Modern research thoughts and methods on bio-active components of TCM formulae / 中国天然药物

TCM formulae are the important guidances for clinical application of traditional Chinese medicines, which follow the principles of diagnosis and treatment in TCM. Elucidating the bio-active components of TCM formulae is the key to the modernization and internationalization of traditional Chinese medicines. With the rapid development of modern instruments and technology, many new theories, methods and strategies are emerging, which upgrade the research of TCM formulae into a higher level. Only when the medicinal efficacy, bio-active components, function mechanism of TCM formulae are understood, we can guarantee TCM safety and quality control. In this paper, we summarized the latest modern research thoughts and methods on bio-active components of TCM formulae including formula decomposition study, serum pharmacology and serum pharmacochemistry, association analysis, biochromatography, network pharmacology, metabolomics and proteomics, so as to provide reference for the research and development of TCM in the future.

Quantitative proteomics revealed extensive microenvironmental changes after stem cell transplantation in ischemic stroke / 医学前沿

The local microenvironment is essential to stem cell-based therapy for ischemic stroke, and spatiotemporal changes of the microenvironment in the pathological process provide vital clues for understanding the therapeutic mechanisms. However, relevant studies on microenvironmental changes were mainly confined in the acute phase of stroke, and long-term changes remain unclear. This study aimed to investigate the microenvironmental changes in the subacute and chronic phases of ischemic stroke after stem cell transplantation. Herein, induced pluripotent stem cells (iPSCs) and neural stem cells (NSCs) were transplanted into the ischemic brain established by middle cerebral artery occlusion surgery. Positron emission tomography imaging and neurological tests were applied to evaluate the metabolic and neurofunctional alterations of rats transplanted with stem cells. Quantitative proteomics was employed to investigate the protein expression profiles in iPSCs-transplanted brain in the subacute and chronic phases of stroke. Compared with NSCs-transplanted rats, significantly increased glucose metabolism and neurofunctional scores were observed in iPSCs-transplanted rats. Subsequent proteomic data of iPSCs-transplanted rats identified a total of 39 differentially expressed proteins in the subacute and chronic phases, which are involved in various ischemic stroke-related biological processes, including neuronal survival, axonal remodeling, antioxidative stress, and mitochondrial function restoration. Taken together, our study indicated that iPSCs have a positive therapeutic effect in ischemic stroke and emphasized the wide-ranging microenvironmental changes in the subacute and chronic phases.

Proteomics study of Mycoplasma pneumoniae pneumonia reveals the Fc fragment of the IgG-binding protein as a serum biomarker and implicates potential therapeutic targets / 医学前沿

Macrolide and corticosteroid resistance has been reported in patients with Mycoplasma pneumoniae (MP) pneumonia (MPP). MP clearance is difficult to achieve through antibiotic treatment in sensitive patients with severe MPP (SMPP). SMPP in children might progress to airway remodeling and even bronchiolitis/bronchitis obliterans. Therefore, identifying serum biomarkers that indicate MPP progression and exploring new targeted drugs for SMPP treatment require urgency. In this study, serum samples were collected from patients with general MPP (GMPP) and SMPP to conduct proteomics profiling. The Fc fragment of the IgG-binding protein (FCGBP) was identified as the most promising indicator of SMPP. Biological enrichment analysis indicated uncontrolled inflammation in SMPP. ELISA results proved that the FCGBP level in patients with SMPP was substantially higher than that in patients with GMPP. Furthermore, the FCGBP levels showed a decreasing trend in patients with GMPP but the opposite trend in patients with SMPP during disease progression. Connectivity map analyses identified 25 possible targeted drugs for SMPP treatment. Among them, a mechanistic target of rapamycin kinase (mTOR) inhibitor, which is a macrolide compound and a cell proliferation inhibitor, was the most promising candidate for targeting SMPP. To our knowledge, this study was the first proteomics-based characterization of patients with SMPP and GMPP.

Application and Prospect of Platelet Multi-Omics Technology in Study of Blood Stasis Syndrome / 中国结合医学杂志

The abnormality of platelet function plays an important role in the pathogenesis and evolution of blood stasis syndrome (BSS). The explanation of its mechanism is a key scientific issue in the study of cardiovascular and cerebrovascular diseases and treatment. System biology technology provides a good technical platform for further development of platelet multi-omics, which is conducive to the scientific interpretation of the biological mechanism of BSS. The article summarized the pathogenesis of platelets in BSS, the mechanism of action of blood activating and stasis resolving drugs, and the application of genomics, proteomics, and metabonomics in platelet research, and put forward the concept of "plateletomics in BSS". Through the combination and cross-validation of multi-omics technology, it mainly focuses on the clinical and basic research of cardiovascular and cerebrovascular diseases; through the interactive verification of multi-omics technology and system biology, it mainly focuses on the platelet function and secretion system. The article systematically explains the molecular biological mechanism of platelet activation, aggregation, release, and other stages in the formation and development of BSS, and provides a new research idea and method for clarifying the pathogenesis of BSS and the mechanism of action of blood activating and stasis resolving drugs.

Effect of PAIP1 on the metastatic potential and prognostic significance in oral squamous cell carcinoma / 国际口腔科学杂志·英文版

Poly Adenylate Binding Protein Interacting protein 1 (PAIP1) plays a critical role in translation initiation and is associated with the several cancer types. However, its function and clinical significance have not yet been described in oral squamous cell carcinoma (OSCC) and its associated features like lymph node metastasis (LNM). Here, we used the data available from Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), and Clinical Proteomic Tumor Analysis Consortium (CPTAC) to analyze PAIP1 expression in oral cancer. The publicly available data suggests that PAIP1 mRNA and protein levels were increased in OSCC. The high PAIP1 expression was more evident in samples with advanced stage, LNM, and worse pattern of invasion. Moreover, the in vitro experiments revealed that PAIP1 knockdown attenuated colony forming, the aggressiveness of OSCC cell lines, decreasing MMP9 activity and SRC phosphorylation. Importantly, we found a correlation between PAIP1 and pSRC through the analysis of the IHC scores and CPTAC data in patient samples. Our findings suggest that PAIP1 could be an independent prognostic factor in OSCC with LNM and a suitable therapeutic target to improve OSCC patient outcomes.

