Cysteine Protease Inhibitor Research Articles

TFAP2A Promotes Cell Progression and Suppresses Ferroptosis in Lung Adenocarcinoma via Activating Transcription of CST1.

Lung adenocarcinoma (LUAD) is a common type of lung cancer with complicated pathological mechanism. Transcription Factor AP-2 Alpha (TFAP2A) and Cysteine protease inhibitor 1 (CST1) are upregulated genes in LUAD samples, accordingly, we focused on clarifying the role of TFAP2A/CST1 axis in LUAD. Expression analysis was performed using real-time quantitative polymerase chain reaction and western blot. Cellular behaviors were detected by colony formation assay, EdU assay, wound healing assay and flow cytometry. Ferroptosis was assessed by oxidative indicators, Fe2+ level and related proteins. TFAP2A and CST1 interaction was analyzed via ChIP assay and dual-luciferase reporter assay. TFAP2A function in vivo was evaluated by xenograft tumor assay. CST1 was overexpressed in LUAD samples and cells. Downregulation of CST1 inhibited proliferation, migration but it promoted apoptosis and ferroptosis of LUAD cells. TFAP2A interacted with the promoter of CST1 to up-regulate CST1 expression. TFAP2A regulated the malignant behaviors and ferroptosis of LUAD cells by targeting CST1. TFAP2A affected LUAD tumor growth via mediating CST1. All these data proved that TFAP2A/CST1 axis contributed to proliferation, migration while it suppressed apoptosis and ferroptosis in LUAD.

Changes in Protease Activity of Ginger Rhizome during Postharvest Storage

It has been reported that ripe ginger rhizomes contain proteolytic enzymes. In this study, we investigated the fluctuations in protease activity from ginger rhizomes stored after harvest for the utilization of proteases. The juice from ginger rhizomes that had been stored for 4 months after harvest exhibited the highest specific protease activity. Additionally, juices with high specific protease activity could form soymilk and cow milk gels. Electrophoresis experiments revealed that the protein bands in ginger rhizome juice were degraded by the proteases contained in the juice. This degradation was prevented by adding the cysteine protease inhibitor E-64.

Abstract 4135985: Association of Plasma Cystatin-C with Cancer Risk in Individuals with and without Cardiovascular and Chronic Kidney Disease: An Atherosclerosis Risk in Communities (ARIC) Study

Background: While previous studies suggested a relationship between circulating Cystatin-C (Cys-C), a cysteine protease inhibitor involved in regulating tissue inflammation and a renal filtration marker, and both cancer and CVD, they often lacked long-term follow-up or did not account for the impact of CVD on the relationship between Cys-C and cancer. Methods: We included participants from the Atherosclerosis Risk in Communities (ARIC) study followed from visit 2 (1990-1992) through 2015. Plasma Cys-C level was measured by SomaScan. Other renal filtration markers beta-2 microglobulin (B2M) and beta-trace protein (BTP) were used to compare their cancer association with Cys-C. Incident cancer was ascertained by state cancer registry linkage supplemented with medical records. After adjusting for age, sex, race, and study center, adjusted hazard ratios (aHR) of total and site-specific cancers were estimated using Cox proportional hazards regression stratified by baseline chronic kidney disease (CKD) and CVD status. Results: Among 10,869 individuals (median age of 56.9 years, 55% female, 25% Black, 74% White), 3352 incident cancers were ascertained over a median follow-up of 22.9 years. Among 9585 individuals with no history of CKD or CVD, higher Cys-C was significantly associated with a higher risk of total (aHR 1.22, 95%CI 1.02-1.46), bladder, lung, colorectal, and hematologic malignancies. Among 1,050 individuals with CVD, but not CKD, Cys-C level was not associated with total cancer (aHR 1.22, 95%CI 0.74-2.01), but was significantly inversely associated with colorectal (aHR 0.19, 95%CI 0.05-0.76) and positively associated with post-menopausal breast (aHR 4.52, 95%CI 1.05-19.40) cancer risk. In individuals with CKD but not CVD, Cys-C was negatively associated with bladder (HR 0.08, 95%CI 0.0-0.77) and lung (0.23, 95%CI 0.06-0.82) cancers. Lastly, those with both CKD and CVD showed higher hematopoietic and lymphatic cancer with higher Cys-C (HR 4.68, 95%CI 1.32-16.60). Similar patterns were observed for B2M and BTP proteins. Conclusions: Our study highlights the intricate relationship between various renal filtration markers and cancer risk. It suggests that they may play a significant role in cancer development among the general population and CVD patients but not CKD patients. Further research should explore the biological mechanism underlying these associations with even more CKD cases to refine risk estimates. Funding: NHLBI, NCI, NPCR

