Protein Lysates Research Articles

The orphan receptor Nur77 binds cytoplasmic LPS to activate the non-canonical NLRP3 inflammasome

Intracellular sensing of lipopolysaccharide (LPS) by murine caspase-11 or human caspase-4 initiates a protease cascade, termed the non-canonical inflammasome, that results in gasdermin D (GSDMD) processing and subsequent NLRP3 inflammasome activation. In an effort aimed at identifying additional sensors for intracellular LPS by biochemical screening, we identified the nuclear orphan receptor Nur77 as an LPS-binding protein in macrophage lysates. Nr4a1-/- macrophages exhibited impaired activation of the NLRP3 inflammasome, but not caspase-11, in response to LPS. Biochemical mapping revealed that Nur77 bound LPS directly through a domain in its C terminus. Yeast two-hybrid assays identified NLRP3 as a binding partner for Nur77. The association between Nur77 and NLRP3 required the presence of LPS and dsDNA. The source of dsDNA was the mitochondria, requiring the formation of gasdermin-D pores. Invivo, Nur77 deficiency ameliorated host response to endotoxins. Thus, Nur77 functions as an intracellular LPS sensor, binding mitochondrial DNA and LPS to activate the non-canonical NLRP3 inflammasome.

Epigallocatechin-3-Gallate Prevents the Acquisition of a Cancer Stem Cell Phenotype in Ovarian Cancer Tumorspheres through the Inhibition of Src/JAK/STAT3 Signaling

Three-dimensional tumorsphere cultures recapitulate the expression of several cancer stem cell (CSC) biomarkers and represent an effective in vitro platform to screen the anti-CSC properties of drugs. Whereas ovarian carcinoma is among the leading causes of death for women, ovarian CSC (OvCSC), a highly malignant subpopulation of ovarian cancer cells, is thought to be responsible for therapy resistance, metastasis, and tumor relapse. Epigallocatechin-3-gallate (EGCG), a diet-derived active polyphenol found in green tea leaves, can suppress ovarian cancer cell proliferation and induce apoptosis. However, its capacity to prevent the acquisition of cancer stemness traits in ovarian malignancies remains unclear. Here, we exploited the in vitro three-dimensional tumorsphere culture model to explore the capacity of EGCG to alter CSC biomarkers expression, signal transducing events and cell chemotaxis. Total RNA and protein lysates were isolated from human ES-2 ovarian cancer cell tumorspheres for gene assessment by RT-qPCR and protein expression by immunoblot. Real-time cell chemotaxis was assessed with xCELLigence. Compared with their parental adherent cells, tumorspheres expressed increased levels of the CSC markers NANOG, SOX2, PROM1, and Fibronectin. EGCG treatment reduced dose-dependently tumorspheres size and inhibited the transcriptional regulation of those genes. Src and JAK/STAT3 signaling pathways appeared to be relevant for CSC phenotype and chemotactic response. In conclusion, these data highlight and support the chemopreventive benefits of the diet-derived EGCG and its capacity to target intracellular transducing events that regulate the acquisition of an invasive CSC phenotype.

A serological assay to detect and differentiate rodent exposure to soft tick and hard tick relapsing fever infections in the United States

