Biology subjects

Chen, P.

Publications and source records attributed to Chen, P..

At least 91 records · Page 5Linked to original sources

bioRxiv2024

Making Aptamers More Antibody-like: Targeting AXL in Vivo Using a Bottlebrush Polymer-Conjugated Aptamer

The overexpression of receptor tyrosine kinase AXL is linked to acquired drug resistance in cancer treatments. Aptamers, acting as antibody surrogates, have been envisioned as potential inhibitors for AXL. However, aptamers face difficult pharmacological challenges including rapid degradation and clearance. Herein, we report a phosphodiester-backboned bottlebrush polymer as a carrier for conjugated aptamers. Termed pacDNA, the conjugate improves aptamer specificity in vivo, prolongs blood retention, and enhances overall aptamer bioactivity. Treatment with pacDNA in AXL-overexpressing cell lines significantly inhibits AXL phosphorylation, resulting in reduced cancer cell migration and invasion. In a non-small cell lung cancer xenograft model (NCI-H1299), pacDNA treatment leads to single-agent reduction in tumor growth. These results highlight the potential of bottlebrush polymers in the field of aptamer therapeutics.

cancer biology↗

bioRxiv2024

Bottlebrush polymers with sequence-controlled backbones for enhanced oligonucleotide delivery

The clinical translation of oligonucleotide-based thera-peutics continues to encounter challenges in delivery. In this study, we introduce a novel class of delivery vehicles for oligonucleotides, which are based on polyethylene glycol (PEG) bottlebrush polymers with sequence-defined backbones. Using solid-phase synthesis and bespoke phosphoramidites, the oligonucleotide and the polymer backbone can both be assembled on the solid support. The synthesis allows chemical modifiers such as carbon 18 (C18) units to be incorporated into the backbone in specific patterns to modulate the cell-materials interactions. Subsequently, PEG side chains were grafted onto the polymer segment of the resulting polymer-oligonucleotide conjugate, yielding bottlebrush polymers. We report an optimal pattern of the C18 modifier that leads to improved cellular uptake, plasma phar-macokinetics, biodistribution, and antisense activity in vivo. Our results provide valuable insights into the pacDNA structure-property relationship and suggest a possibility of tuning the polymer backbone to meet the specific delivery requirements of various diseases. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/616318v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1a332e7org.highwire.dtl.DTLVardef@1630ab1org.highwire.dtl.DTLVardef@15306dforg.highwire.dtl.DTLVardef@1e83f0e_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Micro-C reveals MORC/ApiAP2-mediated links between distant, functionally related genes in the human malaria parasite

Genome organization plays a significant role in silencing heterochromatinized genes in the most virulent human malaria parasite, Plasmodium falciparum. However, it remains unclear how heterochromatinized genes spatially cluster or if active genes are also organized in a specific manner. We used Micro-C to achieve a near-nucleosome resolution DNA-DNA contact map, which revealed new inter- and intrachromosomal heterochromatic and euchromatic structures in the blood stage parasite. We observed subtelomeric fold structures that facilitate interactions amongst heterochromatinized genes involved in antigenic variation. In addition, we identified long-range intra- and interchromosomal interactions amongst active, stage-specific genes. Both structures are mediated by AP2-P, an ApiAP2 transcription factor, and a putative MORC chromatin remodeler, and functional specificity is achieved via combinatorial binding with other sequence-specific DNA-binding factors. This study provides unprecedented insight into the organizational machinery used by this medically important eukaryotic parasite to spatially coordinate genes underlying antigenic variation and to co-activate stage-specific genes.

molecular biology↗

bioRxiv2024

Optimized semi-specific PCR amplification using arbitrarily degenerate primer for genome-wide genotyping and its application in peanut genetic diversity study

