Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 47
Filter
1.
N Engl J Med ; 390(22): 2047-2060, 2024 Jun 13.
Article in English | MEDLINE | ID: mdl-38865660

ABSTRACT

BACKGROUND: The risk of second tumors after chimeric antigen receptor (CAR) T-cell therapy, especially the risk of T-cell neoplasms related to viral vector integration, is an emerging concern. METHODS: We reviewed our clinical experience with adoptive cellular CAR T-cell therapy at our institution since 2016 and ascertained the occurrence of second tumors. In one case of secondary T-cell lymphoma, a broad array of molecular, genetic, and cellular techniques were used to interrogate the tumor, the CAR T cells, and the normal hematopoietic cells in the patient. RESULTS: A total of 724 patients who had received T-cell therapies at our center were included in the study. A lethal T-cell lymphoma was identified in a patient who had received axicabtagene ciloleucel therapy for diffuse large B-cell lymphoma, and both lymphomas were deeply profiled. Each lymphoma had molecularly distinct immunophenotypes and genomic profiles, but both were positive for Epstein-Barr virus and were associated with DNMT3A and TET2 mutant clonal hematopoiesis. No evidence of oncogenic retroviral integration was found with the use of multiple techniques. CONCLUSIONS: Our results highlight the rarity of second tumors and provide a framework for defining clonal relationships and viral vector monitoring. (Funded by the National Cancer Institute and others.).


Subject(s)
Antineoplastic Agents, Immunological , Immunotherapy, Adoptive , Lymphoma, Large B-Cell, Diffuse , Lymphoma, T-Cell , Neoplasms, Second Primary , Receptors, Chimeric Antigen , Female , Humans , Middle Aged , Biological Products/adverse effects , Biological Products/therapeutic use , Clonal Hematopoiesis , Herpesvirus 4, Human/immunology , Herpesvirus 4, Human/genetics , Immunotherapy, Adoptive/adverse effects , Lymphoma, Large B-Cell, Diffuse/genetics , Lymphoma, Large B-Cell, Diffuse/immunology , Lymphoma, Large B-Cell, Diffuse/therapy , Lymphoma, T-Cell/etiology , Lymphoma, T-Cell/genetics , Lymphoma, T-Cell/immunology , Lymphoma, T-Cell/therapy , Neoplasms, Second Primary/genetics , Neoplasms, Second Primary/etiology , Receptors, Chimeric Antigen/immunology , Receptors, Chimeric Antigen/therapeutic use , Antineoplastic Agents, Immunological/adverse effects , Antineoplastic Agents, Immunological/therapeutic use , Virus Integration
2.
Cell Mol Life Sci ; 80(12): 376, 2023 Nov 27.
Article in English | MEDLINE | ID: mdl-38010414

ABSTRACT

Apolipoproteins co-deposit with amyloids, yet apolipoprotein-amyloid interactions are enigmatic. To understand how apoE interacts with Alzheimer's amyloid-ß (Aß) peptide in fibrillary deposits, the NMR structure of full-length human apoE was docked to four structures of patient-derived Aß1-40 and Aß1-42 fibrils determined previously using cryo-electron microscopy or solid-state NMR. Similar docking was done using the NMR structure of human apoC-III. In all complexes, conformational changes in apolipoproteins were required to expose large hydrophobic faces of their amphipathic α-helices for sub-stoichiometric binding to hydrophobic surfaces on sides or ends of fibrils. Basic residues flanking the hydrophobic helical faces in apolipoproteins interacted favorably with acidic residue ladders in some amyloid polymorphs. Molecular dynamics simulations of selected apoE-fibril complexes confirmed their stability. Amyloid binding via cryptic sites, which became available upon opening of flexibly linked apolipoprotein α-helices, resembled apolipoprotein-lipid binding. This mechanism probably extends to other apolipoprotein-amyloid interactions. Apolipoprotein binding alongside fibrils could interfere with fibril fragmentation and secondary nucleation, while binding at the fibril ends could halt amyloid elongation and dissolution in a polymorph-specific manner. The proposed mechanism is supported by extensive prior experimental evidence and helps reconcile disparate reports on apoE's role in Aß aggregation. Furthermore, apoE domain opening and direct interaction of Arg/Cys158 with amyloid potentially contributes to isoform-specific effects in Alzheimer's disease. In summary, current modeling supported by prior experimental studies suggests similar mechanisms for apolipoprotein-amyloid and apolipoprotein-lipid interactions; explains why apolipoproteins co-deposit with amyloids; and helps reconcile conflicting reports on the chaperone-like apoE action in Aß aggregation.


