Pre-disease Stage Research Articles

Detecting tipping points of complex diseases by network information entropy.

The progression of complex diseases often involves abrupt and non-linear changes characterized by sudden shifts that trigger critical transformations. Identifying these critical states or tipping points is crucial for understanding disease progression and developing effective interventions. To address this challenge, we have developed a model-free method named Network Information Entropy of Edges (NIEE). Leveraging dynamic network biomarkers, sample-specific networks, and information entropy theories, NIEE can detect critical states or tipping points in diverse data types, including bulk, single-sample expression data. By applying NIEE to real disease datasets, we successfully identified critical predisease stages and tipping points before disease onset. Our findings underscore NIEE's potential to enhance comprehension of complex disease development.

Evaluation of the effect of Bala Tailam Nasya and Baladi Kwatha Pana in the management of Avabahuka - A Pilot Study

Avabahuka is a disease mainly affects the Amsa Sandhi (shoulder joint) which is painful, affecting the normal routine life style of an individual. The sedentary and restless lifestyles of people, and lack of priority to physical exercise, have an effect on the body that can cause disease. The main Dosha involved Avabahuka is Vatadosha and the treatment adopted for this are like Snayu-Sandhi-Asthi-Gata-Vata treatment. In Frozen Shoulder synovial inflammation occurs followed by capsular fibrosis. The shoulder joint becomes gradually painful and stiff with a reduction in range of motion. The current pilot study aim is to investigate the impact of Nasya with Baladi Taila and Baladi Kwath in Avabahuka. There are references for Nasya Karma in Avabahuka. Acharya Sushruta and others have considered it as Vataja Vikara. Amsa Shosha can be considered a pre-disease stage in which loss or dryness of the Shleshaka Kapha is found, as well as other symptoms like Shula during movement of shoulder joint.

Single-cell RNA sequencing analysis reveals the heterogeneity of IL-10 producing regulatory B cells in lupus-prone mice.

B cells can have both pathogenic and protective roles in autoimmune diseases, including systemic lupus erythematosus (SLE). Deficiencies in the number or immunosuppressive function of IL-10 producing regulatory B cells (Bregs) can cause exacerbated autoimmune inflammation. However, the exact role of Bregs in lupus pathogenesis has not been elucidated. We carried out gene expression analysis by scRNA-seq to characterize differences in splenic Breg subsets and molecular profiles through stages of disease progression in lupus-prone mice. Transcriptome-based changes in Bregs from mice with active disease were confirmed by phenotypic analysis. We found that a loss of marginal zone (MZ) lineage Bregs, an increase in plasmablast/plasma cell (PB-PC) lineage Bregs, and overall increases in inflammatory gene signatures were characteristic of active disease as compared to Bregs from the pre-disease stage. However, the frequencies of both MZ Bregs and PB-PCs expressing IL-10 were significantly decreased in active-disease mice. Overall, we have identified changes to the repertoire and transcriptional landscape of Breg subsets associated with active disease that provide insights into the role of Bregs in lupus pathogenesis. These results could inform the design of Breg-targeted therapies and interventions to restore Breg suppressive function in autoimmunity.

The Psychological Experiences of Patients Isolating at Home during Covid Treatment in Turkey

The global COVID-19 pandemic affected patients’ mental health and well-being, however subjective psychological experiences of the patients treated at home were not adequately addressed. The aim of this study was to evaluate the psychological experiences of COVID-19 patients who received home treatments, in Turkey. The experiences of COVID-19 patients (n = 26) were examined within the stages of pre-disease, disease, and post-disease by following a phenomenological approach. Data were collected through semi-structured in-depth interviews conducted via telephone and the internet and analyzed according to the Miles and Huberman model. Low-risk perception and worry fluctuations dominate in the pre-disease stage among those who were affected by the disease. Patients experienced challenging psychological experiences such as isolation, anxiety, concerns for beloved ones, and stigmatization during the treatment. As a result of these strains, their symptomatic, instrumental, and psychological needs became evident. When the disease was overcome, many patients achieved post-disease strength along with some psychological changes in their lives. Psychological experiences according to the stages of the disease can be an important indicator for mental health interventions in public health and medical social services to be provided in possible future pandemics and for the establishment of social adjustement of patients. Future research is required that can guide social services that examine the in the short and long term mental health of COVID-19 patients in depth.

