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  • 1
    In: The Journal of Neuroscience, Society for Neuroscience, Vol. 38, No. 44 ( 2018-10-31), p. 9600-9613
    Abstract: Fear learning and memory are vital for livings to survive, dysfunctions in which have been implicated in various neuropsychiatric disorders. Appropriate neuronal activation in amygdala is critical for fear memory. However, the underlying regulatory mechanisms are not well understood. Here we report that Neogenin, a DCC (deleted in colorectal cancer) family receptor, which plays important roles in axon navigation and adult neurogenesis, is enriched in excitatory neurons in BLA (Basolateral amygdala). Fear memory is impaired in male Neogenin mutant mice. The number of cFos + neurons in response to tone-cued fear training was reduced in mutant mice, indicating aberrant neuronal activation in the absence of Neogenin. Electrophysiological studies show that Neogenin mutation reduced the cortical afferent input to BLA pyramidal neurons and compromised both induction and maintenance of Long-Term Potentiation evoked by stimulating cortical afferent, suggesting a role of Neogenin in synaptic plasticity. Concomitantly, there was a reduction in spine density and in frequency of miniature excitatory postsynaptic currents (mEPSCs), but not miniature inhibitory postsynaptic currents, suggesting a role of Neogenin in forming excitatory synapses. Finally, ablating Neogenin in the BLA in adult male mice impaired fear memory likely by reducing mEPSC frequency in BLA excitatory neurons. These results reveal an unrecognized function of Neogenin in amygdala for information processing by promoting and maintaining neurotransmission and synaptic plasticity and provide insight into molecular mechanisms of neuronal activation in amygdala. SIGNIFICANCE STATEMENT Appropriate neuronal activation in amygdala is critical for information processing. However, the underlying regulatory mechanisms are not well understood. Neogenin is known to regulate axon navigation and adult neurogenesis. Here we show that it is critical for neurotransmission and synaptic plasticity in the amygdala and thus fear memory by using a combination of genetic, electrophysiological, behavioral techniques. Our studies identify a novel function of Neogenin and provide insight into molecular mechanisms of neuronal activation in amygdala for fear processing.
    Type of Medium: Online Resource
    ISSN: 0270-6474 , 1529-2401
    Language: English
    Publisher: Society for Neuroscience
    Publication Date: 2018
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  • 2
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2011
    In:  Proceedings of the National Academy of Sciences Vol. 108, No. 35 ( 2011-08-30)
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 108, No. 35 ( 2011-08-30)
    Abstract: To address these issues, we examined the ubiquitination and degradation of ERα and ERβ in the hippocampal CA1 region of female rats following long-term deprivation or natural aging. In addition, we determined the role of CHIP in ubiquitination and degradation of ERα/ERβ and examined whether changes in ERα/ERβ were correlated with changes in the sensitivity of the hippocampal CA1 to neuroprotection during natural aging. Here, we show that ERα in the rat hippocampal CA1 region but not the uterus undergoes enhanced interaction with the enzyme CHIP and Bag-1 that leads to its ubiquitination/proteasomal degradation following long-term deprivation. Estrogen treatment initiated before but not after long-term deprivation prevented the enhanced ERα-CHIP/Bag-1 interaction and ERα ubiquitination/degradation, and it was fully neuroprotective against GCI. Administration of a proteasomal inhibitor or antisense oligonucleotides to CHIP reversed the long-term deprivation-induced down-regulation of ERα. Important questions are whether these observations in the long-term deprivation model are relevant to natural aging and whether there is an