bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome‐wide mapping of large organized heterochromatin domains reveals hotspots of epigenetic and transcriptional changes associated with myeloid differentiation and acute myeloid leukemia (565.1)
Authors: Grigoryev Sergei , Salzberg Anna , Berg Arthur , Harris‐Becker Abigail , Loughran Thomas , Claxton David 
Published: June 2021

Acute myeloid leukemia (AML) is a highly malignant blood cancer with the lowest survival rate among the four major types of leukemia. The objective of this study was to conduct a genome‐wide mapping of the epigenetic states in the normal myeloid and leukemia cells and to identify the chromosomal domains undergoing epigenetic and transcriptional destabilization. We hypothesized that large‐scale epigenetic changes manifested by heterochromatin markers, histone H3 di‐ and tri‐methylation at lysine 9, may interfere with transcription and promote AML. We used ChIP‐sequencing to conduct a detailed whole‐genomic characterization of H3(K9) methylation. For this study, we used primary AML myeloblasts, normal granulocytes, CD34+ hematopoietic progenitors, and cultured K562 cells as an epigenomic reference. Using ChIP‐sequencing, we mapped genome‐wide topography of histone H3(K9) methylation and its transitions in the process of myeloid differentiation and characterized spatial and functional relationship between histone H3(K9) methylation and transcriptional changes in AML. Aided by application of genome‐wide bioinformatic analysis using a hidden Markov model we were able to reveal multiple associations of chromatin modification topographies with transcription in leukemia and specific chromosomal domains undergoing both epigenetic and transcriptional changes. We expect that the observed epigenomic transitions may serve for AML prognosis as well as targets for its epigenetic therapy.Grant Funding Source: Supported by Pennsylvania Department of Health
A mitochondrial bioenergetic hypothesis for autism spectrum disorder (570.3)
Authors: Chalkia Dimitra , Derbeneva Olga , Lvova Maria , Lakatos Anita , Leipzig Jeremy , Hadley Dexter , Hakonarson Hakon , Wallace Douglas 
Published: June 2021

We are testing the hypothesis that a significant proportion of the risk for developing Autism Spectrum Disorder (ASD) is the result of inheriting partial defects in genes for mitochondrial bioenergetics. To test our hypothesis, first we determined if ancient human mtDNA variation is associated with ASD risk. To accomplish this, we used two independently generated and genotyped cohorts, the Autism Genetic Resource Exchange (AGRE) and the CHOP Autism Case‐Control (ACC). These pre‐existing mtDNA SNP data were generated by Illumina chip analysis. We deduced the mtDNA haplogroups for all samples and utilized cases and controls that harbored European haplogroups. Generalized linear modeling analysis of the AGRE cohort suggests that J mitochondrial lineage and T2 haplogroup are risk factors for ASD (J lineage: OR = 2.22, CI=1.21‐4.05, p=0.0094; T2 haplogroup: OR= 1.79, CI= 1.26‐2.55, p=0.0012). Congruently, in the ACC cohort we found that haplogroup T2 is strongly associated with ASD and represents a risk factor (OR=1.45, CI=1.04‐2.03, p=0.0284). These data demonstrate that ASD risk is modified by mtDNA haplogroup thus supporting our mitochondrial bioenergetic hypothesis of ASD.Grant Funding Source: Supported by Simons Foundation Autism Research Initiative and National Institutes of Health
Lipoic acid induced weight loss (575.6)
Authors: Sanchez‐Cardenas Marina 
Published: June 2021

Lipoic Acid Induced Weight Loss Over 1.4 billion adults worldwide are considered overweight or obese. Obesity occurs when a person’s body initiates a cycle in which glucose imbalances promote lipogenesis and increases oxidative stress which may cause certain diseases. Prior research has demonstrated that Lipoic Acid (LA) has the ability to act as an insulin mimic as well as an antioxidant. Its insulin mimic capabilities allow it to regulate glucose levels and its antioxidant potential may protect against oxidative damage. However, very little research has been done on its possible beneficial effects in combating obesity. This study aims to demonstrate how supplementation with LA assists in weight loss with no change in life style. The results showed a significant decrease in body mass (in weight) in mice supplemented with LA when compared to those that were not exposed to LA. This study proposes the initial steps to facilitating the prevention of obesity and its related health complications through supplementation.Grant Funding Source: Supported by Title V STEM
Distinct gene expression pattern of osteoblastic cells derived from bone marrow and calvaria of osteoporotic rats (576.1)
Authors: Bombonato‐Prado Karina , de Azevedo Fernanda , Semeghini Mayara , Rosa Adalberto , Beloti Márcio , Siéssere Selma 
Published: June 2021