Proteomic characterization of four subtypes of M2 macrophages derived from human THP-1 cells / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

Macrophages are widely distributed immune cells that contribute to tissue homeostasis. Human THP-1 cells have been widely used in various macrophage-associated studies, especially those involving pro-inflammatory M1 and anti-inflammatory M2 phenotypes. However, the molecular characterization of four M2 subtypes (M2a, M2b, M2c, and M2d) derived from THP-1 has not been fully investigated. In this study, we systematically analyzed the protein expression profiles of human THP-1-derived macrophages (M0, M1, M2a, M2b, M2c, and M2d) using quantitative proteomics approaches. The commonly and specially regulated proteins of the four M2 subtypes and their potential biological functions were further investigated. The results showed that M2a and M2b, and M2c and M2d have very similar protein expression profiles. These data could serve as an important resource for studies of macrophages using THP-1 cells, and provide a reference to distinguish different M2 subtypes in macrophage-associated diseases for subsequent clinical research.

Sequencing and Proteomic Analysis of Exosomes from Apheresis Platelets in Different Storage Periods / 中国实验血液学杂志

OBJECTIVE@#To investigate the changes of gene sequencing and proteomics of apheresis platelet (AP) exosomes in different storage periods and predict the function of AP exosomes in different storage periods.@*METHODS@#Platelets at different storage periods of 0 day (D0), 3 day (D3) and 5 day (D5) were collected, exosomes were extracted with Gradient centrifugation; gene sequencing and proteomic analysis were used to analyze the exosomes, and biological functions of platelet exosomes were analyzed and predicted by bioinformatics. Liquid mass spectrometry (LMS) was used to detect the changes and function prediction of exosomes proteins. The small RNA sequencing library was prepared, and the constructed library was sequenced and bioinformatics technology was used for data analysis.@*RESULTS@#AP exosome iTRAQ protein analysis showed that AP exosomes stored in D3 with 55 up-regulated proteins and 94 down-regulated proteins (P<0.05, FC<0.83 or FC>1.2), while AP exosomes stored in D5 with 292 up-regulated proteins and 53 down-regulated proteins (P<0.05, FC<0.83 or FC>1.2) as compared with D0. KEGG pathway analysis showed that the proteins were mainly involved in transport and metabolism, immune system, cancer, membrane transport and other processes. There were statistically significant differences between AP exosome miRNAs in different storage days (P<0.01). The number of miRNA up-regulated and down-regulated was 374 and 255 as compared with the number of platelet exosomes miRNA stored in D3 and D0, while that was 297 and 242 in D5 and D0, and 252 and 327 in D5 and D3, respectively. The target genes of differential platelet exosome miRNAs were analyzed by GO enrichment. Target genes of differential miRNA were mainly involved in membrane composition, mainly played molecular functions binding to proteins, and participated in biological processes of transcriptional regulation.@*CONCLUSION@#The exosome differential proteins and miRNAs in D5 are significantly different from those in the D0 of APs, and they are involved in various biological processes.

Proteomics of serum exosomes in children in the acute stage of Kawasaki disease: a prospective study / 中国当代儿科杂志

OBJECTIVES@#To study the biological processes and functions of serum exosomes in children in the acute stage of Kawasaki disease (KD), so as to provide new biomarkers for the early diagnosis of KD.@*METHODS@#In this prospective study, 13 children with KD who were treated in Children's Hospital of Soochow University from June 2019 to August 2020 were enrolled as the KD group, and 13 children who were hospitalized due to bacterial infection during the same period were enrolled as the control group. Whole blood was collected on the next morning after admission, serum samples were obtained by centrifugation, and exosomes were extracted through ultracentrifugation. Serum exosomes were analyzed by label-free quantitative proteomics, and differentially expressed proteins (DEPs) were screened out for functional enrichment analysis. A protein-protein interaction (PPI) network was plotted, and unique proteins were validated by targeted proteomics.@*RESULTS@#A total of 131 DEPs were screened out for the two groups, among which 27 proteins were detected in both groups. There were 48 unique DEPs in the KD group, among which 23 were upregulated and 25 were downregulated, and these proteins acted on "complement and coagulation cascades" and "the MAPK signaling pathway". Validation by targeted proteomics showed that FGG, SERPING1, C1R, C1QA, IGHG4, and C1QC proteins were quantifiable in the KD group. A total of 29 proteins were only expressed in the control group, among which 12 were upregulated and 17 were downregulated. Four proteins were quantifiable based on targeted proteomics, i.e., VWF, ECM1, F13A1, and TTR. A PPI network was plotted for each group. In the KD group, FGG and C1QC had close interaction with other proteins, while in the control group, VWF had close interaction with other proteins.@*CONCLUSIONS@#The serum exosomes FGG and C1QC in children in the acute stage of KD are expected to become the biomarkers for the early diagnosis of KD. For children with unexplained fever, detection of FGG, C1QC1, and VWF may help with etiological screening.

