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Dendritic cell (DC) activation and function are underpinned by profound changes in cellular metabolism. Several studies indicate that the ability of DCs to promote tolerance is dependent on catabolic metabolism. Yet the contribution of AMP-activated kinase (AMPK), a central energy sensor promoting catabolism, to DC tolerogenicity remains unknown. Here, we show that AMPK activation renders human monocyte-derived DCs tolerogenic as evidenced by an enhanced ability to drive differentiation of regulatory T cells, a process dependent on increased RALDH activity. This is accompanied by several metabolic changes, including increased breakdown of glycerophospholipids, enhanced mitochondrial fission-dependent fatty acid oxidation, and upregulated glucose catabolism. This metabolic rewiring is functionally important as we found interference with these metabolic processes to reduce to various degrees AMPK-induced RALDH activity as well as the tolerogenic capacity of moDCs. Altogether, our findings reveal a key role for AMPK signaling in shaping DC tolerogenicity and suggest AMPK as a target to direct DC-driven tolerogenic responses in therapeutic settings., (© 2024 Brombacher et al.)

Background: Sporozoites (SPZ), the infective form of Plasmodium falciparum malaria, can be inoculated into the human host skin by Anopheline mosquitoes. These SPZ migrate at approximately 1 µm/s to find a blood vessel and travel to the liver where they infect hepatocytes and multiply. In the skin they are still low in number (50-100 SPZ) and vulnerable to immune attack by antibodies and skin macrophages. This is why whole SPZ and SPZ proteins are used as the basis for most malaria vaccines currently deployed and undergoing late clinical testing. Mosquitoes typically inoculate SPZ into a human host between 14 and 25 days after their previous infective blood meal. However, it is unknown whether residing time within the mosquito affects SPZ condition, infectivity or immunogenicity. This study aimed to unravel how the age of P. falciparum SPZ in salivary glands (14, 17, or 20 days post blood meal) affects their infectivity and the ensuing immune responses., Methods: SPZ numbers, viability by live/dead staining, motility using dedicated sporozoite motility orienting and organizing tool software (SMOOT), and infectivity of HC-04.j7 liver cells at 14, 17 and 20 days after mosquito feeding have been investigated. In vitro co-culture assays with SPZ stimulated monocyte-derived macrophages (MoMɸ) and CD8 + T-cells, analysed by flow cytometry, were used to investigate immune responses., Results: SPZ age did not result in different SPZ numbers or viability. However, a markedly different motility pattern, whereby motility decreased from 89% at day 14 to 80% at day 17 and 71% at day 20 was observed (p ≤ 0.0001). Similarly, infectivity of day 20 SPZ dropped to ~ 50% compared with day 14 SPZ (p = 0.004). MoMɸ were better able to take up day 14 SPZ than day 20 SPZ (from 7.6% to 4.1%, p = 0.03) and displayed an increased expression of pro-inflammatory CD80, IL-6 (p = 0.005), regulatory markers PDL1 (p = 0.02), IL-10 (p = 0.009) and cytokines upon phagocytosis of younger SPZ. Interestingly, co-culture of these cells with CD8 + T-cells revealed a decreased expression of activation marker CD137 and cytokine IFNγ compared to their day 20 counterparts. These findings suggest that older (day 17-20) P. falciparum SPZ are less infectious and have decreased immune regulatory potential., Conclusion: Overall, this data is a first step in enhancing the understanding of how mosquito residing time affects P. falciparum SPZ and could impact the understanding of the P. falciparum infectious reservoir and the potency of whole SPZ vaccines., (© 2024. The Author(s).)

Background: Underutilization of and lack of access to low vision services (LVS) has been reported internationally. The purpose of this study was to identify barriers and facilitators in LVS referral procedures and service delivery from both the perspective of people with visual impairment and professionals from different eye care providers in the Netherlands., Methods: A qualitative study in the Netherlands was conducted. Barriers and facilitators were explored through semi structured interviews with older adults with macular degeneration, diabetic retinopathy and/or glaucoma (n = 14), and healthcare professionals including ophthalmologists and LVS professionals (n = 16). Framework analysis was used for analyzing the interviews with Atlas.ti software., Results: According to both patients and professionals, facilitators in LVS access and utilization are having motivation, self-advocacy, high participation needs and social support, as well as being negatively impacted by the impairment. Both samples found having good communication skills and informing patients about LVS as a healthcare provider to facilitate access. A long patient-provider relationship and the Dutch healthcare system were also mentioned as facilitators. Professionals additionally found long disease duration and the presence of low vision optometric services in the ophthalmic practice to promote access. Barriers that were reported by patients and professionals are lack of motivation, self-advocacy and acceptance of the impairment in patients. In addition, having low participation needs as a patient, lack of information provision by providers and time constraints in the ophthalmic practice were mentioned as barriers. Professionals also reported lack of social support, short disease duration of patients, a short patient-provider relationship and lack of coordination of care in the ophthalmic practice to hinder access., Conclusions: Findings suggest that providers' lack of information provision about LVS, especially to patients who are less assertive, hamper referral to LVS. Providers should have attention for patients' LVS needs and actively inform them and their social network about LVS to facilitate access. Educating and training providers about how and when to address LVS may help to reduce barriers in the referral pathways. In addition, referral procedures may benefit from tools that make providers more aware of LVS., (© 2023. The Author(s).)

Although the prevalence of Acanthamoeba keratitis (AK) is rare, its incidence in contact lens wearers has increased. Acanthamoeba infections can lead to the loss of vision if the diagnosis and treatment are delayed. In this study, we investigated the diagnostic potential of two antibodies raised against the adenylyl cyclase-associated protein (ACAP) and periplasmic binding protein (PBP) of A. castellanii in the AK mouse model. The specificity of ACAP and PBP antibodies to Acanthamoeba was confirmed by immunocytochemistry. AK mouse models were produced by corneal infections with A. castellanii trophozoites for 7 days and 21 days. Enzyme-linked immunosorbent assay results revealed that both ACAP and PBP antibodies successfully detected Acanthamoeba antigens in the tears and eyeball lysates of the AK mouse model. The detection levels of Acanthamoeba antigens were similar at both infection time points. Anti- Acanthamoeba IgG, IgA, and IgM antibodies were evaluated from the sera of the AK mouse model. Notably, IgM and IgA antibody responses were highest and lowest at both time points, respectively. Our findings revealed that both ACAP and PBP antibodies could detect Acanthamoeba antigens in the tears and eyeball lysates of the AK mouse model. These results provide important information for understanding Acanthamoeba infections and developing a new diagnostic tool for AK.

