Baldur: Bayesian Hierarchical Modeling for Label-Free Proteomics with Gamma Regressing Mean-Variance Trends.

Label-free proteomics is a fast-growing methodology to infer abundances in mass spectrometry proteomics. Extensive research has focused on spectral quantification and peptide identification. However, research toward modeling and understanding quantitative proteomics data is scarce. Here we propose a Bayesian hierarchical decision model (Baldur) to test for differences in means between conditions for proteins, peptides, and post-translational modifications. We developed a Bayesian regression model to characterize local mean-variance trends in data, to estimate measurement uncertainty and hyperparameters for the decision model. A key contribution is the development of a new gamma regression model that describes the mean-variance dependency as a mixture of a common and a latent trend-allowing for localized trend estimates. We then evaluate the performance of Baldur, limma-trend, and t test on six benchmark datasets: five total proteomics and one post-translational modification dataset. We find that Baldur drastically improves the decision in noisier post-translational modification data over limma-trend and t test. In addition, we see significant improvements using Baldur over the other methods in the total proteomics datasets. Finally, we analyzed Baldur's performance when increasing the number of replicates and found that the method always increases precision with sample size, while showing robust control of the false positive rate. We conclude that our model vastly improves over popular data analysis methods (limma-trend and t test) in several spike-in datasets by achieving a high true positive detection rate, while greatly reducing the false-positive rate.

NetSeekR: a network analysis pipeline for RNA-Seq time series data.

BACKGROUND: Recent development of bioinformatics tools for Next Generation Sequencing data has facilitated complex analyses and prompted large scale experimental designs for comparative genomics. When combined with the advances in network inference tools, this can lead to powerful methodologies for mining genomics data, allowing development of pipelines that stretch from sequence reads mapping to network inference. However, integrating various methods and tools available over different platforms requires a programmatic framework to fully exploit their analytic capabilities. Integrating multiple genomic analysis tools faces challenges from standardization of input and output formats, normalization of results for performing comparative analyses, to developing intuitive and easy to control scripts and interfaces for the genomic analysis pipeline. RESULTS: We describe here NetSeekR, a network analysis R package that includes the capacity to analyze time series of RNA-Seq data, to perform correlation and regulatory network inferences and to use network analysis methods to summarize the results of a comparative genomics study. The software pipeline includes alignment of reads, differential gene expression analysis, correlation network analysis, regulatory network analysis, gene ontology enrichment analysis and network visualization of differentially expressed genes. The implementation provides support for multiple RNA-Seq read mapping methods and allows comparative analysis of the results obtained by different bioinformatics methods. CONCLUSION: Our methodology increases the level of integration of genomics data analysis tools to network inference, facilitating hypothesis building, functional analysis and genomics discovery from large scale NGS data. When combined with network analysis and simulation tools, the pipeline allows for developing systems biology methods using large scale genomics data.

Arabidopsis thimet oligopeptidases are redox-sensitive enzymes active in the local and systemic plant immune response.

Upon pathogen infection, receptors in plants will activate a localized immune response, the effector-triggered immunity (ETI), and a systemic immune response, the systemic acquired response (SAR). Infection also induces oscillations in the redox environment of plant cells, triggering response mechanisms involving sensitive cysteine residues that subsequently alter protein function. Arabidopsis thaliana thimet oligopeptidases TOP1 and TOP2 are required for plant defense against pathogens and the oxidative stress response. Herein, we evaluated the biochemical attributes of TOP isoforms to determine their redox sensitivity using ex vivo Escherichia coli cultures and recombinant proteins. Moreover, we explored the link between their redox regulation and plant immunity in wild-type and mutant Arabidopsis lines. These analyses revealed that redox regulation of TOPs occurs through two mechanisms: (1) oxidative dimerization of full-length TOP1 via intermolecular disulfides engaging cysteines in the N-terminal signal peptide, and (2) oxidative activation of all TOPs via cysteines that are unique and conserved. Further, we detected increased TOP activity in wild-type plants undergoing ETI or SAR following inoculation with Pseudomonas syringae strains. Mutants unable to express the chloroplast NADPH-dependent thioredoxin reductase C (NTRC) showed elevated TOP activity under unstressed conditions and were SAR-incompetent. A top1top2 knockout mutant challenged with P. syringae exhibited misregulation of ROS-induced gene expression in pathogen-inoculated and distal tissues. Furthermore, TOP1 and TOP2 could cleave a peptide derived from the immune component ROC1 with distinct efficiencies at common and specific sites. We propose that Arabidopsis TOPs are thiol-regulated peptidases active in redox-mediated signaling of local and systemic immunity.

