Biology subjects

Ren, D.

Publications and source records attributed to Ren, D..

24 records · Page 2Linked to original sources

bioRxiv2021

Systemic and local immune response to intraocular AAV vector administration in non-human primates

The positive clinical outcomes in adeno-associated virus (AAV)-mediated retinal gene therapy have often been attributed to the low immunogenicity of AAVs along with the immune-privilege of the eye. However, several recent preclinical studies and clinical trials have shown potential for inflammatory responses to AAV mediated gene therapy. Our current understanding of the factors contributing to intraocular inflammation such as the existence of serum antibodies against AAVs prior to injection and their contribution to increases in antibody levels post-injection is incomplete. The parameters that regulate the generation of new antibodies in response to the AAV capsid or transgene post-injection after intraocular administration are also insufficiently described. In this study we carried out a retrospective analysis of the pre-existing serum antibodies in correlation with changes in antibody levels after intraocular injections of AAV in non-human primates (NHPs). We analyzed NHP serums for the presence of both Binding Antibodies (BABs), as well as a subset of these called Neutralizing Antibodies (NABs) that impede AAV transduction upon binding. We observed significantly higher pre-existing serum BABs against AAV8 compared to other serotypes. We observed a dose-dependent increase in both BABs and NABs in the serums collected post-injection, irrespective of the serotype or the mode of injection. Lastly, we were able to demonstrate a co-relation between the serum BAB levels with clinical grading of inflammation and levels of transgene expression.

immunology↗

bioRxiv2021

New insights into the earlier evolutionary history of epiphytic macrolichens

Lichens are well known as pioneer organisms colonizing bare surfaces such as rocks and therefore have been hypothesized to play a role in the early formation of terrestrial ecosystems. Given the rarity of fossil evidence, our understanding of the evolutionary history of lichen-forming fungi is primarily based on molecular dating approaches. These studies suggest extant clades of macrolichens diversified after the K-Pg boundary. Here we corroborate the mid-Mesozoic fossil Daohugouthallus ciliiferus as an epiphytic macrolichen that predates the K-Pg boundary by 100 Mys. Based on new material and geometric morphometric analysis, we demonstrate that the Jurassic fossil is morphologically most similar to Parmeliaceae, but cannot be placed in Parmeliaceae or other similar family-level clades forming macrolichens as these evolved much later. Consequently, a new family, Daohugouthallaceae, is proposed here to accommodate this fossil, which reveals macrolichens may have been diverse long before the Cenozoic diversification of extant lineages.

paleontology↗

bioRxiv2021

Ovipositor and mouthparts in a fossil insect support a novel ecological role for early orthopterans in Pennsylvanian forests

Lobeattid insects represented a high portion of the earliest known, Pennsylvanian insect faunas. However, their systematic affinities and their role as foliage feeders which severely influenced their ecosystems remain debated. We investigated hundreds of samples of a new lobeattid species from the Xiaheyan locality using Reflectance Transforming Imaging combined with geometric morphometrics in order to assess its morphology, infer its ecological role, and phylogenetic position. Ctenoptilus frequens sp. nov. possessed a sword-shaped ovipositor whose valves interlocked by two ball-and-socket mechanisms. This unambiguously supports lobeattids as stem-relatives of all Orthoptera (crickets, grasshoppers, katydids). Given the herein presented and other remains, it follows that this group experienced an early diversification coupled with high levels of abundance. The ovipositor shape additionally indicates that ground was the preferred substrate for eggs. Visible mouthparts made it possible to assess the efficiency of the mandibular food uptake system in comparison to a wide array of recent species. The new species was omnivorous which explains the paucity of external damage on contemporaneous plant foliage.

evolutionary biology↗

bioRxiv2020

Epilepsy-associated Mutations in the Calcium-sensing Receptor Disrupt the Regulation of NALCN Sodium-leak Channel by Extracellular Calcium in Neurons

