'Hard' and 'soft' principles defining the structure, function and regulation of keratin intermediate filaments

Increased circulating cytokeratin 19 fragment levels in preterm neonates receiving mechanical ventilation are associated with poor outcome

Invasive mechanical ventilation and oxygen toxicity are postnatal contributors to chronic lung disease of prematurity, also known as bronchopulmonary dysplasia (BPD). Cyfra 21-1 is a soluble fragment of cytokeratin 19, which belongs to the cytoskeleton stabilizing epithelial intermediate filaments. As a biomarker of structural integrity, Cyfra 21-1 might be associated with airway injury and lung hypoplasia in neonates. Serum Cyfra 21-1 concentrations for 80 preterm and 80 healthy term newborns were measured within 48 h after birth. Preterm infants with the combined endpoint BPD/mortality had significantly higher Cyfra 21-1 levels compared with those without fulfilling BPD/mortality criteria (P = 0.01). Also, severe RDS (>grade III) was associated with higher Cyfra levels (P = 0.01). Total duration of oxygen therapy was more than five times longer in neonates with high Cyfra 21-1 levels (P = 0.01). Infants with higher Cyfra 21-1 values were more likely to receive mechanical ventilation (50% vs. 17.5%). However, the duration of mechanical ventilation was similar between groups. The median Cyfra value was 1.93 ng/mL (IQR: 1.68-2.53 ng/mL) in healthy term neonates and 8.5 ng/mL (IQR: 3.6-16.0 ng/mL) in preterm infants. Using ROC analysis, we calculated a Cyfra cutoff > 8.5 ng/mL to predict BPD/death with an AUC of 0.795 (P = 0.004), a sensitivity of 88.9%, and a specificity of 55%. Mortality was predicted with a cutoff > 17.4 ng/mL (AUC: 0.94; P = 0.001), a sensitivity of 100%, and a specificity of 84%. These findings suggest that Cyfra 21-1 concentration might be useful to predict poor outcome in premature infants.

The application of cytokeratin-18 as a biomarker for drug-induced liver injury

Drug-induced liver injury (DILI) is a frequent and dangerous adverse effect faced during preclinical and clinical drug therapy. DILI is a leading cause of candidate drug attrition, withdrawal and in clinic, is the primary cause of acute liver failure. Traditional diagnostic markers for DILI include alanine aminotransferase (ALT), aspartate aminotransferase (AST) and alkaline phosphatase (ALP). Yet, these routinely used diagnostic markers have several noteworthy limitations, restricting their sensitivity, specificity and accuracy in diagnosing DILI. Consequently, new biomarkers for DILI need to be identified.A potential biomarker for DILI is cytokeratin-18 (CK18), an intermediate filament protein highly abundant in hepatocytes and cholangiocytes. Extensively researched in a variety of clinical settings, both full length and cleaved forms of CK18 can diagnose early-stage DILI and provide insight into the mechanism of hepatocellular injury compared to traditionally used diagnostic markers. However, relatively little research has been conducted on CK18 in preclinical models of DILI. In particular, CK18 and its relationship with DILI is yet to be characterised in an in vivo rat model. Such characterization of CK18 and ccCK18 responses may enable their use as translational biomarkers for hepatotoxicity and facilitate management of clinical DILI risk in drug development. The aim of this review is to discuss the application of CK18 as a biomarker for DILI. Specifically, this review will highlight the properties of CK18, summarise clinical research that utilised CK18 to diagnose DILI and examine the current challenges preventing the characterisation of CK18 in an in vivo rat model of DILI.

Assembly and recognition of keratins: A structural perspective

Keratins are one of the major components of cytoskeletal network and assemble into fibrous structures named intermediate filaments (IFs), which are important for maintaining the mechanical properties of cells and tissues. Over the past decades, evidence has shown that the functions of keratins go beyond providing mechanical support for cells, they interact with multiple cellular components and are widely involved in the pathways of cell proliferation, differentiation, motility and death. However, the structural details of keratins and IFs are largely missing and many questions remain regarding the mechanisms of keratin assembly and recognition. Here we briefly review the current structural models and assembly of keratins as well as the interactions of keratins with the binding partners, which may provide a structural view for understanding the mechanisms of keratins in the biological activities and the related diseases.

One-Pot Process: Microwave-Assisted Keratin Extraction and Direct Electrospinning to Obtain Keratin-Based Bioplastic

Poultry feathers are among the most abundant and polluting keratin-rich waste biomasses. In this work, we developed a one-pot microwave-assisted process for eco-friendly keratin extraction from poultry feathers followed by a direct electrospinning (ES) of the raw extract, without further purification, to obtain keratin-based bioplastics. This microwave-assisted keratin extraction (MAE) was conducted in acetic acid 70% v/v. The effects of extraction time, solvent/feathers ratio, and heating mode (MAE vs. conventional heating) on the extraction yield were investigated. The highest keratin yield (26 ± 1% w/w with respect to initial feathers) was obtained after 5 h of MAE. Waste-derived keratin were blended with gelatin to fabricate keratin-based biodegradable and biocompatible bioplastics via ES, using 3-(Glycidyloxypropyl)trimethoxysilane (GPTMS) as a cross-linking agent. A full characterization of their thermal, mechanical, and barrier properties was performed by differential scanning calorimetry, thermogravimetric analysis, uniaxial tensile tests, and water permeability measurements. Their morphology and protein structure were investigated using scanning electron microscopy and attenuated total reflection-infrared spectroscopy. All these characterizations highlighted that the properties of the keratin-based bioplastics can be modulated by changing keratin and GPTMS concentrations. These bioplastics could be applied in areas such as bio-packaging and filtration/purification membranes.

Keratin 8 mutations in transgenic mice predispose to lung injury

Keratin 8 (K8) is the cytoskeletal intermediate filament protein of simple-type epithelia. Mutations in K8 predispose the affected individual and transgenic mouse to liver disease. However, the role of K8 in the lung has not been reported in mutant transgenic mouse models. Here, we investigated the susceptibility of two different transgenic mice expressing K8 Gly62-Cys (Gly62 replaced with Cys) or Ser74-Ala (Ser74 replaced with Ala) to lung injury. The mutant transgenic mice were highly susceptible to two independent acute and chronic lung injuries compared with control mice. Both K8 Gly62-Cys mice and K8 Ser74-Ala mice showed markedly increased mouse lethality (∼74% mutant mice versus ∼34% control mice) and more severe lung damage, with increased inflammation and apoptosis, under L-arginine-mediated acute lung injury. Moreover, the K8 Ser74-Ala mice had more severe lung damage, with extensive hemorrhage and prominent fibrosis, under bleomycin-induced chronic lung injury. Our study provides the first direct evidence that K8 mutations predispose to lung injury in transgenic mice.

A KRT71 Loss-of-Function Variant Results in Inner Root Sheath Dysplasia and Recessive Congenital Hypotrichosis of Hereford Cattle

Genodermatoses, such as heritable skin disorders, mostly represent Mendelian conditions. Congenital hypotrichosis (HY) characterize a condition of being born with less hair than normal. The purpose of this study was to characterize the clinicopathological phenotype of a breed-specific non-syndromic form of HY in Hereford cattle and to identify the causative genetic variant for this recessive disorder. Affected calves showed a very short, fine, wooly, kinky and curly coat over all parts of the body, with a major expression in the ears, the inner part of the limbs, and in the thoracic-abdominal region. Histopathology showed a severely altered morphology of the inner root sheath (IRS) of the hair follicle with abnormal Huxley and Henle’s layers and severely dysplastic hair shafts. A genome-wide association study revealed an association signal on chromosome 5. Homozygosity mapping in a subset of cases refined the HY locus to a 690 kb critical interval encompassing a cluster of type II keratin encoding genes. Protein-coding exons of six positional candidate genes with known hair or hair follicle function were re-sequenced. This revealed a protein-changing variant in the KRT71 gene that encodes a type II keratin specifically expressed in the IRS of the hair follicle (c.281delTGTGCCCA; p.Met94AsnfsX14). Besides obvious phenocopies, a perfect concordance between the presence of this most likely pathogenic loss-of-function variant located in the head domain of KRT71 and the HY phenotype was found. This recessive KRT71-related form of hypotrichosis provides a novel large animal model for similar human conditions. The results have been incorporated in the Online Mendelian Inheritance in Animals (OMIA) database (OMIA 002114-9913).