TLR7 expression increases with disease progression and mediates expansion of distinct B cell subsets in primary Sjögren’s Disease

Abstract Primary Sjögren’s Disease (pSD) is a systemic autoimmune disorder in which the exocrine tissue exhibits chronic inflammation. Additionally, patients often experience diminished tear and saliva production along with many extra-glandular disease manifestations. The causes of pSD are poorly understood and no curative treatments are available. Previous studies in our lab conducted in a pSD mouse model demonstrated that TLR7 agonism accelerates pSD pathogenesis and drives expansion of age-associated B cells (ABCs). To extend our prior work, we hypothesized that pSD splenocytes show heightened TLR7 expression and activation, and expansion of B cell subsets linked to autoimmunity relies on TLR7 in pSD mice. We harvested the spleens of pSD females at three different disease time points (pre-disease, clinical disease and advanced stage disease) and performed flow cytometry. Parallel experiments were performed using age and sex-matched healthy controls. Splenocytes were also cultured with the TLR7 agonist Imiquimod (Imq) and IL-6 secretion assessed by ELISA. In addition, spleens were isolated from TLR7-deficient pSD females at the clinical disease stage and flow cytometry was performed. We found splenocytes derived from pSD animals at the clinical disease stage secreted higher levels of IL-6 in response to Imq stimulation as compared to those derived from healthy control animals. TLR7 +B cells and ABCs (B220 +, CD23 −, CD21 −, T-bet +) increased with disease progression in pSD mice. In pSD mice lacking TLR7, ABCs and germinal center B cells were decreased compared to the TLR7-sufficient pSD parental strain. Thus, splenocytes from pSD mice show enhanced sensitivity to TLR7 and TLR7 signaling mediates expansion of ABC subset in pSD. NIH/NIDCR T32 DE023056 NIH/NIDCR R01 DE029472

Single-Cell RNA Sequencing Reveals Disease Stage-Dependent Transcriptomic Profiles of Regulatory B Cells in Systemic Lupus Erythematosus

Abstract Systemic lupus erythematosus (SLE) is an autoimmune disease associated with abnormal activation of immune cells. Regulatory B (Breg) cells are a B cell subset that negatively regulate immune responses via secretion of immunoregulatory cytokines interleukin (IL)-10, IL-35, and transforming growth factor (TGF)-β. We had previously shown that in lupus-prone MRL/lpr mice, pre-disease Breg cells were more potent in suppressing autoimmunity than active-disease Breg cells. In this study, using single-cell RNA (scRNA) sequencing, we profiled ~10,000 Breg cells from female MRL/lpr mice at the pre-disease (6–8 weeks of age) vs. active-disease (10–12 weeks of age) stages. Based on known markers of Breg subsets, scRNA analysis identified respective clusters as transtional-2 marginal zone precursor B cells (T2-MZP), marginal zone B cells (MZB), transitional 1 B cells (T1), germinal center B cells (GC), and B1 B cells. Our data showed that the pre-disease Breg cells were predominantly T2-MZP and MZB cells. Follicular B cells outside the marginal zone, on the other hand, are significantly increased in the active-disease stage. Two long noncoding RNAs (lncRNAs), Malat1 and Xist, were significantly increased in active-disease Breg cells, where the expression of Lglas3, Slpi, and Spp1 was also increased. Notably, active-disease Breg cells exhibited an exhausted phenotype with increased expression of T-bet (Tbx21). Collectively, our findings suggest that the SLE disease stage-dependent functions of Breg cells are regulated at the transcriptional level. In future experiments, we will determine whether the immunosuppressive functions of active-disease Breg cells can be restored by knocking down the differentially overexpressed genes.

Inhibitory Effects of Extracellular Vesicles from iPS-Cell-Derived Mesenchymal Stem Cells on the Onset of Sialadenitis in Sjögren's Syndrome Are Mediated by Immunomodulatory Splenocytes and Improved by Inhibiting miR-125b.