Synthesis of α-fluorocinnamate derivatives as novel cathepsin S inhibitors with in vitro antiproliferative activity against pancreatic cancer cells

Cathepsins, key members of the papain-like family of cysteine proteases, are crucial for proteolysis processes within human cells, including osteolysis, immunomodulation and apoptosis. Recent research has highlighted the significant role of cathepsins, particularly the L, S, K, and B subtypes, in pancreatic cancer. This has driven the development of novel cathepsin inhibitors as potential treatments to inhibit tumor progression, migration and invasion. Targeting cathepsin S (CatS) has shown promise in reducing tumor progression and enhancing the efficacy of chemotherapeutic agents in preclinical models. Building on our previous work where we employed ethyl p-aminocinnamate ester derivatives for covalent inhibition of cysteine proteases, herein we have designed and synthesized three new derivatives basing on an isosteric replacement (H–F) at the level of cinnamate moiety. These derivatives emerged as potent covalent inhibitors of CatS (1.8–2.6 µM) with 2F showing also weak inhibition activity against CatL (20 %) and CatB (29 %). In vitro assays of 2F against pancreatic cancer cell lines BXPC3 and CAPAN1 revealed significant antiproliferative activity, with IC50 = 5.79 µM and 20.75 µM, respectively. These findings underscore the potential of α-fluorocinnamate-based cysteine protease inhibitors as promising candidates for further development in targeting CatS and CatL with the aim to reduce pancreatic cancer cell proliferation.

In vitro proteolysis mirrors intact muscle maturation in beef carcasses

An in vitro assay was developed to study protease activity during the maturation of beef postmortem. Myofibrils were purified from the semitendinosus and used as a sentinel for assessing the activity of endogenous proteases in longissimus thoracis et lumborum (LTL) and the extensor carpi radialis (ER) over time postmortem in beef carcasses. Samples were collected from each muscle at 0, 1, 2, 7, and 14 d of aging and snap frozen. Samples were powdered and added to an in vitro proteolysis assay containing buffer and purified myofibrils. Aliquots were collected at 0, 2, 120, 480, and 1440 min of incubation, and intact desmin and troponin T were quantified. Digestions at 0 and 1 d using either muscle had little desmin degradation during the entire digestion period. In contrast, LTL muscle collected at 2, 7, and 14 d had the greatest proteolytic capacity as indicated by disappearance of intact desmin by 480 and 1440 min incubation. Though degradation ensued using powdered ER muscle, disappearance of intact proteins was limited. Degradation in vitro paralleled that observed in intact muscle. Addition of ethylene glycol tetra-acetic acid (EGTA), a cysteine protease inhibitor, and calpastatin inhibited proteolysis and suggest proteolytic activity observed in muscles and detected in our proteolysis assays is due to an active calpain protease. Collectively, our data show an active protease is minimal in bovine muscle until 48 h postmortem in the LTL muscle and suggest an in vitro assay containing purified myofibrils is a potential tool for studying temporal changes in proteolysis during the maturation and tenderization of beef across muscles.

Profiling Cysteine Proteases Activities in Neuroinflammatory Cells.