Twenty years in the 21st century: research approaches and techniques in modern system biology for mechanisms of Chinese medicinal processing / 中国中药杂志

Clarifying the mechanisms of Chinese medicinal processing is pivotal to the modernization of Chinese medicine. Research on Chinese medicinal processing gives priority to the mechanisms of the processing in enhancing efficacy, reducing toxicity, and repurposing medicinals. During the past 20 years, scholars have carried out in-depth studies on the mechanisms of Chinese medicinal processing via modern system biology. They mainly focused on the changes of medicinal properties and efficacy caused by processing using techniques of modern pharmacology and molecular biology, spectrum-efficacy correlation, and biophoton emission. However, these techniques fail to reflect the holistic view of traditional Chinese medicine. With the introduction of system biology, multi-omics techno-logies(genomics, transcriptomics, proteomics, and metabolomics) have surged, which have been applied to the research on the mec-hanisms of Chinese medicinal processing. These multi-omics technologies have advantages in the research on holism. This study aims to summarize the research techniques and approaches in system biology for mechanisms of Chinese medicinal processing in the past 20 years and analyze the limitations and advantages of them. It is concluded that the multi-omics techniques of system biology can reconstruct the mechanisms of Chinese medicinal processing. This study provides a new direction for further research on the mechanisms of Chinese medicinal processing.

Comparative proteomic profiling of hippocampi in mice treated with Jingui Shenqi Pills and Liuwei Dihuang Pills / 中国中药杂志

The effects of Jingui Shenqi Pills(Jingui) and Liuwei Dihuang Pills(Liuwei) which respectively tonify kidney Yang and kidney Yin on brain function have attracted great attention, while the differences of protein expression regulated by Jingui and Liuwei remain to be studied. This study explored the difference of protein expression profiles in the hippocampi of mice orally administrated with the two drugs for 7 days. The protein expression was quantified using LC-MS/MS. The results showed that among the 5 860 proteins tested, 151, 282 and 75 proteins responded to Jingui alone, Liuwei alone, and both drugs, respectively. The ratio of up-regulated proteins to down-regulated proteins was 1.627 in Jingui group while only 0.56 in Liuwei group. The proteins up-regulated by Jingui were mainly involved in membrane transport, synaptic vesicle cycle, serotonergic synapse, dopaminergic synapse and so on, suggesting that Jingui may play a role in promoting the transport of neurotransmitter in the nervous system. The proteins down-regulated by Liuwei were mainly involved in membrane transport, synapse, ion transport(potassium and sodium transport), neurotransmitter transport, innate and acquired immune responses, complement activation, inflammatory response, etc. In particular, Liuwei showed obvious down-regulation effect on the members of solute carrier(SLC) superfamily, which suggested that Liuwei had potential inhibitory effect on membrane excitation and transport. Finally, consistent results were obtained in the normal mouse and the mouse model with corticosterone-induced depressive-like behavior. This study provides an experimental basis for understanding the effect of Jingui and Liuwei on brain function from protein network.

Mechanism analysis of repeatedly steamed and sundried Rehmanniae Radix Praeparata in delaying brain aging in ovariectomized mice based on proteomics / 中国中药杂志

The present study explored the effect and mechanism of repeatedly steamed and sundried Rehmanniae Radix Praeparata(RRP) in delaying brain aging in ovariectomized mice. After ovariectomy, the mice were randomly divided into a model group, an estradiol valerate group(0.3 mg·kg~(-1)), and low-(1.0 g·kg~(-1)), medium-(2.0 g·kg~(-1)), and high-dose(4.0 g·kg~(-1)) RRP groups, and a sham operation group was also set up, with 15 mice in each group. One week after the operation, intragastric administration was carried out for 15 consecutive weeks. The step-down test and Morris water maze test were used to detect the behavioral changes of mice. HE staining and Nissl staining were used to observe the morphological changes of mouse brain tissues. Immunohistochemistry was used to detect the expression of Aβ and ER_β in mouse brain tissues. The serum estrogen levels and cholinesterase and cholinesterase transferase levels in brain tissues of mice were detected by assay kits. The extracted hippocampal protein was detected by the Nano-ESI-LC-MS system, identified by the Protein Discovery, and analyzed quantitatively and qualitatively by the SIEVE. The PANTHER Classification System was used for GO analysis and KEGG pathway enrichment analysis of the differential proteins. Compared with the sham operation group, the model group showed decreased learning and memory ability, shortened step-down latency(P<0.05), prolonged escape latency(P<0.05), reduced platform crossings and residence time in the target quadrant, scattered nerve cells in the hippocampus with enlarged intercellular space, increased expression of Aβ-positive cells(P<0.05), declining expression of ER_β-positive cells and estrogen level(P<0.05), and weakened cholinergic function(P<0.05). Compared with the model group, the RRP groups showed improved learning and memory ability, prolonged step-down latency(P<0.05), increased estrogen level(P<0.05), neatly arranged nerve cells in the hippocampus with complete morphology, declining Aβ-positive cells, and elevated expression of ER_β-positive cells. A total of 146 differential proteins were screened out by proteomics, and KEGG pathway enrichment yielded 75 signaling pathways. The number of proteins involved in the dopaminergic synapse signaling pathway was the largest, with 13 proteins involved. In summary, RRP can delay brain aging presumedly by increasing the level of estrogen, mediating the dopaminergic synapse signaling pathway, and improving cholinergic function.

Cucumber downy mildew and the mechanisms of host resistance: a review / 生物工程学报

The cultivation and production of cucumber are seriously affected by downy mildew caused by Pseudoperonospora cubensis. Downy mildew damages leaves, stems and inflorescences, and then reduces the yield and quality of cucumber. This review summarized the research advances in cucumber downy mildew, including pathogen detection and defense pathways, regulatory factors, mining of pathogens-resistant candidate genes, proteomic and genomic analysis, and development of QTL remarks. This review may facilitate clarifying the resistance mechanisms of cucumber to downy mildew.

Advances of chromatogram retention time alignment algorithms in proteomics / 生物工程学报

Chromatography is a basic process in the current proteomics workflow, and the retention time alignment of the chromatogram is one of the important steps to effectively improve the identification and quantification accuracy. After years of development, a series of algorithms for retention time alignment have been developed. This review summarizes the advances of chromatographic retention time alignment algorithms and tools for proteomics analysis from the perspective of proteomics users, and discusses the development and future application directions.