Extracellular vesicles (EVs) from allogeneic-tissue-derived mesenchymal stem cells (MSCs) are promising to improve Sjögren's syndrome (SS) treatment, but their application is hindered by high variations in and limited expandability of tissue MSCs. We derived standardized and scalable MSCs from iPS cells (iMSCs) and reported that EVs from young but not aging iMSCs (iEVs) inhibited sialadenitis onset in SS mouse models. Here, we aim to determine cellular mechanisms and optimization approaches of SS-inhibitory effects of iEVs. In NOD.B10.H2b mice at the pre-disease stage of SS, we examined the biodistribution and recipient cells of iEVs with imaging, flow cytometry, and qRT-PCR. Intravenously infused iEVs accumulated in the spleen but not salivary glands or cervical lymph nodes and were mainly taken up by macrophages. In the spleen, young but not aging iEVs increased M2 macrophages, decreased Th17 cells, and changed expression of related immunomodulatory molecules. Loading miR-125b inhibitors into aging iEVs significantly improved their effects on repressing sialadenitis onset and regulating immunomodulatory splenocytes. These data indicated that young but not aging iEVs suppress SS onset by regulating immunomodulatory splenocytes, and inhibiting miR-125b in aging iEVs restores such effects, which is promising to maximize production of effective iEVs from highly expanded iMSCs for future clinical application.

Mitochondrial dysfunction in chromaffin cells from the R6/1 mouse model of Huntington's disease: Impact on exocytosis and calcium current regulation

From a pathogenic perspective, Huntington's disease (HD) is being considered as a synaptopathy. As such, alterations in brain neurotransmitter release occur. As the activity of the sympathoadrenal axis is centrally controlled, deficits in the exocytotic release of catecholamine release may also occur. In fact, in chromaffin cells (CCs) of the adrenal medulla of the R6/1 model of HD, decrease of secretion and altered kinetics of the exocytotic fusion pore have been reported. Those alterations could be linked to mitochondrial deficits occurring in peripheral CCs, similar to those described in brain mitochondria. Here we have inquired about alterations in mitochondrial structure and function and their impact on exocytosis and calcium channel currents (ICa). We have monitored various parameters linked to those events, in wild type (WT) and the R6/1 mouse model of HD at a pre-disease stage (2 months age, 2 m), and when motor deficits are present (7 months age, 7 m). In isolated CCs from 7 m and in the adrenal medulla of R6/1 mice, we found the following alterations (with respect 7 m WT mice): (i) augmented fragmented mitochondria and oxidative stress with increased oxidized glutathione; (ii) decreased basal and maximal respiration; (iii) diminution of ATP cell levels; (iv) mitochondrial depolarization; (v) drastic decrease of catecholamine release with poorer potentiation by protonophore FCCP; (vi) decreased ICa inhibition by FCCP; and (vii) lesser potentiation by BayK8644 of ICa and smaller prolongation of current deactivation. Of note was the fact several of these alterations were already manifested in CCs from 2 m R6/1 mice at pre-disease stages. Based on those results, a plausible hypothesis can be raised in the sense that altered mitochondrial function seems to be an early primary event in HD pathogenesis. This is in line with an increasing number of mitochondrial, metabolic, and inflammatory alterations being recently reported in various HD peripheral tissues.

Pre-disease Detection Using Dynamical Network Biomarkers in Gene Regulatory Networks with Cell-to-cell Interaction

Dynamical Network Biomarkers (DNB) theory has been proposed as a method for detecting diseases at a very early stage. The progression of a disease can be regarded as a bifurcation phenomenon of the underlying dynamical system associated with the corresponding gene network. By identifying large fluctuations of the gene expression level occurring just before the bifurcation, we can detect the pre-disease stage without identifying the mathematical model of the dynamical system. However, the existing DNB theory mainly focuses on a single gene network representing averaged dynamics of multiple cells not explicitly handling a group of cells with cell-to-cell interaction. In this study, we extend the DNB theory to the case where cell-to-cell interaction is also taken into account. Ultimately, our analysis reveals that the pre-disease stage can be detected from the observation of the average gene expression when the bifurcation is induced by the intrinsic dynamics of the cells, whereas it remains undetectable when the bifurcation is produced by the interaction.

The Role of Genetics in Clinically Suspect Arthralgia and Rheumatoid Arthritis Development: A Large Cross-Sectional Study.