Human cases of relapsing fever (RF) in North America are caused primarily by Borrelia hermsii and Borrelia turicatae, which are spread by argasid (soft) ticks, and by Borrelia miyamotoi, which is transmitted by ixodid (hard) ticks. In some regions of the United States, the ranges of the hard and soft tick RF species are known to overlap; in many areas, recorded ranges of RF spirochetes overlap with Lyme disease (LD) group Borrelia spirochetes. Identification of RF clusters or cases detected in unusual geographic localities might prompt public health agencies to investigate environmental exposures, enabling prevention of additional cases through locally targeted mitigation. However, exposure risks and mitigation strategies differ among hard and soft tick RF, prompting a need for additional diagnostic strategies that differentiate hard tick from soft tick RF. We evaluated the ability of new and previously described recombinant antigens in serological assays to differentiate among prior exposures in mice to LD, soft or hard tick RF spirochetes. We extracted whole-cell protein lysates from RF Borrelia cultures and synthesized six recombinant RF antigens (Borrelia immunogenic protein A (BipA) derived from four species of RF Borrelia, glycerophosphodiester phosphodiesterase (GlpQ), and Borrelia miyamotoi membrane antigen A (BmaA)) to detect reactivity in laboratory derived (Peromyscus sp. and Mus sp.) mouse serum infected with RF and LD Borrelia species. Among 44 Borrelia exposed mouse samples tested, all five mice exposed to LD spirochetes were correctly differentiated from the 39 mice exposed to RF Borrelia using the recombinant targets. Of the 39 mice exposed to RF spirochetes, 28 were accurately categorized to species of exposure (71%). Segregation among soft tick RF species (Borrelia hermsii, Borrelia parkeri and Borrelia turicatae) was inadequate (58%) owing to observed cross-reactivity among recombinant BipA protein targets. However, among the 28 samples accurately separated to species, all were accurately assigned to soft tick or hard tick RF type. Although not adequately specific to accurately categorize exposure to soft tick RF species, the recombinant BipA protein targets from soft and hard tick RF species show utility in accurately discriminating mouse exposures to LD or RF Borrelia, and accurately segregate hard tick from soft tick RF Borrelia exposure.

A21 ROLE OF SIALIC ACID O-ACETYLATION IN MAINTAINING MUCUS INTEGRITY AND HOMEOSTASIS OF THE COLONIC MUCOSA

Abstract Background The mucus network provides innate immune defense to protect our gastrointestinal tract from pathogens, and promote homeostasis with our resident microbiota. This network is constituted by the mucin MUC2 (Muc2 in mouse), which is ~80% complex O-linked glycans by weight. Sialic acid (Sia) is a key capping monosaccharide on complex O-glycans which has recently been linked to preserving mucus integrity. Sia can undergo enzymatic modifications including the addition of O-acetyl groups. The 9-O-acetyltransferase CasD1 is responsible for the 9-OAc Sia variants. Functionally, the OAc-modification is known to inhibit microbial sialidase activities which may preserve Sia’s protective roles on mucins. However, the extent of these OAc modifications in human and murine Mucin-2, and how they influence mucus function is unclear. Purpose: To determine whether and how Sia O-acetylation on colonic mucus regulates mucus integrity, host-microbe interactions, and colitis susceptibility. Method We used viral-derived probes that target specific OAc-Sia analogues on mucus on sections from human feces and mouse feces and colon tissues to visualize their spatial arrangement and microbial interaction in situ. For glycomics, OAc-Sia analogues were quantitated on purified human MUC2 and mouse Muc2 by HPLC-MS after derivatization with 4,5-dimethyl-1,2-diaminobenzamine (DMBA). O-glycans were released via non-reductive ammonia-catalyzed β-elimination and analyzed by mass spectrometry. For in vivo work, we generated intestinal epithelial cell-specific Casd1 KO mice (Casd1flox/flox;VillinCre or IEC Casd1-/- mice) and analyzed their mucins. Sialidase activities were quantified in the supernatants of colon fecal materials from WT and IEC Casd1-/- mutants mice using a fluorogenic substrate 4-MU-NeuNAc. Colitis susceptibility was monitored using 1.5% w/v Dextran Sodium Sulfate (DSS). Result(s) We found Sias on both human MUC2 and murine Muc2 were heavily O-acetylated, with ~75% and ~45% of Sias having 9-OAc-based modification in humans and mice respectively, and were distributed throughout the niche and barrier layers of mucus in situ. IEC Casd1-/- mice were viable and healthy with knockdown confirmed by 9-OAc staining, western blot of protein lysates and mucins, and sialylomics. The mucus encapsulation appeared overall intact regardless of OAc status. However, IEC Casd1-/- mice showed heightened susceptibility to 1.5% DSS colitis, linked to thinning of the mucus in IEC Casd1-/- vs WT littermates after challenge. Consistent with the role of OAc Sia in sialidase inhibition, loss of OAc Sia was associated with increased sialidase activities as assessed by heightened 4 MU signal in fecal supernatants in WT vs littermate IEC Casd1-/- mice. O-glycomics also showed reduction in the number of sialylated O-glycan structures upon loss of 9-OAc Sia. Conclusion(s) Sia O-acetylation appears important in maintaining key aspects of Sia-dependent mucus function and protecting from inflammatory insult. Please acknowledge all funding agencies by checking the applicable boxes below: CCC Disclosure of Interest None Declared

