Biology subjects

Winter, J. M.

Publications and source records attributed to Winter, J. M..

At least 19 recordsLinked to original sources

bioRxiv2025

IDBac: an open-access web platform and compendium for the identification of bacteria by MALDI-TOF mass spectrometry.

The identification and analysis of bacteria is central to the microbiological sciences. While gene sequencing methods have been the standard to achieve this, use of MALDI-TOF mass spectrometry (MS), particularly in clinical microbiology, provides high-throughput identification to the subspecies level. However, biotyping has yet to be adopted outside of clinical settings due to the lack of a centralized public database of MS protein signatures that would facilitate isolate identification via spectral comparison. Further, current platforms lack meaningful ways to compare multiple properties from large numbers of bacterial isolates. Herein we present the IDBac web platform, a crowd-sourced central knowledgebase of protein MS signatures of >1400 strains spanning 6 bacterial phyla. Accompanying the knowledgebase is analysis infrastructure to identify unknown isolates, probe relationships within culture collections using metadata integration, and visualize specialized metabolite differences within groups of closely related bacteria. To highlight this utility and encourage wide community contribution, examples of each are presented.

microbiology↗

bioRxiv2025

Global Footprint of the Multidrug Resistance Island Ec17R and Resistance Gene Co-Occurrence in Pathogenic Escherichia coli Isolates

Multidrug resistant (MDR) bacterial pathogens are a major threat to global health, limiting treatment options for common infections. Extraintestinal Pathogenic Escherichia coli (ExPEC), a leading cause of bloodstream and urinary tract infections (UTIs), are often resistant to one or more antibiotic classes. Previously, we identified a clonal group of ExPEC strains (P1A) that persisted over a 5-year period from 2012 to 2016 within a female patient who suffered from frequent recurrent UTIs. A subset of these isolates carried a plasmid-borne MDR island (Ec17R) harboring 17 resistance genes. Sampling of fecal and urine samples in 2019 indicated that the patient remained colonized with the P1A lineage, including Ec17R-positive strains, over 7 years after collection of the first P1A isolates in 2012. Highlighting the public health relevance and mobility of Ec17R, we found that Ec17R-like islands are globally distributed across diverse bacterial species from various environmental, agricultural, and clinical sources, including multiple ExPEC isolates from local pediatric patients. By applying clustering approaches and Bayesian network modeling to 267 pediatric ExPEC isolates, we found that functionally distinct classes of resistance genes (including several heavy metal resistance genes) have a high probability of co-occurrence, possibly reflecting carriage within MDR islands like Ec17R. Finally, we observed that strains within the P1A lineage are recalcitrant to antibiotics for which they have no known resistance mechanisms, suggesting that these pathogens have means beyond their formidable array of resistance genes to survive within a host for years despite the administration of numerous, robust antimicrobial treatments. SIGNIFICANCEMultidrug resistance (MDR) in bacteria is a growing global health crisis that compromises our ability to treat routine infections. In this study, we investigated a clonal lineage of pathogenic Escherichia coli that persisted for many years in a patient with recurrent urinary tract infections. A subset of the E. coli strains carried by this patient possessed a large genomic island encoding resistance to multiple antibiotic classes. This MDR island is globally distributed across diverse bacterial species and niches, from clinical samples to agricultural and environmental reservoirs. Using probabilistic modeling of nearly 300 clinical isolates, we identified networks of resistance gene co-occurrence that link antibiotic and heavy metal resistance, suggesting the potential for environmental pollutants to contribute to MDR dissemination. Notably, patient-derived isolates also survived certain clinically relevant antibiotic treatments despite lacking known resistance mechanisms, highlighting tolerance and persistence as important, often overlooked drivers of therapeutic failure.

microbiology↗

bioRxiv2025

SeqForge: A scalable platform for alignment-based searches, motif detection, and sequence curation across meta/genomic datasets