Integrative network-centric approach reveals signaling pathways associated with plant resistance and susceptibility to Pseudomonas syringae.

Plant protein kinases form redundant signaling pathways to perceive microbial pathogens and activate immunity. Bacterial pathogens repress cellular immune responses by secreting effectors, some of which bind and inhibit multiple host kinases. To understand how broadly bacterial effectors may bind protein kinases and the function of these kinase interactors, we first tested kinase-effector (K-E) interactions using the Pseudomonas syringae pv. tomato-tomato pathosystem. We tested interactions between five individual effectors (HopAI1, AvrPto, HopA1, HopM1, and HopAF1) and 279 tomato kinases in tomato cells. Over half of the tested kinases interacted with at least one effector, and 48% of these kinases interacted with more than three effectors, suggesting a role in the defense. Next, we characterized the role of select multi-effector-interacting kinases and revealed their roles in basal resistance, effector-triggered immunity (ETI), or programmed cell death (PCD). The immune function of several of these kinases was only detectable in the presence of effectors, suggesting that these kinases are critical when particular cell functions are perturbed or that their role is typically masked. To visualize the kinase networks underlying the cellular responses, we derived signal-specific networks. A comparison of the networks revealed a limited overlap between ETI and basal immunity networks. In addition, the basal immune network complexity increased when exposed to some of the effectors. The networks were used to successfully predict the role of a new set of kinases in basal immunity. Our work indicates the complexity of the larger kinase-based defense network and demonstrates how virulence- and avirulence-associated bacterial effectors alter sectors of the defense network.

Proteome-Wide Analysis of Cysteine Reactivity during Effector-Triggered Immunity.

A surge in the accumulation of oxidants generates shifts in the cellular redox potential during early stages of plant infection with pathogens and activation of effector-triggered immunity (ETI). The redoxome, defined as the proteome-wide oxidative modifications of proteins caused by oxidants, has a well-known impact on stress responses in metazoans. However, the identity of proteins and the residues sensitive to oxidation during the plant immune response remain largely unknown. Previous studies of the thimet oligopeptidases TOP1 and TOP2 placed them in the salicylic acid dependent branch of ETI, with a current model wherein TOPs sustain interconnected organellar and cytosolic pathways that modulate the oxidative burst and development of cell death. Herein, we characterized the ETI redoxomes in Arabidopsis (Arabidopsis thaliana) wild-type Col-0 and top1top2 mutant plants using a differential alkylation-based enrichment technique coupled with label-free mass spectrometry-based quantification. We identified cysteines sensitive to oxidation in a wide range of protein families at multiple time points after pathogen infection. Differences were detected between Col-0 and top1top2 redoxomes regarding the identity and number of oxidized cysteines, and the amplitude of time-dependent fluctuations in protein oxidation. Our results support a determining role for TOPs in maintaining the proper level and dynamics of proteome oxidation during ETI. This study significantly expands the repertoire of oxidation-sensitive plant proteins and can guide future mechanistic studies.

The Effects of Capsaicin on Gastrointestinal Cancers.

