Dephosphorylation of T517 on Hemocyanin Is Required for Antibacterial Activity in Penaeus vannamei.

Posttranslational modifications expand the functions of immune-related proteins, especially during infections. The respiratory glycoprotein, hemocyanin, has been implicated in many other functions, but the role of phosphorylation modification in its functional diversity is not fully understood. In this study, we show that Penaeus vannamei hemocyanin (PvHMC) undergoes phosphorylation modification during bacterial infection. Dephosphorylation of PvHMC mediated by P. vannamei protein phosphatase 2A catalytic increases its in vitro antibacterial activity, whereas phosphorylation by P. vannamei casein kinase 2 catalytic subunit α decreases its oxygen-carrying capacity and attenuates its in vitro antibacterial activity. Mechanistically, we show that Thr517 is a critical phosphorylation modification site on PvHMC to modulate its functions, which when mutated attenuates the action of P. vannamei casein kinase 2 catalytic subunit α and P. vannamei protein phosphatase 2A catalytic, and hence abolishes the antibacterial activity of PvHMC. Our results reveal that phosphorylation of PvHMC modulates its antimicrobial functions in penaeid shrimp.

Function of hemocyanin-mediated succinate dehydrogenase in glucose metabolism and immunity of Penaeus vannamei.

Succinate dehydrogenase (SDH) is a crucial enzyme in the tricarboxylic acid cycle (TCA) and has established roles in immune function. However, the understanding of SDH in Penaeus vannamei, particularly its involvement in immune responses, is currently limited. Through affinity proteomics, a potential interaction between hemocyanin (HMC) and SDH in shrimp has been identified. The successful cloning of PvSDH in this study has revealed a high degree of evolutionary conservation. Additionally, it has been found that hemocyanin regulates SDH not only at the transcriptional and enzymatic levels but also through confirmed protein-protein interactions observed via Co-immunoprecipitation (CoIP) assay. Moreover, by combining PvHMC knockdown and Vibrio parahaemolyticus challenge, it was demonstrated that fumaric acid, a product of SDH, enhances the host's immune resistance to pathogen infection by modulating the expression of antimicrobial peptides. This research provides new insights into HMC as a crucial regulator of SDH, potentially impacting glycometabolism and the dynamics of immune responses.

The evolutionary adaptation of shrimp hemocyanin subtypes and the consequences on their structure and functions.

Hemocyanin is the main respiratory protein of arthropods and is formed by hexameric and/or oligomeric subunits. Due to changes in the living environment and gene rearrangement, various hemocyanin subtypes and subunits evolved in crustaceans. This paper reviews the various hemocyanin subtypes and isoforms in shrimp and analyses published genomic data of sixteen hemocyanin family genes from Litopenaeus vannamei to explore the evolution of hemocyanin genes, subunits, and protein structure. Analysis of hemocyanin subtypes distribution and structure in various tissues was also performed and related to multiple and tissue-specific functions, i.e., immunological activity, immune signaling, phenoloxidase activity, modulation of microbiota homeostasis, and energy metabolism. The functional diversity of shrimp hemocyanin due to molecular polymorphism, transcriptional regulation, alternative splicing, degradation into functional peptides, interaction with other proteins or genes, and structural differences will also be highlighted for future research. Inferences would be drawn from other crustaceans to explain how evolution has changed the structure-function of hemocyanin and its implication for evolutionary research into the multifunctionality of hemocyanin and other related proteins in shrimp.

Deacetylation of K481 and K484 on Penaeid Shrimp Hemocyanin Is Critical for Antibacterial Activity.

