Biology subjects

Rasmussen, J.

Publications and source records attributed to Rasmussen, J..

11 recordsLinked to original sources

bioRxiv2026

A mammalian fibroblast zoo reveals barriers to cross-species virus replication and differential regulation of antiviral immunity

Virus zoonosis represents a continual threat to humans. Viruses emerge in humans directly or indirectly through interactions with mammals. However, our understanding of virus-host susceptibility across the diversity of mammals is limited and experimental model systems are restricted to a very small set of model organisms. Mammals are highly diverse and different habitats, lifestyles, diets, and exposures to different pathogens have driven substantial genetic diversity. We generated a library of primary fibroblasts across 86 mammalian species and used these cells to build an atlas of virus-host susceptibility across a panel of arboviruses that infect diverse mammals including humans. Perturbing the innate immune system revealed some virus-host pairs where restriction is controlled by the immune system and others where there is an incompatibility with host factors. Transcriptomic profiling of the library in response to virus sensing mimicked by poly(I:C) or antiviral signaling with type I interferon reveals a core set of conserved genes that respond as well as substantial species- and order-specific responses. Together these data provide a comparative atlas of innate immune responses across mammals and offer a window into how these systems have evolved across animals.

immunology↗

bioRxiv2026

MRI-based dental maturity in newborns reflects prenatal exposures and predicts timing of primary tooth eruption

Primary tooth development is shaped by prenatal experience and has consequences for childhood caries and lifelong oral health. However, evidence linking prenatal conditions to dental development has relied largely on postnatal proxies, such as parent-recalled eruption timing, that conflate prenatal programming with postnatal exposures. Here, we directly phenotype developing dentition in vivo using routinely acquired neonatal brain MRI. Using T2-weighted imaging from the HEALthy Brain and Child Development Study, we trained a 3D U-Net on 100 semi-automatic labels and applied the model to 1,433 quality-controlled neonatal scans. Automated post-processing extracted quantitative features of tooth volume, mineralization, and arch geometry. These features were used to predict postmenstrual age at MRI and to derive a bias-corrected tooth age gap (TAG), indexing relative dental maturity at birth. The segmentation model achieved mean cross-validated Dice = 0.94. Dental features predicted postmenstrual age with R2 = 0.30 and mean absolute error = 6.7 days, outperforming standard anthropometric measures (R2 = 0.22). In adjusted models, TAG varied by infant sex and was associated with gestational age at delivery, maternal pre-pregnancy BMI, and prenatal tobacco use. In infants with longitudinal dental follow-up, greater dental maturity at birth predicted earlier first tooth emergence and more teeth at one year. Automated segmentation and age prediction generalized to an independent cohort. These findings establish neonatal dental MRI phenotyping as an objective, scalable index of dental maturation and a potential readout of prenatal influences on a developmental system relevant to lifelong oral health. Significance StatementPrimary tooth development begins before birth and is shaped by intrauterine experience, with consequences for eruption timing, enamel quality, childhood caries, and lifelong oral health. Yet newborn dentition has been difficult to study because unerupted primary teeth are not routinely measurable at birth, forcing reliance on postnatal proxies that mix prenatal influences with later exposures. We show that standard newborn brain MRI can be repurposed to quantify dental maturity before postnatal exposures accumulate. Applied to 1,433 newborns, this open-source pipeline provides spatially localized measures of unerupted tooth development and links neonatal dental maturity to clinical, environmental, and eruption outcomes. These findings establish neonatal dental MRI as a scalable tool for studying how intrauterine experience becomes biologically embedded in dental development.

developmental biology↗

bioRxiv2025

Insulin stimulated upregulation of OCTN2 carnitine transporters is impaired in patients with Primary carnitine deficiency

BackgroundPrimary carnitine deficiency (PCD) is an autosomal recessive disorder characterized by a lack of functional carnitine transporters OCTN2 (Organic Cation/Carnitine Transporter 2), which has been linked to several cases of sudden death in young Faroese individuals. It causes low carnitine levels and can present with hypoketotic hypoglycemia, skeletal and cardiac myopathy. Patients are treated with L-carnitine, and even while receiving treatment, skeletal muscle carnitine levels are only approximately 7% of normal. The regulation of the carnitine transporter, OCTN2, is not fully understood, but a combination of hypercarnitinaemia with hyperinsulinemia upregulates skeletal muscle carnitine uptake and OCTN2 mRNA expression. ObjectiveThe question arises as to whether hyperinsulinemia increases the efficiency of L-carnitine supplementation in PCD. The present study investigates the regulatory mechanisms behind insulin-induced carnitine uptake, and whether the combination of hypercarnitinaemia and hyperinsulinaemia increases skeletal muscle carnitine levels in patients with PCD. In addition to our main goals, we also explored the measurement of whole-body fat oxidation at rest and during exercise MethodNine patients with PCD (homozygous for the c.95 A > G, pN32S mutation) and nine healthy controls matched to age and body mass index (BMI) participated in the study. A six hour hyperinsulinemic clamp was supplemented with infusion of L-carnitine the last five hours. Skeletal muscle biopsies were collected before and after the clamp and carnitine content was measured. Furthermore, confocal microscopy was used to access regulation of OCTN2 and GLUT4 positive vesicles due to insulin stimulation and additionally whole body fat oxidation was measured with indirect calorimetry. ResultsWe found that the combination of hypercarnitinaemia with hyperinsulinemia did not increase skeletal muscle total carnitine levels significantly for neither patients with PCD [4.5 (SE 0.6) to 5.3 (SE 0.5) mmol {middle dot} kg-1] (P = 0.28) nor controls [19.8 (SE 0.6) to 21.2 (SE 0.5) mmol {middle dot} kg-1] (P = 0.053). The muscle carnitine profile showed that patients with PCD have low levels of total and free carnitine in skeletal muscle, but normal levels of acetylcarnitines corresponding to 60% of total carnitine (normal is [~]16% of total muscle carnitine). The results from confocal microscopy indicate that insulin regulates skeletal muscle carnitine uptake by stimulating OCTN2 recruitment from intracellular storages to the plasma membrane. This regulatory mechanism is however impaired in patients with PCD. Furthermore, we found that PCD patients were more dependent on carbohydrates at rest. In regard to fat oxidation, no difference was found between PCD and control group during short-term exercise. ConclusionsThe study indicates that insulin stimulates translocation of OCTN2 to the plasma membrane in healthy controls, a mechanism that seems to be impaired in patients with PCD. The combination of hypercarnitinaemia with hyperinsulinemia did not increase skeletal muscle total carnitine levels significantly (P = 0.28) in patients with PCD.