age-related critical period for neuroprotection in the hippocampus. Here, we show that these observations do extend to natural aging, because aged (24-mo-old) rats showed enhanced CHIP/Bag-1 interaction, ubiquitination, and degradation of both hippocampal ERα and ERβ as well as, importantly, a correlated loss of neuroprotection against GCI. In contrast, estrogen administration to middle-aged (10-mo-old) rats was still capable of exerting neuroprotection. As a whole, the study provides support for a critical period for neuroprotection of the hippocampus. Previous work by our laboratory and others revealed that long-term estrogen deprivation leads to a loss of neuroprotection in animal models of focal and global cerebral ischemia (GCI). Furthermore, we recently showed that the loss of neuroprotection of the hippocampal CA1 region was correlated with a significant decrease in the α- but not β-subunit of the ER ( 2 ). This decrease in ERα and estrogen sensitivity was tissue-specific, because ERα did not decrease in the uterus following long-term deprivation and the uterus, unlike the hippocampal CA1 region, remained sensitive to the action of estrogen. The mechanisms underlying the decrease of ERα in the hippocampal CA1 region following long-term deprivation are unknown. Previous work in breast cancer cells demonstrated that the enzyme CHIP binds and promotes degradation of the unliganded ERα via the ubiquitin-proteasome degradation pathway ( 3 , 4 ). Because long-term deprivation results in very low serum estrogen levels, we hypothesized that the reduced levels of ERα in the hippocampal CA1 following long-term deprivation may be attributable to CHIP-mediated proteasomal degradation of ERα. Furthermore, because long-term deprivation is only a model of aging, it was important to determine whether ERα levels and estrogen sensitivity of the hippocampal CA1 region are similarly attenuated with natural aging. The beneficial effects of estrogen, or 17β-estradiol, replacement on cardiovascular disease and neurodegenerative diseases, such as stroke and Alzheimer's disease, are well known ( 1 ). However, the National Institutes of Health's Women's Health Initiative (WHI), a 15-y study of more than 12,000 postmenopausal women, surprisingly failed to observe a protective effect of hormone replacement therapy on the cardiovascular system and reported a small but significant increase in risk for stroke and dementia. The average age of subjects in the WHI study was 63 y, far past the onset of menopause. It has been suggested that there may be a “critical period” for the beneficial protective effect of estrogen on the brain and that the hormone may need to be administered around menopause or earlier to observe a beneficial effect on the cardiovascular and neural systems. Here, we provide evidence supporting the existence of a critical period for the neuroprotective effect of estrogen in the hippocampal CA1 region, a region critical for cognition, learning, and memory. We further demonstrate a potential mechanism for the critical period by demonstrating that an enzyme called carboxyl terminus of Hsc70-interacting protein (CHIP) binds and promotes degradation of the α-subunit of the estrogen receptor (ER) in the female rat hippocampal CA1 region following long-term estrogen deprivation and natural aging. We show that in periods of low circulating estrogen levels, the unliganded ER displays increased binding to CHIP, leading to its ubiquitination, a posttranslational modification ( Fig. P1 ). We also show enhanced interaction of ER and CHIP with the protein, Bcl-2–associated athanogene 1 (Bag-1), which has been implicated in the delivery of ubiquitinated proteins to the proteasome, a cellular organelle where protein degradation occurs. The proteasomal degradation of ER is proposed to underlie decreased sensitivity of the hippocampus to the hormone and a corresponding loss of neuroprotection that was observed after long-term deprivation and in aged rats ( Fig. P1 ).