Although invertebrates' innate immunity relies on several immune-like molecules, the diversity of these molecules and their immune response mechanisms are not well understood. Here, we show that Penaeus vannamei hemocyanin (PvHMC) undergoes specific deacetylation under Vibrio parahaemolyticus and LPS challenge. In vitro deacetylation of PvHMC increases its binding capacity with LPS and antibacterial activity against Gram-negative bacteria. Lysine residues K481 and K484 on the Ig-like domain of PvHMC are the main acetylation sites modulated by the acetyltransferase TIP60 and deacetylase HDAC3. Deacetylation of PvHMC on K481 and K484 allows PvHMC to form a positively charged binding pocket that interacts directly with LPS, whereas acetylation abrogates the positive charge to decrease PvHMC-LPS attraction. Besides, V. parahaemolyticus and LPS challenge increases the expression of Pvhdac3 to induce PvHMC deacetylation. This work indicates that, during bacterial infections, deacetylation of hemocyanin is crucial for binding with LPS to clear Gram-negative bacteria in crustaceans.

Waste for Waste: Interface-Intensified Durable Superhydrophilic-Superoleophobic Collagen Fiber Membrane for Efficient Separation of Cationic Surfactant-Stabilized Oil-in-Water Emulsions.

Cationic surfactant-stabilized oil-in-water emulsions pose a significant challenge in separation due to the presence of surfactants. Herein, we develop a collagen-fiber-based CFM-PMDA-TiO2 membrane with unique infiltration properties capable of efficiently separating cationic surfactant-stabilized oil-in-water emulsions by exploiting the charge-demulsification effect. The membrane exhibits superhydrophilic and submerged superoleophobic properties, making it highly suitable for separating a wide range of commercially available cationic surfactant-stabilized oil-in-water microemulsions and nanoemulsions, which demonstrates an exceptional separation efficiency as high as 99.86% and an impressive flux of up to 1436.40 L m-2 h-1. Furthermore, even after a strong subjecting of the membrane to sandpaper abrasion and a full 15 time use, the separation efficacy of oil-in-water emulsions is retained, highlighting the durability, reusability, and economic viability. We propose that these features are enabled by the electrostatic interactions triggered from pyromellitic dianhydride (PMDA) and superhydrophilic-superoleophobic membrane intensified by the TiO2 on the unique collagen fiber membrane. Outcomes emphasize the versatility and potential of our membrane in addressing emulsified oily wastewater hurdles.

Prevention and potential repair of colitis: Beneficial effects and regulatory mechanisms of food-derived anti-inflammatory peptides.

Intestinal inflammatory diseases are increasingly prevalent worldwide, and their pathogenesis is still not fully understood. As of late, studies have discovered that food-derived peptides have specific anti-inflammatory activity and can play a positive role in intestinal health. At the same time, it has broad application prospects in the prevention and treatment of colitis because of its wide source, fast absorption, and high safety. This article reviews the structure-activity and quantity-effect relationships of food-derived peptides for their anti-inflammatory effects. It then discusses their mechanism of action in inhibiting colitis from four aspects. Food-derived anti-inflammatory peptides can delay the progression of the disease by stimulating innate immunity, inhibiting inflammation, and promoting wound healing. Further experiments showed that food-derived anti-inflammatory peptides could prevent and treat colitis through four mechanisms: (a) regulation of inflammatory cytokines; (b) regulation of inflammatory pathways; (c) regulation of intestinal epithelial barrier; (d) regulation of intestinal flora balance. However, due to the treatment of colitis having limitations, there is an urgent to develop food-derived anti-inflammatory peptides as a treatment or adjunctive treatment for colitis. This review highlights the positive effects of food-derived peptides on colitis and anticipates the appearance of mitigating peptides for the therapy of colitis.

The Microbial Composition of Penaeid Shrimps' Hepatopancreas Is Modulated by Hemocyanin.

