Biology subjects

Ly, K.

Publications and source records attributed to Ly, K..

18 recordsLinked to original sources

bioRxiv2026

Biomimetic scaffolds mimic human subretinal debris for preclinical testing of prosthetic vision

Photovoltaic subretinal prostheses replace the lost photoreceptors in patients blinded by atrophic age-related macular degeneration (AMD) and provide central vision by electrically stimulating the inner retinal neurons. Subretinal debris in geographic atrophy separate the inner nuclear layer from the implant by tens of micrometers, increasing the stimulation threshold and reducing the pattern contrast. Absence of this separating layer in animal models diminishes the accuracy of preclinical testing of the next-generation implants, especially with smaller pixels. We developed three-dimensional biomimetic scaffolds nanoprinted onto photovoltaic arrays to provide a precisely controlled separation between the implants and target neurons in animal models of retinal degeneration. Gap sizes of the scaffolds were adjusted to meet the following requirements: they should allow light penetration to the implant, provide unobstructed flow of electric current, but preclude migration of cells into their 3-D structure. Gaps of 3 m were found to be optimal as they restricted cellular migration and maintained the inner nuclear layer above both planar and pillar electrode arrays. Scaffolds did not measurably alter the photovoltaic response and accurately reproduced the distance dependence of stimulation threshold. Following implantation, the initially fluid-filled intra-scaffold space was progressively filled by cellular matter matching the density of the subretinal debris. This transition is expected to increase resistivity of the scaffold to that of tissue, which was evidenced by concurrently improved grating acuity. These results establish a model of the controlled separation between the implant and the target neurons reproducing the features of subretinal debris in geographic atrophy of human patients, thereby providing a platform for accurate preclinical evaluation of the subretinal implants.

bioengineering↗

bioRxiv2026

Identification of Direct and Network-Mediated Activation of Retinal Ganglion Cells from Visually Evoked Potentials Using Machine Learning

ObjectiveTo preserve the encoding of visual information in prosthetic vision as close to natural as possible, subretinal photovoltaic implants, which replace the lost photoreceptors, strive to stimulate the second-order retinal neurons, the bipolar cells, while avoiding direct activation of the downstream retinal ganglion cells. To assess the range of such selective subretinal activation, we implanted the devices in rodent models of retinal degeneration and measured the stimulation thresholds based on the visually evoked potentials. After assessment of the bipolar cell-mediated thresholds, direct activation of retinal ganglion cells was measured following intraocular injection of synaptic blockers. Since these chemicals are toxic to the retina, this procedure can only be done once in each animal. ApproachWe developed a machine-learning model that identifies the stimulation pathway directly from the recorded visually evoked potentials, eliminating the need for synaptic blockers. The model was trained on recordings from rats implanted with PRIMA subretinal arrays and evaluated on two additional implant architectures, a second rat species, and a different anesthesia protocol. Main ResultsThe classifier achieved a balanced accuracy of 92% in cross-validation on the training data. Generalization to all unseen experimental conditions yielded an average balanced accuracy of 91%. Integrated Gradients analysis showed that combined bipolar and ganglion cell responses were driven by the early P1 component, while bipolar cell responses relied on later waveform components, consistent with thalamocortical processing dynamics. SignificanceThe described computational alternative to pharmacological blockers should improve the experimental throughput, allow multiple recordings over the lifetime of the same animal, and might be applicable to optimization of the stimulation settings in patients.

bioengineering↗

bioRxiv2026

Meditope-Enabled Chimeric Antigen Receptors Facilitate Plug-and-Play Control of T Cells

