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Since cardiac inflammation has been considered an important mechanism involved in heart failure, an anti-inflammatory treatment could control cardiac inflammation and mitigate the worsening of cardiac remodeling. This study evaluated the effects of dexamethasone (DEX) and ramipril treatment on inflammation and cardiac fibrosis in an experimental model of heart failure induced by supravalvular aortic stenosis. Wistar rats (21d) were submitted to an aortic stenosis (AS) protocol. After 21 weeks, an echocardiogram and a maximal exercise test were performed, and after 24 weeks, rats were treated with DEX, ramipril or saline for 14d. The left ventricle (LV) was removed for histological and inflammatory marker analyses. The AS group showed exercise intolerance (−32% vs. Sham), higher relative wall thickness (+63%), collagen deposition and capillary rarefaction, followed by cardiac disfunction. Both treatments were effective in reducing cardiac inflammation, but only DEX attenuated the increased relative wall thickness (−17%) and only ramipril reduced LV fibrosis. In conclusion, both DEX and ramipril decreased cardiac inflammatory markers, which probably contributed to the reduced cardiac fibrosis and relative wall thickness; however, treated AS rats did not show any improvement in cardiac function. Despite the complex pharmacological treatment of heart failure, treatment with an anti-inflammatory could delay the patient’s poor prognosis.

FUNDAMENTO: A Tolerância ao Esforço Físico (TEF) é uma medida de condicionamento cardiorrespiratório. A capacidade aeróbica é reduzida na Insuficiência Cardíaca (IC), embora não haja dados disponíveis sobre esse parâmetro em animais com disfunção ventricular e sem sinais de IC. OBJETIVO: Avaliar a TEF em ratos com disfunção ventricular diastólica isolada ou associada com disfunção sistólica induzida pela Estenose da Aorta ascendente (EAo). MÉTODOS: Ratos Wistar machos jovens (20-30 dias de idade) foram divididos em Grupo Controle (GC, n = 11) e Grupo EAo (n = 12). Os animais foram avaliados em 6 e 18 semanas após a cirurgia para EAo. O teste ergométrico foi feito até a exaustão e foram avaliadas a velocidade da esteira e a concentração de lactato [LAC] no limiar de lactato, velocidade da esteira e [LAC] na exaustão, e tempo total do teste. RESULTADOS: Dados ecocardiográficos revelaram remodelação do átrio esquerdo e hipertrofia concêntrica ventricular esquerda em 6 e 18 semanas. A fração de encurtamento endocárdico mostrou-se maior no grupo EAo do que no GC em 6 e 18 semanas. A fração de encurtamento da parede média mostrou-se maior no grupo EAo do que no GC em 6 semanas. O índice cardíaco mostrou-se semelhante no GC e no grupo EAo em 6 e 18 semanas, tendo diminuído entre 6-18 semanas em ambos os grupos. A razão entre a onda E a onda A foi maior no GC do que no grupo EAo em ambos os períodos e não se alterou em ambos os grupos entre a semana 6 e a semana 18. Os parâmetros do teste de esforço na esteira foram semelhantes nos dois grupos tanto na semana 6 quanto na semana 18. CONCLUSÃO: Embora a EAo promova a disfunção diastólica isolada ou associada à disfunção sistólica, em 6 ou 18 semanas, ela não é suficiente para alterar a tolerância ao esforço físico.

