Distinct Differences In Expression Research Articles

Multi-omics integration to identify the genetic expression and protein signature of dilated and ischemic cardiomyopathy.

Heart failure (HF) is a complex clinical syndrome leading to high morbidity. In this study, we aimed to identify the gene expression and protein signature of HF main causes, namely dilated cardiomyopathy (DCM) and ischemic cardiomyopathy (ICM). Omics data were accessed through GEO repository for transcriptomic and PRIDE repository for proteomic datasets. Sets of differentially expressed genes and proteins comprising DCM (DiSig) and ICM (IsSig) signatures were analyzed by a multilayered bioinformatics approach. Enrichment analysis via the Gene Ontology was performed through the Metascape platform to explore biological pathways. Protein-protein interaction networks were analyzed via STRING db and Network Analyst. Intersection of transcriptomic and proteomic analysis showed 10 differentially expressed genes/proteins in DiSig (AEBP1, CA3, HBA2, HBB, HSPA2, MYH6, SERPINA3, SOD3, THBS4, UCHL1) and 15 differentially expressed genes/proteins in IsSig (AEBP1, APOA1, BGN, CA3, CFH, COL14A1, HBA2, HBB, HSPA2, LTBP2, LUM, MFAP4, SOD3, THBS4, UCHL1). Common and distinct biological pathways between DiSig and IsSig were retrieved, allowing for their molecular characterization. Extracellular matrix organization, cellular response to stress and transforming growth factor-beta were common between two subphenotypes. Muscle tissue development was dysregulated solely in DiSig, while immune cells activation and migration in IsSig. Our bioinformatics approach sheds light on the molecular background of HF etiopathology showing molecular similarities as well as distinct expression differences between DCM and ICM. DiSig and IsSig encompass an array of "cross-validated" genes at both transcriptomic and proteomic level, which can serve as novel pharmacological targets and possible diagnostic biomarkers.

Abstract 2201: Epithelial, stromal, and immune changes associated with lung squamous premalignant lesion severity identified by single-cell RNA-seq

Abstract Background: Bronchial pre-malignant lesions (PMLs) are the putative precursors for bronchial squamous cell carcinoma. PMLs represent a spectrum of histologies, from low-grade lesions (hyperplasia, metaplasia) to high-grade lesions (dysplasia, carcinoma in situ). The majority of these lesions will regress or remain stable without clinical intervention while a subset of lesions will progress to invasive carcinoma. We performed single-cell RNA sequencing (scRNAseq) of these lesions to elucidate the cross-talk between epithelial, stromal, and immune populations in lesions of increasing histological grade. Methods: Thirty lesions from seventeen participants were biopsied via bronchoscopy. Cells were sorted by CD45+/- FACS gating and sequenced with the Cel-Seq2 protocol. Celda was used to bi-cluster genes into modules and cells into clusters. Cells were filtered by mitochondrial percentage (%mito < 50%), minimum UMI counts (nUMI > 300), and doublet detection. Cell types were labeled by marker gene expression. Results: After filtering low quality cells, we analyzed 4,382 cells. We observed expected smoking related shifts in epithelial cell type proportions, including an increase in secretory cells (χ2 = 31.39, p = 2.11 X 10-8) and a decrease in ciliated cells (χ2 = 4.83, p = 0.028) among current smokers. Distinct differences in expression of transcriptional modules were observed between KRT5+ (basal) cells from different histologic grades. Basal cells from high grade lesions expressed smoking detoxification and cell cycle gene programs, while low grade lesion basal cells expressed differentiation gene programs. We also identified a group of cells from CIS lesions involved in an epithelial-to-mesenchymal transition, marked by an increase in SPARC and COL4A1 expression and a decrease in CDH1 expression. Subpopulations of immune cells identified include macrophages, CD4/8+ T, B, dendritic cells, and natural killer cells. Several clusters of CD4+ and CD8+ T cells displayed an exhausted phenotype, marked by the expression of PD-1, CTLA4, LAG3, and TIGIT. Samples with high grade histology (dysplasia, carcinoma in situ) were enriched in CD4+ Tregs and myeloid cells compared to low grade histology samples (hyperplasia, metaplasia), which were enriched in Natural Killer and cytotoxic CD8+ T cells (χ2 = 298.95, p = 0.001). Discussion: Our results suggest that changes in specific transcriptional programs are associated with the transition of epithelial cells to more invasive states and that changes in immune populations are associated with increasing histological grade. These signatures can suggest novel avenues for chemoprevention and cancer interception. Citation Format: Conor Shea, Lukas Kalinke, Kitty De Jong, Kate Gowers, Diane Ding, Sherry Zhang, Gang Liu, Jack Cunningham, Ipsita Dey-Guha, Mark Hennon, Sai Yendamuri, Christopher Stevenson, Avrum Spira, Mary E. Reid, Marc E. Lenburg, Sam M. Janes, Jennifer E. Beane, Sarah A. Mazzilli, Joshua D. Campbell. Epithelial, stromal, and immune changes associated with lung squamous premalignant lesion severity identified by single-cell RNA-seq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2201.