Chimeric antigen receptor (CAR) T cells have transformed cancer treatment, yet challenges for achieving broader clinical success remain, including overcoming tumor antigen heterogeneity and limited T cell fitness. To address these challenges and enhance CAR T cell functionality, we leveraged meditope technology, a lock-and-key platform where Fab regions of antibodies are modified to bind a small cyclic peptide termed meditope (meP). We developed a panel of meditope-enabled Fab-based CARs (meCARs), which show selective binding to the meP and comparable activity to traditional single-chain variable fragment (scFv)-based CARs. Focusing on HER2-targeted meCARs for evaluating platform utility, we exploited the modularity of the meditope platform to detect meCAR T cells using meP-fused fluorescent agents, promote meCAR T cell expansion via meP-fused IL-15 cytokine, and broaden tumor antigen targeting through meP-fused antibodies to address tumor heterogeneity. These findings establish the meditope technology as a versatile strategy to augment CAR T cell functionality and overcome key limitations of current CAR-based therapies.

bioengineering↗

bioRxiv2026

Division state reveals hidden genetic regulation during T cell activation and identifies immune disease-linked gene programmes

A major challenge in human genetics is to connect disease-associated variants to the cellular functions they perturb. Variants associated with immune-mediated disease have implicated CD4 T-cell activation as a disease-causal process; however, it remains unresolved whether these variants act on pathways initiating cell division, driving effector differentiation, or maintaining proliferative capacity. Activated T cells comprise mixtures of cells that have undergone different numbers of divisions, potentially obscuring genetic effects that act at specific stages of this process. Here, we study CD4 T-cell activation through cell division using division-resolved single-cell transcriptomics of naive, memory and regulatory T cells. We show that division state constitutes an important axis of transcriptional organisation, with approximately one third of genes exhibiting division-dependent regulation across shared and subset-specific programmes. We develop CellDivider, a machine-learning model that accurately infers proliferative state directly from single-cell transcriptomes, enabling a scalable approach for cohort level mapping of variant effects on cell proliferation phenotypes. Incorporating inferred division state into single-cell eQTL models reveals regulatory effects that are attenuated or missed when cells are analysed by activation time alone. Finally, we resolve gene expression programmes that govern distinct stages of T cell activation and proliferation. We show that polygenic immune disease risk preferentially converges on early activation and differentiation modules, rather than on proliferative capacity itself. Consistent with this model, division-resolved analysis of the pleiotropic immune risk gene RPS26 localises its genetic effects to early division states, providing mechanistic insight into its broad disease associations. Together, these findings illustrate how resolving dynamic cellular consequences of activation sharpens variant-to-function inference in immune disease genetics.

genetics↗

bioRxiv2025

Residual photoreceptors affect the response of a degenerate retina to electrical stimulation

Patients with age-related macular degeneration (AMD) implanted with the PRIMA photovoltaic subretinal prosthesis demonstrated letter acuity closely matching the devices 100 {micro}m pixel size. Improving visual acuity requires smaller pixels, which, in turn, require relaxation of electric field confinement to maintain effective stimulation of bipolar cells. Eliminating local return electrodes broadens the electric field but may inadvertently engage residual photoreceptors adjacent to the implant, thereby altering electrically evoked visual percepts. Here we quantify the contribution of residual photoreceptors to electrically evoked retinal responses across various implant configurations. Monopolar photovoltaic arrays with 20 {micro}m pixels and bipolar arrays with 100 {micro}m pixels were implanted subretinally in Long Evans rats, resulting in local degeneration of photoreceptors directly above the device. Responses were compared with those obtained in RCS rats, which lack functional photoreceptors. Implants were activated by patterns of 880 nm laser at pulse durations varying from 0.5 to 10 ms. Visually evoked potentials were measured in scotopic and photopic conditions, with and without the intravitreal application of mGluR6 agonist L-AP4 to block photoreceptor-driven ON pathways. Experimental thresholds were interpreted using a computational model of retinal network activation in distinct electric field geometries. In locally degenerate retina stimulated with monopolar arrays, blocking photoreceptor input yielded a rheobase (0.06 mW/mm{superscript 2}) and chronaxie ([~]3 ms) of the stimulation threshold, matching that measured in fully degenerate RCS retina, indicating direct activation of bipolar cells. In contrast, when photoreceptor input was intact, stimulation thresholds decreased significantly, and dark adaptation further modulated the threshold in a pulse-duration dependent manner. Bipolar arrays provided identical thresholds in locally degenerate and fully degenerate retina (0.2 mW/mm{superscript 2}) when stimulation was confined to the implant center; however, shifting stimulation to the implants edge lowered the thresholds, revealing a contribution from adjacent photoreceptors. These findings demonstrate that residual photoreceptors can substantially influence responses evoked by subretinal prostheses in a degenerate retina, with direct consequences for perceptual uniformity in patients, such as edge brightening. These results provide guidance for design of the next-generation higher-resolution implants, supporting the use of local return electrodes to maximize resolution while minimizing the effect of photoreceptors in clinical applications.

