Biology subjects

Lu, H.

Publications and source records attributed to Lu, H..

At least 163 records · Page 9Linked to original sources

bioRxiv2023

Community-based Reconstruction and Simulation of a Full-scale Model of Region CA1 of Rat Hippocampus

The CA1 region of the hippocampus is one of the most studied regions of the rodent brain, thought to play an important role in cognitive functions such as memory and spatial navigation. Despite a wealth of experimental data on its structure and function, it has been challenging to reconcile information obtained from diverse experimental approaches. To address this challenge, we present a community-driven, full-scale in silico model of the rat CA1 that integrates a broad range of experimental data, from synapse to network, including the reconstruction of its principal afferents, the Schaffer collaterals, and a model of the effects that acetylcholine has on the system. We tested and validated each model component and the final network model, and made input data, assumptions, and strategies explicit and transparent. The unique flexibility of the model allows scientists to address a range of scientific questions. In this article, we describe the methods used to set up simulations that reproduce and extend in vitro and in vivo experiments. Among several applications in the article, we focus on theta rhythm, a prominent hippocampal oscillation associated with various behavioral correlates and use our computer model to reproduce and reconcile experimental findings. Finally, we make data, code and model available through the hippocampushub.eu portal, which also provides an extensive set of analyses of the model and a user-friendly interface to facilitate adoption and usage. This neuroscience community-driven model represents a valuable tool for integrating diverse experimental data and provides a foundation for further research into the complex workings of the hippocampal CA1 region.

neuroscience↗

bioRxiv2023

Population genomics reveals extensive inbreeding and purging of mutational load in wild Amur tigers

The inbreeding is a big threat for the persistence of genetic diversity in small and isolated populations of endangered species. The homozygous genome could exacerbate inbreeding depression by introducing homozygous deleterious alleles in the population. However, purging of inbreeding loads as they become homozygotes in small populations could alleviate the depression. The Amur tiger (Panthera tigris altaica) is typically exists in small population living in forests in Northeast Asia and is among the most endangered animals on the planet with great symbolic significance of conservation. By comparing with captive individuals, we revealed substantially higher and more extensive inbreeding in the wild Amur tiger population (FROH=0.51) than in captive Amur tigers (FROH=0.26). We further found much less mutational loads in wild populations when compared with captive Amur tigers. However, the frequency of loss of function and deleterious nonsynonymous mutations inside ROH regions are much lower than that in non-ROH regions in both wild and captive Amur tigers, indicating the purging may had occurred in both populations but much effective in the wild population. In addition, we found the average frequency of deleterious alleles was much lower than that of neutral alleles in the wild population, indicating that the purifying selection contributed to the purging of mutational loads in the wild Amur tigers. These findings provide valuable genome-wide evidence to support the making of future conservation plans of wild Amur tigers.

genomics↗

bioRxiv2023

Skin permeable polymer for noninvasive transdermal insulin delivery

Subcutaneous injection of insulin is the current standard medication for many diabetic patients. Convenient and painless noninvasive transdermal insulin delivery has long been pursued but yet succeeded due to no such technologies for large biomacromolecules. We find a tertiary amine oxide-based polyzwitterion, OPDMA, that can efficiently penetrate both the stratum corneum (SC) and viable epidermis into circulation. So its conjugate with insulin, OPDMA-I, applied on the skin can exhibit hypoglycemic effects as efficiently as subcutaneously injected insulin in type-1 diabetic mice and minipigs. The unique pH-dependent cationic-to-zwitterionic transition of OPDMA in the characteristic acidic-to-neutral pH gradient from the skin surface to deep SC enables fast transdermal delivery of OPDMA and its conjugate. On the skin, OPDMA binds to carboxylic acids in the acidic sebum layer, enriching OPDMA-I on the SC. As pH increases in deeper SC layers, binding between OPDMA-I and the skin weakens gradually, allowing for diffusion through inter-corneocyte gaps and penetration into viable epidermis and finally entering the systemic circulation via dermal lymphatic vessels. This process does not alter SC microstructures or cause any physiological changes in the skin. This study represents a groundbreaking example of noninvasive transdermal protein delivery.