Aquatic organisms have to produce proteins or factors that help maintain a stable relationship with microbiota and prevent colonization by pathogenic microorganisms. In crustaceans and other aquatic invertebrates, relatively few of these host factors have been characterized. In this study, we show that the respiratory glycoprotein hemocyanin is a crucial host factor that modulates microbial composition and diversity in the hepatopancreas of penaeid shrimp. Diseased penaeid shrimp (Penaeus vannamei), had an empty gastrointestinal tract with atrophied hepatopancreas, expressed low hemocyanin, and high total bacterial abundance, with Vibrio as the dominant bacteria. Similarly, shrimp depleted of hemocyanin had mitochondrial depolarization, increased reactive oxygen species (ROS) levels, and dysregulation of several energy metabolism-related genes. Hemocyanin silencing together with ROS scavenger (N-acetylcysteine) treatment improved microbial diversity and decreased Vibrio dominance in the hepatopancreas. However, fecal microbiota transplantation after hemocyanin knockdown could not restore the microbial composition in the hepatopancreas. Collectively, our data provide, to our knowledge, new insight into the pivotal role of hemocyanin in modulating microbial composition in penaeid shrimp hepatopancreas via its effect on mitochondrial integrity, energy metabolism, and ROS production.

Modulation of SREBP Expression and Fatty Acid Levels by Bacteria-Induced ER Stress Is Mediated by Hemocyanin in Penaeid Shrimp.

Many environmental and pathogenic insults induce endoplasmic reticulum (ER) stress in animals, especially in aquatic ecosystems, where these factors are crucial for life. In penaeid shrimp, pathogens and environmental stressors induce hemocyanin expression, but the involvement of hemocyanin in ER stress response is unknown. We demonstrate that in response to pathogenic bacteria (Vibrio parahaemolyticus and Streptococcus iniae), hemocyanin, ER stress proteins (Bip, Xbp1s, and Chop), and sterol regulatory element binding protein (SREBP) are induced to alter fatty acid levels in Penaeus vannamei. Interestingly, hemocyanin interacts with ER stress proteins to modulate SREBP expression, while ER stress inhibition with 4-Phenylbutyric acid or hemocyanin knockdown attenuates the expression of ER stress proteins, SREBP, and fatty acid levels. Contrarily, hemocyanin knockdown followed by tunicamycin treatment (ER stress activator) increased their expression. Thus, hemocyanin mediates ER stress during pathogen challenge, which consequently modulates SREBP to regulate the expression of downstream lipogenic genes and fatty acid levels. Our findings reveal a novel mechanism employed by penaeid shrimp to counteract pathogen-induced ER stress.

Screening of Acetylcholinesterase Inhibitors by Capillary Electrophoresis with Oriented-Immobilized Enzyme Microreactors Based on Gold Nanoparticles.

A facial and efficient method for the screening of acetylcholinesterase (AChE) inhibitors by capillary electrophoresis was developed. Based on the specific affinity of concanavalin A (Con A) for binding to the glycosyl group of AChE, enzyme molecules were oriented-immobilized on the surface of gold nanoparticles (AuNPs@Con A@AChE). Then, these modified nanoparticles were bounded to the capillary inlet (about 1.0 cm) by electrostatic self-assembly to obtain the oriented-immobilized enzyme microreactor (OIMER). Compared to an IMER with a free enzyme, the peak area of the product obtained by the OIMER increased by 52.6%. The Michaelis-Menten constant (Km) was as low as (0.061 ± 0.003) mmol/L. The method exhibits good repeatability with a relative standard deviation (RSD) of 1.3% for 100 consecutive runs. The system was successfully applied to detect the IC50 values of donepezil and four components from Chinese medicinal plants. This work demonstrates the potential of this method as a low cost, simple, and accurate screening method for other enzyme inhibitors.

A Novel Cold-Adapted and High-Alkaline Alginate Lyase with Potential for Alginate Oligosaccharides Preparation.