Gastrointestinal (GI) cancers are a group of diseases with very high positions in the ranking of cancer incidence and mortality. While they show common features regarding the molecular mechanisms involved in cancer development, organ-specific pathophysiological processes may trigger distinct signaling pathways and intricate interactions with inflammatory cells from the tumoral milieu and mediators involved in tumorigenesis. The treatment of GI cancers is a topic of increasing interest due to the severity of these diseases, their impact on the patients' survivability and quality of life, and the burden they set on the healthcare system. As the efficiency of existing drugs is hindered by chemoresistance and adverse reactions when administered in high doses, new therapies are sought, and emerging drugs, formulations, and substance synergies are the focus of a growing number of studies. A class of chemicals with great potential through anti-inflammatory, anti-oxidant, and anti-tumoral effects is phytochemicals, and capsaicin in particular is the subject of intensive research looking to validate its position in complementing cancer treatment. Our paper thoroughly reviews the available scientific evidence concerning the effects of capsaicin on major GI cancers and its interactions with the molecular pathways involved in the course of these diseases.

Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions.

BACKGROUND: Gene families are sets of structurally and evolutionarily related genes - in one or multiple species - that typically share a conserved biological function. As such, the identification and subsequent analyses of entire gene families are widely employed in the fields of evolutionary and functional genomics of both well established and newly sequenced plant genomes. Currently, plant gene families are typically identified using one of two major ways: 1) HMM-profile based searches using models built on Arabidopsis thaliana genes or 2) coding sequence homology searches using curated databases. Integrated databases containing functionally annotated genes and gene families have been developed for model organisms and several important crops; however, a comprehensive methodology for gene family annotation is currently lacking, preventing automated annotation of newly sequenced genomes. RESULTS: This paper proposes a combined measure of homology identification, motif conservation, phylogenomic and integrated gene expression analyses to define gene family structures in multiple plant species. The MAP3K gene families in seven plant species, including two currently unexamined species Gossypium hirsutum, and Zostera marina, were characterized to reveal new insights into their collective function and evolution and demonstrate the effectiveness of our novel methodology. CONCLUSION: Compared with recent reports, this methodology performs significantly better for the identification and analysis of gene family members in several monocots/dicots, diploid as well as polyploid plant species.

Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics.

BACKGROUND: Several methods to handle data generated from bottom-up proteomics via liquid chromatography-mass spectrometry, particularly for peptide-centric quantification dealing with post-translational modification (PTM) analysis like reversible cysteine oxidation are evaluated. The paper proposes a pipeline based on the R programming language to analyze PTMs from peptide-centric label-free quantitative proteomics data. RESULTS: Our methodology includes variance stabilization, normalization, and missing data imputation to account for the large dynamic range of PTM measurements. It also corrects biases from an enrichment protocol and reduces the random and systematic errors associated with label-free quantification. The performance of the methodology is tested by performing proteome-wide differential PTM quantitation using linear models analysis (limma). We objectively compare two imputation methods along with significance testing when using multiple-imputation for missing data. CONCLUSION: Identifying PTMs in large-scale datasets is a problem with distinct characteristics that require new methods for handling missing data imputation and differential proteome analysis. Linear models in combination with multiple-imputation could significantly outperform a t-test-based decision method.

Proteomics and Proteogenomics Analysis of Sweetpotato ( Ipomoea batatas) Leaf and Root.

Two complementary protein extraction methodologies coupled with an automated proteomic platform were employed to analyze tissue-specific proteomes and characterize biological and metabolic processes in sweetpotato. A total of 74 255 peptides corresponding to 4321 nonredundant proteins were successfully identified. Data were compared to predicted protein accessions for Ipomoea species and mapped on the sweetpotato transcriptome and haplotype-resolved genome. The two methodologies exhibited differences in the number and class of the unique proteins extracted. Overall, 39 916 peptides mapped to 3143 unique proteins in leaves, and 34 339 peptides mapped to 2928 unique proteins in roots. Primary metabolism and protein translation processes were enriched in leaves, whereas genetic pathways associated with protein folding, transport, sorting, as well as pathways in the primary carbohydrate metabolism were enriched in storage roots. A proteogenomics analysis successfully mapped 90.4% of the total uniquely identified peptides against the sweetpotato transcriptome and genome, predicted 741 new protein-coding genes, and specified 2056 loci where gene annotations can be further improved. The proteogenomics results provide evidence for the translation of new open reading frames (ORFs), alternative ORFs, exon extensions, and intronic ORF sequences. Data are available via ProteomeXchange with identifier PXD012999.