BackgroundThe rapid increase in publicly available microbial and metagenomic data has created a growing demand for tools that can efficiently perform custom large-scale comparative searches and functional annotation. While BLAST+ remains the standard for sequence similarity searches, population-level studies often require custom scripting and manual curation of results, which can present barriers for many researchers. ResultsWe developed SeqForge, a scalable, modular command-line toolkit that streamlines alignment-based searches and motif mining across large genomic datasets. SeqForge automates BLAST+ database creation and querying, integrates amino acid motif discovery, enables sequence and contig extraction, and curates results into structured, easily parsed formats. The platform supports diverse input formats, parallelized execution for high-performance computing environments, and built-in visualization tools. Benchmarking demonstrates that SeqForge achieves near-linear runtime scaling for computationally intensive modules while maintaining modest memory usage. ConclusionsSeqForge lowers the computational barrier for large-scale meta/genomic exploration, enabling researchers to perform population-scale BLAST searches, motif detection, and sequence curation without custom scripting. The toolkit is freely available and platform-independent, making it suitable for both personal workstations and high-performance computing environments.

bioinformatics↗

bioRxiv2024

A Ketogenic Diet Sensitizes Pancreatic Cancer to Inhibition of Glutamine Metabolism

Pancreatic cancer is the third leading cause of cancer death in the United States, and while conventional chemotherapy remains the standard treatment, responses are poor. Safe and alternative therapeutic strategies are urgently needed1. A ketogenic diet has been shown to have anti-tumor effects across diverse cancer types but will unlikely have a significant effect alone. However, the diet shifts metabolism in tumors to create new vulnerabilities that can be targeted (1). Modulators of glutamine metabolism have shown promise in pre-clinical models but have failed to have a marked impact against cancer in the clinic. We show that a ketogenic diet increases TCA and glutamine-associated metabolites in murine pancreatic cancer models and under metabolic conditions that simulate a ketogenic diet in vitro. The metabolic shift leads to increased reliance on glutamine-mediated anaplerosis to compensate for low glucose abundance associated with a ketogenic diet. As a result, glutamine metabolism inhibitors, such as DON and CB839 in combination with a ketogenic diet had robust anti-cancer effects. These findings provide rationale to study the use of a ketogenic diet with glutamine targeted therapies in a clinical context. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/604377v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1ebeefforg.highwire.dtl.DTLVardef@97e2ceorg.highwire.dtl.DTLVardef@1ab45c3org.highwire.dtl.DTLVardef@1713540_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical Abstract Description: Mechanistic rationale for combining a ketogenic diet and glutamine metabolism inhibitors. The combination of low glucose from a ketogenic diet and pharmacologic glutamine inhibition impairs nutrient input to mitochondria, reducing cancer growth.

cancer biology↗

bioRxiv2024

Resistance Gene Association and Inference Network (ReGAIN): A Bioinformatics Pipeline for Assessing Probabilistic Co-Occurrence Between Resistance Genes in Bacterial Pathogens

The rampant rise of multidrug resistant (MDR) bacterial pathogens poses a severe health threat, necessitating innovative tools to unravel the complex genetic underpinnings of antimicrobial resistance. Despite significant strides in developing genomic tools for detecting resistance genes, a gap remains in analyzing organism-specific patterns of resistance gene co-occurrence. Addressing this deficiency, we developed the Resistance Gene Association and Inference Network (ReGAIN), a novel web-based and command line genomic platform that uses Bayesian network structure learning to identify and map resistance gene networks in bacterial pathogens. ReGAIN not only detects resistance genes using well- established methods, but also elucidates their complex interplay, critical for understanding MDR phenotypes. Focusing on ESKAPE pathogens, ReGAIN yielded a queryable database for investigating resistance gene co-occurrence, enriching resistome analyses, and providing new insights into the dynamics of antimicrobial resistance. Furthermore, the versatility of ReGAIN extends beyond antibiotic resistance genes to include assessment of co-occurrence patterns among heavy metal resistance and virulence determinants, providing a comprehensive overview of key gene relationships impacting both disease progression and treatment outcomes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/582197v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@158a667org.highwire.dtl.DTLVardef@114c965org.highwire.dtl.DTLVardef@1b24504org.highwire.dtl.DTLVardef@d112af_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