To investigate whether established genetic predictors for rheumatoid arthritis (RA) differentiate healthy controls, patients with clinically suspect arthralgia (CSA), and RA patients. Using analyses of variance, chi-square tests, and mean risk difference analyses, we investigated the association of an RA polygenic risk score (PRS) and HLA shared epitope (HLA-SE) with all participant groups, both unstratified and stratified for anti-citrullinated protein antibody (ACPA) status. We used 3 separate data sets sampled from the same Dutch population (1,015 healthy controls, 479 CSA patients, and 1,146 early classified RA patients). CSA patients were assessed for conversion to inflammatory arthritis over a period of 2 years, after which they were classified as either CSA converters (n=84) or CSA nonconverters (n=395). The PRS was increased in RA patients (mean ± SD PRS 1.31 ± 0.96) compared to the complete CSA group (1.07 ± 0.94) and compared to CSA converters (1.12 ± 0.94). In ACPA- strata, PRS distributions differed strongly when comparing the complete CSA group (mean ± SD PRS 1.05 ± 0.94) and CSA converters (0.97 ± 0.87) to RA patients (1.20 ± 0.94), while in the ACPA+ strata, the complete CSA group (1.25 ± 0.99) differed clearly from healthy controls (1.05 ± 0.94) and RA patients (1.41 ± 0.96). HLA-SE was more prevalent in the RA group (prevalence 0.64) than the complete CSA group (0.45), with small differences between RA patients and CSA converters (0.64 versus 0.60) and larger differences between CSA converters and CSA nonconverters (0.60 versus 0.42). HLA-SE prevalence differed more strongly within the ACPA+ strata as follows: healthy controls (prevalence 0.43), CSA nonconverters (0.48), complete CSA group (0.59), CSA converters (0.66), and RA patients (0.79). We observed that genetic predisposition increased across pre-RA participant groups. The RA PRS differed in early classified RA and inflammatory pre-disease stages, regardless of ACPA stratification. HLA-SE prevalence differed between arthritis patients, particularly ACPA+ patients, and healthy controls. Genetics seem to fulfill different etiologic roles.

A Natural History of Disease Framework for Improving the Prevention, Management, and Research on Post-viral Fatigue Syndrome and Other Forms of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome.

We propose a framework for the treatment, rehabilitation, and research into Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) using a natural history of disease approach to outline the distinct disease stages, with an emphasis on cases following infection to provide insights into prevention. Moving away from the method of subtyping patients based on the various phenotypic presentations and instead reframing along the lines of disease progression could help with defining the distinct stages of disease, each of which would benefit from large prospective cohort studies to accurately describe the pathological mechanisms taking place therein. With a better understanding of these mechanisms, management and research can be tailored specifically for each disease stage. Pre-disease and early disease stages call for management strategies that may decrease the risk of long-term morbidity, by focusing on avoidance of further insults, adequate rest to enable recovery, and pacing of activities. Later disease stages require a more holistic and tailored management approach, with treatment—as this becomes available—targeting the alleviation of symptoms and multi-systemic dysfunction. More stringent and standardised use of case definitions in research is critical to improve generalisability of results and to create the strong evidence-based policies for management that are currently lacking in ME/CFS.

THE ROLE OF GROUP 3 INNATE LYMPHOID CELLS (ILC3) IN GM-CSF/CSF2RB-DEPENDENT INTESTINAL HOMEOSTASIS IN CROHN’S DISEASE

Abstract Inflammatory Bowel Disease (IBD) is comprised of two subtypes, Crohn’s disease (CD) and ulcerative colitis (UC). Genome-wide association studies (GWAS) of IBD identified 240 loci significantly associated with IBD risk. CSF2RB, one of the identified IBD-associated genes and the receptor for GM-CSF signaling, is responsible for maintaining intestinal homeostasis through retinoic acid (RA) production by macrophages and dendritic cells. GM-CSF (Sargramostim) treatment showed a promising result for preventing intestinal injury and inflammation in both a murine and our novel zebrafish model. However, due to GM-CSF-neutralizing antibodies present in patients, Sargramostim failed in a large cohort Phase II clinical trial. This GM-CSF-dependent homeostasis relies on the balance of innate lymphoid cells (ILCs). In human patients, we report that during inflammation in CD, there is a decrease of NCR+ ILC3s while proinflammatory ILC1s rapidly increase. Neutralizing GM-CSF auto-antibodies were detected in the pre-disease stage (ILC1 low & ILC3 low) in CD patients, a different result from CSF2RB frameshift allele carriers (ILC1 low & ILC3 high) (Figure 1). We developed a novel zebrafish model to mimic the acute and chronic nature of IBD disease pathogenicity in vivo. In our model, human GM-CSF treatment significantly alleviated intestinal injury but showed no effect during mucosal healing. With a CRISPR knockout csf2rb zebrafish line, we showed this protective effect is CSF2RB-dependent. Using single-cell technologies, DSS-induced injury increases rorc+ ILC3s. These ILC3 cell proportion changes were diminished in csf2rb-/- zebrafish (Figure 2). Figure 1. Distinct ILC subpopulations between anti-GM-CSF antibodies and CSFRB mutation carriers. Scatter plot of the PC1 values of the ILC3 gene list (ILC3-PC) (y axis) against the PC1 values of the ILC1 gene list (ILC1-PC) (x axis). Both ILC1-PC and ILC3-PC were derived from PCA analysis of signature gene lists of ILC1 and ILC3 cell types against a sub-dataset of the bulk mRNAseq samples from the MSCCR. Red dot indicate patient with anti-GM-CSF antibody. The logarithm antibody titer was shown with the intensity of red color. The green dots indicate the CSF2RB heterozygote carriers. Figure 2. GM-CSF protects against DSS-induced intestinal injury and regulates ILC3. (A-B) Treatment of human GM-CSF significantly reduces intestinal injury in dose-dependent manner in WT (A) but not CSF2RB-/- (B). ***, P< 0.001 (C) Analyzing scRNAseq data of zebrafish intestine cells, RORC+ (ILC3) cell proportion over total immune cells increases with DSS injury and decreases with human GM-CSF co-treatment. There is no RORC+ cell proportion change in CSF2RB-/-. (D) Modeling of GM-CSF in preventing ILC3 expansion and attenuating ILC3-related proinflammatory cytokines during intestinal injury. Our studies illuminate mechanisms of GM-CSF in perpetuating gut homeostasis through maintaining and regulating ILC3s. This novel aspect of regulating IBD pathogenesis through ILCs may lead to novel therapeutic targets.

