Forced enhancer-promoter rewiring to alter gene expression in animal models

Transcriptional enhancers can be in physical proximity of their target genes via chromatin looping. The enhancer at the β-globin locus (locus control region [LCR]) contacts the fetal-type (HBG) and adult-type (HBB) β-globin genes during corresponding developmental stages. We have demonstrated previously that forcing proximity between the LCR and HBG genes in cultured adult-stage erythroid cells can activate HBG transcription. Activation of HBG expression in erythroid cells is of benefit to patients with sickle cell disease. Here, using the β-globin locus as a model, we provide proof of concept at the organismal level that forced enhancer rewiring might present a strategy to alter gene expression for therapeutic purposes. Hematopoietic stem and progenitor cells (HSPCs) from mice bearing human β-globin genes were transduced with lentiviral vectors expressing a synthetic transcription factor (ZF-Ldb1) that fosters LCR-HBG contacts. When engrafted into host animals, HSPCs gave rise to adult-type erythroid cells with elevated HBG expression. Vectors containing ZF-Ldb1 were optimized for activity in cultured human and rhesus macaque erythroid cells. Upon transplantation into rhesus macaques, erythroid cells from HSPCs expressing ZF-Ldb1 displayed elevated HBG production. These findings in two animal models suggest that forced redirection of gene-regulatory elements may be used to alter gene expression to treat disease.

Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation

Over the last 3 decades ATP-dependent chromatin remodelers have been thought to recognize chromatin at the level of single nucleosomes rather than higher-order organization of more than one nucleosome. We show the yeast ISW1a remodeler has such higher-order structural specificity, as manifested by large allosteric changes that activate the nucleosome remodeling and spacing activities of ISW1a when bound to dinucleosomes. Although the ATPase domain of Isw1 docks at the SHL2 position when ISW1a is bound to either mono- or di-nucleosomes, there are major differences in the interactions of the catalytic subunit Isw1 with the acidic pocket of nucleosomes and the accessory subunit Ioc3 with nucleosomal DNA. By mutational analysis and uncoupling of ISW1a's dinucleosome specificity, we find that dinucleosome recognition is required by ISW1a for proper chromatin organization at promoters; as well as transcription regulation in combination with the histone acetyltransferase NuA4 and histone H2A.Z exchanger SWR1.

Nano-enabled biosensing systems for intelligent healthcare: towards COVID-19 management

Biosensors are emerging as efficient (sensitive and selective) and affordable analytical diagnostic tools for early-stage disease detection, as required for personalized health wellness management. Low-level detection of a targeted disease biomarker (pM level) has emerged extremely useful to evaluate the progression of disease under therapy. Such collected bioinformatics and its multi-aspects-oriented analytics is in demand to explore the effectiveness of a prescribed treatment, optimize therapy, and correlate biomarker level with disease pathogenesis. Owing to nanotechnology-enabled advancements in sensing unit fabrication, device integration, interfacing, packaging, and sensing performance at point-of-care (POC) has rendered diagnostics according to the requirements of disease management and patient disease profile i.e. in a personalized manner. Efforts are continuously being made to promote the state of art biosensing technology as a next-generation non-invasive disease diagnostics methodology. Keeping this in view, this progressive opinion article describes personalized health care management related analytical tools which can provide access to better health for everyone, with overreaching aim to manage healthy tomorrow timely. Considering accomplishments and predictions, such affordable intelligent diagnostics tools are urgently required to manage COVID-19 pandemic, a life-threatening respiratory infectious disease, where a rapid, selective and sensitive detection of human beta severe acute respiratory system coronavirus (SARS-COoV-2) protein is the key factor.

Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling

Nucleosomes are the fundamental building blocks of chromatin that regulate DNA access and are composed of histone octamers. ATP-dependent chromatin remodelers like ISW2 regulate chromatin access by translationally moving nucleosomes to different DNA regions. We find that histone octamers are more pliable than previously assumed and distorted by ISW2 early in remodeling before DNA enters nucleosomes and the ATPase motor moves processively on nucleosomal DNA. Uncoupling the ATPase activity of ISW2 from nucleosome movement with deletion of the SANT domain from the C terminus of the Isw2 catalytic subunit traps remodeling intermediates in which the histone octamer structure is changed. We find restricting histone movement by chemical crosslinking also traps remodeling intermediates resembling those seen early in ISW2 remodeling with loss of the SANT domain. Other evidence shows histone octamers are intrinsically prone to changing their conformation and can be distorted merely by H3-H4 tetramer disulfide crosslinking.

Domain-focused CRISPR screen identifies HRI as a fetal hemoglobin regulator in human erythroid cells

Increasing fetal hemoglobin (HbF) levels in adult red blood cells provides clinical benefit to patients with sickle cell disease and some forms of β-thalassemia. To identify potentially druggable HbF regulators in adult human erythroid cells, we employed a protein kinase domain-focused CRISPR-Cas9-based genetic screen with a newly optimized single-guide RNA scaffold. The screen uncovered the heme-regulated inhibitor HRI (also known as EIF2AK1), an erythroid-specific kinase that controls protein translation, as an HbF repressor. HRI depletion markedly increased HbF production in a specific manner and reduced sickling in cultured erythroid cells. Diminished expression of the HbF repressor BCL11A accounted in large part for the effects of HRI depletion. Taken together, these results suggest HRI as a potential therapeutic target for hemoglobinopathies.

Geospatial distribution of metal(loid)s and human health risk assessment due to intake of contaminated groundwater around an industrial hub of northern India

The study focused on analyzing concentrations of metal(loid)s, their geospatial distribution in groundwater around an industrial hub of northern India. Human health risk posed due to the intake of contaminated groundwater was also evaluated. For this, 240 samples were assayed using inductively coupled plasma emission spectrophotometer. For risk assessment, the methodology proposed by US Environmental Protection Agency was adopted. Geometric mean of Al, As, Mo, Cd, Co, Cr, Fe, Mn, Ni, Pb, Se, and Zn was 193.13, 27.35, 4.22, 2.85, 92.81, 14.97, 271.78, 25.76, 54.75, 19.50, 16.94, and 1830.27 μg/l, respectively. Levels of Al (84%), As (63%), Ni (63%), Pb (49%), and Se (41%) exceeded the Bureau of Indian Standards (BIS). Principal component analysis is accounted for ~ 88% of the total variance and reflected pollution loads of Al, As, Mo, Cr, Fe, Se, and Pb in the groundwater. Based on it, four sources of metal(loid)s, namely geogenic (34.55%), mixed (industrial and agricultural, 26.76%), waste dumping (15.31%), and industrial (11.25%) were identified. Semi-variogram mapping model demonstrated significant geospatial variations of the metal(loid)s. Hazard index (HI) suggested potential non-carcinogenic risks to the inhabitants due to As, Al, Ni, Se, and Pb, which were the largest contributors. Based on maximum concentrations of metal(loid)s, HI for child and adult was above unity. Arsenic was identified as the most hazardous pollutant that may have chronic carcinogenic health implications. At western side of study area, carcinogenic health risks exceeded critical threshold of 1 × 10^-4, indicating that As posed health risks to residents by intake of groundwater.

Nucleosome mobilization by ISW2 requires the concerted action of the ATPase and SLIDE domains

The ISWI family of ATP-dependent chromatin remodelers represses transcription by changing nucleosome positioning. The interactions with extranucleosomal DNA and the requirement of a minimal length of extranucleosomal DNA by ISWI mediate the spacing of nucleosomes. ISW2 from Saccharomyces cerevisiae, a member of the ISWI family, has a conserved domain called SLIDE (SANT-like ISWI domain), whose binding to extranucleosomal DNA ~19 bp from the edge of nucleosomes is required for efficiently pushing DNA into nucleosomes and maintaining the unidirectional movement of nucleosomes, as reported here. Loss of SLIDE binding does not perturb ATPase domain binding to the SHL2 site of nucleosomes or its initial movement of DNA inside of nucleosomes. ISW2 has therefore two distinct roles in mobilizing nucleosomes, with the ATPase domain translocating and moving DNA inside nucleosomes, and the SLIDE domain facilitating the entry of linker DNA into nucleosomes.