A new activity-based probe (ABP) of cysteine proteases (FGA139) has been designed and synthesized. The design of the ABP has been done based upon the chemical structure of an irreversible inhibitor of cysteine proteases by attaching a bodipy fluorophore at the N-terminus of the peptide backbone. The synthetic route of the probe has a metathesis and a "click" reaction as key steps. Although some studies have been reported about the role played by cysteine proteases in neurodegenerative diseases, there are not definitive conclusions. The obtained ABP has been employed as a chemical tool to profile activities of cysteine proteases cathepsins B, L, and calpain in neurodegenerative cell models through confocal imaging. Colocalization of the probe to specific antibodies of the proteases and competitive experiments with non-fluorescent inhibitors confirm the specificity of the ABP. From a theranostic perspective, our findings strongly suggest that FGA139 exhibits a protective role in various cell lines against oxidative stress or pro-inflammatory toxicity and it effectively attenuates macrophage activation triggered by LPS.

Cathepsin B- and L-like Protease Activities Are Induced During Developmental Barley Leaf Senescence.

Leaf senescence is a developmental process allowing nutrient remobilization to sink organs. Previously cysteine proteases have been found to be highly expressed during leaf senescence in different plant species. Using biochemical and immunoblotting approaches, we characterized developmental senescence of barley (Hordeum vulgare L. var. 'GemCraft') leaves collected from 0 to 6 weeks after the onset of flowering. A decrease in total protein and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) large subunits occurred in parallel with an increase in proteolytic activity measured using the fluorogenic substrates Z-RR-AMC, Z-FR-AMC, and casein labeled with fluorescein isothiocyanate (casein-FITC). Aminopeptidase activity detected with R-AMC peaked at week 3 and then decreased, reaching a low level by week 6. Maximal proteolytic activity with Z-FR-AMC and Z-RR-AMC was detected from pH 4.0 to pH 5.5 and pH 6.5 to pH 7.4, respectively, while two pH optima (pH 3.6 to pH 4.5 and pH 6.5 to pH 7.4) were found for casein-FITC. Compound E-64, an irreversible cysteine protease inhibitor, and CAA0225, a selective cathepsin L inhibitor, effectively inhibited proteolytic activity with IC50 values in the nanomolar range. CA-074, a selective cathepsin B inhibitor, was less potent under the same experimental conditions, with IC50 in the micromolar range. Inhibition by leupeptin and phenylmethylsulfonyl fluoride (PMSF) was weak, and pepstatin A, an inhibitor of aspartic acid proteases, had no effect at the concentrations studied (up to 0.2 mM). Maximal proteolytic activity with the aminopeptidase substrate R-AMC was detected from pH 7.0 to pH 8.0. The pH profile of DCG-04 (a biotinylated activity probe derived from E-64) binding corresponded to that found with Z-FR-AMC, suggesting that the major active proteases are related to cathepsins B and L. Moreover, immunoblotting detected increased levels of barley SAG12 orthologs and aleurain, confirming a possible role of these enzymes in senescing leaves.

Single-cell transcriptome profiles and E−64 inhibitor data reveal the essential role of cysteine proteases in the ontogeny of Ichthyophthirius multifiliis

Ichthyophthiriasis (Ich), also known as white spot disease, causes significant economic losses to fish farmers once an outbreak occurs. For fish survival, it is therefore crucial to understand the pathogenic mechanism and find effective prevention methods. In this study, we obtained data for four stages (theront, trophont, protomont and tomont) of Ichthyophthirius multifiliis by single-cell RNA sequencing (scRNA-seq). We found that the invasion-related proteins encoded by highly expressed genes in the theront stage mainly belong to the leishmanolysin family proteins, heat shock proteins, transmembrane proteins and cysteine proteases (CPs). Additionally, the exosome pathway appears to play a significant role in the invasion process of the theront. Since cysteine proteases are expressed at all stages of the I. multifiliis, and five CP-related genes were significantly upregulated at the theront stage of its life cycle — two of which are enriched in the exosome pathway — we incubated I. multifiliis theronts and protomonts with cysteine protease inhibitor (E−64). Our findings revealed that E−64 could kill both stages of the parasite in vitro and affected tomont division and subsequent release. Furthermore, infection experiment showed that E−64 could significantly inhibit the invasion of theronts. Based on our preliminary analysis from the transcriptomic and E−64 experiments, we have confirmed that CPs play a crucial role in I. multifiliis. This research establishes a foundation for future strategies in the prevention and control of Ich.