Internal hernia after laparoscopic colorectal surgery: an under-reported potentially severe complication. A systematic review and meta-analysis.

BACKGROUND: Internal hernia following laparoscopic colorectal surgery is often under-reported. The aim of this review was to evaluate the occurrence rate of internal hernia following laparoscopic colorectal surgery, and to describe clinical presentation and management strategies. METHODS: A comprehensive literature review was conducted including MEDLINE/Pubmed, EMBASE, SCOPUS, clinicaltrials.gov, and the Cochrane Database of Systematic Reviews through April 2018. The review was conducted according to MOOSE guidelines. Quality was appraised with the Methodological Index for Non-Randomized Studies (MINORS) tool. Meta-analysis was performed using a random effects model. Studies reporting data on internal hernia after laparoscopic colorectal surgery were included. RESULTS: Ten observational studies with a total of 8453 patients were included. All included articles were non-comparative prospective or retrospective cohort studies with an average MINORS score of 8.3 (range 6-11). Summary estimate of proportion of patients developing internal hernia after laparoscopic colorectal resection was 0.5% (95% CI 0.3-0.8%). Heterogeneity was moderate (I2 46%, p = 0.03) and study size (> 1000 vs. <1000 patients) was found to have a significant contribution to heterogeneity (p = 0.002). Thirty patients (90.9%) required surgery, with 5 non-fatal and 3 fatal postoperative complications. Quality of some studies was limited; some patients were followed up for less than 1 year; primary surgical procedures included different laparoscopic approaches. CONCLUSIONS: Occurrence rate of internal hernia after laparoscopic colorectal resection is around 5 per 1000 patients. Small-sized studies are likely to overestimate the occurrence of internal hernia. Need for reoperation is high with a substantial risk of mortality.

MAPK target networks in Arabidopsis thaliana revealed using functional protein microarrays.

Signaling through mitogen-activated protein kinases (MPKs) cascades is a complex and fundamental process in eukaryotes, requiring MPK-activating kinases (MKKs) and MKK-activating kinases (MKKKs). However, to date only a limited number of MKK-MPK interactions and MPK phosphorylation substrates have been revealed. We determined which Arabidopsis thaliana MKKs preferentially activate 10 different MPKs in vivo and used the activated MPKs to probe high-density protein microarrays to determine their phosphorylation targets. Our analyses revealed known and novel signaling modules encompassing 570 MPK phosphorylation substrates; these substrates were enriched in transcription factors involved in the regulation of development, defense, and stress responses. Selected MPK substrates were validated by in planta reconstitution experiments. A subset of activated and wild-type MKKs induced cell death, indicating a possible role for these MKKs in the regulation of cell death. Interestingly, MKK7- and MKK9-induced death requires Sgt1, a known regulator of cell death induced during plant innate immunity. Our predicted MKK-MPK phosphorylation network constitutes a valuable resource to understand the function and specificity of MPK signaling systems.

GOOD TO KNOW: The ALPPS Procedure - Embracing a New Technique.

