The p.E152K-STIM1 mutation deregulates Ca2+ signaling contributing to chronic pancreatitis.

Since deregulation of intracellular Ca2+ can lead to intracellular trypsin activation, and stromal interaction molecule-1 (STIM1) protein is the main regulator of Ca2+ homeostasis in pancreatic acinar cells, we explored the Ca2+ signaling in 37 STIM1 variants found in three pancreatitis patient cohorts. Extensive functional analysis of one particular variant, p.E152K, identified in three patients, provided a plausible link between dysregulated Ca2+ signaling within pancreatic acinar cells and chronic pancreatitis susceptibility. Specifically, p.E152K, located within the STIM1 EF-hand and sterile α-motif domain, increased the release of Ca2+ from the endoplasmic reticulum in patient-derived fibroblasts and transfected HEK293T cells. This event was mediated by altered STIM1-sarco/endoplasmic reticulum calcium transport ATPase (SERCA) conformational change and enhanced SERCA pump activity leading to increased store-operated Ca2+ entry (SOCE). In pancreatic AR42J cells expressing the p.E152K variant, Ca2+ signaling perturbations correlated with defects in trypsin activation and secretion, and increased cytotoxicity after cholecystokinin stimulation.This article has an associated First Person interview with the first author of the paper.

Lupus Nephritis Risk Factors and Biomarkers: An Update.

Lupus nephritis (LN) represents the most severe organ manifestation of systemic lupus erythematosus (SLE) in terms of morbidity and mortality. To reduce these risks, tremendous efforts have been made in the last decade to characterize the different steps of the disease and to develop biomarkers in order to better (i) unravel the pre-SLE stage (e.g., anti-nuclear antibodies and interferon signature); (ii) more timely initiation of therapy by improving early and accurate LN diagnosis (e.g., pathologic classification was revised); (iii) monitor disease activity and therapeutic response (e.g., recommendation to re-biopsy, new urinary biomarkers); (iv) prevent disease flares (e.g., serologic and urinary biomarkers); (v) mitigate the deterioration in the renal function; and (vi) reduce side effects with new therapeutic guidelines and novel therapies. However, progress is poor in terms of improvement with early death attributed to active SLE or infections, while later deaths are related to the chronicity of the disease and the use of toxic therapies. Consequently, an individualized treat-to-target strategy is mandatory, and for that, there is an unmet need to develop a set of accurate biomarkers to be used as the standard of care and adapted to each stage of the disease.

Long non-coding RNA Xist contribution in systemic lupus erythematosus and rheumatoid arthritis.

Growing evidence points towards the role of the long non-coding (lnc)-RNA Xist expressed in female cells as a predominant key actor for the sex bias observed in systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). Indeed, in female cells, lnc-Xist controls transcription directly by spreading across the inactivated X chromosome (Xi) and indirectly by sequestring miRNAs as a sponge. The inactivation process at Xi is altered in lymphocytes from SLE women and associated with important variations in ribonucleoproteins (RNP) associated with lnc-Xist. In fibroblast-like synoviocytes (FLS) and osteoclasts from RA women, proinflammatory and proliferative pathways are upregulated due to the sequestration effect exerted by lnc-Xist overexpression on miRNAs. The key role played by lnc-Xist in SLE and RA is further supported by it's knock down that recapitulates the SLE B cell extrafollicular profile and controls RA associated FLS proinflammatory cytokine production and proliferation.

Interplay of Environmental, Individual and Genetic Factors in Rheumatoid Arthritis Provocation.

In this review, we explore systemization of knowledge about the triggering effects of non-genetic factors in pathogenic mechanisms that contribute to the development of rheumatoid arthritis (RA). Possible mechanisms involving environmental and individual factors in RA pathogenesis were analyzed, namely, infections, mental stress, sleep deprivation ecology, age, perinatal and gender factors, eating habits, obesity and smoking. The non-genetic factors modulate basic processes in the body with the impact of these factors being non-specific, but these common challenges may be decisive for advancement of the disease in the predisposed body at risk for RA. The provocation of this particular disease is associated with the presence of congenital loci minoris resistentia. The more frequent non-genetic factors form tangles of interdependent relationships and, thereby, several interdependent external factors hit one vulnerable basic process at once, either provoking or reinforcing each other. Understanding the specific mechanisms by which environmental and individual factors impact an individual under RA risk in the preclinical stages can contribute to early disease diagnosis and, if the factor is modifiable, might be useful for the prevention or delay of its development.