Osteoporosis is one of the most important diseases associated with aging. The aim of this study was to determine if there is a distinct expression of genes associated with osteoblast differentiation in bone marrow mesenchymal stem cells (MSCs) and calvaria osteoblastic cells (COs) of rats induced to osteoporosis through ovariectomy. Cells from bone marrow and calvaria of control and osteoporotic rats were cultured in osteogenic medium and divided into four different groups: calvaria/control (CC); calvaria/osteoporosis (CO); bone marrow/control (MC) and bone marrow/osteoporosis (MO). After 3, 7 and 10 days, real‐time RT‐PCR for key bone markers was carried out in quintuplicate (n=5) and data were compared by Kruskal‐Wallis and Mann‐Whitney tests (p<0.05). Alkaline phosphatase and runt‐related transcription factor 2 expressions were significantly increased in MO and decreased in CO in all periods. Osteocalcin expression was significantly increased in MO at 7 and 10 days, and decreased in CO in all periods. The ratio of receptor activator of nuclear factor kappa‐B ligand /osteoprotegerin expression was significantly decreased in MO at 7 and 10 days and in CO in all periods. Our results show a distinct gene expression pattern for MSCs and COs after osteoporosis induction and suggest that MSCs undergo a metabolic adjustment in order to compensate the effects of estrogen decrease in this osteoporosis model.Grant Funding Source: Supported by FAPESP
GRK5 knockout mice created by TALEN‐mediated gene targeting (576.2)
Authors: Min Kwan‐Sik , Nanjidsuren Tsevelmaa , Park Chae‐Won , Seo Eun‐Bi , Kang Myung‐Hwa 
Published: June 2021

G protein‐coupled receptor kinase 5 (GRK5) is one of the seven GRK family members whose primary function is to desensitize G protein‐coupled receptors (GPCRs). In recently, GRK5 deficiency has been linked to early Alzheimer disease (AD), but the mechanism by which GRK5 deficiency may accelerate to AD pathogenesis remains elusive. The GRK5 mRNA is expressed widely in brain and peripheral tissues, with highest expression evident heart, lung, and placenta. In cellular model systems, GRK5 can phosphorylate several neuronal GPCRs including ß2 adrenergic, M2‐muscarinic, secretin, angiotensin AT1, and thyroid stimulating hormone receptors. Transcription activator‐like effector nucleases (TALENs) are programmable nucleases that join FokI endonucleases with the modular DNA‐binding domain of TALEs and highly effective in inducing mutations at specific genome loci. TALEN‐mediated mutagenesis in zygotes is a potential alternative to conventional gene targeting in mice. In the presented study, we report the generation of mice with genetic knockout of the GRK gene using TALENs. We designed TALEN vectors for exon 1, 3 and 5 of mouse GRK5 gene and tested their ability to alter the each surrogate vector in 293T cells. We prepared of mRNAs for the linearized TALEN using the mMessage mMachine T7 Ultra kit. mRNAs (4ng/μl) was injected into cytoplasm of 180 one‐cell embryos. After incubation for 24 hours, the selected two‐cell embryos transferred into the oviduct of seven pseudopregnant C57BL/6 mice. We confirmed the genotype of Fo mice by sequencing and T7E1 assay.Grant Funding Source: Supported by BK 21 plus program, the Ministry of Education, Science and Technology, Korea
Impact of resistance training on testosterone levels in individuals with moderate to severe chronic obstructive pulmonary disease (576.3)
Authors: Kuzel Aaron , Kaelin Mark 
Published: June 2021