How mechanistic target of rapamycin complex 1 (mTORC1), a key regulator of cellular metabolism, affects dendritic cell (DC) metabolism and T cell-priming capacity has primarily been investigated in vitro, but how mTORC1 regulates this in vivo remains poorly defined. Here, using mice deficient for mTORC1 component raptor in DCs, we find that loss of mTORC1 negatively affects glycolytic and fatty acid metabolism and maturation of conventional DCs, particularly cDC1s. Nonetheless, antigen-specific CD8 + T cell responses to infection are not compromised and are even enhanced following skin immunization. This is associated with increased activation of Langerhans cells and a subpopulation of EpCAM-expressing cDC1s, of which the latter show an increased physical interaction with CD8 + T cells in situ. Together, this work reveals that mTORC1 limits CD8 + T cell priming in vivo by differentially orchestrating the metabolism and immunogenicity of distinct antigen-presenting cell subsets, which may have implications for clinical use of mTOR inhibitors., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

The High and Intensive Care model (HIC) was developed to reduce coercion and improve the quality of acute mental health care in the Netherlands. This study aimed to identify drivers of change which motivate professionals and management to implement HIC, and to identify facilitators and barriers to the implementation process. 41 interviews were conducted with multiple disciplines on 29 closed acute admission wards for adult psychiatric patients of 21 mental healthcare institutions in the Netherlands. The interviews were analysed by means of thematic analysis, consisting of the steps of open coding, axial coding and selective coding. Findings reveal three major drivers of change: the combination of existing interventions in one overall approach to reduce coercion, the focus on contact and cooperation and the alignment with recovery oriented care. Facilitators to implementation of HIC were leadership, involving staff, making choices about what to implement first, using positive feedback and celebrating successes, training and reflection, and providing operationalizable goals. Barriers included the lack of formal organizational support, resistance to change, shortage of staff and use of flex workers, time restraints and costs, lack of knowledge, lack of facilities, and envisaged shortcomings of the HIC standards. Drivers of change motivate staff to implement HIC. In the process of implementation, attention to facilitators and barriers on the level of culture, structure and practice is needed., (© 2021. The Author(s).)

The HIV-protease inhibitor nelfinavir has shown broad anticancer activity in various preclinical and clinical contexts. In patients with advanced, proteasome inhibitor (PI)-refractory multiple myeloma, nelfinavir-based therapy resulted in 65% partial response or better, suggesting that this may be a highly active chemotherapeutic option in this setting. The broad anticancer mechanism of action of nelfinavir implies that it interferes with fundamental aspects of cancer cell biology. We combined proteome-wide affinity-purification of nelfinavir-interacting proteins with genome-wide CRISPR/Cas9-based screening to identify protein partners that interact with nelfinavir in an activity-dependent manner alongside candidate genetic contributors affecting nelfinavir cytotoxicity. Nelfinavir had multiple activity-specific binding partners embedded in lipid bilayers of mitochondria and the endoplasmic reticulum. Nelfinavir affected the fluidity and composition of lipid-rich membranes, disrupted mitochondrial respiration, blocked vesicular transport, and affected the function of membrane-embedded drug efflux transporter ABCB1, triggering the integrated stress response. Sensitivity to nelfinavir was dependent on ADIPOR2, which maintains membrane fluidity by promoting fatty acid desaturation and incorporation into phospholipids. Supplementation with fatty acids prevented the nelfinavir-induced effect on mitochondrial metabolism, drug-efflux transporters, and stress-response activation. Conversely, depletion of fatty acids/cholesterol pools by the FDA-approved drug ezetimibe showed a synergistic anticancer activity with nelfinavir in vitro . These results identify the modification of lipid-rich membranes by nelfinavir as a novel mechanism of action to achieve broad anticancer activity, which may be suitable for the treatment of PI-refractory multiple myeloma. SIGNIFICANCE: Nelfinavir induces lipid bilayer stress in cellular organelles that disrupts mitochondrial respiration and transmembrane protein transport, resulting in broad anticancer activity via metabolic rewiring and activation of the unfolded protein response., (©2021 The Authors; Published by the American Association for Cancer Research.)

Naegleria fowleri is a free-living amoeba that is ubiquitous in diverse natural environments. It causes a fatal brain infection in humans known as primary amoebic meningoencephalitis. Despite the medical importance of the parasitic disease, there is a great lack of knowledge about the biology and pathogenicity of N. fowleri . In this study, we identified and characterized a novel cysteine protease inhibitor of N. fowleri (NfCPI). NfCPI is a typical cysteine protease inhibitor belonging to the cystatin family with a Gln-Val-Val-Ala-Gly (QVVAG) motif, a characteristic motif conserved in the cystatin family of proteins. Bacterially expressed recombinant NfCPI has a dimeric structure and exhibits inhibitory activity against several cysteine proteases including cathespin Bs of N. fowleri at a broad range of pH values. Expression profiles of nfcpi revealed that the gene was highly expressed during encystation and cyst of the amoeba. Western blot and immunofluorescence assays also support its high level of expression in cysts. These findings collectively suggest that NfCPI may play a critical role in encystation or cyst formation of N. fowleri by regulating cysteine proteases that may mediate encystation or mature cyst formation of the amoeba. More comprehensive studies to investigate the roles of NfCPI in encystation and its target proteases are necessary to elucidate the regulatory mechanism and the biological significance of NfCPI.

Purpose: Posttraumatic stress disorder (PTSD) is a mental health problem with a negative impact on quality of life. Little is known about the relationship between PTSD and visual impairment. According to diagnostic criteria for PTSD, vision loss in itself is generally not considered as a traumatic event. PTSD in people with visual impairment is more likely to be the result of traumatic events, which are not directly related, or are only indirectly related to, visual impairment. The purpose of this systematic review was to describe and discuss the literature on the development of PTSD in people with visual impairment., Methods: A literature search in PubMed, Embase, PsycINFO and Web of Science was performed up to 15 November 2019 in collaboration with a medical information specialist. Additional search strategies included hand searches of references of retrieved papers and free-text hand searches in Google Scholar. Thematic content analysis of the extracted data was carried out in order to identify main themes and subthemes., Results: Findings from 13 articles are presented in a narrative manner along three main themes: (1) posttraumatic stress disorder; (2) traumatic events and (3) impact of traumatic events. People with visual impairments may be at higher risk of being exposed to certain potentially traumatic events. Limited/restricted access to situational information during events may contribute to the stressfulness of the experience. Furthermore, visual impairment may shape the impact of traumatic events., Conclusions: The current evidence suggests some unique experiences and challenges for people who are visually impaired. PTSD was prevalent in this population, and prevalence rates ranged from 4% to 50%. Future research may focus on gaining insight into the extent and burden of PTSD, and exploring help-seeking behaviour and treatment needs among those with visual impairment and PTSD., (© 2021 The Authors. Ophthalmic and Physiological Optics published by John Wiley & Sons Ltd on behalf of College of Optometrists.)

Acanthamoeba castellanii, the causative agent of Acanthamoeba keratitis (AK), occurs mainly in contact lens users with poor eye hygiene. The findings of many in vitro studies of AK, as well as the testing of therapeutic drugs, need validation in in vivo experiments. BALB/c mice were used in this study to establish in vivo AK model. A. castellanii cell suspensions (equal mixtures of trophozoites and cysts) were loaded onto 2-mm contact lens pieces and inserted into mouse eyes that were scratched using an ophthalmic surgical blade under anesthesia and the eyelids of the mice were sutured. The AK signs were grossly observed and PCR was performed using P-FLA primers to amplify the Acanthamoeba 18S-rRNA gene from mouse ocular tissue. The experimental AK mouse model was characterized by typical hazy blurring and melting of the mouse cornea established on day 1 post-inoculation. AK was induced with at least 0.3 × 10 5 A. castellanii cells (optimal number, 5 × 10 4 ), and the infection persisted for two months. The PCR products amplified from the extracted mouse eye DNA confirmed the development of Acanthamoeba-induced keratitis during the infection periods. In conclusion, the present AK mouse model may serve as an important in vivo model for the development of various therapeutic drugs against AK.