Abstract P2-26-15: CCR7 expression in Inflammatory breast cancer

Abstract Background: Inflammatory breast cancer is an aggressive breast cancer characterized by florid congestion of lymphovascular spaces by tumor emboli. CCR7 is an immune cell receptor that mediates traffic of immune cells into lymphatics that can be expressed on tumor cells. An RNA-seq screen of tumor promoting mammary glands in mice identified CCR7 as an upregulated signal in mammary glands that promoted IBC-like skin invasion. We examined the expression of CCR7 in IBC cell lines and patients to determine the prevalence of this receptor in IBC. Methods: Protein lysates from IBC and non-IBC cell lines were subjected to immunoblotting using anti CCR7 (R&D systems). An IBC tissue microarray from post-chemotherapy mastectomy specimens of 39 patients, each with three replicates was subjected to immunohistochemical staining for CCR7 (Invitrogen, catalog number MA5-31992) performed using a Leica Bond RX autostainer with an incubation time of 60 minutes at 1:15,000 after 20 minutes of heat-induced antigen retrieval at pH 6.0. In 15 cases there were no tumor cells observed in the cores. Staining was scored by an expert breast pathologist for intensity and percent tumor stained. Staining patterns were scored. Descriptive statistics were examined for representation by receptor subtype. Results: CCR7 staining was strong in all lines examined including MCF7, SUM149, SUM190, MDA-IBC, and SUM159. Among 24 IBC patient cores with tumor in the tissue, 23 (96%) expressed CCR7 in tumor, 15 with complete membranous staining and 9 with incomplete membranous staining. In one case with LVSI the emboli were CCR7 positive. Among the 24 positive cases, 22 were 3+ intensity while two were 2+. Nine CCR7+ cases were estrogen receptor (ER) ER+, 8 ER-, and 6 unknown. HER2 status is pending. Conclusions: CCR7 expression is present across tumor subtypes in IBC cell lines and in both ER+ and ER- patient tumors. Given developing novel pharmacologic targeting of CCR7, this target warrants further investigation in IBC and other breast cancers. Citation Format: Wintana Balema, Savitri Krishnamurthy, Alison Lawrence, Megan Rodriguez, Richard Larson, Natalie Fowlkes, Naoto T. Ueno, Wendy Woodward. CCR7 expression in Inflammatory breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-26-15.

Ezrin and Its Phosphorylated Thr567 Form Are Key Regulators of Human Extravillous Trophoblast Motility and Invasion.

The protein ezrin has been shown to enhance cancer cell motility and invasion leading to malignant behaviours in solid tumours, but a similar regulatory function in the early physiological reproduction state is, however, much less clear. We speculated that ezrin may play a key role in promoting first-trimester extravillous trophoblast (EVT) migration/invasion. Ezrin, as well as its Thr567 phosphorylation, were found in all trophoblasts studied, whether primary cells or lines. Interestingly, the proteins were seen in a distinct cellular localisation in long, extended protrusions in specific regions of cells. Loss-of-function experiments were carried out in EVT HTR8/SVneo and Swan71, as well as primary cells, using either ezrin siRNAs or the phosphorylation Thr567 inhibitor NSC668394, resulting in significant reductions in both cell motility and cellular invasion, albeit with differences between the cells used. Our analysis further demonstrated that an increase in focal adhesion was, in part, able to explain some of the molecular mechanisms involved. Data collected using human placental sections and protein lysates further showed that ezrin expression was significantly higher during the early stage of placentation and, importantly, clearly seen in the EVT anchoring columns, further supporting the potential role of ezrin in regulating migration and invasion in vivo.

