Biology subjects

Mirzaei, M.

Publications and source records attributed to Mirzaei, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Sex-specific retina-brain signatures link ERα/ERβ imbalance with gliosis in Alzheimer's disease

Women face a twofold higher lifetime risk of Alzheimers disease (AD) than men, yet the mechanisms underlying female-biased vulnerability and sex-specific disease signatures across the retina-brain axis remain unknown. By integrating clinicopathological and proteomic datasets from paired retinal and brain tissues from 182 donors, we identified sex-divergent molecular and pathological features across the AD continuum. Despite comparable retinal and cerebral amyloid and tau burdens between sexes, females exhibited a more severe neuroinflammatory-neurodegenerative phenotype with intensified gliosis and tissue atrophy, whereas males displayed a dominant vasculopathy, marked by increased retinal vascular A{beta}40 deposition, tight-junction disruption, and cerebral amyloid angiopathy. In females, this profile coincided with inflammation-associated estrogen receptor (ER)- remodeling and reduced global and astrocytic-nuclear ER-{beta}, which associated more strongly with cognitive decline than in males. These results indicate that comparable AD proteinopathy is associated with divergent downstream consequences across the retina-brain axis and identify astrocytic ER/ER{beta} imbalance as a sex-linked glial mechanism associated with female vulnerability in AD.

neuroscience↗

bioRxiv2026

Synergistic retinal UCHL1 dysregulation and synaptic vulnerability reflect Alzheimer's disease severity

Synaptic failure predicts cognitive decline in Alzheimers disease (AD), yet its impact and molecular drivers in the human retina remain unclear. Leveraging the retina as an accessible central nervous system (CNS) proxy, we integrated spatially resolved histopathology of retinal cross-sections with ultrastructural, proteomic, and biochemical profiling across independent postmortem cohorts spanning normal cognition, mild cognitive impairment due to AD (MCI), and AD dementia. We uncover early, progressive degeneration of excitatory glutamatergic synapses, evidenced by losses of presynaptic vesicular glutamate transporter 1 (VGLUT1) and synaptophysin, and postsynaptic density protein 95 (PSD95) and N-methyl-D-aspartate receptor subunit 2A (NMDAR2A), accompanied by disruption of synaptic ultrastructure. Retinal synaptic loss tightly associates with local accumulation of amyloid-{beta} 42 (A{beta}42) and immature tau species, heightened oxidative stress, and upregulation of the A{beta}-binding death receptor p75 neurotrophin receptor (p75NTR). Notably, the synapse-enriched deubiquitinase ubiquitin C-terminal hydrolase L1 (UCHL1) is profoundly dysregulated, correlates with synaptic integrity and cognition, and emerges as the strongest retinal predictor of Braak stage and cognitive status in multivariable machine-learning models. Together, these findings position retinal A{beta}/p75NTR-mediated UCHL1 imbalance as a proteostasis-synapse mechanistic hub and candidate biomarker reflecting AD severity.

neuroscience↗

bioRxiv2025

Pre-clinical validation of a novel AAV-mediated gene therapy for KCNV2 retinopathy improves visual function in a mouse model and expression in patient organoids

Voltage-gated (Kv) potassium channels are critical for neuronal physiology, and their dysfunction can lead to serious consequences. For example, mutations in the silent modulatory Kv8.2 subunit are known to cause irreversible inherited blindness (KCNV2 retinopathy). This is a currently incurable condition that causes lifelong visual loss, reduced visual acuity, photoaversion, night blindness and abnormal colour vision, alongside a distinctive supernormal electrophysiological (ERG) retinal response to light. In this study, we demonstrate that AAV-mediated gene replacement therapy delivering a codon-optimised human KCNV2 gene subretinally into Kv8.2 knock-out mice significantly restores retinal function. Treated mice exhibited improved ERG responses and correct expression of KCNV2 and its encoded Kv8.2 protein in photoreceptors. Recovery of visually guided scotopic and photopic optomotor responses to wildtype levels was achieved at lower vector doses, highlighting dose-dependent efficacy. Furthermore, treatment of human retinal organoids derived from a KCNV2 patient iPSC line resulted in substantial Kv8.2 protein rescue. This work provides the first preclinical proof-of-concept for the safety and therapeutic potential of gene therapy for KCNV2 retinopathy, laying a strong foundation for future clinical trials.