Time-series transcriptome comparison reveals the gene regulation network under salt stress in soybean (Glycine max) roots

BackgroundSoil salinity is a primary factor limiting soybean (Glycine max) productivity. Breeding soybean for tolerance to high salt conditions is therefore critical for increasing yield. To explore the molecular mechanism of soybean responses to salt stress, we performed a comparative transcriptome time-series analysis of root samples collected from two soybean cultivars with contrasting salt sensitivity.ResultsThe salt-tolerant cultivar ‘Qi Huang No.34’ (QH34) showed more differential expression of genes than the salt-sensitive cultivar ‘Dong Nong No.50’ (DN50). We identified 17,477 genes responsive to salt stress, of which 6644 exhibited distinct expression differences between the two soybean cultivars. We constructed the corresponding co-expression network and performed Gene Ontology term and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. The results suggested that phytohormone signaling, oxidoreduction, phenylpropanoid biosynthesis, the mitogen-activated protein kinase pathway and ribosome metabolism may play crucial roles in response to salt stress.ConclusionsOur comparative analysis offers a comprehensive understanding of the genes involved in responding to salt stress and maintaining cell homeostasis in soybean. The regulatory gene networks constructed here also provide valuable molecular resources for future functional studies and breeding of soybean with improved tolerance to salinity.

Abstract 2212: Cellular and molecular changes associated with lung squamous premalignant lesion severity identified by single-cell RNA-seq

Abstract Background: Sampling the bronchial airway during bronchoscopies in screening populations at high risk for lung cancer has increased detection of squamous bronchial pre-malignant lesions (PML). The majority of these lesions will regress or remain stable without any clinical intervention. However, a subset of lesions will progress to invasive malignancy. In this work, we investigate the gene expression changes in epithelial cell states and immune cell proportion shifts associated with premalignant histologic stage using single-cell RNA sequencing to begin to identify molecular features associated with PML regression or progression. Methods: Cells (n=3,325) were isolated from 11 endobronchial biopsies from 9 patients, where biopsy histology range from normal, dysplasia, carcinoma in situ (CIS) and squamous cell carcinoma. Immune cells (CD45+) and epithelial cells (CD45− EPCAM+) were sorted into separate 96-well plates using fluorescence activated cell sorting (FACS) and sequenced using CEL-Seq2 single cell RNA seq protocol. Results: After filtering low quality cells, we profiled 2,998 cells (1,052 CD45+ and 1,946 CD45−) with an average of 1,190 genes per cell. Within the epithelial cells, we focused on basal cells as they are the airway progenitor cells. We observed distinct differences in expression of KRT5+ (basal) cells between different histologic grades, where KRT5+ cells present in a hyperplasic lesion expressed multiple secretory cell markers suggesting they were transitioning to a secretory cell phenotype and KRT5+ cells from a CIS lesion from a current smoker expressed higher levels of smoking inducible genes, such as GSTM1 and CYP1A1. Lastly, KRT5+ cells from a lung squamous carcinoma tumor expressed higher levels of many genes related to cell cycle progression. Among the immune populations, low-grade PMLs with non-dysplastic histology were enriched for CD8+ T cells, whereas higher-grade PMLs and an invasive tumor were enriched for myeloid cells. Conclusions: To date, we have begun to identify histology-associated cellular and molecular profiles in bronchial premalignancy and early-stage carcinoma. Future resampling of these patients and expansion of cases will allow us to discover biomarkers associated with lesion progression and molecular targets for lung cancer interception. Citation Format: Conor Shea, Lukas Kalinke, Kitty De Jong, Kate Gowers, Diane Ding, Sherry Zhang, Gang Liu, Jack Cunningham, Ipsita Dey-Guha, Mark Hennon, Sai Yendumuri, Christopher Stevenson, Steven Dubinett, Avrum Spira, Marc Lenburg, Samuel Janes, Mary Reid, Jennifer Beane, Sarah Mazzilli, Joshua D. Campbell. Cellular and molecular changes associated with lung squamous premalignant lesion severity identified by single-cell RNA-seq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2212.