Neonatal exposure to phenobarbital potentiates schizophrenia-like behavioral outcomes in the rat

Previous work has indicated an association between seizures early in life and increased risk of psychiatric disorders, including schizophrenia. However, because early-life seizures are commonly treated with antiepileptic drugs (AEDs) such as phenobarbital, the possibility that drug treatment may affect later-life psychiatric outcomes needs to be evaluated. We therefore tested the hypothesis that phenobarbital exposure in the neonatal rat increases the risk of schizophrenia-like behavioral abnormalities in adulthood. Thus, in this study, we examined the effects of a single acute neonatal exposure to phenobarbital on adult behavioral outcomes in the rat neonatal ventral hippocampal (nVH) lesion model of schizophrenia. We compared these outcomes to those in rats a) without nVH lesions and b) with nVH lesions, without phenobarbital. The tasks used for behavioral evaluation were: amphetamine-induced locomotion, prepulse inhibition, elevated plus-maze, and novel object recognition task. We found that neonatal phenobarbital treatment (in the absence of nVH lesions) was sufficient to disrupt sensorimotor gating (as tested by prepulse inhibition) in adulthood to an extent equivalent to nVH lesions. Additionally, neonatal phenobarbital exposure enhanced the locomotor response to amphetamine in adult animals with and without nVH lesions. Our findings suggest that neonatal exposure to phenobarbital can predispose to schizophrenia-like behavioral abnormalities. Our findings underscore the importance of examining AED exposure early in life as a potential risk factor for later-life neuropsychiatric abnormalities in clinical populations.

Steroidal feedback on photoperiodic induction of testicular growth and development in two bird species

Present study was performed to demonstrate the effect of exogenous administration of testosterone propionate on photoperiodic induction of testicular growth and development in brahminy myna (Sturnus pagodarum) and baya weaver (Ploceus philippinus). Two groups of brahminy myna and baya weaver (n=5 each) were exposed to 15L:9D (group-I) and 9L:15D (group-II), and received 30 microg of TP bird(-1) for 15 days. Then, the photoperiod was reversed; the one receiving 15L was exposed to 9L and vice versa. Observations on body mass and testis volume were taken at the beginning and at 15 days interval. In brahminy myna, a significant change in body mass occurred under 9L:15D, transfer to 15L:9D, but not under 15L:9D group, transfer to 9L:15D. Also, testes were stimulated under 15L:9D transferred to 9L:15D, but not under 9L:15D transferred to 15L:9D. In baya weaver, body mass increased under 15L:9D and 9L:15D for first 15 days and was maintained until the end of the experiment. Testes enlarged gradually in both groups (15L:9D and 9L:15D transfer to vice versa), but it regressed in 15L:9D group, transferred to 9L:15D after 45 days. Taken together it appears that body mass response indicates the photoperiodic effect and gonadal response indicates the hormonal effect. Finally results conclude that the photoperiod and circulating testosterone levels feedback on to hypothalamus regulates reproductive cycle in these birds.

