Biology subjects

Borchers, C. H.

Publications and source records attributed to Borchers, C. H..

17 recordsLinked to original sources

bioRxiv2026

PHENOMS: Open-Source Software for Rust-Accelerated Hydrogen-Bond Analysis in Molecular Dynamics Simulations

Hydrogen-deuterium exchange mass spectrometry (HDX-MS) provides powerful insight into protein structure and dynamics, but interpretation of protection patterns at atomic resolution often requires complementary computational modeling. We present PHENOMS, an open-source Python package that integrates molecular dynamics trajectories with HDX-MS data to analyze backbone hydrogen-bond networks by tracking how individual hydrogen bonds and residue-residue contacts form, break, and reorganize throughout the simulations. This residue-level analysis can reveal local structural changes that may be missed by conventional global trajectory metrics. PHENOMS employs a multithreaded, Rust-accelerated computational engine that achieved an average 16-fold speedup (up to 100-fold) over widely used Python-based MD analysis packages in our benchmarks, while retaining individual hydrogen-bond resolution in every trajectory frame. We demonstrate PHENOMS through multiple retrospective case studies using published and in-house datasets, showing that it can recapitulate HDX-MS protection patterns, identify key residues that drive coordinated structural changes, and benchmark the computational efficiency of the approach. With automated quality-control workflows, PHENOMS provides a framework for integrating hydrogen-bond analysis with HDX-MS data or serves as a standalone, high-throughput tool for analyzing MD trajectories for broader applications in protein engineering, drug discovery, and structural biology.

biophysics↗

bioRxiv2026

Endogenous insulin mediates dynamic coordination between pancreatic cancer and systemic metabolism

Pancreatic ductal adenocarcinoma (PDAC) is commonly associated with obesity, diabetes, and cachexia. The pancreatic anabolic hormone, insulin, is implicated in each of these metabolic diseases, but how insulin levels affect tumor growth and relevant host physiological factors, was unclear. To address this, we transplanted orthotopic PDAC patient-derived organoids into mice consuming a hyperinsulinemia-inducing high-fat diet (HFD). We found that insulin concentrations were higher in tumors compared to circulation. Genetically reducing insulin levels reduced PDAC growth, particularly in HFD-fed mature male mice. In turn, we found the presence of pancreatic tumors increased glucose clearance and limited the expected dietary-induced gains in insulin, weight and fat mass. Interestingly, tumor growth in normal-chow-fed mice, but not HFD-fed mice, was associated with declining circulating insulin levels, as well as declines in fat and muscle mass. Together, these data provide new insights into the complex, insulin-centred interplay between PDAC and the hosts systemic metabolism that underlie cancer-associated metabolic dysfunction.

cancer biology↗

bioRxiv2026

Cardiomyocyte pyruvate dehydrogenase kinase 1 knockout activates Rho-mediated remodeling and decreases fatty acyl availability in female mice

Pyruvate dehydrogenase kinase 1 (PDK1) inhibits pyruvate dehydrogenase (PDH) and therefore may regulate the balance between glucose and fatty acid oxidation in cardiomyocytes. We assessed metabolism and function in tamoxifen-inducible, cardiomyocyte-specific Pdk1 knockout (Pdk1cKO) mice, including both males and females fed a high fat diet, to resolve the role of PDK1 in the heart. Female, but not male, Pdk1cKO hearts showed the expected increase in cardiac PDH activity. Though cardiac function was largely preserved, female Pdk1cKO hearts had smaller left ventricles. Proteomics and phosphoproteomics revealed no change in classical hypertrophic markers but downregulated aerobic respiration alongside upregulated Ca2+ handling and Rho signalling, suggesting metabolic remodeling with altered cardiomyocyte contractility and cytoarchitecture in Pdk1cKO hearts. Concordantly, lipidomics revealed membrane remodeling marked by elevated saturated phosphatidylcholine in female Pdk1cKO hearts and decreased triacylglycerols, free fatty acids and fatty acid uptake proteins (CD36, FABP3). These findings reveal novel, female-predominant cardiometabolic roles for PDK1.