Purpose: Individuals with chronic obstructive pulmonary disease (COPD) exhibit decreased airflow and loss of diffusion area in the respiratory tree. Furthermore, current research suggests that low testosterone is a significant risk factor for these individuals. As testosterone levels decrease, the number and intensity of disease exacerbations significantly increases. The purpose of this study is to determine the impact of resistance training on testosterone levels in patients with COPD.Methods: Bellarmine University’s Institutional Review Board approved the study in October 2013. Six individuals (1 male, 5 females) with moderate to severe COPD enrolled in an 11 week resistance training program. Average FEV1% and pack years of the subjects are 57 + 17 and 59.3 + 43.5, respectively. Subjects initial evaluation consisted of the Senior Fitness Test (SFT), the St. George’s Respiratory Questionnaire (SGRQ) and salivary assays of testosterone to determine baseline functional mobility, health related quality of life and free testosterone levels.Results: Initial evaluations revealed below average functional mobility in these subjects compared to their age‐related peers in the following tests: Chair Stand Test ‐21% + 0.14%, Arm Curl ‐7% + 0.14%, Back Scratch ‐14% + 0.35, 8ft Up and Go Test ‐22% + 0.15%, 6‐minute walk ‐22% + 0.33%. Scores for the SGRQ came in at 37.74 points higher than those reported by healthy respondents. At the time of submission, initial testosterone collection remains in progress.Conclusions: Results of the SFT and SGRQ clearly demonstrate impaired functional mobility and self‐reported quality of life in this population.
Cerebrospinal fluid sphingolipids and acid sphingomyelinase change with beta amyloid levels in Alzheimer’s disease (576.5)
Authors: Ormseth Cora , Chiang Jiarong , Arakaki Xianghong , Harrington Michael , Fonteh Alfred 
Published: June 2021

Background: Sphingolipids (SP) and sphingomyelinase (SMase) play a role in amyloid processing. Thus, their cerebrospinal fluid (CSF) levels may change with beta amyloid concentration in Alzheimer’s disease (AD).Methods: Using liquid chromatography tandem mass spectrometry, we identified SP classes and species in two CSF fractions: nanometer‐sized particles (NP) representative of brain membrane metabolism and the NP‐depleted supernatant fluid (SF) representative of interstitial metabolism. We compared SP levels and SMase activity between 70 cognitively healthy CH study participants, 40 participants with mild cognitive impairment (MCI), and 29 with probable AD.Results: CSF fractions are differentially enriched with the SP classes and molecular species. In AD, SP metabolism was altered in both CSF fractions. The NP fraction had the greatest change in sphingomyelin (SM) species: concentrations of three species [SM(34:2), SM(34:1), SM(35:1)] were lower in AD and three [SM(34:2), SM(40:1), SM(41:2)] were lower in MCI compared with CH controls. Acid SMase activity decreased by 44 % in AD and correlated positively with the amyloid β42 levels in CSF from CH controls.Conclusions: Altered SP metabolism in dementia combined with decreased acid SMase activity and its lost association with CSF amyloid β42 levels in AD underscore these as potential disease biomarkers, and acid SMase as a target for AD research.Grant Funding Source: L.K. Whittier and the Helen Posthuma Foundations
Influence of environmental factors on the activity of enzymes of purine nucleotide metabolism (577.1)
Authors: Ilderbayev Oralbek , Abduldayeva Aigul , Nurmukanov Dulat , Rachyzhanova Saule 
Published: June 2021

There is an experimental study of combined influence of 2 Gy dose gamma‐radiation and chrysotile‐asbest dust in the remote period on activity of enzymes of the purine’s nucleotides metabolism: 5’‐nucleotidase (5’‐NT), adenosindesaminase (ADA) and adenilatdesaminase (AMF‐ase) in different organs and tissues.Research results showed that combined effect of chrysotile dust and ionizing radiation in the remote period causes increase of 5'‐NT, ADA, AMF‐ase activity in the liver. In case of conjuncted action 5'‐NT, ADA, AMF‐ase’s activity increases in 1.6; in 2.5 and in 6.0 times accordingly. The activity of 5'‐NT, AMF‐ase in adrenal medulla and lymphocytes of animals’ peripheral blood credibly increased. The ADA’s activity had not changed.Taking into account the obtained results we can say that adrenal medulla tissues and lymphocytes of blood after the combined action of radiation and dust responses considerable intensification of the processes of anabolism and catabolism in the remote period, which marked as the secondary character of changes.The combined action of radiation and asbest dust causes considerable interruption of purine metabolism enzymes’ level, which characterized by strain of adaptive‐compensate mechanisms after the influence of dust‐radiation factor.
Novel ligands for human pregnane X receptor differentially regulate CYP3A4 promoter activity (579.1)
Authors: Banerjee Monimoy , Chen Taosheng 
Published: June 2021