Response to complete and skeleton photoperiods in subtropical male house sparrow, Passer domesticus (Linnaeus)

To examine the importance of the inductive light period of a skeleton photoperiod in relation to the endogenous circadian rhythm of photoinducibility mediating photoperiodic induction, P. domesticus were exposed for 28 weeks to a series of skeleton photoperiods, viz. 6L:4D:1L:13D, 6L:6D:1L:11D. 6L:8D:1L:9D and 6L:14D:1L:3D. The inductive effects of 1 hr light pulse at night varied depending on the time of its placement. To compare the inductive effects of complete and its corresponding skeleton photoperiods, birds in the second experiment were subjected for 20 weeks to 12L:12D and 6L:5D:1L:12D given daily or interposed on alternate days with constant darkness (12L:12D/DD and 6L:5D:1L:12D/DD). There was a difference in the rate and magnitude of response between the complete and skeleton photoperiods. It appears that the subtropical house sparrow uses photoperiodic strategy in regulation of its seasonal testicular responses similar to that is reported for its temperate population.

Neonatal ventral hippocampus lesion leads to reductions in nerve growth factor inducible-B mRNA in the prefrontal cortex and increased amphetamine response in the nucleus accumbens and dorsal striatum

Converging evidence in schizophrenia suggests prefrontal cortical neuronal deficits that correlate with exaggerated subcortical dopamine (DA) functions: Excitotoxic lesion of the ventral hippocampus (VH) in neonatal rats is widely considered a putative animal model of schizophrenia as they lead to characteristic post-pubertal emergence of behavioral and cognitive abnormalities suggesting a developmental change in the neural circuits comprising the prefrontal cortex (PFC) and subcortical DA. Nerve growth factor inducible-B (NGFI-B, also known as Nur77), an orphan nuclear receptor and transcriptional regulator, is constitutively expressed in the target structures of DA pathways. It acts as an immediate early gene with rapid modulation of its mRNA expression by stress, DA and antipsychotic drugs. The present study assessed the effects of neonatal VH (nVH) lesion and amphetamine treatment on the expression of NGFI-B mRNA in pre- and post-pubertal rats. Sprague-Dawley rat pups received bilateral injection of ibotenic acid or phosphate buffered saline in VH at postnatal (PD) 7. At PD35 and PD56, groups of sham and lesioned animals were administered with D-amphetamine (1.5 mg/kg) or saline and killed 20 min later. In situ hybridization analyses showed that the basal level of NGFI-B mRNA in saline-treated lesioned rats was significantly reduced in the medial PFC (mPFC) and cingulate cortex (CC) only at post-pubertal (PD56) age. No significant difference in NGFI-B mRNA levels was seen in the dorsal striatum or nucleus accumbens (NAcc). Amphetamine treatment increased the expression of NGFI-B mRNA in the mPFC, CC, striatum and NAcc in both control and lesioned animals of both ages. Interestingly, however, striatal and NAcc regions of lesioned rats showed a significantly greater effect of amphetamine at PD56. The data suggest that nVH lesions lead to delayed changes in PFC gene expression along with functional DAergic hyperactivity in subcortical regions.

Alterations in signal transduction cascade in young and adult rat brain and lymphocytes

Signal transduction cascade, phosphoinositide metabolism, and protein kinases were studied from discrete areas of rat brain like cerebral hemispheres, cerebellum, brainstem, and diencephalon as well as lymphocytes isolated from three different age groups of rats; young (1 month), young adult (3-4 months), and adult (12 months) rats. The activities of protein kinase A, protein kinase C, phospholipase A(2) and phospholipase C and inositol 1, 4, 5-triphosphate, diacylglycerol, cyclic adenosine monophosphate contents were assayed from different brain areas and lymphocytes from these three age group rats. An upregulatory effect on the signal transduction system was observed from 1 month to 3-4-month age group, whereas, the brain tissue and lymphocytes of adult rats showed lower contents and activities of signal transduction components as compared to young adults. In view of the established 'cross talk' between signal transduction system, the present results suggests that molecular/cellular changes in brain and immune cells signal transduction pathway along with neuronal cell loss may contribute to age-related decline in nervous as well as immune system functions.

