Biology subjects

Knudsen, L.

Publications and source records attributed to Knudsen, L..

12 recordsLinked to original sources

bioRxiv2026

Functional MRI of the Human Hippocampus at 10.5T: Pushing the Boundaries of Spatial Resolution

Although the hippocampus is central to human cognition, its deep location within the medial temporal lobe has historically limited fMRI signal quality. Here, we leverage an ultrahigh-field 10.5T fMRI system, which provides inherently higher signal-to-noise ratio than commonly used lower-field systems, to overcome these limitations and achieve unprecedented 0.5 mm isotropic resolution. This advancement allows for comprehensive hippocampal coverage with robust image quality, facilitating the study of functional microcircuits in individual subjects and paving the way for high-precision clinical diagnostics.

neuroscience↗

bioRxiv2026

Bridging the gap with invasive imaging: promises and challenges of a new generation of ultrahigh resolution fMRI

The human neocortex is organized into six laminae forming the structural basis for feedforward and feedback connections across the brain, yet their functional contributions have remained largely inaccessible for non-invasive imaging methods. Leveraging the ultrahigh field of a 10.5 Tesla scanner, we acquired anatomical and functional MRI data at 0.37mm ([~]0.05 {micro}L) and 0.35mm ([~]0.04 {micro}L) isotropic resolution, respectively, approaching the scale of individual cortical layers in humans. Using the Stria of Gennari as an in-vivo anatomical landmark, we extend our previous finding that feedforward visual activation in layer IV of the primary visual cortex during visual stimulation was resolved in laminar BOLD profiles. These laminar features were reproducible across sessions and were not clearly visible with more typical 0.8 mm resolutions at 7T, underscoring the benefits of further increases in magnetic field strength and resolution. This imaging domain, however, comes with increasing challenges of distortion, alignment, and cortical depth estimation, which must be addressed and mitigated to realize its benefits. In this paper we discuss the promises and challenges of this new regime of high resolutions. Our findings showcase the potential of ultrahigh field, ultrahigh resolution human fMRI to bridge the gap with invasive imaging of cortical layers.

neuroscience↗

bioRxiv2025

To the homeRNAmax: Developing an Improved Blood Self-Collection and Stabilization Platform for Remote Transcriptomic Studies

Shifting human subjects research from research sites to participants homes removes barriers to participation, including transportation and scheduling difficulties. Previously, we developed homeRNA, a kit for immediate stabilization of RNA in self-collected blood using a custom-engineered tube containing RNA stabilizer fluid. The stabilized RNA is extracted and used for downstream gene expression analysis. Here, we introduce homeRNAmax, which improves our original design by interfacing with a commercially available blood collection tube (BD Microtainer), allowing homeRNAmax to be used with any blood collection method that uses this tube and doubling the possible sample volume that can be collected and stabilized compared to the original homeRNA. Through a pilot study (n=19 participants), we show that homeRNAmax (with the Tasso+ blood collection device) produces RNA samples of sufficient quality (mean RIN=7.8) and yield (mean yield=1.93 g) for downstream analysis and can reach participants across the United States, who generally (n=17/19) found the homeRNAmax kit easy to use. A key aspect of the homeRNA and homeRNAmax platforms is a fluidic feature that prevents the RNA stabilizer from spilling, however our previous work had not yet fully characterized the mechanism of this feature. Here, we developed a theoretical model of the spill-resistant feature. In brief, fluid in the tube is suspended due to a balance of pressures; an increase in air volume within the tube reduces the air pressure above the fluid, creating a small vacuum, and preventing fluid leakage. Overall, we show that homeRNAmax is a user-friendly, effective tool for remote blood RNA stabilization.

bioengineering↗

bioRxiv2025

The pleuroparenchymal fibroelastosis atlas reveals aberrant cell states and their zonation as an alternate roadmap to lung fibrosis

