Biology subjects

Nguyen, D. N.

Publications and source records attributed to Nguyen, D. N..

At least 19 recordsLinked to original sources

bioRxiv2026

CRISPR-dPCR: A unified multiplex digital PCR framework for quantitative characterization of targeted knock-in

Accurate characterization of CRISPR knock-in requires distinguishing site-specific integration from total donor abundance and donor-derived background while measuring editing at the target site. Here, we present CRISPR-dPCR, a modular multiplex digital PCR framework combining a locked nucleic acid-enhanced cut-site assay with junction-based detection and two orthogonal short-amplicon strategies: Poisson linkage and homology-arm subtraction. We evaluated assay modules across genomic loci, neuroblastoma models and primary human T cells, with selected assays compared on two dPCR platforms. In genotype-defined clones and mixtures with low residual donor, homology-arm subtraction most closely recovered expected knock-in abundance. Linkage provided highly specific evidence of target-cargo association without junction-spanning amplification, whereas junction assays supplied boundary-specific confirmation but were more sensitive to amplicon length and multiplexing. Five-channel panels integrated cut-site editing, donor abundance, copy-number normalization and site-specific knock-in in a single reaction. Residual donor DNA limited quantitative interpretation, particularly in early post-editing samples. Modular extensions quantified defined unintended outcomes, including chromosomal translocations. CRISPR-dPCR integrates complementary measurements into a scalable analytical framework for genome-editing research, cell and gene therapy product development and applications in longitudinal clinical monitoring of targeted integration and transgene persistence.

molecular biology↗

bioRxiv2026

NAD metabolism mediates a sex-specific protection against early life infections

Sex influences early-life immunity and infection outcomes, yet how metabolic mechanisms regulate these effects remain unclear. As nicotinamide adenine dinucleotide (NAD) can support mitochondrial metabolism and immune function, here we explore how NAD metabolism contributes to sex-specific protection against infections in early life. First, in two independent cohorts of 700 and 386 children, we found that females at birth had higher blood NAD levels than males, and strikingly higher birth NAD levels were associated with reduced infection burdens during the first 3 years of life in females, but with tendency of increased burdens in males. At 18 months, plasma nicotinamide associated with sex-specific cytokine responses to antigen challenges and showed a stronger positive association with tricarboxylic acid cycle (TCA) activity in females. Next, we verified the causal effects of NAD metabolism on infection protection by testing the supplementation of NAD precursor nicotinamide riboside (NR) in infected newborn piglets, used as a translational model of infection-sensitive infants. NR treatment improved survival, bacterial clearance, and disease tolerance only in females, but not in males. Mechanistically, NR increased levels of hepatic TCA cycle metabolites fumarate and malate, and enhanced hepatic inflammatory, hormonal, and mitochondrial-associated transcriptional programs, again only in females. Finally, the sex-specific immune functions mediated by NR were also validated in blood and immune cells in vitro. Collectively, we identified NAD metabolism as a sex-dependent immunometabolic mediator in early-life infection. Our findings suggest the potential of sex-stratified nutritional interventions in infection-sensitive infants.

immunology↗

bioRxiv2026

Glucose restriction reduces systemic, but not cardiac, inflammation during neonatal sepsis in preterm pigs

Introduction: Preterm infants are highly susceptible to sepsis and hyperglycemia may exacerbate inflammation and worsen outcomes. We examined how glucose provision influences systemic and cardiac responses during neonatal sepsis in preterm pigs. Methods: Preterm piglets (90 % gestation) were infused with Staphylococcus epidermidis to induce sepsis. In Experiment 1, three ventilated and anesthetized piglets were continuously monitored for mean arterial pressure (MAP) and blood gases to characterize acute cardiovascular and metabolic deterioration. In Experiment 2, thirty-three piglets were randomized to standard (14 g/kg/day) or reduced (3.5 g/kg/day) glucose provision, with or without infection, and followed for 20h. Results: Infection in Experiment 1 caused progressive hypotension, acidosis, and hypoxia, mirroring clinical neonatal sepsis. In Experiment 2, reduced glucose provision improved survival (77 % vs 46 %, p = 0.06) and attenuated systemic inflammation, with lower IL-6 and higher IL-10 concentrations. Infection induced mild cardiac neutrophil infiltration, without affecting plasma troponin T but clearly reduced cardiomyocyte mitotic density and triggered upregulation of inflammatory transcriptional pathways (NF-{kappa}B, JAK-STAT) and suppression of oxidative phosphorylation. In infected animals. glucose restriction preserved cardiomyocyte mitotic density but did not alter cardiac structure, injury markers or gene expression. Conclusion: Neonatal infection induced circulatory failure, suppression of cardiomyocyte proliferation and upregulation of inflammatory genes in cardiac tissue, while reduced glucose provision mitigated systemic immune responses and preserved cardiomyocyte proliferation.