neuroscience↗

bioRxiv2025

PI5P4Kα Regulates Iron Balance to Promote Metabolic Fitness in Pancreatic Cancer

Phosphoinositide kinases generate distinct phosphoinositides that regulate processes that maintain cellular fitness. Phosphatidylinositol 5-phosphate 4-kinases (PI5P4Ks) have garnered interest for their role in cancer metabolism and cellular trafficking; however, their function in pancreatic ductal adenocarcinoma (PDAC) remains unexplored. Given the unique metabolic demands of PDAC cells, which heavily rely on altered trafficking pathways to support their growth, investigating PI5P4Ks in this context may reveal critical insights. We identify PI5P4K as a regulator of PDAC cell fitness through its key role in maintaining iron homeostasis. PI5P4K depletion causes metabolic disruptions and reduced intracellular iron import, leading to the induction of apoptosis in PDAC cells that is reversed by iron supplementation. Notably, we find that PI5P4K knockdown suppresses tumor growth in a xenograft mouse model of PDAC. These results not only illuminate the mechanistic underpinnings of PI5P4K function in PDAC but also position it as a promising therapeutic target for this disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC="FIGDIR/small/647654v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@17f52e5org.highwire.dtl.DTLVardef@1b78c1org.highwire.dtl.DTLVardef@194e09aorg.highwire.dtl.DTLVardef@125b3c9_HPS_FORMAT_FIGEXP M_FIG C_FIG Schematic representation of the novel function and implication of PI5P4K in PDAC. PI5P4K is upregulated in PDAC to support the ferro-addiction and heightened metabolic requirements of the tumor. When PI5P4K is inhibited, the PDAC cells undergo apoptotic cell death due to iron depletion. PI5P4K-depleted PDAC cells upregulate autophagy as an adaptive response but is not sufficient to defend against apoptotic cell death.

cancer biology↗

bioRxiv2025

Maximizing the fidelity of a photovoltaic subretinal prosthesis for human patients

ObjectivePRIMA subretinal implants provide prosthetic vision to patients blinded by age-related macular degeneration, with acuity closely matching the sampling limit of the pixel pitch: a single 100{micro}m pixel per line of a letter corresponds to 20/420 acuity. Decreasing the pixel size in the same flat geometry is difficult due to the constrained electric field, especially considering a 40{micro}m thick debris layer separating the implant from the target neurons. Here we optimize the electrode design to help overcome such limitations. ApproachAn end-to-end modeling pipeline combines the retinal photovoltaic implant simulator (RPSim) based on the Xyce circuit simulator with an interface to COMSOL Multiphysics for electric field modelling. It was used to generate and characterize implants in an open-loop sampling-based optimization. Implant performance was evaluated with respect to voltage drop across bipolar cells (representing the stimulation strength), pattern contrast, and neural selectivity. Main ResultsThe highest selectivity in stimulation of bipolar cells was achieved with arrays having active electrodes on pillars and return electrodes connected in a mesh surrounding the photovoltaic pixels in the array. Such a design, even with pixels down to 20{micro}m, provides stimulation strength exceeding, and contrast similar to that of flat 100{micro}m PRIMA pixels. SignificanceUsing a novel 3-D electrode design, the pitch of the photovoltaic array can be decreased to 20{micro}m, while providing performance that exceeds the flat 100{micro}m PRIMA pixels. In humans, 20{micro}m resolution on the retina corresponds to a visual acuity of 20/80 - a five times improvement compared to the current clinical device.