Proteolytic degradation of seed proteins of vetch species (Vicia L. subgenus Vicia) of section Peregrinae Kupicha during SDS-electrophoresis and its prevention

Background. Due to its simplicity and good reproducibility, SDS-electrophoresis of seed proteins is widely used for investigating the gene pool of legumes and other plants, for species and varietal identification, analyzing the intraspecific variability, and registering collection material. The data obtained by this method agree well with the DNA analysis results complement them. Typically, legume seed proteins, including representatives of the genus Vicia L., show clear informative SDS electrophoretic profiles. When analyzing seed accessions of vetch species of the section Peregrinae Kupicha using standard approaches previously developed at VIR and approved by ISTA (the International Seed Testing Association), clear electrophoretic protein profiles could not be obtained for many accessions. This called into question the applicability of standard approaches to identifying vetch species in the section Peregrinae. The objective of the work was to clarify the nature of seed proteins degradation in representatives of the Peregrinae section and to find ways to prevent it to ensure the possibility of carrying out species identification and registration of all accessions in the vetch collection using a unified approach. Material and methods. Seed proteins of a number of vetch species Vicia L. from sections Bithynicae (B. Fedtsch.) Maxted, Hypechusa (Alef.) Aschers. et Graebner, Microcarinae Maxted and Peregrinae, members of the subgenus Vicia, were analyzed by SDS-electrophoresis using the standard method of protein extraction from flour with 0.025 M Tris-glycine buffer pH 8.3 at room temperature and its modifications, including heating the extract at 80°C or 100°C with or without the addition of 2-mercaptoethanol, as well as the addition of cysteine and serine protease inhibitors. Results and discussion. An analysis of seed proteins of representatives of most sections of the subgenus Vicia yielded informative species-specific protein profiles, whereas species of the section Peregrinae were characterized by the protein profiles, which indicated protein degradation, and species of this section differed in the frequency of such profile occurrence. While such profiles were obtained for all seeds of seven accessions of V. aintabensis Boiss & Hausskn. ex Boiss differing in geographical origin, year and place of regeneration, and 12 out of 13 of V. peregrine L. accessions demonstrated profiles of partially or completely degraded proteins, complete seed protein profiles were obtained for six out of nine V. michauxii Sprengel accessions. A change in conditions for protein isolation, namely replacement of their extraction from flour with Tris-glycine buffer pH 8.3 at room temperature with extraction in the same buffer by a short-term heating at 100°C in the presence of 2-mercaptoethanol, made it possible to obtain complete protein profiles for all accessions representing the section Peregrinae. The protein profiles of representatives of other vetch sections, as well as the profile of soybean proteins used as a standard for legume species identification, did not differ from the original ones under the modified conditions. Conclusions. The obtained results suggest that protein degradation in species of the Peregrinae section is associated with the abnormal activity of endogenous seed proteases under standard protein extraction conditions, and this trait is determined genotypically. A new modification of the method for isolating proteins from seeds makes it possible to apply the generally accepted approaches based on SDS-electrophoresis in the analysis of the gene pool of the Peregrinae section of the subgenus Vicia, as well as other vetch species.

Design and Synthesis of Benzimidazole Carboxamide Cysteine Protease Inhibitors as Promising Anti-leishmanial Agents.