Cultivated peanut (Arachis hypogaea L.) is an important legume crop with a large genome size but a limited genetic diversity. Evaluating the genetic variation among diverse peanut germplasms using genome-wide molecular markers is an effective strategy to explore its genetic diversity and thereby facilitate peanut improvement. In this study, we introduced a novel whole-genome genotyping (WGG) technique named dRAPD-seq (degenerate Random Amplification Polymorphic DNA and sequencing), which relies on semi-specific PCR amplification by arbitrarily degenerate (AD) primer and next-generation sequencing (NGS), and demonstrated its robust reproducibility and high accuracy. Subsequently, we applied dRAPD-seq to investigate the genetic relatedness within a population of 101 diverse peanut accessions and identified a low genetic diversity among these accessions. Our phylogenetic tree, population structure analyses, and principal component analysis (PCA) indicated that this population could be clustered into three subpopulations, largely corresponding to three botanical types. In conclusion, this research not only introduced a cost-effective and easy-to-conduct WGG method but also provided valuable insights for utilizing these peanut accessions in future breeding programs.

genomics↗

bioRxiv2024

A single-nucleus census of immune and non-immune cell types for the major immune organ systems of chicken.

In the avian host, comprehensively cataloging immune cell types, their transcriptome profiles, and varying molecular responses to pathogen challenges are necessary steps toward a better understanding of the interplay between genetics and disease resilience. We present a first nuclei atlas of immune cell types derived from the three main immune organs of layer chickens, including spleen, bursa, and thymus. In bursa we also present, an accounting of cell type activation with the bacterial toxin lipopolysaccharide (LPS). Our analysis includes 36,370 total nuclei and 16, 12, and 12 transcriptionally distinct clusters for spleen, bursa, and thymus, respectively. We discover nuclei molecular profiles that uniquely distinguish states of the transcriptome within cell type that could serve as new means to characterize avian immune subtypes. We further subcluster refined immune cell type classifications, specifically highlighting the transcriptomic diversity of B and T cell subtypes. In the bursa, inferred intercellular communication and signaling pathway enrichment analyses across immune and non-immune cell types demonstrate the unappreciated complexity of the B cell repertoire in a model mimicking systemic bacterial infection. This census of all cell types in both primary and one major secondary avian immune organ system, although preliminary, provides a first review of how nuclei transcribe numerous genes, known and unknown, a critical prerequisite for the study avian immunogenetics by cell type.

immunology↗

bioRxiv2024

The AP2/ERF transcription factor HcERF5 confers drought tolerance via ABA-mediated signaling in kenaf

The APETALA2/ethylene response factor (AP2/ERFs) are pivotal in regulating abiotic stress responses in plants. However, the specific role of ERFs in kenafs response to drought stress remains unclear. In this study, a transcription factors HcERF5 was isolated from kenaf and its role in drought stress tolerance was analyzed. HcERF5 was found to localize in both nucleus and cytoplasm and could be significantly induced by polyethylene glycol-6000 (PEG-6000) and abscisic acid (ABA) in kenaf seedlings. In transgenic Arabidopsis expressing the HcERF5 promoter-driven {beta}-glucuronidase (GUS), strong GUS activity was observed in roots, stems, and leaves. Overexpression of HcERF5 in Arabidopsis enhanced seed germination rates under drought or ABA stress and improved drought tolerance in seedlings by increasing antioxidant enzyme activities, whereas aterf5 knockout lines exhibited the opposite trend. Additionally, HcERF5 overexpressing Arabidopsis showed significantly increased drought tolerance and reduced sensitivity to ABA. Furthermore, virus-induced gene silencing (VIGS) of HcERF5 in kenaf reduced drought tolerance, as evidenced by decreased antioxidant enzyme activity, increased stomatal aperture, and elevated levels of malondialdehyde (MDA), reactive oxygen species (ROS), and proline under drought stress. RNA-seq analysis further revealed that HcERF5 directly regulated ABA signaling pathway. Yeast-two-hybrid (Y2H) assays revealed 29 proteins that interact with HcERF5. Among them, the expression of downstream drought stress-related genes HcPRK, HcRD22, HcMAP2, HcCAB, HcCS, and HcCCoAOMT3 were significantly reduced in HcERF5-silenced plants. Overall, this study highlights the significant potential of HcERF5 in enhancing drought tolerance in kenaf. HighlightO_LIHcERF5 overexpression enhanced drought tolerance in kenaf, however silencing increased drought sensitivity. C_LIO_LIHcERF5 regulates ABA synthesis and increases kenaf stomatal conductance and density under drought stress. C_LIO_LIHcERF5 regulates plant hormone signal transduction, MAPK signalling, and phenylpropanoid biosynthesis in kenaf under drought stress. C_LIO_LIProtein interaction revealed HcERF5 interacts with six stress-response genes. C_LI