molecular biology↗

bioRxiv2026

Sex-dependent control of renal tubular homeostasis and stress tolerance by KDM6A

Biological sex is an important determinant of kidney disease susceptibility and outcomes. The epigenetic modifier KDM6A is an X chromosome-expressed lysine demethylase and molecular scaffold that escapes X chromosome inactivation. Here, we compared the effects of deletion of KDM6A from kidney tubule epithelial cells in female and male mice (KDM6ATubKO). Knockout of KDM6A from tubule cells aggravated kidney fibrosis caused by unilateral ureteral obstruction (UUO) in female mice, whereas male mice were unaffected by KDM6A absence. Unexpectedly, female (but not male) KDM6ATubKO mice developed spontaneous glucosuria that, when stressed by ligation of one ureter, presented as polyuria and a Fanconi renotubular syndrome-like picture affecting the unobstructed kidney. Absence of KDM6A from tubule epithelial cells of female mice caused mitochondrial circularization, tubule cell vacuolization with focal atrophy and lymphoid infiltration, and diminished sodium/glucose cotransporter 2 (SGLT2). Spatial transcriptomics and untargeted metabolomics revealed that knockout of KDM6A in female mice caused a shift in gene programs and metabolic pathways indicative of tubule cell metabolic dysfunction. In male mice, transcripts of the Y chromosome-expressed gametolog of Kdm6a, Uty were present in tubule epithelial cells at levels comparable to Kdm6a and they were upregulated with UUO. In summary, KDM6A is essential for normal tubule epithelial cell homeostasis in females but not in males. KDM6A and UTY are a dynamically regulated X-Y gene pair with at least partial compensatory overlap in function necessary for the preservation of kidney health and stress tolerance. Graphical abstract. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/740137v1_ufig1.gif" ALT="Figure 1000"> View larger version (29K): org.highwire.dtl.DTLVardef@9186b8org.highwire.dtl.DTLVardef@23d4cborg.highwire.dtl.DTLVardef@67741eorg.highwire.dtl.DTLVardef@1f85dc7_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2026

Lithocholic acid modulates the growth of butyrate-producing bacteria and is decreased in the feces of stunted children

Bile acids modulate the intestinal microbiota and serve as key signaling molecules in host physiology. Bile acid dysregulation has been implicated in nutritional and inflammatory diseases; however, data on the pool of bile acids present in stunted children or children suffering of environmental enteric dysfunction (EED) is limited, particularly in the upper intestinal compartment where disease phenotypes are most relevant. In this study, we performed a targeted metabolomics approach on 75 bile acids and their derivatives, including gastric and duodenal aspirates and fecal samples from almost 1000 children from two Sub-Saharan cities. We found that levels of secondary bile acids, especially lithocholic acid, are significantly lower in the feces of stunted and EED children, while ursocholic acid and its derivatives are significantly higher. Levels of primary and sulfated bile acids are also increased in the feces of children with EED. Microbiota sequencing revealed that high lithocholic acid levels are positively associated with butyrate-producing bacteria, while negatively associated with oral taxa like Streptococcus and Veillonella. In vitro tests on a panel of reference strains showed that oral bacteria bioaccumulate and are inhibited by a variety of bile acids, while lithocholic and chenodeoxycholic acids modulate the growth of several butyrate-producing bacteria. This effect was even stronger with tauro- or glycol-conjugated bile acids. Exposing stool-derived in vitro communities from children in Afribiota to these bile acids confirmed their positive impact on butyrate producers and negative effect on overgrowing oral taxa. Our findings suggest that secondary bile acids, reduced in stunting and EED, modulate the growth of butyrate-producing bacteria while suppressing harmful oral taxa, highlighting their potential as tools to modulate microbiota composition.

microbiology↗

bioRxiv2026

A Multiomic Analysis of Cachectic Mice Reveals Cancer Driven Suppression of Muscle Stem Cell Differentiation