More than 20 protozoan species of Leishmania are responsible for causing Leishmaniasis, an infection spread by blood-feeding phlebotomine sandflies. A narrow pool of drugs is currently available rendering the current drug stratagem to treat this infection . Development of novel, less toxic, and more effective regimens is thus a need of the hour. Design and synthesis of benzo[d]imidazole carboxamides as agents to combat Leishmaniasis are also required. 14 benzo[d]imidazole carboxamides were synthesized and gauged against L. donovani promastigotes and intramacrophage amastigote forms. All of the tested compounds exhibited significant anti-promastigote properties with IC50 well below 10 uM. Compounds 4a, 4b, and 4d, showing the highest anti-parasitic activity against promastigote forms (IC50 0.91- 1.33 μM), were also found to be associated with better anti-leishmanial potential (IC50 0.78- 1.67 μM) against the intramacrophage amastigotes comparable to Amphotericin-B (0.13 μM), a drug used for Leishmaniasis. Compound (4a), namely N-(2-(trifluoromethyl)-1Hbenzo[ d]imidazol-5-yl)benzo[d][1,3]-5-carboxamide-dioxole, was found to be most potent against L. donovani amastigotes among all the tested compounds, and demonstrated better antileishmanial properties (IC50 0.78 μM) when compared to the standard. Compound 4a was also assessed for its toxicity profile against THP-1 human monocytic cells. To establish the molecular target(s) in silico, molecular docking studies were performed against cysteine protease, a putative virulence factor of Leishmania parasites, and nucleoside diphosphate kinase, an enzyme with a critical role in nucleotide recycling, also associated with resistance in Leishmania strains. Compound 4a showed better binding affinity than the standard to these targets; furthermore, the molecular dynamic simulation studies further affirmed the stability of compound 4a, within the active site of the targets. In vitro, cysteine protease inhibitory activity (IC50 8.53 μM) using Bz-Arg-AMC hydrochloride fluorogenic peptide substrate established the promising potential of 4a as a cysteine protease inhibitor. Computational ADMET analysis indicated appropriate pharmacokinetic profile and physicochemical characteristics for all members of the synthesized library. Both in vitro and in silico studies indicate that the synthesized imidazole carboxamides can act as potent hits and that N-(2-(trifluoromethyl)-1H-benzo[d]imidazol-5- yl)benzo[d][1,3]-5-carboxamide-dioxole 4a can be an effective hit molecule which can be further developed into potent lead molecule (s) to fight Leishmania donovani.

Discovery of a Highly Promising Disulfide Derivative Scaffold as Inhibitor of SARS-CoV-2 Main Protease.

The main protease (Mpro) of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) represents a promising target for antiviral drugs aimed at combating COVID-19. Consequently, the development of Mpro inhibitor is an ideal strategy for combating the virus. In this study, we identified twenty-two dithiocarbamates (1 a-h), dithiocarbamate-Cu(II) complexes (2 a-hCu) and disulfide derivatives (2 a-e, 2 i) as potent inhibitors of Mpro, with IC50 value range of 0.09-0.72, 0.9-24.7, and 15.1-111 μM, respectively, through FRET screening. The enzyme kinetics, inhibition mode, jump dilution, and DTT assay revealed that 1 g may be a partial reversible inhibitor, while 2 d and 2 f-Cu are the irreversible and dose- and time-dependent inhibitors, potentially covalently binding to the target. Binding of 2 d, 2 f-Cu, and 1 g to Mpro was found to decrease the stability of the protein. Additionally, DTT assays and thermal shift assays indicated that 2 f-Cu and 2 d are the nonspecific and promiscuous cysteine protease inhibitor. ICP-MS implied that the inhibitory activity of 2 f-Cu may stem from the uptake of Cu(II) by the enzyme. Cytotoxicity assays demonstrated that 2 d and 1 g exhibit low cytotoxicity, whereas 2 f-Cu show certain cytotoxicity in L929 cells. Overall, this work presents two promising scaffolds for the development of Mpro inhibitors to combat COVID-19.

