Biology subjects

Mak, T.

Publications and source records attributed to Mak, T..

11 recordsLinked to original sources

bioRxiv2025

2-Methoxyestradiol Treatment Prevents Graft-versus-Host Disease While Preserving Graft-versus-Leukemia Effect in Mice

2-Methoxyestradiol (2ME2, Panzem) is an endogenous metabolite that is well-tolerated in phase I/II clinical trials for variety of tumors. The plasma levels of 2ME2 may increase up to 1,000-fold during pregnancy and correlate temporally with the remission of rheumatoid arthritis (RA) and multiple sclerosis (MS) symptoms. The anti-inflammatory properties of 2ME2 were recently established in the mouse model of MS, and the mechanism of action is the ability of 2ME2 to inhibit lymphocyte proliferation, cytokine production and T cell polarization. Herein, we have demonstrated that 2ME2 treatment can significantly reduce the mortality and morbidity associated with graft-versus-host disease (GVHD). There is a lower number of donor-derived CD4+ and CD8+ T cells in the peripheral lymph node and Peyers patches of 2ME2-treated mice compared to control recipients. Moreover, 2ME2 exposure can significantly decrease the production of IFN-{gamma} and IL-2 in donor-derived CD4+ T cells and serum in GVHD mice. However, 2ME2 treatment has no effect on the differentiation of CD8+ effector T cells in vivo and their cytolytic activity remains intact. Furthermore, 2ME2 therapy is effective in preventing GVHD while preserving graft-versus leukemia (GVL) activity in mice. Our findings indicate that 2ME2 could be a novel and effective treatment for GVHD patients.

immunology↗

bioRxiv2025

Human Milk Oligosaccharides Modulate Inflammatory Responses and Lipid Metabolism in a Human Intestinal Organoid Model

Human milk oligosaccharides (HMOs) are a major component of human breast milk and have significant protective effects on infant gut health. HMOs are also present in the amniotic fluid surrounding the developing fetus in the womb. Beginning at 10 weeks of gestational age, HMOs enter the fetal gut through the swallowing of amniotic fluid. The effects of this earliest exposure to HMOs on the gut epithelium, which pre-term infants partially miss, remains unknown. In this study, we investigate the effect of a blend of HMOs, including 2-fucosyllactose (2FL), 3-sialyllactose (3SL), and difucosyllactose (DFL), on intestinal epithelial cells, examining their role in steady-state conditions and during inflammation. By utilizing advanced intestinal epithelial organoid models derived from fetal and pediatric donors, we reveal developmental-stage-specific responses to this HMO blend, as well as its potential to mitigate inflammatory damage. These findings offer important insights into the role of HMOs in early-life nutrition and gut health, lending compelling evidence to support their inclusion in infant nutrition strategies.

cell biology↗

bioRxiv2024

Food Fermentation in Space Is Possible, Distinctive, and Beneficial

Space exploration is expanding, which demands new technologies and enables new scientific questions. Food, as a bridge between disciplines, can bring these fundamental and applied goals together. Here we investigate whether food fermentation in space is possible, and if so, how it compares with fermentation on Earth. We fermented a miso, a traditional Japanese condiment, on the International Space Station over 30 days, and compared it with two earthbound controls. Using a specially-built environmental sensing box, we gathered metadata for temperature, relative humidity, pressure, and radiation. We analyzed the three misos with shotgun metagenomics to investigate the microbial communities composition and safety; whole genome sequencing to investigate the mutation rate of Aspergillus oryzae; untargeted metabolomics to quantify aromatic compounds, amino acids and organic acids; colorimetry to quantify color; and sensory analysis to describe the misos flavours and quantify liking and sensory difference. Across these datasets, we found that overall, the space miso is recognizable as a miso, suggesting fermentation in space is possible. We also found certain differences in the space miso: specifically the presence of Bacillus velezensis, a higher mutation rate of A. oryzae, higher attributions of roasted and nutty flavours, and the most different sensory impression. Taken together, these observations suggest unique features of the space environment--what we might call space terroir--which could be harnessed to create more flavorful, nourishing foods for long-term space missions and to address fundamental questions about the biology of novel environments. Significance StatementOur study presents, to our knowledge, the first time a food product has been fermented in space. We demonstrate that fermentation in space is possible with safe and successful results, a proof of concept that offers fermentation as a new tool for space research and future long-term space exploration missions. We also document how the space environment shapes the fermentation process in unique ways, suggesting a space terroir. These findings on the feasibility and novelty of fermentation in space open up directions for further multidisciplinary research across science, health, systems design, and society and culture.