immunology↗

bioRxiv2026

LNP-mediated BCL11A Editing Corrects Sickling Phenotypes and Preserves HSPC Fitness Compared to Electroporation

Hemoglobinopathies, including sickle cell disease (SCD) and thalassemia syndromes, affect millions of individuals worldwide who have limited access to curative therapies. Autologous hematopoietic stem cell transplant following ex vivo CRISPR editing of the BCL11A erythroid enhancer reactivates fetal hemoglobin (HbF) and achieves an effective cure, but the resource constraints of clinically approved procedures for editing by electroporation (EP) severely limit widespread implementation. We directly compared the functional outcomes of EP delivery of Cas9 ribonucleoprotein with lipid nanoparticle (LNP) delivery of Cas9 mRNA in primary human HSPCs obtained from healthy HbAA donors and from patients with SCD. While higher editing rates are achieved with EP, LNP-treated HSPCs exhibited greater viability and cell yields that persisted throughout a multi-stage in vitro erythroid differentiation protocol. By day 20, the yield of mature red blood cells (CD71lowCD235ahigh) was lowest in the EP cohorts. Across treatment groups, we observed HbF induction proportional to indel frequency. LNP editing of SCD patient-derived HSPCs as low as 25% modified alleles still caused HbF production and reduced the propensity for sickling of in vitro differentiated RBCs. These findings highlight the critical trade-offs among manufacturing ease, delivery-associated toxicity, and functional performance across two modalities of therapeutic genome editing for hemoglobinopathies.

bioengineering↗

bioRxiv2026

Reduced parenteral glucose supply in preterm neonatal infection ameliorates the pulmonary damage

Preterm infants are acutely susceptible to neonatal sepsis, a syndrome characterized by systemic pro-inflammatory activity and life-threatening multi-organ dysfunction. However, the specific pulmonary pathological response to sepsis and the potential for metabolic interventions to mitigate lung injury remain poorly characterized. Herein, we evaluated the impact of varying parenteral glucose regimens on pulmonary outcomes during severe infection using a preterm piglet model. Genome-wide gene expression analysis was used to characterize lung transcriptome profiles. The relationships between gene expression and circulating biochemical and immune profiles were also investigated. Our findings demonstrate that significant pulmonary tissue damage is a hallmark of neonatal sepsis. A reduced-glucose regimen markedly attenuated pulmonary tissue damage while simultaneously alleviating systemic metabolic acidosis and hyperlactatemia. Mechanistically, lung transcriptome profiling revealed a profound activation of pathways associated with inflammatory signaling, programmed cell death, and the dysregulation of glucose, amino acid, and lipid metabolism. The low-glucose intervention effectively mitigated these widespread molecular and metabolic disturbances, suggesting a restorative effect on the pulmonary transcriptome landscape. To facilitate further mechanistic exploration and the identification of novel therapeutic targets, we developed the NeoSepPulmoExplorer (https://pharmaco-omicslab.shinyapps.io/NeoSepPulmoExplorer/), an interactive web-based toolkit for better mechanistic understanding and the identification of potential treatment targets. These results collectively underscore the importance of metabolic modulation in preserving organ function, though further translational studies are requisite to improve clinical outcomes in septic neonates.

immunology↗

bioRxiv2025

Ketone and glycolytic metabolism are key modulators of inflammation during neonatal sepsis