Genome-Wide Survey Reveals Transcriptional Differences Underlying the Contrasting Trichome Phenotypes of Two Sister Desert Poplars.

Trichomes, which are widely used as an important diagnostic characteristic in plant species delimitation, play important roles in plant defense and adaptation to adverse environments. In this study, we used two sister poplar species, Populus pruinosa and Populus euphratica—which have, respectively, dense and sparse trichomes—to examine the genetic differences associated with these contrasting phenotypes. The results showed that 42 and 45 genes could be identified as candidate genes related to trichomes in P. pruinosa and P. euphratica, respectively; most of these genes possessed high degrees of diversification in their coding sequences, but they were similar in intron/exon structure in the two species. We also found that most of the candidate trichome genes were expressed at higher levels in P. pruinosa, which has dense trichomes, than in P. euphratica, where there are few trichomes. Based on analyses of transcriptional profiles, a total of 195 genes, including many transcription factors, were found to show distinct differences in expression. The results of gene function annotation suggested that the genes identified as having contrasting levels of expression level are mainly associated with trichome elongation, ATPase activity, and hormone transduction. Changes in the expression of these and other related genes with high sequence diversification may have contributed to the contrast in the pattern of trichome phenotypes between the two species.

Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles

Rice has developed several morphological and physiological strategies to adapt to phosphate starvation in the soil. In order to elucidate the molecular basis of response to phosphate starvation, we performed mRNA sequencing of 4 rice cultivars with variation in growth response to Pi starvation as indicated by the shoot/root dry weight ratio. Approximately 254 million sequence reads were mapped onto the IRGSP-1.0 reference rice genome sequence and an average of about 5,000 transcripts from each cultivar were found to be responsive under phosphate starvation. Comparative analysis of the RNA-Seq profiles of the 4 cultivars revealed similarities as well as distinct differences in expression of these responsive transcripts. We elucidated a set of core responsive transcripts including annotated and unannotated transcripts commonly expressed in the 4 cultivars but with different levels of expression. De novo assembly of unmapped reads to the Nipponbare genome generated a set of sequence contigs representing potential new transcripts that may be involved in tolerance to phosphate starvation. This study can be used for identification of genes and gene networks associated with environmental stress and the development of novel strategies for improving tolerance to phosphate starvation in rice and other cereal crops.Electronic supplementary materialThe online version of this article (doi:10.1007/s11103-013-0106-4) contains supplementary material, which is available to authorized users.