Objective: Having a visual impairment is known to be associated with an increased vulnerability to (potentially) traumatic events. Little is known about how people with visual impairment experience and process such events. This qualitative study aimed to provide more insight into experiences with traumatic events, consequences of traumatic events and post-traumatic stress disorder (PTSD)-related care among people with visual impairment and PTSD., Methods: Eighteen persons with visual impairment and (a history of) PTSD were interviewed. Among them were 14 women and 4 men aged between 23 and 66 years. Recruitment of participants was done through health professionals from two low-vision service centres and a patient association for people with eye diseases and visual impairment in The Netherlands. Interviews focused on experiences with (1) traumatic events, (2) consequences of traumatic events and (3) PTSD-related care. Thematic content analysis of interview data was performed using ATLAS.ti. The COnsolidated criteria for REporting Qualitative research (COREQ) checklist was used to check for completeness and transparency of the study. Data were collected between 2018 and 2020., Results: The most commonly reported traumatic events were sexual and physical abuse. Many participants experienced that their impairment had negatively affected their acceptance by others, independence and self-esteem, increasing their vulnerability for traumatic events. Additionally, having a visual impairment negatively impacted participants' ability to respond to situations and aggravated post-traumatic stress reactions. Existing treatments seem suitable for people with visual impairment when accommodated to the impairment., Conclusions: Having a visual impairment may affect traumatic events and post-traumatic stress reactions, particularly by contributing to low self-esteem, problems in social interactions and a lack of visual information. Insights from this study provide starting points for adapting pretraumatic and post-traumatic care to the needs of people with visual impairment., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2021. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Patients suffering from exsudative retinal diseases may experience severe central vision loss and this might have impact on their daily activities and quality of life. To measure the disabilities these patients may have, the use of the Impact of Vision Impairment Profile questionnaire is recommended. The aim of this study was to translate the original English 28-item Impact of Vision Impairment Profile (IVI) into the Dutch language and evaluate its comprehensibility, comprehensiveness and relevance as evidence of content validity. The translation process was performed using standardized methods. Content validity was assessed by cognitive debriefing using a Three-Step Test-Interview (TSTI) method for participants diagnosed with exudative retinal diseases. Step 1 and 2 focused on assessment of comprehensibility of items, step 3 on comprehensiveness and relevance. Audio-recorded qualitative data was analyzed using Atlas.ti. Data regarding comprehensibility problems was further categorized into item-specific problems and general problems., Results: Few minor discrepancies in wording were found after translation. After conducting 12 cognitive interviews, data saturation was reached. All participants reported comprehensibility problems resulting from specific items, these were; sentence structure, vocabulary and formulation, influence of conditions or composite items and influence of comorbid disorders. Several general comprehensibility problems resulting from instructions or response categories were detected. The main general comprehensibility problem resulted from the layout of the Dutch-IVI. Most participants considered the included items as relevant and indicated that they covered the problems that occur due to vision impairment., Conclusions: Minor problems in the Dutch translation were detected and adjusted. The layout and instructions of the Dutch-IVI resulted in some comprehensibility problems. The Dutch-IVI appeared to be at risk of being interpreted as a generic patient reported outcome measure, instead of a disease-specific instrument, mainly due to the influence of co-morbidities. Adaptations should improve validity and reliability of the Dutch-IVI, however, cross-cultural comparisons may be at stake.

IgG Abs are crucial for various immune functions, including neutralization, phagocytosis, and Ab-dependent cellular cytotoxicity. In this study, we identified another function of IgG by showing that IgG immune complexes elicit distinct cytokine profiles by human myeloid immune cells, which are dependent on FcγR activation by the different IgG subclasses. Using monoclonal IgG subclasses with identical Ag specificity, our data demonstrate that the production of Th17-inducing cytokines, such as TNF, IL-1β, and IL-23, is particularly dependent on IgG2, whereas type I IFN responses are controlled by IgG3, and IgG1 is able to regulate both. In addition, we identified that subclass-specific cytokine production is orchestrated at the posttranscriptional level through distinct glycolytic reprogramming of human myeloid immune cells. Combined, these data identify that IgG subclasses provide pathogen- and cell type-specific immunity through differential metabolic reprogramming by FcγRs. These findings may be relevant for future design of Ab-related therapies in the context of infectious diseases, chronic inflammation, and cancer., (Copyright © 2020 by The American Association of Immunologists, Inc.)

Purpose: In Kenya, the employment rate for persons with disabilities is about 1% compared to 73.8% for the general population, and the situation is even worse for persons with mental disabilities. Persons with mental disabilities are often regarded as "mad", and stand little or no chance of employment. We undertook an exploratory study with employers and potential employers to understand factors that hinder or facilitate their employment and to gain insight into employers' perceptions of mental disability. Materials and methods: We adopted a mixed method study design, including in-depth interviews ( n  = 10) and questionnaires ( n  = 158) with (potential) employers in Kenya to explore the barriers and facilitators of employment for persons with mental disabilities. Results: Out of the 158 employers who completed the questionnaire, only 15.4% had ever employed persons with mental disabilities. The perceptions that these persons are not productive and may be violent was associated with an unwillingness to employ them (OR: 10.11, 95%CI: 2.87-35.59 and OR: 3.6, 95%CI: 1.34-9.64, respectively). The possession of skills was the highest reported facilitator of employing persons with mental disabilities. Employers suggested that information about mental illness and the disclosure by prospective employees with mental disabilities are relevant for the provision of reasonable accommodation in the workplace. Conclusion: Possession of skills and disclosure by persons with mental disabilities could improve their employability. Information targeted at all actors including employers, employees, government, and policymakers is necessary for balancing employers and employees expectations.Implications for rehabilitationDisabled persons' organisations or mental disability programs that seek to improve the employment of persons with mental disabilities should incorporate methods that address employer expectations through dialogue to find mutual benefits.Employers require essential information about mental illness, and guidance and support in order to provide reasonable accommodation in the workplace for persons with mental disabilities.Disabled persons' organisations and inclusive employment programs should share the positive experiences of employers of persons with mental disabilities with employers who are unaware of the work abilities of persons with mental disabilities to stimulate adoption of inclusive practices.

Helminths like Schistosoma mansoni release excretory/secretory (E/S) products that modulate host immunity to enable infection. Extracellular vesicles (EVs) are among these E/S products, yet molecular mechanisms and functionality of S. mansoni EV interaction with host immune cells is unknown. Here we demonstrate that EVs released by S. mansoni schistosomula are internalised by human monocyte-derived dendritic cells (moDCs). Importantly, we show that this uptake was mainly mediated via DC-SIGN (CD209). Blocking DC-SIGN almost completely abrogated EV uptake, while blocking mannose receptor (MR, CD206) or dendritic cell immunoreceptor (DCIR, CLEC4A) had no effect on EV uptake. Mass spectrometric analysis of EV glycans revealed the presence of surface N-glycans with terminal Galβ1-4(Fucα1-3)GlcNAc (LewisX) motifs, and a wide array of fucosylated lipid-linked glycans, including LewisX, a known ligand for DC-SIGN. Stimulation of moDCs with schistosomula EVs led to increased expression of costimulatory molecules CD86 and CD80 and regulatory surface marker PD-L1. Furthermore, schistosomula EVs increased expression of IL-12 and IL-10 by moDCs, which was partly dependent on the interaction with DC-SIGN. These results provide the first evidence that glycosylation of S. mansoni EVs facilitates the interaction with host immune cells and reveals a role for DC-SIGN and EV-associated glycoconjugates in parasite-induced immune modulation., (© 2020 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group on behalf of The International Society for Extracellular Vesicles.)