BackgroundPleuroparenchymal fibroelastosis (PPFE) is a progressive interstitial lung disease with higher prevalence in females, histologically characterized by intra-alveolar fibrosis with septal elastosis (AFE). Effective treatments are lacking, highlighting the need to dissect its pathogenesis at single-cell resolution. MethodsWe performed single-nucleus RNA sequencing (snRNAseq) on explanted lungs from a German (n=23) and a French cohort (n=17) of PPFE patients, and controls (n=16). Identified cell populations were localized by immunofluorescence and multiplex RNA in-situ hybridization. Hierarchical phase-contrast computed tomography (HiP-CT) and micro-CT provided 3D spatial context. Reanalyzed snRNAseq data from a Belgian IPF cohort (n=9) served as disease comparator. FindingsWe present the first snRNAseq atlas of PPFEs cellular and structural landscape based on a European multinational cohort. 24 PPFE patients were female (60.0%), while 34 were non-smokers (85.0%). 519,920 nuclear transcriptomes from PPFE and IPF patients, and controls were profiled. We identified PPFE-specific accumulations of MFAP5+PI16+SFRP2+ adventitial and LEPR+ITGA8+SFRP2+DIO2+ elastofibrotic fibroblasts as main drivers of elastotic remodeling in PPFE. Multiple PPFE fibroblast subsets acquire an inflammatory activation state as highlighted by the expression of CXCL12 and CXCL14. This is accompanied by a marked increase in lymphocytes and the formation of tertiary lymphoid structures (TLS) in a disease that was previously considered to be purely elastofibrotic. We identified CTHRC1+ fibrotic fibroblasts and Aberrant Basaloid cells in PPFE as well, forming the "Usual Fibrotic Niche". 3D reconstruction of the pronounced COL15A1+ vascular conglomerate at the border of the elastofibrotic and subpleural fibrosis indicates communication with interlobar veins. Last, we observed a zonation of the PPFE lesion, constructed by the above-mentioned PPFE-associated cell types. InterpretationOur unprecedented cellular and molecular survey uncovers previously unobserved PPFE-specific inflammatory and elastogenic fibroblast populations, as well as the presence of CTHRC1+ fibroblasts and Aberrant Basaloid cells common to other fibrotic ILDs. These findings provide the foundation for including PPFE patients in current antifibrotic trials, as well as development of PPFE-specific therapies. FundingSupported mainly by the Else Kroner-Fresenius Foundation, the German Center for Lung Research and the Fondation du Souffle.

cell biology↗

bioRxiv2025

A Numerical Alternative to MR Thermometry for Safety Validation of Multi-Channel RF Transmit Coils

PurposeThis study proposes an alternative approach to MR thermometry (MRT) for the safety validation of multi-channel RF transmit coils and demonstrates its use to enable human studies at 10.5T. MethodsTo ensure patient safety, specific absorption rate (SAR) limits established under international guidelines must not be exceeded. Predicting SAR on state-of-the-art parallel transmit systems relies on electromagnetic simulations, which require extensive experimental validation. Despite a well-established validation workflow, SAR prediction errors are unavoidable and must be quantified as a safety margin. While MRT tests are commonly used for this purpose, their technical challenges necessitate an alternative. The proposed technique propagates the error between experimentally and numerically acquired B+distributions to the uncertainty in simulated peak local SAR using Monte-Carlo simulations without the need for MRT. This method was validated using a 16-channel transceiver coil for imaging the human torso (henceforth referred to as a "body" coil) at 10.5T with two excitation scenarios, as well as an 8-channel 10.5T head coil with four excitation scenarios. ResultsThe proposed numerical technique proved more conservative than existing MRT-based SAR error quantification methods across all tested scenarios. Its application to validate three state-of-the-art head coils (16Tx/32Rx, 16Tx/80Rx, and 16Tx/128Rx) led to regulatory approval for human head imaging and high-quality functional as well as diffusion MRI results at 10.5T. ConclusionA numerical alternative to MRT requires only the experimental acquisition of B+ maps for comparison with simulations, enabling the quantification of uncertainty in SAR prediction. This technique was applied to three 16-channel transmit arrays, each used in conjunction with high-channel-count receive arrays for in vivo imaging.

neuroscience↗

bioRxiv2024

Spanning spatial scales with functional imaging in the human brain; initial experiences at 10.5 Tesla

One of the most important frontiers in the efforts to improve functional imaging of brain activity (fMRI) is the recent push to increase the magnetic fields for human imaging beyond 10 Tesla. Having established safety, large gains in signal-to-noise-ratio (SNR), and novel radiofrequency arrays that capture the higher SNR, here we demonstrate major gains in the spatial resolution, sensitivity, and functional contrast of BOLD (Blood Oxygenation Level Dependent) based human fMRI at 10.5 Tesla. Using image reconstruction methods developed to minimize blurring, we also demonstrate that ultrahigh resolutions achieved at 10.5 Tesla suppress large-vein confounds in gradient-recalled-echo BOLD fMRI, thus improving the fidelity of functional signals relative to neuronal activity and yielding accurate cortical depth-profiles for layer-specific activation. Together, these multiplicative benefits deliver much needed increases in precision and resolution for meso-scale fMRI applications and illustrate the transformative potential of human functional imaging at magnetic fields that exceed 10 Tesla.

neuroscience↗

bioRxiv2024

Aberrant and Ectopic Cell Populations of the Fibrotic Pushing Border in Restrictive Allograft Syndrome after Lung Transplantation