Epigenetics in Primary Sjögren's Syndrome.

Primary Sjögren's syndrome (SjS) is a chronic and systemic autoimmune epithelitis with predominant female incidence, which is characterized by exocrine gland dysfunction. Incompletely understood, the etiology of SjS is multi-factorial and evidence is growing to consider that epigenetic factors are playing a crucial role in its development. Independent from DNA sequence mutations, epigenetics is described as inheritable and reversible processes that modify gene expression. Epigenetic modifications reported in minor salivary gland and lymphocytes from SjS patients are related to (i) an abnormal DNA methylation process inducing in turn defective control of normally repressed genes involving such matters as autoantigens, retrotransposons, and the X chromosome in women; (ii) altered nucleosome positioning associated with autoantibody production; and (iii) altered control of microRNA. Results from epigenome-wide association studies have further revealed the importance of the interferon pathway in disease progression, the calcium signaling pathway for controlling fluid secretions, and a cell-specific cross talk with risk factors associated with SjS. Importantly, epigenetic modifications are reversible thus opening opportunities for therapeutic procedures in this currently incurable disease.

Apoptotic resistance in chronic lymphocytic leukemia and therapeutic perspectives.

Increased resistance to apoptosis represents a key oncogenic mechanism in chronic lymphocytic leukemia (CLL) that has been attributed to the upregulation of the anti-apoptotic B cell lymphoma 2 (Bcl-2) family members. Such an observation was associated with the development of molecules inhibiting Bcl-2 activity, and among them, BH3-mimetics represent a novel class of therapeutic compounds. In 2016, venetoclax became the first approved oral inhibitor of Bcl-2, and it has been used with success in patients with CLL who present with a 17p deletion or TP53 mutations and in those who have received at least one prior therapy. However, its mechanism for controlling relapses, and its optimal use in terms of duration and combinations with other drugs, remain unknown. Therefore, this review focuses on the mechanisms controlling apoptosis, CLL B cell strategies to prevent apoptosis including in response to BH3-mimetics, and arguments supporting the use of BH3-mimetics in association with other therapies in order to limit compensatory mechanisms.

Molecular Dynamics Simulations of Membrane-Bound STIM1 to Investigate Conformational Changes during STIM1 Activation upon Calcium Release.

Calcium is involved in important intracellular processes, such as intracellular signaling from cell membrane receptors to the nucleus. Typically, calcium levels are kept at less than 100 nM in the nucleus and cytosol, but some calcium is stored in the endoplasmic reticulum (ER) lumen for rapid release to activate intracellular calcium-dependent functions. Stromal interacting molecule 1 (STIM1) plays a critical role in early sensing of changes in the ER's calcium level, especially when there is a sudden release of stored calcium from the ER. Inactive STIM1, which has a bound calcium ion, is activated upon ion release. Following activation of STIM1, there is STIM1-assisted initiation of extracellular calcium entry through channels in the cell membrane. This extracellular calcium entering the cell then amplifies intracellular calcium-dependent actions. At the end of the process, ER levels of stored calcium are reestablished. The main focus of this work was to study the conformational changes accompanying homo- or heterodimerization of STIM1. For this purpose, the ER luminal portion of STIM1 (residues 58-236), which includes the sterile alpha motif (SAM) domain plus the calcium-binding EF-hand domains 1 and 2 attached to the STIM1 transmembrane region (TM), was modeled and embedded in a virtual membrane. Next, molecular dynamics simulations were performed to study the conformational changes that take place during STIM1 activation and subsequent protein-protein interactions. Indeed, the simulations revealed exposure of residues in the EF-hand domains, which may be important for dimerization steps. Altogether, understanding conformational changes in STIM1 can help in drug discovery when targeting this key protein in intracellular calcium functions.

Cupriphilic compounds to aid in proteasome inhibition.