microbiology↗

bioRxiv2021

Identification of SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of the nsp14 RNA Cap Methyltransferase

The COVID-19 pandemic has presented itself as one of the most critical public health challenges of the century, with SARS-CoV-2 being the third member of the Coronaviridae family to cause fatal disease in humans. There is currently only one antiviral compound, remdesivir, that can be used for the treatment of COVID-19. In order to identify additional potential therapeutics, we investigated the enzymatic proteins encoded in the SARS-CoV-2 genome. In this study, we focussed on the viral RNA cap methyltransferases, which play a key role in enabling viral protein translation and facilitating viral escape from the immune system. We expressed and purified both the guanine-N7 methyltransferase nsp14, and the nsp16 2-O-methyltransferase with its activating cofactor, nsp10. We performed an in vitro high-throughput screen for inhibitors of nsp14 using a custom compound library of over 5,000 pharmaceutical compounds that have previously been characterised in either clinical or basic research. We identified 4 compounds as potential inhibitors of nsp14, all of which also show antiviral capacity in a cell based model of SARS-CoV-2 infection. Three of the 4 compounds also exhibited synergistic effects on viral replication with remdesivir.

bioengineering↗

bioRxiv2020

Universal Spectrum Identifier for mass spectra

Mass spectra provide the ultimate evidence for supporting the findings of mass spectrometry (MS) proteomics studies in publications, and it is therefore crucial to be able to trace the conclusions back to the spectra. The Universal Spectrum Identifier (USI) provides a standardized mechanism for encoding a virtual path to any mass spectrum contained in datasets deposited to public proteomics repositories. USIs enable greater transparency for providing spectral evidence in support of key findings in publications, with more than 1 billion USI identifications from over 3 billion spectra already available through ProteomeXchange repositories.

bioinformatics↗

bioRxiv2020

Influence of the microenvironment on the modulation of the host response by the typhoid toxin

Bacterial genotoxins cause DNA damage in eukaryotic cells, resulting in activation of the DNA damage response (DDR) in vitro. These toxins are produced by Gram negative bacteria, enriched in the microbiota of Inflammatory Bowel Disease (IBD) and colorectal cancer (CRC) patients. However, their role in infection remains poorly characterized. We have addressed the role of the typhoid toxin in the modulation of the host-microbial interaction in health and disease. Infection with a genotoxigenic Salmonella protected mice from intestinal inflammation. The toxin-induced DNA damage caused senescence in vivo, which was uncoupled from the inflammatory response, and associated with the maintenance of an anti-inflammatory environment. This effect was lost when infection occurred in mice suffering from inflammatory conditions that mimic Ulcerative Colitis, a form of IBD. These data highlight a complex context-dependent crosstalk between bacterial genotoxins-induced DDR and the host immune response, underlining an unexpected role for bacterial genotoxins.

immunology↗

bioRxiv2019

Antibody responses to immunization require sensory neurons

Mammals store memories in the nervous and immune systems. Sensory neurons have been implicated in enhancing neurological memory, but whether neurons participate during immunity to novel antigens is unknown. Here, mice rendered deficient in transient receptor potential vanilloid 1 (TRPV1)-expressing sensory neurons, termed "nociceptors," fail to develop competent antibody responses to KLH and hapten-NP. Moreover, selective optogenetic stimulation of TRPV1 neurons during immunization significantly enhanced antibody responses to antigens. Thus, TRPV1 nociceptors mediate antibody responses to novel antigen, and stimulating TRPV1 nociceptors enhances antibody responses during immunization. This is the first genetic and selective functional evidence that nociceptors are required during immunization to produce antigen-specific antibodies. SummaryThe first genetic and selective functional evidence showing that TRPV1-expressing nociceptors are required for competent antibody responses to novel antigen, and stimulating TRPV1 nociceptors enhances antibody responses to novel antigen.

immunology↗

bioRxiv2019

β-cell dedifferentiation is associated with epithelial-mesenchymal transition triggered by miR-7-mediated repression of mSwi/Snf complex