neuroscience↗

bioRxiv2025

Patient induced pluripotent stem cells identify specificities of a reticular pseudodrusen phenotype in age-related macular degeneration

BackgroundAge-related macular degeneration (AMD) is a leading cause of vision loss. Reticular pseudodrusen (RPD), deposits on the apical side of the retinal pigment epithelium (RPE), signify a distinctive and critical AMD phenotype. Yet, their molecular basis and relationship to the conventional drusen seen in AMD remain unclear. ResultsWe generated induced pluripotent stem cell-derived RPE cells from a clinically phenotyped cohort comprising only individuals with conventional drusen (AMD/RPD-) or drusen coexisting with RPD (AMD/RPD+). From these cells, we generated single-cell transcriptomics, proteomics, and functional data to identify differences between the two cohorts. We show that AMD/RPD+ RPE cells exhibit enrichment in extracellular matrix (ECM) remodelling, cytoskeletal, and hypoxia-responsive programs, whereas AMD/RPD- RPE cells display a relatively greater representation of mitochondrial and protein homeostasis pathways. Both subtypes engaged pathways classically linked to ageing, including ECM remodelling and mitochondrial function, but differed in the direction and extent of these changes. Expression and protein quantitative trait loci (QTLs) highlight shared genetic influences on mitochondrial and iron-handling pathways, while disease-interacting eQTLs and transcriptome-wide association study identify regulatory signals that are distinctive of the RPD subtype within AMD, including through regulation of ECM. Functionally, all iPSC-derived RPE formed drusen-like deposits in vitro: AMD/RPD-lines generated more basal deposits, whereas AMD/RPD+ cells exhibited greater structural instability under bisretinoid-induced stress. ConclusionsThese findings indicate that AMD with and without RPD represent mechanistically distinct entities and provide novel insight into the molecular mechanisms underlying disease heterogeneity in AMD.

genetics↗

bioRxiv2025

Identification of Chlamydia pneumoniae and NLRP3 inflammasome activation in Alzheimer's disease retina

Chlamydia pneumoniae (Cp), an obligate intracellular bacterium, has been implicated in Alzheimers disease (AD), yet its role in retinal pathology remains unexplored. We analyzed postmortem tissues from 95 human donors and found 2.9-4.1-fold increases in Cp inclusions in AD retinas and brains, with no significant elevation in mild cognitive impairment (MCI). Proteomics revealed dysregulation of retinal and brain bacterial infection-related proteins and NLRP3 inflammasome pathways. NLRP3 expression was markedly elevated in MCI and AD retinas, and its activation was evident by increased N-terminal gasdermin D (NGSDMD) and mature interleukin-1{beta}. Retinal Cp strongly correlated with A{beta}42 and NLRP3 inflammasome components, which tightly linked to cleaved caspase-3-apoptotic and NGSDMD-pyroptotic cell death. Although retinal microgliosis was elevated in AD, Cp-associated microglia were reduced by 62%, suggesting impaired Cp phagocytosis. Higher retinal Cp burden correlated with APOE{varepsilon}4, Braak stage, and cognitive deficit. Machine learning identified retinal Cp or NLRP3 combined with A{beta}42 as strong predictors of AD diagnosis, staging, and cognitive impairment. Our findings suggest that Cp infection contributes to AD dementia but not initiating pathology, whereas early NLRP3 activation may promote disease development, warranting studies on Cps role in AD pathogenesis and early antibiotic or inflammasome-targeted therapies.

neuroscience↗

bioRxiv2024

Epigenetic derepression of H3K9me3 mitigates Alzheimer-related pathology and improves cognition via immunomodulation and Vgf induction