Alginate oligosaccharides (AOs) prepared through enzymatic reaction by diverse alginate lyases under relatively controllable and moderate conditions possess versatile biological activities. But widely used commercial alginate lyases are still rather rare due to their poor properties (e.g., lower activity, worse thermostability, ion tolerance, etc.). In this work, the alginate lyase Alyw208, derived from Vibrio sp. W2, was expressed in Yarrowia lipolytica of food grade and characterized in order to obtain an enzyme with excellent properties adapted to industrial requirements. Alyw208 classified into the polysaccharide lyase (PL) 7 family showed maximum activity at 35 °C and pH 10.0, indicating its cold-adapted and high-alkaline properties. Furthermore, Alyw208 preserved over 70% of the relative activity within the range of 10-55 °C, with a broader temperature range for the activity compared to other alginate-degrading enzymes with cold adaptation. Recombinant Alyw208 was significantly activated with 1.5 M NaCl to around 2.1 times relative activity. In addition, the endolytic Alyw208 was polyG-preferred, but identified as a bifunctional alginate lyase that could degrade both polyM and polyG effectively, releasing AOs with degrees of polymerization (DPs) of 2-6 and alginate monomers as the final products (that is, DPs 1-6). Alyw208 has been suggested with favorable properties to be a potent candidate for biotechnological and industrial applications.

Ammonia stress affects the structure and function of hemocyanin in Penaeus vannamei.

Anthropogenic factors and climate change have serious effects on the aquatic ecosystem and aquaculture. Among water pollutants, ammonia has the greatest impact on aquaculture organisms such as penaeid shrimp because it makes them more susceptible to infections. In this study, we explored the effects of ammonia stress (0, 50, 100, and 150 mg/L) on the molecular structure and functions of the multifunctional respiratory protein hemocyanin (HMC) in Penaeus vannamei. While the mRNA expression of Penaeus vannamei hemocyanin (PvHMC) was up-regulated after ammonia stress, both plasma hemocyanin protein and oxyhemocyanin (OxyHMC) levels decreased. Moreover, ammonia stress changed the molecular structure of hemocyanin, modulated the expression of protein phosphatase 2 A (PP2A) and casein kinase 2α (CK2α) to regulate the phosphorylation modification of hemocyanin, and enhanced its degradation into fragments by trypsin. Under moderate ammonia stress conditions, hemocyanin also undergoes glycosylation to improve its in vitro antibacterial activity and binding with Gram-negative (Vibrio parahaemolyticus) and Gram-positive (Staphylococcus aureus) bacteria, albeit differently. The current findings indicate that P. vannamei hemocyanin undergoes adaptive molecular modifications under ammonia stress enabling the shrimp to survive and counteract the consequences of the stress.

Mesenchymal stem cells enhance the impact of KIR receptor-ligand mismatching on acute graft-versus-host disease following allogeneic hematopoietic stem cell transplantation in patients with acute myeloid leukemia but not in those with acute lymphocytic leukemia.

Killer cell immunoglobulin-like receptor (KIR) receptor-ligand mismatch has been shown to be protective for acute and chronic graft-versus-host disease (aGVHD, cGVHD) following allogeneic hematopoietic stem cell transplantation (allo-HSCT) for acute leukemia. Mesenchymal stem cells (MSC) have been considered as one of the most promising prophylaxis for severe GVHD. However, there are no prospective or retrospective studies determining whether they can work synergistically on GVHD. To investigate the potential influence of KIR matching and MSCs, and their synergism on aGVHD and cGVHD after allo-HSCT in acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) patients. Data from 104 patients with AML and 50 patients with ALL treated with allo-HSCT in the transplantation unit were retrospectively analyzed. KIR genotyping was performed by the PCR-SSO method. The amplicons were quantified on the Luminex 200 flow analyzer and analyzed using the Quick-Type for Lifecodes software to generate KIR data. Cox proportional hazards models were used in multivariate analyses. KIR receptor-ligand matching was associated with an increased risk of grade II-IV aGVHD compared to KIR receptor-ligand mismatching (p < 0.001) in AML patients, but KIR ligand-mismatching had no significant effect on aGVHD or cGVHD in ALL patients. In contrast, MSCs reduced the incidence of grade II-IV aGVHD in both AML and ALL patients (AML: p = 0.006; ALL: p = 0.008) regardless of KIR mismatching. The combination of KIR receptor-ligand mismatch and MSC transplantation significantly suppressed grade II-IV aGVHD occurrence in AML patients (p = 0.039). In the KIR mismatch group, the incidence of aGVHD was 2.8% in patients receiving MSC compared to 14.6% in those who did not (p = 0.047). KIR receptor-ligand mismatch, MSC transplantation and their combined use significantly reduced the risk of aGVHD after allo-HSCT. These data provide a clinically applicable strategy to reduce aGVHD, thus improving allo-HSCT outcome.