RationaleRestrictive allograft syndrome (RAS) is a major cause of mortality in patients following lung transplantation due to rapid progressive fibrosis in the pulmonary graft. We have only limited knowledge of the cellular and molecular mechanisms that characterize the fibrosis in the RAS lung. ObjectiveTo elucidate cellularly-resolved transcriptomic and histologic characteristics of the structural cells in human RAS lungs. MethodsSingle-nuclei RNA-sequencing was performed in peripheral lung tissues from 15 RAS patients undergoing lung re-transplantation, and from 9 healthy control lungs. Findings were validated and complemented by various histologic techniques, including immunofluorescence, RNAscope, combined Elastica van Gieson-immunohistochemistry stains, and micro-CT scans. Measurement and Main resultsDifferential gene expression analysis of our single-nuclei RNA-sequencing data revealed in human RAS lungs previously undescribed and uniquely distributed aberrant basaloid cells, ectopic COL15A1+ vascular endothelial cells, and CTHRC1+ fibrotic fibroblasts, all first characterized in idiopathic pulmonary fibrosis (IPF). In contrast to IPF, RAS lacks the cellular equivalent of bronchiolization. Histologic stains confirmed our transcriptomic discoveries and disclosed distinctive distribution patterns: Aberrant basaloid cells are primarily localized at the edge of the fibrotic pushing border, forming together with the juxtaposed CTHRC1+ fibrotic fibroblasts the fibrotic niche of alveolar fibroelastosis (AFE), the histopathological hallmark in RAS lungs. On the endothelial side, PRX+ alveolar microvasculature is lost in AFE areas. Micro-CT scans revealed that blood supply, now facilitated by expanded and ectopic COL15A1+ VE cells, changes from pulmonary to systemic perfusion. Last, our data reveals potential therapeutically-modifiable expression patterns in RAS, including genes coding for the integrin subunits v{beta}6, activators of TGF{beta}. ConclusionConsidering the marked clinical, histologic and etiologic dissimilarities of RAS and IPF, our snRNAseq study revealed a surprising general principle of cellular and molecular pathogenesis in the fibrosing lung: the entity-spanning composition of the fibrotic niche by a) aberrant basaloid cells localized at the fibrotic pushing border, b) ectopic COL15A1+ vascular ECs and c) effector CTHRC1+ fibrotic fibroblasts. This general principle justifies a flexible but cellular pathogenesis-guided transferability of potential therapeutic approaches between progressive fibrotic lung diseases.

cell biology↗

bioRxiv2024

Laminar fMRI in the locked-in stage of amyotrophic lateral sclerosis shows preserved activity in layer Vb of primary motor cortex

Amyotrophic lateral sclerosis (ALS) affects the cerebral cortex layer-dependently, most notably by the foremost targeting of upper motor neurons (UMNs) sited in layer Vb. Previous studies have shown a retained ability of paralysed patients to activate residual cortical motor networks, even in late-stage ALS. However, it is currently unknown whether such activation reflects a retained capacity to process sensorimotor inputs or if it is a result of actual motor output. Given the distinct function of individual cortical layers, layer-specific functional measurements may provide insight to this question. In this study, using submillimetre resolution laminar fMRI, we assessed the layer-dependent activation associated with attempted (motor) and passive (somatosensory) movements in a locked-in stage ALS patient. We found robust activation in both superficial and deep layers of primary motor cortex. The peak activation in deep layers was localised to layer Vb. These findings demonstrate preserved activity in deep output layers of M1, possibly reflecting a retained ability to engage residual UMNs despite years of paralysis. Our study underscores the capacity of laminar fMRI to discern subtle cortical activity and elucidates a promising pathway for probing in vivo human ALS pathology with unprecedented resolution.

neuroscience↗

bioRxiv2023

The laminar pattern of proprioceptive activation in human primary motor cortex

The primary motor cortex (M1) has traditionally been viewed as a motor output generator. However, its vital role in proprioceptive somatosensation is increasingly being recognized. Yet, our understanding of proprioceptive somatosensation in M1 at the laminar scale is limited, largely due to methodological challenges. Empirical findings in primates and rodents suggest a pronounced role of superficial cortical layers, but the involvement of deep layers has yet to be examined in humans. Submillimeter resolution fMRI has emerged in recent years, paving the way for the study of layer-dependent activity in humans (laminar fMRI). In the present study, laminar fMRI was employed to investigate the laminar pattern of proprioceptive somatosensation on M1 deep layer activation using passive finger movements as proprioceptive stimulation. Significant M1 deep layer activation was observed in response to proprioceptive stimulation across 10 healthy subjects using vascular space occupancy (VASO) at 7T. For further validation, two additional subjects were scanned using a balanced steady-state free precession (bSSFP) sequence with ultrahigh (0.3 mm) in-plane resolution, yielding converging results. These results were interpreted in the light of previous laminar fMRI studies and the active inference account of motor control. We suggest that a considerable proportion of M1 deep layer activation is due to proprioceptive influence and that deep layers of M1 constitute a key component in proprioceptive circuits.