bioengineering↗

bioRxiv2025

Noncanonical PI(4,5)P2 coordinates lysosome positioning through cholesterol trafficking

In p53-deficient cancers, targeting cholesterol metabolism has emerged as a promising therapeutic approach, given that p53 loss dysregulates sterol regulatory element-binding protein 2 (SREBP-2) pathways, thereby enhancing cholesterol biosynthesis. While cholesterol synthesis inhibitors such as statins have shown initial success, their efficacy is often compromised by the development of acquired resistance. Consequently, new strategies are being explored to disrupt cholesterol homeostasis more comprehensively by inhibiting its synthesis and intracellular transport. In this study, we investigate a previously underexplored function of PI5P4Ks, which catalyzes the conversion of PI(5)P to PI(4,5)P2 at intracellular membranes. Our findings reveal that PI5P4Ks play a key role in facilitating lysosomal cholesterol transport, regulating lysosome positioning, and sustaining growth signaling via the mTOR pathway. While PI5P4Ks have previously been implicated in mTOR signaling and tumor proliferation in p53-deficient contexts, this work elucidates an upstream mechanism that unifies these earlier observations.

cell biology↗

bioRxiv2024

Varying recombination landscapes between individuals are driven by polymorphic transposable elements

AbstractsMeiotic recombination is a prominent force shaping genome evolution, and understanding the causes for varying recombination landscapes within and between species has remained a central, though challenging, question. Recombination rates are widely observed to negatively associate with the abundance of transposable elements (TEs), selfish genetic elements that move between genomic locations. While such associations are usually interpreted as recombination influencing the efficacy of selection at removing TEs, accumulating findings suggest that TEs could instead be the cause rather than the consequence. To test this prediction, we formally investigated the influence of polymorphic, putatively active TEs on recombination rates. We developed and benchmarked a novel approach that uses PacBio long-read sequencing to efficiently, accurately, and cost-effectively identify crossovers (COs), a key recombination product, among large numbers of pooled recombinant individuals. By applying this approach to Drosophila strains with distinct TE insertion profiles, we found that polymorphic TEs, especially RNA-based TEs and TEs with local enrichment of repressive marks, reduce the occurrence of COs. Such an effect leads to different CO frequencies between homologous sequences with and without TEs, contributing to varying CO maps between individuals. The suppressive effect of TEs on CO is further supported by two orthogonal approaches-analyzing the distributions of COs in panels of recombinant inbred lines in relation to TE polymorphism and applying marker-assisted estimations of CO frequencies to isogenic strains with and without transgenically inserted TEs. Our investigations reveal how the constantly changing mobilome can actively modify recombination landscapes, shaping genome evolution within and between species.

genomics↗

bioRxiv2024

Oseltamivir (Tamiflu), a Commonly Prescribed Antiviral Drug, Mitigates Hearing Loss in Mice

Hearing loss affects up to 10% of all people worldwide, but currently there is only one FDA-approved drug for its prevention in a subgroup of cisplatin-treated pediatric patients. Here, we performed an unbiased screen of 1,300 FDA-approved drugs for protection against cisplatin-induced cell death in an inner ear cell line, and identified oseltamivir phosphate (brand name Tamiflu), a common influenza antiviral drug, as a top candidate. Oseltamivir phosphate was found to be otoprotective by oral delivery in multiple established cisplatin and noise exposure mouse models. The drug conferred permanent hearing protection of 15-25 dB SPL for both female and male mice. Oseltamivir treatment reduced in mice outer hair cells death after cisplatin treatment and mitigated cochlear synaptopathy after noise exposure. A potential binding protein, ERK1/2, associated with inflammation, was shown to be activated with cisplatin treatment and reduced by oseltamivir cotreatment in cochlear explants. Importantly, the number of infiltrating immune cells to the cochleae in mice post noise exposure, were significantly reduced with oseltamivir treatment, suggesting an anti-inflammatory mechanism of action. Our results support oseltamivir, a widespread drug for influenza with low side effects, as a promising otoprotective therapeutic candidate in both cisplatin chemotherapy and traumatic noise exposure.