Exploiting Caenorhabditis elegans to discover human gut microbiota-mediated intervention strategies in protein conformational diseases.

Exploiting Caenorhabditis elegans to discover human gut microbiota-mediated intervention strategies in protein conformational diseases.

Integrated Measurement for Early Detection (MIDO) as a digital strategy for timely assessment of non-communicable disease profiles and factors associated with unawareness and control: a retrospective observational study in primary healthcare facilities in Mexico

ObjectivesThe Carlos Slim Foundation implemented the Integrated Measurement for Early Detection (MIDO), a screening strategy for non-communicable diseases (NCDs) in Mexico as part of CASALUD, a portfolio of digital health...

RUNX3 Promotes the Development of MDS/MPN Overlap Syndrome Via Enhancing Expression of Myc in the Absence of Tet2

The RUNX transcription factors have a critical role in normal and malignant hematopoiesis including myeloproliferative neoplasms (MPN) and myelodysplastic syndromes (MDS). RUNX3 is expressed in various hematopoietic cells, and the reduced expression of RUNX3 due to promoter DNA hyper-methylation is seen in patients with acute lymphoid leukemia, indicating a tumor suppressive role of RUNX3. The loss of Runx3 promotes the development of MPN-like disease in mice. However, loss-of-function mutations and/or a deletion of RUNX3 are rarely observed in patients with myeloid malignancies. In fact, given that enhanced levels of RUNX3 expression are found in a part of patients with AML and MDS, RUNX3 may play an oncogenic role for myeloid malignancies.To determine how RUNX3 over-expression promotes the development of myeloid malignancies, we generated a mouse model of RUNX3 -induced MDS/MPN by utilizing Tet2 -deficient hematopoietic stem cells (HSCs). Since TET2 loss-of-function mutations initiate the transformation of HSCs, we harvested bone marrow CD150+CD34-LSK HSCs from tamoxifen-treated Cre-ERT2 (WT) and Cre-ERT2;Tet2Δ/Δ (Tet2 KO) mice, and transduced expression of 3xFLAG-tagged RUNX3 by using a retrovirus vector in vitro. Then, we transplanted them into lethally-irradiated Ly5.1+ recipient mice together with wild-type competitor cells. We observed that Tet2 KO mice died dominantly due to MPN-like disease, whereas RUNX3 -expressing Tet2 wild-type (RUNX3/WT) HSCs neither competed wild-type bone marrow cells nor developed hematological malignancies in mice by 12 months post transplantation. In contrast, RUNX3 -expressing Tet2 KO (RUNX3/Tet2 KO) HSCs preferentially generated myeloid cells, but not lymphoid cells, and subsequently competed wild-type cells in the PB and the BM. We found that 7 out of 18 RUNX3/Tet2 KO mice developed lethal MDS/MPN diseases despite a longer latency. At the time of sacrifice, RUNX3-Tet2 KO mice showed severe pancytopenia accompanied with dyplastic blood cells including pseudo-Pelger neutrophils and micro megakaryocytes. In addition, these moribund mice significantly enlarged spleen due to the expansion of myeloid cells. FACS analysis demonstrated that the expansion of LSK hematopoietic stem/progenitor cells (HSPCs) in the BM and the spleen, consistent with the features of extramedullary hematopoiesis. Thus, RUNX3/Tet2 KO mice recapitulated the phenotypic features of human MDS/MPN overlap syndrome, indicating that RUNX3 over-expression is prerequisite to the development of MDS/MPN in the absence of Tet2, although it has an adverse effect on the function of Tet2 -present HSCs, reminiscent with a tumor suppressive function of RUNX3 as seen in Runx3 KO mice.To understand the underlying molecular mechanism in the pathogenesis of RUNX3 -induced MDS/MPN, we