We investigated the role of histone 3 lysine 9 trimethylation (H3K9me3), an epigenetic mechanism involved in the repression of synaptic plasticity and memory-related genes, within aging and Alzheimers disease (AD). Our study reveals that elevated cortical H3K9me3 strongly correlates with cognitive dysfunction in individuals with mild cognitive impairment (MCI) and AD. In old (18 months) and younger (14 months) APPSWE/PS1{Delta}E9 and 3xTg AD mouse models, inhibiting SUV39H1 methyltransferase with ETP69, substantially reduces cerebral H3K9me3 levels and attenuates amyloid-{beta} burden, tau pathology, and gliosis. Administration of ETP69 further promotes dendritic spine formation, leading to rapid and sustained improvements in cognitive function. Proteomics analysis indicates that a significant proportion of dysregulated proteins in the brains of AD-model mice are reversed by ETP69. These proteins are enriched for synaptic plasticity and learning-related pathways. ETP69 exerts its effects through multiple neuroprotective mechanisms, including regulation of neuroinflammation, induction of both blood and cerebral-infiltrating monocytes involved in cerebral A{beta} clearance. Moreover, ETP69 activates brain-derived neurotrophic factor (Bdnf) network, and particularly its downstream effector neurosecretory protein Vgf. These findings support the pharmacological inhibition of H3K9me3-mediated gene silencing to reverse AD-related pathology and cognitive decline.

neuroscience↗

bioRxiv2024

Proteomic Profiling of Mesenchymal Stem Cell-Derived Extracellular Vesicles: Impact of Isolation Methods on Protein Cargo

Extracellular vesicles (EVs) are nanosized vesicles with a lipid bilayer that are secreted by cells and play a critical role in cell-to-cell communication. Despite the promising reports regarding their diagnostic and therapeutic potential, the utilization of EVs in the clinical setting is limited due to insufficient information about their cargo and a lack of standardization in isolation and analysis methods. Considering protein cargos in EVs as key contributors to their therapeutic potency, we conducted a tandem mass tag (TMT) quantitative proteomics analysis of three subpopulations of mesenchymal stem cell (MSC)-derived EVs obtained through three different isolation techniques: ultracentrifugation (UC), high-speed centrifugation (HS), and ultracentrifugation on sucrose cushion (SU). Subsequently, we checked EV marker expression, size distribution, and morphological characterization, followed by bioinformatic analysis. The bioinformatic analysis of the proteome results revealed that these subpopulations exhibit distinct molecular and functional characteristics. The choice of isolation method impacts the proteome of isolated EVs by isolating different subpopulations of EVs. Specifically, EVs isolated through the high-speed centrifugation (HS) method exhibited a higher abundance of ribosomal and mitochondrial proteins. Functional apoptosis assays comparing isolated mitochondria with different EV isolation methods revealed that HS-EVs, but not other EVs, induced early apoptosis in cancer cells. On the other hand, EVs isolated using the sucrose cushion (SU) and ultracentrifugation (UC) methods demonstrated a higher abundance of proteins primarily involved in the immune response, cellLJcell interactions, and extracellular matrix interactions. Our analyses unveil notable disparities in proteins and associated biological functions among EV subpopulations, underscoring the importance of meticulously selecting isolation methods and resultant EV subpopulations based on the intended application.

cell biology↗

bioRxiv2024

Long-term Exposure to Methyl Jasmonate Increases Myrosinases TGG1 and TGG2 in Arabidopsis coi1 and myc2,3,4 Mutants

Plants are constantly subjected to stresses such as wounding or herbivore attacks, which continuously activate the JA signaling pathway in nature. However, knowledge about the effect of long-term activation of the JA signaling pathway on plant defense response remains limited. THIOGLUCOSIDE GLUCOHYDROLASE 1 (TGG1) and TGG2 are enzymes that activate defensive metabolites, namely glucosinolates, which are involved in defense against herbivores and pathogens. Here, we show that prolonged exposure to the wounding hormone methyl jasmonate (MeJA) enhances TGG1 and TGG2 expression independent of the canonical jasmonic acid (JA) signaling pathway in Arabidopsis thaliana rosette leaves. We found that airborne MeJA treatment for up to 5 d enhanced both TGG1 and TGG2 gene expression and their protein levels in Arabidopsis leaves. Notably, TGG1 and TGG2 gene expressions significantly upregulated in two JA signaling pathway mutants, namely coi1-16 and myc2,3,4, following 5 d of MeJA treatment. TGG1 and TGG2 proteins accumulate in specialized myrosin cells of rosette leaves. Myrosin cell area expands in response to MeJA treatment in a leaf-age-dependent manner. Consistent with this, the expression of FAMA, a transcription factor known to regulate TGG1 and TGG2 gene expression, also increased in a leaf-age-dependent manner after 5 d of MeJA treatment. Taken together, our results suggest the existence of a non-canonical JA signaling pathway that is activated by long-term exposure to MeJA and regulates the expression of defense-related genes TGG1 and TGG2.