bioengineering↗

bioRxiv2023

Spatiotemporal transcriptome atlas of human embryos after gastrulation

The spatial and temporal atlas of gene expression in the human embryo at early gestation is critical in understanding embryo development, organogenesis, and disease origins. We obtained the spatiotemporal transcriptome from 90 sagittal sections of 16 whole human embryos from 3 to 8 post-conception weeks by Stereo-seq with high resolution and ultra-large field, establishing the development trajectory/regulatory profiling of 49 organs. We uncovered the organ-specific regulons as potential lineage-determining factors and identified the new regulatory networks during heart and brain development. The atlas refines the key organs/cell types vulnerable to virus infection and genetic disorders, and, reveals the dynamics of allelic gene expression in specific organs at different stages. These results present the first comprehensive delineation of the spatiotemporal transcriptomic dynamics of human organogenesis. One Sentence SummaryThe spatiotemporal transcriptome atlas presents a comprehensive delineation of human embryogenesis after gastrulation.

developmental biology↗

bioRxiv2023

Pharmacological Induction of mesenchymal-epithelial transition chemosensitizes breast cancer cells and prevents metastatic progression

The epithelial-mesenchymal transition (EMT) is a developmental program co-opted by tumor cells that aids the initiation of the metastatic cascade. Tumor cells that undergo EMT are relatively chemoresistant, and there are currently no therapeutic avenues specifically targeting cells that have acquired mesenchymal traits. We show that treatment of mesenchymal-like triple-negative breast cancer (TNBC) cells with the microtubule-destabilizing chemotherapeutic eribulin, which is FDA-approved for the treatment of advanced breast cancer, leads to a mesenchymal-epithelial transition (MET). This MET is accompanied by loss of metastatic propensity and sensitization to subsequent treatment with other FDA-approved chemotherapeutics. We uncover a novel epigenetic mechanism of action that supports eribulin pretreatment as a path to MET induction that curtails metastatic progression and the evolution of therapy resistance. SummaryWhile the advent of targeted therapy has led to vast improvements in outcomes for certain types of breast cancer, a mainstay for triple-negative breast cancer (TNBC) remains cytotoxic chemotherapy. A major clinical hurdle in successfully managing this disease is the eventual development of therapeutic resistance and disease relapse in more aggressive forms. Our data reveal that epigenetic modulation of EMT state using the FDA-approved therapeutic eribulin curtails metastatic propensity of breast tumors and, when administered in the treatment-naive setting, sensitizes to subsequent treatment with other chemotherapeutics.

cancer biology↗

bioRxiv2023

On-chip brain slice stimulation: precise control of electric fields and tissue orientation

Non-invasive brain stimulation modalities, including transcranial direct current stimulation (tDCS), are widely used in neuroscience and clinical practice to modulate brain function and treat neuropsychiatric diseases. DC stimulation of ex vivo brain tissue slices has been a method used to understand mechanisms imparted by tDCS. However, delivering spatiotemporally uniform direct current electric fields (dcEFs) that have precisely engineered magnitudes and are also exempt from toxic electrochemical by-products are both significant limitations in conventional experimental setups. As a consequence, bioelectronic dose-response interrelations, the role of EF orientation, and the biomechanisms of prolonged or repeated stimulation over several days all remain not well understood. Here we developed a platform with fluidic, electrochemical, and magnetically-induced spatial control. Fluidically, the chamber geometrically confines precise dcEF delivery to the enclosed brain slice and allows for tissue recovery in order to monitor post-stimulation effects. Electrochemically, conducting hydrogel electrodes mitigate stimulation-induced faradaic reactions typical of commonly-used metal electrodes. Magnetically, we applied ferromagnetic substrates beneath the tissue and used an external permanent magnet to enable in situ rotational control in relation to the dcEF. By combining the microfluidic chamber with live-cell calcium imaging and electrophysiological recordings, we showcased the potential to study the acute and lasting effects of dcEFs with the potential of providing multi-session stimulation. This on-chip bioelectronic platform presents a modernized yet simple solution to electrically stimulate explanted tissue by offering more environmental control to users, which unlocks new opportunities to conduct thorough brain stimulation mechanistic investigations. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/536696v1_ufig1.gif" ALT="Figure 1"> View larger version (85K): org.highwire.dtl.DTLVardef@10bac4dorg.highwire.dtl.DTLVardef@15d1dd3org.highwire.dtl.DTLVardef@5119c8org.highwire.dtl.DTLVardef@73b554_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