FUNDAMENTO: Treinamento físico (TF) aumenta a sensibilidade dos hormônios tireoidianos (HT) e a expressão gênica de estruturas moleculares envolvidas no movimento intracelular de cálcio do miocárdio, enquanto a restrição alimentar (RIA) promove efeitos contrários ao TF. OBJETIVO: Avaliar os efeitos da associação TF e RIA sobre os níveis plasmáticos dos HT e a produção de mRNA dos receptores HT e estruturas moleculares do movimento de cálcio do miocárdio de ratos. MÉTODOS: Utilizaram-se ratos Wistar Kyoto divididos em: controle (C, n = 7), RIA (R50, n = 7), exercício físico (EX, n = 7) e exercício físico + RIA (EX50, n = 7). A RIA foi de 50% e o TF foi natação (1 hora/dia, cinco sessões/semana, 12 semanas consecutivas). Avaliaram-se as concentrações séricas de triiodotironina (T3), tiroxina (T4) e hormônio tireotrófico (TSH). O mRNA da bomba de cálcio do retículo sarcoplasmático (SERCA2a), fosfolamban (PLB), trocador Na+/Ca+2 (NCX), canal lento de cálcio (canal-L), rianodina (RYR), calsequestrina (CQS) e receptor de HT (TRα1 e TRβ1) do miocárdio foram avaliados por reação em cadeia da polimerase (PCR) em tempo real. RESULTADOS: RIA reduziu o T4, TSH e mRNA do TRα1 e aumentou a expressão da PLB, NCX e canal-L. TF aumentou a expressão do TRβ1, canal-L e NCX. A associação TF e RIA reduziu T4 e TSH e aumentou o mRNA do TRβ1, SERCA2a, NCX, PLB e correlação do TRβ1 com a CQS e NCX. CONCLUSÃO: Associação TF e RIA aumentou o mRNA das estruturas moleculares cálcio transiente, porém o eixo HT-receptor não parece participar da transcrição gênica dessas estruturas.FUNDAMENTO: Entrenamiento físico (EF) aumenta la sensibilidad de las hormonas tiroideas (HT) y la expresión génica de estructuras moleculares envueltas en el movimiento intracelular de calcio del miocardio, mientras que la restricción alimenticia (RA) promueve efectos contrarios al EF. OBJETIVO: Evaluar los efectos de la asociación EF y RA sobre los niveles plasmáticos de los HT y la producción de ARNm de los receptores HT y estructuras moleculares del movimiento de calcio del miocardio de ratones. MÉTODOS: Se utilizaron ratones Wistar Kyoto divididos en: control (C, n = 7), RA (R50, n = 7), ejercicio físico (EX, n = 7) y ejercicio físico + RA (EX50, n = 7). La RA fue de 50% y el EF fue natación (1 hora/día, cinco sesiones/semana, 12 semanas consecutivas). Se evaluaron las concentraciones séricas de triyodotironina (T3), tiroxina (T4) y hormona tireotrófico (TSH). El ARNm de la bomba de calcio del retículo sarcoplasmático (SERCA2a), fosfolamban (PLB), intercambiador Na+/Ca+2 (NCX), canal lento de calcio (canal-L), rianodina (RYR), calsequestrina (CQS) y receptor de HT (TRα1 y TRβ1) del miocardio fueron evaluados por reacción en cadena de la polimerasa (PCR) en tiempo real. RESULTADOS: RA redujo el T4, TSH y ARNm del TRα1 y aumentó la expresión de la PLB, NCX y canal-L. EF aumentó la expresión del TRβ1, canal-L y NCX. La asociación EF y RA redujo T4 y TSH y aumentó el ARNm del TRβ1, SERCA2a, NCX, PLB y correlación del TRβ1 con la CQS y NCX. CONCLUSIÓN: Asociación EF y RA aumentó el ARNm de las estructuras moleculares calcio transiente, sin embargo el eje HT-receptor no parece participar de la transcripción génica de esas estructuras.BACKGROUND: Chronic exercise and food restriction (FR) have directionally opposite changes in transcription of molecular structures of calcium handling and thyroid hormone (TH) status. OBJECTIVE: Evaluate the association of chronic exercise and FR on serum thyroid hormones and gene transcription of molecular structures of intracellular calcium transients and thyroid receptors in myocardium of rats. METHODS: Male Wistar Kyoto rats, divided into two groups: control (C, n = 7), FR (R50, n = 7), chronic exercise (EX, n = 7) and chronic exercise + FR (EX50, n = 7). FR was of 50% and exercise was swimming (1 hour/day, 5 days/week, during 12 weeks). Serum concentrations of T3, T4 and TSH were determined. The mRNA gene expression of the sarcoplasmatic reticulum calcium pump (SERCA2a), phospholamban (PLB), Na+/Ca+2 exchanger (NCX), calcium channel L-type (L-channel), ryanodine (RYR), calsequestrin (CQS) and HT receptor (TRα1 and TRβ1) of the myocardium was performed by PCR real-time. RESULTS: FR reduced serum levels of T4 and TSH and TRα1 mRNA and increased the expression of PLB, NCX and L-channel. Exercise increased the TRβ1 receptor, L-channel and NCX. The association of exercise and FR reduced plasma T4 and TSH, TRβ1 mRNA increase, SERCA2a, NCX and PLB, and there was a significant correlation of TRβ1 with CQS and NXC. CONCLUSION: Chronic exercise and food restriction increased the mRNA of transient Ca2+ proteins; however, TH-receptor axis cannot participate in the transcription of mRNA of myocardial calcium transient proteins.