Human pregnane X receptor (hPXR) also known as xenobiotic sensing nuclear receptor (SXR) is a member of nuclear receptor family and a critical regulator of the expression of genes involved in drug metabolism and clearance. The pregnane X receptor (PXR) regulates drug metabolism by regulating the expression of drug‐metabolizing enzymes such as cytochrome P450 3A4 (CYP3A4), which is involved in the metabolism of >50% of clinically prescribed drugs. It also plays an important role in cancer drug resistance by regulating the expression of MDR1. Activity of PXR can be modulated by agonists or antagonists. There are several agonists for PXR have been reported but the reported antagonists for PXR are limited. Therefore, there is still need to develop novel ligands for PXR. Here, we report the virtual screening of ~25,000 natural product derivatives from the ZINC database using the MOE docking software tool against the PXR‐Rifampicin complex X‐ray crystal structure. Our screening resulted in identification of compounds based on the lowest S scores which measures binding energy. All of these ligands were docked within the ligand binding pocket forming interactions with several hydrophobic amino acid residues. Further, all these main compounds and analogs were synthesized to verify with biological assays. We found that the compounds that bind directly to PXR, as revealed in an intrinsic tryptophan fluorescence assay, modulate CYP3A4 promoter activity differentially in HepG2 cells. Mutational analysis and docking studies showed that these compounds bind broadly in the ligand binding pocket but interact with different amino acid residues. The mechanism of binding and the functional group of the ligands that are important for distinguishing agonists/antagonists were also investigated.Grant Funding Source: Supported by the ALSAC, St. Jude CRH, NIH, NCI.
Circadian clock control of hepatic metabolism via nuclear receptor SHP (579.3)
Authors: Lee Sang Min , Zhang Yuxia , Tsuchiya Hiroyuki , Smalling Rana , Jetten Anton , Wang Li 
Published: June 2021

Objective: In mammals, circadian rhythms are essential for coordinating the timing of various metabolic processes. SHP interacts with many nuclear receptors to regulate the expression of multiple metabolic genes in the liver. This study investigates the role of SHP in controlling the rhythmicity of metabolites and liver clock genes. Methods: RNA‐sequencing (RNA‐seq) and qPCR were used to examine the rhythmic expression of liver clock and metabolic genes in Shp+/+ and Shp−/− mice on a C57BL/6 background (n=3‐5/group). GC/MS was used to identify the oscillation of metabolites in serum and liver. In vitro assays include: transient transfection, luciferase reporter assay, ChIP assay, gel‐shift assay, Co‐IP, Western blots, adenovirus overexpression and siRNA knockdown. Results: The transcriptomics and metabolomics analyses revealed a global alteration in the rhythm of metabolic genes and intermediate metabolites in glucose, lipid, amino acid, and bile acid homeostasis in the Shp−/− mice. Several components of the liver clock including Npas2 and Rorα/γ were sharply induced in Shp−/− liver. SHP inhibited Npas2 transcription through direct interaction with Rorγ to repress Rorγ transactivation of the Npas2 promoter and by directly interacting with Rev‐erbα to enhance its inhibition on the Npas2 promoter activation by Rorα. Conversely, Npas2 controlled the circadian rhythm of SHP by binding rhythmically to the SHP promoter. The Shp−/− mice exhibited higher locomotor activity which was consistent with their increased Pgc‐1α and energy metabolism. Conclusions: These novel findings identified SHP as an integral component of the liver circadian network.Grant Funding Source: Supported by AHA post‐doc fellowship (S.L), and DK080440 and AHA GIA (L.W).
Three polymorphisms and susceptibility to breast cancer development: a Turkish study population (58.1)
Authors: Bayram Banu , Özkurt Mete , Erkasap Nilüfer , İhtiyar Enver , Erkasap Serdar 
Published: June 2021

