Biology subjects

Lee, E. J.

Publications and source records attributed to Lee, E. J..

27 records · Page 2Linked to original sources

bioRxiv2021

Spatiotemporal characterization of glial cell activation in an Alzheimer's disease model by spatially resolved transcriptome

The pathophysiological changes that occur with the progression of Alzheimers disease (AD) are well known, but understanding the spatiotemporal heterogeneity of the brain is needed. Here, we investigated the spatially resolved transcriptome in a 5XFAD AD model of different ages to understand regional changes at the molecular level. We identified early alterations in the white matter (WM) of the AD model before the definite accumulation of amyloid plaques in the gray matter (GM). Changes in the early stage of the disease were involved primarily in glial cell activation in WM, whereas the changes were prominent in the later stage of pathology in GM. We confirmed that disease-associated microglia (DAM) and astrocyte (DAA) signatures also showed initial changes in WM and that activation spreads to GM. Trajectory inference using microglial gene sets revealed the subdivision of DAMs with different spatial patterns. Taken together, these results help to understand the spatiotemporal changes associated with reactive glial cells as a major pathophysiology of AD and provide information for diagnosis and prognosis based on spatiotemporal changes caused by amyloid accumulation in AD.

neuroscience↗

bioRxiv2021

Odor Blocking Of Stress

Scents have been employed for millennia to allay fear and stress, but whether they do so is poorly understood. In response to fear and stress, hypothalamic corticotropin releasing hormone neurons (CRHNs) induce increases in blood stress hormones. Here, we find that certain structurally and perceptually dissimilar odorants can block mouse stress hormone responses to three potent stressors: physical restraint, predator odor, and male-male social confrontation. Both odorants activate GABAergic inhibitory neurons presynaptic to CRHNs in the hypothalamic ventromedial nucleus (VMH). Stimulation of those neurons inhibits restraint-induced activation of CRHNs and stress hormone increase, mimicking a blocking odorant. Conversely, their silencing prevents odorant blocking of both responses. Notably, we also observed odor blocking of stressor activation in neurons presynaptic to CRHNs in the bed nucleus of the stria terminalis (BNST). Together, these findings indicate that selected odorants can indeed block stress responses, and that odor blocking can occur via two routes: a direct route in which blocking odor signals directly inhibit CRHNs and an indirect route in which they inhibit stressor activation of neurons presynaptic to CRHNs and prevent them from transmitting stress signals to CRHNs.

neuroscience↗

bioRxiv2021

Extracellular vesicles induce aggressive phenotype of luminal breast cancer cells by PKM2 phosphorylation

The aerobic glycolysis is a hallmark of cancer glucose metabolism. Several studies have suggested that cancer-derived extracellular vesicles (EVs) can modulate glucose metabolism in adjacent cells and promote disease progression. Here we suggest that EVs originated from cancer cell with highly glycolytic activity can modulate glucose metabolism in the recipient cancer cells with relative low glycolytic activity, and further induce cell proliferation. Two types of breast cancer cell lines with different levels of glycolytic activity, MDA-MB-231 of a claudin low-type breast cancer cell and MCF7 of luminal type breast cancer cell, were selected and co-cultured using indirect co-culture system such as transwell system or microfluidic system. Glucose uptake of the recipient MCF7 cells was markedly increased after co-culture with MDA-MB-231 cells. MCF7 cells after co-culture with MDA-MB-231-tdTomato cells represented multiple tdTomato signal inside the cell, which proved that EVs originated from MDA-MB-231-tdTomato were transferred to MCF7 cell. In addition, serine phosphorylation of PKM2 necessary for tumorigenesis was highly activated, and tyrosine phosphorylation of PKM2 suggesting activated aerobic glycolysis was also increased in the co-cultured MCF7 cells. Proteomic profiling of the co-cultured MCF7 cells revealed the proliferation and dedifferentiation of MCF7 cells, and further confirmed epithelial-mesenchymal transition (EMT), which is a key phenomenon for cancer metastasis. In the transcriptomic analysis, glycolysis increased in co-cultured MCF7 cells, and the component analysis of genes associated with glycolysis revealed that the next major component after cytoplasm was extracellular exosome. Proteomic analysis of EVs revealed that there were important proteins in the EV such as EGFR, ERBB2 and MAPK for phosphorylating PKM2. This phenomenon suggests the potential for aggressive cancer cells to affect other cancer cells through EV mediators.