It has been found that tumor cells and tissues, compared to normal cells, have higher levels of copper and possibly other metal ions. This presents a potential vulnerability of tumor cells that can serve as a physiological difference between cancer cells and normal cells and allows design of compounds that selectively target tumor cells while sparing normal cells. Recently we have identified compounds that have potential to inhibit the proteasome in tumor cells and induce cell death by mobilizing endogenous tumor copper resulting in in cellulo activation of the compound. These compounds hence act as pro-drugs, becoming active drugs in tumor cells with high copper content but remaining essentially inactive in normal cells, thereby greatly reducing adverse effects in patients. Such use would be of significant benefit in early detection and treatment of cancers, in particular, aggressive cancers such as pancreatic cancer which is usually not detected until it has reached an advanced stage. Six compounds were identified following virtual screening of the NCI Diversity Set with our proteasome computer model followed by confirmation with a biochemical assay that showed significant inhibition of the proteasome by the compounds in the presence of copper ions. In a dose response assay, NSC 37408 (6,7-dihydroxy-1-benzofuran-3-one), our best compound, exhibited an IC50 of 3µM in the presence of 100nM copper.

Stromal interaction molecules as important therapeutic targets in diseases with dysregulated calcium flux.

Calcium ions have important roles in cellular processes including intracellular signaling, protein folding, enzyme activation and initiation of programmed cell death. Cells maintain low levels of calcium in their cytosol in order to regulate these processes. When activation of calcium-dependent processes is needed, cells can release calcium stored in the endoplasmic reticulum (ER) into the cytosol to initiate the processes. This can also initiate activation of plasma membrane channels that allow entry of additional calcium from the extracellular milieu. The change in calcium levels is referred to as calcium flux. A key protein involved in initiation of calcium flux is Stromal Interaction Molecule 1 (STIM1), which has recently been identified as a sensor of ER calcium levels. STIM1 is an ER transmembrane protein that is activated by a drop in ER calcium levels. Upon activation, STIM1 interacts with a plasma membrane protein, ORAI1, to activate ORAI-containing calcium-selective plasma membrane channels. Dysregulation of calcium flux has been reported in cancers, autoimmune diseases and other diseases. STIM1 is a promising target in drug discovery due to its key role early in calcium flux. Here we review the involvement and importance of STIM1 in diseases and why STIM1 is a viable target for drug discovery. This article is part of a Special Issue entitled: Calcium signaling in health and disease. Guest Editors: Geert Bultynck, Jacques Haiech, Claus W. Heizmann, Joachim Krebs, and Marc Moreau.

Polyamine Dysregulation and Nucleolar Disruption in Alzheimer's Disease.

A hypothesis of Alzheimer's disease etiology is proposed describing how cellular stress induces excessive polyamine synthesis and recycling which can disrupt nucleoli. Polyamines are essential in nucleolar functions, such as RNA folding and ribonucleoprotein assembly. Changes in the nucleolar pool of anionic RNA and cationic polyamines acting as counterions can cause significant nucleolar dynamics. Polyamine synthesis reduces S-adenosylmethionine which, at low levels, triggers tau phosphorylation. Also, polyamine recycling reduces acetyl-CoA needed for acetylcholine, which is low in Alzheimer's disease. Extraordinary nucleolar expansion and/or contraction can disrupt epigenetic control in peri-nucleolar chromatin, such as chromosome 14 with the presenilin-1 gene; chromosome 21 with the amyloid precursor protein gene; chromosome 17 with the tau gene; chromosome 19 with the APOE4 gene; and the inactive X chromosome (Xi; aka "nucleolar satellite") with normally silent spermine synthase (polyamine synthesis) and spermidine/spermine-N1-acetyltransferase (polyamine recycling) alleles. Chromosomes 17, 19 and the Xi have high concentrations of Alu elements which can be transcribed by RNA polymerase III if positioned nucleosomes are displaced from the Alu elements. A sudden flood of Alu RNA transcripts can competitively bind nucleolin which is usually bound to Alu sequences in structural RNAs that stabilize the nucleolar heterochromatic shell. This Alu competition leads to loss of nucleolar integrity with leaking of nucleolar polyamines that cause aggregation of phosphorylated tau. The hypothesis was developed with key word searches (e.g., PubMed) using relevant terms (e.g., Alzheimer's, lupus, nucleolin) based on a systems biology approach and exploring autoimmune disease tautology, gaining synergistic insights from other diseases.

