Biology subjects

Tan, C. Y.

Publications and source records attributed to Tan, C. Y..

5 recordsLinked to original sources

bioRxiv2024

A commensal-derived sugar protects against metabolic disease

Obesity is a worsening global epidemic that is regulated by the microbiota through unknown bacterial factors. We discovered a human commensal bacterium, Clostridium immunis, that treats obesity by secreting a phosphocholine-modified exopolysaccharide. Loss- and gain-of-function bacterial mutants involving the phosphocholine biosynthesis locus (licABC) revealed the phosphocholine moiety is critically required to protect against metabolic disease. This C. immunis exopolysaccharide decreases small-intestinal and visceral fat levels of IL-22, which increases metabolic activity specifically in visceral adipose tissue. Importantly, phosphocholine biosynthesis genes are less abundant in humans with obesity or hypertriglyceridemia, findings that suggest the role of bacterial phosphocholine is conserved across mice and humans. These results define a bacterial molecule--and its key structural motif--that provides immunometabolic control of obesity. More broadly, they highlight a clinically translatable strategy to reduce visceral fat.

microbiology↗

bioRxiv2024

Interplay between particle size and microbial ecology in the gut microbiome

Physical particles can serve as critical abiotic factors that structure the ecology of microbial communities. For non-human vertebrate gut microbiomes, fecal particle size (FPS) has been known to be shaped by chewing efficiency and diet. However, little is known about what drives FPS in the human gut. Here, we analyzed FPS by laser diffraction across a total of 76 individuals and found FPS to be strongly individualized. Surprisingly, a behavioral intervention with 41 volunteers designed to increase chewing efficiency did not impact FPS. Dietary patterns could also not be associated with FPS. Instead, we found evidence that mammalian and human gut microbiomes shaped FPS. Fecal samples from germ-free and antibiotic-treated mice exhibited increased FPS relative to colonized mice. In humans, markers of longer transit time were correlated with smaller FPS. Gut microbiota diversity and composition were also associated with FPS. Finally, ex vivo culture experiments using human fecal microbiota from distinct donors showed that differences in microbiota community composition can drive variation in particle size. Together, our results support an ecological model in which the human gut microbiome plays a key role in reducing the size of food particles during digestion, and that the microbiomes of individuals vary in this capacity. These new insights also suggest FPS in humans to be governed by processes beyond those found in other mammals and emphasize the importance of gut microbiota in shaping their own abiotic environment.

microbiology↗

bioRxiv2024

Commensal bacteria inhibit viral infections via a tryptophan metabolite

Clinical outcomes following viral exposures exhibit substantial interindividual variability. Although developing evidence suggests commensal bacteria modulate viral infections, the specific bacteria and mechanisms remain underexplored. Here we define a pathway by which viral infections are inhibited by specific tryptophan-catabolizing bacteria. Using HIV as a model, we bioinformatically associated and experimentally validated several bacterial species that inhibited viral replication. This activity required the aromatic amino acid aminotransferase (ArAT) to metabolize tryptophan into 3-indolelactic acid, which agonizes the aryl hydrocarbon receptor (AhR). Given that AhR regulates multiple viral infections, we found that commensal bacteria also inhibit cytomegalovirus (CMV) in an ArAT-dependent manner. Finally, we confirmed that ArAT is associated with protection against disease outcomes in three distinct human cohorts at-risk for HIV, CMV, or symptomatic COVID-19. Taken together, our results provide mechanistic insight into how commensal bacteria impact viral infections, thereby adding to an emerging field focused on host-commensal-virus interactions.

microbiology↗

bioRxiv2020

Non-invasive, label-free optical analysis to detect aneuploidy within the inner cell mass of the preimplantation embryo