Using OMICS technologies to analyze the mechanisms of synthetic microbial co-culture systems: a review / 生物工程学报

In recent years, the interaction mechanisms underpinning the synthetic microbial co-culture systems have gained increasing attention due to their potentials in various biotechnological applications. Exploration of the inter-species mechanisms underpinning the synthetic microbial co-culture system could contribute to a better understanding of the theoretical basis to further optimize the existing co-culture systems, and design new synthetic co-culture system for large-scale application. OMICS technologies such as genomics, transcriptomics, proteomics, and metabolomics could analyze the biological processes in a high throughput manner. Multi-omics analysis could achieve a "global view" of various members in the microbial co-culture systems, which presents opportunities in understanding synthetic microbial consortia better. This article summarizes recent advances in understanding the mechanisms of synthetic microbial co-culture systems using omics technologies, from the aspects of metabolic network, energy metabolism, signal transduction, membrane transport, stress response, community stability and structural rationality. All these findings could provide important theoretical basis for future application of the microbial co-culture systems with the aids of emerging biotechnologies such as synthetic biology and genome editing.

A map of neutrophil granules by proteomics / Mapa dos neutrófilos por proteômica (OU) Mapa dos grânulos do neutrófilo por proteômica

Neutrophils are polymorphonuclear leukocytes that play a key role in the organism defense. These cells enroll in a range of actions to ensure pathogen elimination and orchestrate both innate and adaptative immune responses. The main physiological structures of neutrophils are their storage organelles that are essential since the cells activation and participate in all their functions. The storage organelles are divided into 2 types: granules and secretory vesicles. The granules are subdivided into azurophilic, specific and gelatinase. The granules are distinguished by their protein content, and since they play an important role on the neutrophil function, the knowledge of the proteins stored in these organelles can help to better understand these cells. Some proteins are present in high abundance and are used as markers for each storage organelle. These proteins are myeloperoxidase (MPO) for azurophil granules, neutrophil gelatinase associated with lipocalin-2 (NGAL) and lactoferrin (LTF) for specific granules, matrix metalloproteinase-9 (MMP9) for gelatinase granules and alkaline phosphatase (AP) for secretory vesicles. The isolation of neutrophils granules, however, is challenging and the existing procedures rely on large sample volumes, about 400 mL of peripheral blood or 3 x 108 neutrophils, not allowing for multiple biological and technical replicates. Therefore, the aim of this study was to develop a miniaturized neutrophil granules isolation method and to use biochemical assays, mass spectrometry-based proteomics and a machine learning approach to investigate the protein content of the neutrophils storage organelles. With that in mind, 40 mL of the peripheral blood of three apparently healthy volunteers were collected. The neutrophils were isolated, disrupted using nitrogen cavitation and organelles were fractionated with a discontinuous 3-layer Percoll density gradient. The presence of granules markers in each fraction was assessed using western blot , gelatin zymography and enzymatic assays. The isolation was proven successful and allowed for a reasonable separation of all neutrophils storage organelles in a gradient of less than 1 mL, about 37 times smaller than the methodsdescribed in the literature. Moreover, mass spectrometry-based proteomics identified 369 proteins in at least 3 of the 5 samples, and using a machine learning strategy, the localization of 140 proteins was predicted with confidence. Furthermore, this study was the first to investigate the proteome of neutrophil granules using technical and biological replicates, creating a reliable database for further studies. In conclusion, the developed miniaturized method is reproducible, cheaper, and reliable. In addition, it provides a resource for further studies exploring neutrophil granules protein content and mobilization during activation with different stimuli

Neutrófilos são leucócitos polimorfonucleares que possuem papel fundamental na defesa do organismo. Essas células desempenham diversas ações a fim de assegurar a eliminação de um patógeno e, além disso, orquestram a resposta imune inata e adaptativa. O conjunto composto pelos grânulos de armazenamento e as vesículas secretórias compõe a principal estrutura fisiológica dos neutrófilos. Estes componentes são essenciais desde a ativação celular, participando de todas as funcionalidades desta célula. Os grânulos são subdivididos em azurófilos, específicos e gelatinase. Eles podem ser distinguidos por meio de seu conteúdo proteico e, como são importantes na funcionalidade dos neutrófilos, identificar quais proteínas são armazenadas nestas organelas é imprescindível para entender melhor essa célula como um todo. Algumas proteínas, estão presentes de forma abundante e, portanto, são utilizadas como marcadores dos grânulos. Tais proteínas são mieloperoxidase (MPO) para os grânulos azurófilos, gelatinase de neutrófilo associada a lipocalina (NGAL) e lactoferrina (LTF) para os específicos, metaloproteinase de matrix 9 (MMP9) para os grânulos de gelatinase e fosfatase alcalina (AP) para as vesículas secretórias. Isolar estas estruturas, no entanto, é desafiador visto que os protocolos existentes na literatura utilizam grandes volumes de amostra, cerca de 400 mL de sangue ou 3 x 108 neutrófilos, para apenas um isolamento, impedindo a realização de replicatas técnicas e biológicas. Desta forma, o objetivo do presente estudo foi desenvolver um protocolo miniaturizado de isolamento dos grânulos neutrofílicos e utilizar métodos bioquímicos, de proteômica e machine learning para investigar o conteúdo proteico destas estruturas celulares. Para isto, 40 mL de sangue periférico de três voluntários aparentemente saudáveis foi coletado. Os neutrófilos foram então isolados, lisados com cavitação de nitrogênio e o fracionamento subcelular foi realizado baseado em um gradiente descontínuo de 3 camadas de Percoll. O método de isolamento foi avaliado através da investigação dos marcadores utilizando western blotting (WB), zimografia de gelatina e ensaios enzimáticos em cada fração coletada. O isolamento demonstrou-se eficiente e permitiu uma ótima separação dos grânulosem um gradiente menor que 1 mL, cerca de 37 vezes menor que os métodos atualmente descritos na literatura. Além disso, a análise proteômica foi capaz de identificar 369 proteínas presentes em pelo menos 3 das 5 réplicas investigadas e, utilizando ferramentas de machine learning, 140 proteínas foram classificadas como pertencentes a um dos tipos de grânulos ou vesícula secretória com alto nível de confiabilidade. Por fim, o presente estudo foi o primeiro a investigar o proteoma dos grânulos utilizando replicatas técnicas e biológicas, criando e fornecendo uma base de dados robusta que poderá ser utilizada em estudos futuros. Conclui-se, portanto, que a metodologia miniaturizada desenvolvida é eficaz, reprodutível e mais barata, além de permitir estudos mais complexos e profundos sobre o proteoma dos grânulos dos neutrófilos em diferentes momentos celulares, tais como quando ativados via estímulos distintos