Cancer cachexia affects a large proportion of cancer patients, inducing a rapid decline in muscle mass. Patients with cachexia have a worse prognosis and are less responsive to cancer therapies. The exact cause of cachexia remains unknown, nor are there any effective treatments for the condition. In this study, we use the C26 adenocarcinoma cell line to determine how cancer cells affect myofiber and muscle stem cell function. We determined that C26 cancer cells adapt to the host environment, in both male and female mice, greatly altering their transcriptome to promote their survival and growth. C26 cells directly communicate with muscle stem cells via GDF15 and MMP9. These circulatory factors cause the muscle stem cells to upregulate the EMT pathway and become less capable of undergoing differentiation and contributing to muscle regeneration. Muscle stem cells from tumor bearing mice are less proliferative and less prone to differentiation, Chromatin accessibility data shows that there are fewer accessible myogenic regulatory binding sites. Cytokine array determined that circulating GDF15 and MMP9 were highly upregulated and were derived form C26 tumor cells. However, blocking tumor derived GDF15 is not sufficient to prevent the onset of cachexia and rescue the loss of muscle stem cell function. Together, these findings establish a new conceptual paradigm in which cancer orchestrates muscle wasting through coordinated transcriptional, metabolic, and epigenetic suppression of muscle stem cell differentiation.

cell biology↗

bioRxiv2025

IRP1 deficiency alters mitochondrial metabolism and protects against metabolic syndrome pathologies

Iron regulatory protein 1 (IRP1) is a post-transcriptional regulator of cellular iron metabolism. In mice, loss of IRP1 causes polycythemia through translational de-repression of hypoxia-inducible factor 2 (HIF2) mRNA, which increases renal erythropoietin production. Here we show that Irp1-/- mice develop fasting hypoglycemia and are protected against high-fat diet-induced hyperglycemia and hepatic steatosis. Discovery-based proteomics of Irp1-/- livers revealed a mitochondrial dysfunction signature. Seahorse flux analysis in primary hepatocytes and differentiated skeletal muscle myotubes confirmed impaired respiratory capacity, with a shift from oxidative phosphorylation to glycolytic ATP production. This metabolic rewiring was associated with enhanced insulin sensitivity and increased glucose uptake in skeletal muscle. Under metabolic stress, IRP1 deficiency altered the redox balance of mitochondrial iron, resulting in inefficient energy production and accumulation of amino acids and metabolites in skeletal muscle, rendering them unavailable for hepatic gluconeogenesis. These findings identify IRP1 as a critical regulator of systemic energy homeostasis.

pathology↗

bioRxiv2025

A Hit Prioritization Strategy for Compound Library Screening Using LiP-MS and Molecular Dynamics Simulations Applied to KRas G12D Inhibitors

An important step in screening small molecule libraries for drug discovery is hit prioritization and validation to rule out false positives, which is usually performed using biochemical and biophysical assays. The development of orthogonal assays that are highly sensitive and can accelerate the hit-to-lead process is valuable. Limited proteolysis combined with mass spectrometry (LiP-MS) is a technique used to study changes in protein structure upon ligand binding. In LiP-MS, proteins are exposed to low concentrations of proteases under native conditions. The resulting proteolytic pattern is sensitive to protein structure at the cleavage site, which can change upon ligand binding. We characterized the interaction of small molecule inhibitors of the KRas G12D mutant oncoprotein by LiP-MS combined with molecular dynamics (MD). Intact mass spectrometry and top-down analysis were used to detect and identify KRas G12D cleavage products in the presence and absence of inhibitors, thereby locating the cleavage sites in the protein. Cleavage sites protected upon compound binding correlated well with the switch II binding site. The degree of cleavage depends on binding affinity and the presence of specific functional groups in the inhibitors structure. A comparison of MD simulations for the ligand-free and ligand-bound proteins revealed the atomistic mechanisms by which the cleavage sites, located in flexible and disordered regions, are stabilized upon compound binding. We suggest that LiP-MS combined with MD (LiP-MS-MD) could be valuable in small molecule screening campaigns and add to the repertoire of available methods for high-quality hit selection in early-stage drug discovery.

biophysics↗

bioRxiv2025

Characterization of the KRas G12D-inhibitor interactions by HDX-MS and molecular dynamics simulations