Increase of Claudin-5, ICAM-1 and eNOS expressions in human brain endothelial cells by ammonium chloride

Abstract Objectives Lysosomal dysfunction could lead to a failure in the degradation process of waste materials, especially for the elimination of aggregated, misfolded and senescence proteins or organelles. Human brain endothelial cells (HBECs) are a part of the blood-brain barrier and any disruption of lysosomal functions could affect the cellular functions of the HBECs. Protein expression studies on the cells could give an insight to associate lysosomal dysfunction on HBECs homeostasis. The aim of this study was to measure the cellular changes via the expression of several proteins such as Claudin-5, which is a tight junction protein; intracellular adhesion molecule 1 (ICAM-1), an inflammatory marker and endothelial nitric oxide synthase (eNOS), which provides nitric oxide (NO) for vasodilation. These components are important in maintaining homeostasis as the imbalance could lead to endothelial impairment linked brain related disorders such as neurodegenerative disease. Methods HBECs were treated with 10 mM ammonium chloride, which is a lysosome inhibitor for 1 h. The protein lysates were collected and subjected for ICAM-1 and Claudin-5 measurement by capillary immunoassay instrument, while eNOS by ELISA. Results Claudin-5 and ICAM-1 expression significantly increased (p<0.05). The ELISA results showed eNOS increment (p<0.001) compared to control. Lysosome inhibitor could be associated with accumulation of organelles that can stimulates inflammation and initial cellular responses. Conclusions Inhibition of lysosome by the inhibitor increases protein expressions related with endothelial function.

Comparative Analysis of Protein Folding Stability-Based Profiling Methods for Characterization of Biological Phenotypes.

Recently, a new suite of mass spectrometry-based proteomic methods has been developed that enables evaluation of protein folding stability on the proteomic scale. These methods utilize chemical and thermal denaturation approaches (SPROX and TPP, respectively) as well as proteolysis strategies (DARTS, LiP, and PP) to assess protein folding stability. The analytical capabilities of these technique have been well-established for protein target discovery applications. However, less is known about the relative advantages and disadvantages of using these different strategies to characterize biological phenotypes. Reported here is a comparative study of SPROX, TPP, LiP, and conventional protein expression level measurements using both a mouse model of aging and a mammalian cell culture model of breast cancer. Analyses on proteins in brain tissue cell lysates derived from 1- and 18-month-old mice (n = 4-5 at each time point) and on proteins in cell lysates derived from the MCF-7 and MCF-10A cell lines revealed a majority of the differentially stabilized protein hits in each phenotype analysis had unchanged expression levels. In both phenotype analyses, TPP generated the largest number and fraction of differentially stabilized protein hits. Only a quarter of all the protein hits identified in each phenotype analysis had a differential stability that was detected using multiple techniques. This work also reports the first peptide-level analysis of TPP data, which was required for the correct interpretation of the phenotype analyses performed here. Studies on selected protein stability hits also uncovered phenotype-related functional changes.

Transport Mechanism for Nuclear Localization of Irradiation-Activated EGFR Measured by Single-Molecule Pull-Down Assay.

Nuclear transport of epidermal growth factor receptor (EGFR) is considered to be a key cause of radiation resistance in cancer therapy. Here, we showed that irradiation-activated EGFR binds to the nuclear transport protein karyopherin alpha (KPNA) rather than karyopherin subunit beta 1 (KPNB1), through a single-molecule pull-down assay, which allows measurement of the binding affinity by single proteins in cell lysate without an additional purification step. We also obtained kinetic parameters for the binding between the phosphorylated nuclear localization signal (NLS) peptide of EGFR (645RRRHIVRKRpTLRR657) and KPNA. This observation may help developing small molecules to modulate nuclear transport, which potentially reduces the radiation resistance during irradiation therapy.

Atrial cardiomyocytes from a canine model of atrial fibrillation demonstrate reduced force development and altered expression of contractile proteins.