Partial least squares for efficient models of fecal indicator bacteria on Great Lakes beaches.

At public beaches, it is now common to mitigate the impact of water-borne pathogens by posting a swimmer's advisory when the concentration of fecal indicator bacteria (FIB) exceeds an action threshold. Since culturing the bacteria delays public notification when dangerous conditions exist, regression models are sometimes used to predict the FIB concentration based on readily-available environmental measurements. It is hard to know which environmental parameters are relevant to predicting FIB concentration, and the parameters are usually correlated, which can hurt the predictive power of a regression model. Here the method of partial least squares (PLS) is introduced to automate the regression modeling process. Model selection is reduced to the process of setting a tuning parameter to control the decision threshold that separates predicted exceedances of the standard from predicted non-exceedances. The method is validated by application to four Great Lakes beaches during the summer of 2010. Performance of the PLS models compares favorably to that of the existing state-of-the-art regression models at these four sites.

Graves' Disease in a Young Patient With Turner's Syndrome: The Genetic Association.

INTRODUCTION: Autoimmune diseases occur more often in females, suggesting a key role for the X chromosome. Curiously, individuals with Turner syndrome (TS), with fewer copies of X-linked genes, are prone to develop autoimmune conditions. Hashimoto's thyroiditis (HT) is described with a relatively high frequency in patients with TS while the association with Graves' disease (GD) is rare. Here we report a rare case of TS with GD in a young patient. METHOD: A 14-year-old girl presented with hyperthyroid symptoms and eye signs that developed over the past six months. She had somatic stigmata of TS. TS was diagnosed by karyotyping (45,XO/46,XX del Xq22) and GD was diagnosed by a thyroid function test and the presence of autoantibodies. She was treated effectively with carbimazole for GD. Estrogen replacement therapy was also initiated to induce the development of secondary sex characteristics. CONCLUSION: X chromosome inactivation, an epigenetic process that establishes and maintains dosage compensation of X-linked genes, is especially vulnerable to disruption and may contribute to an autoimmune disease process. The occurrence of autoimmune diseases in patients with TS is discussed with regard to possible abnormalities in X-linked dosage compensation.

Cerebrospinal fluid YKL-40 level evolution is associated with autoimmune encephalitis remission.

Objective: Because of its heterogeneity in clinical presentation and course, predicting autoimmune encephalitis (AIE) evolution remains challenging. Hence, our aim was to explore the correlation of several biomarkers with the clinical course of disease. Methods: Thirty-seven cases of AIE were selected retrospectively and divided into active (N = 9), improved (N = 12) and remission (N = 16) AIE according to their disease evolution. Nine proteins were tested in both serum and cerebrospinal fluid (CSF) at diagnosis (T0) and during the follow-up (T1), in particular activated MMP-9 (MMP-9A) and YKL-40 (or chitinase 3-like 1). Results: From diagnosis to revaluation, AIE remission was associated with decreased YKL-40 and MMP-9A levels in the CSF, and with decreased NfL and NfH levels in the serum. The changes in YKL-40 concentrations in the CSF were associated with (1) still active AIE when increasing >10% (P-value = 0.0093); (2) partial improvement or remission when the changes were between +9% and -20% (P-value = 0.0173); and remission with a reduction > -20% (P-value = 0.0072; overall difference between the three groups: P-value = 0.0088). At T1, the CSF YKL-40 levels were significantly decreased between active and improved as well as improved and remission AIE groups but with no calculable threshold because of patient heterogeneity. Conclusion: The concentration of YKL-40, a cytokine-like proinflammatory protein produced by glial cells, is correlated in the CSF with the clinical course of AIE. Its introduction as a biomarker may assist in following disease activity and in evaluating therapeutic response.

Virtual target screening: validation using kinase inhibitors.