Study questionCan label-free, non-invasive optical imaging by hyperspectral microscopy discern between euploid and aneuploid cells within the inner cell mass of the mouse preimplantation embryo? Summary answerHyperspectral microscopy shows a variance in metabolic activity which enables discrimination between euploid and aneuploid cells. What is known alreadyEuploid/aneuploid mosaicism affects up to 17.3% of human blastocyst embryos with trophectoderm biopsy or spent media currently utilised to diagnose aneuploidy and mosaicism in clinical in vitro fertilisation. Based on their design, these approaches will fail to diagnose the presence or proportion of aneuploid cells within the fetal lineage (inner cell mass (ICM)) of some blastocyst embryos. Study design, size, durationThe impact of aneuploidy on cellular metabolism of primary human fibroblast cells and mouse embryos was assessed by a fluorescence microscope adapted for imaging with multiple spectral channels (hyperspectral imaging). Primary human fibroblast cells with known ploidy were subjected to hyperspectral imaging to record native cell fluorescence (euploid n= 467; aneuploid n= 969). For mouse embryos, 50-70 individual euploid and aneuploid blastomeres (8-cell stage embryo) and chimeric blastocysts (40-50 per group: euploid; aneuploid; or 1:1 and 1:3 ratio of euploid:aneuploid) were utilised for hyperspectral imaging. Participants/materials, setting, methodsTwo models were employed: (i) Primary human fibroblasts with known karyotype and (ii) a mouse model of embryo aneuploidy where mouse embryos were treated with reversine, a reversible spindle assembly checkpoint inhibitor, during the 4-to 8-cell division. Individual blastomeres were dissociated from reversine treated (aneuploid) and control (euploid) 8-cell embryos and either imaged directly or used to generate chimeric blastocysts with differing ratios of euploid:aneuploid cells. Individual blastomeres and embryos were subjected to hyperspectral imaging. Changes in cellular metabolism were determined by quantification of metabolic cofactors (inferred from their autofluorescence signature): reduced nicotinamide adenine dinucleotide (NAD(P)H), flavins with the subsequent calculation of the optical redox ratio (ORR: Flavins/[NAD(P)H + Flavins]). Mathematical algorithms were applied to extract features from the autofluorescence signals of each cell/blastomere/inner cell mass to discriminate between euploid and aneuploid. Main results and the role of chanceAn increase in the relative abundance of NAD(P)H with a decrease in flavins led to a significant reduction in the ORR for aneuploid cells in both primary human fibroblasts and individual mouse blastomeres (P < 0.05). Mathematical algorithms were able to achieve good separation between (i) euploid and aneuploid primary human fibroblast cells, (ii) euploid and aneuploid mouse blastomeres cells and (iii) euploid and aneuploid chimeric blastocysts and (iv) 1:1 and 1:3 chimeric blastocysts. The accuracy of these separations was supported by receiver operating characteristic curves with areas under the curve of 0.85, 0.99, 0.87 and 0.88, respectively. We believe that the role of chance is low as multiple cellular models (human somatic cells and mouse embryos) demonstrated a consistent shift in cellular metabolism in response to aneuploidy as well as the robust capacity of mathematical features to separate euploid and aneuploid cells in a statistically significant manner. Limitations, reasons for cautionThere would be added value in determining the degree of embryo mosaicism by sequencing the inner cell mass (ICM) of individual blastocysts to correlate with metabolic profile and level of discrimination achieved using the mathematical features approach. Wider implications of the findingsHyperspectral imaging was able to discriminate between euploid and aneuploid human fibroblasts and mouse embryos. This may lead to the development of an accurate and non-invasive optical approach to assess mosaicism within the ICM of human embryos in the absence of fluorescent tags. Study funding/competing interest(s)K.R.D. is supported by a Mid-Career Fellowship from the Hospital Research Foundation (C-MCF-58-2019). This study was funded by the Australian Research Council Centre of Excellence for Nanoscale Biophotonics (CEI40100003). The authors declare that there is no conflict of interest.

cell biology↗

bioRxiv2019

Hepatitis C virus infection is inhibited by a non-canonical antiviral signaling pathway targeted by NS3-NS4A

The hepatitis C virus (HCV) NS3-NS4A protease complex is required for viral replication and is the major viral innate immune evasion factor. NS3-NS4A evades antiviral innate immunity by inactivating several proteins, including MAVS, the signaling adaptor for RIG-I and MDA5, and Riplet, an E3 ubiquitin ligase that activates RIG-I. Here, we identified a Tyr-16-Phe (Y16F) change in the NS4A transmembrane domain that prevents NS3-NS4A targeting of Riplet but not MAVS. This Y16F substitution reduces HCV replication in Huh7 cells, but not in Huh-7.5 cells, known to lack RIG-I signaling. Surprisingly, deletion of RIG-I in Huh7 cells did not restore Y16F viral replication. Rather, we found that Huh-7.5 cells lack Riplet expression and that addition of Riplet to these cells reduced HCV Y16F replication. In addition, IRF3 deletion in Huh7 cells was sufficient to restore HCV Y16F replication, and the Y16F protease lacked the ability to prevent IRF3 activation or interferon induction. Taken together, these data reveal that the NS4A Y16 residue regulates a non-canonical Riplet-IRF3-dependent, but RIG-I-MAVS-independent, signaling pathway that limits HCV infection.\n\nImportanceThe HCV NS3-NS4A protease complex facilitates viral replication by cleaving and inactivating the antiviral innate immune signaling proteins MAVS and Riplet, which are essential for RIG-I activation. NS3-NS4A therefore prevents IRF3 activation and interferon induction during HCV infection. Here, we uncover an amino acid residue within the NS4A transmembrane domain that is essential for inactivation of Riplet, but does not affect MAVS cleavage by NS3-NS4A. Our study reveals that Riplet is involved in a RIG-I- and MAVS-independent signaling pathway that activates IRF3 and that this pathway is normally inactivated by NS3-NS4A during HCV infection. Our study selectively uncouples these distinct regulatory mechanisms within NS3-NS4A and defines a new role for Riplet in the antiviral response to HCV. As Riplet is known to be inhibited by other RNA viruses, such as such influenza A virus, this innate immune signaling pathway may also be important in controlling other RNA virus infections.

microbiology↗