Neonatal sepsis is a life-threatening condition in preterm infants, primarily due to a dysregulated immunometabolic response to infection. Sepsis and infection mortality are associated with excessive glycolysis-induced inflammation, impaired mitochondrial oxidative phosphorylation (OXPHOS) and loss of disease tolerance. Reduced glucose intake can reverse these dysregulations, but it is unclear how the mechanistic control of glycolysis-OXPHOS balance drives defense strategies and infection outcomes. Here, in a preterm piglet model of neonatal sepsis, glycolysis inhibition with 2-deoxyglucose (2-DG) completely prevents acute infection mortality, reduces systemic inflammation and markers of liver injury, accompanied by enhanced mitochondrial metabolism and disease tolerance. Strikingly, this protection by 2-DG is conferred despite elevated blood glucose levels and higher bacterial burdens than the infected controls. Alternatively, partial replacement of glucose intake with the ketone beta-hydroxybutyrate (BHB) abolishes sepsis-related mortality via improving disease tolerance and clinical parameters. This intervention also shifts the hepatic transcriptome away from inflammatory signaling and towards mitochondrial metabolism. In macrophages in vitro, BHB also exerts anti-inflammatory effects independently of metabolic modulation via the HCAR2 receptor. Finally, data from a cohort of 700 infants confirm an association of plasma BHB levels and anti-inflammatory state. These findings demonstrate that metabolic reprogramming through glycolysis inhibition or ketone supplementation is a promising therapeutic strategy to enhance disease tolerance and improve sepsis outcomes in neonates.

immunology↗

bioRxiv2025

Harnessing systemic glycolysis-TCA cycle axis to boost the host defense against newborn infection

Energy metabolism and immune response are tightly connected, but it is poorly understood how this interplay is regulated in early life to dictate host defense strategy, infection risks and severity. This interplay is particularly relevant for preterm, low birthweight or otherwise immunocompromised infants, who have poor metabolic control and increased risks of sepsis. Here, we utilized data from the COPSAC2010 cohort with 700 mother-child pairs and showed that plasma levels of TCA cycle metabolites in early life were associated with reduced childhood risk of bacterial infection and an attenuated systemic inflammatory response. Next, we explored how two distinct nutritional strategies, which were aimed at boosting TCA cycle activity instead of glycolysis, impacted neonatal host defense against a serious bloodstream infection in preterm piglets. Substituting galactose for glucose in parenteral nutrition enhanced disease tolerance in early phase of infection and overall glucose homeostasis, improving survival. Further, combining glucose restriction with supplementation of glucogenic amino acids conferred glycemic control and completely prevented sepsis and abnormal changes of organ injury markers. Mechanistically, this intervention enhanced both disease resistance and tolerance, accompanied by metabolic rewiring from glycolysis towards gluconeogenesis, TCA cycle activity and oxidative phosphorylation. Thus, optimized nutritional strategies controlling the interplay of energy metabolism and host defense may be lifesaving for infected infants. In briefNewborns rely on two distinct defense strategies to combat infections in early life. Disease resistance, fueled by aerobic glycolysis, seeks to actively eliminate microorganisms while disease tolerance, fueled by mitochondrial oxidative phosphorylation, seeks to reduce collateral tissue damage during infections. We found that in healthy human newborns, increased plasma levels of metabolites from the tricarboxylic acid (TCA) cycle were associated with lower burden of childhood infections and reduced pro-inflammatory status. In a newborn animal model of bloodstream infection, nutritional strategies boosting systemic TCA cycle activity, while reducing aerobic glycolysis, enhanced both host disease tolerance and resistance, thereby improving survival. These findings could pave a path for improved infection management in human newborns. HighlightsO_LIIn healthy children, higher plasma levels of TCA cycle metabolites are associated with lower infection risks and systemic inflammation. C_LIO_LIIn a neonatal infection model, the supply of galactose, instead of glucose, improves host glucose homeostasis and TCA cycle activity, improving disease tolerance and survival. C_LIO_LIA combination of glucose restriction and glucogenic amino acid supply also improves TCA cycle activity, enhancing both disease resistance and tolerance and completely preventing lethal sepsis. C_LI

immunology↗

bioRxiv2025

Characterization of a virulent bacteriophage consortium targeting Enterobacteriaceae from inflamed preterm gut mucosa