Effect of diabetes on calcium/calmodulin dependent protein kinase-II from rat brain

Changes in the protein levels and activity of Ca2+/Calmodulin dependent protein kinase II (CaM kinase II) level were studied in cytosolic and particulate fractions from cerebral hemisphere, cerebellum, brain stem, thalamus and hypothalamus regions of rat brain after 4 and 12 weeks of induction of diabetes. Streptozotocin induced diabetes, resulted in pronounced increase of CaM kinase II activity as determined by the kinase activity assay. The total amount of enzyme protein (alpha-subunit specific) also showed increase as revealed by western blotting. Parallel studies were also made in age matched control rats and insulin treated diabetic rats. The increase in CaM kinase II activity was more pronounced in the 12 weeks diabetic group. Insulin treatment of diabetic rats, resulted in recovery of enzyme activity near to control values from majority of the brain regions studied. The expression of alpha-subunit specific CaM kinase II correlates with the enzyme activity in the diabetic rat brain.

Impact of diabetes on CNS: role of signal transduction cascade

Diabetic neuropathy is the most common secondary complication of diabetes mellitus. Several pathogenetic factors have been proposed for diabetic neuropathy. The present investigation was undertaken to study different components of signal transduction from discrete brain regions from streptozotocin-induced diabetic rats. Rats were sacrificed after 1 and 3 months of induction of diabetes, and a control group was also studied in parallel to ascertain the specificity of diabetes-associated changes. Blood glucose level and protein content of discrete brain regions were also estimated. Signal transduction cascade components like protein kinase A, protein kinase C, cAMP, phospholipase C, phospholipase A2, diacylglycerol and inositol phosphate levels were assayed in control and diabetic groups of rats. Significant attenuation in phosphoinositide metabolism along with activation of protein kinase activities were observed. These findings provide evidence to suggest a mechanism linking changes in signal transduction cascade, which is observed in 1- and 3-month diabetic rats, which ultimately leads to development of diabetic neuropathy.

Role of opioidergic and monoaminergic neurotransmission in the GnRH release mechanism of EBP-primed OVX rats

We examined the effect of intracerebroventricular (i.c.v.) administration of mu-opioid agonist, morphine, and its antagonist naloxone followed by morphine on the activities of monoamine-metabolizing enzymes, namely tyrosine hydroxylase (TH) and monoamine oxidase (MAO) along with adenosinetriphosphatase (Na+, K+ -ATPase), the enzyme responsible for the maintenance of ionic gradients across the membrane, in seven discrete regions of brain from estrogen- and progesterone-primed ovariectomized rats. TH activity decreased after morphine treatment in some areas such as the median eminence-arcuate region (ME-ARC), the amygdala, and the thalamus, showing statistically significant change. MAO activity increased in all the areas studied, but more appreciable change was observed in medial preoptic area (mPOA), the ME-ARC region, and the cortex. Pronounced increase in Na+, K+ -ATPase enzyme activity was observed after the drug treatment. Naloxone given prior to morphine injection resulted in recovery of the enzyme activities in most of the areas studied. Our study may provide insights into the precise opioidergic modulation of gonadotropin releasing hormone (GnRH) release mechanisms through the involvement of monoaminergic system, elucidating the basis of various neuronal dysfunctions and their management in opioid addicts.

The impact of diabetes on CNS. Role of bioenergetic defects

To address the problem of the pathogenesis in diabetic neuropathy, rats were made diabetic by streptozotocin administration, and discrete brain regions, such as cortex, cerebellum, brainstem, thalamus, and hypothalamus, were sampled for assay of activities of electron transport chain complexes I-IV at 1 and 3 mo after induction of diabetes. Significant decrease was seen in activities of dinitrophenylhydrazine DNPH-coenzyme Q reductase (complex I), coenzyme Q cytochrome-c reductase (complex III), and cytochrome-c oxidase (complex IV) from discrete brain regions with more pronounced changes in complex I. The decline in the complex I, III, and IV activity was more severe in the 3-mo group. Succinate dehydrogenase (SDH) coenzyme Q reductase (complex II), which is an enzyme shared by tricarboxylic acid (TCA) cycle and electron transport chain, showed a significant increase under the same set of conditions. These results suggest that the bioenergetic impairment has an important role in the pathophysiology of diabetes.