Genetic insight into sick sinus syndrome

Aims

The aim of this study was to use human genetics to investigate the pathogenesis of sick sinus syndrome (SSS) and the role of risk factors in its development.

Methods and results

We performed a genome-wide association study of 6469 SSS cases and 1 000 187 controls from deCODE genetics, the Copenhagen Hospital Biobank, UK Biobank, and the HUNT study. Variants at six loci associated with SSS, a reported missense variant in MYH6, known atrial fibrillation (AF)/electrocardiogram variants at PITX2, ZFHX3, TTN/CCDC141, and SCN10A and a low-frequency (MAF = 1.1–1.8%) missense variant, p.Gly62Cys in KRT8 encoding the intermediate filament protein keratin 8. A full genotypic model best described the p.Gly62Cys association (P = 1.6 × 10⁻²⁰), with an odds ratio (OR) of 1.44 for heterozygotes and a disproportionally large OR of 13.99 for homozygotes. All the SSS variants increased the risk of pacemaker implantation. Their association with AF varied and p.Gly62Cys was the only variant not associating with any other arrhythmia or cardiovascular disease. We tested 17 exposure phenotypes in polygenic score (PGS) and Mendelian randomization analyses. Only two associated with the risk of SSS in Mendelian randomization, AF, and lower heart rate, suggesting causality. Powerful PGS analyses provided convincing evidence against causal associations for body mass index, cholesterol, triglycerides, and type 2 diabetes (P > 0.05).

Conclusion

We report the associations of variants at six loci with SSS, including a missense variant in KRT8 that confers high risk in homozygotes and points to a mechanism specific to SSS development. Mendelian randomization supports a causal role for AF in the development of SSS.

Comparative Genomics Analysis of Keratin-Degrading Chryseobacterium Species Reveals Their Keratinolytic Potential for Secondary Metabolite Production

A promising keratin-degrading strain from the genus Chryseobacterium (Chryseobacterium sp. KMC2) was investigated using comparative genomic tools against three publicly available reference genomes to reveal the keratinolytic potential for biosynthesis of valuable secondary metabolites. Genomic features and metabolic potential of four species were compared, showing genomic differences but similar functional categories. Eleven different secondary metabolite gene clusters of interest were mined from the four genomes successfully, including five common ones shared across all genomes. Among the common metabolites, we identified gene clusters involved in biosynthesis of flexirubin-type pigment, microviridin, and siderophore, showing remarkable conservation across the four genomes. Unique secondary metabolite gene clusters were also discovered, for example, ladderane from Chryseobacterium sp. KMC2. Additionally, this study provides a more comprehensive understanding of the potential metabolic pathways of keratin utilization in Chryseobacterium sp. KMC2, with the involvement of amino acid metabolism, TCA cycle, glycolysis/gluconeogenesis, propanoate metabolism, and sulfate reduction. This work uncovers the biosynthesis of secondary metabolite gene clusters from four keratinolytic Chryseobacterium species and shades lights on the keratinolytic potential of Chryseobacterium sp. KMC2 from a genome-mining perspective, can provide alternatives to valorize keratinous materials into high-value bioactive natural products.

Generation of a tissue-specific transgenic model for K8 phosphomutants: A tool to investigate the role of K8 phosphorylation during skin carcinogenesis in vivo

Keratin 8/18, the predominant keratin pair of simple epithelia, is known to be aberrantly expressed in several squamous cell carcinomas (SCCs), where its expression is often correlated with increased invasion, neoplastic progression, and poor prognosis. The majority of keratin 8/18 structural and regulatory functions are governed by posttranslational modifications, particularly phosphorylation. Apart from filament reorganization, cellular processes including cell cycle, cell growth, cellular stress, and apoptosis are known to be orchestrated by K8 phosphorylation at specific residues in the head and tail domains. Even though deregulation of K8 phosphorylation at two significant sites (Serine⁷³ /Serine⁴³¹ ) has been implicated in neoplastic progression of SCCs by various in vitro studies, including ours, it is reported to be highly context-dependent. Therefore, to delineate the precise role of Kereatin 8 phosphorylation in cancer initiation and progression, we have developed the tissue-specific transgenic mouse model expressing Keratin 8 wild type and phosphodead mutants under Keratin 14 promoter. Subjecting these mice to 7,12-dimethylbenz(a)anthracene/12-O-tetradecanoylphorbol-13-acetate-mediated skin carcinogenesis revealed that Keratin 8 phosphorylation may lead to an early onset of tumors compared to Keratin 8 wild-type expressing mice. Conclusively, the transgenic mouse model developed in the present study ascertained a positive impact of Keratin 8 phosphorylation on the neoplastic transformation of skin-squamous cells.

Id4 Suppresses the Growth and Invasion of Colorectal Cancer HCT116 Cells through CK18-Related Inhibition of AKT and EMT Signaling

Id4 is one of the inhibitors of DNA-binding proteins (Id) and involved in the pathogenesis of numerous cancers. The specific mechanism underlying the Id4-mediated regulation of proliferation, invasion, and metastasis of colorectal cancer (CRC) cells is still largely unclear. In the present study, results showed CRC cells had a lower baseline Id4 expression than normal intestinal epithelial NCM460 cells. In order to explore the role of Id4 in the tumorigenicity, CRC HCT116 cells with stable Id4 expression were used, and results showed Id4 overexpression arrested the cell cycle at the G0/G1 phase, inhibited the cell proliferation and the colony formation, as well as suppressed the migration and invasion. In the in vivo model, Id4 overexpression inhibited the tumor growth and metastasis in the nude mice. Furthermore, Id4 overexpression upregulated the expression of proteins associated with cell proliferation, inhibited the PI3K/AKT pathway, and suppressed epithelial-mesenchymal transition (EMT) of HCT116 cells. Moreover, Id4 significantly decreased cytokeratin 18 (CK18) expression, but CK18 overexpression in Id4 expressing HCT116-Id4 cells rescued the activation of AKT, p-AKT, MMP2, MMP7, and E-cadherin. Collectively, our study indicated Id4 may inhibit CRC growth and metastasis through inhibiting the PI3K/AKT pathway in a CK18-dependent manner and suppressing EMT. Id4 may become a target for the treatment of CRC.

Smart and Sustainable Hair Products Based on Chitin-Derived Compounds

According to previous research studies, consumers worldwide are searching for new natural-oriented hair products that are both skin and environmentally friendly. Worldwide waste and air pollution, with the consequent environmental disasters, represent the greatest risk to human health and economy, further increased by the COVID-19 pandemic. Among others, non-biodegradable molecules are present in hair products (fossil-based additives, surfactants, etc.) and macromolecules (plastics). Plastics waste is considered the most serious problem, representing a forecast amount of 460 million tons per year by 2030, 12% of which is reused or recycled. Most plastics consumed, therefore, go to landfills and incineration, also if their recycling is considered an important driver of industrial profitability. Thus, the use of biopolymers represents an interesting alternative to produce biodegradable goods and tissues. After an introduction to the worldwide waste problem and the hair structure, the present review proposes the possibility to make biodegradable tissues that, realized by chitin nanofibrils and nano-lignin as natural polymers, may be used to produce an innovative and smart cosmetic hairline. Chitin-derived compounds are considered interesting polymers to produce non-woven tissues able to repair the hair damages provoked by the aggressiveness of both the environment and some aggressive cosmetic treatments, such as setting, bleaching, permanent waving, and oxidative coloring. The possible activity, that positively charged polymers such as chitin could have, has been speculated, interfering with the constitution and organization of the hair fibrils’ structure, which is negatively charged. The possibility of selecting biopolymers for their packaging is also discussed. Moreover, the use of these biopolymers, obtained from forestry-agro-food waste, may be of help to safeguard the further consumption of natural raw materials, necessary for future generations, also maintaining the earth’s biodiversity.