Hydrogen-deuterium exchange (HDX) combined with mass spectrometry (MS) is a powerful technique for studying changes in protein structure and dynamics upon ligand binding. Protein-ligand complexes can result in increased protection of peptide-bond amides in HDX indicating protein structure stabilization. We have characterized the interaction of lead inhibitor candidates towards the KRas G12D oncoprotein by intact protein and bottom-up HDX-MS in combination with molecular dynamics (MD) simulations. Significant differences in HDX protection were detected upon inhibitor binding in the flexible switch-II pocket of the protein. We identified a correlation between ligand binding affinities and corresponding changes in protection. MD simulations of the free and inhibitor-bound KRas G12D proteins revealed changes in the hydrogen bond network of backbone amides in the switch-II region upon inhibitor binding, explaining the observed HDX protection. This combined HDX-MS and MD analysis approach provides a mechanistic picture of the KRas G12D protein-inhibitor interactions and may be a useful tool for future drug design efforts.

biophysics↗

bioRxiv2024

SysQuan: repurposing SILAC mice for the affordable absolute quantitation of the human proteome

Relative quantitation, used by most MS-based proteomics laboratories to determine protein fold-changes, requires samples being processed and analyzed together for best comparability through minimizing batch differences. This limits the adoption of MS-based proteomics in population-wide studies, and the detection of subtle but relevant changes in heterogeneous samples. Absolute quantitation circumvents these limitations and enables comparison of results across laboratories, studies, and longitudinally. However, high costs of the essential stable isotope labeled (SIL) standards prevents widespread access and limits the number of quantifiable proteins. Our new approach, called "SysQuan", repurposes SILAC mouse tissues/biofluids as system-wide internal standards for matched human samples to enable absolute quantitation of, theoretically, two-thirds of the human proteome using 157,086 shared tryptic peptides. We demonstrate that SysQuan enables quantification of 70% and 31% of the liver and plasma proteomes, respectively. We demonstrate for 14 metabolic proteins that abundant SIL mouse tissues enable cost-effective reverse absolute quantitation in, theoretically, 1000s of human samples. Moreover, 10,000s of light/heavy doublets in untargeted SysQuan datasets enable unique post-acquisition absolute quantitation. SysQuan empowers researchers to replace relative quantitation with affordable absolute quantitation at scale, making data comparable across laboratories, diseases and tissues, enabling completely novel study designs and increasing reusability of data in repositories. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/622109v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@c7a58org.highwire.dtl.DTLVardef@1344320org.highwire.dtl.DTLVardef@2321e3org.highwire.dtl.DTLVardef@85bf2d_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2023

Proteomic evidence of astrocytic dysfunction in the olfactory bulb of depressed suicides

The olfactory bulb (OB), a major structure of the limbic system, has been understudied in human investigations of psychopathologies such as depression. To explore more directly the molecular features of the OB in depression, a global comparative proteome analysis was carried out with human post-mortem OB samples from 11 males having suffered from depression and 12 healthy controls. We identified 188 differentially abundant proteins (with adjusted p<0.05) between depressed cases and controls. Gene ontology and gene enrichment analyses suggested that these proteins are involved in biological processes including the complement and coagulation cascades. Cell type enrichment analysis displayed a significant reduction in several canonical astrocytic proteins in OBs from depressed patients. Furthermore, using RNA-fluorescence in-situ hybridization, we observed a decrease in the percentage of ALDH1L1+ cells expressing canonical astrocytic markers including ALDOC, NFIA, GJA1 (connexin 43) and SLC1A3 (EAAT1). These results are consistent with previous reports of downregulated astrocytic marker expression in other brain regions in depressed patients. We also conducted a comparative phosphoproteomic analysis of OB samples and found a dysregulation of proteins involved in neuronal and astrocytic functions. To determine whether OB astrocytic abnormalities is specific to humans, we also performed proteomics on the OB of socially defeated male mice, a commonly used model of depression. Cell-type specific analysis revealed that in socially defeated animals, the most striking OB protein alterations were associated with oligodendrocyte- lineage cells rather than with astrocytes, highlighting an important species difference. Overall, this study further highlights cerebral astrocytic abnormalities as a consistent feature of depression in humans.

neuroscience↗

bioRxiv2023

Clinical proteomics reveals vulnerabilities in non-invasive breast ductal carcinoma and drives personalized treatment strategies.