Alterations in free radical scavenger system profile of type I diabetic rat brain

The activities of the enzymes related to glutathione synthesis, degradation, and functions as well as reactive oxygen scavenging enzymes were analyzed in different brain regions, such as cerebral hemisphere, cerebellum, brainstem, thalamus, and hypothalamus after 1 and 3 mo of streptozotocin-induced diabetes in rats. Parallel studies were also made in age-matched control rats and insulin-treated diabetic rats. The content of glutathione (GSH) and its synthesizing enzyme gamma-glutamylcystein synthetase and also superoxide dismutase (SOD) and catalase activities (reactive oxygen scavenging enzymes) were significantly decreased from almost all the brain regions studied. However, glutathione peroxidase (GPx), glutathione reductase (GR), glutathione S-transferase (GST), gamma-glutamyl transpeptidase (gamma-GTP), and glutamine synthetase (GS) activities were increased in the diabetic rat brain. Insulin treatment to the diabetic rats resulted in partial to full recovery in these enzymes activities. The present results emphasize the potentially serious alterations of brain free radical scavenger system in uncontrolled Type I diabetes.

Effect of starvation and insulin-induced hypoglycemia on oxidative stress scavenger system and electron transport chain complexes from rat brain, liver, and kidney

Considerable evidence suggests that oxidative stress plays an important role in tissue damage associated with hypoglycemia and other metabolic disorders. The altered brain neurotransmitters metabolism, cerebral electrolyte contents, and impaired blood-brain barrier function may contribute to CNS dysfunction in hypoglycemia. The present study elucidates the effect of starvation and insulin-induced hypoglycemia on the free radical scavanger system--reduced glutathione (GSH) content, glutathione S-transferase (GST), glutathione peroxidase (GPx), glutathione reductase (GR), gamma-glutamyl transpeptidase (gamma-GTP), gamma-glutamyl cystein synthetase (gamma-GCS), catalase and superoxide dismutase (SOD), and mitochondrial electron transport chain (ETC) complexes I-IV from three different regions of rat brain, namely cerebral hemispheres (CH), cerebellum (CB), and brainstem (BS). Peripheral organs, such as liver and kidney, were also studied. Significant changes in these enzymic activities were observed. The analysis of such alterations is important in ultimately determining the basis of neuronal dysfunction during metabolic stress conditions, such as hypoglycemia, and also defining the nature of these changes may help to develop therapeutic means to cure metabolically stressed tissues.

Effect of a composite Indian herbal preparation, CIHP(III) on avoidance learning during endurance performance of rats

A nine week cross over study (5 weeks drug administration and 4 weeks withdrawal) was performed to see the effect of a composite Indian herbal preparation (CIHP III), viz. Mentat, on avoidance learning during endurance performance of albino rats. Runimex, a circular runway was used for this purpose. The number of stimuli viz. electrical shock of 10 mv, in drug treated rats at an oral dose of 47.86 mg/100 g body wt/single dose/day for 5 days were significantly reduced as compared to rats not taking any drug. The number of stimuli decreased significantly when the drug was started in the control group. No change in avoidance learning was observed over the period of 9 weeks in another group of rats. Results indicate significant improvement in avoidance learning during endurance performance due to the intake of CIHP(III).

Effect of age on susceptibility of carcinogen benzidine-hydrochloride

Susceptibility of carcinogen (benzidine hydrochloride) was checked by degranulation technique in rats of three different (young, adult and old) age groups. The dose response curves of these three different groups showed different per cent degranulation. Comparative data of dose response of benzidine hydrochloride observed on the basis of RNA/Protein ratio basis showed that old animals were more susceptible to carcinogens than young and adult animals.