Objective: Genetic variations like polymorphisms underlie differences in our susceptibility to diseases. According to our literature reviews we have found three polymorphisms which contribute to breast cancer development from different pathways. However genetic variations of polymorphism vary between populations according to gene pools, life style and gene‐environment interactions. Based on these findings we aimed to investigate the association between p53 gene codon 72 polymorphism, MTHFR gene C677T polymorphism and PAI‐1 gene 4G/5G polymorphism and breast cancer in a Turkish study population.Material and Methods: Genomic DNA was extracted from 100 women (52 with breast cancer and 48 controls) in the study. PCR technique was used to amplify extracted DNA with proper primers for each polymorphism. For identifying genotypes PCR products were assessed with UV transilluminator by being exposed to agarose gel electrophoresis.Results: According to genotype distributions and allele frequencies of three polymorphisms there were no statistical differences between breast cancer patients and control group.Conclusion: As a conclusion of our study we may assert that p53 gene codon 72, MTHFR gene C677T and PAI‐1 gene 4G/5G polymorphisms should not be considered as susceptibility factors for breast cancer development. However polymorphism studies with larger numbers of the population provides more meaningful results. The significance of our result remains to be further investigated in different and even larger populations, combined with other polymorphisms considered as susceptibility factors for breast cancer.
An innovative role of thyroid receptor β in triple‐negative breast cancer (58.4)
Authors: Gelsomino Luca , Guowei Gu , Kyle Covington , Babarinde Toyin , Zhou Jianlin , Rechoum Yassine , Corona‐Rodriguez Arnoldo , O'Malley Bert , Mangelsdorf David , Minna John , Webb Paul , Ando' Sebastiano , Fuqua Suzanne 
Published: June 2021

Background Currently endocrine treatment is the most effective therapeutic strategy in patients affected by estrogen‐receptor (ERα) positive breast cancer cells. In contrast, treatment of triple‐negative breast cancer (TNBC) is a major clinical problem due to the lack of useful therapeutic targets. Microarray analysis demonstrated that THRβ is one of the most expressed receptors in TNBC cells. Aim of our study was to evaluate THRβ’s role in TNBC.Experimental Design and Methods Microarray and predicition analysis, qRT‐PCR, THRβ shRNAs for stable clones using pGIPZ lentiviral vectors, MTT, soft‐agar assays, immunoprecipitation and proximity ligation assays.Results Statistical analysis using a published dataset1 showed that patients with low THRβ have a poor clinical outcome. ShTHRβ stable clones were resistant to chemodrugs (doxorubicin and docetaxel), while specific THRβ agonists increased sensitivity to these agents. Interestingly, THRβ agonists through post‐traslational modifications enhanced ERα expression and activity rendering the cells sensitive to the inhibitory effects of the antiestrogen tamoxifen on growth.Conclusion THRβ might represent a predicitive and prognostic marker in TNBC patients. THRβ agonists can enhance chemosensitivity and by restoring ERα expression make cells targetable for hormone therapy.
Development and characterization of a multi‐drug resistant Her‐2/neu positive breast cancer cell line (58.6)
Authors: Tang Yuan , Lamberti Giuseppina , Curran Elizabeth , Kiani Mohammad , Wang Bin 
Published: June 2021

Research has shown that ~ 25% ‐ 30% breast cancers overexpress Her‐2/neu receptor. The major problem in the management of Her‐2/neu overexpressed breast cancer is its multi‐drug resistantce (MDR). P‐glycoprotein (P‐gp) mediated MDR has been recognized as one of the major mechanisms in drug resistance in breast cancer. Therefore, developing a breast cancer cell line with both Her‐2/neu and MDR positive becomes necessary.Dual positive breast cancer cell line was developed by transfection of the multidrug resistance gene (MDR1 gene) to human breast carcinoma cell line BT‐474 (Her‐2/neu +), followed by selection on clochicine. The presence of membrane protein Her‐2 and P‐gp were tested by immunohistochemical methods. The multidrug resistance was tested by the treatment efficacy of doxorubicin.The overexpression of p‐glycoprotein in multidrug resistant cells and the presence of membrane protein Her‐2 were confirmed by immunocytochemistry staining as well as Western Blot. Fluorescence imaging study showed that drug resistant BT‐474 cells uptake much more Her‐2/neu tagged nanoparticles than non‐tagged ones. Cytotoxicity test shows that the transfected BT‐474 is 10 times more resistant than its drug sensitive counterpart.In conclusion, we have successfully developed and characterized Her‐2/neu and MDR dual positive breast cancer cell line which can serve as a platform for testing new therapeutic strategies.Grant Funding Source: Supported by Susan G. Komen for the Cure foundation