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2011
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  • 3
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2015
    In:  Proceedings of the National Academy of Sciences Vol. 112, No. 47 ( 2015-11-24), p. 14670-14675
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 112, No. 47 ( 2015-11-24), p. 14670-14675
    Abstract: Noninvasive prenatal testing (NIPT) using sequencing of fetal cell-free DNA from maternal plasma has enabled accurate prenatal diagnosis of aneuploidy and become increasingly accepted in clinical practice. We investigated whether NIPT using semiconductor sequencing platform (SSP) could reliably detect subchromosomal deletions/duplications in women carrying high-risk fetuses. We first showed that increasing concentration of abnormal DNA and sequencing depth improved detection. Subsequently, we analyzed plasma from 1,456 pregnant women to develop a method for estimating fetal DNA concentration based on the size distribution of DNA fragments. Finally, we collected plasma from 1,476 pregnant women with fetal structural abnormalities detected on ultrasound who also underwent an invasive diagnostic procedure. We used SSP of maternal plasma DNA to detect subchromosomal abnormalities and validated our results with array comparative genomic hybridization (aCGH). With 3.5 million reads, SSP detected 56 of 78 (71.8%) subchromosomal abnormalities detected by aCGH. With increased sequencing depth up to 10 million reads and restriction of the size of abnormalities to more than 1 Mb, sensitivity improved to 69 of 73 (94.5%). Of 55 false-positive samples, 35 were caused by deletions/duplications present in maternal DNA, indicating the necessity of a validation test to exclude maternal karyotype abnormalities. This study shows that detection of fetal subchromosomal abnormalities is a viable extension of NIPT based on SSP. Although we focused on the application of cell-free DNA sequencing for NIPT, we believe that this method has broader applications for genetic diagnosis, such as analysis of circulating tumor DNA for detection of cancer.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2015
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  • 4
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 380, No. 6643 ( 2023-04-28)
    Abstract: Thousands of genetic variants have been associated with human diseases and traits through genome-wide association studies (GWASs). Translating these discoveries into improved therapeutics requires discerning which variants among hundreds of candidates are causally related to disease risk. To date, only a handful of causal variants have been confirmed. Here, we leverage 100 million years of mammalian evolution to address this major challenge. RATIONALE We compared genomes from hundreds of mammals and identified bases with unusually few variants (evolutionarily constrained). Constraint is a measure of functional importance that is agnostic to cell type or developmental stage. It can be applied to investigate any heritable disease or trait and is complementary to resources using cell type– and time point–specific functional assays like Encyclopedia of DNA Elements (ENCODE) and Genotype-Tissue Expression (GTEx). RESULTS Using constraint calculated across placental mammals, 3.3% of bases in the human genome are significantly constrained, including 57.6% of coding bases. Most constrained bases (80.7%) are noncoding. Common variants (allele frequency ≥ 5%) and low-frequency variants (0.5% ≤ allele frequency 〈 5%) are depleted for constrained bases (1.85 versus 3.26% expected by chance, P 〈 2.2 × 10 −308 ). Pathogenic ClinVar variants are more constrained than benign variants ( P 〈 2.2 × 10 −16 ). The most constrained common variants are more enriched for disease single-nucleotide polymorphism (SNP)–heritability in 63 independent GWASs. The enrichment of SNP-heritability in constrained regions is greater (7.8-fold) than previously reported in mammals and is even higher in primates (11.1-fold). It exceeds the enrichment of SNP-heritability in nonsynonymous coding variants (7.2-fold) and fine-mapped expression quantitative trait loci (eQTL)–SNPs (4.8-fold). The enrichment peaks near constrained bases, with a log-linear decrease of SNP-heritability enrichment as a function of the distance to a constrained base. Zoonomia constraint scores improve functionally informed fine-mapping. Variants at sites constrained in mammals and primates have greater posterior inclusion probabilities and higher per-SNP contributions. In addition, using both constraint and functional annotations improves polygenic risk score accuracy across a range of traits. Finally, incorporating constraint information into the analysis of noncoding somatic variants in medulloblastomas identifies new