neuroscience↗

bioRxiv2023

The lipid Gb3 promotes germinal center B cell responses and anti-viral immunity

Influenza viruses escape immunity due to rapid antigenic evolution, which requires vaccination strategies that allow for broadly protective antibody responses. Here, we demonstrate that the lipid globotriaosylceramide (Gb3) expressed on germinal center (GC) B cells is essential for the production of high-affinity antibodies. Mechanistically, Gb3 binds and disengages CD19 from its chaperone CD81 for subsequent translocation to the B cell receptor (BCR) complex to trigger signaling. Abundance of Gb3 amplifies the PI3-kinase/Akt/Foxo1 pathway to drive affinity maturation. Moreover, this lipid regulates MHC-II expression to increase diversity of T follicular helper (Tfh) and GC B cells reactive with subdominant epitopes. In influenza infection, Gb3 promotes broadly reactive antibody responses and cross-protection. Thus, we show that Gb3 determines affinity as well as breadth in B cell immunity and propose this lipid as novel vaccine adjuvant against viral infection. One Sentence SummaryGb3 abundance on GC B cells selects antibodies with high affinity and broad epitope reactivities, which are cross-protective against heterologous influenza infection.

immunology↗

bioRxiv2023

Hyperglycosylation of prosaposin in tumor DCs promotes immune escape in cancer

Tumors develop strategies to evade immunity by suppressing antigen presentation. Here, we show that prosaposin drives CD8 T cell-mediated tumor immunity and that its hyperglycosylation in tumor DCs leads to cancer immune escape. We found that lysosomal prosaposin and its single saposin cognates mediated disintegration of tumor cell-derived apoptotic bodies to facilitate presentation of membrane-associated antigen and T cell activation. In the tumor microenvironment, TGF-{beta} induced hyperglycosylation of prosaposin and its subsequent secretion, which ultimately caused depletion of lysosomal saposins. In melanoma patients, we found similar prosaposin hyperglycosylation in tumor-associated DCs, and reconstitution with prosaposin rescued activation of tumor-infiltrating T cells. Targeting tumor DCs with recombinant prosaposin triggered cancer protection and enhanced immune checkpoint therapy. Our studies demonstrate a critical function of prosaposin in tumor immunity and escape and introduce a novel principle of prosaposin-based cancer immunotherapy. One Sentence SummaryProsaposin facilitates antigen cross-presentation and tumor immunity and its hyperglycosylation leads to immune evasion.

immunology↗

bioRxiv2023

Leveraging IFNγ/CD38 regulation to unmask and target leukemia stem cells in acute myelogenous leukemia

Elimination of drug-resistant leukemia stem cells (LSCs) represents a major challenge to achieve a cure in acute myeloid leukemia (AML). Although AML blasts generally retain high levels of surface CD38 (CD38pos), the presence of CD34 and lack of CD38 expression (CD34posCD38neg) are immunophenotypic features of both LSC-enriched AML blasts and normal hematopoietic stem cells (HSCs). We report that IFN-{gamma} induces CD38 upregulation in LSC-enriched CD34posCD38neg AML blasts, but not in CD34posCD38neg HSCs. To leverage the IFN-{gamma} mediated CD38 up-regulation in LSCs for clinical application, we created a compact, single-chain CD38-CD3-T cell engager (CD38-BIONIC) able to direct T cells against CD38pos blasts. Activated CD4pos and CD8pos T cells not only kill AML blasts but also produce IFN{gamma}, which leads to CD38 expression on CD34posCD38neg LSC-enriched blasts. These cells then become CD38-BIONIC targets. The net result is an immune-mediated killing of both CD38neg and CD38pos AML blasts, which culminates in LSC depletion. Statement of significanceThis work represents a potential advancement in the treatment of AML, as it involves the release of IFN-{gamma} by T cells to induce CD38 expression and thus sensitizing leukemia stem cells, which have been resistant to current treatment regimens, to CD38-directed T cell engagers.