Preterm infants have a high risk of intestinal inflammation which can progress to necrotizing enterocolitis (NEC). The gut microbial colonization commencing at birth is essential for proper intestinal maturation, but this process is often disrupted in preterm infants, leading to dysbiosis and increased risk of developing NEC. Bacteriophages (phages), viruses that specifically infect bacteria, are an important constituent of the gut microbiome and protects the gut epithelium against invading bacteria. This study aimed to isolate and characterize phages for use as a preventive measure against NEC-associated bacteria. We initially cultured Enterobacteriaceae from ileal mucosa of preterm piglets that exhibited severe NEC-like pathology. We then screened 23 donor fecal samples for inhibition of bacterial growth and isolated a collection of unique phages to use further. The phages were characterized by whole genome sequencing, host receptor binding determination, and immune cell activation in vitro. The final phage collection consisted of ten virulent phages within five genera, representing myovirus, podovirus and siphovirus morphologies. All phages in the collection induced expression of both pro-and anti-inflammatory genes in co-culture with macrophage-like THP-1 cells, but to different extents than Escherichia coli. Ultimately, we selected one phage for a high-dose oral administration to newborn piglets and assessed its infectivity and presence in different gut segments. This intervention did not result in any direct side effects, while both infective phages and signatures of phage DNA were detected in the intestinal content and mucosa. Having characterized a set of rationally selected virulent phages, we support the advancement of phage therapy as a potential protection against NEC.

microbiology↗

bioRxiv2025

The Lipidome Landscape of Amiodarone Toxicity: An in vivo Lipid-centric Multi-Omics Study

Amiodarone is an effective therapy for arrhythmias, its prolonged management may lead to significant adverse drug reactions. Amiodarone-induced hepatoxicity is described by phospholipidosis, hepatic steatosis, cholestatic hepatitis, and cirrhosis. However, the systemic and hepatic lipidome disturbances and underlying toxicological mechanisms remain comprehensively elucidated. Untargeted lipidomics were utilized to analyze serum and liver samples from the rats orally administered a daily dose of amiodarone of either 100 or 300 mg/kg for one week. Changes in the expression of hepatic lipid-related genes were also examined utilizing transcriptomics. We found a higher magnitude of lipidome alterations in the 300 mg/kg than those in the 100 mg/kg groups. Treated animals showed elevated abundances of phosphatidylcholines, ether-linked phosphatidylcholines, sphingomyelins, and ceramides, and decreased levels of triacylglycerols, ether-linked triacylglycerols, and fatty acids. We also found 199 lipid-related differentially expressed hepatic genes between the 300 mg/kg group versus controls, implying lipid metabolism and signaling pathways disturbances. Specifically, elevation of serum phosphatidylcholines and ether-linked phosphatidylcholines, as well as hepatic bismonoacylglycerophosphates were associated with reduced expression of phospholipase genes and elevated expression of glycerophospholipid biosynthesis genes, possibly driving phospholipidosis. Perturbations of sphingolipid metabolism might also be the key events for amiodarone-induced toxicity. Alterations in gene expression levels related to lipid storage and metabolism, mitochondria functions, and energy homeostasis were also found. Collectively, our study characterized the sophisticated perturbations in the lipidome and transcriptome of amiodarone-treated rats and suggested potential mechanisms responsible for amiodarone-induced hepatotoxicity.

pharmacology and toxicology↗

bioRxiv2024

Chemostat culturing reduces fecal eukaryotic virus load and delays diarrhea after virome transplantation

Fecal virome transfer (FVT) shows promise in reducing necrotizing enterocolitis (NEC), likely due to donor bacteriophages preventing the gut dysbiosis preceding disease. However, concurrent transfer of eukaryotic viruses may carry a risk of infection for the recipient. To increase safety, we investigated chemostat propagation as a method to eliminate eukaryotic viruses from donor feces while maintaining a diverse and reproducible bacteriophage community. Donor feces was collected from healthy suckling piglets and inoculated into a fermenter containing growth media supplemented with lactose and milk oligosaccharides (MOs). During continuous medium exchange (20% volume/h), dilution significantly reduced eukaryotic viruses. Viral richness was concurrently reduced although still preserving a stable community of 200-250 bacteriophages. Inclusion of MOs in the medium ensured higher bacterial richness and a bacterial community closer resembling donor feces. Fecal Lactobacillaceae bacteria were lost during cultivation but partially replaced by members of the Bacteroidota phylum in MO-supplemented cultures, accompanied by phages predicted to have Parabacteroides as host. After cultivation, virus-like particles (VLPs) were isolated, and their ability to reduce NEC incidence tested in vivo. Preterm piglets were delivered by cesarean section and received either the lactose- or MO-propagated viromes by oral route (n = 14-15/group). These were compared with groups receiving the same dose of donor fecal virome (1010 VLPs/kg) or vehicle control. The piglets were subsequently fed infant formula for 96 hours followed by euthanasia and tissue sampling. Both chemostat-propagated viromes effectively mitigated diarrhea compared to the donor virome. The donor virome partially engrafted in recipients and led to higher levels of Lactobacillaceae bacteria and Lactobacillaceae targeting phages. However, these signatures were lost in recipients of chemostat-propagated viromes, and only minor microbiome effects and no NEC prevention were observed. To conclude, we provide in vivo proof-of-concept for chemostat propagation of fecal viruses as a means to deplete eukaryotic viruses and in turn reduce side effects in newborn virome recipients. However, chemostat culture conditions need further optimization to preserve the donor phageome.