Ductal carcinoma in situ (DCIS) is the most common type (80%) of noninvasive breast lesions. The lack of validated prognostic markers, limited patient numbers and variable tissue quality significantly impact diagnosis, risk stratification, patient enrolment, and results of clinical studies. We performed label-free quantitative proteomics on 50 clinical formalin-fixed, paraffin embedded biopsies, validating 22 putative biomarkers from independent genetic studies. Our comprehensive proteomic phenotyping reveals more than 380 differentially expressed proteins and metabolic vulnerabilities, that can inform new therapeutic strategies for DCIS and IDC. Due to the readily druggable nature of proteins and metabolites, this study is of high interest for clinical research and pharmaceutical industry. To further evaluate our findings, and to promote the clinical translation of our study, we developed a highly multiplexed targeted proteomics assay for 90 proteins associated with cancer metabolism, RNA regulation and signature cancer pathways, such as Pi3K/AKT/mTOR and EGFR/RAS/RAF.

cancer biology↗

bioRxiv2022

Insulin receptors in pancreatic acinar cells contribute to KrasG12D-driven cancer initiation in the context of diet-induced obesity

The rising pancreatic cancer incidence due to obesity and type 2 diabetes is closely tied to hyperinsulinemia, an independent cancer risk factor. Previous studies demonstrated reducing insulin production suppressed pancreatic intraepithelial neoplasia (PanIN) pre-cancerous lesions in Kras-mutant mice. However, the pathophysiological and molecular mechanisms remained unknown and in particular it was unclear whether hyperinsulinemia affected PanIN precursor cells directly or indirectly. Here, we demonstrate that insulin receptors (Insr) in KrasG12D-expressing pancreatic acinar cells are dispensable for glucose homeostasis, but necessary for hyperinsulinemia-driven PanIN formation in the context of diet-induced hyperinsulinemia and obesity. Mechanistically, this was attributed to amplified digestive enzyme protein translation, triggering of local inflammation and PanIN metaplasia in vivo. In vitro, insulin dose-dependently increased acinar-to-ductal metaplasia formation in a trypsin- and Insr-dependent manner. Collectively, our data shed light on the mechanisms connecting obesity-driven hyperinsulinemia and pancreatic cancer development.

cancer biology↗

bioRxiv2020

Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein

Detection of viral RNA by PCR is currently the main diagnostic tool for COVID-19 [1]. The PCR-based test, however, shows limited sensitivity, especially at early and late stages of the disease development [2,3], and is relatively time consuming. Fast and reliable complementary methods for detecting the viral infection would be of help in the current pandemia conditions. Mass-spectrometry is one of such possibilities. We have developed a mass-spectrometry based method for the detection of the SARS CoV-2 virus in nasopharynx epithelial swabs, based on the detection of the viral nucleocapsid N protein. The N protein of the SARS-COV-2 virus, the most abundant protein in the virion, is the best candidate for mass-spectrometric detection of the infection, and MS-based detection of several peptides from the SARS-COoV-2 nucleoprotein has been reported earlier by the Sinz group [4]. Our approach shows confident identification of the N protein in patient samples even with the lowest viral loads and a much simpler preparation procedure. Our main protocol consists of virus inactivation by heating and adding of isopropanol, and tryptic digestion of the proteins sedimented from the swabs followed by MS analysis. A set of unique peptides, produced as a result of proteolysis of the nucleocapsid phosphoprotein of SARS-CoV-2, is detected. The obtained results can further be used to create fast parallel mass-spectrometric approaches for the detection of the virus in the nasopharyngeal mucosa, saliva, sputum and other physiological fluids.

molecular biology↗

bioRxiv2019

Endothelial specific PER2 at the crossroads of light elicited circadian amplitude enhancement as novel cardioprotective strategy and transcriptional regulation of HIF1A-dependent metabolic adaptation to myocardial ischemia