cancer biology↗

bioRxiv2022

Early life tolerance depends on a subset of specialized dendritic cells and is reinforced by the skin microbiota

Early life establishment of tolerance to commensal bacteria at barrier surfaces carries enduring implications for immune health but remains poorly understood. Here we show that this process is controlled by microbial interaction with a specialized subset of antigen presenting cells. More particularly, we identify CD301b+ type 2 conventional dendritic cells (DC) as a subset in neonatal skin specifically capable of uptake, presentation and generation of regulatory T cells (Tregs) to commensal antigens. In early life, CD301b+ DC2 are enriched for programs of phagocytosis and maturation, while also expressing tolerogenic markers. In both human and murine skin, these signatures were reinforced by microbial uptake. In contrast to their adult counterparts or other early life DC subsets, neonatal CD301b+ DC2 highly expressed the retinoic acid-producing enzyme, RALDH2, deletion of which limited commensal-specific Tregs. Thus, synergistic interactions between bacteria and a specialized DC subset critically support early life tolerance at the cutaneous interface.

immunology↗

bioRxiv2021

Microbial signals and lymphotoxin drive TNF-independent death of A20 and ABIN-1 deficient epithelium

Anti-TNF antibodies are effective for treating patients with inflammatory bowel disease (IBD), but many patients fail to respond to anti-TNF therapy, highlighting the importance of TNF-independent disease. We previously demonstrated that acute deletion of two IBD susceptibility genes, A20 (Tnfaip3) and Abin-1 (Tnip1), in intestinal epithelial cells (IECs) sensitizes mice to both TNF-dependent and TNF-independent death. Here we show that TNF-independent IEC death after A20 and Abin-1 deletion is rescued by germ-free derivation or deletion of MyD88, while deletion of Trif provides only partial protection. Combined deletion of Ripk3 and Casp8, which inhibits both apoptotic and necroptotic death, completely protects against death after acute deletion of A20 and Abin-1 in IECs. A20 and Abin-1-deficient IECs are sensitized to TNF-independent, TNFR-1-mediated death in response to lymphotoxin alpha (LT) homotrimers. Blockade of LT in vivo reduces weight loss and improves survival when combined with partial deletion of MyD88. These data show that microbial signals, MyD88, and LT all contribute to TNF-independent intestinal injury. SUMMARYHere we show that germ-free derivation, MyD88 deletion, combined Ripk3 and Casp8 deletion, or anti-LT, all reduce TNF-independent intestinal injury after A20 and Abin-1 deletion.

immunology↗

bioRxiv2021

Late-in-life treadmill-training rejuvenates autophagy, protein aggregate clearance, and function in mouse hearts.

