Biology subjects

Wong, N.

Publications and source records attributed to Wong, N..

21 records · Page 2Linked to original sources

bioRxiv2020

MealTime-MS: A Machine Learning-Guided Real-Time Mass SpectrometryAnalysis for Protein Identification and Efficient DynamicExclusion

Mass spectrometry-based proteomics technologies are the prime methods for the high-throughput identification of proteins in complex biological samples. Nevertheless, there are still technical limitations that hinder the ability of mass spectrometry to identify low abundance proteins in complex samples. Characterizing such proteins is essential to provide a comprehensive understanding of the biological processes taking place in cells and tissues. Still today, most mass spectrometry-based proteomics approaches use a data-dependent acquisition strategy, which favors the collection of mass spectra from proteins of higher abundance. Since the computational identification of proteins from proteomics data is typically performed after mass spectrometry analysis, large numbers of mass spectra are typically redundantly acquired from the same abundant proteins, and little to no mass spectra are acquired for proteins of lower abundance. We therefore propose a novel supervised learning algorithm that identifies proteins in real-time as mass spectrometry data are acquired and prevents further data collection from confidently identified proteins to ultimately free mass spectrometry resources to improve the identification sensitivity of low abundance proteins. We use real-time simulations of a previously performed mass spectrometry analysis of a HEK293 cell lysate to show that our approach can identify 92.1% of the proteins detected in the experiment using 66.2% of the MS2 spectra. We also demonstrate that our approach outperforms a previously proposed method, is sufficiently fast for real-time mass spectrometry analysis, and is flexible. Finally, MealTime-MS efficient usage of mass spectrometry resources will provide a more comprehensive characterization of proteomes in complex samples.

bioinformatics↗

bioRxiv2019

Lfc/Arhgef2 regulates mitotic spindle orientation in hematopoietic stem and progenitor cells and is essential for productive hematopoiesis

How hematopoietic stem cells (HSCs) coordinate their divisional axis relative to supportive niche cells and whether or not their divisional orientation is important for stem cell-driven hematopoiesis is poorly understood. Single cell RNA sequencing data from patients with the inherited bone marrow failure Shwachman-Diamond syndrome (SDS) show that ARHGEF2, a RhoA-specific guanine nucleotide exchange factor (GEF) and determinant of mitotic spindle orientation, is one of a restricted group of genes specifically downregulated in SDS HSCs and multipotent progenitors. Here, we describe Lfc/Arhgef2 as an important regulator of hematopoiesis in vivo. Transplanted Lfc/Arhgef2-/- bone marrow shows impaired hematopoietic recovery and a production deficit of long-term HSCs. These phenotypes cannot be explained by differences in numbers of transplanted HSCs, their cell cycle status, level of apoptosis, progenitor output or homing ability. Using live imaging of dividing hematopoietic stem and progenitor cells (HSPCs), we show an increased frequency of misoriented divisions in the absence of Lfc/Arhgef2. Functional ARHGEF2 knockdown in human HSCs also impairs their ability to regenerate hematopoiesis, culminating in significantly smaller hematopoietic xenografts. Together, these data provide evidence demonstrating a conserved role for Lfc/Arhgef2 in orienting HSPC division and suggest that HSCs divide in certain orientations to establish hematopoiesis, the loss of which leads to their exhaustion in a mechanism that may underlie certain bone marrow failure syndromes.

cell biology↗

bioRxiv2017

IRF4 haploinsufficiency in a family with Whipples disease

The pathogenesis of Whipples disease (WD) remains largely unknown, as WD strikes only a very small minority of the individuals infected with Tropheryma whipplei (Tw). Asymptomatic carriage of Tw is less rare. We studied a large multiplex French kindred, containing four otherwise healthy WD patients (mean age: 76.7 years) and five healthy carriers of Tw (mean age: 55 years). We used a strategy combining genome-wide linkage analysis and whole-exome sequencing to test the hypothesis that WD is inherited in an autosomal dominant (AD) manner, with age-dependent incomplete penetrance. WD was linked to 12 genomic regions covering 27 megabases in the four patients. These regions contained only one very rare non-synonymous variation: the R98W variant of IRF4. The five Tw carriers were heterozygous for R98W. Interferon regulatory factor 4 (IRF4) is a transcription factor with pleiotropic roles in immunity. We showed that R98W was a loss-of-function allele, like only five other exceedingly rare IRF4 alleles of a total of 39 rare and common non-synonymous alleles tested. Furthermore, heterozygosity for R98W led to a distinctive pattern of transcription in leukocytes following stimulation with BCG or Tw. Finally, we found that IRF4 had evolved under purifying selection and that R98W was not dominant-negative, suggesting that the IRF4 deficiency in this kindred was due to haploinsufficiency. Overall, haploinsufficiency at the IRF4 locus selectively underlies WD in this multiplex kindred. This deficiency displays AD inheritance with incomplete penetrance, and chronic carriage probably precedes WD by several decades in Tw-infected heterozygotes.

immunology↗