performed gene expression analysis in HSPCs isolated from WT, RUNX3/WT, Tet2 KO and RUNX3/Tet2 KO mice at pre-disease and MDS/MPN stages. Gene Set Enrichment Analysis (GSEA) demonstrated that RUNX3/Tet2 KO MDS/MPN cells significantly enhanced expression of c-Myc target genes, compared to either WT cells or RUNX3/Tet2 KO cells at the pre-disease stage. While RUNX3/Tet2 KO cells showed negative enrichments of differentiation-related pathway genes, compared to WT cells, we found that those MDS/MPN cells enhanced expression of cell cycle, ribosome, and mitochondria-related biological pathways, in which c-Myc may regulate target genes and contribute to the transformation. In order to determine whether RUNX3 directly activates expression of c-Myc, we performed ChIP-sequencing by using an anti-FLAG antibody in RUNX3/Tet2 KO bone marrow cells, and found that c-Myc 3' distal enhancer regions showed conserved binding sites for Runx transcription factors. In addition, we found that RUNX3 -expressing human AML cells showed higher sensitivity to JQ1, a BRD4 inhibitor, following the significant reduction of both RUNX3 and C-MYC expression. The growth inhibition by JQ1 was rescued by ectopic expression of RUNX3 .In conclusion, RUNX3 and c-Myc collaborated to activate the function of oncogenic enhancers, in which Tet2 deficiency may alter the epigenetic status for allowing the bindings of these transcription factors, to an extent not seen in RUNX3-expressing alone. We demonstrated that RUNX3 functions as either an oncogene or a tumor suppressor for myeloid malignancies in the context dependent manner. DisclosuresHarada:Celgene: Research Funding; NIPPON SHINYAKU CO.: Speakers Bureau; NOVARTIS: Research Funding.

A metaheuristic multi-objective optimization method for dynamical network biomarker identification as pre-disease stage signal

Deciphering the signals that are attached to the transition from normal to disease stage is crucial in preventive medicine to understand the progression of complex diseases. Between normal and disease stages there exists the pre-disease stage, in which the disease is yet reversible towards the normal stage. Traditionally, molecular biomarkers have been used to identify the pre-disease stage. However, they have limitations because they have an individual and static nature. In complex diseases, the dynamics and interplays of certain genes have to be taken into account in order to identify the pre-disease stage. Therefore, in complex diseases, it is necessary to use dynamical network biomarkers (DNBs). The development of time-course omics data has been crucial to the use of DNBs as biomarker. In this article, a new two-step method is proposed for the identification of DNBs as pre-disease stage signal. In the first step, the relevant genes in the dataset are pre-filtered using a differential gene expression analysis. In the second step, the DNBs are identified, from a multi-objective optimization viewpoint, by using an Artificial Bee Colony based on Dominance (ABCD) algorithm. Specifically, identified DNBs optimize three objectives: they are the smallest gene network that shows the strongest signal in the earliest time-point of the disease progression and best correlates with the disease phenotype. The proposed method has been evaluated with five time-course microarray datasets and the results have been compared with five methods from other authors, surpassing their results. The effectiveness of the proposed method has been also proved with a leave-one-out cross-validation and a Gene Ontology term enrichment. In fact, the proposed method obtains values around 90% for accuracy, precision, recall, and F1 scores.