Consistent daylight oscillations and abundant oxygen availability are fundamental to human health. While both are connected from an evolutionary and cellular perspective, only oxygen is an established therapy in cardiovascular medicine. Here, we probe the mechanistic intersection between light-(Period 2, PER2) and oxygen-(hypoxia inducible factor, HIF1A) sensing pathways in cellular adaptation to low oxygen conditions with respect to myocardial ischemia. Using a whole genome array from daylight exposed wildtype or Per2-/- mice, an affinity purification-mass spectrometry-based proteomics screen for PER2 targets in hypoxic human endothelial cells, and targeted metabolomics from human healthy volunteers after daylight therapy, we investigated the intersection of light and hypoxia elicited pathways. Housing mice under daylight conditions prior to myocardial ischemia and reperfusion (IR)-injury, uncovered circadian PER2 amplitude enhancement as novel cardioprotective strategy, mimicking HIF1A metabolic adaptation to myocardial ischemia in a PER2 regulated manner. Whole genome array analysis from daylight exposed wildtype and Per2-/- mice or myocardial IR-injury in endothelial specific PER2 deficient mice (Per2loxP/loxP-VE-Cadherin -Cre) revealed a critical role for light elicited PER2 in maintaining the endothelial barrier function during myocardial ischemia. Mechanistic studies in human endothelia pointed towards a master transcriptional regulatory role for endothelial PER2 in metabolic reprograming to hypoxia via HIF1A, which was mimicked during normoxic PER2 stabilization. Translational investigation of light elicited pathways in human healthy volunteers found similar increases of PER2 or mimicking of HIF1A dependent metabolism. These studies identify light elicited circadian amplitude enhancement of endothelial PER2 as a novel cardioprotective strategy. Furthermore, these studies identify PER2 as critical control point of endothelial metabolic reprograming to maintain vascular integrity during myocardial IR-injury and implicate the use of daylight therapy to increase endothelial PER2 signaling as a strategy for the treatment of coronary artery disease.

cell biology↗

bioRxiv2017

Short-term stabilities of 21 amino acids in dried blood spots

BACKGROUNDDried blood spots (DBSs) have potential use in remote health applications for individual and population diagnosis, and can enable epidemiological surveillance for known and unknown diseases. The preparation and transportation of DBSs from remote settings often exposes these cards to extreme environmental stress that may impact the quality of the diagnostic data. Given these risks, it is essential to investigate the individual stabilities of biomarkers in DBSs. This paper details the stability of routinely-analyzed amino acids (AAs) on DBSs under environmental conditions that simulate a global health workflow.\n\nMETHODSThe extractions of 21 AAs from three sets of DBSs prepared on cellulose and cotton filter paper were optimized for quantitation by dansylation-UPLC/MRM-MS. The effects of sunlight exposure, temperature, humidity, and storage time were studied.\n\nRESULTSThe AAs were stable in DBSs after 4-hour sunlight exposure, and after storage at -20 and 4 {degrees}C for 30 days. At 25 and 40 {degrees}C, only 7 AAs showed significant concentration decreases over time, while 2 showed concentration increases. The changes were accelerated by high humidity. Histidine was the least stable AA under the conditions tested.\n\nCONCLUSIONSThis study provides quantitative data on the short-term stabilities of 21 AAs in DBSs on cellulose and cotton-based filter paper, under environmental conditions that simulate a global-health workflow. These results highlight the importance of assessing the stability of clinically-relevant biomarkers in DBSs. Based on the measured stabilities, we recommend that higher-temperature and high-humidity storage of DBS samples be avoided for AA analysis in remote health applications.

biochemistry↗

bioRxiv2017

Affinity-mass spectrometric technologies for quantitative proteomics in biological fluids

Proteins are the functional molecules in organisms and are therefore excellent biomarker candidates for a diversity of diseases. Immunoassays and mass spectrometry (MS) are two major technologies being used in proteomics; however, they either lack specificity or sensitivity. An emerging trend is to combine immunoassays with MS (which we call \"affinity-MS\"). This is an important milestone in quantitative proteomics, making it possible to measure low-abundance proteins with high specificity. The targeted enrichment and the assignment of mass-to-charge ratios to different molecules provide two selection criteria, making affinity-MS highly specific. Picogram-per-milliliter limits of detection have been obtained for many proteins. Furthermore, multiplexing capacity of >150 proteins has been achieved. This article reviews different formats of affinity-enrichment methods, and demonstrates how they are interfaced with both electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) MS. The pros and cons of these techniques are compared, and future prospectives are discussed.

molecular biology↗