Immunoproteasome Deficiency Modifies the Alternative Pathway of NFκB Signaling

Immunoproteasome is a protease abundant in immune cells and also present, albeit at lower concentrations, in cells outside the immune system. Recent evidence supports a novel role for the immunoproteasome in the cellular stress response potentially through regulation of NFκB signaling, which is the primary response to multiple stressors. The current study tests whether the Classical or Alternative Pathways are regulated by immunoproteasome following chronic TNFα exposure in cultured retinal pigment epithelial cells isolated from wild-type mice and mice deficient in one (LMP2, L2) or two (LMP7 and MECL-1, L7M1) immunoproteasome subunits. Assays were performed to assess the expression of NFκB responsive genes, the content and activity of NFκB transcription factors (p65, p50, p52, cRel, RelB), and expression and content of regulatory proteins (IκBα, A20, RPS3). Major findings include distinct differences in expression of NFκB responsive genes in both KO cells. The mechanism responsible for the altered gene expression could not be established for L7M1 since no major differences in NFκB transcription factor content or activation were observed. However, L2 cells exhibited substantially higher content and diminished activation of NFκB transcription factors associated with the Alternative Pathway and delayed termination of the Classical Pathway. These results provide strong experimental evidence supporting a role for immunoproteasome in modulating NFκB signaling.

Contrasting Requirement for Reactive Oxygen Species for the Suppressive Function of Naturally Occurring Regulatory T Cells but Not Induced Regulatory T Cells.

AbstractAbstract 2146 Background:Naturally-occurring, thymus-derived regulatory T cells (nTregs) have clinically important roles in suppression of autoimmunity and graft versus host disease but are maladaptive in the tumor microenvironment where their activity results in the suppression of anti-tumor immunity. Induced regulatory T cells (iTregs) arise in the periphery under the influence of TGF-beta and have related phenotypic features and function. However, the mechanisms by which nTregs and iTregs impart suppression remain poorly understood. We have previously shown that NADPH oxidase derived reactive oxygen species (ROS) are important for nTreg suppressive function. We extend these observations and find distinct differences in the effect of antioxidants and NADPH oxidase inhibitors on blocking nTreg function but not iTreg function thus implying a role for ROS in the function of the former but not the latter. The contrasting requirement for ROS is further supported by distinct differences in expression of oxidant related genes in nTregs and iTregs. Methods:Murine nTregs were isolated by flow cytometric sorting for CD4+CD25++ T cells. Murine iTregs were induced from spleen sorted naïve T cells (CD4+CD44-) by incubating with TGF-beta and IL-2 and the resulting cells were sorted for the CD25++ subset. For suppression assays, nTregs and iTregs were incubated for three days with CFSE-labeled conventional T cells (Tc; CD4+CD25−) with antioxidants or NADPH oxidase inhibitors, as indicated. The proliferation of Tc co-incubated with Tregs was compared to their proliferation in identical conditions lacking Tregs in classical suppression assays. In some cases, nTregs and iTregs were co-incubated with CFSE-labeled Tc for two days in conditions identical to suppression assays to activate their suppressive function then resorted and subjected to RNA extraction and analysis of mRNA expression of a series of oxidant related genes. Results and Discussion:The antioxidants n-acetylcysteine (NAC; 1mM) and beta-mercaptoethanol (B-ME; 50 uM) had only small effects on suppression imparted by iTregs (p<0.01) while they completely blocked suppression by nTregs (see figure; p<0.0001). NADPH oxidase inhibitors VAS2870 (100nM) and diphenyleneiodonium (DPI; 10nM) demonstrated only mild effects on suppression by iTregs (p<0.01) while markedly reducing suppression by nTregs (p<0.001; see figure). iTregs derived from mice lacking a functional NADPH oxidase complex due to a mutation in the NADPH oxidase subunit NCF1 (NCF1−/−) demonstrated suppressive activity that was similar to wild type (NCF+/+) iTregs, thus genetically confirming no role for NADPH oxidase derived ROS for iTreg-mediated suppression. To evaluate dynamic functional differences between nTregs and iTregs, the expression of a series of ROS related genes was analyzed in purified Tregs with activated suppressive function. This demonstrated overexpression of two genes involved in oxidant detoxification in nTregs: sulfiredoxin1 (SRXN1; >16 fold overexpression in nTregs vs iTregs; mean of 3 experiments) and glutathione peroxidase 3 (GPX3; approximately 3-fold overexpression in nTregs vs iTregs; mean of 3 experiments). Overexpression of SRXN1 and GPX3 in nTregs was confirmed with additional unrelated assays. SRXN1 is a transcriptional target for the cytoprotective transcription factor nuclear factor erythroid 2-related factor 2 (NRF2). Therefore, we separately evaluated NRF2 expression and found approximately 2.5-fold mean overexpression in nTregs vs iTregs. Thus, because ROS is an important mediator of nTreg suppressive function we hypothesize that activation of NRF2, and downstream antioxidants such as SRXN1, are critical for the oxidant protection of nTregs themselves during suppression. Conclusions:Our findings illustrate fundamental differences in suppressive mechanisms employed by murine nTregs and iTregs and highlight a role for ROS in the former but not the latter. [Display omitted] Disclosures:No relevant conflicts of interest to declare.