microbiology↗

bioRxiv2024

A Comprehensive Engineering Strategy Improves Potency and Manufacturability of a Near Pan-neutralizing Antibody Against HIV

Anti-HIV envelope broadly neutralizing antibodies (bnAbs) are alternatives to conventional antiretrovirals with the potential to prevent and treat infection, reduce latent reservoirs, and/or mediate a functional cure. Clinical trials with "first generation" bnAbs used alone or in combination show promising antiviral effects but also highlight that additional engineering of "enhanced" antibodies will be required for optimal clinical utility, while preserving or enhancing cGMP manufacturing capability. Here we report the engineering of an anti-CD4 binding-site (CD4bs) bnAb, N49P9.3, purified from the plasma of an HIV elite-neutralizer. Through a series of rational modifications we produced a variant that demonstrates: enhanced potency; superior antiviral activity in combination with other bnAbs; low polyreactivity; and longer circulating half-life. Additional engineering for manufacturing produced a final variant, eN49P9, with properties conducive to cGMP production. Overall, these efforts demonstrate the feasibility of developing enhanced anti-CD4bs bnAbs with greatly improved antiviral properties as well as potential translational value.

bioengineering↗

bioRxiv2024

Protection against necrotizing enterocolitis by fecal filtrate transfer requires an active donor virome

Necrotizing enterocolitis (NEC) remains a frequent catastrophic disease in preterm infants, but fecal filtrate transfer (FFT) has been identified as a promising prophylactic therapy in preclinical studies. This study examined the importance of the FFT virome viability on gut colonization and NEC occurrence. We established an ultraviolet irradiation-based viral inactivation protocol and demonstrated total loss of infectivity of a viral mock community. Using this protocol, we inactivated an aliquot of sterile-filtered donor feces and compared the response in preterm piglets subjected to experimental NEC induction. Gut pathology and barrier properties were assessed, and bacterial and viral compositions were determined by 16S rRNA amplicon and viral metagenomics sequencing, respectively. Native FFT decreased NEC severity and proinflammatory cytokines, but inactivated FFT (iFFT) completely abolished these effects. Mild side effects in the form of diarrhea manifested earlier in recipients of native FFT than iFFT or controls. A distinct gut colonization pattern of increased viral heterogeneity increased bacterial homogeneity and reduction in pathobionts like Clostridium perfringens and Escherichia was observed in the group receiving native FFT, but not in the iFFT group. The present study uncovered a clear distinction between active and inactivated transferred viromes in the ability to modulate gut colonization after preterm birth and decrease NEC. FFT efficacy is potentially driven by active bacteriophages targeting pathogenic bacteria.

microbiology↗

bioRxiv2024

Endoplasmic reticulum stress inhibition preserves mitochondrial function and cell survival during early onset of isoniazid-induced oxidative stress