Epidermal growth factor stimulates exosomal microRNA-21 derived from mesenchymal stem cells to ameliorate aGVHD by modulating regulatory T cells.

Regulatory T cells (Tregs), a subset of CD4+ T cells, may exert inhibitory effects on alloimmune responses including acute graft-versus-host disease (aGVHD), and several microRNAs are implicated in the pathophysiological process of GVHD. Therefore, we aimed in the present study to characterize the functional relevance of epidermal growth factor (EGF)-stimulated microRNA-21 (miR-21) in regulating bone marrow-derived mesenchymal stem cells (BMSCs) in a mouse model of aGVHD. We first isolated and cultured BMSCs and Tregs. Then, we examined effects of miR-21 knockdown or overexpression and EGF on cell activities of BMSCs and the expression of PTEN, Foxp3, AKT phosphorylation, and extent of c-jun phosphorylation by gain- and loss-of-function approaches. The results showed that miR-21 promoted the proliferation, invasion, and migration of BMSCs. Furthermore, miR-21 in BMSCs-derived exosomes inhibited PTEN, but enhanced AKT phosphorylation and Foxp3 expression in Tregs. In addition, EGF enhanced c-jun phosphorylation to elevate the miR-21 expression. Furthermore, EGF significantly increased the efficacy of BMSCs in a mouse model of aGVHD, manifesting in reduced IFN-γ expression and lesser organ damage. Moreover, EGF treatment promoted the Foxp3 expression of Tregs in BMSCs-treated aGVHD mice. Taken together, EGF induced the BMSCs-derived exosomal miR-21 expression, which enhanced Foxp3 expression in Tregs, thereby improving the therapeutic effect of BMSCs on aGVHD.

Collagen Peptides Derived from Sipunculus nudus Accelerate Wound Healing.

Marine collagen peptides have high potential in promoting skin wound healing. This study aimed to investigate wound healing activity of collagen peptides derived from Sipunculus nudus (SNCP). The effects of SNCP on promoting healing were studied through a whole cortex wound model in mice. Results showed that SNCP consisted of peptides with a molecular weight less than 5 kDa accounted for 81.95%, rich in Gly and Arg. SNCP possessed outstanding capacity to induce human umbilical vein endothelial cells (HUVEC), human immortalized keratinocytes (HaCaT) and human skin fibroblasts (HSF) cells proliferation and migration in vitro. In vivo, SNCP could markedly improve the healing rate and shorten the scab removal time, possessing a scar-free healing effect. Compared with the negative control group, the expression level of tumor necrosis factor-α, interleukin-1ß and transforming growth factor-ß1 (TGF-ß1) in the SNCP group was significantly down-regulated at 7 days post-wounding (p < 0.01). Moreover, the mRNA level of mothers against decapentaplegic homolog 7 (Smad7) in SNCP group was up-regulated (p < 0.01); in contrast, type II TGF-ß receptors, collagen I and α-smooth muscle actin were significantly down-regulated at 28 days (p < 0.01). These results indicate that SNCP possessed excellent activity of accelerating wound healing and inhibiting scar formation, and its mechanism was closely related to reducing inflammation, improving collagen deposition and recombination and blockade of the TGF-ß/Smads signal pathway. Therefore, SNCP may have promising clinical applications in skin wound repair and scar inhibition.