Subject(s)
Alzheimer Disease , Amyloid beta-Peptides , Apolipoproteins E , Humans , Alzheimer Disease/metabolism , Amyloid/metabolism , Amyloid beta-Peptides/metabolism , Apolipoproteins/chemistry , Apolipoproteins/metabolism , Apolipoproteins E/metabolism , Brain/metabolism , Cryoelectron Microscopy , Molecular Dynamics Simulation , Peptide Fragments/metabolism
3.
Horm Behav ; 155: 105411, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37659358

ABSTRACT

Premenopausal hysterectomy is associated with a greater relative risk of dementia. We previously demonstrated cognitive impairments in adult rats six weeks after hysterectomy with ovarian conservation compared with intact sham-controls and other gynecological surgery variations. Here, we investigated whether hysterectomy-induced cognitive impairments are transient or persistent. Adult rats received sham-control, ovariectomy (Ovx), hysterectomy, or Ovx-hysterectomy surgery. Spatial working memory, reference memory, and anxiety-like behavior were tested either six-weeks post-surgery, in adulthood; seven-months post-surgery, in early middle-age; or twelve-months post-surgery, in late middle-age. Hysterectomy in adulthood yielded spatial working memory deficits at short-, moderate-, and long-term post-surgery intervals. Serum hormone levels did not differ between ovary-intact, but differed from Ovx, groups. Hysterectomy had no significant impact on healthy ovarian follicle or corpora lutea counts for any post-surgery timepoint compared with intact sham-controls. Frontal cortex, dorsal hippocampus, and entorhinal cortex were assessed for activity-dependent markers. In entorhinal cortex, there were alterations in FOSB and ΔFOSB expression during the early middle-age timepoint, and phosphorylated ERK1/2 levels at the adult timepoint. Collectively, results suggest a primary role for the uterus in regulating cognition, and that memory-related neural pathways may be modified following gynecological surgery. This is the first preclinical report of long-term effects of hysterectomy with and without ovarian conservation on cognition, endocrine, ovarian, and brain assessments, initiating a comprehensive framework of gynecological surgery effects. Translationally, findings underscore critical needs to decipher how gynecological surgeries, especially those involving the uterus, impact the brain and its functions, the ovaries, and overall aging from a systems perspective.


Subject(s)
Hysterectomy , Ovary , Female , Humans , Rats , Animals , Ovariectomy/adverse effects , Brain , Cognition , Maze Learning
4.
bioRxiv ; 2023 Aug 06.
Article in English | MEDLINE | ID: mdl-37577501

ABSTRACT

Apolipoproteins co-deposit with amyloids, yet apolipoprotein-amyloid interactions are enigmatic. To understand how apoE interacts with Alzheimer's amyloid-ß (Aß) peptide in fibrillary deposits, the NMR structure of full-length human apoE was docked to four structures of patient-derived Aß1-40 and Aß1-42 fibrils determined previously using cryo-electron microscopy or solid-state NMR. Similar docking was done using the NMR structure of human apoC-III. In all complexes, conformational changes in apolipoproteins were required to expose large hydrophobic faces of their amphipathic α-helices for sub-stoichiometric binding to hydrophobic surfaces on sides or ends of fibrils. Basic residues flanking the hydrophobic helical faces in apolipoproteins interacted favorably with acidic residue ladders in some amyloid polymorphs. Molecular dynamics simulations of selected apoE-fibril complexes confirmed their stability. Amyloid binding via cryptic sites, which became available upon opening of flexibly linked apolipoprotein α-helices, resembled apolipoprotein-lipid binding. This mechanism probably extends to other apolipoprotein-amyloid interactions. Apolipoprotein binding alongside fibrils could interfere with fibril fragmentation and secondary nucleation, while binding at the fibril ends could halt amyloid elongation and dissolution in a polymorph-specific manner. The proposed mechanism is supported by extensive prior experimental evidence and helps reconcile disparate reports on apoE's role in Aß aggregation. Furthermore, apoE domain opening and direct interaction of Arg/Cys158 with amyloid potentially contributes to isoform-specific effects in Alzheimer's disease. In summary, current modeling supported by prior experimental studies suggests similar mechanisms for apolipoprotein-amyloid and apolipoprotein-lipid interactions; explains why apolipoproteins co-deposit with amyloids; and helps reconcile conflicting reports on the chaperone-like apoE action in Aß aggregation.