BACKGROUND: Hepatic resection is the only potentially curative treatment for primary liver tumors and hepatic metastases. The most frightening postoperative complication of extensive hepatectomies is liver failure due to insufficient future liver remnant (FLR). The ALPPS technique (Associating Liver Partition and Portal vein Ligation for Staged hepatectomy) effectively increased the resectability of otherwise inoperable liver tumors (primary or secondary malignant liver tumor) by achieving a rapid and an effective hypertrophy of the FLR, which lowers postoperative liver failure risk. AIM: To present the ALPPS classic right trisectionectomy and its technical variants which were invented to decrease the high rate of post-operative morbidity and mortality, reported in early case series. TECHNIQUE: ALPPS involves two stages. The first surgical procedure consists in the ligation of the right portal branch and the partition of the liver at the site of the falciform ligament (insitu splitting). In contrast to a classical hepatectomy, the tumoral hemiliver is left in situ and remains vascularized by the right hepatic artery only. The biliary and systemic venous drainages represented by the right biliary duct and respectively the hepatic veins, are preserved. The second step of the procedure is usually performed within 7 to 15 days after the firststage. The tumoral hemiliver is removed by sectioning the right hepatic artery, the biliary duct and the systemic venous pedicle. Conclusions: The ALPPS technique is a therapeutic method for inoperable liver tumors by standard methods of hepatectomy ± portal vein ligation (PVL). By careful patient selection and technical adjustment to the particular conditions of each case, better outcomes have been achieved, leading toan increasing number of surgeons who perform ALPPS.

ABC transporter PEN3/PDR8/ABCG36 interacts with calmodulin that, like PEN3, is required for Arabidopsis nonhost resistance.

Nonhost resistance (NHR) is the most prevalent form of plant immunity. In Arabidopsis, NHR requires membrane-localized ATP-binding cassette (ABC) transporter PENETRATION (PEN) 3. Upon perception of pathogen-associated molecular patterns, PEN3 becomes phosphorylated, suggestive of PEN3 regulation by post-translational modification. Here, we investigated the PEN3 protein interaction network. We probed the Arabidopsis protein microarray AtPMA-5000 with the N-terminal cytoplasmic domain of PEN3. Several of the proteins identified to interact with PEN3 in vitro represent cellular Ca(2+) sensors, including calmodulin (CaM) 3, CaM7 and several CaM-like proteins, pointing to the importance of Ca(2+) sensing to PEN3-mediated NHR. We demonstrated co-localization of PEN3 and CaM7, and we confirmed PEN3-CaM interaction in vitro and in vivo by PEN3 pull-down with CaM Sepharose, CaM overlay assay and bimolecular fluorescence complementation. We also show that just like in pen3, NHR to the nonadapted fungal pathogens Phakopsora pachyrhizi and Blumeria graminis f.sp. hordei is compromised in the Arabidopsis cam7 and pen3 cam7 mutants. Our study discloses CaM7 as a PEN3-interacting protein crucial to Arabidopsis NHR and emphasizes the importance of Ca(2+) sensing to plant immunity.

The Arabidopsis oligopeptidases TOP1 and TOP2 are salicylic acid targets that modulate SA-mediated signaling and the immune response.

Salicylic acid (SA) is a small phenolic molecule with hormonal properties, and is an essential component of the immune response. SA exerts its functions by interacting with protein targets; however, the specific cellular components modulated by SA and critical for immune signal transduction are largely unknown. To uncover cellular activities targeted by SA, we probed Arabidopsis protein microarrays with a functional analog of SA. We demonstrate that thimet oligopeptidases (TOPs) constitute a class of SA-binding enzymes. Biochemical evidence demonstrated that SA interacts with TOPs and inhibits their peptidase activities to various degrees both in vitro and in plant extracts. Functional characterization of mutants with altered TOP expression indicated that TOP1 and TOP2 mediate SA-dependent signaling and are necessary for the immune response to avirulent pathogens. Our results support a model whereby TOP1 and TOP2 act in separate pathways to modulate SA-mediated cellular processes.

The tomato kinome and the tomato kinase library ORFeome: novel resources for the study of kinases and signal transduction in tomato and solanaceae species.

