- by Sharifi, O., Neier, K. E., Valenzuela, A. E., Torres, C. G., Korf, I., Lein, P. J., Yasui, D. H., LaSalle, J.Etiologies of neurodevelopmental disorders involve genes and environment however their interactions are understudied. Rett Syndrome (RTT) is an X-linked, dominant neurodevelopmental disorder caused by mutations in MECP2, encoding the epigenetic regulator methyl CpG binding protein. Epigenetic features of MECP2 expression due to X-linked cellular mosaicism and the variability in severity and timing of progression in RTT suggest interaction with environmental neurotoxicants such as lipophilic polychlorinated biphenyls (PCBs). To understand shared mechanisms, we exposed WT and Mecp2e1-/+ female mice to a […]
- by Levin, N., Saylan, C. C., Lapin, J., Demyanenko, Y., Yang, K. L., Sidda, J., Nesvizhskii, A., Wilhelm, M., Mohammed, S.We built and characterised a mass spectrometer capable of performing CID (both beam type and resonant type), UVPD, EID and ECD in an automated fashion during an LCMS type experiment. We exploited this ability to generate large datasets through multienzyme deep proteomics experiments for characterisation of these activation techniques. As a further step, motivated by the complexity generated by these dissociation techniques, we developed a single Prosit deep learning model for fragment ion intensity prediction covering all of these techniques. […]
- by Oliinyk, D., Heymann, T., Henneberg, L., Bardziukova, A., Thielert, M., Kjaergaard, J., Vasconez, S., Oeller, M., Rodriguez, E., Rosenberger, F. A., Mann, M.Mass spectrometry (MS)-based phosphoproteomics has transformed our understanding of cell signaling, yet current workflows face limitations in sensitivity and spatial resolution when applied to sub-microgram scale protein inputs. Here, we present nanoPhos, a robust method for ultra-sensitive phosphoproteomics, which allows deep coverage at high throughput and is compatible with Deep Visual Proteomics (DVP). It employs loss-less solid phase extraction capture (SPEC) for sample preparation and protein processing, followed by automated zero-volume phosphopeptide enrichment using Fe(III)-NTA cartridges. nanoPhos identifies over 55,000 […]
- by Reimer, J., Page, J., Saha, P., Shen, S., Zhu, X., Qian, S., Mammen, M., Qu, J., Sethi, S., Broderick, G. J.The fourth leading cause of death in the US, Chronic Obstructive Pulmonary Disease (COPD) is punctuated by frequent viral and bacterial infections causing severe acute exacerbations (AECOPD) and increased mortality. In previous work we have shown that altered immune cell signaling may confer increased and persistent susceptibility to infection. Here we continue this investigation by conducting broad-spectrum proteomic profiling of circulating white blood cells to assemble an empirical protein-protein interaction network associated with frequency of infectious exacerbation. In a novel […]
- by Woessmann, J., Petrosius, V., Schovsbo, S., Arrey, T. N., Furtwaengler, B., Op de Beeck, J., Damoc, E., Porse, B. T., Schoof, E. M.Cellular differentiation processes are largely orchestrated by variation in transcription factor (TF) abundance. Since these proteins are usually expressed at extremely low levels, studying TF-driven cellular processes using single-cell proteomics by mass spectrometry (scp-MS) has been challenging. Here we present informed DIA (iDIA), an acquisition method tailored towards low-input and scp-MS. iDIA combines targeted and global proteomics in a single acquisition scheme and is by design universally applicable on different MS instrumentation. By combining wide window (ww)PRM scans with DIA […]
- by Mighell, T., Lehner, B.G-protein coupled receptors (GPCRs) are the most abundant class of human receptors and drug targets. The vast majority of GPCR drugs bind the conserved orthosteric pocket, which can lead to non-specificity and toxicity. Precision modalities such as biased signaling and allosteric modulation could lead to GPCR therapeutics with improved efficacy and safety profiles. The rational design of precision therapies is, however, limited by the lack of high-resolution functional understanding of GPCRs. Here we present a general approach to chart high-resolution […]
- by Simpson, M. J., Plank, M. J.Parameter inference is a critical step in the process of interpreting biological data using mathematical models. Inference provides a means of deriving quantitative, mechanistic insights from sparse, noisy data. While methods for parameter inference, parameter identifiability, and model prediction are well-developed for deterministic continuum models, working with biological applications often requires stochastic modelling approaches to capture inherent variability and randomness that can be prominent in biological measurements and data. Random walk models are especially useful for capturing spatiotemporal processes, such […]