FUNDAMENTO: A Tolerância ao Esforço Físico (TEF) é uma medida de condicionamento cardiorrespiratório. A capacidade aeróbica é reduzida na Insuficiência Cardíaca (IC), embora não haja dados disponíveis sobre esse parâmetro em animais com disfunção ventricular e sem sinais de IC. OBJETIVO: Avaliar a TEF em ratos com disfunção ventricular diastólica isolada ou associada com disfunção sistólica induzida pela Estenose da Aorta ascendente (EAo). MÉTODOS: Ratos Wistar machos jovens (20-30 dias de idade) foram divididos em Grupo Controle (GC, n = 11) e Grupo EAo (n = 12). Os animais foram avaliados em 6 e 18 semanas após a cirurgia para EAo. O teste ergométrico foi feito até a exaustão e foram avaliadas a velocidade da esteira e a concentração de lactato [LAC] no limiar de lactato, velocidade da esteira e [LAC] na exaustão, e tempo total do teste. RESULTADOS: Dados ecocardiográficos revelaram remodelação do átrio esquerdo e hipertrofia concêntrica ventricular esquerda em 6 e 18 semanas. A fração de encurtamento endocárdico mostrou-se maior no grupo EAo do que no GC em 6 e 18 semanas. A fração de encurtamento da parede média mostrou-se maior no grupo EAo do que no GC em 6 semanas. O índice cardíaco mostrou-se semelhante no GC e no grupo EAo em 6 e 18 semanas, tendo diminuído entre 6-18 semanas em ambos os grupos. A razão entre a onda E a onda A foi maior no GC do que no grupo EAo em ambos os períodos e não se alterou em ambos os grupos entre a semana 6 e a semana 18. Os parâmetros do teste de esforço na esteira foram semelhantes nos dois grupos tanto na semana 6 quanto na semana 18. CONCLUSÃO: Embora a EAo promova a disfunção diastólica isolada ou associada à disfunção sistólica, em 6 ou 18 semanas, ela não é suficiente para alterar a tolerância ao esforço físico.BACKGROUND: Physical stress tolerance (ST) is a measurement of cardiorespiratory fitness. Aerobic capacity is reduced in heart failure (HF) although there is no data available on this parameter in animals with ventricular dysfunction and no signs of HF. OBJECTIVE: Evaluate ST in rats with ventricular diastolic dysfunction isolated or associated with systolic dysfunction induced by ascending aortic stenosis (AoS). METHODS: Young male Wistar rats (20-30 days old), divided in: control group (CG, n=11) and AoSG group, (n=12). Animals were assessed at 6 and 18 weeks after AoS surgery. Treadmill exercise test was until exhaustion and evaluated treadmill speed and lactate concentration [LAC] at lactate threshold, treadmill speed and [LAC] at exhaustion, and total testing time. RESULTS: Echocardiography data revealed remodeling of the left atrium and left ventricular concentric hypertrophy at 6 and 18 weeks. Endocardial fractional shortening was greater in AoSG than CG at 6 and 18 weeks. Midwall fractional shortening was greater in AoSG than in CG only 6 week. Cardiac index was similar in CG and AoSG at 6 and 18 weeks and decreased between from 6 to 18 weeks in both groups. The E wave to A wave ratio was greater in CG than in AoSG at both periods and did not change in both groups between week 6 and 18. Treadmill stress testing parameters were similar in both groups at 6 or 18 weeks. CONCLUSION: Although AoS promotes isolated diastolic dysfunction or associated with systolic dysfunction at 6 or 18 weeks, it is not sufficient to modify physical stress tolerance.

Cigarette smoking is a major preventable cause of morbidity and mortality. While quitting smoking is the best option, switching from cigarettes to non-combustible alternatives (NCAs) such as e-vapor products is a viable harm reduction approach for smokers who would otherwise continue to smoke. A key challenge for the clinical assessment of NCAs is that self-reported product use can be unreliable, compromising the proper evaluation of their risk reduction potential. In this cross-sectional study of 205 healthy volunteers, we combined comprehensive exposure characterization with in-depth multi-omics profiling to compare effects across four study groups: cigarette smokers (CS), e-vapor users (EV), former smokers (FS), and never smokers (NS). Multi-omics analyses included metabolomics, transcriptomics, DNA methylomics, proteomics, and lipidomics. Comparison of the molecular effects between CS and NS recapitulated several previous observations, such as increased inflammatory markers in CS. Generally, FS and EV demonstrated intermediate molecular effects between the NS and CS groups. Stratification of the FS and EV by combustion exposure markers suggested that this position on the spectrum between CS and NS was partially driven by non-compliance/dual use. Overall, this study highlights the importance of in-depth exposure characterization before biological effect characterization for any NCA assessment study., (© 2024. The Author(s).)