molecular biology↗

bioRxiv2024

Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics

Identifying pharmacological probes for human proteins represents a key opportunity to accelerate the discovery of new therapeutics. High-content screening approaches to expand the ligandable proteome offer the potential to expedite the discovery of novel chemical probes to study protein function. Screening libraries of reactive fragments by chemoproteomics offers a compelling approach to ligand discovery, however, optimising sample throughput, proteomic depth, and data reproducibility remains a key challenge. We report a versatile, label-free quantification proteomics platform for competitive profiling of cysteine-reactive fragments against the native proteome. This high-throughput platform combines SP4 plate-based sample preparation with rapid chromatographic gradients. Data-independent acquisition performed on a Bruker timsTOF Pro 2 consistently identified [~]23,000 cysteine sites per run, with a total of [~]32,000 cysteine sites profiled in HEK293T and Jurkat lysate. Crucially, this depth in cysteinome coverage is met with high data completeness, enabling robust identification of liganded proteins. In this study, 80 reactive fragments were screened in two cell lines identifying >400 ligand-protein interactions. Hits were validated through concentration-response experiments and the platform was utilised for hit expansion and live cell experiments. This label-free platform represents a significant step forward in high-throughput proteomics to evaluate ligandability of cysteines across the human proteome.

systems biology↗

bioRxiv2024

Beyond Auditory Relay: Dissecting the Inferior Colliculus's Role in Sensory Prediction, Cognitive Decision-Making, and Reward Prediction

The Inferior Colliculus (IC) has traditionally been regarded as an important relay in the auditory pathway, primarily involved in relaying auditory information from the brainstem to the thalamus. However, this study uncovers the multifaceted role of the IC in bridging auditory processing, sensory prediction, and reward prediction. Through extracellular recordings in monkeys engaged in a sound duration-based deviation detection task, we observed a "climbing effect" in neuronal firing rates, indicative of an enhanced response over sound sequences linked to sensory prediction rather than reward anticipation. Moreover, our findings demonstrate reward prediction errors within the IC, highlighting its complex integration in auditory and reward processing. Further analysis revealed a direct correlation between IC neuronal activity and behavioral choices, suggesting its involvement in decision-making processes. This research highlights a more complex role for the IC than traditionally understood, showcasing its integral role in cognitive and sensory processing and emphasizing its importance in integrated brain functions.