Discovery of a new drug using lipid-based formulation targeting G12D mutated KRAS4B through non-covalent bonds

One of the most common drivers in human cancer is KRAS4B. In recent years, the promising KRAS targeted drug development has attracted significant new research interest and reignited the field of RAS therapeutics. To signal, oncogenic KRAS4B not only requires a sufficient nucleotide exchange, but also needs to recruit effectors by exposing its effector-binding sites while anchoring to plasma membrane where KRAS4B-mediated signaling events occur. Phosphodiesterase-{delta} plays an important role in sequestering KRAS4B from the cytoplasm and targeting it to cellular membranes. In this work, we have designed a drug LIG1 using lipid-based formulation to directly target both the switch-II pocket of KRAS4B-G12D and phosphodiesterase-{delta}. LIG1 was found to lock KRAS4B in its GDP-bound state while the effector-binding domain is blocked by the interface of the plasma membrane which hinders the nucleotide exchange while simultaneously it can affect the GTP-bound KRAS4B to shift from an active state to its inactive state. LIG1 is also observed to stably accommodate itself in the prenyl-binding pocket of phosphodiesterase-{delta} which impairs KRAS4B enrichment at the membrane and suppress the proliferation of KRAS4B-dependent cancer cells. In this work we report a drug based on lipid-based formulation that can foster drug discovery efforts for the targeting of oncogenes of the RAS family and beyond.

molecular biology↗

bioRxiv2023

standard-GEM: standardization of open-source genome-scale metabolic models

The field of metabolic modelling at the genomescale continues to grow with more models being created and curated. This comes with an increasing demand for adopting common principles regarding transparency and versioning, in addition to standardisation efforts regarding file formats, annotation and testing. Here, we present a standardised template for git-based and GitHub-hosted genome-scale metabolic models (GEMs) supporting both new models and curated ones, following FAIR principles (findability, accessibility, interoperability, and reusability), and incorporating bestpractices. standard-GEM facilitates the reuse of GEMs across web services and platforms in the metabolic modelling field and enables automatic validation of GEMs. The use of this template for new models, and its adoption for existing ones, paves the way for increasing model quality, openness, and accessibility with minimal effort. Availabilitystandard-GEM is available from github.com/MetabolicAtlas/standard-GEM under the conditions of the CC BY 4.0 licence along with additional supporting material.

systems biology↗

bioRxiv2023

Repetitive transcranial magnetic stimulation (rTMS) triggers dose-dependent homeostatic rewiring in recurrent neuronal networks