Chronic effects of microcystin-LR at environmental relevant concentrations on photosynthesis of Typha angustifolia Linn.

Understanding the growth and development of aquatic plants in eutrophic water is of great significance for the selection of potential candidate plant for use in the phytoremediation of eutrophic aquatic ecosystems. The present study aimed to investigate the chronic effects of microcystin-LR (MC-LR) on photosynthesis in the leaves of Typha angustifolia Linn. Photosynthetic activity was stimulated in the leaves following exposure to 4.6 µg L-1 MC-LR for six weeks based on the enhancement of Ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco) activity and net photosynthetic rate (PN). However, PN decreased significantly after exposure to 49.1 or 98.3 µg L-1 MC-LR, via non-stomatal limitation by reducing the chlorophyll a and b contents and Rubisco activity. In addition, glycolate oxidase (GO) and serine:glyoxylate aminotransferase (SGAT) activities decreased significantly, indicating that the photorespiration pathway was affected adversely. The intercellular carbon dioxide (Ci) concentration decreased significantly following exposure to 98.3 µg L-1 MC-LR, accompanied with decreases in PN and stomatal conductivity (gs), indicating that stomatal limitation on the photosynthesis system in T. angustifolia L. was observed after exposure to 98.3 µg L-1 MC-LR. Under long-term exposure to MC-LR (49.1-98.3 µg L-1), oxidation stress was severe in the aquatic plant, and non-stomatal limitation or stomatal limitation effects on the photosynthesis system were obvious, resulting in decreases in photosynthesis rates.

[Wound-healing acceleration of mice skin by Sipunculus nudus extract and its mechanism].

In order to explore the effect of Sipunculus nudus extract (SNE) on skin wound healing in mice and its mechanism, hemostasis effect of SNE was measured, the mouse skin wound model was established by full-thickness excision. The morphological changes of the wound were observed after the treatment with SNE and the healing rate was measured. The changes of wound histology were observed by hematoxylin eosin (HE) staining, Masson staining and transmission electron microscope (TEM). The expression of cell factors and related proteins was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Results showed that the SNE possessed hemostatic function. SNE could obviously improve the healing rate of wound in mouse and shorten time of scab removal compared with the none-treatment (NT) group ( P < 0.05).The pathological histology analysis results showed complete epidermal regeneration, with remarkable capillary and collagen fiber observed in the SNE group. The expression level of tumor necrosis factor-α (TNF -α), interleukin-1ß (IL-1ß) and transforming growth factor-ß1 (TGF-ß1) in SNE group was significantly lower than that of the NT group on 7 d ( P < 0.05). Moreover, compared with the NT group, the gene expressions level of Smad7 was significantly increased and the level of type II TGF-ß receptors (TGF-ßRII), collagen I (COL1A1) and α-smooth muscle actin (α-SMA) were significantly reduced in the SNE group on 28 d ( P < 0.05), but the difference was not statistically significant compared to Yunnanbaiyao group (PC group) ( P > 0.05). These results indicated that SNE possessed obvious activity of accelerating wound healing and inhibiting scar formation, and its mechanism was closely related to hemostatic function, regulation of inflammatory factors, collagen deposition, collagen fiber remodeling and intervening TGF-ß/Smads signal pathway. Therefore, SNE may have promising clinical applications in skin wound repair and scar inhibition.

Primordial follicle activation is affected by the absence of Sohlh1 in mice.