Signs of carcinogenicity induced by parathion, malathion, and estrogen in human breast epithelial cells (Review)

Cancer development is a multistep process that may be induced by a variety of compounds. Environmental substances, such as pesticides, have been associated with different human diseases. Organophosphorus pesticides (OPs) are among the most commonly used insecticides. Despite the fact that organophosphorus has been associated with an increased risk of cancer, particularly hormone-mediated cancer, few prospective studies have examined the use of individual insecticides. Reported results have demonstrated that OPs and estrogen induce a cascade of events indicative of the transformation of human breast epithelial cells. In vitro studies analyzing an immortalized non-tumorigenic human breast epithelial cell line may provide us with an approach to analyzing cell transformation under the effects of OPs in the presence of estrogen. The results suggested hormone-mediated effects of these insecticides on the risk of cancer among women. It can be concluded that, through experimental models, the initiation of cancer can be studied by analyzing the steps that transform normal breast cells to malignant ones through certain substances, such as pesticides and estrogen. Such substances cause genomic instability, and therefore tumor formation in the animal, and signs of carcinogenesis in vitro. Cancer initiation has been associated with an increase in genomic instability, indicated by the inactivation of tumor-suppressor genes and activation of oncogenes in the presence of malathion, parathion, and estrogen. In the present study, a comprehensive summary of the impact of OPs in human and rat breast cancer, specifically their effects on the cell cycle, signaling pathways linked to epidermal growth factor, drug metabolism, and genomic instability in an MCF-10F estrogen receptor-negative breast cell line is provided.

Host-cell dependent role of phosphorylated keratin 8 during influenza A/NWS/33 virus (H1N1) infection in mammalian cells

In this study, we investigated the involvement of keratin 8 during human influenza A/NWS/33 virus (H1N1) infection in semi-permissive rhesus monkey-kidney (LLC-MK2) and permissive human type II alveolar epithelial (A549) cells. In A549 cells, keratin 8 showed major expression and phosphorylation levels. Influenza A/NWS/33 virus was able to subvert keratin 8 structural organization at late stages of infection in both cell models, promoting keratin 8 phosphorylation in A549 cells at early phases of infection. Accordingly, partial colocalizations of the viral nucleoprotein with keratin 8 and its phosphorylated form were assessed by confocal microscopy at early stages of infection in A549 cells. The employment of chemical activators of phosphorylation resulted in structural changes as well as increased phosphorylation of keratin 8 in both cell models, favoring the influenza A/NWS/33 virus's replicative efficiency in A549 but not in LLC-MK2 cells. In A549 and human larynx epidermoid carcinoma (HEp-2) cells inoculated with respiratory secretions from pediatric patients positive for, respectively, influenza A virus or respiratory syncytial virus, the keratin 8 phosphorylation level had increased only in the case of influenza A virus infection. The results obtained suggest that in A549 cells the influenza virus is able to induce keratin 8 phosphorylation thereby enhancing its replicative efficiency.

Structure of Keratin

Keratins, as a group of insoluble and filament-forming proteins, mainly exist in certain epithelial cells of vertebrates. Keratinous materials are made up of cells filled with keratins, while they are the toughest biological materials such as the human hair, wool and horns of mammals and feathers, claws, and beaks of birds and reptiles which usually used for protection, defense, hunting and as armor. They generally exhibit a sophisticated hierarchical structure ranging from nanoscale to centimeter-scale: polypeptide chain structures, intermediated filaments/matrix structures, and lamellar structures. Therefore, more and more attention has been paid to the investigation of the relationship between structure and properties of keratins, and a series of biomimetic materials based on keratin came into being. In this chapter, we mainly introduce the hierarchical structure, the secondary structure, and the molecular structure of keratins, including α- and β-keratin, to promote the development of novel keratin-based biomimetic materials designs.

Current Biomarkers for Precision Medicine in Breast Cancer

Breast cancer has become the prototypical solid tumor where targets have been identified within the tumor allowing for personalized approach for systemic therapy. Biomarkers are beginning to play an important role in preparing the way for precision treatment. Mandatory biomarkers for every newly diagnosed case of breast cancer are estrogen receptors and progesterone receptors in selecting patients for endocrine treatment and HER2 for identifying patients likely to benefit from antiHER2 therapy. Although methodological problems exist in the determination of Ki67, because of its clearly established clinical value, wide availability, and low costs relative to the available multianalyte signatures, Ki67 may be used for determining prognosis, especially if values are low or high. Also, the androgen receptor (AR) pathway is emerging as a potential therapeutic target in breast cancer. AR-targeted treatments for breast cancer are in development and have shown promising preliminary results. While, most established biomarkers in breast cancer require tissue samples, serum tumor markers are easily accessible and require a less invasive procedure. Among them, tissue polypeptide-specific antigen (TPS), a specific epitope structure of a peptide in serum associated with human cytokeratin 18, is linked to the proliferative activity of tumors. TPS may be a valuable and independent prognostic biomarker for breast cancer.In order to accelerate progress towards precision treatment for women with breast cancer, we need additional predictive biomarker, especially for enhancing the positive predictive value for endocrine and antiHER2 therapies, as well as biomarkers for predicting response to specific forms of chemotherapy.

Seasonal morphology and immunoreactivity of cytokeratin and atrial natriuretic peptide in dromedary camel poll glands

Poll glands are characteristic feature of dromedary camels; although they yield a yellowish offensive secretion, especially during rutting (breeding) season, their function is not yet exactly specified. The present study shows the seasonal morphology and immunoreactivity of cytokeratin (CK) and atrial natriuretic peptide (ANP) in the camel poll gland; the result could clearly specify the role of the gland in camel reproduction. Poll glands are compound tubulo-alveolar in structure. During rutting season, the secretory units showed wide lumina and simple squamous epithelium surrounded by myoepithelial cells; the lumina became narrower and the epithelium changed to simple cuboidal during non-rutting season. Many glandular lobules showed abundant interlobular connective tissue with fewer and smaller secretory units during non-rutting season compared to rutting season. Positive CK and ANP immunoreactivity was detected in the cytoplasm of epithelial cells of secretory units and ducts together with the myoepithelial cells and blood vessels. Although CK immunoreactivity was more intense during rutting season in comparison to non-rutting season, there was no seasonal variation in ANP immunoreactivity. During both seasons, while the glandular capsule, connective tissue septa, interstitium showed negative CK immunoreactions, they reacted moderately to ANP. In conclusion, the poll gland undergoes annual structural and functional changes which are suggested to correlate with the male seasonal sexual behaviour. Further, the biological role of CK and ANP proteins together with their immunohistochemical expression in the camel poll gland suggests a stimulatory effect in the glandular secretory cells, and hence, they might modify camel sexual activity.

Keratin intermediate filaments in the colon: guardians of epithelial homeostasis

Keratin intermediate filament proteins are major cytoskeletal components of the mammalian simple layered columnar epithelium in the gastrointestinal tract. Human colon crypt epithelial cells express keratins 18, 19 and 20 as the major type I keratins, and keratin 8 as the type II keratin. Keratin expression patterns vary between species, and mouse colonocytes express keratin 7 as a second type II keratin. Colonic keratin patterns change during cell differentiation, such that K20 increases in the more differentiated crypt cells closer to the central lumen. Keratins provide a structural and mechanical scaffold to support cellular stability, integrity and stress protection in this rapidly regenerating tissue. They participate in central colonocyte processes including barrier function, ion transport, differentiation, proliferation and inflammatory signaling. The cell-specific keratin compositions in different epithelial tissues has allowed for the utilization of keratin-based diagnostic methods. Since the keratin expression pattern in tumors often resembles that in the primary tissue, it can be used to recognize metastases of colonic origin. This review focuses on recent findings on the biological functions of mammalian colon epithelial keratins obtained from pivotal in vivo models. We also discuss the diagnostic value of keratins in chronic colonic disease and known keratin alterations in colon pathologies. This review describes the biochemical properties of keratins and their molecular actions in colonic epithelial cells and highlights diagnostic data in colorectal cancer and inflammatory bowel disease patients, which may facilitate the recognition of disease subtypes and the establishment of personal therapies in the future.