- by Chiba, G., Kamei, K.-i. F., Oda, A. H., Ohta, K., Wakamoto, Y.Understanding how specific genetic changes lead organisms to different phenotypes is the cornerstone of genetics. However, even a single gene perturbation can cause global changes in gene expression profiles. Consequently, predicting which genes will be affected by a particular genetic perturbation remains a challenge. Here, we analyze changes in genome-wide gene expression profiles caused by single-gene perturbations in bacterial, worm, and human cells and show a simple rule that genes that intrinsically maintain the ratio of expression levels (stoichiometry) with […]
- by Estevez, S. R., Baltusyte, G., Youssef, G., Han, N.We present a generalisable, interpretable machine learning framework for therapeutic target discovery using single-cell transcriptomics, protein interaction networks, and drug proximity analysis. The pipeline integrates feature selection via gradient boosting classifiers, systems-level network inference, and in silico drug repurposing, enabling the identification of actionable targets with cellular specificity. As a proof of concept, we apply the method to clear cell renal cell carcinoma (ccRCC), an aggressive kidney cancer with limited treatment options. The model identifies 96 tumour-intrinsic genes, refines them […]
- by Gizardin-Fredon, H., Terrosu, S., Pichard, S., Korkut, D., Braun, C., Poterszman, A., Charenton, C., Cianferani, S.Protein-protein interactions (PPIs) underpin nearly all cellular processes; therefore, mapping PPI and protein-protein association networks is critical for understanding how biological systems function in health and disease. However, many functionally relevant PPIs are transient and mediated by weak affinity interactions, making them challenging to detect. Using chemical cross-linking together with mass spectrometry (XL-MS) has emerged as an important category of methods for mapping PPIs, including those that are more dynamic and transient, although XL-MS workflows face limitations which hinder their […]
- by Jain, P., Jolly, M. K., George, J. T.Cells invariably encounter unpredictable changes in their microenvironment and undergo adaptation by orchestrating considerable alterations in their molecular states that often result in appreciable phenotypic changes. The timescale of molecular and, therefore, cellular adaptation depends on how quickly the memory of past environmental encounters is lost (and therefore forgotten) by the cell (e.g., degradation rate of proteins unfavorable to the current environment). Here, we study the dynamical implications of two distinct memory mechanisms on cellular responses to a changing environment. […]
- by Shi, L., Uzuni, A., Wang, X. K., Pressler, M., Harle, D. W., Chakrabarti, S., Macedo, R., Belay, K., Gordillo, C. A., Raps, E., Zhang, J. Y. A., Nazaret, A., Fan, J. L., Jin, Y., Shen, X., Fuller, J. S., Azad, T., Huang, J., Chainani, P., Abrams, J. A., Del Portillo, A., Mapara, M. Y., Alhamar, M., Sykes, M., McFaline-Figueroa, J., Azizi, E., Reshef, R.Allogeneic hematopoietic cell transplantation (alloHCT) is curative for various hematologic diseases but often leads to acute graft-versus-host disease (GVHD), a potentially life-threatening complication. We leverage GVHD as a uniquely tractable disease model to dissect complex T-cell-mediated pathology in 27 alloHCT recipients. We integrate pre-transplant identification of alloreactive T-cells with longitudinal tracking across blood and gut, using mixed lymphocyte reaction-based clonal "fingerprinting", TCR clonotyping, single-cell RNA/TCR sequencing, and spatial transcriptomics. Using DecompTCR, a novel computational tool for longitudinal TCR analysis, we […]
- by Parsa, M. S., Aminian-Dehkordi, J., Mofrad, M.Understanding gut microbiome dynamics gut requires deciphering complex, metabolically driven interactions beyond taxonomic profiles. We present SIMBA, a novel framework that integrates mechanistic metabolic simulations with a graph neural network (GNN) to predict microbial abundances and uncover cross-feeding relationships. By simulating pairwise interactions among gut microbes using metabolic networks, we generate biologically grounded graphs that capture metabolite cross-feeding and functional relationships. Our custom GNN, enhanced with edge-aware attention, is trained through a multi-stage pipeline combining self-supervised learning, simulation-based pretraining, and […]