Atrial fibrillation (AF) is the most common cardiac rhythm disturbance and associates with worse outcomes in cardiac contractile-related diseases including cardiomyopathy. As most studies surrounding AF focus on the electrophysiology of the disease, there is little known about cardiomyocyte contractile function in AF. We used atrial tissue from an established atrial tachypacing canine model of AF. Whole protein lysates were collected from the atria to conduct mass spectrometry analysis showing dysregulation of numerous molecular pathways, including contractility. Skinned atrial cardiomyocytes were isolated from the tissue for force calcium and passive tension experiments. Force calcium experiments showed a significant reduction in the maximum force of contraction of AF cardiomyocytes. To explain this, myosin heavy chain (MHC) isoform expression was evaluated because isoform switching is known to alter force of contraction. Decreased percent beta expression was found, explaining the reduction of force due to MHC alpha's capacity for reduced force of contraction. AF cardiomyocytes showed increased calcium sensitivity of force development, which may translate to prolonged contraction with slower relaxation in vivo. A significant reduction in S100A1 was seen in the AF samples via mass spectrometry, which is associated with increased calcium sensitivity. Prolonged contraction along with reduced force of each contraction could support the development of atrial clots. Atrial cardiomyocytes from the AF hearts demonstrated a significant reduction in the passive tension. Evaluation of titin isoform expression, which is known to alter passive tension, showed increased titin degradation, supporting the capacity for atrial dilation in vivo. Discerning the role of contractility in the pathology of atrial fibrillation could provide novel avenues of AF treatment, especially in instances where it is associated with contractile diseases.

Dissecting molecular regulation of unconventional protein secretion.

Many elegant studies have revealed conserved molecular principles underlying the classical ER-Golgi-Secretory pathway for protein secretion. However, over the past two decades, several cytoplasmic proteins involved in innate immunity, angiogenesis, and neuronal pathogenicity have been shown to be secreted via ER-Golgi independent, “unconventional” secretory routes. Thus, understanding the molecular regulation of unconventional cytoplasmic protein secretion (UCPS) is of considerable interest. Our current studies are focused on 1) identifying unconventionally secreted proteins using an unbiased high-throughput mass-spectrometry based approach and 2) identifying regulators of UCPS using whole-genome CRISPR screening. By comparing levels of a given protein in conditioned media and cell lysates, our analysis effectively discriminates between authentically secreted proteins and non-secreted proteins released into the extracellular media from dead or dying cells. Coupling this approach with treatment of cells with Brefeldin-A, an inhibitor of ER-Golgi traffic, we have identified Brefeldin-A resistant peptides derived from candidate unconventionally secreted proteins from Huh7 (hepatocyte) and THP1 (immune) cell lines and primary endothelial cells. As expected, most highly secreted proteins from these cell lines were observed to contain signal peptides, presumably mediating traffic through the conventional ER/Golgi secretory pathway, with a minor fraction of the secretome consisting of unconventionally secreted proteins. Our analysis has identified several novel candidate UCPS cargoes, as well as confirming previously reported UCPS cargoes including metallothionein and leukocyte elastase inhibitor. A preliminary whole genome CRISPR screen for modulators of secretion for the known UCPS cargo, interleukin-1β (IL-1β), identified PIK3C2A (a lipid kinase known to be localized to the endo-lysosomal system), molecular motor proteins, and other protein kinases as candidate regulators of UCPS. Our preliminary studies also suggest significant heterogeneity in the regulation of UCPS across cell types, with PIK3C2A selectively influencing IL-1β secretion in non-pyroptotic cells.

Molecular and immunological characterization of the calcyclin binding protein in rodent malaria parasite

Malaria remains as a global life-threatening disorder due to the emergence of resistance against standard antimalarials. Consequently, there is a serious need to better understand the biology of the malaria parasite in order to determine appropriate targets for new interventions. Calcyclin binding protein (CacyBP) is a multi-functional and multi-ligand protein that is not well characterized in malaria disease. In this study, we have cloned CacyBP from rodent species Plasmodium yoelii nigeriensis and purified the recombinant protein to carry out its detailed molecular, biophysical and immunological characterization. Molecular characterization indicates that PyCacyBP is a ∼27 kDa protein in parasite lysate and exists in monomer and dimer forms. Bioinformatic analysis of CacyBP showed significant sequence and structural similarities between rodent and human malaria parasites. CacyBP is expressed in all blood stages of P. yoelii nigeriensis parasite. In silico studies proposed the immunogenic potential of CacyBP. The rPyCacyBP immunized mice exhibited elevated levels of IgG1, IgG2a, IgG2b and IgG3 in their serum. Notably, cellular immune response in splenocytes from immunized mice showed increased expression of pro-inflammatory cytokines such as IL-12, IFN-γ and TNF-α. This CacyBP exhibited pro-inflammatory immune response in rodent host. These finding revealed that CacyBP may have the potential to boost the host immunity for protection against malaria infection. The present study provides basis for further exploration of the biological function of CacyBP in malaria parasite.