Bacterial Diversity and Chemical Ecology of Natural Product-Producing Bacteria from Great Salt Lake Sediment

Great Salt Lake (GSL), located northwest of Salt Lake City, UT, is the largest terminal lake in the United States. While the average salinity of seawater is [~]3.3%, the salinity in GSL ranges between 5-28%. In addition to being a hypersaline environment, GSL also contains toxic concentrations of heavy metals, such as arsenic, mercury, and lead. The extreme environment of GSL makes it an intriguing subject of study, both for its unique microbiome and its potential to harbor novel natural product-producing bacteria, which could be used as resources for the discovery of biologically active compounds. Though work has been done to survey and catalogue bacteria found in GSL, the Lakes microbiome is largely unexplored, and little-to-no work has been done to characterize the natural product potential of GSL microbes. Here, we investigate the bacterial diversity of two important regions within GSL, describe the first genomic characterization of Actinomycetota isolated from GSL sediment, including the identification of a new Saccharomonospora species, and provide the first survey of the natural product potential of GSL bacteria.

ecology↗

bioRxiv2023

Targeting wild-type IDH1 enhances chemosensitivity in pancreatic cancer

Pancreatic cancer (PC) is one of the most aggressive types of cancer, with a five-year overall survival rate of 11% among all-comers. Current systemic therapeutic options are limited to cytotoxic chemotherapies which have limited clinical efficacy and are often associated with development of drug resistance. Analysis of The Cancer Genome Atlas showed that wild-type isocitrate dehydrogenase (wtIDH1) is overexpressed in pancreatic tumors. In this study, we focus on the potential roles of wtIDH1 in pancreatic cancer chemoresistance. We found that treatment of pancreatic cancer cells with chemotherapy induced expression of wtIDH1, and this serves as a key resistance factor. The enzyme is protective to cancer cells under chemotherapy-induced oxidative stress by producing NADPH and alpha-ketoglutarate to maintain redox balance and mitochondrial function. An FDA-approved mutant IDH1 inhibitor, ivosidenib (AG-120), is actually a potent wtDH1 inhibitor under a nutrient-deprived microenvironment, reflective of the pancreatic cancer microenvironment. Suppression of wtIDH1 impairs redox balance, results in increased ROS levels, and enhances chemotherapy induced apoptosis in pancreatic cancer vis ROS damage in vitro. In vivo experiments further revealed that inhibiting wtIDH1 enhances chemotherapy anti-tumor effects in patient-derived xenografts and murine models of pancreatic cancer. Pharmacologic wtIDH1 inhibition with ivosidenib represents an attractive option for combination therapies with cytotoxic chemotherapy for patients with pancreatic cancer. Based on these data, we have initiated phase Ib trial combining ivosidenib and multi-agent chemotherapy in patients with pancreatic cancer (NCT05209074).

cancer biology↗

bioRxiv2022

Phosphate Starvation Signaling Increases Mitochondrial Membrane Potential through Respiration-independent Mechanisms

Mitochondrial membrane potential directly powers many critical functions of mitochondria, including ATP production, mitochondrial protein import, and metabolite transport. Its loss is a cardinal feature of aging and mitochondrial diseases, and cells closely monitor membrane potential as an indicator of mitochondrial health. Given its central importance, it is logical that cells would modulate mitochondrial membrane potential in response to demand and environmental cues, but there has been little exploration of this question. We report that loss of the Sit4 protein phosphatase in yeast increases mitochondrial membrane potential, both through inducing the electron transport chain and the phosphate starvation response. Indeed, a similarly elevated mitochondrial membrane potential is also elicited simply by phosphate starvation or by abrogation of the Pho85-dependent phosphate sensing pathway. This enhanced membrane potential is primarily driven by an unexpected activity of the ADP/ATP carrier. We also demonstrate that this connection between phosphate limitation and enhancement of the mitochondrial membrane potential is also observed in primary and immortalized mammalian cells as well as in Drosophila. These data suggest that mitochondrial membrane potential is subject to environmental stimuli and intracellular signaling regulation and raise the possibility for therapeutic enhancement of mitochondrial functions even with defective mitochondria.