Most mammalian neurons have a resting membrane potential (RMP) of ~ -50 mV to -70 mV, significantly above the equilibrium potential of K+ (EK) of ~ -90 mV. The resting Na+-leak conductance is a major mechanism by which neurons maintain their RMPs above EK. In the hippocampal neurons, the TTX-insensitive, voltage-independent Na+ leak is mediated by the NALCN cation channel. Extracellular Ca2+ (Ca2+e) also controls the sizes of NALCN current (INALCN) in a G-protein-dependent fashion. The molecular identities of the basal Na+ conductances and their regulation in other regions in the central nervous system and in the peripheral nervous system are less established. Here we show that neurons cultured from mouse cortices, ventral tegmental area, spinal cord and dorsal root ganglia all have a NALCN-dependent basal Na+-leak conductance that is absent in NALCN knockout mice. Like in hippocampal neurons, a decrease in [Ca2+]e increases INALCN. Using shRNA knockdown, we show that the regulation of INALCN by Ca2+e in neurons requires the Ca2+-sensing G-protein-coupled receptor CaSR. Surprisingly, the functional coupling from [Ca2+]e to NALCN requires CaSRs distal C-terminal domain that is dispensable for the receptors ability to couple [Ca2+]e to its canonical signaling targets such as PLC and MAPK. In addition, several epilepsy-associated human CaSR mutations, though sparing the receptors ability to sense Ca2+e to maintain systemic [Ca2+], disrupt the ability of CaSR to regulate NALCN. These findings uncover a unique mechanism by which CaSR regulates neuronal excitability via NALCN in the central and peripheral nervous system.

physiology↗

bioRxiv2020

Lyl-1 marks and regulates primitive macrophages and microglia development

During ontogeny, macrophages (M{Phi}) populations emerge in the Yolk Sac (YS) via two distinct progenitor waves, prior to hematopoietic stem cell development. M{Phi}-progenitors from the primitive/"early EMP" and transient-definitive/"late EMP" waves both contribute to various resident-M{Phi} populations in the developing embryonic organs. Identifying factors that modulates early stages of M{Phi}-progenitor development may lead to a better understanding of defective function of specific resident-M{Phi} subsets. Here we show that primitive macrophage (M{Phi}Prim) progenitors in the YS express Lyl-1, a bHLH transcription factor related to SCL/Tal-1. Transcriptomic analysis of YS M{Phi}-progenitors indicated that M{Phi}Prim progenitors present at embryonic day (E) 9 are clearly distinct from those present at later stages. Disruption of Lyl-1 basic helix-loop-helix domain led initially to an early increased emergence of M{Phi}Prim progenitors, and later to their defective differentiation. These defects were associated with a disrupted expression of gene sets related to embryonic patterning and neurodevelopment. Lyl-1-deficiency also induced a reduced production of mature M{Phi}/microglia in the early brain, as well as a transient reduction of the microglia pool at midgestation and in the newborn. We thus identify Lyl-1 as a critical regulator of M{Phi}Prim and microglia development, which disruption may impair resident-M{Phi} function during organogenesis. Key points1- Yolk sac primitive macrophage progenitors and microglia/Border Associated macrophages express Lyl-1. 2- Lyl-1-deficiency impairs primitive macrophage and microglia development and leads to the up-regulation of gene sets related to embryo patterning and neuro-development.

developmental biology↗

bioRxiv2019

RADAR: Differential analysis of MeRIP-seq data with a random effect model

Epitranscriptome profiling using MeRIP-seq is a powerful technique for in vivo functional studies of reversible RNA modifications. We develop RADAR, a comprehensive analytical tool for detecting differentially methylated loci in MeRIP-seq data. RADAR enables accurate identification of altered methylation sites by accommodating variability of pre-immunoprecipitation expression level and post-immunoprecipitation count using different strategies. In addition, it is compatible with complex study design when covariates need to be incorporated in the analysis. Through simulation and real datasets analyses, we show that RADAR leads to more accurate and reproducible differential methylation analysis results than alternatives, which is available at https://github.com/scottzijiezhang/RADAR.

bioinformatics↗