A comprehensive understanding of isoniazid (INH)-mediated hepatotoxic effects is essential for developing strategies to predict and prevent severe liver toxicity in tuberculosis treatment. Our study utilized multi-omics profiling to investigate the toxic effects of INH, revealing significant involvement of endoplasmic reticulum (ER) stress, mitochondrial impairment, redox imbalance, and altered metabolism. Followed-up mechanistic studies revealed that INH triggered the generation of cytosolic reactive oxygen species (ROS) and the activation of the Nrf2 signaling pathway prior to mitochondrial ROS accumulation. Subsequently, INH disrupted mitochondrial function by impairing respiratory complexes I-IV and caused mitochondrial membrane proton leaks without affecting ATP synthase activity, together leading to mitochondrial depolarization and reduced ATP production. These disturbances enhanced mitochondrial fission and mitophagy. While much attention has been given to mitochondrial dysfunction and oxidative stress in INH-induced hepatotoxicity, our findings highlight the potential of inhibiting ER stress during early INH exposure to mitigate cytosolic and mitochondrial oxidative stress. We further revealed the critical role of Nrf2 signaling in protecting liver cells under INH-induced oxidative stress by maintaining redox homeostasis and enabling metabolic reprogramming via regulating the expression of antioxidant genes and cellular lipid abundance. We also identified other antioxidant pathways (e.g., selenocompound metabolism, HIF-1 signaling pathway, and pentose phosphate pathway) as potential alternative mechanisms besides Nrf2 signaling in response to INH-induced oxidative stress. In conclusion, our research emphasizes the importance of ER stress, redox imbalance, metabolic changes, and mitochondrial dysfunction underlying INH-induced hepatotoxicity.

pharmacology and toxicology↗

bioRxiv2024

Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) in primary human immune cells and hematopoietic stem cells

Peptide-enabled ribonucleoprotein delivery for CRISPR engineering (PERC) is a new approach for ex vivo genome editing of primary human cells. PERC uses a single amphiphilic peptide reagent to mediate intracellular delivery of the same pre-formed CRISPR ribonucleoprotein enzymes that are broadly used in research and therapeutics, resulting in high-efficiency editing of stimulated immune cells and cultured hematopoietic stem and progenitor cells (HSPCs). PERC facilitates nuclease-mediated gene knockout, precise transgene knock-in, and base editing. PERC involves mixing the CRISPR ribonucleoprotein enzyme with peptide and then incubating the formulation with cultured cells. For efficient transgene knock-in, adeno-associated virus (AAV) bearing homology-directed repair template DNA may be included. In contrast to electroporation, PERC is appealing as it requires no dedicated hardware and has less impact on cell phenotype and viability. Due to the gentle nature of PERC, delivery can be performed multiple times without substantial impact to cell health or phenotype. Here we report methods for improved PERC-mediated editing of T cells as well as novel methods for PERC-mediated editing of HSPCs, including knockout and precise knock-in. Editing efficiencies can surpass 90% using either Cas9 or Cas12a in primary T cells or HSPCs. Because PERC calls for only three readily available reagents - protein, RNA, and peptide - and does not require dedicated hardware for any step, PERC demands no special expertise and is exceptionally straightforward to adopt. The inherent compatibility of PERC with established cell engineering pipelines makes this approach appealing for rapid deployment in research and clinical settings.

bioengineering↗

bioRxiv2024

NKp30 and NKG2D contribute to natural killer recognition of HIV-infected cells

Natural killer (NK) cells respond rapidly in early HIV-1 infection. HIV-1 prevention and control strategies harnessing NK cells could be enabled by mechanistic understanding of how NK cells recognize HIV-infected T cells. Here, we profiled the phenotype of human primary NK cells responsive to autologous HIV-1-infected CD4+ T cells in vitro. We characterized the patterns of NK cell ligand expression on CD4+ T cells at baseline and after infection with a panel of transmitted/founder HIV-1 strains to identify key receptor-ligand pairings. CRISPR editing of CD4+ T cells to knockout the NKp30 ligand B7-H6, or the NKG2D ligands MICB or ULBP2 reduced NK cell responses to HIV-infected cells in some donors. In contrast, overexpression of NKp30 or NKG2D in NK cells enhanced their targeting of HIV-infected cells. Collectively, we identified receptor-ligand pairs including NKp30:B7-H6 and NKG2D:MICB/ULBP2 that contribute to NK cell recognition of HIV-infected cells.

immunology↗

bioRxiv2024

Reduced glucose supply during neonatal infection attenuates neurological and renal pathology via modulation of innate and Th1 immunity