5.
Behav Brain Res ; 448: 114442, 2023 06 25.
Article in English | MEDLINE | ID: mdl-37085118

ABSTRACT

Progestogens are a key component of menopausal hormone therapies. While some progestogens can be detrimental to cognition, there is preclinical evidence that progestogens with a strong progesterone-receptor affinity benefit some molecular mechanisms believed to underlie cognitive function. Thus, a progestin that maximizes progesterone-receptor affinity and minimizes affinities to other receptors may be cognitively beneficial. We evaluated segesterone-acetate (SGA), a 19-norprogesterone derivative with a strong progesterone-receptor affinity and no androgenic or estrogenic-receptor activity, hypothesizing that it would enhance cognition. Middle-aged rats underwent Sham or Ovariectomy (Ovx) surgery followed by administration of medroxyprogesterone-acetate (MPA; used as a positive control as we have previously shown MPA-induced cognitive deficits), SGA (low or high dose), or vehicle (one Sham and one Ovx group). Spatial working and reference memory, delayed retention, and anxiety-like behavior were assessed, as were memory- and hormone- related protein assays within the frontal cortex, dorsal hippocampus, and entorhinal cortex. Low-dose SGA impaired spatial working memory, while high-dose SGA had a more extensive detrimental impact, negatively affecting spatial reference memory and delayed retention. Replicating previous findings, MPA impaired spatial reference memory and delayed retention. SGA, but not MPA, alleviated Ovx-induced anxiety-like behaviors. On two working memory measures, IGF-1R expression correlated with better working memory only in rats without hormone manipulation; any hormone manipulation or combination of hormone manipulations used herein altered this relationship. These findings suggest that SGA impairs spatial cognition after surgical menopause, and that surgical menopause with or without progestin administration disrupts relationships between a growth factor critical to neuroplasticity.


Subject(s)
Progesterone , Progestins , Animals , Female , Rats , Acetates , Anxiety/drug therapy , Intercellular Signaling Peptides and Proteins , Menopause/physiology , Ovariectomy , Progesterone/pharmacology , Progestins/pharmacology
6.
Cancer Cell ; 41(1): 210-225.e5, 2023 01 09.
Article in English | MEDLINE | ID: mdl-36584673

ABSTRACT

Most relapsed/refractory large B cell lymphoma (r/rLBCL) patients receiving anti-CD19 chimeric antigen receptor (CAR19) T cells relapse. To characterize determinants of resistance, we profiled over 700 longitudinal specimens from two independent cohorts (n = 65 and n = 73) of r/rLBCL patients treated with axicabtagene ciloleucel. A method for simultaneous profiling of circulating tumor DNA (ctDNA), cell-free CAR19 (cfCAR19) retroviral fragments, and cell-free T cell receptor rearrangements (cfTCR) enabled integration of tumor and both engineered and non-engineered T cell effector-mediated factors for assessing treatment failure and predicting outcomes. Alterations in multiple classes of genes are associated with resistance, including B cell identity (PAX5 and IRF8), immune checkpoints (CD274), and those affecting the microenvironment (TMEM30A). Somatic tumor alterations affect CAR19 therapy at multiple levels, including CAR19 T cell expansion, persistence, and tumor microenvironment. Further, CAR19 T cells play a reciprocal role in shaping tumor genotype and phenotype. We envision these findings will facilitate improved chimeric antigen receptor (CAR) T cells and personalized therapeutic approaches.