Rhodesain inhibitors on the edge of reversibility-irreversibility

A comparative study of Michael acceptor and keto-Michael acceptor inhibitors of the cysteine protease rhodesain has been performed. Five new inhibitors have been prepared bearing the peptide structure of the known cysteine protease inhibitor K11777 and differing on the warhead. For the preparation of the Michael acceptor warhead, a Horner-Wadsworth-Emmons reaction was used. In the synthetic routes of the keto-Michael acceptor warheads, keto-enoate and keto-vinyl sulfone, a metathesis reaction and a radical sulfonylation were the key steps, respectively. Interestingly, keto-Michael acceptors inhibited rhodesain through a dual mode of action, showing reversibility at low inhibitor concentrations and irreversibility at high inhibitor concentrations.

Efficacy of a cysteine protease inhibitor compared with enalapril in murine heart failure models

Cysteine proteases calpains contribute to heart failure (HF), but it remains unknown whether their inhibition provides any benefit compared to standard pharmacological treatment for HF. Here, we characterize the pharmacological properties of NPO-2270 (NPO) as a potent inhibitor of cysteine proteases. Then, we describe that acute administration of NPO in rodent models of transient ischemia at the time of reperfusion reduces myocardial infarction, while its chronic oral administration attenuates adverse remodeling and cardiac dysfunction induced by ischemic and non-ischemic pathological stimuli more effectively than enalapril when given at the same dose. Finally, we provide evidence showing that the effects of NPO correlate with calpain inhibition and the preservation of the T-tubule morphology, due at least in part to reduced cleavage of the calpain substrate junctophilin-2. Together, our data highlight the potential of cysteine protease inhibition with NPO as a therapeutic strategy for the treatment of heart failure.

To Explore Potential Natural Inhibitors of Cysteine Proteases to Combat Human African Trypanosomiasis and Chagas Disease.

Human African Trypanosomiasis (HAT), also known as sleeping sickness, and Chagas disease are neglected tropical diseases caused by Trypanosoma brucei and Trypanosoma cruzi, respectively. These diseases present significant challenges in treatment due to the toxicity, low efficacy, and drug-resistant strains associated with current therapies. Cysteine proteases play vital roles in the life cycles of these parasites, making them potential targets for therapeutic intervention. Natural inhibitors sourced from plants, marine organisms, and microorganisms show promise for developing novel therapies. This review surveys the potential of natural inhibitors as therapeutic agents against HAT and Chagas disease. It compiles PubMed and PubChem information from various studies to provide an overview of their activities and characteristics, including their ability to inhibit cysteine proteases, modulate the host immune response, and interfere with other parasite proteins. Several natural inhibitors, such as berberine, curcumin, and tannins, have been identified and characterized. These inhibitors have demonstrated encouraging outcomes in both in vitro and in vivo experiments, indicating their potential as therapeutic agents for HAT and Chagas disease. Natural inhibitors of cysteine proteases offer a promising avenue for developing novel therapies against HAT and Chagas disease. Further research is needed to identify additional natural inhibitors and optimize their efficacy and safety for human use. The significance of this study lies in its potential to contribute to the discovery of effective, safe, and affordable treatments for these neglected tropical diseases.

Development of a new experimental NMR strategy for covalent cysteine protease inhibitors screening: toward enhanced drug discovery.

In the development of antiviral drugs, proteases and polymerases are among the most important targets. Cysteine proteases, also known as thiol proteases, catalyze the degradation of proteins by cleaving peptide bonds using the nucleophilic thiol group of cysteine. As part of our research, we are examining how cysteine, an essential amino acid found in the active site of the main protease (Mpro) enzyme in SARS-CoV-2, interacts with electrophilic groups present in ethacrynic acid (EA) and compounds 4, 6, and 8 to form sulfur-carbon bonds. Nuclear magnetic resonance (NMR) spectroscopy was used to monitor the reaction rate between cysteine and Michael acceptors. We found that the inhibitory activity of these compounds towards Mpro is correlated to their chemical reactivity toward cysteine. This approach may serve as a valuable tool in drug development for detecting potential covalent inhibitors of Mpro and other cysteine proteases.

