Biology subjects

Du, E.

Publications and source records attributed to Du, E..

9 recordsLinked to original sources

bioRxiv2024

Engineered paediatric tumours retain patient tumour genotype and phenotype for precision medicine.

Precision medicine for paediatric and adult cancers that includes drug sensitivity profiling, can identify effective therapies for individual patients. However, obtaining adequate biopsy samples for high-throughput (HTP) screening remains challenging, with tumours needing to be expanded in culture or patient-derived xenografts - this is time-consuming and often unsuccessful. Herein, we have developed paediatric patient-derived tumour models using an engineered extracellular matrix (ECM) tissue mimic hydrogel system and HTP 3D bioprinting. Gene expression analysis from neuroblastoma and sarcoma patients identified key components of the ECM in these tumour types. Engineered hydrogels with ECM-mimic peptides were used to create patient-specific tumour organoids, modelling tumour growth conditions. Expanded tumour organoids recapitulated the genetic and phenotypic characteristics of the original tumours and retained tumourgenicity. Screening of these models identified individualised drug sensitivities. Our approach offers a timely and clinically relevant technology platform for precision medicine in paediatric cancers, potentially transforming preclinical testing across cancer types.

cancer biology↗

bioRxiv2024

Mapping Plasmodium transitions and interactions in the Anopheles female

The human malaria parasite, Plasmodium falciparum, relies exclusively on Anopheles mosquitoes for transmission. Once ingested during blood feeding, most parasites die in the mosquito midgut lumen or during epithelium traversal1. How surviving ookinetes interact with midgut cells and form oocysts is poorly known, yet these steps are essential to initiate a remarkable growth process culminating in the production of thousands of infectious sporozoites2. Here, using single-cell RNA sequencing of both parasites and mosquito cells across different developmental stages and metabolic conditions, we unveil key transitions and mosquito-parasite interactions occurring in the midgut. Functional analyses uncover processes regulating oocyst growth and identify the transcription factor PfSIP2 as essential for sporozoite infection of human hepatocytes. Combining shared mosquito-parasite barcode analysis with confocal microscopy, we reveal that parasites preferentially interact with midgut progenitor cells during epithelial crossing, potentially using their basal location as an exit landmark. Additionally, we show tight connections between extracellular late oocysts and surrounding muscle cells that may ensure parasites adherence to the midgut. We confirm our major findings in several mosquito-parasite combinations, including field-derived parasites. Our study provides fundamental insight into the molecular events characterizing previously inaccessible biological transitions and mosquito-parasite interactions, and identifies candidates for transmission-blocking strategies.

microbiology↗

bioRxiv2024

Genome-wide association study for age-related hearing loss in CFW mice

Age-related hearing impairment is the most common cause of hearing loss and is one of the most prevalent conditions affecting the elderly globally. It is influenced by a combination of environmental and genetic factors. The mouse and human inner ears are functionally and genetically homologous. Investigating the genetic basis of age-related hearing loss (ARHL) in an outbred mouse model may lead to a better understanding of the molecular mechanisms of this condition. We used Carworth Farms White (CFW) outbred mice, because they are genetically diverse and exhibit variation in the onset and severity of ARHL. The goal of this study was to identify genetic loci involved in regulating ARHL. Hearing at a range of frequencies was measured using Auditory Brainstem Response (ABR) thresholds in 946 male and female CFW mice at the age of 1, 6, and 10 months. We obtained genotypes at 4.18 million single nucleotide polymorphisms (SNP) using low-coverage (mean coverage 0.27x) whole-genome sequencing followed by imputation using STITCH. To determine the accuracy of the genotypes we sequenced 8 samples at >30x coverage and used calls from those samples to estimate the discordance rate, which was 0.45%. We performed genetic analysis for the ABR thresholds for each frequency at each age, and for the time of onset of deafness for each frequency. The SNP heritability ranged from 0 to 42% for different traits. Genome-wide association analysis identified several regions associated with ARHL that contained potential candidate genes, including Dnah11, Rapgef5, Cpne4, Prkag2, and Nek11. We confirmed, using functional study, that Prkag2 deficiency causes age-related hearing loss at high frequency in mice; this makes Prkag2 a candidate gene for further studies. This work helps to identify genetic risk factors for ARHL and to define novel therapeutic targets for the treatment and prevention of ARHL.