Subject(s)
Lymphoma, Large B-Cell, Diffuse , Receptors, Chimeric Antigen , Humans , Receptors, Chimeric Antigen/genetics , Neoplasm Recurrence, Local/drug therapy , Lymphoma, Large B-Cell, Diffuse/therapy , Lymphoma, Large B-Cell, Diffuse/drug therapy , Immunotherapy, Adoptive/methods , T-Lymphocytes , Antigens, CD19/genetics , Tumor Microenvironment
7.
Benef Microbes ; 14(5): 433-443, 2023 Nov 20.
Article in English | MEDLINE | ID: mdl-38656097

ABSTRACT

In this study, we analyse the influence of nutrition during the early neonatal period on the development and prevention of atopic dermatitis (AD) in children with a history of very low birth weight (VLBW). A retrospective cohort study was performed of VLBW preterm infants to assess the risk of their developing AD during childhood, according to nutrition with breastmilk and/or probiotic supplementation during the neonatal period. The analysis focused on nutritional and early childhood follow-up data for 437 newborns, of whom 184 received probiotics up to 36 weeks postmenstrual age. AD was present in 23.5% of the study sample. Of the children who did not develop AD, 44.9% had received probiotics from birth to 36 weeks of gestational age. Therefore, the administration of probiotics to infants at less than 36 weeks postmenstrual age is associated with a protective effect against the development of AD (odds ratio (OR) 0.57; 95% confidence interval (CI) 0.34-0.93). Moreover, a protective interaction was observed between probiotic administration and breastmilk (OR 0.46; 95% CI 0.25-0.82). The adjusted data in the regression model allow us to observe a statistically significant association with the protective effect of Lacticaseibacillus rhamnosus with the development of AD at school age (OR 0.55; 95% CI 0.30-0.99). Probiotic supplementation in VLBW newborns is associated with a decreased risk of subsequent development of AD. Breastmilk strengthens the protective effect of probiotics against the development of AD.


Subject(s)
Dermatitis, Atopic , Infant, Very Low Birth Weight , Lacticaseibacillus rhamnosus , Milk, Human , Probiotics , Humans , Dermatitis, Atopic/prevention & control , Retrospective Studies , Infant, Newborn , Probiotics/administration & dosage , Female , Male , Infant, Premature , Infant
8.
OTA Int ; 5(4): e220, 2022 Dec.
Article in English | MEDLINE | ID: mdl-36569109

ABSTRACT

Objectives: The aim of this study was to evaluate functional and radiographic results after open reduction and internal fixation of distal humeral fractures using precontoured locking plates. Our main hypothesis was that patients older than 65 years have inferior outcomes compared with younger patients. Methods: All patients treated for a distal humeral fracture with precontoured locking plates between 2006 and 2017 at a level 1 trauma center were identified. Included patients underwent a clinical examination, and new radiographs were obtained. Functional outcomes were evaluated using Quick Disability of the Arm, Shoulder and Hand, Mayo Elbow Performance Score, visual analog scale elbow satisfaction, and range of motion. Complications and reoperations were recorded. Results: Fifty-seven patients with a median age of 60 years were included in this study. Median Quick Disability of the Arm, Shoulder and Hand was 14, and median Mayo Elbow Performance Score was 85. There was no difference in functional scores in patients younger than 65 years or 65 years or older. However, the median flexion-extension arc was 121 degrees in patients younger than 65 years and 111 degrees in patients 65 years or older (P = 0.01). The overall complication rate was 68%, and 24 patients had at least 1 reoperation. Ulnar neuropathy was the most common complication followed by reduced range of motion. Conclusions: Operative management of distal humeral fractures with precontoured locking plates provides good functional outcome. The patient-reported outcomes were good, independent of patient age. The implant failure rate is low with precontoured locking plates; however, the complication rate remains high, and reoperations are common. Level of Evidence: Level 4, retrospective study.