Cellular State Transformations Using Deep Learning for Precision Medicine Applications

We introduce the Transcriptome State Perturbation Generator (TSPG) as a novel deep-learning method to identify changes in genomic expression that occur between tissue states using generative adversarial networks. TSPG learns the transcriptome perturbations from RNA-sequencing data required to shift from a source to a target class. We apply TSPG as an effective method of detecting biologically relevant alternate expression patterns between normal and tumor human tissue samples. We demonstrate that the application of TSPG to expression data obtained from a biopsy sample of a patient's kidney cancer can identify patient-specific differentially expressed genes between their individual tumor sample and a target class of healthy kidney gene expression. By utilizing TSPG in a precision medicine application in which the patient sample is not replicated (i.e., n=1), we present a novel technique of determining significant transcriptional aberrations that can be used to help identify potential targeted therapies.

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We present the Transcriptome State Perturbation Generator (TSPG) application

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We apply TSPG to The Cancer Genome Atlas data to perturb gene expression states

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TSPG was used to learn patient-specific (n = 1) gene expression tumor alterations

Deep learning has shown tremendous success in image and natural language processing; however, attempts to apply the tools of machine learning to better understanding biological systems are still in the stage of early adoption. We propose a novel deep-learning tool that can be used to process samples of RNA-sequencing data. By applying the Transcriptome State Perturbation Generator to human samples, we show that deep learning derives insight into the gene expression shifts required for transition between two biological conditions (e.g., normal versus tumor). RNA-sequencing data derived from a single patient's tumor were analyzed using this tool to determine gene expression aberrations specific to that patient's tumor. As medicine shifts from cohort-based population studies to individual-based precision treatments, our example demonstrates that deep learning is a powerful ally in the quest to understand how complex biological systems have shifted for a single patient.

A Polymorphism at the microRNA Binding Site in the 3' Untranslated Region of KRT81 Is Associated with Breast Cancer

Single nucleotide polymorphisms in miRNA binding sites (miR-SNPs) are associated with cancer risk. We assessed the relationship between five miR-SNPs in the 3' untranslated region (3'-UTR) of RYR3 (rs1044129), KIAA0423 (rs1053667), C14orf101 (rs4901706), GOLGA7 (rs11337), and KRT81 (rs3660) and the risk of breast cancer (BC). The CC genotype of rs3660 located in the 3'-UTR of KRT81 was identified for its association with lower BC risk (odds ratio, 0.093; 95% confidence interval, 0.045-0.193; p = 0.000). Immunnochemical analysis and Renilla luciferase reporter assays indicated that the CC genotype of KRT81 was associated with lower expression of KRT81 (p < 0.05). The subsequently functional analysis showed that knockdown the KRT81 could inhibit proliferation and promote apoptosis of the MDA-MB-231 BC cells (p < 0.05) with monocyte chemotactic protein-1 (MCP-1) deregulation. Meanwhile, KRT81 overexpression could promote the proliferation and inhibit the apoptosis of MCF-7 BC cells (p < 0.05). Our data demonstrated that the KRT81 expressional change modulated by rs3660 miR-SNP could modify the carcinogenesis of BC, thereby KRT81 would be a new target for BC treatment.

Tumor microtubes connect pancreatic cancer cells in an Arp2/3 complex-dependent manner

Actin-based tubular connections between cells have been observed in many cell types. Termed "tunneling nanotubes (TNTs)," "membrane nanotubes," "tumor microtubes (TMTs)," or "cytonemes," these protrusions interconnect cells in dynamic networks. Structural features in these protrusions vary between cellular systems, including tubule diameter and the presence of microtubules. We find tubular protrusions, which we classify as TMTs, in a pancreatic cancer cell line, Dartmouth-Hitchcock Pancreatic Cancer (DHPC)-018. TMTs are present in DHPC-018-derived tumors in mice, as well as in a mouse model of pancreatic cancer and a subset of primary human tumors. DHPC-018 TMTs have heterogeneous diameter (0.39-5.85 µm, median 1.92 µm) and contain actin filaments, microtubules, and cytokeratin 19-based intermediate filaments. TMTs do not allow intercellular transfer of cytoplasmic GFP. Actin filaments are cortical within the protrusion, as opposed to TNTs, in which filaments run down the center. TMTs are dynamic in length, but are long lived (median >60 min). Inhibition of actin polymerization, but not microtubules, results in TMT loss. Extracellular calcium is necessary for TMT maintenance. A second class of tubular protrusion, which we term cell-substrate protrusion, has similar width range and cytoskeletal features but makes contact with the substratum as opposed to another cell. Similar to previous work on TNTs, we find two assembly mechanisms for TMTs, which we term "pull-away" and "search-and-capture." Inhibition of Arp2/3 complex inhibits TMT assembly by both mechanisms. This work demonstrates that the actin architecture of TMTs in pancreatic cancer cells is fundamentally different from that of TNTs and demonstrates the role of Arp2/3 complex in TMT assembly.

Biotransformation of keratin waste to amino acids and active peptides based on cell-free catalysis

BACKGROUND

Keratin is the primary constituent of the vertebrate epidermis and epidermal appendages, as well as the main waste product generated during poultry processing from feathers, hair, scales, nails, etc. Keratin is generally hard, stubborn and difficult to hydrolyze; however, it is also inexpensive and contains more than 85% protein. Currently, tens of millions of tons of keratin waste are produced each year worldwide; however, no effective methods for the recovery of keratin waste have been reported thus far, making such research urgent. Keratinase has been reported to be useful for keratin waste recovery; however, nearly all keratinases are unable to hydrolyze keratin after they are detached from living cell systems. This may be due to low keratinase activity and lack of synergistic factors.

RESULTS

Herein, the keratinase gene from Bacillus licheniformis BBE11-1 was successfully expressed in Bacillus subtilis WB600, allowing for improved activity of the recombinant keratinase KerZ1 to 45.14 KU/mL via promoter substitution and screening of the ribosome-binding sites. Further, real-time control of temperature, pH, dissolved oxygen, and feed strategy allowed the activity of KerZ1 to reach 426.60 KU/mL in a 15-L fermenter, accounting for a 3552-fold increase compared to the wild-type keratinase (120.1 U/mL). Most importantly, we proposed a method based on the synergistic action of keratinase KerZ1 and sodium sulfite, to hydrolyze feathers into amino acids. In specific, 100 g/L of feather waste can be successfully converted into 56.6% amino acids within 12 h, while supporting the production of dozens of bioactive peptides.

CONCLUSIONS

The activity of recombinant keratinase can be greatly enhanced via transcription and translational regulation in Bacillus subtilis. The synergistic action of keratinase and sulfite can rapidly degrade feather waste and produce amino acids and polypeptides.