Abstract 5288: Tumor-endothelial 3D spheroids for dynamic imaging of cancer progression

Abstract The increasing use of anti-angiogenic drugs for the treatment of cancer has emerged from the explosion of knowledge about the process of tumor angiogenesis. However, the clinical results of using such drugs have been relatively modest and new agents are likely needed. A robust pre-clinical model of cellular mechanisms governing tumor angiogenesis may improve our ability to develop strategies for tumor specific drug delivery with superior pharmacokinetics, controlled biodistribution, efficacy, and safety profiles. We have developed a system to grow 3D-cultures of tumor and endothelial cells in hanging drops of medium. Subsequently, we transplant these spheroidal cultures into the dorsal skin fold window chamber of mice for intravital multiphoton imaging of neovasculature and disease progression. Our initial observation was that there was a marked difference in neovascularization from the GFP-tumor-endothelial spheroids in comparison to GFP-tumor spheroids in the window chamber mouse model. Molecular analysis using an antibody array showed a pronounced upregulation of angiogenic factors in the tumor tissue derived from the tumor-endothelial spheroid compared to the spheroid grown with tumor cells alone. Interleukin-1α, FGF-1α, CCN3/NOV, PIGF-2, MMP-3, MMP-8 and MMP-9 were seven identified proteins that showed distinct differences in expression between the two spheroid types. Further, the relative increase in tumor growth of tumor-endothelial spheroids implanted on the rear hind limb was much faster than the tumor cell alone spheroid and resulted in evidence of greater metastasis to the lung. We thus strongly believe that the 3D tumor-endothelial spheroid implanted in the dorsal fold window chamber of mice is a more realistic and informative model for dynamic imaging of critical aspects of tumor angiogenesis and the study of metastasis. Efforts are underway to monitor molecular and cellular events related to radiation exposure combined with anti-angiogenic agents of varying mechanisms of action to determine prudent new avenues for therapeutic success. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5288. doi:10.1158/1538-7445.AM2011-5288

Developmental expression of non-coding RNAs in Chlamydia trachomatis during normal and persistent growth

Chlamydia trachomatis is an obligate intracellular bacterium that exhibits a unique biphasic developmental cycle that can be disrupted by growth in the presence of IFN-γ and β-lactams, giving rise to an abnormal growth state termed persistence. Here we have examined the expression of a family of non-coding RNAs (ncRNAs) that are differentially expressed during the developmental cycle and the induction of persistence and reactivation. ncRNAs were initially identified using an intergenic tiling microarray and were confirmed by northern blotting. ncRNAs were mapped, characterized and compared with the previously described chlamydial ncRNAs. The 5′- and 3′-ends of the ncRNAs were determined using an RNA circularization procedure. Promoter predictions indicated that all ncRNAs were expressed from σ66 promoters and eight ncRNAs contained non-templated 3′-poly-A or poly-AG additions. Expression of ncRNAs was studied by northern blotting during (i) the normal developmental cycle, (ii) IFN-γ-induced persistence and (iii) carbenicillin-induced persistence. Differential temporal expression during the developmental cycle was seen for all ncRNAs and distinct differences in expression were seen during IFN-γ and carbenicillin-induced persistence and reactivation. A heterologous co-expression system was used to demonstrate that one of the identified ncRNAs regulated the expression of FtsI by inducing degradation of ftsI mRNA.