9.
IEEE J Biomed Health Inform ; 26(9): 4785-4793, 2022 09.
Article in English | MEDLINE | ID: mdl-35820010

ABSTRACT

Non-small cell lung cancer (NSCLC) is the most prevalent form of lung cancer and a leading cause of cancer-related deaths worldwide. Using an integrative approach, we analyzed a publicly available merged NSCLC transcriptome dataset using machine learning, protein-protein interaction (PPI) networks and bayesian modeling to pinpoint key cellular factors and pathways likely to be involved with the onset and progression of NSCLC. First, we generated multiple prediction models using various machine learning classifiers to classify NSCLC and healthy cohorts. Our models achieved prediction accuracies ranging from 0.83 to 1.0, with XGBoost emerging as the best performer. Next, using functional enrichment analysis (and gene co-expression network analysis with WGCNA) of the machine learning feature-selected genes, we determined that genes involved in Rho GTPase signaling that modulate actin stability and cytoskeleton were likely to be crucial in NSCLC. We further assembled a PPI network for the feature-selected genes that was partitioned using Markov clustering to detect protein complexes functionally relevant to NSCLC. Finally, we modeled the perturbations in RhoGDI signaling using a bayesian network; our simulations suggest that aberrations in ARHGEF19 and/or RAC2 gene activities contributed to impaired MAPK signaling and disrupted actin and cytoskeleton organization and were arguably key contributors to the onset of tumorigenesis in NSCLC. We hypothesize that targeted measures to restore aberrant ARHGEF19 and/or RAC2 functions could conceivably rescue the cancerous phenotype in NSCLC. Our findings offer promising avenues for early predictive biomarker discovery, targeted therapeutic intervention and improved clinical outcomes in NSCLC.


Subject(s)
Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Actins/metabolism , Bayes Theorem , Carcinoma, Non-Small-Cell Lung/genetics , Guanine Nucleotide Exchange Factors , Humans , Lung Neoplasms/genetics , Lung Neoplasms/metabolism , Signal Transduction/genetics , rho-Specific Guanine Nucleotide Dissociation Inhibitors
10.
Front Psychiatry ; 12: 768722, 2021.
Article in English | MEDLINE | ID: mdl-34925096

ABSTRACT

It is a common pathway for patients with the behavioral variant of frontotemporal dementia (bvFTD) to be first misdiagnosed with a primary psychiatric disorder, a considerable proportion of them being diagnosed with bipolar disorder (BD). Conversely, not rarely patients presenting in late life with a first episode of mania or atypically severe depression are initially considered to have dementia before the diagnosis of late-onset BD is reached. Beyond some shared features that make these conditions particularly prone to confusion, especially in the elderly, the relationship between bvFTD and BD is far from simple. Patients with BD often have cognitive complaints as part of their psychiatric disorder but are at an increased risk of developing dementia, including FTD. Likewise, apathy and disinhibition, common features of depression and mania, respectively, are among the core features of the bvFTD syndrome, not to mention that depression may coexist with dementia. In this article, we take advantage of the current knowledge on the neurobiology of these two nosologic entities to review their historical and conceptual interplay, highlighting the clinical, genetic and neuroimaging features that may be shared by both disorders or unique to each of them.

12.
FEBS Open Bio ; 10(11): 2427-2436, 2020 11.
Article in English | MEDLINE | ID: mdl-32961634

ABSTRACT

Idiopathic pulmonary fibrosis (IPF) is a severe lung disease with poor survival that warrants early and precise diagnosis for timely therapeutic intervention. Despite accumulating genomic, transcriptomic, proteomic, and lipidomic data on IPF, evidence from water-soluble metabolomics is limited. To identify biomarkers for IPF from water-soluble metabolomic data, we measured the levels of various metabolites in bronchoalveolar lavage fluid (BALF) and serum samples from a bleomycin-induced murine pulmonary fibrotic model using gas chromatography/mass spectrometry. Thirty-two of 73 BALF metabolites and 29 of 74 serum metabolites were annotated. We observed that the levels of proline and methionine were higher in BALF but lower in serum than those in the control. Furthermore, analysis of public RNA-Seq data from the lungs of patients with IPF revealed that proline- and methionine-related genes were significantly upregulated compared to those in the lungs of healthy controls. These results suggest that proline and methionine may be potential biomarkers for IPF and may help to deepen our understanding of the pathophysiology of the disease. Based on our results, we propose a model capable of recapitulating the proline and methionine metabolism of fibrotic lungs, thereby providing better means for studying the disease and developing novel therapeutic strategies for IPF.