cancer biology↗

bioRxiv2020

Inverse oculomotor responses of achiasmatic mice expressing a transfer-defective Vax1 mutant

In binocular animals that exhibit stereoscopic visual responses, the axons of retinal ganglion cells (RGCs) connect to brain areas bilaterally by forming a commissure called the optic chiasm (OC). Ventral anterior homeobox 1 (Vax1) contributes to formation of the OC, acting endogenously in optic pathway cells and exogenously in growing RGC axons. Here, we generated Vax1AA/AA mice expressing the Vax1AA mutant, which is incapable of intercellular transfer. We found that RGC axons cannot take up Vax1AA protein from Vax1AA/AA mouse optic stalk (OS) cells, of which maturation is delayed, and fail to access the midline. Consequently, RGC axons of Vax1AA/AA mice connect exclusively to ipsilateral brain areas, resulting in the reduced visual acuity and the abnormal oculomotor responses. Together, our study provides physiological evidences for the necessity of intercellular transfer of Vax1 and the importance of the bilateral RGC axon projection in visuomotor responses.

developmental biology↗

bioRxiv2020

Synergistic effect of deoxynucleosides and AAV gene therapy for thymidine kinase 2 deficiency

Autosomal recessive thymidine kinase 2 (TK2) mutations causes TK2 deficiency, which typically manifests as a progressive and fatal mitochondrial myopathy in infants and children. Treatment with deoxycytidine and thymidine ameliorates mitochondrial defects and extends lifespan of Tk2 knock-in mouse (TK2-/-); however, efficacy is limited by age- and tissue-dependent expression of the cytosolic enzymes Tk1 and Dck. Thus, therapies aimed at systemic restoration of TK2 activity are needed. Here, we demonstrate that delivery of human TK2 cDNA to Tk2-/- mice using AAV9 efficiently rescued Tk2 activity in all the tissues tested except kidney, delayed disease onset, and increased lifespan. Sequential treatment of Tk2-/- mice with AAV9 first followed by AAV2 at different ages allowed us to reduce the viral dose while further prolonging the lifespan. Furthermore, addition of deoxycytidine and deoxythymidine supplementation to AAV9 + AAV2 treated Tk2-/- mice dramatically improved mtDNA copy numbers in liver and kidney, animal growth, and lifespan. These data indicate that combined pharmacological and gene therapies may be highly efficacious for human TK2 deficiency.

genetics↗

bioRxiv2020

Targeted Eicosanoid Profiling Reveals MicroRNA-155 Shifts PGE2/PGD2 Balance Towards Oncogenic State

microRNA-155 is a strong oncogenic microRNAs with multiple functions. To reveal its novel function in cancer metabolism, we performed a targeted metabolomic analysis of icosanoids, the key metabolites of inflammation-related carcinogenesis. We found miR-155-depleted cells expressed unbalanced prostaglandins, especially in PGE2 and PGD2. Subsequent analysis of primary cancer cells and 20 TNBC specimen indicated a positive correlation between miR-155 and PGE2/PGD2 ratio. Mechanistically, miR-155 controls the prostaglandin shift by up-regulating PGE2-producing enzymes PTGES/PTGES2 and down-regulating PGD2-producing enzyme PTGDS. Further analysis showed that the up-regulation of PTGES2 is driven by miR-155-cMYC axis whereas PTGES is transactivated by miR-155-KLF4 axis, indicating a dual-regulatory mode for the metabolic enzyme expression drives a shift in PGE2/PGD2 balance. Lastly, we show the miR-155-driven cellular proliferation is significantly restored by the siRNA of PTGES1/2, of which expression also correlates with patients survival. Taken altogether, our study reveals an unprecedented oncogenic function of miR-155 on prostaglandin regulation.

cancer biology↗

bioRxiv2020

Out-of-register parallel β-sheets and antiparallel β-sheets coexist in 150 kDa oligomers formed by Aβ(1-42)