An exploratory study on the effect of choline and folate deficiency on levels of vascularization proteins and transcription factors in first trimester trophoblast HTR-8/SVneo cells.

We studied the effect of choline and folate deficiencies on levels of predetermined placental proteins during early development. We incubated HTR-8/SVneo cells under choline and folate deficiency conditions and measured levels of some placental proteins using ELISA methods. Concentrations of LRP2 protein in cell lysates were higher in cells incubated in choline and folate deficient media compared to the control media (mean [SD]=2.95 [1.30] vs. 1.65 [0.27] ng/mg protein, p=0.004). The levels of LRP2 protein in lysates of cells incubated in choline and folate deficient media were significantly higher than the concentrations in lysates of cells incubated in choline deficient but folate sufficient media (1.96 [0.28] ng/mg protein) or those incubated in choline sufficient but folate deficient media (1.77 [0.24] ng/mg protein) (p < 0.05 for both). The cellular levels of CDX2 protein were significantly higher in cells incubated in choline and folate deficient media compared to the control media (1.78 [0.60] vs. 0.99 [0.42] pg/mg protein, p =0.002); and compared to CDX2 levels in cells incubated in choline deficient but folate sufficient media (0.87 [0.13] pg/mg protein, p < 0.001) or in choline sufficient but folate deficient media (0.96 [0.16] pg/mg protein, p < 0.001). The levels of sFLT-1 and IGF1 in culture media and that of EOMES in HTR-8/SVneo cell lysates remained unchanged under all deficiency conditions. LRP2 and CDX2 are likely to be molecular targets for early choline and folate deficiencies in human trophoblast cells. The results should be confirmed in animal models and in other models of placental cells.

Role of overexpression mTORC1 in diabetes mellitus type 2: activation PI3K/Akt pathway

The objective of this study is investigating the role of excessive activation PI3K/Akt/mTORC1 in diabetes mellitus type 2. It’s known that the PI3K/Akt/mTORC1 pathway is involved in the pathogenesis of cancer. Study design was carried out in accordance with the guidelines of the Helsinki Declaration that included normal patients as control (n = 15), second group included patients with diabetes mellitus type 2 (n = 22) while, third group included patients with malignancy positive mTORC1 (n = 22). 81 women were examined and enrolled in this study with age from 40 to 75-year-old. Diabetes mellitus type 2 compensation was assessed by determining the level of HbA1c by the method of ion-exchange chromatography, using the BIO-RAD D-10 analyzer, PRAS40 was determined in units depending on the amount of protein in the blood cell lysates.

Lipocalin-2 promotes acute lung inflammation and oxidative stress by enhancing macrophage iron accumulation.