Proteomics: a tool to investigate of composition and function of HDL in hyperlipidemia / Proteômica: uma ferramenta para a investigação da composição e função da HDL em hiperlipidemia

The inverse relationship between HDL-C (high-density lipoprotein cholesterol) and cardiovascular disease is well established. However, it is consensus that the cholesterol content present in HDL does not capture its complexity, and other metrics need to be explored. HDL is a heterogeneous, protein-enriched particle with functions going beyond lipid metabolism. In this way, its protein content seems to be attractive to investigate its behavior in the face of pathologies. Many of the proteins with important function in HDL are in low abundance (<1% of total proteins), which makes their detection challenging. Quantitative proteomics allows detecting proteins with high precision and robustness in complex matrix. However, quantitative proteomics is still poorly explored in the context of HDL. In this sense, in the second chapter of this thesis, the analytical performance of two quantitative methodologies was carefully investigated. These methods achieved adequate linearity and high precision using labeled peptides in a pool HDL, in addition to comparable ability to differentiate proteins from HDL subclasses of healthy subjects. Another bottleneck that waits for a solution in proteomics is the lack of standardization in data processing and analysis after mass spectrometry acquisition. In addition, interest in the cardioprotective properties of omega-3 is growing, but little is known about its effects on the HDL proteome. Thus, in the third chapter of this thesis, we compared five protein quantification strategies using Skyline and MaxDIA software platforms in order to investigate the HDL proteome from mice submitted to a high-fat diet supplemented or not with omega-3. MaxDIA with label-free quantification (MaxLFQ) achieved high precision to show that polyunsaturated fatty acids remodel the HDL proteome to a less inflammatory profile. Therefore, the two studies presented in this thesis begin to open new paths for a deeper and more reliable understanding of HDL, both at the level of protein quantification by mass spectrometry and after data acquisition

A inversa relação entre HDL-C (do inglês, high-density lipoprotein cholesterol) e doenças cardiovasculares é bem estabelecida. No entanto, é consenso que o conteúdo de colesterol presente na HDL não captura sua complexidade, e outras métricas precisam ser exploradas. A HDL é uma partícula heterogênea, enriquecida em proteínas, com funções que vão além do metabolismo de lipídeos. Dessa forma, seu conteúdo proteico parece ser mais atrativo para exprimir seu comportamento frente às patologias. Muitas das proteínas com função importante estão em baixa abundância (<1% do total de proteínas), o que torna a detecção desafiadora. Métodos quantitativos de proteômica permitem detectar proteínas com alta precisão e robustez em matrizes complexas. No entanto, a proteômica quantitativa ainda é pouco explorada no contexto da HDL. Nesse sentido, no segundo capítulo dessa tese, a performance analítica de dois métodos quantitativos foi criteriosamente investigada, os quais alcançaram adequada linearidade e alta precisão usando peptídeos marcados em um pool de HDL, além de comparável habilidade em diferenciar as proteínas das subclasses da HDL de indivíduos saudáveis. Outro gargalo que aguarda por solução em proteômica é a falta de padronização no processamento e análise de dados após a aquisição por espectrometria de massas. Além disso, é crescente o interesse das propriedades cardioprotetivas do ômega-3, porém pouco se conhece sobre seus efeitos no proteoma da HDL. Então, no terceiro capítulo dessa tese, comparamos cinco estratégias de quantificação de proteínas utilizando os softwares Skyline e MaxDIA com o intuito de comparar o proteoma da HDL de camundongos submetidos a uma dieta hiperlipídica suplementados ou não com ômega-3. MaxDIA com quantificação label-free (MaxLFQ) apresentou alta precisão para mostrar que o ômega-3 remodela o proteoma da HDL para um perfil menos inflamatório. Portanto, os dois estudos apresentados nessa tesa começam a abrir novos caminhos para o entendimento mais profundo e confiável da HDL tanto por meio da quantificação das proteínas por espectrometria de massas quanto após à aquisição dos dados

Identificação de moduladores da sinalização celular no câncer de cólon e metástases hepáticas como ferramenta para descoberta de alvos terapêuticos / Identification of cell signaling modulators in colon cancer and liver metastases as a tool for discovering therapeutic targets