Repetitive transcranial magnetic stimulation (rTMS) is a non-invasive brain stimulation technique used to induce neuronal plasticity in healthy individuals and patients. Designing effective and reproducible rTMS protocols poses a major challenge in the field as the underlying biomechanisms remain elusive. Current clinical protocol designs are often based on studies reporting rTMS-induced long-term potentiation or depression of synaptic transmission. Herein, we employed computational modeling to explore the effects of rTMS on long-term structural plasticity and changes in network connectivity. We simulated a recurrent neuronal network with homeostatic structural plasticity between excitatory neurons, and demonstrated that this mechanism was sensitive to specific parameters of the stimulation protocol (i.e., frequency, intensity, and duration of stimulation). The feedback-inhibition initiated by network stimulation influenced the net stimulation outcome and hindered the rTMS-induced homeostatic structural plasticity, highlighting the role of inhibitory networks. These findings suggest a novel mechanism for the lasting effects of rTMS, i.e., rTMS-induced homeostatic structural plasticity, and highlight the importance of network inhibition in careful protocol design, standardization, and optimization of stimulation. Author summaryThe cellular and molecular mechanisms of clinically employed repetitive transcranial magnetic stimulation (rTMS) protocols remain not well understood. However, it is clear that stimulation outcomes depend heavily on protocol designs. Current protocol designs are mainly based on experimental studies that explored functional synaptic plasticity, such as long-term potentiation of excitatory neurotransmission. Using a computational approach, we sought to address the dose-dependent effects of rTMS on the structural remodeling of stimulated and non-stimulated connected networks. Our results suggest a new mechanism of action--activity-dependent homeostatic structural remodeling--through which rTMS may assert its lasting effects on neuronal networks. We showed that the effect of rTMS on structural plasticity critically depends on stimulation intensity, frequency, and duration and that recurrent inhibition can affect the outcome of rTMS-induced homeostatic structural plasticity. These findings emphasize the use of computational approaches for an optimized rTMS protocol design, which may support the development of more effective rTMS-based therapies.

neuroscience↗

bioRxiv2023

Interplay between homeostatic synaptic scaling and homeostatic structural plasticity maintains the robust firing rate of neural networks

AbstractCritical network states and neural plasticity are essential for flexible behavior in dynamic envi-ronments, allowing for efficient information processing and experience-dependent learning. Synaptic-weight-based Hebbian plasticity and homeostatic synaptic scaling were considered the key mechanisms in enabling memory while stabilizing network dynamics. However, the role of structural plasticity as a homeostatic mechanism is less consistently reported, especially under activity inhibition, leading to an incomplete understanding of its functional impact. In this study, we combined live-cell microscopy of eGPF-labeled neurons in organotypic entorhinal-hippocampal tissue cultures with computational modeling to investigate the response of spine-number-based structural plasticity to activity perturba-tions and its interaction with homeostatic synaptic scaling. Tracking individual dendritic segments, we demonstrated that inhibiting excitatory neurotransmission does not monotonically regulate den-dritic spine density. Specifically, inhibition of AMPA receptors with a low concentration of 2,3-dioxo-6-nitro-7-sulfamoyl-benzo[f]quinoxaline (NBQX, 200 nM) significantly increased spine density, while complete AMPA receptors blockade with 50 {micro}M NBQX reduced spine density. Motivated by these findings, we developed network simulations incorporating a bi-phasic structural plasticity rule governing activity-dependent synapse formation. We showed that this biphasic rule maintained neu-ral activity homeostasis under stimulation and permitted either synapse formation or synapse loss, depending on the degree of activity deprivation. Homeostatic synaptic scaling affected the recurrent connectivity, modulated the network activity, and influenced the outcome of structural plasticity. Specifically, it reduced stimulation-triggered synapse loss by downscaling synaptic weights and res-cued silencing-induced synapse loss by upscaling recurrent inputs, thus reactivating silent neurons. Our interaction between these mechanisms offers an explanation for divergent findings in the existing literature. In summary, calcium-based synaptic scaling and homeostatic structural plasticity rules compete and compensate for one another, ensuring efficient and robust control of firing rate home-ostasis. Significance StatementO_LIThis work combined systematic computer simulations and in vitro experiments to explore the in-terplay between homeostatic structural plasticity and synaptic scaling under conditions of activity deprivation. C_LIO_LIWe identified a non-monotonic relationship between neural activity and spine numbers, where par-tial inhibition of synaptic transmissions increased spine density, while complete inhibition reduced it. C_LIO_LIPartial inhibition led to increased spine sizes across all initial spine sizes, whereas complete inhibition selectively increased the size of relatively large spines. C_LIO_LIA biphasic, spine-number-based homeostatic structural plasticity (HSP) rule reconciled previously divergent experimental findings regarding activity-dependent changes in spine density. C_LIO_LIUsing an engineering and complex systems framework, we proposed that the biphasic HSP rule incorporates a negative feedback mechanism and acts as a redundant and heterogeneous mechanism alongside the synaptic-weight-based homeostatic synaptic scaling (HSS) rule. C_LIO_LIBy comparing simulation and experimental results, we demonstrated the necessity of HSP-HSS interplay in maintaining firing rate homeostasis. C_LIO_LIBoth plasticity rules are driven by intracellular calcium concentration, which reflects cumulative neural activity. Thus, we propose that integral feedback control is critical in firing rate homeostasis. C_LI