Neonatal lactocrine deficiency affects the adult porcine endometrial transcriptome at pregnancy day 13

Reproductive performance of female pigs that do not receive sufficient colostrum from birth is permanently impaired. Whether lactocrine deficiency, reflected by low serum immunoglobulin immunocrit (iCrit), affects patterns of endometrial gene expression during the periattachment period of early pregnancy is unknown. Here, objectives were to determine effects of low iCrit at birth on the adult endometrial transcriptome on pregnancy day (PxD) 13. On the first day of postnatal life, gilts were assigned to high or low iCrit groups. Adult high (n = 8) and low (n = 7) iCrit gilts were bred (PxD 0), and humanely slaughtered on PxD 13 when tissues and fluids were collected. The endometrial transcriptome was defined for each group using mRNAseq and microRNAseq. Reads were mapped to the Sus scrofa 11.1 genome build. Mature microRNAs were annotated using miRBase 21. Differential expression was defined based on fold change (≥ ±1.5). Lactocrine deficiency did not affect corpora lutea number, uterine horn length, uterine wet weight, conceptus recovery, or uterine luminal fluid estrogen content on PxD 13. However, mRNAseq revealed 1157 differentially expressed endometrial mRNAs in high versus low iCrit gilts. Differentially expressed genes had functions related to solute transport, endometrial receptivity, and immune response. Six differentially expressed endometrial microRNAs included five predicted to target 62 differentially expressed mRNAs, affecting similar biological processes. Thus, lactocrine deficiency on the first day of postnatal life can alter uterine developmental trajectory with lasting effects on endometrial responses to pregnancy as reflected at the level of the transcriptome on PxD 13.

KRT8 phosphorylation regulates the epithelial-mesenchymal transition in retinal pigment epithelial cells through autophagy modulation

Proliferative vitreoretinopathy (PVR) is a severe ocular disease which results in complex retinal detachment and irreversible vision loss. The epithelial-mesenchymal transition (EMT) of retinal pigment epithelial (RPE) cells is considered to be critical in the pathogenesis of PVR. In this study, we focused on the potential impact of keratin 8 (KRT8) phosphorylation and autophagy on TGF-β2-induced EMT of RPE cells and explored the relationship between them. Using immunofluorescence and Western blot analysis, the co-localization of KRT8 and autophagy marker, as well as the abundance of phosphorylated KRT8 (p-KRT8) expression, was observed within subretinal and epiretinal membranes from PVR patients. Moreover, during TGF-β2-induced EMT process, we found that p-KRT8 was enhanced in RPE cells, which accompanied by an increase in autophagic flux. Inhibition of autophagy with pharmacological inhibitors or specific siRNAs was associated with a reduction in cell migration and the synthesis of several EMT markers. In the meantime, we demonstrated that p-KRT8 was correlated with the autophagy progression during the EMT of RPE cells. Knockdown the expression or mutagenesis of the critical phosphorylated site of KRT8 would induce autophagy impairment, through affecting the fusion of autophagosomes and lysosomes. Therefore, this study may provide a new insight into the pathogenesis of PVR and suggests the potential therapeutic value of p-KRT8 in the prevention and treatment of PVR.

Cytokeratin 5 alters β-catenin dynamics in breast cancer cells

Estrogen receptor (ER) positive breast cancers often contain subpopulations of cells that express the intermediate filament protein cytokeratin 5 (CK5). CK5+ cells are enriched in cancer stem cell (CSC) properties, can be induced by progestins, and predict poor prognosis in ER+ breast cancer. We established through CK5 knockout and overexpression in ER+ breast cancer cell lines that CK5 is important for tumorsphere formation, prompting us to speculate that CK5 has regulatory activity in CSCs. To interrogate CK5 interacting proteins that may be functionally cooperative, we performed immunoprecipitation-mass spectrometry for CK5 in ER+ breast cancer cells. Focusing on proteins with signaling activity, we identified β-catenin, a key transcription factor of the Wnt signaling pathway and cell adhesion molecule, as a CK5 interactor, which we confirmed by co-immunoprecipitation in several breast cancer models. We interrogated the dual functions of β-catenin in relation to CK5. Knockout or knockdown of CK5 ablated β-catenin transcriptional activity in response to progestins and Wnt stimuli. Conversely, CK5 induced by progestins or overexpression was sufficient to promote loss of β-catenin at the cell membrane and total E-cadherin loss. A breast cancer patient-derived xenograft showed similar loss of membrane β-catenin and E-cadherin in CK5+ but not intratumoral CK5− cells and single cell RNA sequencing found the top enriched pathways in the CK5+ cell cluster were cell junction remodeling and signaling. This report highlights that CK5 actively remodels cell morphology and that blockade of CK5-β-catenin interaction may reverse the detrimental properties of CK5+ breast cancer cells.

Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures

The capacity of microbes to degrade recalcitrant materials has been extensively explored for environmental remediation and industrial production. Significant achievements have been made with single strains, but focus is now going toward the use of microbial consortia owning to their functional stability and efficiency. However, assembly of simplified microbial consortia (SMC) from complex environmental communities is still far from trivial due to large diversity and the effect of biotic interactions. Here we propose a strategy, based on enrichment and dilution-to-extinction cultures, to construct SMC with reduced diversity for degradation of keratinous materials. Serial dilutions were performed on a keratinolytic microbial consortium pre-enriched from a soil sample, monitoring the dilution effect on community growth and enzymatic activities. An appropriate dilution regime (10-9) was selected to construct a SMC library from the enriched microbial consortium. Further sequencing analysis and keratinolytic activity assays demonstrated that obtained SMC displayed actual reduced microbial diversity, together with various taxonomic composition, and biodegradation capabilities. More importantly, several SMC possessed equivalent levels of keratinolytic efficiency compared to the initial consortium, showing that simplification can be achieved without loss of function and efficiency. This methodology is also applicable to other types of recalcitrant material degradation involving microbial consortia, thus considerably broadening its application scope.

Keratin 18 is an integral part of the intermediate filament network in murine skeletal muscle

Intermediate filaments (IFs) contribute to force transmission, cellular integrity, and signaling in skeletal muscle. We previously identified keratin 19 (Krt19) as a muscle IF protein. We now report the presence of a second type I muscle keratin, Krt18. Krt18 mRNA levels are about half those for Krt19 and only 1:1,000th those for desmin; the protein was nevertheless detectable in immunoblots. Muscle function, measured by maximal isometric force in vivo, was moderately compromised in Krt18-knockout (Krt18-KO) or dominant-negative mutant mice (Krt18 DN), but structure was unaltered. Exogenous Krt18, introduced by electroporation, was localized in a reticulum around the contractile apparatus in wild-type muscle and to a lesser extent in muscle lacking Krt19 or desmin or both proteins. Exogenous Krt19, which was either reticular or aggregated in controls, became reticular more frequently in Krt19-null than in Krt18-null, desmin-null, or double-null muscles. Desmin was assembled into the reticulum normally in all genotypes. Notably, all three IF proteins appeared in overlapping reticular structures. We assessed the effect of Krt18 on susceptibility to injury in vivo by electroporating siRNA into tibialis anterior (TA) muscles of control and Krt19-KO mice and testing 2 wk later. Results showed a 33% strength deficit (reduction in maximal torque after injury) compared with siRNA-treated controls. Conversely, electroporation of siRNA to Krt19 into Krt18-null TA yielded a strength deficit of 18% after injury compared with controls. Our results suggest that Krt18 plays a complementary role to Krt19 in skeletal muscle in both assembling keratin-based filaments and transducing contractile force.

Human Hair: Scaffold Materials for Regenerative Medicine

This chapter reviews the studies of keratin-based biomaterials in the past and discusses the advancement of it in recent years. Keratin, as a protein-based biopolymer, possesses excellent biocompatibility and biodegradability. In addition, keratin has abundant disulfide bonds, which result in its unique and tough structure. However, the property also results in dissolubility, which causes difficult process ability. Over the past years, much research utilizes different methodologies to extract keratins. Different kinds of extraction methods affect the characteristics of keratins and give a wide variety of application forms. The features of different methods are discussed and summarized in the following.