cell biology↗

bioRxiv2022

Biosynthesis of the Fungal Nonribosomal Peptide Penilumamide A and Biochemical Characterization of a Pterin-Specific Adenylation Domain

We report the characterization of the penilumamide A biosynthetic gene cluster from the marine-derived fungus Aspergillus flavipes CNL-338. In vitro reconstitution studies demonstrated that three Plm nonribosomal peptide synthetases encoding four modules are required for constructing the lumazine-containing tripeptide. Further investigations using dissected adenylation domains determined substrate specificity for methionine and anthranilic acid and led to the first biochemical characterization of an adenylation domain with selectivity for a pterin-derived building block. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/505926v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@dfc4aeorg.highwire.dtl.DTLVardef@e9a4fdorg.highwire.dtl.DTLVardef@14ee7beorg.highwire.dtl.DTLVardef@1508021_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2022

Surgical techniques and tips for a reliable murine model of primary and metastatic pancreatic cancer

For patients with pancreatic cancer, survival rates lag behind other common cancers. This is in part due to the relative resistance to conventional chemotherapeutics and novel immune- or targeted-therapies. Ongoing research efforts are needed to identify and validate effective therapies. It is the unfortunate reality that a significant proportion of pre-clinical success does not translate into improved patient outcomes, likely due to a multitude of factors. In the current research landscape, flank xenograft models are commonly utilized to study pancreatic cancer, as this technique is fast, fairly non-invasive, and reliable. However, this model is not anatomically or physiologically accurate, does not impact other intra-abdominal organs, and experiments are often ended based on tumor size rather than systemic illness. Orthotopic injections of cancer cells directly into the pancreas for study of localized disease or into the spleen for study of hepatic metastases can be performed via a quick, reliable, minimally invasive surgical procedure with minimal morbidity and mortality. Existing methodologic reports are often sparse. Thus, there are significant knowledge and technical gaps for researchers attempting these techniques for the first time. In the current report, details of orthotopic pancreatic injections and splenic injections for metastatic disease are provided. Details of commonly encountered operative issues and mistakes are presented with suggestions to improve performance are described. A summary of expected outcomes is also provided herein.

cancer biology↗

bioRxiv2022

Wild-type IDH1 inhibition enhances chemotherapy response in melanoma

Malignant melanoma is one of the most common types of cancer in the United States. Despite recent and well-described progress in melanoma treatment, advanced disease still carries a poor prognosis for many patients and chemotherapy has been appropriately abandoned as a front-line option. Wild-type isocitrate dehydrogenase 1 (wtIDH1) has recently been implicated as a metabolic dependency in cancer. The enzyme is protective to cancer cells under metabolic stress, including oxidative damage by conventional chemotherapy and nutrient limitation characteristic of the tumor microenvironment. Specifically, the cytosolic enzyme generates NADPH to maintain redox homeostasis. IDH1 also supports mitochondrial function through anaplerosis of its reaction product, -ketoglutarate. We show that melanoma patients express higher levels of the wtIDH1 enzyme compared to normal skin tissue, and elevated wtIDH1 expression portends poor patient survival. Knockdown of IDH1 by RNA interference inhibited cell proliferation and migration under low nutrient levels. Suppression of IDH1 expression in melanoma also decreased NADPH and glutathione levels, resulting in increased reactive oxygen species. An FDA-approved inhibitor of mutant IDH1, ivosidenib (AG-120), exhibited potent anti-wtIDH1 properties under low magnesium and nutrient levels, reflective of the tumor microenvironment in natura. Similarly, findings were replicated in murine models of melanoma. Further, wtIDH1 inhibition was synergistic to conventional anti-melanoma chemotherapy in pre-clinical models. This work points to a novel and readily available combination treatment strategy for patients with advanced and refractory melanoma.

cancer biology↗

bioRxiv2022

Genome Mining and Biochemical Characterization of a Bifunctional Type I Diterpene Synthase from a Marine-Derived Fungus