neuroscience↗

bioRxiv2023

An expanded GCaMP reporter toolkit for functional imaging in C. elegans

In living organisms, changes in calcium flux are integral to many different cellular functions and are especially critical for the activity of neurons and myocytes. Genetically encoded calcium indicators (GECIs) have been popular tools for reporting changes in calcium levels in vivo. In particular, GCaMP, derived from GFP, are the most widely used GECIs and have become an invaluable toolkit for neurophysiological studies. Recently, new variants of GCaMP, which offer a greater variety of temporal dynamics and improved brightness, have been developed. However, these variants are not readily available to the Caenorhabditis elegans research community. This work reports a set of GCaMP6 and jGCaMP7 reporters optimized for C. elegans studies. Our toolkit provides reporters with improved dynamic range, varied kinetics, and targeted subcellular localizations. Besides optimized routine uses, this set of reporters are also well-suited for studies requiring fast imaging speeds and low magnification or low-cost platforms.

neuroscience↗

bioRxiv2023

Single-Cell Map of Dynamic Multicellular Ecosystem of Radiation-Induced Intestinal Injury

Intestine is a highly radiation-sensitive organ that could be injured during the radiotherapy for abdominal or pelvic cavity tumors. However, the dynamic change of the intestinal microenvironment related to radiation-induced intestine injury (RIII) is still unclear. Using single-cell RNA sequencing, we pictured a dynamic landscape of the intestinal microenvironment during RIII and regeneration. We showed that the multicellular ecosystem of intestine exhibited heterogeneous radiosensitivities. We revealed the distinct dynamic patterns of three subtypes of intestinal stem cells (ISCs), and the cellular trajectory analysis suggested a complex interconversion pattern among them. For the immune cells, we found that Ly6c+ monocytes can give rise to both pro-inflammatory macrophages and resident macrophages after RIII. Besides, through cellular communication analysis, we identified a positive feedback loop between the macrophages and endothelial cells, which could amplify the inflammatory response induced by radiation. Overall, our study provides a valuable single-cell map of the dynamic multicellular ecosystem during RIII and regeneration, which may facilitate the understanding of the mechanism of RIII.

cell biology↗

bioRxiv2023

Zero-shot learning enables instant denoising and super-resolution in optical fluorescence microscopy

Computational super-resolution (SR) methods, including conventional analytical algorithms and deep learning models, have substantially improved optical microscopy. Among them, supervised deep neural networks have demonstrated outstanding SR performance, however, demanding abundant high-quality training data, which are laborious and even impractical to acquire due to the high dynamics of living cells. Here, we develop zero-shot deconvolution networks (ZS-DeconvNet) that instantly enhance the resolution of microscope images by more than 1.5-fold over the diffraction limit with 10-fold lower fluorescence than ordinary SR imaging conditions in an unsupervised manner without the need for either ground truths or additional data acquisition. We demonstrate the versatile applicability of ZS-DeconvNet on multiple imaging modalities, including total internal reflection fluorescence microscopy, three-dimensional (3D) wide-field microscopy, confocal microscopy, lattice light-sheet microscopy, and multimodal structured illumination microscopy (SIM), which enables multi-color, long-term, super-resolution 2D/3D imaging of subcellular bioprocesses from mitotic single cells to multicellular embryos of mouse and C. elegans.