O câncer de cólon é uma das principais causas de morte por câncer em todo mundo e aproximadamente 50% dos pacientes desenvolvem metástases hepáticas durante o curso da doença. Ainda que a ressecção cirúrgica proporcione sobrevida de 5 anos ao redor de 40%, a maior parte dos pacientes apresenta doença irressecável ao diagnóstico. Neste caso, o cenário é devastador devido à resistência das células tumorais ao tratamento padrão com quimioterapia e/ou anticorpo monoclonal. Apesar dos avanços alcançados pelo rastreamento genômico das metástases, o conhecimento sobre o envolvimento de transcritos e proteínas específicas na atividade de sinalização e recrutamento de populações imunes ainda é limitado nessa doença. Considerando o grande potencial de descoberta e inovação que pode ser alcançado, este projeto propôs o desenvolvimento de uma meta-análise de dados públicos para a exploração de metástases hepáticas e a caracterização proteômica de metástases hepáticas inicialmente irressecáveis em busca de alvos promissores que possam ser explorados em novas opções terapêuticas. As principais etapas metodológicas incluem (1) desenvolvimento de um modelo de integração de dados para a obtenção, processamento e análise de aproximadamente 3.5 mil amostras de RNA-seq, microarray e proteômica de metástases hepáticas inicialmente ressecáveis, tumores primários do cólon e tecidos não-neoplásicos, (2) rastreamento por espectrometria de massas de 30 biópsias pareadas, sendo 15 de metástases hepáticas inicialmente irressecáveis e 15 de tecidos não-neoplásicos adjacentes, (3) investigação de potenciais moduladores da sinalização oncogênica associada à resistência à terapia e (4) exploração dos resultados em um conjunto independente com aproximadamente 138 mil células obtidas por single-cell RNA-seq em busca de associações entre alvos, vias de sinalização e populações imunes. Após a análise de espectrometria de massas e integração de dados da metaanálise, das 46 proteínas diferencialmente reguladas entre metástases hepáticas inicialmente irressecáveis e tecidos não-neoplásicos, TGFB1, CDH2, APOA1, TNFR2, EGFR, MDH2, ITIH2, YWHAZ, PCBP1, TOP2A e ENO1 (todas com aumento de regulação nas metástases) e CXCL14, PLA2G2A e CAV1 (com diminuição de regulação nas metástases) prosseguiram na análise. Dessas, PLA2G2A e CAV1 não foram estatisticamente confirmadas após comparação com cinco estudos independentes. Também foi identificada a ativação nas metástases de importantes vias como JAK-STAT (z-score=3,18), VEGF (z-score=2,67), WNT (z-score=3,22), PI3K (z-score=3,99), MAPK (z-score=2,85), EGFR (z-score=2,49) e NFkB (zscore=4,11). Em seguida observamos pela análise de single-cell RNA-seq que a presença de TGFB1, TNFR2 e EGFR estava associada a maior polarização de neutrófilos e células Tregs em metástases hepáticas, sugerindo uma participação desses alvos no recrutamento dessas populações imunes ou em conjunto durante o desenvolvimento, estabelecimento dessas células no fígado e progressão da doença. Tanto TGFB1 (p=0,01) quanto TNFR2 (p=0,048) foram associados a pior sobrevida global em pacientes metastáticos e apresentaram AUC=0,95 na separação entre câncer primário no cólon e metástases no fígado. Especificamente sobre a comparação entre metástases inicialmente ressecáveis e irressecáveis, apesar de termos identificado alguns alvos com mais de 10-fold de diferença (YWHAZ, AHNAK, HNRNPH1, PCBP1 e TGFB1) apenas TGFB1 prosseguiu em todas as análises, porém, esses resultados sugerem a exploração posterior desses candidatos em novos estudos. Quando buscamos por alvos relacionados à resistência à terapia, nossa estratégia selecionou 32 proteínas diferencialmente reguladas nas metástases resistentes, com envolvimento de CDH2 (p=0,002), CXCL14 (p=0,05), SERPINA1 (p=0,012) e LRGR (p=0,049) com pior sobrevida global em pacientes metastáticos. Nesses tumores também foi observada uma tendência de ativação das vias TGF-ß e TNF-α, já descritas na literatura devido a participação no desenvolvimento e progressão de metástases, além de favorer um perfil de resistência às células tumorais. Por meio de uma análise de deconvolução também observamos maior presença de células Tregs em pacientes resistentes. Essa relação entre Tregs/LGR5 também já foi associada a pior prognóstico em outros tipos de cânceres e suportam uma participação de ambos em um possível mecanismo de resistência desses tumores. Com base nos resultados obtidos, acreditamos oferecer um conjunto de dados inéditos que podem modificar o prognóstico e diagnóstico das metástases hepáticas, bem como contribuir para que os pacientes tenham novas opções terapêuticas com melhora na sobrevida