Lipids play a vital role as essential components of all prokaryotic and eukaryotic cells. Constant technological improvements in mass spectrometry have made lipidomics a powerful analytical tool for monitoring tissue lipidome compositions in homeostatic as well as disease states. This paper presents a step-by-step protocol for a shotgun lipid analysis method that supports the simultaneous detection and quantification of a few hundred molecular lipid species in different tissue and biofluid samples at high throughput. This method leverages automated nano-flow direct injection of a total lipid extract spiked with labeled internal standards without chromatographic separation into a high-resolution mass spectrometry instrument. Starting from sub-microgram amounts of rodent tissue, the MS analysis takes 10 min per sample and covers up to 400 lipids from 14 lipid classes in mouse lung tissue. The method presented here is well suited for studying disease mechanisms and identifying and quantifying biomarkers that indicate early toxicity or beneficial effects within rodent tissues.

Aims: Smoking is an important risk factor for the development of chronic obstructive pulmonary disease and cardiovascular diseases. This study aimed to further elucidate the role of ceramides, as a key lipid class dysregulated in disease states., Main Methods: In this article we developed and validated LC-MS/MS method for ceramides (Cer(d18:1/16:0), Cer(d18:1/18:0), Cer(d18:1/24:0) and Cer(d18:1/24:1(15Z)) for the absolute quantification. We deployed it together with proteomics and transcriptomic analysis to assess the effects of cigarette smoke (CS) from the reference cigarette as well as aerosols from heat-not-burn (HnB) tobacco and e-vapor products in apolipoprotein E-deficient (ApoE -/- ) mice over several time points., Key Findings: In the lungs, CS exposure substantially elevated the ratios of Cer(d18:1/24:0) and Cer(d18:1/24:1) to Cer(d18:1/18:0) in two independent ApoE -/- mouse inhalation studies. Data from previous studies, in both ApoE -/- and wild-type mice, further confirmed the reproducibility of this finding. Elevation of these ceramide ratios was also observed in plasma/serum, the liver, and-for the Cer(d18:1/24:1(15Z)) to Cer(d18:1/18:0) ratio-the abdominal aorta. Also, the levels of acid ceramidase (Asah1) and glucocerebrosidase (Gba)-lysosomal enzymes involved in the hydrolysis of glucosylceramides-were consistently elevated in the lungs after CS exposure. In contrast, exposure to HnB tobacco product and e-vapor aerosols did not induce significant changes in the ceramide profiles or associated enzymes., Significance: Our work in mice contributes to the accumulating evidence on the importance of ceramide ratios as biologically relevant markers for respiratory disorders, adding to their already demonstrated role in cardiovascular disease risk assessment in humans., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

Cigarette smoke (CS) causes adverse health effects and, for smoker who do not quit, modified risk tobacco products (MRTPs) can be an alternative to reduce the risk of developing smoking-related diseases. Standard toxicological endpoints can lack sensitivity, with systems toxicology approaches yielding broader insights into toxicological mechanisms. In a 6-month systems toxicology study on ApoE -/- mice, we conducted an integrative multi-omics analysis to assess the effects of aerosols from the Carbon Heated Tobacco Product (CHTP) 1.2 and Tobacco Heating System (THS) 2.2-a potential and a candidate MRTP based on the heat-not-burn (HnB) principle-compared with CS at matched nicotine concentrations. Molecular exposure effects in the lungs were measured by mRNA/microRNA transcriptomics, proteomics, metabolomics, and lipidomics. Integrative data analysis included Multi-Omics Factor Analysis and multi-modality functional network interpretation. Across all five data modalities, CS exposure was associated with an increased inflammatory and oxidative stress response, and lipid/surfactant alterations. Upon HnB aerosol exposure these effects were much more limited or absent, with reversal of CS-induced effects upon cessation and switching to CHTP 1.2. Functional network analysis revealed CS-induced complex immunoregulatory interactions across the investigated molecular layers (e.g., itaconate, quinolinate, and miR-146) and highlighted the engagement of the heme-Hmox-bilirubin oxidative stress axis by CS. This work exemplifies how multi-omics approaches can be leveraged within systems toxicology studies and the generated multi-omics data set can facilitate the development of analysis methods and can yield further insights into the effects of toxicological exposures on the lung of mice., (© 2020 The Authors.)