Computational methods involving virtual screening could potentially be employed to discover new biomolecular targets for an individual molecule of interest (MOI). However, existing scoring functions may not accurately differentiate proteins to which the MOI binds from a larger set of macromolecules in a protein structural database. An MOI will most likely have varying degrees of predicted binding affinities to many protein targets. However, correctly interpreting a docking score as a hit for the MOI docked to any individual protein can be problematic. In our method, which we term "Virtual Target Screening (VTS)", a set of small drug-like molecules are docked against each structure in the protein library to produce benchmark statistics. This calibration provides a reference for each protein so that hits can be identified for an MOI. VTS can then be used as tool for: drug repositioning (repurposing), specificity and toxicity testing, identifying potential metabolites, probing protein structures for allosteric sites, and testing focused libraries (collection of MOIs with similar chemotypes) for selectivity. To validate our VTS method, twenty kinase inhibitors were docked to a collection of calibrated protein structures. Here, we report our results where VTS predicted protein kinases as hits in preference to other proteins in our database. Concurrently, a graphical interface for VTS was developed.

Evaluating the performance of volunteers in mapping invasive plants in public conservation lands.

Citizen science programs are touted as useful tools for engaging the public in science and for collecting important data for scientists and resource managers. To accomplish the latter, it must be shown that data collected by volunteers is sufficiently accurate and reliable. We engaged 119 volunteers over three years to map and estimate abundance of invasive plants in New York and New Jersey parklands. We tested their accuracy via collected pressed samples and by subsampling their transect points. We also compared the performances of volunteers and botanical experts. Our results support the notion that volunteer participation can enhance the data generated by scientists alone. We found that the quality of data collected might be affected by the environment in which the data are collected. We suggest that giving consideration to how people learn can not only help to achieve educational goals but can also help to produce more data to be used in scientific study.

Species densities, assembly order, and competence jointly determine the diversity-disease relationship.

Since species vary in abundance and host competence (i.e., ability to get infected and transmit a pathogen), changes in species composition caused by biodiversity loss impacts disease dynamics. Forecasting effects of species composition on disease depends on community (dis)assembly, processes determining how species are added to (or lost from) communities. We simulated community assembly by planting mesocosms, nested along a richness gradient, and tested how relationships between richness, species assembly order, and overall density affect disease risk. Mesocosms with up to six crop species of varying competence were inoculated with a soilborne fungal pathogen, Rhizoctonia solani. Disease was measured as species-level prevalence, community-level prevalence, and total number of diseased plants. Regardless of metric, richness limited disease when species assembly order negatively correlated with competence and total density remained unchanged with richness. When density increased with richness or species assembled randomly, richness primarily correlated positively or weakly with disease. Our results align with theoretical expectations and represent the first empirical study to test the influence of species densities, assembly order, and competence on diversity-disease relationships.

Identification of altered cell signaling pathways using proteomic profiling in stable and progressive chronic lymphocytic leukemia.

Chronic lymphocytic leukemia (CLL) is characterized by significant biologic and clinical heterogeneity. This study was designed to explore CLL B-cells' proteomic profile in order to identify biologic processes affected at an early stage and during disease evolution as stable or progressive. Purified B cells from 11 untreated CLL patients were tested at two time points by liquid chromatography-tandem mass spectrometry. Patients included in the study evolved to either progressive (n = 6) or stable disease (n = 5). First, at an early stage of the disease (Binet stage A), based on the relative abundance levels of 389 differentially expressed proteins (DEPs), samples were separated into stable and progressive clusters with the main differentiating factor being the RNA splicing pathway. Next, in order to test how the DEPs affect RNA splicing, a RNA-Seq study was conducted showing 4217 differentially spliced genes between the two clusters. Distinct longitudinal evolutions were observed with predominantly proteomic modifications in the stable CLL group and spliced genes in the progressive CLL group. Splicing events were shown to be six times more frequent in the progressive CLL group. The main aberrant biologic processes controlled by DEPs and spliced genes in the progressive group were cytoskeletal organization, Wnt/ß-catenin signaling, and mitochondrial and inositol phosphate metabolism with a downstream impact on CLL B-cell survival and migration. This study suggests that proteomic profiles at the early stage of CLL can discriminate progressive from stable disease and that RNA splicing dysregulation underlies CLL evolution, which opens new perspectives in terms of biomarkers and therapy.

Shp2 protein tyrosine phosphatase inhibitor activity of estramustine phosphate and its triterpenoid analogs.