Activation of B10 cells via gut microbiota in the pathogenesis of systemic lupus erythematosus

Abstract Systemic Lupus Erythematosus(SLE), a disease of various genetic and environmental origins, is often characterized by immune complexes causing inflammation and damage in various organ systems, such as the brain, kidneys, lung, joint, and skin. Current treatment for SLE include steroidal and nonsteroidal anti-inflammatory drugs, antimalarial agents, and immunosuppressive medications. These treatments primarily reduce symptoms, and patients may develop side effects with long-term care. The gut microbiome has an important role in various metabolic and immunological diseases. A previous study found that increased Lactobacillus colonization restored the mucosal barrier, and increased abundance in these bacteria attenuated SLE symptoms through reversing a ‘leaky gut’. This allows for potential therapies of SLE with probiotics. In preliminary trials, vancomycin treatment during active disease killed gram-positive bacteria, but spared Lactobacillus, and attenuated symptoms. Surprisingly, significantly decreased amounts of CD10+CD19+ B cells that produce IL-10 (B10) were found when vancomycin was given before the onset of lupus. Vancomycin treatment before disease onset significantly removed bacterial DNA from the gut and circulation, causing exacerbation of clinical symptoms. Oral gavage of activated B10 cells in vancomycin treated mice rescued the negative effects of vancomycin treated mice at the pre-disease stage. This work suggests that a form of oral tolerance induced by bacterial DNA-mediated expansion of B10 cells suppress disease onset in the autoimmune-prone MRL/lpr mouse model. Future studies are warranted to further define the mechanism behind bacterial DNA promoting B10 cells.

TLR9 stimulation by the gut microbiota promotes tissue-specific immunosuppression in autoimmune-prone MRL/lpr mice

Abstract To investigate the ability of gut microbiota to modify immune regulation in autoimmune disease, we treated lupus-prone mice with oral vancomycin prior to disease development, and subsequently administered bacterial DNA isolated from commensal bacteria. Vancomycin given prior to disease initiation promotes exacerbation of autoimmune disease, likely due to a decrease in the frequency of B regulatory (Breg) cells, whereas vancomycin given after autoimmune disease onset has suppressive effects on disease phenotype in MRL/lpr mice. Bacterial DNA administration during the pre-disease stage promoted Breg cell production and suppressed autoimmune disease parameters in MRL/lpr mice. Further, we showed that activation of toll-like receptor 9 (TLR9) on B cells was involved in the suppressive effects of bacterial DNA seen in the MRL/lpr mouse model. We found that during the pre-disease period, joint treatment with vancomycin and oral administration of a TLR9 specific agonist, ODN 1826, promoted Breg cells in the lamina propria, increased total CD8+ T cells and effector memory CD44 expressingCD8+ T cells in the spleen, and suppressed Th17 and IFNγ producing CD4+ T cells in the mesenteric lymph nodes. Oral ODN 1826 administration also increased the Treg/Th17 ratio in the mesenteric lymph nodes. The alterations in suppressive vs. proinflammatory cell phenotypes by oral exposure to ODN 1826 suggests that the suppressive effects of bacterial DNA from the gut microbiota are modulated through TLR9 activation in a tissue-specific manner.

Detection of Early Disease Risk Factors Associated with Metabolic Syndrome: A New Era with the NMR Metabolomics Assessment.

The metabolic syndrome is a multifactorial disease developed due to accumulation and chronification of several risk factors associated with disrupted metabolism. The early detection of the biomarkers by NMR spectroscopy could be helpful to prevent multifactorial diseases. The exposure of each risk factor can be detected by traditional molecular markers but the current biomarkers have not been enough precise to detect the primary stages of disease. Thus, there is a need to obtain novel molecular markers of pre-disease stages. A promising source of new molecular markers are metabolomics standing out the research of biomarkers in NMR approaches. An increasing number of nutritionists integrate metabolomics into their study design, making nutrimetabolomics one of the most promising avenues for improving personalized nutrition. This review highlight the major five risk factors associated with metabolic syndrome and related diseases including carbohydrate dysfunction, dyslipidemia, oxidative stress, inflammation, and gut microbiota dysbiosis. Together, it is proposed a profile of metabolites of each risk factor obtained from NMR approaches to target them using personalized nutrition, which will improve the quality of life for these patients.