Modified risk tobacco products (MRTPs) have the potential to reduce smoking-related health risks. The Carbon Heated Tobacco Product 1.2 (CHTP1.2) is a potential MRTP that uses a pressed carbon heat source to generate an aerosol by heating tobacco. Here, we report the results from the systems toxicology arm of a 90-day rat inhalation study (OECD test guideline 413) to assess the effects of CHTP1.2 aerosol compared with cigarette smoke (CS). Transcriptomics, proteomics, and lipidomics analyses complemented the standard endpoints. In the respiratory nasal epithelium, CS induced an adaptive tissue and inflammatory response, which was much weaker after CHTP1.2 aerosol exposure, mostly limited to the highest CHTP1.2 concentration (at twice the 3R4F CS concentration: 50 vs. 23 μg nicotine/L), in female rats. In the lungs, the effects of CS exposure included inflammatory and cellular stress responses, which were absent or much lower after CHTP1.2 aerosol exposure. Outside of the respiratory tract, CS and CHTP1.2 aerosol induced effects that were previously associated with exposure to any nicotine-containing aerosol, e.g., lower lipid concentrations in serum. Overall, this systems toxicology analysis complements and confirms the results from classical toxicological endpoints and further suggests potentially reduced respiratory health risks of CHTP1.2., (Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Unlabelled: Smoking is associated with several serious diseases, such as lung cancer and chronic obstructive pulmonary disease (COPD). Within our systems toxicology framework, we are assessing whether potential modified risk tobacco products (MRTP) can reduce smoking-related health risks compared to conventional cigarettes. In this article, we evaluated to what extent 2D-PAGE/MALDI MS/MS (2D-PAGE) can complement the iTRAQ LC-MS/MS results from a previously reported mouse inhalation study, in which we assessed a prototypic MRTP (pMRTP). Selected differentially expressed proteins identified by both LC-MS/MS and 2D-PAGE approaches were further verified using reverse-phase protein microarrays. LC-MS/MS captured the effects of cigarette smoke (CS) on the lung proteome more comprehensively than 2D-PAGE. However, an integrated analysis of both proteomics data sets showed that 2D-PAGE data complement the LC-MS/MS results by supporting the overall trend of lower effects of pMRTP aerosol than CS on the lung proteome. Biological effects of CS exposure supported by both methods included increases in immune-related, surfactant metabolism, proteasome, and actin cytoskeleton protein clusters. Overall, while 2D-PAGE has its value, especially as a complementary method for the analysis of effects on intact proteins, LC-MS/MS approaches will likely be the method of choice for proteome analysis in systems toxicology investigations., Significance: Quantitative proteomics is anticipated to play a growing role within systems toxicology assessment frameworks in the future. To further understand how different proteomics technologies can contribute to toxicity assessment, we conducted a quantitative proteomics analysis using 2D-PAGE and isobaric tag-based LC-MS/MS approaches and compared the results produced from the 2 approaches. Using a prototypic modified risk tobacco product (pMRTP) as our test item, we show compared with cigarette smoke, how 2D-PAGE results can complement and support LC-MS/MS data, demonstrating the much lower effects of pMRTP aerosol than cigarette smoke on the mouse lung proteome. The combined analysis of 2D-PAGE and LC-MS/MS data identified an effect of cigarette smoke on the proteasome and actin cytoskeleton in the lung., (Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.)

The liver is one of the most important organs involved in elimination of xenobiotic and potentially toxic substances. Cigarette smoke (CS) contains more than 7000 chemicals, including those that exert biological effects and cause smoking-related diseases. Though CS is not directly hepatotoxic, a growing body of evidence suggests that it may exacerbate pre-existing chronic liver disease. In this study, we integrated toxicological endpoints with molecular measurements and computational analyses to investigate effects of exposures on the livers of Apoe(-/- )mice. Mice were exposed to 3R4F reference CS, to an aerosol from the Tobacco Heating System (THS) 2.2, a candidate modified risk tobacco product (MRTP) or to filtered air (Sham) for up to 8 months. THS2.2 takes advantage of a "heat-not-burn" technology that, by heating tobacco, avoids pyrogenesis and pyrosynthesis. After CS exposure for 2 months, some groups were either switched to the MRTP or filtered air. While no group showed clear signs of hepatotoxicity, integrative analysis of proteomics and transcriptomics data showed a CS-dependent impairment of specific biological networks. These networks included lipid and xenobiotic metabolism and iron homeostasis that likely contributed synergistically to exacerbating oxidative stress. In contrast, most proteomic and transcriptomic changes were lower in mice exposed to THS2.2 and in the cessation and switching groups compared to the CS group. Our findings elucidate the complex biological responses of the liver to CS exposure. Furthermore, they provide evidence that THS2.2 aerosol has reduced biological effects, as compared with CS, on the livers of Apoe(-/- )mice.