genetics↗

bioRxiv2023

Interplay between nutrient transporters ensures fertility in the malaria mosquito Anopheles gambiae

Females from many mosquito species feed on blood to acquire nutrients for egg development. The oogenetic cycle has been characterized in the arboviral vector Aedes aegypti, where after a bloodmeal, the lipid transporter lipophorin (Lp) shuttles lipids from the midgut and fat body to the ovaries, and a yolk precursor protein, vitellogenin (Vg), is deposited into the oocyte by receptor-mediated endocytosis. Our understanding of how the roles of these two nutrient transporters are mutually coordinated is however limited in this and other mosquito species. Here, we demonstrate that in the malaria mosquito Anopheles gambiae, Lp and Vg are reciprocally regulated in a timely manner to optimize egg development and ensure fertility. Defective lipid transport via Lp silencing triggers abortive ovarian follicle development, leading to misregulation of Vg and aberrant yolk granules. Conversely, depletion of Vg causes an upregulation of Lp in the fat body in a manner that appears to be at least partially dependent on target of rapamycin (TOR) signaling, resulting in excess lipid accumulation in the developing follicles. Embryos deposited by Vg-depleted mothers are completely infertile, and are arrested early during development, likely due to severely reduced amino acid levels and protein synthesis. Our findings demonstrate that the mutual regulation of these two nutrient transporters is essential to safeguard fertility by ensuring correct nutrient balance in the developing oocyte, and validate Vg and Lp as two potential candidates for mosquito control. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/543516v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1c9b326org.highwire.dtl.DTLVardef@1109e59org.highwire.dtl.DTLVardef@c263borg.highwire.dtl.DTLVardef@1a1f9df_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Selective loss of specific subsets of hair cell and spiral ganglion cell types in an outbred mouse model of age-related hearing loss

Age-related hearing loss (ARHL) is the most common cause of hearing loss and one of the most prevalent conditions affecting the elderly worldwide. Despite evidence from our lab and others about its polygenic nature, little is known about the specific genes, cell types and pathways involved in ARHL, impeding the development of therapeutic interventions. In this manuscript, we describe, for the first time, the complete cell-type specific transcriptome of the aging mouse cochlea using snRNA-seq in an outbred mouse model in relation to auditory threshold variation. Cochlear cell types were identified using unsupervised clustering and annotated via a three-tiered approach - first by linking to expression of known marker genes, then using the NS-Forest algorithm to select minimum cluster-specific marker genes and reduce dimensional feature space for statistical comparison of our clusters with existing publicly-available data sets on the gEAR website (https://umgear.org/), and finally, by validating and refining the annotations using Multiplexed Error Robust Fluorescence In Situ Hybridization (MERFISH) and the cluster-specific marker genes as probes. We report on 60 unique cell-types expanding the number of defined cochlear cell types by more than two times. Importantly, we show significant specific cell type increases and decreases associated with loss of hearing acuity implicating specific subsets of hair cell subtypes, ganglion cell subtypes, and cell subtypes withing the stria vascularis in this model of ARHL. These results provide a view into the cellular and molecular mechanisms responsible for age-related hearing loss and pathways for therapeutic targeting.

genomics↗

bioRxiv2020

Electrical impedance detection of sickle cell vaso-occlusion in microfluidic capillary structures

Sickle cell disease (SCD) is primarily associated with episodic vaso-occlusive events. Poorly deformable sickle cells may get stuck in small blood vessels, slow down or block blood flow, leading to local hypoxia that damages tissues and organs. In this paper, we present a novel electrical impedance sensing technique for detection of the progressive occlusion by sickle cells in microfluidic capillary structures. Changes in both resistance and reactance of the sickle blood flow were observed at multiple low frequencies (< 500 kHz), upon the deoxygenation and reoxygenation processes. In contrast, no obvious impedance changes were observed in the flow of normal blood cells and sickle blood cells treated with anti-sickling agent. Accuracy of the impedance-based detection of the vaso-occlusion process was verified by microscopic observation. The results show the distinct sensing performance of sickle cell vaso-occlusion by electrical impedance, which does not require sophisticated optical microscopy or video processing. The low frequency impedance sensing can be achieved by replacing the benchtop equipment with low-cost, high precision impedance converter system, allowing for detection of sickle cell vaso-occlusion in point-of-care settings.