Colon cancer is one of the leading causes of cancer death worldwide and approximately 50% of patients develop liver metastases during the course of the disease. Although surgical resection provides a 5-year survival rate of around 40%, most patients have unresectable disease at diagnosis. In this case, the scenario is devastating due to the resistance of tumor cells to standard treatment with chemotherapy and/or monoclonal antibody. Despite the advances achieved by genomic tracking of metastases, the involvement of specific transcripts and proteins in the signaling activity and recruitment of immune populations is still limited in this disease. Considering the great potential for discovery and innovation that can be achieved, this project proposed the development of a meta-analysis for the exploration of liver metastases and the proteomic characterization of initially unresectable liver metastases in search of promising targets that can be explored in new therapeutics options. Key methodological steps include (1) development of a data integration model for obtaining, processing and analyzing approximately 3,500 RNA-seq, microarray and proteomic samples from initially resectable liver metastases, primary colon tumors and non-neoplastic tissues, (2) mass spectrometry screening of 30 paired biopsies, 15 from initially unresectable liver metastases and 15 from adjacent non-neoplastic tissues, (3) investigation of potential modulators of oncogenic signaling associated with therapy resistance, and (4) exploration of the results in an independent pool of approximately 138,000 cells obtained by single-cell RNA-seq in search of associations between targets, signaling pathways and immune populations. After mass spectrometry analysis and integration of metaanalysis data, of the 46 differentially regulated proteins between initially unresectable liver metastases and non-neoplastic tissues, TGFB1, CDH2, APOA1, TNFR2, EGFR, MDH2, ITIH2, YWHAZ, PCBP1, TOP2A and ENO1 (all with upregulation in metastases) and CXCL14, PLA2G2A and CAV1 (with downregulation in metastases) continued in the analysis. Of these, PLA2G2A and CAV1 were not statistically confirmed after comparison with five independent studies. We identified activation of important pathways such as JAK-STAT (zscore=3.18), VEGF (z-score=2.67), WNT (z-score=3.22), PI3K (z-score=3.99), MAPK (z- score=2.85), EGFR (z-score=2.49) and NFkB (z-score=4.11). Then we observed by single-cell RNA-seq analysis that the presence of TGFB1, TNFR2 and EGFR was associated with greater polarization of neutrophils and Treg cells in liver metastases, suggesting a participation of these targets in the recruitment of these immune populations or together during development, establishment of these cells in the liver and disease progression. Both TGFB1 (p=0.01) and TNFR2 (p=0.048) were associated with worse overall survival in patients with metastatic disease and had AUC=0.95 separating primary colon cancer from liver metastases. Specifically, regarding the comparison between initially resectable and unresectable metastases, although we identified some targets with more than 10-fold difference (YWHAZ, AHNAK, HNRNPH1, PCBP1 and TGFB1) only TGFB1 continued in all analyses, however, these results suggest the exploration of these candidates in further studies. When looking for targets related to therapy resistance, our strategy selected 32 proteins differentially regulated in resistant metastases, with involvement of CDH2 (p=0.002), CXCL14 (p=0.05), SERPINA1 (p=0.012) and LRGR (p=0.049) with poor overall survival in metastatic patients. In these tumors, a tendency of activation of the TGF-ß and TNF-α pathways was also observed, already described in the literature due to their participation in the development and progression of metastases, in addition to favoring a resistance profile to tumor cells. By means of a deconvolution analysis, we also observed a greater presence of Treg cells in resistant patients. This relationship between Tregs/LGR5 has also been associated with a worse prognosis in other types of cancers and supports the participation of both in a possible mechanism of resistance in these tumors. Based on the results obtained, we believe to offer a set of unpublished data that can modify the prognosis and diagnosis of liver metastases, as well as contribute to patients having new therapeutic options with improved survival

Proteomic analysis of human keratinocytes under UVA-induced stress / Análise proteômica de queratinócitos humanos sob estresse induzido por luz UVA

The solar ultraviolet (UV) radiation that reaches the Earth is composed of 95% of UVA (320 to 400 nm) and 5% of UVB (280 to 320 nm) radiation. UVB is carcinogenic, generating potentially mutagenic DNA lesions. The solar UVA radiation also causes DNA damage, but this fact does not fully account for its biological impact. UVA is absorbed by non-DNA cellular chromophores, generating reactive oxygen species such as singlet oxygen. Knowing the proteome mediates stress responses in cells, here we investigated the cellular effects of a non-cytotoxic dose of UVA radiation, equivalent to about 20 minutes of midday sun exposure, on the proteome of human keratinocytes. Using a combination of mass spectrometry-based proteomics, bioinformatics, and conventional biochemical assays, we analyzed two aspects of UVA-induced stress: spatial remodeling of the proteome in subcellular compartments 30 minutes after stress and long-term changes in protein levels and secretion (24 hours and 7 days postirradiation). In the first part of this thesis, we quantified and assigned subcellular localization for over 3000 proteins, of which about 600 potentially redistribute upon UVA exposure. Protein redistributions were accompanied by redox modulations, mitochondrial fragmentation and DNA damage. In the second part of the work, our results showed that primary human keratinocytes enter senescence upon exposure to a single dose of UVA, mounting antioxidant and inflammatory responses. Cells under UVA-induced senescence further elicit paracrine responses in neighboring premalignant HaCaT epithelial cells via inflammatory mediators. Altogether, these results reiterate the role of UVA radiation as a potent metabolic stressor in the skin

A radiação ultravioleta (UV) solar que atinge a superfície terrestre é composta por 95% de radiação UVA (320 a 400 nm) e 5% de radiação UVB (280 a 320 nm). A radiação UVB é carcinogênica e gera lesões potencialmente mutagênicas no DNA. A radiação UVA solar também gera danos no DNA, mas a genotoxicidade dessa radiação não explica inteiramente o seu impacto biológico. Atualmente, sabe-se que a radiação UVA é absorvida por cromóforos celulares, gerando espécies reativas de oxigênio, como o oxigênio singlete. Sabendo que o proteoma é um mediador de respostas ao estresse celular, nós investigamos os efeitos celulares de uma dose não-citotóxica de radiação UVA, equivalente a cerca de 20 minutos de exposição ao sol, no proteoma de queratinócitos humanos. Utilizando espectrometria de massas, bioinformática e ensaios bioquímicos convencionais, nós analisamos dois aspectos do estresse induzido por radiação UVA: o remodelamento espacial do proteoma 30 minutos depois do estresse e alterações nos níveis e na secreção de proteínas no longo prazo (24 horas e 7 dias depois da irradiação). Na primeira parte desta tese, nós quantificamos e atribuímos classificações de localização subcelular a mais de 3000 proteínas. Dentre essas proteínas, 600 tem potencialmente a sua distribuição subcelular alterada em resposta à radiação. As redistribuições subcelulares são acompanhadas de modulações redox, fragmentação mitocondrial e danos no DNA. Na segunda parte da tese, os nossos resultados mostraram que queratinócitos humanos primários entram em senescência sob exposição a uma única dose de radiação UVA, montando respostas antioxidantes e pró-inflamatórias. Células sob senescência induzida por UVA, por sua vez, desencadeiam respostas parácrinas em queratinócitos pré-tumorais (células HaCaT) por meio de mediadores inflamatórios. Em conjunto, esses resultados reiteram o papel da radiação UVA como um potente estressor metabólico em células da pele

Análise proteômica de células BEAS-2B expostas a benzo[α]pireno e nicotinamida ribosídeo / Proteomic Analysis of BEAS-2B cells exposed to benzo[α]pyrene and nicotinamide riboside