Keratin Associations with Synthetic, Biosynthetic and Natural Polymers: An Extensive Review

Among the biopolymers from animal sources, keratin is one the most abundant, with a major contribution from side stream products from cattle, ovine and poultry industry, offering many opportunities to produce cost-effective and sustainable advanced materials. Although many reviews have discussed the application of keratin in polymer-based biomaterials, little attention has been paid to its potential in association with other polymer matrices. Thus, herein, we present an extensive literature review summarizing keratin's compatibility with other synthetic, biosynthetic and natural polymers, and its effect on the materials' final properties in a myriad of applications. First, we revise the historical context of keratin use, describe its structure, chemical toolset and methods of extraction, overview and differentiate keratins obtained from different sources, highlight the main areas where keratin associations have been applied, and describe the possibilities offered by its chemical toolset. Finally, we contextualize keratin's potential for addressing current issues in materials sciences, focusing on the effect of keratin when associated to other polymers' matrices from biomedical to engineering applications, and beyond.

Effect of Microwave or Ultrasound Irradiation in the Extraction from Feather Keratin

The extraction of feather keratin biopolymer structures was studied using chicken feathers as a biomass material by the cold acid hydrolysis reaction; the recrystallization stage was performed using microwave or ultrasound irradiation, and conduction heating was used as a reference. The microwave or ultrasound irradiation modified the texture and the morphology of the obtained materials, and they can be controlled depending on the time exposure and the power of the irradiation; this has high relevance in the design of new materials to obtain nanostructures depending on the specific application. It was found that the microwave irradiation promotes the growth of the beta sheet over the alpha helix, and in the case of ultrasound irradiation, the growth is reversed being similar to the conduction heating; the porosity properties remain invariant, modifying the particle sizes depending on the exposure time and power of irradiation. Therefore, the feather keratin biopolymer, when modified by microwaves and ultrasound in the recrystallization stage, is a fibrous protein that has good mechanical, structural, morphological, and thermal properties with potential applications such as development of biocompatible materials with cellular interaction and in catalysis as catalytic and enzymatic support to mention just a few.

The Equine Hoof: Laminitis, Progenitor (Stem) Cells, and Therapy Development

The equine hoof capsule, composed of modified epidermis and dermis, is vital for protecting the third phalanx from forces of locomotion. There are descriptions of laminitis, defined as inflammation of sensitive hoof tissues but recognized as pathologic changes with or without inflammatory mediators, in the earliest records of domesticated horses. Laminitis can range from mild to serious, and signs can be acute, chronic, or transition from acute, severe inflammation to permanently abnormal tissue. Damage within the intricate dermal and epidermal connections of the primary and secondary lamellae is often associated with lifelong changes in hoof growth, repair, and conformation. Decades of research contribute to contemporary standards of care that include systemic and local therapies as well as mechanical hoof support. Despite this, consistent mechanisms to restore healthy tissue formation following a laminitic insult are lacking. Endogenous and exogenous progenitor cell contributions to healthy tissue formation is established for most tissues. There is comparably little information about equine hoof progenitor cells. Equine hoof anatomy, laminitis, and progenitor cells are covered in this review. The potential of progenitor cells to advance in vitro equine hoof tissue models and translate to clinical therapies may significantly improve prevention and treatment of a devastating condition that has afflicted equine companions throughout history.

Biomarkers in Head and Neck Cancer an Update

The study is aimed at establishing the purpose of tumour markers, their application, classification, diagnostic and therapeutic roles in the management of head and neck cancer. A literature review using Medline, Scopus, Google Scholar, the Cochrane Database of Systematic Reviews and the Cochrane central register of controlled trials for articles published between 1993 and 2016 on tumour markers and their role in head and neck cancer was performed. A broader search of prognostic markers in head and neck cancer was also carried out to avoid missing other pertinent markers. Natural history, tumour biology, stage and prognostic factors influence the outcome of management in patients with Head and Neck Squamous cell carcinoma (HNSCC). Evaluation of the cellular lineage and histogenic origin of diverse neoplasms can be done using tumour biomarkers. Identifying predictive tumour markers can lead to improvement in preventive management of HNSCC. There has been remarkable advancement in molecular technology with gene expression and proteomic profiling. Integration of specific tumour markers into routine clinical practice requires substantiation through well designed clinical trials. The investigation of tumour markers is imperative as they influence the prognosis of HNSCC and provide the potential to improve outcomes of treatment through targeted therapy. We have outlined recent tumour biomarkers in this review which have significant role in diagnosis, screening and prognostication in HNSCC. Recent advancement in clinical applications, therapeutic strategies of tumour markers has been highlighted.

Keratins regulate Hsp70-mediated nuclear localization of p38 mitogen-activated protein kinase

Intermediate filament protein keratin 8 (K8) binds to heat shock protein 70 (Hsp70) and p38 MAPK, and is phosphorylated at Ser74 by p38α (MAPK14, hereafter p38). However, a p38 binding site on K8 and the molecular mechanism of K8-p38 interaction related to Hsp70 are unknown. Here, we identify a p38 docking site on K8 (Arg148/149 and Leu159/161) that is highly conserved in other intermediate filaments. A docking-deficient K8 mutation caused increased p38-Hsp70 interaction and enhanced p38 nuclear localization, indicating that the p38 dissociated from mutant K8 makes a complex with Hsp70, which is known as a potential chaperone for p38 nuclear translocation. Comparison of p38 MAPK binding with keratin variants associated with liver disease showed that the K18 I150V variant dramatically reduced binding with p38, which is similar to the effect of the p38 docking-deficient mutation on K8. Because the p38 docking site on K8 (Arg148/149 and Leu159/161) and the K18 Ile150 residue are closely localized in the parallel K8/K18 heterodimer, the K18 I150V mutation might interfere with K8-p38 interaction. These findings show that keratins, functioning as cytoplasmic anchors for p38, modulate p38 nuclear localization and thereby might affect a number of p38-mediated signal transduction pathways.

Keratin 14 is a novel interaction partner of keratinocyte differentiation regulator: receptor-interacting protein kinase 4

The epidermis, the outer layer of the skin, is formed by stratified keratinocyte layers. The self-renewal of the epidermis is provided by sustained proliferation and differentiation of the keratinocyte stem cells localized to the basal layer of the epidermis. Receptor-interacting protein kinase 4 (RIPK4) is an important regulator of keratinocyte differentiation, mutations of which are associated with congenital ectodermal malformations. In an attempt to identify the molecular basis of RIPK4’s function, we applied yeast two-hybrid screen (Y2H) and found basal layer-specific keratin filament component keratin 14 (KRT14) as a novel RIPK4-interacting partner. During keratinocyte differentiation, layer-specific keratin composition is tightly regulated. Likewise, the basal layer specific KRT14/keratin 5 (KRT5) heterodimers are replaced by keratin 1 (KRT1)/keratin 10 (KRT10) in suprabasal layers. The regulation of keratin turnover is under the control of signaling associated with posttranslational modifications in which phosphorylation plays a major role. In this study, we verified the KRT14-RIPK4 interaction, which was identified with Y2H, in mammalian cells and showed that the interaction was direct by using proteins expressed in bacteria. According to our results, the N-terminal kinase domain of RIPK4 is responsible for KRT14-RIPK4 interaction; however, the RIPK4 kinase activity is dispensable for the interaction. In accordance with their interaction, RIPK4 and KRT14 colocalize within the cells, particularly at keratin filaments associated with perinuclear ring-like structures. Moreover, RIPK4 did not show any effect on KRT14/KRT5 heterodimer formation. Our results suggest that RIPK4 may regulate the keratin turnover required for keratinocyte differentiation through interacting with KRT14.

Cdc42 Deficiency Leads To Epidermal Barrier Dysfunction by Regulating Intercellular Junctions and Keratinization of Epidermal Cells during Mouse Skin Development

Rationale: Cdc42 is a Rho GTPase that regulates diverse cellular functions. Here, we used genetic techniques to investigate the role of Cdc42 in epidermal development and epidermal barrier formation.

Methods: Keratinocyte-restricted Cdc42 knockout mice were generated with the Cre-LoxP system under the keratin 14 (K14) promoter. The skin and other tissues were collected from mutant and wild-type mice, and their cellular, molecular, morphological, and physiological features were analyzed.