Identification, molecular profiling and immune functions of cystatin M in silver pomfret (Pampus argenteus)

Cystatins play an important role in various physiological and pathological processes of organisms, including regulating protein metabolism, antigen processing, inflammatory response, nutritional disorders, and controlling enzyme activity. However, research on immunity functions of fish cystatin M is limited. In this study, Pampus argenteus cystatin M (Pacystatin M) was identified and analyzed. Its amino acid sequence was highly conserved in teleosts, and included the conserved cystatin cysteine protease inhibitor motifs. Pacystatin M was highly expressed in the gill, spleen, and intestine, whereas the expression levels of liver and kidney were lower. Furthermore, Nocardia seriolae infection up-regulated the expression of Pacystatin M in the kidney, spleen and liver, with particularly significant expression observed in the liver on day 15 post-infection. Functional analysis indicated that the recombinant Pacystatin M showed increasing inhibitory activity against papain within a certain concentration range, suggesting that the inhibition was likely competitive. Additionally, Pacystatin M demonstrated the ability to inhibit bacterial growth and high thermal stability. These results suggested that Pacystatin M might be involved in the immune response to microbial invasion and provided new reference addressing disease issues in the large-scale farming of silver pomfret.

Phenotypic and transcriptomics characterization uncovers genes underlying tuber yield traits and gene expression marker development in potato under aeroponics.

Transcriptome analysis in potato varieties revealed genes associated with tuber yield-related traits and developed gene expression markers. This study aimed to identify genes involved in high tuber yield and its component traits in test potato varieties (Kufri Frysona, Kufri Khyati, and Kufri Mohan) compared to control (Kufri Sutlej). The aeroponic evaluation showed significant differences in yield-related traits in the varieties. Total RNA sequencing was performed using tuber and leaf tissues on the Illumina platform. The high-quality reads (QV > 25) mapping with the reference potato genomes revealed statistically significant (P < 0.05) differentially expressed genes (DEGs) into two categories: up-regulated (> 2 Log2 fold change) and down-regulated (< -2 Log2 fold change). DEGs were characterized by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Collectively, we identified genes participating in sugar metabolism, stress response, transcription factors, phytohormones, kinase proteins, and other genes greatly affecting tuber yield and its related traits. A few selected genes were UDP-glucose glucosyltransferase, glutathion S-transferase, GDSL esterase/lipase, transcription factors (MYB, WRKY, bHLH63, and BURP), phytohormones (auxin-induced protein X10A, and GA20 oxidase), kinase proteins (Kunitz-type tuber invertase inhibitor, BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1) and laccase. Based on the selected 17 peptide sequences representing 13 genes, a phylogeny tree and motifs were analyzed. Real time-quantitative polymerase chain reaction (RT-qPCR) analysis was used to validate the RNA-seq results. RT-qPCR based gene expression markers were developed for the genes such as 101kDa heat shock protein, catechol oxidase B chloroplastic, cysteine protease inhibitor 1, Kunitz-type tuber invertase inhibitor, and laccase to identify high yielding potato genotypes. Thus, our study paved the path for potential genes associated with tuber yield traits in potato under aeroponics.

CST3 alleviates retinal vascular leakage by regulating the Rap1 signaling pathway

Retinal vascular leakage is a major event in several retinal diseases, including diabetic retinopathy (DR). In a previous study, we demonstrated that the aqueous humor concentration of Cystatin C (CST3), a physiological inhibitor of cysteine protease, is negatively correlated with the severity of diabetic macular edema. However, its function in the retina has not been clearly elucidated. In this study, we found a significant decrease in the aqueous humor concentration of CST3 with DR progression. Furthermore, we found that CST3 was expressed in retinal endothelial cells and that its expression was significantly downregulated in high glucose-treated human retinal microvascular endothelial cells (HRMECs) and the retinal vessels of oxygen-induced retinopathy (OIR) mice. Silencing CST3 expression resulted in decreased HRMEC migration and tubule formation ability. Exogenous addition of the CST3 protein significantly improved HRMEC migration and tubular formation. In-vivo experiments demonstrated that CST3 silencing induced retinal vascular leakage in WT mice, while its intravitreal injection significantly reduced retinal leakage in OIR mice. Mechanistically, CST3 promoted the expression of the downstream adhesion molecules, claudin5, VE-cadherin, and ZO-1, in retinal vascular cells by regulating the Rap1 signaling pathway. Therefore, this study revealed a novel mechanism by which CST3 improves retinal vascular function and provided evidence that it is a potential therapeutic target for retinal vascular leakage.