neuroscience↗

bioRxiv2024

Neuron synchronization analyzed through spatial-temporal attention

Across diverse organisms, the temporal dynamics of spiking responses between neurons, the neural synchrony, is crucial for encoding different stimuli. Neural synchrony is especially important in the insect antennal (olfactory) lobe (AL). Previous studies on synchronization, however, rely on pair-wise synchronization metrics including the cross-correlogram and cos-similarity between kernelized spikes train. These pair-wise analyses overlook an important aspect of synchronization which is the interaction at the population neuron level. There are also limited modeling techniques that incorporate the synchronization between neurons in modeling population spike trains. Inspired by recent advancements in machine learning, we leverage a modern attention mechanism to learn a generative normalizing flow that captures neuron population synchronization. Our method not only reveals the spiking mechanism of neurons in the AL region but also produces semi-interpretable attention weights that characterize neuron interactions over time. These automatically learned attention weights allow us to elucidate the known principles of neuron synchronization and further shed light on the functional roles of different cell types (the local interneurons (LNs), and projection neurons (PNs)) in the dynamic neural network in the AL. By varying the balance of excitation and inhibition in this neural circuit, our method further uncovers the pattern between the strength of synchronization and the ratio of an odorant in the mixture. Author SummaryThe olfactory system can accurately compute the mixture of volatile compounds emitted from distant sources, enabling the foraging species to exhibit fast and effective decisions. However, altering ratios of one of the compounds in the mixture could be perceived as a different odor. Leveraging the current understanding of neural synchronization on sensory neural regions of insects, we construct a spatial-temporal attention normalizing flow, which partially replicates the AL regions functionality by learning the spiking mechanics of neurons. Beyond providing insights of the spiking mechanism of neurons in the AL region, our method also produces semi-interpretable attention weights that characterize neuron interaction over time. These automatically learned attention weights allow us to dissect out the principles of neuron synchronization and interaction mechanisms between projection neurons (PNs) and local neurons (LNs). Utilizing our accurate model of these AL functionality, we show evidence that the behavioral relevant compounds are closely clustered together while varying the intensities of one of the behavioral compounds in the mixture could attenuate the synchronization

neuroscience↗

bioRxiv2024

Glycerol Metabolism Contributes to Competition by Oral Streptococci through Production of Hydrogen Peroxide

As a biological byproduct from both humans and microbes, glycerols contribution to microbial homeostasis in the oral cavity remains understudied. Here we examined glycerol metabolism by Streptococcus sanguinis, a commensal associated with oral health. Genetic mutants of glucose-PTS enzyme II (manL), glycerol metabolism (glp and dha pathways), and transcriptional regulators were characterized with regard to glycerol catabolism, growth, production of hydrogen peroxide (H2O2), transcription, and competition with Streptococcus mutans. Biochemical assays identified the glp pathway as a novel source of H2O2 production by S. sanguinis that is independent of pyruvate oxidase (SpxB). Genetic analysis indicated that the glp pathway requires glycerol and a transcriptional regulator, GlpR, for expression and is negatively regulated by PTS, but not the catabolite control protein, CcpA. Conversely, deletion of either manL or ccpA increased expression of spxB and a second, H2O2-non-producing glycerol metabolic pathway (dha), indicative of a mode of regulation consistent with conventional carbon catabolite repression (CCR). In a plate-based antagonism assay and competition assays performed with planktonic and biofilm-grown cells, glycerol greatly benefited the competitive fitness of S. sanguinis against S. mutans. The glp pathway appears to be conserved in several commensal streptococci and actively expressed in caries-free plaque samples. Our study suggests that glycerol metabolism plays a more significant role in the ecology of the oral cavity than previously understood. Commensal streptococci, though not able to use glycerol as a sole carbohydrate for growth, benefit from catabolism of glycerol through production of both ATP and H2O2. ImportanceGlycerol is an abundant carbohydrate found in oral cavity, both due to biological activities of humans and microbes, and as a common ingredient of foods and health care products. However, very little is understood regarding the metabolism of glycerol by some of the most abundant oral bacteria, commensal streptococci. This was in part because most streptococci cannot grow on glycerol as the sole carbon source. Here we show that Streptococcus sanguinis, an oral commensal associated with dental health, can degrade glycerol for persistence and competition through two independent pathways, one of which generates hydrogen peroxide at levels capable of inhibiting a dental pathobiont, Streptococcus mutans. Preliminary studies suggest that several other commensal streptococci are also able to catabolize glycerol, and glycerol-related genes are being actively expressed in human dental plaque samples. Our findings reveal the potential of glycerol to significantly impact microbial homeostasis which warrants further exploration.

