Biology subjects

Jacobs, M. E.

Publications and source records attributed to Jacobs, M. E..

6 recordsLinked to original sources

bioRxiv2025

Image-guided alignment of consecutive multi-modal tissue slides

Multi-modal spatial data analysis often requires precise physical alignment of consecutive tissue sections, a process that can be challenging and typically relies on shared molecular markers or image recognition techniques. Here, we introduce COAST (Consecutive multi-Omics Alignment of Spatial Tissues), a method to reliably physically align consecutive tissue sections to produce a unified multi-modal molecular dataset suitable for downstream applications. COAST relies exclusively on the images associated with spatial data, eliminating the need for common molecular features or prior annotations. We demonstrate the effectiveness of COAST using spatial transcriptomics slides, where it achieves performance comparable to established uni-modal alignment tools. Applying COAST to spatial transcriptomics and metabolomics/lipidomics tissue sections from a mouse model of ischemia reperfusion injury allowed the investigation of lipid/metabolite features of transcriptionally-defined cell types. Overall, COAST offers a streamlined and integrative solution for multi-modal spatial data alignment.

bioinformatics↗

bioRxiv2025

Normothermic human kidney preservation drives iron accumulation and ferroptosis

Ex vivo normothermic machine perfusion has been proposed to protect deceased donor organs, promoting metabolic recovery and allowing quality assessment. However, its benefits for preserving deceased donor kidneys remain ambiguous. We postulate that the use of red blood cells (RBCs) as oxygen carriers and associated secondary hemolysis may in fact cause renal injury, offsetting potential advantages. During 48-hour normothermic perfusion of seven human deceased donor kidneys, we observed progressive hemolysis, leading to iron accumulation in perfusate, tissue, and urine. Untargeted lipidomic analysis revealed profound increases in oxidized phospholipid species in perfused kidneys, pointing towards iron-dependent cell death known as ferroptosis. Next, in twelve additional human kidney perfusions, we demonstrate that either dialysis-based free hemoglobin removal or cell-free perfusion attenuates hemolysis-driven iron accumulation, phospholipid peroxidation, and acute kidney injury. Our findings highlight the pathological role of hemolysis and iron on the kidney, urging restraint in the clinical application of RBC-based kidney perfusion.

physiology↗

bioRxiv2024

Spatial quantitative metabolomics enables identification of remote and sustained ipsilateral cortical metabolic reprogramming after stroke

Mass spectrometry imaging (MSI) has become a cornerstone of spatial biology research. However, various factors that are intrinsic to the technology limit quantitative capacity of MSI-based spatial metabolomics and thus reliable interpretation. Here, we developed a quantitative MSI workflow (Q-MSI), based on isotopically 13C-labeled yeast extract as internal standards, to overcome these pitfalls. Using brain and kidney tissue, we demonstrate that this approach allows for (absolute) quantification of hundreds of metabolites and lipids. Applying our workflow to a stroke model allowed us to not only map metabolic remodeling of the infarct and peri-infarct area over time, but also discover hitherto unnoted remote metabolic remodeling in the histologically unaffected ipsilateral sensorimotor cortex. At day 7 post-stroke, increased levels of neuroprotective lysine and reduced excitatory glutamate levels were found compared to the contralateral cortex. By day 28 post-stroke, lysine and glutamate levels had been normalized, while decreased precursor pools of UDP-GlcNAc and linoleate persisted that have previously been associated with vulnerability. Importantly, traditional normalization strategies not employing internal standards were unable to visualize these differences. Using 13C-labeled yeast extracts as a normalization strategy establishes a new paradigm in quantitative MSI-based spatial metabolomics that greatly enhances reliability and interpretive strength.

biochemistry↗

bioRxiv2023

Preclinical lentiviral vector-mediated hematopoietic stem and progenitor cell gene therapy corrects Pompe disease-related muscle and neurological manifestations