Shp2 protein tyrosine phosphate (PTP) is a novel target for anticancer drug discovery. We identified estramustine phosphate as a Shp2 PTP inhibitor from the National Cancer Institute Approved Oncology Drug set. A focused structure-activity relationship study indicated that the 17-phosphate group is required for the Shp2 PTP inhibitor activity of estramustine phosphate. A search for estramustine phosphate analogs led to identification of two triterpenoids, enoxolone, and celastrol, having Shp2 PTP inhibitor activity. With the previously reported PTP1B inhibitor trodusquemine, our study reveals steroids and triterpenoids with negatively charged phosphate, carboxylate, or sulfonate groups as novel pharmacophores of selective PTP inhibitors.

Knowledge gain and behavioral change in citizen-science programs.

Citizen-science programs are often touted as useful for advancing conservation literacy, scientific knowledge, and increasing scientific-reasoning skills among the public. Guidelines for collaboration among scientists and the public are lacking and the extent to which these citizen-science initiatives change behavior is relatively unstudied. Over two years, we studied 82 participants in a three-day program that included education about non-native invasive plants and collection of data on the occurrence of those plants. Volunteers were given background knowledge about invasive plant ecology and trained on a specific protocol for collecting invasive plant data. They then collected data and later gathered as a group to analyze data and discuss responsible environmental behavior with respect to invasive plants. We tested whether participants without experience in plant identification and with little knowledge of invasive plants increased their knowledge of invasive species ecology, participation increased knowledge of scientific methods, and participation affected behavior. Knowledge of invasive plants increased on average 24%, but participation was insufficient to increase understanding of how scientific research is conducted. Participants reported increased ability to recognize invasive plants and increased awareness of effects of invasive plants on the environment, but this translated into little change in behavior regarding invasive plants. Potential conflicts between scientific goals, educational goals, and the motivation of participants must be considered during program design.

Resumen: Los programas de ciencia-ciudadana a menudo son vendidos como útiles para que el público avance en sus conocimientos sobre conservación, en su conocimiento científico y en el incremento de las habilidades de razonamiento científico. No existen directrices para la colaboración entre científicos y el público y casi no se ha estudiado el grado en que estas iniciativas ciudadanos-ciencia cambian el comportamiento. Durante dos años estudiamos a 82 participantes en un programa de 3 días que incluía educación sobre plantas invasoras no nativas y la recolección de datos sobre la ocurrencia de estas plantas. A los voluntarios se les proporcionó conocimiento básico sobre la ecología de plantas invasoras y fueron entrenados en un protocolo específico para la recolección de datos de plantas invasoras. Posteriormente recolectaron datos y se reunieron para analizarlos y discutir sobre comportamiento ambiental responsable en relación con plantas invasoras. Probamos si los participantes sin experiencia en la identificación de plantas y con poco conocimiento de plantas invasoras incrementaron su conocimiento de ecología de especies invasoras, si la participación incrementó su conocimiento de métodos científicos y si la participación afectó su comportamiento. El conocimiento de plantas invasoras incrementó 24% en promedio, pero la participación no fue suficiente para incrementar el entendimiento de cómo se lleva a cabo la investigación científica. Los participantes reportaron incremento en su habilidad para reconocer plantas invasoras e incremento en la conciencia sobre el efecto de las plantas invasoras sobre el ambiente, pero esto se tradujo en pocos cambios en el comportamiento respecto a las plantas invasoras. Los potenciales conflictos entre las metas científicas, las metas educativas y la motivación de participantes deben ser considerados durante el diseño del programa.

Transition from compensated hypertrophy to systolic heart failure in the spontaneously hypertensive rat: Structure, function, and transcript analysis.

Gene expression, determined by micro-array analysis, and left ventricular (LV) remodeling associated with the transition to systolic heart failure (HF) were examined in the spontaneously hypertensive rat (SHR). By combining transcript and gene set enrichment analysis (GSEA) of the LV with assessment of function and structure in age-matched SHR with and without HF, we aimed to better understand the molecular events underlying the onset of hypertensive HF. Failing hearts demonstrated depressed LV ejection fraction, systolic blood pressure, and LV papillary muscle force while LV end-diastolic and systolic volume and ventricular mass increased. 1431 transcripts were differentially expressed between failing and non-failing animals. GSEA identified multiple enriched gene sets, including those involving inflammation, oxidative stress, cell degradation and cell death, as well as TGF-beta and insulin signaling pathways. Our findings support the concept that these pathways and mechanisms may contribute to deterioration of cardiac function and remodeling associated with hypertensive HF.