ABSTRACT AND KEYWORDSThere is evidence for a progressive decline of protein quality control mechanisms during the process of cardiac aging. This enables the accumulation of protein aggregates and damaged organelles that contribute to age-associated cardiac dysfunction. Macroautophagy (referred to as autophagy) is the process by which post-mitotic cells such as cardiomyocytes clear defective proteins and organelles. We hypothesized that late-in-life exercise training improves autophagy, protein aggregate clearance, and function that is otherwise dysregulated in hearts from old vs adult mice. As expected, 24-month old male C57BL/6J mice (old) exhibited : (i) repressed autophagosome formation and protein aggregate accumulation in the heart; (ii) systolic and diastolic dysfunction; and (iii) reduced exercise capacity, vs. 8-month old (adult) mice (all p< .05). Separate cohorts of 21 month old mice completed a 3-month progressive resistance treadmill-running program (old-ETR) that improved (all < .05) : (i) body composition; (ii) exercise capacity; and (iii) soleus muscle citrate synthase activity, vs. age-matched mice that did not train (old-SED). Importantly, (iv) protein expression of autophagy markers indicated trafficking of the autophagosome to the lysosome increased, (v) protein aggregate clearance improved, and (vi) overall function was enhanced (all p<0.05), in hearts from old-ETR vs. old- SED mice. Dietary maneuvers and pharmacological interventions shown to elevate basal autophagy are reported to mitigate / reverse age-associated cardiac dysfunction. Here we show the first evidence that a physiological intervention initiated late-in-life improves autophagic flux, protein aggregate clearance, and overall function in mouse hearts.

physiology↗

bioRxiv2020

Lineage recording reveals dynamics of cerebral organoid regionalization

Diverse regions develop within cerebral organoids generated from human induced pluripotent stem cells (iPSCs), however it has been a challenge to understand the lineage dynamics associated with brain regionalization. Here we establish an inducible lineage recording system that couples reporter barcodes, inducible CRISPR/Cas9 scarring, and single-cell transcriptomics to analyze lineage relationships during cerebral organoid development. We infer fate-mapped whole organoid phylogenies over a scarring time course, and reconstruct progenitor-neuron lineage trees within microdissected cerebral organoid regions. We observe increased fate restriction over time, and find that iPSC clones used to initiate organoids tend to accumulate in distinct brain regions. We use lineage-coupled spatial transcriptomics to resolve lineage locations as well as confirm clonal enrichment in distinctly patterned brain regions. Using long term 4-D light sheet microscopy to temporally track nuclei in developing cerebral organoids, we link brain region clone enrichment to positions in the neuroectoderm, followed by local proliferation with limited migration during neuroepithelial formation. Our data sheds light on how lineages are established during brain organoid regionalization, and our techniques can be adapted in any iPSC-derived cell culture system to dissect lineage alterations during perturbation or in patient-specific models of disease.Competing Interest StatementThe authors have declared no competing interest.View Full Text

developmental biology↗

bioRxiv2019

Diet induces reproducible alterations in the mouse and human gut microbiome

The degree to which diet reproducibly alters the human and mouse gut microbiota remains unclear. Here, we focus on the consumption of a high-fat diet (HFD), one of the most frequently studied dietary interventions in mice. We employed a subject-level meta-analysis framework for unbiased collection and analysis of publicly available 16S rRNA gene and metagenomic sequencing data from studies examining HFD in rodent models. In total, we re-analyzed 27 studies, 1101 samples, and 106 million reads mapping to 16S rRNA gene sequences. We report reproducible changes in gut microbial community structure both within and between studies, including a significant increase in the Firmicutes phylum and decrease in the Bacteroidetes phylum; however, reduced alpha diversity is not a consistent feature of HFD. Finer taxonomic analysis revealed that the strongest signal of HFD on microbiota species composition is Lactococcus spp., which we demonstrate is a common dietary contaminant through the molecular testing of dietary ingredients, culturing, microscopy, and germ-free mouse experiments. After in silico removal of Lactococcus spp., we employed machine learning to define a unique operational taxonomic unit (OTU)-based signature capable of predicting the dietary intake of mice and demonstrate that phylogenetic and gene-family transformations of this model are capable of accurately predicting human samples in controlled feeding settings (area under the receiver operator curve = 0.75 and 0.88 respectively). Together, these results demonstrate the utility of microbiome meta-analyses in identifying robust bacterial signals for mechanistic studies and creates a framework for the routine meta-analysis of microbiome studies in preclinical models.

microbiology↗