Smoking of combustible cigarettes has a major impact on human health. Using a systems toxicology approach in a model of chronic obstructive pulmonary disease (C57BL/6 mice), we assessed the health consequences in mice of an aerosol derived from a prototype modified risk tobacco product (pMRTP) as compared to conventional cigarettes. We investigated physiological and histological endpoints in parallel with transcriptomics, lipidomics, and proteomics profiles in mice exposed to a reference cigarette (3R4F) smoke or a pMRTP aerosol for up to 7 months. We also included a cessation group and a switching-to-pMRTP group (after 2 months of 3R4F exposure) in addition to the control (fresh air-exposed) group, to understand the potential risk reduction of switching to pMRTP compared with continuous 3R4F exposure and cessation. The present manuscript describes the study design, setup, and implementation, as well as the generation, processing, and quality control analysis of the toxicology and 'omics' datasets that are accessible in public repositories for further analyses.

Chronic obstructive pulmonary disease (COPD) is one of the most prevalent lung diseases. Cigarette smoking is the main risk factor for COPD. In this parallel-group clinical study we investigated to what extent the transitions in a chronic-exposure-to-disease model are reflected in the proteome and cellular transcriptome of induced sputum samples. We selected 60 age- and gender-matched individuals for each of the four study groups: current asymptomatic smokers, smokers with early stage COPD, former smokers, and never smokers. The cell-free sputum supernatant was analyzed by quantitative proteomics and the cellular mRNA fraction by gene expression profiling. The sputum proteome of current smokers clearly reflected the common physiological responses to smoke exposure, including alterations in mucin/trefoil proteins and a prominent xenobiotic/oxidative stress response. The latter response also was observed in the transcriptome, which additionally demonstrated an immune-cell polarization change. The former smoker group showed nearly complete attenuation of these biological effects. Thirteen differentially abundant proteins between the COPD and the asymptomatic smoker group were identified including TIMP1, APOA1, C6orf58, and BPIFB1 (LPLUNC1). In summary, our study demonstrates that sputum profiling can capture the complex and reversible physiological response to cigarette smoke exposure, which appears to be only slightly modulated in early-stage COPD., (Copyright © 2015. Published by Elsevier B.V.)

Current toxicology studies frequently lack measurements at molecular resolution to enable a more mechanism-based and predictive toxicological assessment. Recently, a systems toxicology assessment framework has been proposed, which combines conventional toxicological assessment strategies with system-wide measurement methods and computational analysis approaches from the field of systems biology. Proteomic measurements are an integral component of this integrative strategy because protein alterations closely mirror biological effects, such as biological stress responses or global tissue alterations. Here, we provide an overview of the technical foundations and highlight select applications of proteomics for systems toxicology studies. With a focus on mass spectrometry-based proteomics, we summarize the experimental methods for quantitative proteomics and describe the computational approaches used to derive biological/mechanistic insights from these datasets. To illustrate how proteomics has been successfully employed to address mechanistic questions in toxicology, we summarized several case studies. Overall, we provide the technical and conceptual foundation for the integration of proteomic measurements in a more comprehensive systems toxicology assessment framework. We conclude that, owing to the critical importance of protein-level measurements and recent technological advances, proteomics will be an integral part of integrative systems toxicology approaches in the future.

The use of in vitro cell culture model systems has revealed many potential mediators and candidate biomarkers of various disease phenotypes. To be of clinical utility, the expression of these candidates must be assessed in patient samples such as tissue, urine or blood. However, typical "omic" experiments may produce candidates in such large numbers that it is usually impossible to test all of these in clinical samples. Here, we present a proteomic approach to discover and prioritize candidate biomarkers that are more likely to be found in serum. Using a combination of experimental and in silico approaches, we have demonstrated this approach using an isogenic cell culture model of breast cancer invasion. Differential proteomics (2D-DIGE) was used to discover a number of candidate biomarkers and a subset of these were identified as "extracellular". We tested the validity of this approach by screening serum from breast cancer patients for these candidates and then verified the presence of several of these "extracellular" proteins. This approach provides a pragmatic approach to prioritizing candidates that may be most suitable for downstream assays such as multiple reaction monitoring.