plant biology↗

bioRxiv2024

Aphid resistance segregates independently of cardiac glycoside and glucosinolate content in an Erysimum cheiranthoides (wormseed wallflower) F2 population

Plants in the genus Erysimum produce both glucosinolates and cardiac glycosides as defense against herbivory. Two natural isolates of Erysimum cheiranthoides (wormseed wallflower) differed in their glucosinolate content, cardiac glycoside content, and resistance to Myzus persicae (green peach aphid), a broad generalist herbivore. Both classes of defensive metabolites were produced constitutively and were not induced further by aphid feeding. To investigate the relative importance of glucosinolates and cardiac glycosides in E. cheiranthoides defense, we generated an improved genome assembly, genetic map, and segregating F2 population. Genotypic and phenotypic analysis of the F2 plants identified quantitative trait loci affecting glucosinolates and cardiac glycosides, but not aphid resistance. The abundance of most glucosinolates and cardiac glycosides was positively correlated in the F2 population, indicating that similar processes regulate their biosynthesis and accumulation. Aphid reproduction was positively correlated with glucosinolate content. Although overall cardiac glycoside content had little effect on aphid growth and survival, there was a negative correlation between aphid reproduction and helveticoside abundance. However, this variation in defensive metabolites could not explain the differences in aphid growth on the two parental lines, suggesting that processes other than the abundance of glucosinolates and cardiac glycosides have a predominant effect on aphid resistance in E. cheiranthoides.

plant biology↗

bioRxiv2023

Reversing the escape from herbivory: Knockout of cardiac glycoside biosynthesis in wormseed wallflower (Erysimum cheiranthoides L., Brassicaceae)

O_LIThe chemical arms race between plants and insects is foundational to the generation and maintenance of biological diversity. We asked how the evolution of a novel defensive compound in an already well-defended plant lineage impacts interactions with diverse herbivores. Erysimum cheiranthoides (Brassicaceae), which produces both ancestral glucosinolates and novel cardiac glycosides, served as a model. C_LIO_LIWe analyzed gene expression to identify cardiac glycoside biosynthetic enzymes in E. cheiranthoides and characterized these enzymes via heterologous expression and CRISPR/Cas9 knockout. Using E. cheiranthoides cardiac glycoside-deficient lines, we conducted insect experiments in both the laboratory and field. C_LIO_LIEcCYP87A126 initiates cardiac glycoside biosynthesis via sterol side chain cleavage, and EcCYP716A418 has a role in cardiac glycoside hydroxylation. In EcCYP87A126 knockout lines, cardiac glycoside production was eliminated. Laboratory experiments with these lines revealed that cardiac glycosides were highly effective defenses against two species of glucosinolate-tolerant specialist herbivores but did not protect against all crucifer-feeding specialist herbivores in the field. Cardiac glycosides had lesser to no effect on two broad generalist herbivores. C_LIO_LIThese results begin elucidation of the E. cheiranthoides cardiac glycoside biosynthetic pathway and demonstrate in vivo that cardiac glycoside production allows Erysimum to escape from some, but not all, specialist herbivores. C_LI

ecology↗

bioRxiv2023

A transient protein folding response targets aggregation in the early phase of TDP-43-mediated disease