bioengineering↗

bioRxiv2023

Discovery and characterization of cross-reactive intrahepatic antibodies in severe alcoholic hepatitis

The pathogenesis of antibodies in severe alcoholic hepatitis (SAH) remains unknown. We sought to determine if there was antibody deposition in SAH livers and whether antibodies extracted from SAH livers were cross-reactive against both bacterial antigens and human proteins. We analyzed immunoglobulins (Ig) in explanted livers from SAH patients (n=45) undergoing liver transplantation and tissue from corresponding healthy donors (HD, n=10) and found massive deposition of IgG and IgA isotype antibodies associated with complement fragment C3d and C4d staining in ballooned hepatocytes in SAH livers. Ig extracted from SAH livers, but not patient serum exhibited hepatocyte killing efficacy in an antibody-dependent cell-mediated cytotoxicity (ADCC) assay. Employing human proteome arrays, we profiled the antibodies extracted from explanted SAH, alcoholic cirrhosis (AC), nonalcoholic steatohepatitis (NASH), primary biliary cholangitis (PBC), autoimmune hepatitis (AIH), hepatitis B virus (HBV), hepatitis C virus (HCV) and HD livers and found that antibodies of IgG and IgA isotypes were highly accumulated in SAH and recognized a unique set of human proteins as autoantigens. The use of an E. coli K12 proteome array revealed the presence of unique anti-E. coli antibodies in SAH, AC or PBC livers. Further, both Ig and E. coli captured Ig from SAH livers recognized common autoantigens enriched in several cellular components including cytosol and cytoplasm (IgG and IgA), nucleus, mitochondrion and focal adhesion (IgG). Except IgM from PBC livers, no common autoantigen was recognized by Ig and E. coli captured Ig from AC, HBV, HCV, NASH or AIH suggesting no cross-reacting anti-E. coli autoantibodies. The presence of cross-reacting anti-bacterial IgG and IgA autoantibodies in the liver may participate in the pathogenesis of SAH.

pathology↗

bioRxiv2023

Kinetics and efficacy of antibody drug conjugates in 3D tumour models

Antibody-drug conjugates (ADCs) are emerging targeted agents against cancer. Current studies of ADCs are performed on monolayer cultures which do not mimic the biophysical property of a tumour. Hence, in vitro models that can better predict the efficacy of ADCs in vivo are needed. In this study, we aim to optimise 3-dimentional cancer spheroid systems, which preserve the features of the tumour structure, to test the efficacy of two ADCs (T-DM1 and T-vcMMAE). Firstly, a set of reproducible spheroid models using epithelial ovarian cancer cell lines were established. Subsequently, phenotypic changes in spheroids were characterised upon ADC treatment. The penetration dynamics of ADCs into 3D tumour structure were also studied. Our data revealed that spheroids are less sensitive to ADCs compared to monolayer cultures. Interestingly, the small molecule component of ADCs-the cytotoxic payload-showed a similar decrease in efficacy in spheroids compared to monolayer cultures. Furthermore, we also gained new insight into ADC penetration dynamics and showed that ADCs can fully penetrate a tumour-like spheroid within 24h. The results suggest that although ADCs, as large molecule biological drugs, are likely to have slower penetration dynamics than small molecule compounds such as their cytotoxic payload, they could have comparable capability to kill cancer cells in 3D structures. This may be explained by the fact that multiple cytotoxic payloads are conjugated with each single antibody, which compensates the penetration deficiency of the large molecules. In conclusion, our work confirms that the tumour 3D structure could limit the therapeutic efficacy of ADCs. Nevertheless, optimising ADC design such as adjusting drug-to-antibody ratios could help to overcome this hurdle.