Pompe disease, a rare genetic neuromuscular disorder, is caused by a deficiency of acid alpha-glucosidase (GAA), leading to the accumulation of glycogen in lysosomes and the progressive development of muscle weakness. The current standard treatment, enzyme replacement therapy (ERT), is not curative and demonstrates poor penetration into skeletal muscle and the central and peripheral nervous systems, susceptibility to immune responses against the recombinant enzyme, and the need for high doses and frequent infusions. To overcome these limitations, lentiviral vector-mediated hematopoietic stem and progenitor cell (HSPC) gene therapy has been proposed as a next-generation approach for treating Pompe disease. This study demonstrates the potential of lentiviral HSPC gene therapy to reverse the pathological effects of Pompe disease in a preclinical mouse model. It includes a comprehensive safety assessment via integration site analysis, along with single-cell RNA sequencing analysis of CNS samples to gain insights into the underlying mechanisms of phenotype correction. One Sentence Summary: Preclinical hematopoietic stem cell gene therapy for the treatment of Pompe disease.

neuroscience↗

bioRxiv2023

Advancing multi-day ex vivo kidney perfusion using spatially resolved metabolomics

The ability to preserve metabolically active kidneys ex vivo for multiple days may permit reconditioning, repair and regeneration of deceased donor kidneys. However, the kidneys high metabolic demand limits its functional preservation. Current approaches focus on normothermic machine perfusion (NMP) at 37{degrees}C or hypothermic machine perfusion (HMP) at 4-8{degrees}C. At normothermia, kidneys are metabolically active but ex vivo preservation is limited to hours. During hypothermia kidneys can be preserved up to 24 hours but are metabolically inactive and suffer cold-induced injury. Therefore, we revisited sub normothermic perfusion (at 25{degrees}C) as an alternative approach to preserve human kidneys in a metabolically active state for extended periods of time. In a custom-made platform that includes a cell-free perfusate enriched with TCA cycle fuels, urine recirculation, and continuous hemofiltration we perfused discarded human kidneys up to 8 days. Using spatially resolved single cell resolution isotope tracing we demonstrate active metabolism in all the different renal cell types over this period. However, beyond 4 days cell composition of nephron segments assessed with spatial lipidomics changed substantially and injury markers such as NGAL and LDH increased in the perfusate. Up to 4 days, perfused human discarded donor kidneys maintained metabolic fluxes, functional parameters and allow for reperfusion using a porcine auto transplantation model. These data underpin that extended multi-day metabolic preservation of human kidneys is achievable using a sub normothermic perfusion platform.

bioengineering↗

bioRxiv2021

Screening of Chimeric GAA Variants in a Preclinical Study of Pompe Disease Results in Candidate Vector for Hematopoietic Stem Cell Gene Therapy

Pompe disease is a rare genetic neuromuscular disorder caused by acid alpha-glucosidase (GAA) deficiency resulting in lysosomal glycogen accumulation and progressive myopathy. Enzyme replacement therapy (ERT) is the current standard of care, which prolongs the quality of life for Pompe patients. However, ERT has limitations due to lack of enzyme penetration into the central nervous system (CNS) and skeletal muscles, immunogenicity against the recombinant enzyme, and requires life-long biweekly infusions. In a preclinical mouse model, a clinically relevant promoter to drive lentiviral vector-mediated expression of engineered GAA in autologous hematopoietic stem and progenitor cells (HSPC) was tested with nine unique human chimeric GAA coding sequences incorporating distinct peptide tags and codon-optimization iterations. Vectors including glycosylation independent lysosomal targeting (GILT) tags resulted in effective GAA enzyme delivery into key disease tissues with enhanced reduction of glycogen, myofiber and CNS vacuolation, compared to non-tagged GAA in Gaa knockout mice, a model of Pompe disease. Genetically modified microglial cells in brains were detected at low levels, but provided robust correction. Furthermore, an aminoacid substitution in the tag added to reduced capacity to induce insulin signaling and there was no evidence of off-target effects. This study demonstrated the therapeutic potential of lentiviral HSPC gene therapy exploiting optimized GAA tagged coding sequences to reverse Pompe disease pathology in a preclinical mouse model providing a promising vector candidate for further investigation. One Sentence SummaryA candidate vector for hematopoietic stem cell gene therapy of Pompe disease.

bioengineering↗