neuroscience↗

bioRxiv2023

The use of cultured human alveolar basal cells to mimic honeycomb formation in idiopathic pulmonary fibrosis

Honeycomb cysts (HC) within the alveolar region are distinct histopathological features in the lungs of idiopathic pulmonary fibrosis (IPF) patients. HC are lined with basal cells (BC), or with a bronchiolar-like epithelium composed of basal-, ciliated- and secretory epithelial cells. By using cultured IPF patient-derived alveolar BC, we aimed to establish in vitro- and in vivo models to mimic HC formation in IPF. In order to do so, we cultured the cells (1) on an air liquid interface (ALI) or (2) in a three dimensional (3D) organoid model in vitro, and (3) investigated the cells behavior after instillation into bleomycin-challenged mice in vivo. Under the here tested in vitro- and in vivo conditions, alveolar BC differentiate and formed HC-like structures, which closely resemble HC within the IPF lung. These models therefore represent powerful tools to study HC formation, and its potential therapeutic inhibition in IPF.

cell biology↗

bioRxiv2022

Feasibility of 3T layer-dependent fMRI with GE-BOLD using NORDIC and phase regression

IntroductionFunctional MRI with spatial resolution in the submillimeter domain enables measurements of activation across cortical layers in humans. This is valuable as different types of cortical computations, e.g., feedforward versus feedback related activity, take place in different cortical layers. Layer-dependent fMRI (L-fMRI) studies have almost exclusively employed 7T scanners to overcome the reduced signal stability associated with small voxels. However, such systems are relatively rare and only a subset of those are clinically approved. In the present study, we examined the feasibility of L-fMRI at 3T using NORDIC denoising. Methods5 healthy subjects were scanned on a Siemens MAGNETOM Prisma 3T scanner. To assess across-session reliability, each subject was scanned in 3-8 sessions on 3-4 consecutive days. A 3D gradient echo EPI (GE-EPI) sequence was used for BOLD acquisitions (voxel size 0.82 mm isotopic, TR = 2.2 s) using a block designed finger tapping paradigm. NORDIC denoising was applied to the magnitude and phase time series to overcome limitations in tSNR and the denoised phase time series were subsequently used to correct for large vein contamination through phase regression. Results and conclusionNORDIC denoising resulted in temporal signal-to-noise ratio (tSNR) values comparable to or higher than commonly observed at 7T. Layer-dependent activation profiles could thus be extracted robustly, within and across sessions, from regions of interest located in the hand knob of the primary motor cortex (M1). Phase regression led to substantially reduced superficial bias in obtained layer profiles, although residual macrovascular contribution remained. We believe the present results support the feasibility of L-fMRI at 3T, which might help make L-fMRI available to a much wider community.

neuroscience↗

bioRxiv2020

In vitro culture of aberrant basal-like cells from fibrotic lung tissue

RationaleIn idiopathic pulmonary fibrosis (IPF) atypical epithelial cells are present in the alveolar compartment. Their origin and contribution to IPF pathogenesis is unknown. We recently cultured a distinct population of cells, which readily grew from fibrotic lung tissue, but only rarely from non-fibrotic tissue. Here we aimed to characterize these fibrosis-enriched cells and determine transcriptomic differences between cells derived from IPF and patients with other interstitial lung diseases (ILD). MethodsCells were cultured from peripheral lung tissue of ILD patients and analysed by bulk or single cell RNA sequencing (scRNA-seq), TaqMan-PCR, immunofluorescence (IF), immunoblotting or electron microscopy (EM). ResultsscRNA-seq demonstrated an overall homogeneity and epithelial origin of the cells. The majority of cells expressed basal cell markers (Cytokeratin (KRT) 5 and 17, TP63), of which a fraction co-expressed mesenchymal cell markers (VIM, FN1, CDH2), alveolar (SLC34A2, ABCA3, LPCAT1, EMP2, HOPX) and/or secretory epithelial cell markers (SCGB1A1, MUC4). Interestingly, most of the cells showed closest transcriptomic similarity to recently described aberrant basal-like cells. Cells derived from IPF versus other ILD patients revealed significant transcriptomic differences with an up-regulation of fibrosis-associated and a down-regulation of inflammatory pathways in IPF cells. ConclusionWe here confirm the presence of aberrant basal-like cells in fibrotic lung tissue and, importantly, are the first to describe their in vitro characteristics and a way of culturing these cells in vitro. Cultured basal-like cells co-express epithelial and mesenchymal markers, suggesting a partial epithelial to mesenchymal transition (EMT). A subset of cells co-express alveolar, ciliated or secretory epithelial cell markers, possibly indicating differentiation towards these cell linages. Furthermore, cultured basal-like cells display a disease-specific transcriptome, possibly induced by their specific microenvironment. Our findings will contribute to a better understanding of the cells origin and their potential contribution to IPF pathogenesis.

cell biology↗