Immunohistochemical Expression of Retinoblastoma Protein and p16 in Renal Cell Carcinoma

Introduction: The regulation proteins retinoblastoma protein (pRb) and p16 play an important role in the cell cycle as tumor suppressors. pRb is the main substrate for the function of cyclin-dependent kinases during the cell cycle in the transition from G₁ to S phase. In this study, the immunohistochemical expression of pRb and p16 in renal cell carcinoma (RCC) were examined. Methods: Paraffin-embedded specimens from 94 patients with RCC were examined immunohistologically, using primary antibodies for p16 and pRb (Novocastra) and a biotin-conjugated anti-mouse IgG secondary antibody. Microscopically, the expression of p16 and pRb was evaluated by examination of the staining intensity of 100 cells of each specimen, and compared with epidemiological parameters (tumor size, TNM, nuclear grade and follow-up). Statistical analyses were conducted by SPSS, version 15.0 (SPSS® Inc., Chicago, Ill., USA), the χ² test (Fisher’s exact test), the Kaplan-Meier method and Mantel’s log rank test. Results: All 94 tumors showed a positive reaction for pRb (weakly positive in 67.0%; strongly positive in 33.0%). p16 was expressed in only 52.1% (weakly positive in 48.9%; intermediately positive in 3.2%; no strongly positive expression). The expression of p16-positive tumors was significantly associated with the expression of pRb (p = 0.040). Tumor size, grading, lymph node and distant metastases did not correlate with p16/pRb expression. Conclusion: pRb and p16 control the cell cycle as tumor suppressors. Therefore, in many tumors they are dysregulated. There are distinct differences in expression in various individual RCC. However, in a limited number of cases there was no significant correlation with clinical parameters.

Messenger ribonucleic acid expression profile in peripheral blood cells from RA patients following treatment with an anti-TNF-α monoclonal antibody, infliximab

We monitored the mRNA expression profiles of peripheral blood cells during treatment with a TNF-alpha inhibitor, infliximab, in patients with RA. Using a DNA microarray analysis, we demonstrated a unique set of genes, with distinct baseline and post-treatment changes in expression between responders and non-responders to infliximab treatment. Using a customized low-density cDNA microarray with 747 genes and a reliable data collection system, we monitored the mRNA expression profiles of whole blood cells from 18 RA patients before and after the infusion of infliximab for up to 22 weeks. The clinical response to treatment with infliximab was determined using the ACR response criteria, the disease activity score of 28 joints (DAS28), and individual clinical parameters. The patients were classified as responders or non-responders based on their ACR50% response at 22 weeks. Approximately 15% of the total genes were found to exhibit a >1.5-fold change, compared with their reference values, at one or more time points during the 22 weeks of infliximab therapy. The expression of inflammatory genes, such as IFN-related genes, was strongly correlated with the serum level of CRP and the DAS28. The increased expression of inflammatory genes in responders was normalized within 2 weeks and then remained at a normal level during the treatment period. In contrast, in the non-responders, the elevated expression at baseline, although it was significantly decreased at 2 weeks, returned to the baseline level after 14 weeks. In addition to inflammatory genes, we identified several groups of genes with distinct differences in expression between the responders and non-responders. Our results suggest that a customized low-density microarray is useful for monitoring mRNA expression profiles in peripheral blood cells, enabling us to identify a unique set of genes with differentially regulated expressions in responders and non-responders to a TNF inhibitor among patients with RA.