bioengineering↗

bioRxiv2020

A Portable Impedance Microflow Cytometer for Measuring Cellular Response to Hypoxia

This paper presents the development and testing of a low-cost, portable microflow cytometer based on electrical impedance sensing, for single cell analysis under controlled oxygen microenvironment. The cytometer system is based on an AD5933 impedance analyzer chip, a microfluidic chip, and an Arduino microcontroller operated by a custom Android application. A representative case study on human red blood cells (RBCs) affected by sickle cell disease is conducted to demonstrate the capability of the cytometry system. Equivalent circuit model of a suspending biological cell is used to interpret the electrical impedance of single flowing RBCs. In normal blood, cytoplasmic resistance and membrane capacitance do not change significantly with the change in oxygen tension. In contrast, RBCs affected by sickle cell disease show that upon hypoxia treatment, the cytoplasmic resistance decrease from 11.6 M{Omega} to 23.4 M{Omega}, and membrane capacitance decrease from 1.1 pF to 0.8 pF. Strong correlations are identified between the changes in these subcellular electrical components of single cells and the cell sickling process induced by hypoxia treatment. The representative results reported in this paper suggest that single cell electrical impedance can be used as a sensitive biophysical marker for quantifying cellular response to change in oxygen concentration. The developed flow cytometry system and the methodology can also be extended to analysis of cellular response to hypoxia in other cell types. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/224006v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@147f903org.highwire.dtl.DTLVardef@2d4c35org.highwire.dtl.DTLVardef@1e63b0dorg.highwire.dtl.DTLVardef@2eeb0c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2020

Smartphone-based Sickle Cell Disease Detection and Monitoring for Point-of-Care Settings

Sickle cell disease (SCD) is a worldwide hematological disorder causing painful episodes, anemia, organ damage, stroke, and even deaths. It is more common in sub-Saharan Africa and other resource-limited countries. Conventional laboratory-based diagnostic methods for SCD are time-consuming, complex, and cannot be performed at point-of-care (POC) and home settings. Optical microscope-based classification and counting demands a significant amount of time, extensive setup, and cost along with the skilled human labor to distinguish the normal red blood cells (RBCs) from sickled cells. There is an unmet need to develop a POC and home-based test to diagnose and monitor SCD and reduce mortality in resource-limited settings. An early-stage and timely diagnosis of SCD can help in the effective management of the disease. In this article, we utilized a smartphone-based image acquisition method for capturing RBC images from the SCD patients in normoxia and hypoxia conditions. A computer algorithm is developed to differentiate RBCs from the patients blood before and after cell sickling. Using the developed smartphone-based technique, we obtained similar percentage of sickle cells in blood samples as analyzed by conventional method (standard microscope). The developed method of testing demonstrates the potential utility of the smartphone-based test for reducing the overall cost of screening and management for SCD, thus increasing the practicality of smartphone-based screening technique for SCD in low-resource settings. Our setup does not require any special storage requirements and is particularly useful in assessing the severity of the SCD. This is the characteristic advantage of our technique as compared to other hemoglobin-based POC diagnostic techniques.

bioengineering↗

bioRxiv2018

Nonnegligible role of warming-induced soil drying in regulating warming effect on soil respiration

Based on results of a 26-year soil warming experiment (soil temperature being elevated by 5 {degrees}C) in a Harvard hardwood forest, Melillo et al. demonstrated a four-phase pattern of long-term warming effect on soil respiration, while the mechanisms were not fully elucidated because they neglected the indirect effect due to warming-induced soil drying. By showing a significant correlation between precipitation anomaly and inter-annual variation of warming effect on soil respiration, we suggest a nonnegligible role of warming-induced soil drying in regulating the long-term warming effect on soil respiration. Our analysis recommends further efforts to consider both the direct and indirect (i.e., warming-induced soil drying) warming effects to gain more in-depth understanding of the long-term soil C dynamics.

ecology↗