We report the identification of the tnd biosynthetic cluster from the marine-derived fungal strain Aspergillus flavipes CNL-338 and in vivo characterization of a cryptic type I diterpene synthase. Heterologous expression of the bifunctional terpene synthase TndC in Saccharomyces cerevisiae led to the discovery of a new diterpene backbone, talarodiene, harboring a benzo[a]cyclopenta[d]cyclooctane tricyclic fused ring system. The cyclization mechanism that converts geranylgeranyl diphosphate to the tricyclic hydrocarbon skeleton was investigated using 13C-labeling studies and stable isotope tracer experiments showed the biotransformation of talarodiene into talaronoid C.

bioengineering↗

bioRxiv2022

Increased glucose availability sensitizes pancreatic cancer to chemotherapy

Pancreatic cancer (Pancreatic Ductal Adenocarcinoma; PDAC) is highly resistant to chemotherapy. Effective alternative therapies have yet to emerge, leaving chemotherapy as the best available systematic treatment. The discovery of safe and available adjuncts that improve chemotherapeutic efficacy would potentially improve survival outcomes. We show that a hyperglycemic state enhances the efficacy of conventional single- and multi-agent chemotherapies against PDAC. Molecular analyses of tumors exposed to relatively high glucose levels revealed that a key metabolic pathway, glutathione biosynthesis, is diminished and underlies chemo-sensitization by enhancing oxidative injury to cancer cells. Inhibition of this pathway under normal conditions phenocopied a hyperglycemic state by enhancing chemotherapeutic efficacy in mouse PDAC, while rescuing the pathway under high glucose abrogated the anti-tumor effects observed with chemotherapy.

cancer biology↗

bioRxiv2021

Protein-Metabolite Interactomics Reveals Novel Regulation of Carbohydrate Metabolism

Metabolism is highly interconnected and also has profound effects on other cellular processes. However, the interactions between metabolites and proteins that mediate this connectivity are frequently low affinity and difficult to discover, hampering our understanding of this important area of cellular biochemistry. Therefore, we developed the MIDAS platform, which can identify protein-metabolite interactions with great sensitivity. We analyzed 33 enzymes from central carbon metabolism and identified 830 protein-metabolite interactions that were mostly novel, but also included known regulators, substrates, products and their analogs. We validated previously unknown interactions, including two atomic-resolution structures of novel protein-metabolite complexes. We also found that both ATP and long-chain fatty acyl-CoAs inhibit lactate dehydrogenase A (LDHA), but not LDHB, at physiological concentrations in vitro. Treating cells with long-chain fatty acids caused a loss of pyruvate/lactate interconversion, but only in cells reliant on LDHA. We propose that these regulatory mechanisms are part of the metabolic connectivity that enables survival in an ever-changing nutrient environment, and that MIDAS enables a broader and deeper understanding of that network.

biochemistry↗

bioRxiv2021

Co-deletion of ATAD1 with PTEN primes cells for BIM-mediated apoptosis

PTEN is a potent tumor suppressor gene that is frequently mutated or deleted in human cancers. Such deletions often include portions of the 10q23 locus beyond the bounds of PTEN itself, in many cases resulting in the disruption of additional genes. Coincidental loss of PTEN-adjacent genes might impose vulnerabilities that could either affect patient outcome basally or be exploited therapeutically. Here we describe how the loss of ATAD1, which is adjacent to and frequently co-deleted with PTEN, predisposes cancer cells to apoptosis and correlates with improved survival in cancer patients. ATAD1 directly and specifically extracts the pro-apoptotic BIM protein from mitochondria to inactivate it. Cells lacking ATAD1 are hypersensitive to clinically used proteasome inhibitors, which increase BIM and trigger apoptosis. Thus, we demonstrate that mitochondrial protein quality control interfaces with cell death in a clinically actionable manner.

cancer biology↗

bioRxiv2020

Cancer cells are sensitive to wild-type IDH1 inhibition under nutrient limitation