Results: Loss of Cdc42 in the epidermis in vivo resulted in neonatal lethality and impairment of epidermal barrier formation. Cdc42 deficiency led to the loss of epidermal stem cells. The absence of Cdc42 led to increased thickening of the epidermis, which was associated with increased proliferation and reduced apoptosis of keratinocytes. In addition, Cdc42 deficiency damaged tight junctions, adherens junctions and desmosomes. RNA sequencing results showed that the most significantly altered genes were enriched by the terms of “keratinization” and “cornified envelope” (CE). Among the differentially expressed genes in the CE term, several members of the small proline-rich protein (SPRR) family were upregulated. Further study revealed that there may be a Cdc42-SPRR pathway, which may correlate with epidermal barrier function.

Conclusions: Our study indicates that Cdc42 is essential for epidermal development and epidermal barrier formation. Defects in Cdc42-SPRR signaling may be associated with skin barrier dysfunction and a variety of skin diseases.

Cytokeratin 18 regulates the transcription and alternative splicing of apoptotic‑related genes and pathways in HeLa cells

Cytokeratin 18 (CK18), one of the major components of intermediate filaments (IF) in simple epithelial cells, undergoes caspase-mediated cleavage upon epithelial cell necrosis and apoptosis. CK18 has been used as a biomarker of several cancers and has been reported to be dysregulated in cervical cancers. The effects of dysregulated expression of CK18 at a molecular level are, however, unclear. In the present study, the function of CK18 in HeLa cells, a cell line derived from a cervical cancer cells, was investigated using shRNA knockdown. Reduced levels of CK18 led to a significant decrease in cell apoptosis, compared with control cells. Notably, RNA-seq analysis of the transcriptomes of HeLa cells, with or without CK18 knockdown, revealed that genes in the NF-κB pathway, and certain apoptosis pathways, were under global transcriptional and alternative splicing regulation. Quantitative RT-PCR confirmed the CK18-regulated transcription of apoptotic genes FAS and FADD, as well as immune genes CXCL2 and CD79B, in addition to alternative splicing of FAS and CTNNB1. Western blot analysis further revealed that CK18 knockdown led to reduced expression of CASP8. In conclusion, the present study indicated that CK18 played a role in apoptosis, which may be mediated via a feed-back regulation loop and may involve regulation of transcription and alternative splicing of a number of genes in apoptotic pathways.

Significance of Cytokeratin-1 Single-Nucleotide Polymorphism and Protein Level in Susceptibility to Vocal Leukoplakia and Laryngeal Squamous Cell Carcinoma

OBJECTIVE

To investigate the association between the cytokeratin (CK)-1 single-nucleotide polymorphism (SNP), the protein level of CK-1 and the risk of vocal leukoplakia and laryngeal squamous cell carcinoma (LSCC).

METHODS

In this case-control study, 155 patients with vocal leukoplakia, 323 patients with LSCC, and 266 healthy controls were genotyped for the CK-1 (SNP RS14024) gene using pyrosequencing. The protein expression level of CK-1 was analyzed in vocal leukoplakia, LSCC, and vocal polyp patients by immunohistochemistry (IHC).

RESULTS

Of the CK-1 RS14024 polymorphism, the heterozygote AG and homozygote GG genotype exhibited a significantly increased risk of LSCC (AG: OR = 2.16, p = 0.014; GG: OR = 2.15, p = 0.018) compared to normal controls. A higher protein expression level of CK-1 was detected in patients with LSCC compared to vocal leukoplakia and polyps (both p < 0.001), and a significant increasing trend of CK-1 protein expression level from mild-moderate dysplasia to moderate-severe dysplasia in vocal leukoplakia patients was also observed (p = 0.006).

CONCLUSIONS

This study demonstrates that the CK-1 SNP and high protein expression levels are associated with vocal leukoplakia and LSCC and promote the transformation from vocal leukoplakia to LSCC in a Chinese Han population.

Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing

Background

The C. macropomum is a characiform fish from the Amazon basin that has been hybridized with other pacu species to produce commercial hybrids, such as the tambacu. However, little is known of the functional genomics of the parental species or these hybrid forms. The transcriptome of C. macropomum and tambacu were sequenced using 454 Roche platform (pyrosequencing) techniques to characterize the domains of Gene Ontology (GO) and to evaluate the levels of gene expression in the two organisms.

Results

The 8,188,945 reads were assembled into 400,845 contigs. A total of 58,322 contigs were annotated with a predominance of biological processes for both organisms, as determined by Gene Ontology (GO). Similar numbers of metabolic pathways were identified in both the C. macropomum and the tambacu, with the metabolism category presenting the largest number of transcripts. The BUSCO analysis indicated that our assembly was more than 40% complete. We identified 21,986 genes for the two fishes. The P and Log2FC values indicated significant differences in the levels of gene expression, with a total of 600 up-regulated genes.

Conclusion

In spite of the lack of a reference genome, the functional annotation was successful, and confirmed a considerable difference in the specificity and levels of gene expression between the two organisms. This report provides a comprehensive baseline for the genetic management of these commercially important fishes, in particular for the identification of specific genes that may represent markers involved in the immunity, growth, and fertility of these organisms, with potential practical applications in aquaculture management.

Analyses of histological and transcriptome differences in the skin of short-hair and long-hair rabbits

BACKGROUND

Hair fibre length is an important economic trait of rabbits in fur production. However, molecular mechanisms regulating rabbit hair growth have remained elusive.

RESULTS

Here we aimed to characterise the skin traits and gene expression profiles of short-hair and long-hair rabbits by histological and transcriptome analyses. Haematoxylin-eosin staining was performed to observe the histological structure of the skin of short-hair and long-hair rabbits. Compared to that in short-hair rabbits, a significantly longer anagen phase was observed in long-hair rabbits. In addition, by RNA sequencing, we identified 951 genes that were expressed at significantly different levels in the skin of short-hair and long-hair rabbits. Nine significantly differentially expressed genes were validated by quantitative real-time polymerase chain reaction. A gene ontology analysis revealed that epidermis development, hair follicle development, and lipid metabolic process were significantly enriched. Further, we identified potential functional genes regulating follicle development, lipid metabolic, and apoptosis as well as important pathways including extracellular matrix-receptor interaction and basal cell carcinoma pathway.

CONCLUSIONS

The present study provides transcriptome evidence for the differences in hair growth between short-hair and long-hair rabbits and reveals that lipid metabolism and apoptosis might constitute major factors contributing to hair length.

High KRT8 Expression Independently Predicts Poor Prognosis for Lung Adenocarcinoma Patients

Keratin 8 (KRT8), a type II basic intermediate filament (IF) protein, is essential for the development and metastasis of various cancers. In this study, by analyzing RNA-seq data from the Cancer Genome Atlas (TCGA)-lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), we have determined the expression profile of KRT8, and assessed its prognostic significance and the possible mechanism underlying the dysregulation. Our results showed that KRT8 mRNA expression was significantly up-regulated in both LUAD and LUSC tissues compared with normal lung tissues. The high KRT8 expression group for LUAD patients significantly reduced overall survival (OS) and recurrence-free survival (RFS). Univariate and multivariate analysis revealed that KRT8 expression was an independent prognostic indicator for poor OS and RFS in LUAD patients. However, KRT8 expression had no prognostic value in terms of OS and RFS for LUSC. By exploring DNA copy number alterations (CNAs) of the KRT8 gene in LUAD, we found that DNA low copy gain (+1 and +2) was associated with elevated KRT8 mRNA expression. From the above findings, we have deduced that KRT8 is aberrantly expressed in LUAD tissues and that its expression might independently predict poor OS and RFS for LUAD patients, but not for LUSC patients.