Hmga2 Functions As an Oncogene upon the Deletion of Tet2 and Promotes the Pathogenesis of Myelodysplastic Syndrome

High Mobility Group AT-hook 2 (HMGA2) is a chromatin modifier and its overexpression has been found in a subset of patients with myelodysplastic syndrome (MDS). The high level of HMGA2 expression appears to predict poor prognosis in various tumors; however, it remains unclear how HMGA2 dysregulates expression of target genes to facilitate the transformation. To elucidate the mechanisms by which the overexpression of Hmga2 promotes the development of MDS, we generated an Hmga2-expressing Tet2-deficient (Hmga2-Tet2Δ/Δ) mouse model showing the progressive phenotype of MDS. We found that Hmga2-Tet2Δ/Δ mice had neutropenia and anemia, but variable platelet counts, accompanied by elevated frequencies of mutant cells in myeloid cells. Hmga2-Tet2Δ/Δ mice showed a similar median survival to Tet2Δ/Δ mice (274 days vs 290 days), but shorter survival than Hmga2-Tet2wt/wt mice (274 days vs undetermined). Moribund Hmga2-Tet2Δ/Δ mice showed progressive leukopenia and anemia, accompanied by the emergence of dysplastic neutrophils, myeloblasts and anisocytosis in the PB and BM and dysplastic megakaryocytes in the BM. Hmga2-Tet2Δ/Δ mice had mildly increased spleen weights, and expanded myeloid cells and HSPCs in the spleen without the deposition of fibrosis. During a 12-month observation, we found that Hmga2-Tet2Δ/Δ mice developed lethal MDS/MPN overlap disease (47%), MDS (33%), MPN (13%), and AML (7%), while 6 out of 11 Tet2Δ/Δ mice developed MPN (55%). Hmga2-Tet2wt/wt mice subsequently showed similar blood counts in PB and died without the expansion of leukemic or dysplastic blood cells. Therefore, Hmga2 overexpression did not transform wild-type HSCs but promoted the development of MDS in the absence of Tet2 in vivo. In order to elucidate the molecular mechanisms underlying the transformation of Hmga2-Tet2Δ/Δ cells, we initially performed gene expression profiling by a RNA sequencing analysis in LSK HSPCs isolated from WT, Hmga2-Tet2wt/wt, Tet2Δ/Δ, and Hmga2-Tet2Δ/Δ mice at a pre-disease stage and those isolated from two Hmga2-Tet2Δ/Δ MDS/MPN and AML mice. Hmga2-Tet2Δ/Δ leukemic cells were placed closer to one out of two Hmga2-Tet2Δ/Δ cells at the pre-disease stage, but clearly apart from the other genotype cells, indicating that Hmga2 overexpression and Tet2 loss result in the accumulation of alterations in the transcriptional program during the development of MDS.In order to clarify the mechanisms by which the overexpression of Hmga2 alters the transcriptional program in Tet2-deficient cells, we performed the ChIP-sequencing of FLAG-tagged Hmga2 in bone marrow progenitor cells isolated from WT, Hmga2-Tet2wt/wt, and Hmga2-Tet2Δ/Δ mice. The numbers of Hmga2-binding peaks were markedly lower in Tet2-deficient cells than in Hmga2-Tet2wt/wt cells (2227 peaks versus 11500 peaks). Furthermore, annotated genes adjacent to Hmga2-binding sites partially overlapped in both genotype cells, whereas 2965 out of 3843 genes identified in Tet2 wild-type cells lost the binding peaks of Hmga2 upon the deletion of Tet2. Based on the DNA-binding capacity of Hmga2, the loss of Tet2 remodeled the binding sites of Hmga2 via change in DNA methylation in Hmga2-binding flanking regions, which were not observed in the presence of Tet2, leading to significant enrichments in genes involved in cell-to-cell adhesion and cell morphogenesis in Hmga2-Tet2Δ/Δ cells. Furthermore, we found that the overexpression of Hmga2 and loss of Tet2 resulted in the activation of oncogenic pathways (e.g. TGF-b, TNF-a), but suppressed the expression of genes in the unfolded protein response. Notably, the inhibition of bile acid metabolism to reactivate the unfolded protein response markedly attenuated the proliferation of Hmga2-Tet2Δ/Δ cells. These combinatory effects on the transcriptional program and cellular functions were not redundant to those in either single mutant cell, supporting Hmga2 being a proto-oncogene because its overexpression alone was not sufficient to develop MDS in vivo. Thus, Hmga2 overexpression exerts synergistic, but also gain-of-function effects with the loss of Tet2 to target these key biological pathways and promotes the transformation of Tet2-deficient stem cells. This study also provides a new rationale for targeting the unfolded protein response in MDS cells expressing HMGA2. Disclosures No relevant conflicts of interest to declare.