Alteration of expression levels of the oxidative phosphorylation system (OXPHOS) in breast cancer cell mitochondria

Mitochondria are dynamic intracellular organelles playing a central role in cell metabolism by generating ATP, through the oxidative phosphorylation system (OXPHOS). Altered mitochondrial functions have been identified as causative or contributing factors in some degenerative diseases and are becoming crucial to understanding cancer mechanisms. We report on distinct expression differences between mitochondria of normal and breast-infiltrating ductal carcinoma (IDC) cells. Mitochondria isolated from HMC (human mammary carcinoma) and HMEC (human mammary epithelial cell) cultures were assayed for expression levels of the multi-protein OXPHOS complexes using Western blot and densitometric analyses. Depressed expression levels were detected for all HMC OXPHOS complexes. Drastic signal reduction was observed for the succinate-dehydrogenase complex II iron-sulphur protein SDH-B (3.38%), while decreasing was reported for the NADH-ubiquinone oxidoreductase complex I Fe-S protein 3 NDUFS3 (32.78%) and the ubiquinol-cytochrome c reductase complex III protein 2 UQCRC2 (50.34%). A significant signal dropping was detected for the ATP-synthase complex V F(1)beta subunit (18.07%). For the cytochrome-oxidase complex IV (CO), near-depletion of the mitochondrial-encoded COI (4.37%) and no apparent variation of the COIV (97.26%) subunits were observed. CO and ATP-synthase were also assayed by cryo-immunoelectron microscopy (CIEM) on unfractionated HMC and HEMC cell mitochondria. COI and F(1)beta differential expression, invariance of COIV levels were corroborated, while HMC mitochondria morphology deterioration was highlighted. MitoTracker Red and fluorescence immunolabelling merging confirmed CIEM data. MitoTracker Red and Green co-staining showed mitochondria membrane property modulation. These data describe bioenergetic and phenotypic alterations of IDC cell mitochondria, possibly providing new cancer hallmarks.

Burn size determines the inflammatory and hypermetabolic response

BackgroundIncreased burn size leads to increased mortality of burned patients. Whether mortality is due to inflammation, hypermetabolism or other pathophysiologic contributing factors is not entirely determined. The purpose of the present study was to determine in a large prospective clinical trial whether different burn sizes are associated with differences in inflammation, body composition, protein synthesis, or organ function.MethodsPediatric burned patients were divided into four burn size groups: <40% total body surface area (TBSA) burn, 40–59% TBSA burn, 60–79% TBSA burn, and >80% TBSA burn. Demographic and clinical data, hypermetabolism, the inflammatory response, body composition, the muscle protein net balance, serum and urine hormones and proteins, and cardiac function and changes in liver size were determined.ResultsOne hundred and eighty-nine pediatric patients of similar age and gender distribution were included in the study (<40% TBSA burn, n = 43; 40–59% TBSA burn, n = 79; 60–79% TBSA burn, n = 46; >80% TBSA burn, n = 21). Patients with larger burns had more operations, a greater incidence of infections and sepsis, and higher mortality rates compared with the other groups (P < 0.05). The percentage predicted resting energy expenditure was highest in the >80% TBSA group, followed by the 60–79% TBSA burn group (P < 0.05). Children with >80% burns lost the most body weight, lean body mass, muscle protein and bone mineral content (P < 0.05). The urine cortisol concentration was highest in the 80–99% and 60–79% TBSA burn groups, associated with significant myocardial depression and increased change in liver size (P < 0.05). The cytokine profile showed distinct differences in expression of IL-8, TNF, IL-6, IL-12p70, monocyte chemoattractant protein-1 and granulocyte–macrophage colony-stimulating factor (P < 0.05).ConclusionMorbidity and mortality in burned patients is burn size dependent, starts at a 60% TBSA burn and is due to an increased hypermetabolic and inflammatory reaction, along with impaired cardiac function.