BackgroundPremature infants are highly susceptible to infections that can lead to sepsis with life-threatening organ dysfunctions. The clinical practice of high parenteral glucose supply in preterm infants can exacerbate infection outcomes through excessive glycolysis-induced inflammatory response. This in turn can affect the health of vital preterm organs, including the brain and kidneys. We hypothesized that reducing glucose supply in infected preterm newborns may help protect against pathology in these two key organs. MethodsCaesarean-delivered preterm pigs were nourished with high or low parenteral glucose levels, infected with Staphylococcus epidermidis or saline, and cared for until 22h. Blood, brain, and kidney samples were collected at the end of the study for analyses. ResultsInfection led to multiple pathological changes, increased inflammation and tissue injury and dysfunction in both brain and kidneys of preterm piglets. Reduced glucose supply in infected animals alleviated neurological degradation, hyperemia and enhanced M2 microglial phenotype in the brain. This intervention also reduced plasma creatinine, renal edema, tubular vacuolization and dilatation. Multiple genes related to innate and Th1 immunity in both organs were highly correlated and dampened by reduced glucose supply, but there were clear signs that renal inflammation was closely connected to systemic inflammation while neuroinflammation was likely driven by immune response to the bacteria translocated into the brain. ConclusionReduced glucose supply can protect brain and kidney health in infected preterm neonates.

immunology↗

bioRxiv2024

Multi-omics phenotyping characterizes molecular divergence underlying different clinical scenarios of inflammatory bowel disease

Clinically heterogeneous spectrum and molecular phenotypes of inflammatory bowel disease (IBD) remain to be comprehensively elucidated. This study set out to explore the serum molecular profiles (I) of IBD subtypes; in association with (II) elevated fecal calprotectin and (III) disease activity states; (IV) upon treatment escalation; and (V) in patients who needed treatment escalation. The serum proteome, metabolome, and lipidome of 75 treated IBD patients were profiled. Single- and multi-omic data analysis was performed to determine differential analytes and integrative biosignatures. (I) Chronic inflammation, and phosphatidylcholine and bile acid homeostasis disturbances underlined the differences between Crohns disease (CD) and ulcerative colitis. (II) Elevated calprotectin was associated with higher levels of inflammatory proteins and sphingomyelins (SM) and lower levels of bile acids, amino acids, and triacylglycerols (TG). Relative to patient remission, active disease state (III) was characterized by decreased SMs and increased inflammatory proteins and TGs. (IV) Treatment escalation was associated with augmented levels of inflammatory response-related proteins and reduced levels of amino acids. Most TG species increased in the post-treatment escalation. Moreover, needed-treatment-escalation patients had significantly lower levels of TGs (V). They also showed increased SMs and decreased signaling receptor binding proteins. Multi-omics analysis revealed biosignatures that captured the differences between groups of each scenario. Eight analytes, including NFASC, ANGPTL4, and chenodeoxycholate, were found in at least three biosignatures. Collectively, disturbances in immune response, bile acid homeostasis, amino acids, and lipids alteration potentially underlie the clinically heterogeneous spectrum of IBD.

systems biology↗

bioRxiv2024

Regulation of defense strategies and host metabolism to survive neonatal infection

Two distinct defense strategies, resistance and tolerance, enable a host to survive infectious diseases. Newborns, constrained by limited energy reserves, predominantly rely on tolerance to cope with infection. However, this approach may fail as pathogen levels surpass a critical threshold, prompting a shift to resistance that can lead to dysregulated immune responses and sepsis. The mechanisms governing the interplay between tolerance and resistance in newborns remain poorly understood. Here, we compare metabolic traits and defense strategies between survivors and non- survivors in Staphylococcus epidermidis (S. epidermidis)-infected preterm piglets, mimicking infection in preterm infants. Relative to non-survivors, survivors displayed elevated resistance during the early phase of infection, followed by stronger tolerance in later stages. Conversely, animals succumbing to sepsis showed clear signs of respiratory and metabolic acidosis, together with exaggerated inflammation and organ dysfunctions. Hepatic transcriptomics revealed a strong association between the tolerance phenotype and heightened oxidative phosphorylation in survivors, coupled with suppressed glycolysis and immune signaling. Plasma metabolomics supported the finding of enhanced mitochondrial metabolism in survivors. Our findings suggest a link between mitochondrial metabolism, disease tolerance, and ultimately improved survival during infections in newborns. Metabolic regulations related to tolerance may be exploited to discover novel therapeutics for neonatal infection. Conflict-of-interest statementThe authors have declared that no conflict of interest exists.

immunology↗