Understanding the mechanisms that drive TDP-43 pathology is integral to combating neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). To address this, we sought to determine the timeline of proteomic alterations across disease course in TDP-43 proteinopathy. Using longitudinal quantitative proteomics analysis of cortex samples from the cytoplasmic TDP-43 rNLS8 mouse model of ALS and FTLD, we identified several distinct protein subsets characterized by temporal alterations in protein abundance across diverse biological pathways, including protein folding, intracellular transport, myelination, and neuronal synaptic function. Remarkably, neurons in the rNLS8 cortex elicited a transitory response primarily comprising protein-folding factors prior to and in the earliest stages of disease progression. This response included increased levels of DnaJ homolog subfamily B member 5, DNAJB5, and proof-of-concept studies showed that DNAJB5 over-expression decreased TDP-43 aggregation in cell and cortical neuron cultures. Conversely, knockout of Dnajb5 exacerbated motor impairments caused by AAV-mediated cytoplasmic TDP-43 expression in the brains and spinal cords of mice. Lastly, the late disease proteomic signatures of rNLS8 mouse cortex strongly correlated with changes in human autopsy-derived TDP-43 proteinopathy tissues, indicating commonality of disease processes. Together, these findings reveal molecular mechanisms that regulate protein levels through distinct stages of ALS and FTLD progression, and suggest that protein folding factors that combat cytoplasmic TDP-43 protein aggregation could be protective in disease. HighlightsO_LIThe first longitudinal map of the cortex proteome throughout TDP-43-driven disease in a mouse model of cytoplasmic TDP-43 proteinopathy (rNLS8 mice). C_LIO_LICytoplasmic TDP-43 accumulation drives many dynamic changes to the cortex proteome, including increases in protein folding factors prior to disease onset. C_LIO_LIThe protein folding factor DNAJB5 decreases TDP-43 aggregation in HEK293 cells and primary cortical neurons and Dnajb5 knockout exacerbates cytoplasmic TDP-43-associated motor impairments in vivo. C_LIO_LIThe proteomic signature of the rNLS8 mouse cortex correlates strongly with postmortem brain tissue from human TDP-43 proteinopathies. C_LIO_LIA new webtool, TDP-map (https://shiny.rcc.uq.edu.au/TDP-map/), allows comparison of transcriptomic and proteomic datasets from mouse and human TDP-43 proteinopathy. C_LI

neuroscience↗

bioRxiv2023

Parsing the effect of co-culture with brain organoids on Diffuse Intrinsic Pontine Glioma (DIPG) using quantitative proteomics

Diffuse Intrinsic Pontine Gliomas (DIPGs) are deadly brain cancers in children for which there is currently no effective treatment. This can partly be attributed to preclinical models that lack essential elements of the in vivo tissue environment, resulting in treatments that appear promising preclinically, but fail to result in effective cures. Recently developed co-culture models combining stem cell-derived brain organoids with brain cancer cells provide tissue dimensionality and a human-relevant tissue-like microenvironment. As these models are technically challenging and time consuming it is imperative to establish whether interaction with the organoid influences DIPG biology and thus warrants their use. To address this question, we cultured DIPG cells with cortical organoids. We created "mosaic" co-cultures enriched for tumour cell-neuronal cell interactions versus "assembloid" co-cultures enriched for tumour cell-tumour cell interactions. Sequential window acquisition of all theoretical mass spectra (SWATH-MS) was used to analyse the proteomes of DIPG fractions isolated by flow-assisted cell sorting. Control proteomes from DIPG spheroids were compared with DIPG cells isolated from mosaic and assembloid co-cultures. This revealed that tumour cell adhesion was reduced, and DNA synthesis and replication were increased, in DIPG cells under either co-culture condition. By contrast, the mosaic co-culture was associated with pathways implicated in dendrite growth. We propose that co-culture with brain organoids is a valuable tool to parse the contribution of the brain microenvironment to DIPG tumour biology.

cancer biology↗

bioRxiv2023

Arabidopsis MEB3 functions as a vacuolar transporter to regulate iron accumulation in roots

Iron is an essential nutrient for plant photosynthesis and development, but excess iron leads to stress. After absorption from the soil, plants store iron in roots and distribute it to shoots via long-distance transport. Vacuole serves as the iron storage organ in root cells, maintaining cellular iron homeostasis, and vacuolar iron transporter (VIT) family proteins have been identified as plant vacuolar iron transporters. However, the contribution of vacuolar iron transporters to the overall iron homeostasis of plants is not fully understood. Here, we show that MEMBRANE PROTEIN OF ER BODY 3 (MEB3), a VIT family member, is a vacuolar iron transporter involved in root-shoot iron distribution in Arabidopsis thaliana. Heterologous expression of Arabidopsis MEB3 in yeast restored the iron resistance phenotype of the vacuolar iron transporter deficient mutant ccc1, indicating that MEB3 regulates iron transport. In Arabidopsis, MEB3 was expressed in almost all tissues, albeit to higher levels in roots and seedlings, and the MEB3 protein localized to the tonoplast. At low iron concentration, meb3 knockout mutants accumulated less iron in shoots, suggesting that MEB3 promotes iron accumulation in shoots. Consistently, meb3 mutants exhibited reduced growth compared with the wild type upon transfer to iron-deficient medium. However, at high iron concentration, meb3 mutants accumulated more iron in shoots and less iron in roots than the wild type, indicating the impairment of proper iron distribution in meb3 mutants. These findings demonstrate that MEB3 is a vacuolar iron transporter involved in root-to-shoot iron distribution.