The role of lysophosphatidic acid in the physiology and pathology of the skin

Lysophosphatidic acid (LPA) is the simplest phospholipid found in nature. LPA is mainly biosynthesized in tissues and cells by autotoxin and PA-PLA1α/PA-PLA1β and is degraded by lipid phosphate phosphatases (LPPs). It is an important component of biofilm, an extracellular signal transmitter and intracellular second messenger. After targeting to endothelial differentiation gene (Edg) family LPA receptors (LPA1, LPA2, LPA3) and non-Edg family LPA receptors (LPA4, LPA5, LPA6), LPA mediates physiological and pathological processes such as embryonic development, angiogenesis, tumor progression, fibrogenesis, wound healing, ischemia/reperfusion injury, and inflammatory reactions. These processes are induced through signaling pathways including mitogen-activated protein kinase (MAPK), phosphatidylinositol-3-kinase (PI3K)/Akt, protein kinase C (PKC)-GSK3β-β-catenin, Rho, Stat, and hypoxia-inducible factor 1-alpha (HIF-1α). LPA is involved in multiple physiological and pathological processes in the skin. It not only regulates skin function but also plays an important role in hair follicle development, skin wound healing, pruritus, skin tumors, and scleroderma. Pharmacological inhibition of LPA synthesis or antagonization of LPA receptors is a new strategy for the treatment of various skin disorders. This review focuses on the current understanding of the pathophysiologic role of LPA in the skin.

Enrichment and characterization of an environmental microbial consortium displaying efficient keratinolytic activity

Keratin refers to a group of insoluble and recalcitrant protein materials. Slaughterhouses produce large amount of keratinous byproducts, which are either disposed or poorly valorized through costly thermochemical processes for animal feed formulation. Learning from nature, keratinolytic microbial consortia stand as a cost-efficient and environmental friendly way to valorize this recalcitrant resource. Directed selection was applied to enrich soil-born microbial consortia, using sequential batch cultivations in keratin medium, while measuring enzymes activity and monitoring consortia compositions via 16S rRNA gene amplicon sequencing. A promising microbial consortium KMCG6, featuring mainly members of Bacteroidetes and Proteobacteria, was obtained. It possessed keratinolytic activity with <25% residual substrate remaining, which also displayed a high degradation reproducibility level after long-term cryopreservation. This work represents an advance in the field of α-keratin degradation with potential for practical applications.

Biofloc technology (BFT): An alternative aquaculture system for prevention of Cyprinid herpesvirus 2 infection in gibel carp (Carassius auratus gibelio)

Gibel carp (Carassius auratus gibelio), a major aquaculture species in China, has emerged in a seriously epizootic disease caused by Cyprinid herpesvirus 2 (CyHV-2). There are no effective methods to prevent or control this serious disease. Biofloc technology (BFT) can improve water quality, reduce pathogens introduction, enhance cultured species immunity and disease resistance. In this study, a 30-day experiment was conducted to investigate the effect of BFT on innate immune response and disease resistance of gibel carp against CyHV-2 infection. Gibel carp was cultured at different total suspended solid (TSS) concentrations of 10, 300, 600, 800 and 1000 mg L^-1, which were named as groups BF0, BF300, BF600, BF800 and BF1000. Results showed that fish in groups BF600/800 had significantly higher weight gain (WG) and specific growth rate (SGR) than them in control group (BF0). The transcriptional levels of seven immune-related genes in BF300/600/800 groups, including myeloid-specific- peroxidase (MPO), keratin 8 (KRT 8), dual specificity phosphatase 1 (DUSP 1), interleukin-11 (IL-11), intelectin (ITLN), purine nucleoside phosphorylase 5α (PNP 5α) and c-type lysozyme (c-lys), were up-regulated significantly compared to BF0 group. Furthermore, cumulative mortality of gibel carp in BF600 group after being challenged with CyHV-2 reduced significantly. In vivo viral replication in kidney demonstrated that CyHV-2 load at 168 h post injection in BF600 group was significantly higher than that in BF0 group. In conclusion, BFT could improve growth, immune response and disease resistance of gibel carp, and the effect was related with TSS concentration. The optimal TSS concentration of 600-800 mg L^-1 was recommended in the present study.

Genetic and Molecular Basis of Feather Diversity in Birds

Feather diversity is striking in many aspects. Although the development of feather has been studied for decades, genetic and genomic studies of feather diversity have begun only recently. Many questions remain to be answered by multidisciplinary approaches. In this review, we discuss three levels of feather diversity: Feather morphotypes, intraspecific variations, and interspecific variations. We summarize recent studies of feather evolution in terms of genetics, genomics, and developmental biology and provide perspectives for future research. Specifically, this review includes the following topics: 1) Diversity of feather morphotype; 2) feather diversity among different breeds of domesticated birds, including variations in pigmentation pattern, in feather length or regional identity, in feather orientation, in feather distribution, and in feather structure; and 3) diversity of feathers among avian species, including plumage color and morph differences between species and the regulatory differences in downy feather development between altricial and precocial birds. Finally, we discussed future research directions.

Methylmercury Intoxication Promotes Metallothionein Response and Cell Damage in Salivary Glands of Rats

Environmental and occupational mercury exposure is considered a major public health issue. Despite being well known that MeHg exposure causes adverse effects in several physiologic functions, MeHg effects on salivary glands still not completely elucidated. Here, we investigated the cellular MeHg-induced damage in the three major salivary glands (parotid, submandibular, and sublingual) of adult rats after chronic, systemic and low doses of MeHg exposure. Rats were exposed by 0.04 mg/kg/day over 60 days. After that, animals were euthanized and all three glands were collected. We evaluated total Hg accumulation, metallothionein I/II (MT I/II), α-smooth muscle actin (α-SMA), and cytokeratin 18 (CK18) immune expression. Our results have showed that MeHg is able to disrupt gland tissue and to induce a protective mechanism by MT I/II expression. We also showed that cell MT production is not enough to protect gland tissue against cellular structural damage seen by reducing marking of cytoskeletal proteins as CK18 and α-SMA. Our data suggest that chronic MeHg exposure in low-daily doses is able to induce cellular damage in rat salivary glands.

Understanding the dynamics of keratin weakening and hydrolysis by proteases

Keratin is the structural protein in hair, nails, feathers and horns. Keratin is recalcitrant, highly disulfide bonded and is generally inaccessible to common proteases. Only certain types of proteases, called keratinases, are able to cleave the peptide bonds within the keratin structure. Due to this outstanding activity, keratinases have potential application in industries such as livestock, cosmetics and pharmaceuticals. Yet, the process of enzymatic keratin degradation is poorly understood, affecting the development of industrial enzyme formulations that may require full or only partial modification or weakening. Here we investigate the dynamics of keratin weakening and hydrolysis, showing that the decrease in hair mechanical strength is associated with cuticle removal and damage to the cortex and complete breakdown is dependent on reducing agents. Proteases with keratinolytic activity were selected and applied to hair with degradation examined by mechanical, biochemical and microscopic techniques. The extent of keratin degradation was highly enhanced by the presence of reducing agents, principally sodium thioglycolate, exceeding 90% degradation within 16 h of enzymatic treatment. Application was extended to feathers showing that the findings are relevant to improving the use of keratinases in a variety of industries. Overall, the outcomes provide valuable insights into the keratin degradation process by enzymes for the optimization of cosmetic and pharmaceutical products and for livestock waste recycling among other important applications.

Keratins and epidermolysis bullosa simplex

Keratin intermediate filaments play an important role in maintaining the integrity of the skin structure. Understanding the importance of this subject is possible with the investigation of keratin defects in epidermolysis bullosa simplex (EBS). Nowadays, in addition to clinical criteria, new molecular diagnostic methods, such as next generation sequencing, can help to distinguish the subgroups of EBS more precisely. Because the most important and most commonly occurring molecular defects in these patients are the defects of keratins 5 and14 (KRT5 and KRT14), comprehending the nature structure of these proteins and their involved processes can be very effective in understanding the pathophysiology of this disease and providing new and effective therapeutic platforms to treat it. Here, we summarized the various aspects of the presence of KRT5 and KRT14 in the epidermis, their relation to the incidence and severity of EBS phenotypes, and the processes with which these proteins can affect them.