candidate driver genes. CONCLUSION Genome-wide measures of evolutionary constraint can help discern which variants are functionally important. This information may accelerate the translation of genomic discoveries into the biological, clinical, and therapeutic knowledge that is required to understand and treat human disease. Using evolutionary constraint in genomic studies of human diseases. ( A ) Constraint was calculated across 240 mammal species, including 43 primates (teal line). ( B ) Pathogenic ClinVar variants ( N = 73,885) are more constrained across mammals than benign variants ( N = 231,642; P 〈 2.2 × 10 −16 ). ( C ) More-constrained bases are more enriched for trait-associated variants (63 GWASs). ( D ) Enrichment of heritability is higher in constrained regions than in functional annotations (left), even in a joint model with 106 annotations (right). ( E ) Fine-mapping (PolyFun) using a model that includes constraint scores identifies an experimentally validated association at rs1421085. Error bars represent 95% confidence intervals. BMI, body mass index; LF, low frequency; PIP, posterior inclusion probability.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2023
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  • 5
    In: Brain, Oxford University Press (OUP), Vol. 136, No. 5 ( 2013-5), p. 1432-1445
    Type of Medium: Online Resource
    ISSN: 1460-2156 , 0006-8950
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    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2013
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  • 6
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2016
    In:  Proceedings of the National Academy of Sciences Vol. 113, No. 27 ( 2016-07-05), p. 7661-7666
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 113, No. 27 ( 2016-07-05), p. 7661-7666
    Abstract: The phenomenon of delayed flowering after the application of nitrogen (N) fertilizer has long been known in agriculture, but the detailed molecular basis for this phenomenon is largely unclear. Here we used a modified method of suppression-subtractive hybridization to identify two key factors involved in N-regulated flowering time control in Arabidopsis thaliana , namely ferredoxin-NADP + -oxidoreductase and the blue-light receptor cryptochrome 1 (CRY1). The expression of both genes is induced by low N levels, and their loss-of-function mutants are insensitive to altered N concentration. Low-N conditions increase both NADPH/NADP + and ATP/AMP ratios, which in turn affect adenosine monophosphate-activated protein kinase (AMPK) activity. Moreover, our results show that the AMPK activity and nuclear localization are rhythmic and inversely correlated with nuclear CRY1 protein abundance. Low-N conditions increase but high-N conditions decrease the expression of several key components of the central oscillator (e.g., CCA1 , LHY , and TOC1 ) and the flowering output genes (e.g., GI and CO ). Taken together, our results suggest that N signaling functions as a modulator of nuclear CRY1 protein abundance, as well as the input signal for the central circadian clock to interfere with the normal flowering process.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2016
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  • 7
    In: The Journal of Neuroscience, Society for Neuroscience, Vol. 29, No. 44 ( 2009-11-04), p. 13823-13836
    Abstract: The goal of this study was to elucidate the mechanisms of 17β-estradiol (E 2 ) antioxidant and neuroprotective actions in stroke. The results reveal a novel extranuclear receptor-mediated antioxidant mechanism for E 2 during stroke, as well as a hypersensitivity of the CA3/CA4 region to ischemic injury after prolonged hypoestrogenicity. E 2 neuroprotection was shown to involve a profound attenuation of NADPH oxidase activation and superoxide production in hippocampal CA1 pyramidal neurons after stroke, an effect mediated by extranuclear estrogen receptor α (ERα)-mediated nongenomic signaling, involving Akt activation and subsequent phosphorylation/inactivation of Rac1, a factor critical for activation of NOX2 NADPH oxidase. Intriguingly, E 2 nongenomic signaling, antioxidant action, and neuroprotection in the CA1 region were lost after long-term E 2 deprivation, and this loss was tissue specific because the uterus remained responsive to E 2 . Correspondingly, a remarkable loss of ERα, but not ERβ, was observed in the CA1 after long-term E 2 deprivation, with no change observed in the uterus. As a whole, the study reveals a novel, membrane-mediated antioxidant mechanism in neurons by E 2 provides support and mechanistic insights for a “critical period” of E 2 replacement in the hippocampus and demonstrates a heretofore unknown hypersensitivity of the CA3/CA4 to ischemic injury after prolonged hypoestrogenicity.