microbiology↗

bioRxiv2024

Escalation of genome defense capacity enables control of an expanding meiotic driver

SummaryFrom RNA interference to chromatin silencing, diverse genome defense pathways silence selfish genetic elements to safeguard genome integrity1,2. Despite their diversity, different defense pathways share a modular organization, where numerous specificity factors identify diverse targets and common effectors silence them. In the PIWI-interacting RNA (piRNA) pathway, which controls selfish elements in the metazoan germline, diverse target RNAs are first identified by complementary base pairing with piRNAs and then silenced by PIWI-clade nucleases via enzymatic cleavage1,3. Such a binary architecture allows the defense systems to be readily adaptable, where new targets can be captured via the innovation of new specificity factors4,5. Thus, our current understanding of genome defense against lineage-specific selfish genes has been largely limited to the evolution of specificity factors, while it remains poorly understood whether other types of innovations are required. Here, we describe a new type of innovation, which escalates the defense capacity of the piRNA pathway to control a recently expanded selfish gene in Drosophila melanogaster. Through an in vivo RNAi screen for repressors of Stellate--a recently evolved and expanded selfish meiotic driver6-8--we discovered a novel defense factor, Trailblazer. Trailblazer is a transcription factor that promotes the expression of two PIWI-clade nucleases, Aub and AGO3, to match Stellate in abundance. Recent innovation in the DNA-binding domain of Trailblazer enabled it to drastically elevate Aub and AGO3 expression in the D. melanogaster lineage, thereby escalating the silencing capacity of the piRNA pathway to control expanded Stellate and safeguard fertility. As copy-number expansion is a recurrent feature of diverse selfish genes across the tree of life9-12, we envision that augmenting the defense capacity to quantitatively match selfish genes is likely a repeatedly employed defense strategy in evolution.

genetics↗

bioRxiv2024

Bola-amphiphilic dendrimer empowers imatinib to target metastatic ovarian cancer stem cells via beta-catenin-HRP2 signaling axis

Ovarian cancer is the leading cause of death among all gynecological malignancies, and drug resistance renders the current chemotherapy agents ineffective for patients with advanced metastatic tumors. We report an effective treatment strategy for targeting metastatic ovarian cancer involving a nanoformulation (Bola/IM) - bola-amphiphilic dendrimer (Bola)-encapsulated imatinib (IM) - to target the critical mediator of ovarian cancer stem cells (CSCs) CD117 (c-Kit). Bola/IM offered significantly more effective targeting of CSCs compared to IM alone, through a novel and tumor-specific {beta}-catenin/HRP2 axis, allowing potent inhibition of cancer cell survival, stemness and metastasis in metastatic and drug-resistant ovarian cancer cells. Promising results were also obtained in clinically relevant patient-derived ascites and organoids, alongside high tumor-oriented accumulation and favorable pharmacokinetic properties in mouse models. Furthermore, Bola/IM displayed synergistic anticancer activity when combined with the first-line chemotherapeutic drug cisplatin in patient-derived xenograft mouse models, without any adverse effects. Our findings support the use of Bola/IM as a nanoformulation to empower IM, providing targeted and potent treatment of metastatic ovarian cancer. Our study thus represents a significant advancement towards addressing the unmet medical need for improved therapies targeting this challenging disease.

cancer biology↗

bioRxiv2024

Multi-step engineered adeno-associated virus enables whole-brain mRNA delivery

Adeno-associated viruses (AAVs) are commonly used vectors for DNA delivery in gene therapy. Here we developed a system that enables the AAV shell to package mRNAs by multi-step introduction of RNA-packaging components and modification of AAV Rep proteins. The resultant mRNA-carrying AAVs (RAAVs) retained most properties of conventional AAVs, including capsid composition, virus morphology, and tissue tropism. These RAAVs could mediate mRNA transfer into target cells and tissues, leading to transient expression of the functional protein. Importantly, intravenously injected RAAVs efficiently crossed the blood-brain barrier (BBB) and infected the whole mouse brain. Thus, the DNA viral vector could be modified for RNA delivery, and our RAAV represents the first highly efficient BBB-crossing mRNA delivery system that could be used for therapeutic purposes via whole-brain infection.