Lipocalin-2 (LCN2) is an acute-phase protein that regulates inflammatory responses to bacteria or lipopolysaccharide (LPS). Although the bacteriostatic role of LCN2 is well studied, the function of LCN2 in acute lung damage remains unclear. Here, LCN2 knockout (KO) mice were used to investigate the role of LCN2 in LPS-treated mice with or without recombinant LCN2 (rLCN2). In addition, we employed patients with pneumonia. RAW264.7 cells were given LCN2 inhibition or rLCN2 with or without iron chelator deferiprone. LCN2 KO mice had a higher survival rate than wild-type (WT) mice after LPS treatment. In addition to elevated LCN2 levels in serum and bronchoalveolar lavage fluid (BALF), LPS treatment also increased LCN2 protein in alveolar macrophage lysates of BALF. LCN2 deletion attenuated neutrophil and macrophage infiltration in the lungs of LPS-treated mice as well as serum and BALF interleukin-6 (IL-6). Circulating proinflammatory cytokines and LCN2-positive macrophages were prominently increased in the BALF of pneumonia patients. In addition to increase of iron-stained macrophages in pneumonia patients, increased iron-stained macrophages and oxidative stress in LPS-treated mice were inhibited by LCN2 deletion. In contrast, rLCN2 pretreatment aggravated lung inflammation and oxidative stress in LPS-treated WT mice and then resulted in higher mortality. In RAW264.7 cells, exogenous LCN2 treatment also increased inflammation and oxidative stress, whereas LCN2 knockdown markedly diminished these effects. Furthermore, deferiprone inhibited inflammation, oxidative stress, and phagocytosis in RAW264.7 cells with high LCN2 levels, as well as LPS-induced acute lung injury in WT and LCN2 KO mice. Thus, these findings suggest that LCN2 plays a key role in inflammation and oxidative stress following acute lung injury and that LCN2 is a potential therapeutic target for pneumonia or acute lung injury.

Miniprep assisted proteomics (MAP) for rapid proteomics sample preparation.

Complete enzymatic digestion of proteins for bottom-up proteomics is substantially improved by use of detergents for denaturation and solubilization. Detergents however, are incompatible with many proteases and highly detrimental to LC-MS/MS. Recently; filter-based methods have seen wide use due to their capacity to remove detergents and harmful reagents prior to digestion and mass spectrometric analysis. We hypothesized that non-specific protein binding to negatively charged silica-based filters would be enhanced by addition of lyotropic salts, similar to DNA purification. We sought to exploit these interactions and investigate if low-cost DNA purification spin-filters, 'Minipreps,' efficiently and reproducibly bind proteins for digestion and LC-MS/MS analysis. We propose a new method, Miniprep Assisted Proteomics (MAP), for sample preparation. We demonstrate binding capacity, performance, recovery and identification rates for proteins and whole-cell lysates using MAP. MAP recovered equivalent or greater protein yields from 0.5-50 μg analyses benchmarked against commercial trapping preparations. Nano UHPLC-MS/MS proteome profiling of lysates of Escherichia coli had 99.3% overlap vs. existing approaches and reproducibility of replicate minipreps was 98.8% at the 1% FDR protein level. Label Free Quantitative proteomics was performed and 91.2% of quantified proteins had a %CV <20% (2044/2241). Miniprep Assisted Proteomics can be performed in minutes, shows low variability, high recovery and proteome depth. This suggests a significant role for adventitious binding in developing new proteomics sample preparation techniques. MAP represents an efficient, ultra-low-cost alternative for sample preparation in a commercially obtainable device that costs ∼$0.50 (USD) per miniprep.

Methods to Measure NLR Oligomerization I: Size Exclusion Chromatography, Co-immunoprecipitation, and Cross-Linking.

Protein oligomerization is a common principle of regulating cellular responses. Oligomerization of NLRs is essential for the formation of NLR signaling platforms and can be detected by several biochemical techniques. Some of these biochemical methods can be combined with functional assays, such as caspase-1 activity assay. Size exclusion chromatography (SEC) allows separation of native protein lysates into different sized complexes by FPLC for follow-up analysis. Using co-immunoprecipitation (co-IP), combined with SEC or on its own, enables subsequent antibody-based purification of NLR complexes and associated proteins, which can then be analyzed by immunoblot and/or subjected to functional caspase-1 activity assay. Native gel electrophoresis also allows detection of the NLR oligomerization state by immunoblot. Chemical cross-linking covalently joins two or more molecules, thus capturing the oligomeric state with high sensitivity and stability. ASC oligomerization has been successfully used as readout for NLR/ALR inflammasome activation in response to various PAMPs and DAMPs in human and mouse macrophages and THP-1 cells. Here, we provide a detailed description of the methods used for NLRP7 oligomerization in response to infection with Staphylococcus aureus (S. aureus) in primary human macrophages, co-immunoprecipitation, and immunoblot analysis of NLRP7 and NLRP3 inflammasome complexes as well as caspase-1 activity assays. Also, ASC oligomerization is shown in response to dsDNA, LPS/ATP, and LPS/nigericin in mouse bone marrow-derived macrophages (BMDMs) and/or THP-1 cells or human primary macrophages.