Protein kinase-driven phosphorylation constitutes the core of cellular signaling. Kinase components of signal transduction pathways are often targeted for inactivation by pathogens. The study of kinases and immune signal transduction in the model crop tomato (Solanum lycopersicum) would benefit from the availability of community-wide resources for large scale and systems-level experimentation. Here, we defined the tomato kinome and performed a comprehensive comparative analysis of the tomato kinome and 15 other plant species. We constructed a tomato kinase library (TOKN 1.0) of over 300 full-length open reading frames (ORF) cloned into a recombination-based vector. We developed a high-throughput pipeline to isolate and transform tomato protoplasts. A subset of the TOKN 1.0 library kinases were expressed in planta, were purified, and were used to generate a functional tomato protein microarray. All resources created were utilized to test known and novel associations between tomato kinases and Pseudomonas syringae DC3000 effectors in a large-scale format. Bsk7 was identified as a component of the plant immune response and a candidate effector target. These resources will enable comprehensive investigations of signaling pathways and host-pathogen interactions in tomato and other Solanaceae spp.

Arabidopsis RTNLB1 and RTNLB2 Reticulon-like proteins regulate intracellular trafficking and activity of the FLS2 immune receptor.

Receptors localized at the plasma membrane are critical for the recognition of pathogens. The molecular determinants that regulate receptor transport to the plasma membrane are poorly understood. In a screen for proteins that interact with the FLAGELIN-SENSITIVE2 (FLS2) receptor using Arabidopsis thaliana protein microarrays, we identified the reticulon-like protein RTNLB1. We showed that FLS2 interacts in vivo with both RTNLB1 and its homolog RTNLB2 and that a Ser-rich region in the N-terminal tail of RTNLB1 is critical for the interaction with FLS2. Transgenic plants that lack RTNLB1 and RTNLB2 (rtnlb1 rtnlb2) or overexpress RTNLB1 (RTNLB1ox) exhibit reduced activation of FLS2-dependent signaling and increased susceptibility to pathogens. In both rtnlb1 rtnlb2 and RTNLB1ox, FLS2 accumulation at the plasma membrane was significantly affected compared with the wild type. Transient overexpression of RTNLB1 led to FLS2 retention in the endoplasmic reticulum (ER) and affected FLS2 glycosylation but not FLS2 stability. Removal of the critical N-terminal Ser-rich region or either of the two Tyr-dependent sorting motifs from RTNLB1 causes partial reversion of the negative effects of excess RTNLB1 on FLS2 transport out of the ER and accumulation at the membrane. The results are consistent with a model whereby RTNLB1 and RTNLB2 regulate the transport of newly synthesized FLS2 to the plasma membrane.

Challenges of Integrating New Technologies for Orthopedic Doctors to Face up to Difficulties during the Pandemic Era.

In the field of orthopedics, competitive progress is growing faster because new technologies used to facilitate the work of physicians are continuously developing. Based on the issues generated in the pandemic era in this field, a research study was developed to identify the intention of orthopedic doctors to integrate new medical technologies. The survey was based on a questionnaire that was used for data collection. The quantitative study registered a sample of 145 orthopedic doctors. The data analysis was performed based on the IBM SPSS program. A multiple linear regression model was applied, which analyzed how the independent variables can influence the dependent variables. After analyzing the data, it was observed that the intention of orthopedic doctors to use new medical technologies is influenced by the advantages and disadvantages perceived by them, the perceived risks, the quality of the medical technologies, the experience of physicians in their use, and their receptivity to other digital tools. The obtained results are highly important both for hospital managers and authorities, illustrating the main factors that influence doctors to use emergent technologies in their clinical work.

Disruptive Technologies for Learning and Further Investigation of the Potential Toxicity Produced by Titanium in the Human Body during the COVID-19 Pandemic Period.