    Type of Medium: Online Resource
    ISSN: 0270-6474 , 1529-2401
    Language: English
    Publisher: Society for Neuroscience
    Publication Date: 2009
    detail.hit.zdb_id: 1475274-8
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  • 8
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 106, No. 50 ( 2009-12-15), p. 21230-21235
    Abstract: Due to its numerous environmental extremes, the Tibetan Plateau—the world's highest plateau—is one of the most challenging areas of modern human settlement. Archaeological evidence dates the earliest settlement on the plateau to the Late Paleolithic, while previous genetic studies have traced the colonization event(s) to no earlier than the Neolithic. To explore whether the genetic continuity on the plateau has an exclusively Neolithic time depth, we studied mitochondrial DNA (mtDNA) genome variation within 6 regional Tibetan populations sampled from Tibet and neighboring areas. Our results confirm that the vast majority of Tibetan matrilineal components can trace their ancestry to Epipaleolithic and Neolithic immigrants from northern China during the mid-Holocene. Significantly, we also identified an infrequent novel haplogroup, M16, that branched off directly from the Eurasian M founder type. Its nearly exclusive distribution in Tibetan populations and ancient age ( 〉 21 kya) suggest that M16 may represent the genetic relics of the Late Paleolithic inhabitants on the plateau. This partial genetic continuity between the Paleolithic inhabitants and the contemporary Tibetan populations bridges the results and inferences from archaeology, history, and genetics.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2009
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 9
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 107, No. 49 ( 2010-12-07), p. 21146-21151
    Abstract: Mutations in superoxide dismutase 1 (SOD1) cause familial ALS. Mutant SOD1 preferentially associates with the cytoplasmic face of mitochondria from spinal cords of rats and mice expressing SOD1 mutations. Two-dimensional gels and multidimensional liquid chromatography, in combination with tandem mass spectrometry, revealed 33 proteins that were increased and 21 proteins that were decreased in SOD1 G93A rat spinal cord mitochondria compared with SOD1 WT spinal cord mitochondria. Analysis of this group of proteins revealed a higher-than-expected proportion involved in complex I and protein import pathways. Direct import assays revealed a 30% decrease in protein import only in spinal cord mitochondria, despite an increase in the mitochondrial import components TOM20, TOM22, and TOM40. Recombinant SOD1 G93A or SOD1 G85R , but not SOD1 WT or a Parkinson's disease-causing, misfolded α-synuclein E46K mutant, decreased protein import by 〉 50% in nontransgenic mitochondria from spinal cord, but not from liver. Thus, altered mitochondrial protein content accompanied by selective decreases in protein import into spinal cord mitochondria comprises part of the mitochondrial damage arising from mutant SOD1.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2010
    detail.hit.zdb_id: 209104-5
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  • 10
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2015
    In:  Proceedings of the National Academy of Sciences Vol. 112, No. 42 ( 2015-10-20)
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 112, No. 42 ( 2015-10-20)
    Abstract: TREX1 is an exonuclease that digests DNA in the cytoplasm. Loss-of-function mutations of TREX1 are linked to Aicardi–Goutieres Syndrome (AGS) and systemic lupus erythematosus (SLE) in humans. Trex1 −/− mice exhibit autoimmune and inflammatory phenotypes that are associated with elevated expression of interferon (IFN)-induced genes (ISGs). Cyclic GMP-AMP (cGAMP) synthase (cGAS) is a cytosolic DNA sensor that activates the IFN pathway. Upon binding to DNA, cGAS is activated to catalyze the synthesis of cGAMP, which functions as a second messenger that binds and activates the adaptor protein STING to induce IFNs and other cytokines. Here we show that genetic ablation of cGas in Trex1 −/− mice eliminated all detectable pathological and molecular phenotypes, including ISG induction, autoantibody production, aberrant T-cell activation, and lethality. Even deletion of just one allele of cGas largely rescued the phenotypes of Trex1 −/− mice. Similarly, deletion of cGas in mice lacking DNaseII, a lysosomal enzyme that digests DNA, rescued the lethal autoimmune phenotypes of the DNaseII −/− mice. Through quantitative mass spectrometry, we found that cGAMP accumulated in mouse tissues deficient in Trex1 or DNaseII and that this accumulation was dependent on cGAS. These results demonstrate that cGAS activation causes the autoimmune diseases in Trex1 −/− and DNaseII −/− mice and suggest that inhibition of cGAS may lead to prevention and treatment of some human autoimmune diseases caused by self-DNA.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2015
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
    SSG: 11
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