The free-living amoebae Naegleria spp. and Acanthamoeba spp. exist in the natural environment and are sometimes causal agents of lethal primary amoebic meningoencephalitis (PAM), amoebic keratitis (AK) and granulomatous amebic encephalitis (GAE) in humans, respectively. To ascertain the existence of free-living amoebae in Korea, water samples were collected from the Korean hydrosphere, Namhangang (southern Han River), an active location for water skiing and recreation. Samples underwent two-step filtration and were cultured on non-nutrient agar medium with inactivated E. coli. The remaining samples were subjected to PCR for primarily the 18S small ribosomal RNA gene and gene sequencing. Similarities in 18S rDNA sequences, in comparison with various reference amoebae in GenBank, showed 86~99% homology with N. gruberi, N. philippinensis, N. clarki, A. polyphaga, A. castellannii, and Hartmannella (Vermamoeba) vermiformis. Therefore, this study will be useful for seasonal detection of free-living amoebae from various Korean hydrospheres in future studies.

Free-living amoeba, Naegleria fowleri, destroys target cells through contact-dependent mechanisms, such as phagocytosis and/or trogocytosis. A previous experiment showed that the nf-actin gene consisted of 1.2 kbp, produced a 50.1 kDa recombinant protein (Nf-actin), and was localized on the cytoskeleton, pseudopodia and amoebastome. In this study, cellular characterization of the nf-actin gene concerned with contact-dependent mechanisms in N fowleri was performed. The nf-actin gene was amplified from a gene-cloned vector, pEXQP5-T7/NT TOPO. The nf-actin gene was introduced into the Ubi-pEGFP-C2 vector, and Ubi-pEGFP-C2/nf-actin was transfected into N fowleri trophozoites. Strong GFP fluorescence was detected in N fowleri trophozoites transfected with Ubi-pEGFP-C2/nf-actin. Expression of EGFP-Nf-actin protein was detected by Western blot analysis. The nf-actin-overexpressing N fowleri showed significantly increased adhesion activity against extracellular matrix components, fibronectin, collagen I and fibrinogen, compared with wild-type N fowleri. Moreover, nf-actin-overexpressing N fowleri showed increased phagocytic activity and cytotoxicity in comparison with wild-type N fowleri. In summary, the overexpressed nf-actin gene has an important function in ability to increase cell adhesion, cytotoxicity and phagocytosis by N fowleri., (© 2019 John Wiley & Sons Ltd.)

C-reactive protein (CRP) is an acute-phase protein produced in high quantities by the liver in response to infection and during chronic inflammatory disorders. Although CRP is known to facilitate the clearance of cell debris and bacteria by phagocytic cells, the role of CRP in additional immunological functions is less clear. This study shows that complexed CRP (phosphocholine [PC]:CRP) (formed by binding of CRP to PC moieties), but not soluble CRP, synergized with specific TLRs to posttranscriptionally amplify TNF, IL-1β, and IL-23 production by human inflammatory macrophages. We identified FcγRI and IIa as the main receptors responsible for initiating PC:CRP-induced inflammation. In addition, we identified the underlying mechanism, which depended on signaling through kinases Syk, PI3K, and AKT2, as well as glycolytic reprogramming. These data indicate that in humans, CRP is not only a marker but also a driver of inflammation by human macrophages. Therefore, although providing host defense against bacteria, PC:CRP-induced inflammation may also exacerbate pathology in the context of disorders such as atherosclerosis., (Copyright © 2019 by The American Association of Immunologists, Inc.)

Acanthamoeba castellanii has ubiquitous distribution and causes primary acanthamoebic keratitis (AK). AK is a common disease in contact lens wearers and results in permanent visual impairment or blindness. In this study, we observed the cytopathic effect, in vitro cytotoxicity, and secretion pattern of cytokines in human corneal epithelial cells (HCECs) induced by A. castellanii trophozoites and/or cysts. Morphological observation revealed that panked dendritic HCECs co-cultured with amoeba cysts had changed into round shape and gradually died. Such changes were more severe in co-culture with cyst than those of co-cultivation with trophozoites. In vitro cytotoxicity assay revealed the highest cytotoxicity to HCECs in the co-culture system with amoeba cysts. A. castellanii induced the expression of IL-1α, IL-6, IL-8, and CXCL1 in HCECs. Secreted levels of IL-1α, IL-6, and IL-8 in HCECs co-cultured with both trophozoites and cysts were increased at an early incubation time (3 and 6 hr). These results suggested that cytopathic changes and pro-inflammatory cytokines release of HCECs in response to A. castellanii, especially amoebic cysts, are an important mechanism for AK development.

Liver Kinase B1 (LKB1) plays a key role in cellular metabolism by controlling AMPK activation. However, its function in dendritic cell (DC) biology has not been addressed. Here, we find that LKB1 functions as a critical brake on DC immunogenicity, and when lost, leads to reduced mitochondrial fitness and increased maturation, migration, and T cell priming of peripheral DCs. Concurrently, loss of LKB1 in DCs enhances their capacity to promote output of regulatory T cells (Tregs) from the thymus, which dominates the outcome of peripheral immune responses, as suggested by increased resistance to asthma and higher susceptibility to cancer in CD11c ΔLKB1 mice. Mechanistically, we find that loss of LKB1 specifically primes thymic CD11b + DCs to facilitate thymic Treg development and expansion, which is independent from AMPK signalling, but dependent on mTOR and enhanced phospholipase C β1-driven CD86 expression. Together, our results identify LKB1 as a critical regulator of DC-driven effector T cell and Treg responses both in the periphery and the thymus.

The molecular mechanisms through which dendritic cells (DCs) prime T helper 2 (Th2) responses, including those elicited by parasitic helminths, remain incompletely understood. Here, we report that soluble egg antigen (SEA) from Schistosoma mansoni, which is well known to drive potent Th2 responses, triggers DCs to produce prostaglandin E2 (PGE2), which subsequently-in an autocrine manner-induces OX40 ligand (OX40L) expression to license these DCs to drive Th2 responses. Mechanistically, SEA was found to promote PGE2 synthesis through Dectin-1 and Dectin-2, and via a downstream signaling cascade involving spleen tyrosine kinase (Syk), extracellular signal-regulated kinase (ERK), cytosolic phospholipase A2 (cPLA2), and cyclooxygenase 1 and 2 (COX-1 and COX-2). In addition, this pathway was activated independently of the actions of omega-1 (ω-1), a previously described Th2-priming glycoprotein present in SEA. These findings were supported by in vivo murine data showing that ω-1-independent Th2 priming by SEA was mediated by Dectin-2 and Syk signaling in DCs. Finally, we found that Dectin-2-/-, and to a lesser extent Dectin-1-/- mice, displayed impaired Th2 responses and reduced egg-driven granuloma formation following S. mansoni infection, highlighting the physiological importance of this pathway in Th2 polarization during a helminth infection. In summary, we identified a novel pathway in DCs involving Dectin-1/2-Syk-PGE2-OX40L through which Th2 immune responses are induced.