We present solid-state NMR measurements of {beta}-strand secondary structure and inter-strand organization within a 150 kDa oligomeric aggregate of the 42-residue variant of the Alzheimers amyloid-{beta} peptide (A{beta}(1-42)). This oligomer is characterized by a structure that cannot be explained by any previously proposed model for aggregated A{beta}. We build upon our previous report of a {beta}-strand spanned by residues 30-42, which arranges into an antiparallel {beta}-sheet. New results presented here indicate that there is a second {beta}-strand formed by residues 11-24. We show negative results for NMR experiments designed to reveal antiparallel {beta}-sheets formed by this {beta}-strand. Remarkably, we show that this strand is organized into a parallel {beta}-sheet despite the co-existence of an antiparallel {beta}-sheet in the same structure. In addition, the in-register parallel {beta}-sheet commonly observed for amyloid fibril structure does not apply to residues 11-24 in the 150 kDa oligomer. Rather, we present evidence for an inter-strand registry shift of 3 residues that alternates in direction between adjacent molecules along the {beta}-sheet. We corroborated this unexpected scheme for {beta}-strand organization using multiple 2-dimensional NMR and 13C-13C dipolar recoupling experiments. Our findings indicate a previously unknown assembly pathway and inspire a suggestion as to why this aggregate does not grow to larger sizes.

biochemistry↗

bioRxiv2018

Connect-seq to superimpose molecular on anatomical neural circuit maps

The mouse brain contains ~100 million neurons interconnected in a vast array of neural circuits. The identities and functions of individual neuronal components of most circuits are undefined. Here we describe a method, termed Connect-seq, which combines retrograde viral tracing and single cell transcriptomics to uncover the molecular identities of upstream neurons in a specific circuit and the signaling molecules they use to communicate. Connect-seq can generate a molecular map that can be superimposed on a neuroanatomical map to permit molecular and genetic interrogation of how the neuronal components of a circuit control its function. Application of this method to hypothalamic neurons controlling physiological responses to fear and stress reveal subsets of upstream neurons that express diverse constellations of signaling molecules and can be distinguished by their anatomical locations.

neuroscience↗

bioRxiv2017

Newly identified relatives of botulinum neurotoxins shed light on their molecular evolution

The evolution of bacterial toxins is a central question to understanding the origins of human pathogens and infectious disease. Through genomic data mining, we traced the evolution of the deadliest known toxin family, clostridial neurotoxins, comprised of tetanus and botulinum neurotoxins (BoNT). We identified numerous uncharacterized lineages of BoNT-related genes in environmental species outside of Clostridium, revealing insights into their molecular ancestry. Phylogenetic analysis pinpointed a sister lineage of BoNT-like toxins in the gram-negative organism, Chryseobacterium piperi, that exhibit distant homology at the sequence level but preserve overall domain architecture. Resequencing and assembly of the C. piperi genome confirmed the presence of BoNT-like proteins encoded within two toxin-rich gene clusters. A C. piperi BoNT-like protein was validated as a novel toxin that induced necrotic cell death in human kidney cells. Mutagenesis of the putative active site abolished toxicity and indicated a zinc metalloprotease-dependent mechanism. The C. piperi toxin did not cleave common SNARE substrates of BoNTs, indicating that BoNTs have diverged from related families in substrate specificity. The new lineages of BoNT-like toxins identified by computational methods represent evolutionary missing links, and suggest an origin of clostridial neurotoxins from ancestral toxins present in environmental bacteria.\n\nSignificance statementThe origins of bacterial toxins that cause human disease is a key question in our understanding of pathogen evolution. To explore this question, we searched genomes for evolutionary relatives of the deadliest biological toxins known to science, botulinum neurotoxins. Genomic and phylogenetic analysis revealed a group of toxins in the Chryseobacterium piperi genome that are a sister lineage to botulinum toxins. Genome sequencing of this organism confirmed the presence of toxin-rich gene clusters, and a predicted C. piperi toxin was shown to induce necrotic cell death in human cells. These newly predicted toxins are missing links in our understanding of botulinum neurotoxin evolution, revealing its origins from an ancestral family of toxins that may be widespread in the environment.

bioinformatics↗