- by Dang, V., Voigt, B., Yang, D., Hoogerbrugge, G., Lee, M., Cox, R., Papoulas, O., McWhite, C. D., Pradeep, R., Leggere, J. C., Gray, R. S., Marcotte, E. M.Protein-protein interactions underlie core brain functions, including neurotransmitter release, receptor activation, and intracellular signaling essential for learning, memory, and cognition. Here, we systematically map conserved brain protein interactions across five vertebrate species-rabbit, chicken, dolphin, pig, and mouse-using co-fractionation and immunoprecipitation mass spectrometry. From 2,197 biochemical fractions, we identify over 81,000 high-confidence interactions among 6,108 conserved proteins. This interaction map (VerteBrain) reveals both regulatory and structural complexes, including extensive synaptonemal protein associations likely involved in inter-neuronal coordination. Conservation across species underscores […]
- by Clark, H. K., Yeung, E., Thirumaligai, R., Giusto, C.Global cellular transcription and growth are tightly coupled to the supercoiling state of a cells genomic DNA. Direct processes that modulate the supercoiling state of genomic DNA thus provide a novel mechanistic route for biological control of cellular dynamics. In this work, we develop a stochastic model of genome-wide transcriptional responses to local DNA supercoiling and show that, despite heterogeneity in the transcription of each individual gene, the overall system converges to a unique stationary distribution. From the stochastic system, […]
- by Carrasco Muriel, J., Groves, T., Nielsen, L. K.Transcriptional regulation–the modulation of gene expression in response to environmental stimuli–is fundamental to cellular function. Identifying groups of co-regulated genes helps elucidate gene functions and characterize how an organism has evolved to respond to various stimuli. In previous works, signal processing algorithms have been applied to characterize the transcriptional regulatory modes, known as iModulons, of bacteria. However, these methods do not quantify uncertainty of the results and are difficult to integrate with different sources of information. In this work, we […]
- by Francis, E. A., Hamid, J., Kumar, A., Rangamani, P.The dynamics of calcium ions (Ca2+) in skeletal muscles link electrochemical activation and contractile force generation. An improved quantitative understanding of the mechanisms by which calcium dynamics modulate force production is crucial for optimizing muscle performance. Recent experimental data suggest that store-operated calcium entry (SOCE), the process of extracellular Ca2+ influx upon depletion of Ca2+ from the sarcoplasmic reticulum (SR), helps delay the onset of muscle fatigue. However, the mechanistic links between SOCE and sustained force generation in muscle remain […]
- by Kitano, E., Demyanenko, Y., Mohammed, S.We evaluate the performance of nonporous C-18 stationary phases in high-speed proteomics workflows. We employed two commercially available sub-2 {micro}m nonporous particle (NPP) materials, ODS-IIIE (1.5 {micro}m) and SOLAD (1.0 {micro}m), to fabricate analytical columns using 150 {micro}m internal diameter (i.d.) fused silica capillaries to ensure compatibility with nano-UHPLC and nano-HPLC pressure regimes. Using long NPP columns (15 – 25 cm) connected to a conventional nano-UHPLC, we found that both materials supported efficient peptide separations within the flow rate and […]
- by Greter, G., Hummel, S., Kuenzli, D., Duenki, N., Ruoho, N., Burkhardt, P., Ganguillet, S., Radiom, M., Moresi, C., Laganenka, L., Hardt, W.-D., Geisel, S., Jordi, S., Misselwitz, B., Yilmaz, B., Slomka, J., Secchi, E., Stocker, R., Slack, E., Arnoldini, M.Spatial structure can determine function and evolution of bacterial communities. The gut microbiota is known to be spatially structured longitudinally along the many meters of the gastrointestinal tract, but micro-scale structure in the gut lumen has not been extensively explored. In samples from mice and humans, we show that upper large-intestinal content behaves as a non-Newtonian fluid that changes its viscoelastic properties under the force of gut contractions. This phenomenon is sufficient to explain micro-scale bacterial clustering in the murine […]
- by Jost, F., Cordes, H.This study presents a novel approach for predicting complete pharmacokinetic (PK) profiles of monoclonal antibodies (mAbs) based solely on their amino acid sequences, addressing a critical gap in early-stage therapeutic antibody development. While current methodologies rely on in vivo testing in specialized models like Tg32 mice or cynomolgus monkeys, our approach enables PK parameter prediction prior to molecule synthesis. Using a dataset of 118 diverse mAbs, we developed a physics-informed neural network (PINN) incorporating a two-compartment PK model. The four […]
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