Increasing the Overall Proteome Coverage by Combining Protein Digestion by Tryp-N and Trypsin.

Mass spectrometry-based proteomics combining more than one protease in parallel facilitates the identification of more peptides and proteins than when a single protease is used. Trypsin cleaves proteins C-terminally to arginine and lysine, while its mirroring protease Tryp-N cleaves N-terminally to the same amino acids. Here, we combine trypsin and Tryp-N with the commercially available S-Trap columns, which purify protein samples and catalyze digestion. Comparison of trypsin or Tryp-N coupled with S-Trap columns demonstrates plasma and cell lysate proteins unique to one protease. We thus suggest the use of both proteases in a complementary manner to obtain deeper proteome coverage.

Identification of Lignan Compounds as New 6-Phosphogluconate Dehydrogenase Inhibitors for Lung Cancer.

Targeting pentose phosphate pathway (PPP) enzymes has emerged as a promising strategy to combat cancer. 6-Phosphogluconate dehydrogenase (6-PGD), the third critical enzyme of the PPP, catalyzes oxidative decarboxylation of 6-phosphogluconate (6-PG) to produce ribulose-5-phosphate (Ru-5-P) and CO2. Overexpression of 6-PGD has been reported in multiple cancers and is recognized as a potential anticancer drug target. The current study is focused on the utilization of indispensable virtual screening tools for structure-based drug discovery. During the study, 17,000 natural compounds were screened against the 3-phosphoglycerate (3-PG) binding site of 6-PGD through a molecular operating environment (MOE), which revealed 115 inhibitors with higher selectivity and binding affinity. Out of the 115 best-fit compounds within the 6-PGD binding cavity, 15 compounds were selected and optimized through stringent in silico ADMET assessment models that justified the desirable pharmacokinetic, pharmacodynamic and physicochemical profiles of 5 ligands. Further protein−ligand stability assessment through molecular dynamics (MD) simulation illustrated three potential hits, secoisolariciresinol, syringaresinol and cleomiscosin A, with stable confirmation. Moreover, 6-PGD inhibitor validation was performed by an in vitro enzymatic assay using human erythrocytes purified 6-PGD protein and A549 cell lysate protein. The results of the in vitro assays supported the in silico findings. In order to gain insight into the anticancer activity of the aforementioned compounds, they were subjected to CLC-Pred, an in silico cytotoxicity browsing tool, which proved their anticancer activity against several cancer cell lines at Pa > 0.5. Additionally, a confirmation for in silico cytotoxicity was made by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay for commercially available hits syringaresinol and cleomiscosin A against lung cancer (A549) cells. The results demonstrated that syringaresinol has an IC50 value of 36.9 μg/mL, while cleomiscosin A has an IC50 value of 133 μg/mL. After MTT, flow cytometry analysis confirmed that compounds induced apoptosis in A549 cells in a dose-dependent manner. This study suggested that the respective lignan compounds can serve as lead candidates for lung cancer therapy via 6-PGD inhibition. Furthermore, in vivo experiments need to be conducted to confirm their efficacy.

High sensitivity CIP2A detection for oral cancer using a rapid transistor-based biosensor module.

Oral squamous cell carcinoma (OSCC) is one of the most common lip and oral cavity cancer types. It requires early detection via various medical technologies to improve the survival rate. While most detection techniques for OSCC require testing in a centralized lab to confirm cancer type, a point of care detection technique is preferred for on-site use and quick result readout. The modular biological sensor utilizing transistor-based technology has been leveraged for testing CIP2A, and optimal transistor gate voltage and load resistance for sensing setup was investigated. Sensitivities of 1 × 10-15 g/ml have been obtained for both detections of pure CIP2A protein and HeLa cell lysate using identical test conditions via serial dilution. The superior time-saving and high accuracy testing provides opportunities for rapid clinical diagnosis in the medical space.