Recently, it has become clear that short-chain fatty acids (SCFAs), and in particular butyrate, have anti-inflammatory properties. Murine studies have shown that butyrate can promote regulatory T cells via the induction of tolerogenic dendritic cells (DCs). However, the effects of SCFAs on human DCs and how they affect their capacity to prime and polarize T-cell responses have not been addressed. Here, we report that butyrate suppresses LPS-induced maturation and metabolic reprogramming of human monocyte-derived DCs (moDCs) and conditions them to polarize naive CD4 + T cells toward IL-10-producing type 1 regulatory T cells (Tr1). This effect was dependent on induction of the retinoic acid-producing enzyme retinaldehyde dehydrogenase 1 in DCs. The induction of retinaldehyde dehydrogenase activity and Tr1 cell differentiation by butyrate was dependent on simultaneous inhibition of histone deacetylases and signaling through G protein-coupled receptor 109A. Taken together, we reveal that butyrate is a potent inducer of tolerogenic human DCs, thereby shedding new light on the cellular and molecular mechanisms through which SCFAs can exert their immunomodulatory effects in humans.

"Thinking too much", and variations such as "thinking a lot", are common idioms of distress across the world. The contextual meaning of this idiom of distress in particular localities remains largely unknown. This paper reports on a systematic study of the content and cause, consequences, and social response and coping related to the local terms |x'an n|a te and |eu-ca n|a te, both translated as "thinking a lot", and was part of a larger ethnographic study among the Khwe of South Africa. Semi-structured exploratory interviews with community members revealed that "thinking a lot" refers to a common experience of reflecting on personal and interpersonal problems. Consequences were described in emotional, psychological, social, behavioral, and physical effects. Coping strategies included social support, distraction, and religious practices. Our contextualized approach revealed meanings and experiences of "thinking a lot" that go beyond a psychological state or psychopathology. The common experience of "thinking a lot" is situated in socio-political, economic, and social context that reflect the marginalized and displaced position of the Khwe. We argue that "thinking a lot" and associated local meanings may vary across settings, may not necessarily indicate psychopathology, and should be understood in individual, interpersonal, community, and socio-political dimensions.

Objective: The aim of this study was to gain better insight into the quality of patient participation in the development of clinical practice guidelines and to contribute to approaches for the monitoring and evaluation of such initiatives. In addition, we explore the potential of a dialogue-based approach for reconciliation of preferences of patients and professionals in the guideline development processes., Methods: The development of the Multidisciplinary Guideline for Employment and Severe Mental Illness in the Netherlands served as a case study. Methods for patient involvement in guideline development included the following: four patient representatives in the development group and advisory committee, two focus group discussions with patients, a dialogue session and eight case studies. To evaluate the quality of patient involvement, we developed a monitoring and evaluation framework including both process and outcome criteria. Data collection included observations, document analysis and semi-structured interviews (n = 26)., Results: The quality of patient involvement was enhanced using different methods, reflection of patient input in the guideline text, a supportive attitude among professionals and attention to patient involvement throughout the process. The quality was lower with respect to representing the diversity of the target group, articulation of the patient perspective in the GDG, and clarity and transparency concerning methods of involvement., Conclusions: The monitoring and evaluation framework was useful in providing detailed insights into patient involvement in guideline development. Patient involvement was evaluated as being of good quality. The dialogue-based approach appears to be a promising method for obtaining integrated stakeholder input in a multidisciplinary setting., (© 2015 John Wiley & Sons Ltd.)

Engagement of Toll-like receptors (TLRs) on dendritic cells (DCs) triggers the expression of a large set of genes involved in DC activation and maturation, which allow them to act efficiently as antigen-presenting cells. Recently, it has become clear that TLR signalling in DCs also results in dramatic metabolic changes that are integral to their changed biology. Here, we describe a detailed protocol on how DC metabolism can be studied after TLR stimulation using the 96-well format Extracellular Flux (XF(e)96) Analyzer from Seahorse Bioscience, a machine that allows one to simultaneously assess rates of oxidative phosphorylation and glycolysis in real-time, in live cells and in a high-throughput manner.

Background and Objectives: The objective of this research is to improve compliance of the medication reconciliation process at the time of patient admission in the Department of Pediatrics at King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia using an innovative evidence-based approach., Materials and Methods: Most of the recent efforts at our institution to revamp the medication reconciliation process have failed. Thus, we implemented an innovative evidence-based approach to improve the compliance of the reconciliation process at admission. This approach focused on the Department of Pediatrics at King Faisal Specialist Hospital and Research Centre (KFSH&RC). We established specific educational and monitoring programs that were run over a two-month period, from June to July 2015. The educational program consisted of focused hands-on daily interactive training sessions presented to a small group of residents, i.e., 5-6 residents per session, for a period of one week. One resident was identified as a "Super-User" to provide ongoing support for the other residents involved in the process. A close monitoring process was also implemented, which included daily follow up and encouragement from three assigned consultants. In addition, periodic independent audit report results prepared by Healthcare Information Technology Affairs (HITA) were communicated to the Department of Pediatrics regarding physician compliance in the medication reconciliation process., Results: Physician compliance for admission medication reconciliation documentation in ICIS ranged from (0-15%) between the first quarter of 2012 and the first quarter 2015, we designated the official hospital audit for the first quarter of 2015 as a baseline audit report. Between the first quarter of 2012 and 2015, the physician compliance for admission medication reconciliation was ranged between 0 to 15% according to the official hospital audit. We implemented our initiative during the months of June and July 2015. During that time, there was a gradual improvement in the number of admission medication reconciliations reported by the independent audits of our general Pediatrics Ward (B1), which represents the majority of pediatric admissions. The 57% of 26 patients had medication reconciliation completed by the first report dated 16 June 2015. This percentage improved to 92% out of a total of 13 patients at the last report on 12 July 2015. This consistent improvement also occurred in other areas where pediatric patients were admitted including the B3-1 (from 88% to 90%), the NICU 1 (from 83% to 100%) and the NICU 2 (from 90% to 100%)., Conclusions: By structuring and implementing intensive educational and monitoring programs, a marked improvement in the compliance of medication reconciliation at the time of admission for the pediatric patient population was achieved. We believe that our department-based results would be generalizable if a similar hospital-wide programme was to be rigorously implemented.

Female domestic workers face many migration-related stressors that affect their mental health, but we know little about the dynamics of stress and coping in different migration phases. This exploratory study aims to assess stress and coping of female migrant domestic workers from the Philippines in different phases of the migration process; prior to migration, in the country of destination and upon return to the Philippines. Data were collected in 2010 using questionnaires (N = 500). Validation of findings took place in a work shop (23 participants) and two focus groups (13 and 8 participants). Stress levels of women were significantly higher abroad than in the Philippines. Stress and coping in the Philippines was primarily related to financial issues, while stress and coping abroad related more strongly loneliness, working conditions and employers. Findings from this study provide insight in the phase-specific and transnational dimensions of stress and coping.

This study is the first in-depth qualitative study of service user involvement in the development of multidisciplinary mental health guidelines in the Netherlands. The study comprised a desk study of guidelines (n = 12) and case studies of service user involvement in five guidelines using document analysis, interviews (n = 24) and observations. The desk study shows that all multidisciplinary mental health guidelines have taken service user perspectives into account to some extent. The five guideline case studies led to the identification of ten main themes. Findings will assist guideline developers in making early, informed decisions on involving service users effectively.

Despite advocacy and demand for psychiatric advance directives (PADs), uptake and implementation in clinical practice is low. We examine why PAD implementation has been difficult globally by reviewing barriers in existing evidence. The review includes 30 studies, and identified 13 barriers, clustered into system level barriers, health professional level barriers, and service user level barriers. The considerable barriers to uptake and implementation hamper PAD use. We propose several potential strategies for overcoming some of the barriers. In order to realise these strategies, additional research is needed, particularly more field-based and operational research to understand processes and difficulties experienced in clinical practice.