Previous studies have reported that only primordial follicles and empty follicles can be found in 7.5 days postparturition (dpp) Sohlh1-/- mouse ovaries and females are infertility. There appears to be a defect in follicle development during the primordial-to-primary follicle transition in Sohlh1-/- mouse ovaries. However, detailed analyses of these phenomena have not been performed. In this study, we used Sohlh1-/- transgenic mice to explore the role of Sohlh1 in folliculogenesis. The results showed that only primordial follicles and empty follicles can be observed in Sohlh1-/- ovaries from 0.5 to 23.5 dpp. The expression of Foxo3 and FOXO3 was downregulated; nucleocytoplasmic shuttling of FOXO3 was normal in 7.5-dpp Sohlh1+/+ but not Sohlh1-/- ovaries; and primordial follicle activation (PFA) was not observed in 7.5-dpp Sohlh1-/- mice. The expression levels of KIT, AKT, and P308-AKT were downregulated (p < 0.05), whereas that of P473-AKT was not significantly changed (p > 0.05). The KIT/PI3K/AKT pathway was inhibited. Furthermore, we conducted a dual luciferase assay and chromatin immunoprecipitation. The results showed that SOHLH1 can upregulate the Kit gene by binding to the -3698 bp E-box motif. The absence of Sohlh1 may affect PFA in mouse ovaries via downregulation of Kit and inhibition of the KIT/PI3K/AKT pathway.

Sohlh1 is required for synaptonemal complex formation by transcriptionally regulating meiotic genes during spermatogenesis in mice.

Gonad-specific transcription factor spermatogenesis- and oogenesis-specific helix-loop-helix transcription factor 1 (SOHLH1) plays a key role in the transcriptional regulation of the expression of differentiating spermatogonial genes. However, its role in spermatocytes (meiotic male germ cells) remains largely unknown. In this study, Sohlh1 knockout (KO) male mice displayed meiotic defects at the zygotene stage during spermatogenesis. Microarray analyses identified 66 upregulated genes and 139 downregulated genes in Sohlh1 KO testes compared with those in wild-type testes at postnatal Day 7.5. Among many of the downregulated genes, Sycp1 and Sycp3, which encode synaptonemal complex proteins 1 and 3 (SYCP1 and SYCP3), respectively, were significantly reduced in Sohlh1 knockout mice. Transmission electron microscopy revealed no formation of the synaptonemal complex in Sohlh1 KO spermatocytes. Luciferase reporter and chromatin-immunoprecipitation assays demonstrated that SOHLH1 enhanced the expression of the Sycp1 and Sycp3 genes by binding the -1276, -708, and -94 basepairs (bp) E-boxes upstream of the Sycp1 promoter and the -64 and -43 bp E-boxes upstream of the Sycp3 promoter. Our data suggest that SOHLH1 transcriptionally regulates the expression of many target genes critical for the meiotic phase of spermatogenesis.

Tumor classification and biomarker discovery based on the 5'isomiR expression level.

BACKGROUND: The miRNA isoforms (isomiRs) have been suggested to regulate the same pathways as the canonical miRNA and play an important biological role in miRNA-mediated gene regulation. Recently, a study has demonstrated that the presence or absence of all isomiRs could efficiently discriminate amongst 32 TCGA cancer types. Besides, an effective reduction of distinguishing isomiR features for multiclass tumor discrimination must have a major impact on our understanding of the disease and treatment of cancer. METHODS: In this study, we have constructed a combination of the genetic algorithms (GA) with Random Forest (RF) algorithms to detect reliable sets of cancer-associated 5'isomiRs from TCGA isomiR expression data for multiclass tumor classification. RESULTS: We obtained 100 sets of the optimal predictive features, each of which comprised of 50-5'isomiRs that could effectively classify with an average sensitivity of 92% samples from 32 different tumor types. We calculated the frequency with which a 5'isomiR found in these sets as measuring its importance for tumor classification. Many highly frequent 5'isomiRs with different 5' loci from canonical miRNAs were detected in these sets, supporting that the isomiRs play a significant role in the multiclass tumor classification. The further functional enrichment analysis showed that the target genes of the 10 most frequently appearing 5'isomiRs were involved in the activity of transcription activator and protein kinase and cell-cell adhesion. CONCLUSIONS: The findings of the present study indicated that the 5'isomiRs might be employed for multiclass tumor classification and the suggested that GA/RF model could perform effective tumor classification by a series of largely independent optimal predictor 5' isomiR sets.