Titanium is considered to be a biocompatible material and is used to a great extent in the pharmaceutical and oral implantology fields. While initially, specialists considered that its use does not cause adverse effects on the human body, as time has gone by, it has become clear that its use can lead to the development of certain diseases. The objective of this study was to identify the way in which digital technologies have the capacity to facilitate information regarding the potential long-term harm caused by titanium device toxicity during the COVID-19 pandemic. In this study, a regression model was developed to identify how a series of independent variables have the ability to influence the dependent variable (respondents' perceptions of how new web technologies have the ability to help future physicians to facilitate information absorption with regard to potential titanium toxicity). The results illustrated that new technologies have the potential to support both the learning process on this topic and the innovation activity by discovering new solutions that will gradually lead to the reduction of the side effects of titanium used in the pharmaceutical and oral implantology fields.

Assessment of tumoral and peritumoral inflammatory reaction in cutaneous malignant melanomas.

Skin cancer is one of the most common types of cancer, with an increasing worldwide incidence in recent decades. The main risk factor for increasing the skin cancer incidence is ultraviolet (UV) radiation. Of the two major forms of skin cancer (melanomas and non-melanotic cancers), the cutaneous melanoma (CM) is the most aggressive form, causing about 80% of the deaths resulted from this type of tumor. Malignant melanoma develops through malignant transformation of melanocytes in the skin because of prolonged exposure to solar or artificial UV. The malignant transformation of the melanocytes in the skin is accompanied by the presence of a local inflammatory reaction that, in the initial stages of carcinogenesis, would oppose to tumor development. Chronic exposure to UV or other etiopathogenic factors induces chronic inflammation, which, by producing inflammatory molecules (cytokines, chemokines, prostaglandins), constitutes a tumoral microenvironment that favors carcinogenesis, tumor invasion, metastasis, and the presence of neoplastic "mutant cells" that avoid the protective action of the immune system. Using immunohistochemistry techniques, we assessed the intra- and peritumoral inflammatory infiltrate cells in CM. The chronic inflammatory infiltrate presented more intense in the peritumoral stroma compared to the intratumoral one, heterogenous, more intensely composed of lymphocytes, plasma cells, macrophages, and mast cells (MCs), the most numerous cells in the inflammatory infiltrate being T-lymphocytes, plasma cells and macrophages; B-lymphocytes and MCs were in a small number, especially intratumorally. Inflammatory cells had a direct contact with tumor cells, blood vessels, connective matrix, suggesting that the inflammatory microenvironment plays an important role in carcinogenesis, tumor invasion, local angiogenesis, and tumor metastasis.

Assessment of tumor microenvironment in gastric adenocarcinoma.

Gastric cancer (GC), despite the current possibilities of early diagnosis and curative treatment, remains a major public health problem, being one of the main causes of cancer, due to its detection in advanced stages. Screening programs applied in Western countries led to low incidence rates in these countries. Helicobacter pylori bacterial infection is considered to be the highest risk factor for the onset of GC because it causes chronic inflammation of the gastric mucosa and damages hydrochloric acid secretory glands, eventually leading to atrophic gastritis, which has a potential to progress to GC. In our study, we aimed at assessing the tumor microenvironment in gastric adenocarcinomas as approximately 90% of GCs are adenocarcinomas. Our study showed that the tumor microenvironment has an extremely complex morphological structure, totally different from the microscopic structure of the gastric wall, consisting of stromal cells, lymphocytes, plasma cells, macrophages, blood vessels, collagen fibers, extracellular connective matrix, other cells. The tumor microenvironment presents phenotypic, cellular and molecular heterogeneity; therefore, the microscopic aspect differs from one tumor to another and even from one region to another in the same tumor. Poorly or moderately differentiated adenocarcinomas show a more intense desmoplastic reaction than well-differentiated ones. Alpha-smooth muscle actin (α-SMA)-positive stromal cells (tumor-associated fibroblasts) and tumor macrophages were the most numerous cells of the tumor microenvironment. The tumor microenvironment is the result of cooperation between tumor cells, cancer-associated fibroblasts, immune system cells and blood vessels. It allows tumor cells to multiply, grow and metastasize.