Responsável por milhões de óbitos anuais e um grande custo para a saúde pública, o câncer é a segunda maior causa de mortes no mundo. Dentre seus diversos tipos, o câncer de pulmão, além da alta incidência, é um dos mais letais. A exposição a substâncias tóxicas provenientes da combustão de matéria orgânica, assim como o consumo de cigarro, são os principais responsáveis pela alta incidência de câncer de pulmão. Dentre estas substâncias, está o benzo[α]pireno (B[α]P), um carcinógeno completo, ou seja, capaz de iniciar e promover o processo de carcinogênese. Resultados anteriores obtidos pelo grupo demonstraram que células BEAS-2B expostas a 1 µM de B[α]P apresentaram alterações das concentrações de metabólitos intracelulares, indução de estresse redox e hipermetilação do DNA. A exposição a 1 µM de nicotinamida ribosídeo (NR), um dos precursores de NAD+, foi capaz de proteger as células BEAS-2B contra a transformação induzida por B[α]P, além de impedir totalmente que células não expostas a B[α]P formassem colônias em soft-agar. A utilização da proteômica neste trabalho permitiu verificar a abundância das proteínas nos quatro diferentes grupos de exposição: Controle, B[α]P, B[α]P + NR e NR. Após 120 h de exposição as células foram coletadas, as proteínas extraídas e preparadas para análise. Foram descobertas 3024 proteínas posteriormente analisadas com o objetivo de elucidar vias possivelmente envolvidas na proteção contra o processo de transfomação maligna. Os grupos NR e Controle demonstram ser mais parecidos em relação ao seu conteúdo, enquanto os grupos B[α]P e B[α]P + NR foram mais semelhantes entre si. A análise de proteínas exclusivas revelou menos processos relacionados ao reparo de DNA no grupo tratado apenas com B[α]P quando comparado com B[α]P + NR. A análise estatística do total de proteínas utilizando o teste ANOVA (p < 0,05, N = 5) revelou 564 proteínas diferencialmente expressas entre os grupos. A clusterização nos permitiu observar a diferença na abundância de proteínas entre os quatro tratamentos. As proteínas estão envolvidas em funções como a regulação do metabolismo, resposta a estresse, transdução de sinal, regulação de expressão gênica e morte celular. Um dos clusters (cluster 1), contendo 59 proteínas, revelou poucos processos na análise de enriquecimento, mas as proteínas contidas nele apresentam funções como controle da divisão celular, apoptose e proteção ao estresse redox. Nele podemos observar que, no geral, o tratamento com B[α]P aumentou a abundância de algumas proteínas, o que foi revertido no grupo B[α]P + NR. O tratamento apenas com NR diminuiu a abundância das proteínas contidas nesse cluster. Outro cluster (cluster 4) apresentou 51 proteínas de abundância diminuída durante a exposição ao B[α]P, o que se reverteu no grupo B[α]P + NR. As proteínas desse cluster estão envolvidas em etapas importantes da via glicolítica, de crescimento, adesão, migração e invasão celular. Apesar de ser descrito que a exposição a NR pode aumentar a eficiência do reparo de DNA, os resultados apresentados nesse trabalho indicam que o efeito protetor pode estar relacionado com a modulação do ciclo celular ou alterações na adesão celular

Responsible for millions of annual deaths and a great health expense, cancer is the second leading cause of death in the world. Among its many types, lung cancer, besides its high incidence, is also one of the most lethal. Exposure to toxic substances resulting from the combustion of organic matter, as well as cigarette consumption, are the mainly responsible for the high incidence of lung cancer. One of these substances is benzo[α]pyrene (B[α]P), a complete carcinogen, able to initiate and promote the carcinogenesis process. Results obtained previously demonstrated that BEAS-2B cells exposed to 1 µM BaP presented alterations in the levels of intracellular metabolites, induction of oxidative stress, and hypermethylation of DNA. The exposure to 1 µM nicotinamide riboside (NR), one of the precursors of NAD+, was able to protect BEAS-2B cells against the transformation induced by B[α]P, moreover, it also totally prevented the colonies formation on soft agar in cells not exposed to B[α]P. The use of proteomics allowed us to verify the abundance of proteins in the four different exposure groups: Control, B[α]P, B[α]P + NR e NR. After 120h of exposure, the cells were collected followed by the extraction of the proteins. A total of 3024 proteins were identified and analyzed aiming to elucidate possible pathways involved in the protective effect against the malignant transformation induced by B[α]P. The NR and Control groups showed to be more similar, while B[α]P and B[α]P + NR were more similar. The analysis of exclusive proteins revealed fewer processes related to DNA repair in B[α]P when compared with B[α]P + NR. The statistical analysis of the total proteins using the ANOVA test (p <0.5, N = 5) revealed 564 proteins differentially expressed between the groups. The heatmap showed the difference in protein abundance between the four treatments. Proteins are involved in functionssuch asthe regulation of metabolism, stress response, signal transduction, regulation of gene expression, and cell death. One of the clusters (cluster 1), containing 59 proteins, revealed a few processes in the enrichment analysis, but the proteins contained in it have functions such as control of cell division, apoptosis, and protection from redox stress. It is possible to observe, in general, treatment with B[α]P increased the abundance of some proteins, which was partially reversed in group B[α]P + NR. On the other hand, the NR treatment decreased the abundance of proteins contained in this cluster. Another cluster (cluster 4) showed 51 proteins of decreased abundance during exposure to B [α] P, which was partially reversed in group B[α]P + NR. The proteins in this cluster are involved in important stages of the glycolytic pathway, also in growth, adhesion, migration, and cell invasion. Although it has been described that exposure to NR can increase the efficiency of DNA repair, the results presented in this work indicate that the protective effect may be related to the modulation of the cell cycle or cell adehsion modifications