plant biology↗

bioRxiv2023

New Features Surrounding the Cdc42-Ste20 Module that Regulates MAP Kinase Signaling in Yeast

Mitogen-activated protein kinase (MAPK) pathways regulate multiple cellular responses, including the response to stress and cell differentiation, and are highly conserved across eukaryotes from yeast to humans. In yeast, the canonical activation of several MAPK pathways includes the interaction of the small GTPase Cdc42p with the p21-activated kinase (PAK) Ste20p. We recently found that the active conformation of Cdc42p is regulated by turnover, which impacts the activity of the pathway that regulates filamentous growth (fMAPK). Here, we show that Ste20p is turned over by the 26S proteasome. Ste20p was stabilized when bound to Cdc42p, presumably to sustain MAPK pathway signaling. Ste20p is a major conduit by which signals flow through the fMAPK pathway; however, by genetic approaches we also identified a Ste20p-independent branch of the fMAPK pathway. Ste20p-dependent signaling required the 14-3-3 proteins, Bmh1p and Bmh2p, while Ste20p-independent signaling required the fMAPK pathway adaptor and Cdc42p-interacting protein, Bem4p. Ste20p-independent signaling was inhibited by one of the GTPase-activating proteins for Cdc42p in the fMAPK pathway, Rga1p, which also dampened basal but not active fMAPK pathway activity. Finally, the polarity adaptor and Cdc42p-interacting protein, Bem1p, which also regulates the fMAPK pathway, interacts with the tetra-span protein Sho1p, connecting a sensor at the plasma membrane to a protein that regulates the GTPase module. Collectively, these data reveal new regulatory features surrounding a Rho-PAK module that may extend to other pathways that control cell differentiation.

biochemistry↗

bioRxiv2021

Acropetal and basipetal cardenolide transport in Erysimum cheiranthoides (wormseed wallflower)

Plant specialized metabolites are often subject to within-plant transport and have tissue-specific distribution patterns. Among plants in the Brassicaceae, the genus Erysimum is unique in producing not only glucosinolates but also cardenolides as defense against insect herbivory. Ten cardenolides were detected with varying abundance in different tissues of Erysimum cheiranthoides (wormseed wallflower). As is predicted by the optimal defense theory, cardenolides were most abundant in young leaves and reproductive tissues. The lowest concentrations were observed in senescing leaves and roots. Crosses between wildtype E. cheiranthoides and a mutant line with an altered cardenolide profile showed that the seed cardenolide phenotype is determined entirely by the maternal genotype. Prior to the development of the first true leaves, seedling cotyledons also had the maternal cardenolide profile. Hypocotyl grafting experiments showed that the root cardenolide profile is determined entirely by the aboveground plant genotype. In further grafting experiments, there was no evidence of cardenolide transport into the leaves, but a mixed cardenolide profile was observed in the stems and inflorescences of plants that had been grafted at vegetative and flowering growth stages, respectively. Together, these results indicate that E. cheiranthoides leaves are a site of cardenolide biosynthesis and therefore also the plant tissue that is most likely to be expressing the relevant biosynthetic genes.

plant biology↗

bioRxiv2021

Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration.

Induced pluripotent stem cells generated from patients with geographic atrophy as well as healthy individuals were differentiated to retinal pigment epithelium (RPE) cells. By integrating transcriptional profiles of 127,659 RPE cells generated from 43 individuals with geographic atrophy and 36 controls with genotype data, we identified 439 expression Quantitative Trait (eQTL) loci in cis that were associated with disease status and specific to subpopulations of RPE cells. We identified loci linked to two genes with known associations with geographic atrophy - PILRB and PRPH2, in addition to 43 genes with significant genotype x disease interactions that are candidates for novel genetic associations for geographic atrophy. On a transcriptome-only level, we identified molecular pathways significantly upregulated in geographic atrophy-RPE including in extracellular cellular matrix reorganisation, neurodegeneration, and mitochondrial functions. We subsequently implemented a large-scale proteomics analysis, confirming modification in proteins associated with these pathways. We also identified six significant protein (p) QTL that regulate protein expression in the RPE cells and in geographic atrophy - two of which share variants with cis-eQTL. Transcriptome-wide association analysis identified genes at loci previously associated with age-related macular degeneration. Further analysis conditional on disease status, implicated statistically significant RPE-specific eQTL. This study uncovers important differences in RPE homeostasis associated with geographic atrophy.