Subject(s)
Biomarkers/metabolism , Lung/metabolism , Lung/pathology , Metabolomics , Pulmonary Fibrosis/genetics , Pulmonary Fibrosis/metabolism , RNA-Seq , Animals , Bronchoalveolar Lavage Fluid/chemistry , Databases, Genetic , Gene Expression Regulation , Humans , Metabolic Networks and Pathways , Metabolome , Methionine/metabolism , Mice, Inbred C57BL , Principal Component Analysis , Proline/metabolism , Pulmonary Fibrosis/blood , Pulmonary Fibrosis/diagnosis
13.
Front Genet ; 11: 585998, 2020.
Article in English | MEDLINE | ID: mdl-33424923

ABSTRACT

While both chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are multifactorial disorders characterized by distinct clinical and pathological features, their commonalities and differences have not been fully elucidated. We sought to investigate the preventive roles of tetraspanins Cd151 and Cd9 -that are involved in diverse cellular processes in lung pathophysiology- in pulmonary fibrosis and emphysema, respectively, and to obtain a deeper understanding of their underlying molecular mechanisms toward facilitating improved therapeutic outcomes. Using an integrative approach, we examined the transcriptomic changes in the lungs of Cd151- and Cd9-deficient mice using functional-enrichment-analysis, pathway-perturbation-analysis and protein-protein-interaction (PPI) network analysis. Circadian-rhythm, extracellular-matrix (ECM), cell-adhesion and inflammatory responses and associated factors were prominently influenced by Cd151-deletion. Conversely, cellular-junctions, focal-adhesion, vascular-remodeling, and TNF-signaling were deeply impacted by Cd9-deletion. We also highlighted a "common core" of factors and signaling cascades that underlie the functions of both Cd151 and Cd9 in lung pathology. Circadian dysregulation following Cd151-deletion seemingly facilitated progressive fibrotic lung phenotype. Conversely, TGF-ß signaling attenuation and TNF-signaling activation emerged as potentially novel functionaries of Cd9-deletion-induced emphysema. Our findings offer promising avenues for developing novel therapeutic treatments for pulmonary fibrosis and emphysema.

14.
ISME J ; 14(1): 259-273, 2020 01.
Article in English | MEDLINE | ID: mdl-31624345

ABSTRACT

Many insects depend on obligate mutualistic bacteria to provide essential nutrients lacking from their diet. Most aphids, whose diet consists of phloem, rely on the bacterial endosymbiont Buchnera aphidicola to supply essential amino acids and B vitamins. However, in some aphid species, provision of these nutrients is partitioned between Buchnera and a younger bacterial partner, whose identity varies across aphid lineages. Little is known about the origin and the evolutionary stability of these di-symbiotic systems. It is also unclear whether the novel symbionts merely compensate for losses in Buchnera or carry new nutritional functions. Using whole-genome endosymbiont sequences of nine Cinara aphids that harbour an Erwinia-related symbiont to complement Buchnera, we show that the Erwinia association arose from a single event of symbiont lifestyle shift, from a free-living to an obligate intracellular one. This event resulted in drastic genome reduction, long-term genome stasis, and co-divergence with aphids. Fluorescence in situ hybridisation reveals that Erwinia inhabits its own bacteriocytes near Buchnera's. Altogether these results depict a scenario for the establishment of Erwinia as an obligate symbiont that mirrors Buchnera's. Additionally, we found that the Erwinia vitamin-biosynthetic genes not only compensate for Buchnera's deficiencies, but also provide a new nutritional function; whose genes have been horizontally acquired from a Sodalis-related bacterium. A subset of these genes have been subsequently transferred to a new Hamiltonella co-obligate symbiont in one specific Cinara lineage. These results show that the establishment and dynamics of multi-partner endosymbioses can be mediated by lateral gene transfers between co-ocurring symbionts.


Subject(s)
Aphids/microbiology , Buchnera/genetics , Erwinia/genetics , Gene Transfer, Horizontal , Symbiosis/genetics , Animals , Vitamins/biosynthesis
15.
Front Genet ; 10: 934, 2019.
Article in English | MEDLINE | ID: mdl-31649722

ABSTRACT

Biological data analysis is the key to new discoveries in disease biology and drug discovery. The rapid proliferation of high-throughput 'omics' data has necessitated a need for tools and platforms that allow the researchers to combine and analyse different types of biological data and obtain biologically relevant knowledge. We had previously developed TargetMine, an integrative data analysis platform for target prioritisation and broad-based biological knowledge discovery. Here, we describe the newly modelled biological data types and the enhanced visual and analytical features of TargetMine. These enhancements have included: an enhanced coverage of gene-gene relations, small molecule metabolite to pathway mappings, an improved literature survey feature, and in silico prediction of gene functional associations such as protein-protein interactions and global gene co-expression. We have also described two usage examples on trans-omics data analysis and extraction of gene-disease associations using MeSH term descriptors. These examples have demonstrated how the newer enhancements in TargetMine have contributed to a more expansive coverage of the biological data space and can help interpret genotype-phenotype relations. TargetMine with its auxiliary toolkit is available at https://targetmine.mizuguchilab.org. The TargetMine source code is available at https://github.com/chenyian-nibio/targetmine-gradle.