Pancreatic cancer cells alter their metabolism to survive cancer-associated stress (1-4). For example, cancer cells must adapt to steep nutrient gradients that characterize the natural tumor microenvironment (TME) (5-7). In the absence of adaptive strategies, harsh metabolic conditions promote the generation of free radicals (8) and impair energy production in tumor cells. Towards this end, wild-type isocitrate dehydrogenase 1 (IDH1) activity is a metabolic requirement for cancer cells living in a harsh metabolic milieu. The cytosolic enzyme interconverts isocitrate and alpha-ketoglutarate, and uses NADP(H) as a cofactor. We show that under low nutrient conditions, the enzymatic reaction favors oxidative decarboxylation to yield NADPH and alpha-ketoglutarate. Metabolic studies showed that the IDH1 products directly support antioxidant defense and mitochondrial function in stressed cancer cells. Genetic IDH1 suppression reduced growth of pancreatic cancer cells in vitro under low nutrient conditions and in mouse models of pancreatic cancer. Surprisingly, allosteric inhibitors of mutant IDH1 proved to be potent wild-type IDH1 inhibitors under conditions specific to the TME, highlighting a natural therapeutic window. The presence of low magnesium enhanced allosteric inhibition by the drug, and ambient low glucose levels enhanced cancer cells dependence on wild-type IDH1. Thus, intrinsic TME conditions sensitized wild-type IDH1 to FDA-approved AG-120 (ivosidenib), and revealed the drug to be a potent single-agent therapeutic in cell culture and diverse in vivo cancer models. This work identified a potentially new repertoire of safe cancer therapies, including a clinically available compound, for the treatment of multiple wild-type IDH1 cancers (e.g., pancreatic).

cancer biology↗

bioRxiv2020

Msp1/ATAD1 restores mitochondrial function in Zellweger Spectrum Disease

Peroxisomal Biogenesis Disorders (PBDs) are a class of inherited metabolic disorders with profound neurological and other phenotypes. The most severe PBDs are caused by mutations in peroxin genes, which result in nonfunctional peroxisomes typically through impaired protein import. In order to better understand the molecular causes of Zellweger Spectrum Disease (ZSD) -the most severe PBDs -, we investigated the fate of peroxisomal mRNAs and proteins in ZSD model systems. We found that loss of peroxisomal import has no effect on peroxin mRNA expression or translational efficiency. Instead, peroxin proteins--still produced at high levels-- aberrantly accumulate on the mitochondrial membrane, impairing respiration and ATP generation. Finally, we rescued mitochondrial function in fibroblasts derived from human patients with ZSD by overexpressing ATAD1, an AAA-ATPase that functions in mitochondrial quality control. These findings might provide a new focus of PBD therapies in supporting quality control pathways that protect mitochondrial function.

cell biology↗

bioRxiv2019

Animal biosynthesis of complex polyketides in a photosynthetic partnership

Animals are rich sources of complex polyketides, including pharmaceuticals, cosmetics, and other products. Most polyketides are associated with microbial or plant metabolism1. For this reason, symbiotic bacteria or dietary organisms are often the true producers of compounds found in animals2,3. Although increasing evidence suggests that animals themselves make some compounds4-7, the origin of most polyketides in animals remains unknown. This problem makes it difficult to supply useful animal compounds as drugs and severely constrains our understanding of chemical diversity and the scope of biosynthesis in nature. Here, we demonstrate that animals produce microbe-like complex polyketides. We report a previously undocumented but widespread branch of fatty acid synthase- (FAS)-like proteins that have been retooled by evolution to synthesize complex products. One FAS-like protein uses only methylmalonyl-CoA as a substrate, otherwise unknown in animal lipid metabolism, and is involved in an intricate partnership between a sea slug and captured chloroplasts. The enzymes complex, methylated polyketide product results from a metabolic interplay between algal chloroplasts and animal host cells, and also likely facilitates the survival of both symbiotic partners, acting as a photoprotectant for plastids and an antioxidant for the slug8-12. Thus, we find that animals can unexpectedly synthesize a large and medically useful class of structurally complex polyketides previously ascribed solely to microbes, and can use them to promote symbiotic organelle maintenance. Because this represents an otherwise uncharacterized branch of polyketide and fatty acid metabolism, we anticipate a large diversity of animal polyketide products and enzymes awaiting discovery.

biochemistry↗