Biology subjects

Chen, W. H.

Publications and source records attributed to Chen, W. H..

5 recordsLinked to original sources

bioRxiv2024

Kinetic patterns of single cell gene expression discriminate between the murine cellular responses to live attenuated and inactivated Yellow Fever vaccines

The success of the live attenuated Yellow Fever vaccine (YF17D) that elicits immunity lasting over thirty years has made it a widely used model to understand the generation of durable protection. We compare the early single-cell level transcriptional response in mice to YF17D and an adjuvanted-inactivated, but less effective version (InYF). Within the first week, we identify 70 kinetic patterns in 45 cellular clusters, majority of which discriminate between the two formulations, some in a tissue and sex-specific manner. Intriguingly, differential transcripts fall into two categories, one whose association with YF17D or InYF is maintained even when decoupled from their cell-type of expression and the other where such cell-plus-gene pairing is critical to maintain differential marker status. We demonstrate applications of this resource, by identifying B cells with varied interferon and antigen responsiveness in relation to each vaccine. This high-resolution dataset is amenable to further biomarker discovery and hypothesis generation.

immunology↗

bioRxiv2024

CountASAP: A Lightweight, Easy to Use Python Package for Processing ASAPseq Data

Declining sequencing costs coupled with the increasing availability of easy-to-use kits for the isolation of DNA and RNA transcripts from single cells have driven a rapid proliferation of studies centered around genomic and transcriptomic data. Simultaneously, a wealth of new techniques have been developed that utilize single cell technologies to interrogate a broad range of cell-biological processes. One recently developed technique, transposase-accessible chromatin with sequencing (ATAC) with select antigen profiling by sequencing (ASAPseq), provides a combination of chromatin accessibility assessments with measurements of cell-surface marker expression levels. While software exists for the characterization of these datasets, there currently exists no tool explicitly designed to reformat ASAP surface marker FASTQ data into a count matrix which can then be used for these downstream analyses. To address this, we created CountASAP, an easy-to-use Python package purposefully designed to transform FASTQ files from ASAP experiments into count matrices compatible with commonly-used downstream bioinformatic analysis packages. CountASAP takes advantage of the independence of the relevant data structures to perform fully parallelized matches of each sequenced read to user-supplied input ASAP oligos and unique cell-identifier sequences.

bioinformatics↗

bioRxiv2023

Impact of Bmal1 rescue and time-restricted feeding on liver and muscle proteomes during the active phase in mice

ObjectiveMolecular clocks and daily feeding cycles support metabolism in peripheral tissues. Although the roles of local clocks and feeding is well defined at the transcriptional level, their impact on governing protein abundances in peripheral tissues is unclear. Here, we determine the relative contributions of the local molecular clock and daily feeding cycles on liver and muscle proteomes during feeding. MethodsLC-MS/MS was performed on liver and skeletal muscle harvested four hours into the dark phase from wild-type (WT), Bmal1 knockout (KO), and liver- and muscle-Bmal1-rescued (LMRE) mice housed under 12-h light/12-h dark cycles with either ad libitum feeding or nighttime-restricted feeding. Additional molecular and metabolic analyses were performed on liver and cultured hepatocytes. ResultsFeeding-fasting cycles had only minimal effects on liver and none on muscle. In contrast, Bmal1 KO altered the abundance of 674 proteins in liver, and 80 in muscle. Rescue of liver and muscle Bmal1 restored 50% of proteins in liver and 25% in muscle. These included proteins involved in carbohydrate metabolism in muscle and in fatty acid oxidation in liver. For liver, proteins involved in de novo lipogenesis were largely dependent on Bmal1 function in other tissues (i.e., the wider clock system). Proteins regulated by BMAL1 were enriched for secreted proteins; we determined that the maintenance of FGF1 abundance requires liver BMAL1, and that autocrine signaling through FGF1 is necessary and sufficient for mitochondrial respiration in hepatocytes. ConclusionsBMAL1 in liver and muscle is a more potent regulator of dark phase proteomes than daily feeding cycles, highlighting the need to assess protein levels in addition to mRNA when investigating clock mechanisms. The proteome is more extensively regulated by BMAL1 in liver than in muscle, and numerous metabolic pathways in peripheral tissues are reliant on the function of the clock system as a whole.

systems biology↗

bioRxiv2021

Functional and structural modifications of influenza antibodies during pregnancy

Pregnancy represents a unique tolerogenic immune state which may alter susceptibility to infection and vaccine-response. Here we characterized humoral immunity to seasonal influenza vaccine strains in pregnant and non-pregnant women. Pregnant women had reduced hemagglutinin subtype-1 (H1)-IgG, IgG1, and IgG2, hemagglutination inhibition and group 1 and 2 stem IgG. However, H1-specific avidity and Fc{gamma}R1 binding increased. Influenza-antibodies in pregnancy had distinct Fc and Fab glycans characterized by di-galactosylation and di-sialylation. In contrast, agalactosylation and bisection were prominent outside of pregnancy. H1-specific Fc-functionality was moderately reduced in pregnancy, although likely compensated by stronger binding to cognate antigen and FcR. Multivariate analysis revealed distinct populations characterized by Fc{gamma}R1 binding, H1-IgG levels, and glycosylation. Pooled sera from pregnant women exhibited longer retention in vivo. Our results demonstrate structural and functional modulation of humoral immunity during pregnancy in an antigen-specific manner towards reduced inflammation, increased retention in circulation, and efficient placental transport.

immunology↗

bioRxiv2021

ALT Neuroblastoma Chemoresistance due to ATM Activation by Telomere Dysfunction is Reversible with the ATM Inhibitor AZD0156

Cancers overcome replicative immortality by activating either telomerase or an alternative lengthening of telomeres (ALT) mechanism. ALT occurs in [~] 25% of high-risk neuroblastomas and relapse or progression in ALT neuroblastoma patients during or after front-line therapy is frequent and almost uniformly fatal. Temozolomide + irinotecan is commonly used as salvage therapy for neuroblastoma. Patient-derived cell-lines and xenografts established from relapsed ALT neuroblastoma patients demonstrated de novo resistance to temozolomide + irinotecan (as SN-38 in vitro, P<0.05) and in vivo (mouse event-free survival (EFS) P<0.0001) relative to telomerase-positive neuroblastomas. We observed that ALT neuroblastoma cells manifest constitutive ATM kinase activation due to spontaneous telomere dysfunction while telomerase- positive tumors lacked constitutive ATM activation or spontaneous telomere DNA damage. We demonstrated that induction of telomere dysfunction resulted in ATM activation that in turn conferred resistance to temozolomide + SN-38 (4.2 fold-change in IC50, P<0.001). ATM kinase shRNA knock-down or inhibition using a clinical-stage small molecule inhibitor (AZD0156) reversed resistance to temozolomide + irinotecan in ALT neuroblastoma cell-lines in vitro (P<0.001) and in 4 ALT xenografts in vivo (EFS P<0.0001). AZD0156 showed modest to no enhancement of temozolomide + irinotecan activity in telomerase-positive neuroblastoma cell lines and xenografts. ATR inhibition using AZD6738 did not enhance temozolomide + SN-38 activity in ALT neuroblastoma cell lines. Thus, resistance to chemotherapy in ALT neuroblastoma occurs via ATM kinase activation and was reversed with the ATM inhibitor AZD0156. Combining AZD0156 with temozolomide + irinotecan warrants clinical testing in neuroblastoma. One Statement SummaryATM activation at telomeres confers resistance to DNA damaging chemotherapy in ALT neuroblastoma that was reversed with ATM knockdown or inhibition.

cancer biology↗