16.
Physiol Rep ; 7(6): e14010, 2019 03.
Article in English | MEDLINE | ID: mdl-30916484

ABSTRACT

Hypertension is a major health concern in the developed world, and its prevalence increases with advancing age. The impact of hypertension on the function of the renal and cardiovascular systems is well studied; however, its influence on the brain regions important for cognition has garnered less attention. We utilized the Cyp1a1-Ren2 xenobiotic-inducible transgenic rat model to mimic both the age of onset and rate of induction of hypertension observed in humans. Male, 15-month-old transgenic rats were fed 0.15% indole-3-carbinol (I3C) chow to slowly induce renin-dependent hypertension over a 6-week period. Systolic blood pressure significantly increased, eventually reaching 200 mmHg by the end of the study period. In contrast, transgenic rats fed a control diet without I3C did not show significant changes in blood pressure (145 mmHg at the end of study). Hypertension was associated with cardiac, aortic, and renal hypertrophy as well as increased collagen deposition in the left ventricle and kidney of the I3C-treated rats. Additionally, rats with hypertension showed reduced savings from prior spatial memory training when tested on the hippocampus-dependent Morris swim task. Motor and sensory functions were found to be unaffected by induction of hypertension. Taken together, these data indicate a profound effect of hypertension not only on the cardiovascular-renal axis but also on brain systems critically important for learning and memory. Future use of this model and approach may empower a more accurate investigation of the influence of aging on the systems responsible for cardiovascular, renal, and neurological health.


Subject(s)
Behavior, Animal , Blood Pressure , Brain/physiopathology , Cytochrome P-450 CYP1A1/metabolism , Hypertension/physiopathology , Hypertension/psychology , Renin-Angiotensin System , Renin/metabolism , Spatial Learning , Animals , Blood Pressure/genetics , Cytochrome P-450 CYP1A1/genetics , Disease Models, Animal , Hypertension/chemically induced , Hypertension/genetics , Indoles , Locomotion , Male , Promoter Regions, Genetic , Rats, Inbred F344 , Rats, Transgenic , Renin/genetics , Renin-Angiotensin System/genetics , Time Factors
17.
J Chem Theory Comput ; 15(5): 3134-3152, 2019 May 14.
Article in English | MEDLINE | ID: mdl-30916955

ABSTRACT

The Automatic Rhodopsin Modeling (ARM) protocol has recently been proposed as a tool for the fast and parallel generation of basic hybrid quantum mechanics/molecular mechanics (QM/MM) models of wild type and mutant rhodopsins. However, in its present version, input preparation requires a few hours long user's manipulation of the template protein structure, which also impairs the reproducibility of the generated models. This limitation, which makes model building semiautomatic rather than fully automatic, comprises four tasks: definition of the retinal chromophore cavity, assignment of protonation states of the ionizable residues, neutralization of the protein with external counterions, and finally congruous generation of single or multiple mutations. In this work, we show that the automation of the original ARM protocol can be extended to a level suitable for performing the above tasks without user's manipulation and with an input preparation time of minutes. The new protocol, called a-ARM, delivers fully reproducible (i.e., user independent) rhodopsin QM/MM models as well as an improved model quality. More specifically, we show that the trend in vertical excitation energies observed for a set of 25 wild type and 14 mutant rhodopsins is predicted by the new protocol better than when using the original. Such an agreement is reflected by an estimated (relative to the probed set) trend deviation of 0.7 ± 0.5 kcal mol-1 (0.03 ± 0.02 eV) and mean absolute error of 1.0 kcal mol-1 (0.04 eV).