neuroscience↗

bioRxiv2021

Indole-3-glycerolphosphate synthase, a branchpoint for the biosynthesis of tryptophan, indole, and benzoxazinoids in maize

The maize (Zea mays) genome encodes three indole-3-glycerolphosphate synthase enzymes (IGPS1, 2, and 3) catalyzing the conversion of 1-(2-carboxyphenylamino)-l-deoxyribulose-5-phosphate to indole-3-glycerolphosphate. Three further maize enzymes (BX1, benzoxazinoneless 1; TSA, tryptophan synthase subunit; and IGL, indole glycerolphosphate lyase) convert indole-3-glycerolphosphate to indole, which is released as a volatile defense signaling compound and also serves as a precursor for the biosynthesis of tryptophan and defense-related benzoxazinoids. Phylogenetic analyses showed that IGPS2 is similar to enzymes found in both monocots and dicots, whereas maize IGPS1 and IGPS3 are in monocot-specific clades. Fusions of yellow fluorescent protein (YFP) with maize IGPS enzymes and indole-3-glycerolphosphate lyases were all localized in chloroplasts. In bimolecular fluorescence complementation assays, IGPS1 interacted strongly with BX1 and IGL, IGPS2 interacted primarily with TSA, and IGPS3 interacted equally with all three indole-3-glycerolphosphate lyases. Whereas IGPS1 and IGPS3 expression was induced by insect feeding, IGPS2 expression was not. Transposon insertions in IGPS1 and IGPS3 reduced the abundance of both benzoxazinoids and free indole. Spodoptera exigua (beet armyworm) larvae show improved growth on igps1 mutant maize plants. Together, these results suggest that IGPS1 and IGPS3 function mainly in the biosynthesis of defensive metabolites, whereas IGPS2 may be involved in the biosynthesis of tryptophan. This metabolic channeling is similar, though less exclusive than that proposed for the three maize indole-3-glycerolphosphate lyases.

plant biology↗

bioRxiv2020

Proteomic and transcriptomic analysis of Microviridae {varphi}X174 infection reveals broad up-regulation of host membrane damage and heat shock responses

Measuring host-bacteriophage dynamics is an important approach to understanding bacterial survival functions and responses to infection. The model Microviridae bacteriophage {varphi}X174 is endemic to the human gut and has been studied for over seventy years but the host response to infection has never been investigated in detail. To address this gap in our understanding of this important interaction within our microbiome we have measured host Escherichia coli C proteomic and transcriptomic response to {varphi}X174 infection. We used mass spectrometry and RNA-seq to identify and quantify all 11 {varphi}X174 proteins and over 1,700 E. coli proteins, enabling us to comprehensively map host pathways involved in {varphi}X174 infection. Most notably, we see significant host responses centered on membrane damage and remodeling, cellular chaperone and translocon activity, and lipoprotein processing, which we speculate is due to the peptidoglycan-disruptive effects of the {varphi}X174 lysis protein E on MraY activity. We also observe the massive upregulation of small heat-shock proteins IbpA/B, along with other heat shock pathway chaperones, and speculate on how the specific characteristics of holdase protein activity may be beneficial for viral infections. Together, this study enables us to begin to understand the proteomic and transcriptomic host responses of E. coli to Microviridae infections and contributes insights to the activities of this important model phage. IMPORTANCEA major part of the healthy human gut microbiome are the Microviridae bacteriophage, exemplified by the model {varphi}X174 phage. Although much has been learned from studying {varphi}X174 over the last half century, until this work, the E. coli host response to infection has never been investigated in detail. We reveal the proteomic and transcriptomic pathways differentially regulated during the {varphi}X174 infection cycle, and uncover the details of a coordinated cellular response to membrane damage that results in increased lipoprotein processing and membrane trafficking, likely due to the phage antibiotic-like lysis protein. We also reveal that small heat shock proteins IbpA/B are massively upregulated during infection and that these holdase chaperones are highly conserved across the domains of life, indicating that reliance on them is likely widespread across viruses.

microbiology↗