bioengineering↗

bioRxiv2024

Protective role of parenthood on age-related brain function in mid- to late-life

The experience of parenthood can profoundly alter ones body, mind, and environment, yet we know little about the long-term associations between parenthood and brain function and aging in adulthood. Here, we investigate the link between number of children parented (parity) and age on brain function in 19,964 females and 17,607 males from the UK Biobank. In both females and males, increased parity was positively associated with functional connectivity, particularly within the somato/motor network. Critically, the spatial topography of parity-linked effects was inversely correlated with the impact of age on functional connectivity across the brain for both females and males, suggesting that a higher number of children is associated with patterns of brain function in the opposite direction to age-related alterations. These results indicate that the changes accompanying parenthood may confer benefits to brain health across the lifespan, highlighting the importance of future work to understand the associated mechanisms.

neuroscience↗

bioRxiv2024

Soft-lithographically defined template for arbitrarily patterned acoustic bioassembly

Acoustic bioassembly is recently regarded as a highly efficient biofabrication tool to generate functional tissue mimics. Despite their capacity of directly patterning live cells with close intercellular proximity, most acoustic bioassembly techniques are currently limited to generate some specific simple types of periodic and symmetric patterns, which represents an urgent challenge to emulate geometrically complex cytoarchitecture in human tissue. To address this challenge, we herein demonstrate a soft-lithographically defined acoustic bioassembly (SLAB) technique that enables to assemble live cells into geometrically defined arbitrary multicellular structures. Particularly, we employed a widely accessible soft lithography technique to fabricate a PDMS construct that works as an amplitude modulation template to define the pressure distribution of near-field acoustic waves. We found that zero pressure areas of the near-field acoustic waves at the PDMS surface distribute above the air-filling regions of the PDMS construct when both the PDMS top layer and air layer are approximately one-tenth of the acoustic wavelength. Using this technique, bioparticles can be assembled into symmetrical or asymmetrical patterns. Specifically, we have demonstrated the SLAB of endothelial spheroids and hepatic cells into liver tissue mimics (LTMs). The functional analysis further indicates that the formed LTMs displayed liver-specific functions, including albumin secretion, urea synthesis, glucose metabolism, and lipid storage. We expect this SLAB technique will be broadly used to construct complex functional tissues for tissue engineering and regenerative medicine.

bioengineering↗

bioRxiv2024

Determining the Youngs Modulus of the Bacterial Cell Envelope

Bacteria experience substantial physical forces in their natural environment including forces caused by osmotic pressure, growth in constrained spaces, and fluid shear. The cell envelope is the primary load-carrying structure of bacteria, but the mechanical properties of the cell envelope are poorly understood; reports of Youngs modulus of the cell envelope of E. coli are widely range from 2 MPa to 18 MPa. We have developed a microfluidic system to apply mechanical loads to hundreds of bacteria at once and demonstrated the utility of the approach for evaluating whole-cell stiffness. Here we extend this technique to determine Youngs modulus of the cell envelope of E. coli and of the pathogens V. cholerae and S. aureus. An optimization-based inverse finite element analysis was used to determine the cell envelope Youngs modulus from observed deformations. The Youngs modulus of the cell envelope was 2.06 {+/-} 0.04 MPa for E. coli, 0.84 {+/-} 0.02 MPa for E. coli treated with a chemical known to reduce cell stiffness, 0.12 {+/-} 0.03 MPa for V. cholerae, and 1.52 {+/-} 0.06 MPa for S. aureus (mean {+/-} SD). The microfluidic approach allows examining hundreds of cells at once and is readily applied to Gram-negative and Gram-positive organisms as well as rod-shaped and cocci cells, allowing further examination of the structural causes of differences in cell envelope Youngs modulus among bacteria species and strains.