18.
PLoS One ; 13(6): e0198256, 2018.
Article in English | MEDLINE | ID: mdl-29870545

ABSTRACT

Enzastaurin is a Protein Kinase C-ß selective inhibitor that was developed to treat cancers. Protein Kinase C-ß is an important enzyme for a variety of neuronal functions; in particular, previous rodent studies have reported deficits in spatial and fear-conditioned learning and memory with lower levels of Protein Kinase C-ß. Due to Enzastaurin's mechanism of action, the present study investigated the consequences of Enzastaurin exposure on learning and memory in 12-month-old Fischer-344 male rats. Rats were treated daily with subcutaneous injections of either vehicle or Enzastaurin, and behaviorally tested using the spatial reference memory Morris Water Maze. Rats treated with Enzastaurin exhibited decreased overnight retention and poorer performance on the latter testing day, indicating a mild, but significant, memory impairment. There were no differences during the probe trial indicating that all animals were able to spatially localize the platform to the proper quadrant by the end of testing. RNA isolated from the hippocampus was analyzed using Next Generation Sequencing (Illumina). No statistically significant transcriptional differences were noted. Our findings suggest that acute Enzastaurin treatment can impair hippocampal-based learning and memory performance, with no effects on transcription in the hippocampus. We propose that care should be taken in future clinical trials that utilize Protein Kinase C-ß inhibitors, to monitor for possible cognitive effects, future research should examine if these effects are fully reversible.


Subject(s)
Aging/metabolism , Behavior, Animal/drug effects , Indoles/adverse effects , Memory Disorders , Memory/drug effects , Protein Kinase C beta/antagonists & inhibitors , Aging/genetics , Animals , Indoles/pharmacology , Male , Memory Disorders/chemically induced , Memory Disorders/enzymology , Protein Kinase C beta/genetics , Protein Kinase C beta/metabolism , Rats , Rats, Inbred F344
20.
J Infect Dis ; 218(5): 748-756, 2018 07 24.
Article in English | MEDLINE | ID: mdl-29684148

ABSTRACT

Background: Respiratory syncytial virus (RSV) disease has no effective treatment. JNJ-53718678 is a fusion inhibitor with selective activity against RSV. Methods: After confirmation of RSV infection or 5 days after inoculation with RSV, participants (n = 69) were randomized to JNJ-53718678 75 mg (n = 15), 200 mg (n = 17), 500 mg (n = 18), or placebo (n = 17) orally once daily for 7 days. Antiviral effects were evaluated by assessing RSV RNA viral load (VL) area under the curve (AUC) from baseline (before the first dose) until discharge, time-to-peak VL, duration of viral shedding, clinical symptoms, and quantity of nasal secretions. Results: Mean VL AUC was lower for individuals treated with different doses of JNJ-53718678 versus placebo (203.8-253.8 vs 432.8 log10 PFUe.hour/mL). Also, mean peak VL, time to peak VL, duration of viral shedding, mean overall symptom score, and nasal secretion weight were lower in each JNJ-53718678-treated group versus placebo. No clear exposure-response relationship was observed. Three participants discontinued due to treatment-emergent adverse events of grade 2 and 1 electrocardiogram change (JNJ-53718678 75 mg and 200 mg, respectively) and grade 2 urticaria (placebo). Conclusions: JNJ-53718678 at all 3 doses substantially reduced VL and clinical disease severity, thus establishing clinical proof of concept and the compound's potential as a novel RSV treatment. Clinical trials registration: ClinicalTrials.gov: NCT02387606; EudraCT number: 2014-005041-41.


Subject(s)
Antiviral Agents/administration & dosage , Imidazolidines/administration & dosage , Indoles/administration & dosage , Respiratory Syncytial Virus Infections/drug therapy , Respiratory Syncytial Virus, Human/drug effects , Administration, Oral , Adolescent , Adult , Antiviral Agents/pharmacology , Drug-Related Side Effects and Adverse Reactions/epidemiology , Drug-Related Side Effects and Adverse Reactions/pathology , Female , Healthy Volunteers , Humans , Imidazolidines/pharmacology , Indoles/pharmacology , Male , Middle Aged , Placebos/administration & dosage , Respiratory Syncytial Virus Infections/pathology , Respiratory Syncytial Virus Infections/prevention & control , Respiratory Syncytial Virus, Human/isolation & purification , Treatment Outcome , Viral Load , Virus Shedding , Young Adult
SELECTION OF CITATIONS
SEARCH DETAIL
...