{beta}-cell dedifferentiation has been revealed as a pathological mechanism underlying pancreatic dysfunction in diabetes. However, little is known on the genetic and epigenetic changes linked with the dedifferentiation of {beta}-cells. We now report that {beta}-cell dedifferentiation is associated with epithelial to mesenchymal transition (EMT) triggered by miR-7-mediated repression of Smarca4/Brg1 expression, a catalytic subunit of the mSwi/Snf chromatin remodeling complexes essential for {beta}-cell transcription factors ({beta}-TFs) activity. miR-7-mediated repression of Brg1 expression in diabetes causes an overall compaction of chromatin structure preventing {beta}-TFs from accessing and transactivating genes maintaining the functional and epithelial identity of {beta}-cells. Concomitantly, loss of {beta}-cell identity impairs the ability of {beta}-TFs Pdx1, Nkx6-1, Neurod1 to repress non-{beta}-cell genes enriched selectively in mesenchymal cells leading to EMT, change in islet microenvironment, and fibrosis. Remarkably, anti-EMT agents normalized glucose tolerance of diabetic mice, thus revealing mesenchymal reprogramming of {beta}-cells as a novel therapeutic target in diabetes. This study sheds light on the genetic signature of dedifferentiated {beta}-cells and highlights how loss of mSwi/Snf activity in diabetes initiating a step-wise remodeling of epigenetic landscapes of {beta}-cells leading to the induction of an EMT process reminiscent of a response to tissue injury.

genomics↗

bioRxiv2019

LFMD: a new likelihood-based method to detect low-frequency mutations without molecular tags

As next-generation sequencing (NGS) and liquid biopsy become more prevalent in research and in the clinic, there is an increasing need for better methods to reduce cost and improve sensitivity and specificity of low-frequency mutation detection (where the Alternative Allele Frequency, or AAF, is less than 1%). Here we propose a likelihood-based approach, called Low-Frequency Mutation Detector (LFMD), which combines the advantages of duplex sequencing (DS) and the bottleneck sequencing system (BotSeqS) to maximize the utilization of duplicate reads. Compared with the existing state-of-the-art methods, DS, Du Novo, UMI-tools, and Unified Consensus Maker, our method achieves higher sensitivity, higher specificity (< 4 x 10-10 errors per base sequenced) and lower cost (reduced by ~70% at best) without involving additional experimental steps, customized adapters or molecular tags. LFMD is useful in areas where high precision is required, such as drug resistance prediction and cancer screening. As an example of LFMDs applications, mitochondrial heterogeneity analysis of 28 human brain samples across different stages of Alzheimers Disease (AD) showed that the canonical oxidative damage related mutations, C:G>A:T, are significantly increased in the mid-stage group. This is consistent with the Mitochondrial Free Radical Theory of Aging, suggesting that AD may be linked to the aging of brain cells induced by oxidative damage.

bioinformatics↗

bioRxiv2018

KS-Burden: Assessing distributional differences of rare variants in dichotomous traits

A number of rare variant tests have been developed to explore the effect of low frequency genetic variations on complex phenotypes. However, an often neglected aspect in these tests is the position of genetic variations. Here we are proposing a way to assess the differences in spatial organization of rare variants by assessing their distributional differences between affected and unaffected subjects. To do so, we have formulated an adaptation of the well know Kolmogorov-Smirnov (KS) test, combining both KS and a simple gene burden approach, called KS-Burden.\n\nThe performance of our test was evaluated under a comprehensive simulations framework using real data and various scenarios. Our results show that the KS-Burden test is able to outperform the commonly used SKAT-O test, as well as others, in the presents of clusters of causal variants within a genomic region. Furthermore, our test is able to maintain competitive statistical power in scenarios unfavorable to its original assumptions. Hence, the KS-Burden test is a valuable alternative to existing tests and provides better statistical power in the presents of causal clusters within a gene.

bioinformatics↗

bioRxiv2018

Polygenic scores without external summary statistics

Polygenic scores (PGS) are estimated scores representing the genetic tendency of an individual for a disease or trait and have become an indispensible tool in a variety of analyses. Typically they are linear combination of the genotypes of a large number of SNPs, with the weights calculated from an external source, such as summary statistics from large meta-analyses. Recently cohorts with genetic data have become very large, such that it would be a waste if the raw data were not made use of in constructing PGS. Making use of raw data in calculating PGS, however, presents us with problems of overfitting. Here we discuss the essence of overfitting as applied in PGS calculations and highlight the difference between overfitting due to the overlap between the target and the discovery data (OTD), and overfitting due to the overlap between the target the the validation data (OTV). We propose two methods -- cross prediction and split validation -- to overcome OTD and OTV respectively. Using these two methods, PGS can be calculated using raw data without overfitting. We show that PGSs thus calculated have better predictive power than those using summary statistics alone for six phenotypes in the UK Biobank data.

genomics↗