BURN SIZE DETERMINES THE INFLAMMATORY AND HYPERMETABOLIC RESPONSE

Background: Increased burn size leads to increased mortality of burned patients. Whether mortality is due to inflammation, hypermetabolism or other factors is not entirely determined. The purpose of the present study was to determine whether different burn sizes are associated with differences in the hypermetabolic and inflammatory response. Patients and Methods: Severely burned pediatric patients were divided into four burn size groups: 0-39% total body surface are burn (TBSA), 40-59% TBSA, 60-79% TBSA and 80-99% TBSA. Demographic and clinical data, serum hormones, and resting energy expenditure (REE) was obtained throughout acute hospital course. Inflammatory markers were determined using the Bioplex Array. Significance was accepted at P < 0.05. Results: Two-hundred twenty one patients were included into this study. Forty-three patients in the 0-39% TBSA, 79 in the 40- 59% TBSA, 78 in the 60-79% TBSA, and 21 in the 80-99% TBSA group. Patients with larger burns had more operations, greater incidence of infections and sepsis, and higher mortality rates compared to the other groups, P < 0.05. Measured REE and percent predicted REE was highest in the 80-99 % TBSA group followed by the 40-59% and 60-79% and lowest in the 0-39 %, P < 0.05. Children suffering from >80% burn lost the most body weight, lean body mass, muscle protein and bone mineral content when compared to the other groups, P < 0.05. Urine cortisol concentration was increased in all groups but highest in the 80-99% TBSA group, P < 0.05. Cytokine profile showed distinct differences in expression between groups with significant differences in almost all cytokines, P < 0.05. Summary: Morbidity and mortality in burned patients is burn size dependent and due to an increased hypermetabolic and inflammatory reaction. These data delineate the importance for anabolic and anti-inflammatory treatment to improve outcome for these patients.

Developmental expression and biochemical properties of a β‐1,4‐endoglucanase family in the soybean cyst nematode, Heterodera glycines

SUMMARY The soybean cyst nematode, Heterodera glycines, produces beta-1,4-endoglucanases (cellulases) that are secreted during infection of soybean. The gene structures of three, hg-eng-4, hg-eng-5 and hg-eng-6, of the six beta-1,4-endoglucanase genes, all family 5 glycosyl hydrolases previously identified from H. glycines, are presented here. Furthermore, we present the detailed expression analyses of beta-1,4-endoglucanase genes as well as the biochemical properties of four H. glycines endoglucanase enzymes. Two of the endoglucanases, HG-ENG-5 and HG-ENG-6, differed significantly in their amino acid sequence of the catalytic domains and their gene structure from that of the other four beta-1,4-endoglucanases. Quantitative real-time RT-PCR revealed distinct developmental expression differences among the hg-eng family members during the early stages of parasitism and relatively low expression levels in late parasitic stages, with the exception of the adult male stage for some eng genes. Recombinant HG-ENGs degraded carboxymethylcellulose and optimum enzyme activity ranged from pH 5.5 for HG-ENG-5 to pH 8 for HG-ENG-6. EDTA, Ca(2+), Co(2+), Mg(2+) and Fe(2+) did not affect enzyme activity of any ENG protein, whereas Zn(2+), Cu(2+) and Mn(2+) inhibited enzyme activity from 23% to 73% in some cases. In tests with 12 different polysaccharide substrates, enzyme activity was restricted to beta-1,4 linkages with all ENG proteins tested. Only HG-ENG-5 and HG-ENG-6 had relatively high activity on xylan and slightly degraded microcrystalline cellulose. Together, these data reveal distinct differences in expression and biochemistry of cyst nematode parasitism genes and proteins, respectively, and cast light on the intricate interactions between a parasitic animal and its plant host.

Chemokine and Chemokine-Receptor Expression in Human Glial Elements: Induction by the HIV Protein, Tat, and Chemokine Autoregulation

Human immunodeficiency virus (HIV) encephalitis is a prominent pathology seen in children infected with HIV. Immunohistochemical analyses of pediatric brain tissue showed distinct differences in expression of C-C chemokines and their receptors between children with HIV encephalitis and those with non-CNS-related pathologies. Evidence suggests that soluble factors such as HIV Tat released from HIV-infected cells may have pathogenic effects. Our results show Tat effects on chemokines and their receptors in microglia and astrocytes as well as chemokine autoregulation in these cells. These results provide evidence for the complex interplay of Tat, chemokines, and chemokine receptors in the inflammatory processes of HIV encephalitis and illustrate an important new role for chemokines as autocrine regulators.