Identification and functional characterization of a novel cystatin in amphioxus, ancient origin of vertebrate type-2 cystatin homologues

Cystatins are well known as a vast superfamily of functional proteins participated in the reversible competitive inhibition of cysteine proteases. Currently, increasing evidences point to the extensive phylogenetic diversity and crucial immune roles of type-2 cystatins in the vertebrate species. However, no information is available regarding the homologue in cephalochordate amphioxus, the representative of most basal living chordates, whose immune regulation are still ambiguous. Here, we clearly identified the presence of type-2 cystatin gene in amphioxus Branchiostoma japonicum, termed Bjcystatin-2, which was structurally characterized by typical wedge-shaped cystatin feature. Evolutionary analyses revealed that Bjcystatin-2 is the putative ancestral type-2 cystatin for chordates, with gene diversity emerging through duplication events. The expression of Bjcystatin-2 showed tissue-specific profile and was inducible upon invasive pathogens. Significantly, the recombinant Bjcystatin-2 exhibited not merely cathepsin L inhibitory activity, but also the ability to bind with bacteria and their characteristic molecules. Furthermore, Bjcystatin-2 also showed the capacity to enhance the macrophage-driven bacterial phagocytosis and to attenuate the generation of pro-inflammatory cytokines within macrophages. In summary, these findings demonstrate that Bjcystatin-2 exhibits dual role acting as both a protease inhibitor and an immunoactive molecule, greatly enriching our understanding of immune defense mechanisms of type-2 cystatin within the amphioxus.

Functional analysis of novel cystatins from Haemaphysalis doenitzi and evaluation of their roles in cypermethrin and λ-cyhalothrin resistance

Currently, the primary strategy for tick control relies on chemical agents. Pyrethrins, which are botanically derived compounds, have demonstrated efficacy in controlling ticks without posing a risk to human or animal health. However, research into pyrethrins' metabolic mechanisms remains sparse. Cystatin, as a reversible binding inhibitor of cysteine protease, may be involved in the initiation of pyrethrin detoxification of Haemaphysalis doenitzi. In this study, two novel cystatins were cloned, HDcyst-3 and HDcyst-4, the relative expression of which was highest in the Malpighian tubules compared with the tick midguts, salivary glands, and ovaries. Prokaryotic expression and in vitro studies revealed that cystatins effectively inhibit the enzymatic activities of cathepsins B and S. RNAi results showed that the reduction of cystatins significantly decreased the engorgement weight, egg mass weight, and egg hatching rate of adult female ticks, and prolonged feeding time by two days. The control rate of rHDcyst-3 and rHDcyst-4 protein vaccination against female adults were 55.9% and 63.2%, respectively. In addition, the tick immersion test showed that cypermethrin and λ-cyhalothrin had significant acaricidal effects against adult unfed H. doenitzi. The qPCR result indicated that compared with the control group, the expression of HDcyst-3 and HDcyst-4 was markedly decreased in the sublethal cypermethrin and λ-cyhalothrin group at LC50. Enzyme activity showed that cypermethrin and λ-cyhalothrin could significantly induce the activities of glutathione S-transferase (GST), carboxylesterase (CarE), and acetylcholinesterase (AchE). The aforementioned results provided indirect evidence that cystatin plays an important role in pyrethrin detoxification and provides a theoretical basis for future acaricide experiments and pest management.