Domestic workers face many migration-related stressors that affect their mental health. Currently there is an emphasis in the literature on these workers' problems and vulnerability, while there is little insight into factors that positively affect their mental health. In this study, we describe a range of factors that potentially contribute to the resilience of female domestic workers from the Philippines, and explore their relation to stress and well-being. The study used an explorative, mixed-methods design. First, data were collected using questionnaires (n = 500) to assess self-perceived stress levels, well-being, personal resources, and social resources. Then, findings from the questionnaires were validated and elaborated on in a workshop (n = 23) and two focus groups (n = 13; n = 8). Results show that participants perceived their well-being abroad as relatively good, while they also experienced high levels of stress. Workers used a variety of resources in dealing with stress. Socially oriented coping strategies and spirituality seemed to play an important role as personal resources, while the influence of reasons for migration was less clear. Employers and (access to) social networks appeared important in determining social resources. Social resources were more often related to stress and well-being than were personal resources. Findings from this study can help to design strengths-based interventions aimed at improving the well-being of female domestic workers and preventing mental health problems. The environmental factors and structural constraints that provide the context for resilience should be further explored as they influence the ability to mobilize resources., (© The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.)

Although differences in immunological responses between populations have been found in terms of vaccine efficacy, immune responses to infections and prevalence of chronic inflammatory diseases, the mechanisms responsible for these differences are not well understood. Therefore, innate cytokine responses mediated by various classes of pattern-recognition receptors including Toll-like receptors (TLR), C-type lectin receptors (CLRs) and nucleotide-binding oligomerisation domain-like receptors (NLRs) were compared between Dutch (European), semi-urban and rural Gabonese (African) children. Whole blood was stimulated for 24 hours and the pro-inflammatory tumor necrosis factor (TNF) and the anti-inflammatory/regulatory interleukin-10 (IL-10) cytokines in culture supernatant were measured by enzyme-linked immunosorbent assay (ELISA). Gabonese children had a lower pro-inflammatory response to poly(I:C) (TLR3 ligand), but a higher pro-inflammatory response to FSL-1 (TLR2/6 ligand), Pam3 (TLR2/1 ligand) and LPS (TLR4 ligand) compared to Dutch children. Anti-inflammatory responses to Pam3 were also higher in Gabonese children. Non-TLR ligands did not induce substantial cytokine production on their own. Interaction between various TLR and non-TLR receptors was further assessed, but no differences were found between the three populations. In conclusion, using a field applicable assay, significant differences were observed in cytokine responses between European and African children to TLR ligands, but not to non-TLR ligands.

Differentiating and quantifying protein differences in complex samples produces significant challenges in sensitivity and specificity. Label-free quantification can draw from two different information sources: precursor intensities and spectral counts. Intensities are accurate for calculating protein relative abundance, but values are often missing due to peptides that are identified sporadically. Spectral counting can reliably reproduce difference lists, but differentiating peptides or quantifying all but the most concentrated protein changes is usually beyond its abilities. Here we developed new software, IDPQuantify, to align multiple replicates using principal component analysis, extract accurate precursor intensities from MS data, and combine intensities with spectral counts for significant gains in differentiation and quantification. We have applied IDPQuantify to three comparative proteomic data sets featuring gold standard protein differences spiked in complicated backgrounds. The software is able to associate peptides with peaks that are otherwise left unidentified to increase the efficiency of protein quantification, especially for low-abundance proteins. By combing intensities with spectral counts from IDPicker, it gains an average of 30% more true positive differences among top differential proteins. IDPQuantify quantifies protein relative abundance accurately in these test data sets to produce good correlations between known and measured concentrations.

Recent reports have attributed an immunoregulatory role to the mammalian target of rapamycin (mTOR), a key serine/threonine protein kinase integrating input from growth factors and nutrients to promote cell growth and differentiation. In the present study, we investigated the role of the mTOR pathway in Th2 induction by human monocyte-derived dendritic cells (moDCs). Using a co-culture system of human lipopolysaccharide (LPS)-matured moDCs and allogeneic naive CD4(+) T cells, we show that inhibition of mTOR by the immunosuppressive drug rapamycin reduced moDC maturation and promoted Th2 skewing. Next, we investigated whether antigens from helminth parasites, the strongest natural inducers of Th2 responses, modulate moDCs via the mTOR pathway. In contrast to rapamycin, neither Schistosoma mansoni-soluble egg antigens (SEA) nor its major immunomodulatory component omega-1 affected the phosphorylation of S6 kinase (S6K) and 4E-binding protein 1 (4E-BP1), downstream targets of mTORC1. Finally, we found that the effects of rapamycin and SEA/omega-1 on Th2 skewing were additive, suggesting two distinct underlying molecular mechanisms. We conclude that conditioning human moDCs to skew immune responses towards Th2 can be achieved via an mTOR-dependent and -independent pathway triggered by rapamycin and helminth antigens, respectively.

Objective: The crisis card is a specific form of psychiatric advance directive, documenting mental clients' treatment preferences in advance of a potential psychiatric crisis. In this paper, we aim to provide insight into implementation issues surrounding the crisis card., Method: A Dutch crisis-card project formed the scope of this study. Data were collected through interviews with 15 participants from six stakeholder groups., Results: Identified implementation issues are: (a) The role of the crisis-card counselor, (b) lack of distribution and familiarity, (c) care professionals' routines, and (d) client readiness., Conclusions and Implications for Practice: The crisis-card counselor appears to play a key role in fostering benefits of the crisis card by supporting clients' perspectives. More structural integration of the crisis card in care processes may enhance its impact, but should be carefully explored., ((PsycINFO Database Record (c) 2013 APA, all rights reserved).)

Objective: Recent trends in health care indicate a shift toward client-centered care and an emphasis on dialog between clients and providers. The aim of this study is to assess the role of video-mediated moral deliberation in stimulating dialog between clients and providers., Methods: A participatory video project carried out in a long-term care facility of a psychiatric hospital was investigated as a case study. Data were collected through interviews, a focus group and a dialog session with providers, clients, managers and a family member., Results: Data analysis produced four themes: (1) the video elicits discussion by affecting viewers; (2) the video raises awareness and discussion of clients' needs and desires; (3) the video and discussion give a voice to clients; and (4) the video and discussions draw attention to client-provider relations., Conclusion: The study shows that video-mediated moral deliberation can be a useful tool for starting dialog between clients and care providers. It can also contribute to changes in care provision by acting as a catalyst., Practice Implications: This study provides an example of how video-mediated moral deliberation can be applied in the context of psychiatric care. Opportunities regarding the usefulness of video-mediated moral deliberation include training purposes and education., (Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.)