biochemistry↗

bioRxiv2023

Development and optimisation of cationic lipid nanoparticles for mRNA delivery

Messenger RNA (mRNA) has been proposed as a therapeutic agent for various diseases, including cancer. To ensure effective transfection of cancer cells, mRNA needs to be transported with a delivery system that protects its integrity and functionality. In this regard, cationic lipid nanoparticles composed of dioleoylphosphatidylethanolamine (DOPE) and 3{beta}-[N-(N,N-dimethylaminoethane)-carbamoyl] cholesterol (DC-Chol) have emerged as common vectors to deliver mRNA. In this project, we aim to use luciferase mRNA as a reporter to synthesise mRNA-loaded cationic lipid nanoparticles, and optimise their mRNA encapsulation and transfection efficiency in ovarian cancer cells. The optimisation process included: 1) adjusting the lipid formulation; 2) adjusting the input mRNA concentration before lipid nanoparticle extrusion; and 3) adjusting the extrusion methods. After optimisation, the encapsulation efficiency was optimised to 62%, thus achieving a relatively high transfection luminescence signal (9.4 times compared to baseline). The lipid nanoparticles also demonstrated stable physical characteristics and high biocompatibility (above 75% cell viability after treatment) within 24 hours. Overall, this project evaluated the synthesis of DOPE/DC-Chol cationic lipid nanoparticles, and optimised their mRNA encapsulation and transfection efficiency in ovarian cancer cell lines. The optimised lipid nanoparticles can be utilised as an ideal system for mRNA delivery, which could be further developed as a potential platform for the immunotherapy in ovarian cancer.

bioengineering↗

bioRxiv2023

A novel lethal cuticular structural protein, AaCPR100A and its upstream interaction protein, G12-like, function in cuticle and egg shell formation in the yellow fever mosquito, Aedes aegypti

AaCPR100A is a structural protein, found in the soft cuticle of Ae. Aegypti. RNAi of AaCPR100A resulted in high mortality in Ae. Aegypti and abnormal egg development in the surviving mosquitoes. Over thirty proteins that could interact with AaCPR100A were screened out by yeast two-hybrid assay, and subsequently, further verification by hybrid and GST pull-down assays identified that G12-like had the strongest interaction with AaCPR100A. RNAi of G12-like suggested it may be related to larva development. Interestingly, the adults in which the G12-like gene was knocked down were sensitive to low temperature, and their egg shell formation, production, and hatching were affected. G12-like has the opposite effect in the upstream expression of AaCPR100A, promoting AaCPR100A function in the larval stage and inhibiting AaCPR100A in the adult stage. In all, functional studies of AaCPR100A and its interaction protein G12-like provide insight into its involvement in cuticle development and formation and egg shell formation.

molecular biology↗

bioRxiv2023

IMPACT: a web server for exploring immunotherapeutic predictive and cancer prognostic biomarkers

Immune checkpoint inhibitors (ICIs) are a breakthrough in oncology treatment, and studies of screening predictive biomarkers of ICIs are emerging. We developed a web server named IMPACT (http://impact.brbiotech.com/) to thoroughly explore immunotherapeutic predictive or prognostic biomarkers. IMPACT contains a large dataset of 6,276 patients treated with ICIs and integrates 11 well-designed function modules, enabling an in-depth solution for biomarkers exploration. Compared with the existing tools, IMPACT was implemented with one exclusive module for interaction analysis and several optimized conventional functions for discovering novel biomarkers. Specifically, the interaction analysis of biomarker-treatment effect is essential to determine whether a biomarker is predictive and/or prognostic for ICIs. Moreover, several optimized functions allow complicated biomarker exploration, including customized selections of variant types in more detail, automatically screening meaningful co-mutations among multiple genes, and selecting cut-off values for gene expression biomarkers. In summary, IMPACT is a comprehensive analysis resource to facilitate biomarker research of ICIs.

bioinformatics↗