bioengineering↗

bioRxiv2024

Biomechanical regulation of cell shapes promotes branching morphogenesis of the ureteric bud epithelium

BackgroundBranching morphogenesis orchestrates organogenesis in many tissues including kidney, where ureteric bud branching determines kidney size and nephron number. Defects in branching morphogenesis result in congenital renal anomalies which manifest as deviations in size, function, and nephron number thus critically compromising the lifelong renal functional capacity established during development. Advances in the genetic and molecular understanding of ureteric bud branching regulation have proved insufficient to improve prognosis of congenital renal defects. Thus, we addressed mechanisms regulating three-dimensional (3D) ureteric bud epithelial cell morphology and cell shape changes during novel branch initiation to uncover the contributions of cellular mechanics on cellular functions and tissue organization in normal and branching-compromised bud tips. MethodsWe explored epithelial cell behavior at all scales by utilizing a combination of mouse genetics and a custom machine-learning segmentation pipeline in MATLAB. Ureteric bud epithelial cell shapes and sizes were quantified in 3D wholemount kidneys. A combination with live imaging of fluorescently labelled UB cells, traction force microscopy, and primary UB cells were used to determine how basic cellular features and niche biomechanics contribute to complex novel branch point determination in the process that aims at gaining optimal growth and epithelial density in a limited space. ResultsMachine learning-based segmentation of tip epithelia identified geometrical round-to-elliptical transformation as a key cell shape change facilitating shifts in growth direction that enable propitious branching complexity. Cell shape and molecular analyses in branching-compromised epithelia demonstrated a failure to condense cell size and conformation. Analysis of branching-compromised ureteric bud derived epithelial cells demonstrated disrupted E-CADHERIN and PAXILLIN mediated adhesive forces and defective cytoskeletal dynamics as detected by fluorescent labelling of actin in primary ureteric bud epithelial cells. Branching-compromised ureteric bud epithelial cells showed wrinkled nuclear shapes and alterations in MYH9-based microtubule organization, which suggest a stiff cellular niche with disturbed sensing of and response to biomechanical cues. ConclusionsOur results indicate that the adhesive forces within the epithelium and towards the niche composed of nephron progenitors must dynamically fluctuate to allow complexity in arborization during new branch formation. The data collectively propose a model where epithelial cell crowding in tandem with stretching transforms individual cells into elliptical and elongated shapes. This creates local curvatures that drive new branch formation during the ampulla-to-asymmetric ampulla transition of ureteric bud.

developmental biology↗

bioRxiv2024

HER2 Prognostic Significance and Therapeutic Implications in Gastric Cardia Adenocarcinoma: Insights from Multi-Omics Profiling

Therapeutic targets for Gastric Cardia Adenocarcinoma (GCA), particularly for HER2- negative patients, are lacking. Here, we conducted multi-omics profiling on 128 GCA patients using mass spectrometry, whole-exome sequencing, RNA-Seq, and metabolomics. We found HER2 to be a favorable prognostic marker for GCA. Employing molecular counting, we categorized patients into HER2-high, -low, and -negative groups. We uncovered an enrichment of DNA repair features in the HER2-high group, while HER2-low and -negative groups exhibited strong inflammation. We found that tumor mutation burden may not be the distinguishing factor among these three groups. We revealed that the HER2-negative and -low groups have a tumor-suppressive immune microenvironment, and HER2 expression is associated with fatty acid metabolic profiles and inflammation in the blood of patients. Our study revealed anti-inflammatory and immune checkpoint inhibition, targeting PD-L2 and the CD47/SIRPA pair, as therapeutic strategies for HER2-negative GCA patients. These findings highlight promising avenues for personalized treatment for GCA.

cancer biology↗