans; Models, Molecular; Protein Isoforms
PubMed: 34885917
DOI: 10.3390/molecules26237331 -
Clinical & Experimental Metastasis Jun 2022Cellular plasticity lies at the core of cancer progression, metastasis, and resistance to treatment. Stemness and epithelial-mesenchymal plasticity in cancer are... (Review)
Review
Cellular plasticity lies at the core of cancer progression, metastasis, and resistance to treatment. Stemness and epithelial-mesenchymal plasticity in cancer are concepts that represent a cancer cell's ability to coopt and adapt normal developmental programs to promote survival and expansion. The cancer stem cell model states that a small subset of cancer cells with stem cell-like properties are responsible for driving tumorigenesis and metastasis while remaining especially resistant to common chemotherapeutic drugs. Epithelial-mesenchymal plasticity describes a cancer cell's ability to transition between epithelial and mesenchymal phenotypes which drives invasion and metastasis. Recent research supports the existence of stable epithelial/mesenchymal hybrid phenotypes which represent highly plastic states with cancer stem cell characteristics. The cell adhesion molecule CD44 is a widely accepted marker for cancer stem cells, and it lies at a functional intersection between signaling networks regulating both stemness and epithelial-mesenchymal plasticity. CD44 expression is complex, with alternative splicing producing many isoforms. Interestingly, not only does the pattern of isoform expression change during transitions between epithelial and mesenchymal phenotypes in cancer, but these isoforms have distinct effects on cell behavior including the promotion of metastasis and stemness. The role of CD44 both downstream and upstream of signaling pathways regulating epithelial-mesenchymal plasticity and stemness make this protein a valuable target for further research and therapeutic intervention.
Topics: Alternative Splicing; Epithelial-Mesenchymal Transition; Humans; Hyaluronan Receptors; Neoplasm Metastasis; Neoplasms; Neoplastic Stem Cells; Protein Isoforms
PubMed: 35023031
DOI: 10.1007/s10585-022-10146-x -
Clinical Pharmacology and Therapeutics Nov 2016Solute carrier (SLC) transporters represent 52 families of membrane transport proteins that function in endogenous compound homeostasis and xenobiotic disposition, and... (Review)
Review
Solute carrier (SLC) transporters represent 52 families of membrane transport proteins that function in endogenous compound homeostasis and xenobiotic disposition, and have been exploited in drug delivery and therapeutic targeting strategies. In particular, the SLC16 family that encodes for the 14 isoforms of the monocarboxylate transporter (MCT) family plays a significant role in the absorption, tissue distribution, and clearance of both endogenous and exogenous compounds. MCTs are required for the transport of essential cell nutrients and for cellular metabolic and pH regulation. Recent publications have indicated their novel roles in disease, and thus their potential as biomarkers and new therapeutic targets in disease are under investigation. More research into MCT isoform function, specificity, expression, and regulation will allow researchers to exploit the potential utility of MCTs in the clinic as therapeutic targets and prognostic factors of disease.
Topics: Humans; Models, Biological; Molecular Targeted Therapy; Monocarboxylic Acid Transporters; Prognosis; Protein Isoforms
PubMed: 27351344
DOI: 10.1002/cpt.418