Activating mutations in KRAS occur in 30% to 40% of colorectal cancers. How mutant KRAS alters cancer cell behavior has been studied intensively, but non-cell autonomous effects of mutant KRAS are less understood. We recently reported that exosomes isolated from mutant KRAS-expressing colon cancer cells enhanced the invasiveness of recipient cells relative to exosomes purified from wild-type KRAS-expressing cells, leading us to hypothesize mutant KRAS might affect neighboring and distant cells by regulating exosome composition and behavior. Herein, we show the results of a comprehensive proteomic analysis of exosomes from parental DLD-1 cells that contain both wild-type and G13D mutant KRAS alleles and isogenically matched derivative cell lines, DKO-1 (mutant KRAS allele only) and DKs-8 (wild-type KRAS allele only). Mutant KRAS status dramatically affects the composition of the exosome proteome. Exosomes from mutant KRAS cells contain many tumor-promoting proteins, including KRAS, EGFR, SRC family kinases, and integrins. DKs-8 cells internalize DKO-1 exosomes, and, notably, DKO-1 exosomes transfer mutant KRAS to DKs-8 cells, leading to enhanced three-dimensional growth of these wild-type KRAS-expressing non-transformed cells. These results have important implications for non-cell autonomous effects of mutant KRAS, such as field effect and tumor progression.

Early diagnosis and curative resection are the predominant factors associated with increased survival in patients with gastric cancer. However, most gastric cancer cases are still diagnosed at later stages. Since most pathologic specimens are archived as FFPE samples, the ability to use them to generate expression profiles can greatly improve cancer biomarker discovery. We sought to uncover new biomarkers for stomach preneoplastic metaplasias and neoplastic lesions by generating proteome profiles using FFPE samples. We combined peptide isoelectric focusing and liquid chromatography-tandem mass spectrometry analysis to generate proteomic profiles from FFPE samples of intestinal-type gastric cancer, metaplasia, and normal mucosa. The expression patterns of selected proteins were analyzed by immunostaining first in single tissue sections from normal stomach, metaplasia, and gastric cancer and later in larger tissue array cohorts. We detected 60 proteins up-regulated and 87 proteins down-regulated during the progression from normal mucosa to metaplasia to gastric cancer. Two of the up-regulated proteins, LTF and DMBT1, were validated as specific markers for spasmolytic polypeptide-expressing metaplasia and intestinal metaplasia, respectively. In cancers, significantly lower levels of DMBT1 or LTF correlated with more advanced disease and worse prognosis. Thus, proteomic profiling using FFPE samples has led to the identification of two novel markers for stomach metaplasias and gastric cancer prognosis., (Copyright © 2012 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)

Omega-1, a glycosylated T2 ribonuclease (RNase) secreted by Schistosoma mansoni eggs and abundantly present in soluble egg antigen, has recently been shown to condition dendritic cells (DCs) to prime Th2 responses. However, the molecular mechanisms underlying this effect remain unknown. We show in this study by site-directed mutagenesis of omega-1 that both the glycosylation and the RNase activity are essential to condition DCs for Th2 polarization. Mechanistically, we demonstrate that omega-1 is bound and internalized via its glycans by the mannose receptor (MR) and subsequently impairs protein synthesis by degrading both ribosomal and messenger RNA. These experiments reveal an unrecognized pathway involving MR and interference with protein synthesis that conditions DCs for Th2 priming.

Liquid chromatography tandem mass spectrometry (LC-MS/MS) based methods provide powerful tools for the quantitative analysis of modified proteins. We have developed a label-free approach using internal reference peptides (IRP) from the target protein for signal normalization without the need for isotope labeling. Ion-trap mass spectrometry and pseudo-selected reaction monitoring (pSRM) were used to acquire full MS/MS and MS(3) spectra from target peptides. Skyline, a widely used software for SRM experiments, was used for chromatographic ion extraction. Phosphopeptides spiked into a BSA background yielded concentration response curves with high correlation coefficients (typically >0.9) and low coefficients of variation (≤15%) over a 200-fold concentration range. Stable isotope dilution (SID) and IRP methods were compared for quantitation of six site-specific phosphorylations in the epidermal growth factor receptor (EGFR) in epidermal growth factor-stimulated A431 cells with or without the addition of EGFR inhibitors cetuximab and gefitinib. Equivalent responses were observed with both IRP and SID methods, although analyses using the IRP method typically had higher median CVs (22-31%) than SID (10-20%). Analyses using both methods were consistent with immunoblot using site-selective antibodies. The ease of implementation and the suitability for targeted quantitative comparisons make this method suitable for broad application in protein biochemistry.

We compared the reproducibility of multiple reaction monitoring (MRM) mass spectrometry-based peptide quantitation in tryptic digests from formalin-fixed, paraffin-embedded (FFPE) and frozen clear cell renal cell carcinoma tissues. The analyses targeted a candidate set of 114 peptides previously identified in shotgun proteomic analyses, of which 104 were detectable in FFPE and frozen tissue. Although signal intensities for MRM of peptides from FFPE tissue were on average 66% of those in frozen tissue, median coefficients of variation (CV) for measurements in FFPE and frozen tissues were nearly identical (18-20%). Measurements of lysine C-terminal peptides and arginine C-terminal peptides from FFPE tissue were similarly reproducible (19.5% and 18.3% median CV, respectively). We further evaluated the precision of MRM-based quantitation by analysis of peptides from the Her2 receptor in FFPE and frozen tissues from a Her2 overexpressing mouse xenograft model of breast cancer and in human FFPE breast cancer specimens. We obtained equivalent MRM measurements of HER2 receptor levels in FFPE and frozen mouse xenografts derived from HER2-overexpressing BT474 cells and HER2-negative Sum159 cells. MRM analyses of 5 HER2-positive and 5 HER-negative human FFPE breast tumors confirmed the results of immunohistochemical analyses, thus demonstrating the feasibility of HER2 protein quantification in FFPE tissue specimens. The data demonstrate that MRM analyses can be performed with equal precision on FFPE and frozen tissues and that lysine-containing peptides can be selected for quantitative comparisons, despite the greater impact of formalin fixation on lysine residues. The data further illustrate the feasibility of applying MRM to quantify clinically important tissue biomarkers in FFPE specimens.

Spectral libraries have emerged as a viable alternative to protein sequence databases for peptide identification. These libraries contain previously detected peptide sequences and their corresponding tandem mass spectra (MS/MS). Search engines can then identify peptides by comparing experimental MS/MS scans to those in the library. Many of these algorithms employ the dot product score for measuring the quality of a spectrum-spectrum match (SSM). This scoring system does not offer a clear statistical interpretation and ignores fragment ion m/z discrepancies in the scoring. We developed a new spectral library search engine, Pepitome, which employs statistical systems for scoring SSMs. Pepitome outperformed the leading library search tool, SpectraST, when analyzing data sets acquired on three different mass spectrometry platforms. We characterized the reliability of spectral library searches by confirming shotgun proteomics identifications through RNA-Seq data. Applying spectral library and database searches on the same sample revealed their complementary nature. Pepitome identifications enabled the automation of quality analysis and quality control (QA/QC) for shotgun proteomics data acquisition pipelines.

Vinyl chloride (VC) is an industrial chemical that is known to be carcinogenic to animals and humans. VC primarily induces hepatic angiosarcomas following high exposures (≥50 ppm). VC is also found in Superfund sites at ppb concentrations as a result of microbial metabolism of trichloroethylene and perchloroethylene. Here, we report a new sensitive LC-MS/MS method to analyze the major DNA adduct formed by VC, 7-(2-oxoethylguanine) (7-OEG). We used this method to analyze tissue DNA from both adult and weanling rats exposed to 1100 ppm [(13)C(2)]-VC for 5 days. After neutral thermal hydrolysis, 7-OEG was derivatized with O-t-butyl hydroxylamine to an oxime adduct, followed by LC-MS/MS analysis. The limit of detection was 1 fmol, and the limit of quantitation was 1.5 fmol on the column. The use of stable isotope VC allowed us to demonstrate for the first time that endogenous 7-OEG was present in tissue DNA. We hypothesized that endogenous 7-OEG was formed from lipid peroxidation and demonstrated the formation of [(13)C(2)]-7-OEG from the reaction of calf thymus DNA with [(13)C(18)]-ethyl linoleate (EtLa) under peroxidizing conditions. The concentrations of endogenous 7-OEG in liver, lung, kidney, spleen, testis, and brain DNA from adult and weanling rats typically ranged from 1.0 to 10.0 adducts per 10(6) guanine. The exogenous 7-OEG in liver DNA from adult rats exposed to 1100 ppm [(13)C(2)]-VC for 5 days was 104.0 ± 23.0 adducts per 10(6) guanine (n = 4), while concentrations in other tissues ranged from 1.0 to 39.0 adducts per 10(6) guanine (n = 4). Although endogenous concentrations of 7-OEG in tissues in weanling rats were similar to those of adult rats, exogenous [(13)C(2)]-7-OEG concentrations were higher in weanlings, averaging 300 adducts per 10(6) guanine in liver. Studies on the persistence of [(13)C(2)]-7-OEG in adult rats sacrificed 2, 4, and 8 weeks postexposure to [(13)C(2)]-VC demonstrated a half-life of 7-OEG of 4 days in both liver and lung.

Summary: The large amount of data produced by proteomics experiments requires effective bioinformatics tools for the integration of data management and data analysis. Here we introduce a suite of tools developed at Vanderbilt University to support production proteomics. We present the Backup Utility Service tool for automated instrument file backup and the ScanSifter tool for data conversion. We also describe a queuing system to coordinate identification pipelines and the File Collector tool for batch copying analytical results. These tools are individually useful but collectively reinforce each other. They are particularly valuable for proteomics core facilities or research institutions that need to manage multiple mass spectrometers. With minor changes, they could support other types of biomolecular resource facilities.

Despite the initial effectiveness of the tyrosine kinase inhibitor lapatinib against HER2 gene-amplified breast cancers, most patients eventually relapse after treatment, implying that tumors acquire mechanisms of drug resistance. To discover these mechanisms, we generated six lapatinib-resistant HER2-overexpressing human breast cancer cell lines. In cells that grew in the presence of lapatinib, HER2 autophosphorylation was undetectable, whereas active phosphoinositide-3 kinase (PI3K)-Akt and mitogen-activated protein kinase (MAPK) were maintained. To identify networks maintaining these signaling pathways, we profiled the tyrosine phosphoproteome of sensitive and resistant cells using an immunoaffinity-enriched mass spectrometry method. We found increased phosphorylation of Src family kinases (SFKs) and putative Src substrates in several resistant cell lines. Treatment of these resistant cells with Src kinase inhibitors partially blocked PI3K-Akt signaling and restored lapatinib sensitivity. Further, SFK mRNA expression was upregulated in primary HER2+ tumors treated with lapatinib. Finally, the combination of lapatinib and the Src inhibitor AZD0530 was more effective than lapatinib alone at inhibiting pAkt and growth of established HER2-positive BT-474 xenografts in athymic mice. These data suggest that increased Src kinase activity is a mechanism of lapatinib resistance and support the combination of HER2 antagonists with Src inhibitors early in the treatment of HER2+ breast cancers in order to prevent or overcome resistance to HER2 inhibitors.

Lung carcinogenesis in humans involves an accumulation of genetic and epigenetic changes that lead to alterations in normal lung epithelium, to in situ carcinoma, and finally to invasive and metastatic cancers. The loss of transforming growth factor β (TGF-β)-induced tumor suppressor function in tumors plays a pivotal role in this process, and our previous studies have shown that resistance to TGF-β in lung cancers occurs mostly through the loss of TGF-β type II receptor expression (TβRII). However, little is known about the mechanism of down-regulation of TβRII and how histone deacetylase (HDAC) inhibitors (HDIs) can restore TGF-β-induced tumor suppressor function. Here we show that HDIs restore TβRII expression and that DNA hypermethylation has no effect on TβRII promoter activity in lung cancer cell lines. TGF-β-induced tumor suppressor function is restored by HDIs in lung cancer cell lines that lack TβRII expression. Activation of mitogen-activated protein kinase/extracellular signal-regulated kinase pathway by either activated Ras or epidermal growth factor signaling is involved in the down-regulation of TβRII through histone deacetylation. We have immunoprecipitated the protein complexes by biotinylated oligonucleotides corresponding to the HDI-responsive element in the TβRII promoter (-127/-75) and identified the proteins/factors using proteomics studies. The transcriptional repressor Meis1/2 is involved in repressing the TβRII promoter activity, possibly through its recruitment by Sp1 and NF-YA to the promoter. These results suggest a mechanism for the downregulation of TβRII in lung cancer and that TGF-β tumor suppressor functions may be restored by HDIs in lung cancer patients with the loss of TβRII expression.

In shotgun proteomics, protein identification by tandem mass spectrometry relies on bioinformatics tools. Despite recent improvements in identification algorithms, a significant number of high quality spectra remain unidentified for various reasons. Here we present ScanRanker, an open-source tool that evaluates the quality of tandem mass spectra via sequence tagging with reliable performance in data from different instruments. The superior performance of ScanRanker enables it not only to find unassigned high quality spectra that evade identification through database search but also to select spectra for de novo sequencing and cross-linking analysis. In addition, we demonstrate that the distribution of ScanRanker scores predicts the richness of identifiable spectra among multiple LC-MS/MS runs in an experiment, and ScanRanker scores assist the process of peptide assignment validation to increase confident spectrum identifications. The source code and executable versions of ScanRanker are available from http://fenchurch.mc.vanderbilt.edu.

Liquid chromatography-multiple reaction monitoring mass spectrometry of peptides using stable isotope dilution (SID) provides a powerful tool for targeted protein quantitation. However, the high cost of labeled peptide standards for SID poses an obstacle to multiple reaction monitoring studies. We compared SID to a labeled reference peptide (LRP) method, which uses a single labeled peptide as a reference standard for all measured peptides, and a label-free (LF) approach, in which quantitation is based on analysis of un-normalized peak areas for detected MRM transitions. We analyzed peptides from the Escherichia coli proteins alkaline phosphatase and β-galactosidase spiked into lysates from human colon adenocarcinoma RKO cells. We also analyzed liquid chromatography-multiple reaction monitoring mass spectrometry data from a recently published interlaboratory study by the National Cancer Institute Clinical Proteomic Technology Assessment for Cancer network (Addona et al. (2009) Nat. Biotechnol. 27: 633-641), in which unlabeled and isotopically labeled synthetic peptides or their corresponding proteins were spiked into human plasma. SID displayed the highest correlation coefficients and lowest coefficient of variation in regression analyses of both peptide and protein spike studies. In protein spike experiments, median coefficient of variation values were about 10% for SID and 20-30% for LRP and LF methods. Power calculations indicated that differences in measurement error between the methods have much less impact on measured protein expression differences than biological variation. All three methods detected significant (p < 0.05) differential expression of three endogenous proteins in a test set of 10 pairs of human lung tumor and control tissues. Further, the LRP and LF methods both detected significant differences (p < 0.05) in levels of seven biomarker candidates between tumors and controls in the same set of lung tissue samples. The data indicate that the LRP and LF methods provide cost-effective alternatives to SID for many quantitative liquid chromatography-multiple reaction monitoring mass spectrometry applications.