molecular biology↗

bioRxiv2024

Sex-specific effects of early life unpredictability on hippocampal and amygdala responses to novelty in adolescents

BackgroundUnpredictable childhood experiences are an understudied form of early life adversity that impacts neurodevelopment in a sex-specific manner. The neurobiological processes by which exposure to early-life unpredictability impacts development and vulnerability to psychopathology remain poorly understood. The present study investigates the sex-specific consequences of early-life unpredictability on the limbic network, focusing on the hippocampus and the amygdala. MethodsParticipants included 150 youth (54% female). Early life unpredictability was assessed using the Questionnaire of Unpredictability in Childhood (QUIC). Participants engaged in a task-fMRI scan between the ages of 8 and 17 (223 total observations) measuring BOLD responses to novel and familiar scenes. ResultsExposure to early-life unpredictability associated with BOLD contrast (novel vs. familiar) in a sex-specific manner. For males, but not females, higher QUIC scores were associated with lower BOLD activation in response to novel vs. familiar stimuli in the hippocampal head and amygdala. Secondary psychophysiological interaction (PPI) analyses revealed complementary sex-specific associations between QUIC and condition-specific functional connectivity between the right and left amygdala, as well as between the right amygdala and hippocampus bilaterally. ConclusionExposure to unpredictability in early life has persistent implications for the functional operations of limbic circuits. Importantly, consistent with emerging experimental animal and human studies, the consequences of early life unpredictability differ for males and females. Further, impacts of early-life unpredictability were independent of other risk factors including lower household income and negative life events, indicating distinct consequences of early-life unpredictability over and above more commonly studied types of early life adversity.

neuroscience↗

bioRxiv2023

Multivariate and Regional Age-Related Change in Basal Ganglia Iron in Neonates

In the perinatal period, reward and cognitive systems begin trajectories, influencing later psychiatric risk. The basal ganglia is important for reward and cognitive processing but early development has not been fully characterized. To assess age-related development, we used a measure of basal ganglia physiology, specifically brain tissue iron, obtained from nT2* signal in rsfMRI, associated with dopaminergic processing. We used data from the Developing Human Connectome Project (N=464) to assess how moving from the prenatal to the postnatal environment affects rsfMRI nT2*, modeling gestational and postnatal age separately for basal ganglia subregions in linear models. We did not find associations with tissue iron and gestational age [Range: 24.29-42.29] but found positive associations with postnatal age [Range:0-17.14] in the pallidum and putamen, but not the caudate. We tested if there was an interaction between preterm birth and postnatal age, finding early preterm infants (GA<35 weeks) had higher iron levels and changed less over time. To assess multivariate change, we used support vector regression to predict age from voxel-wise-nT2* maps. We could predict postnatal but not gestational age when maps were residualized for the other age term. This provides evidence subregions differentially change with postnatal experience and preterm birth may disrupt trajectories.

neuroscience↗

bioRxiv2023

Gestational and postnatal age associations for striatal tissue iron deposition in early infancy

Striatal development is crucial for later motor, cognitive, and reward behavior, but age-related change in striatal physiology during the neonatal period remains understudied. An MRI-based measure of tissue iron deposition, T2*, is a non-invasive way to probe striatal physiology neonatally, linked to dopaminergic processing and cognition in children and adults. Striatal subregions have distinct functions that may come online at different time periods in early life. To identify if there are critical periods before or after birth, we measured if striatal iron accrued with gestational age at birth [range=34.57-41.85 weeks] or postnatal age at scan [range=5-64 days], using MRI to probe the T2* signal in N=83 neonates in three striatal subregions. We found iron increased with postnatal age in the pallidum and putamen but not the caudate. No significant relationship between iron and gestational age was observed. Using a subset of infants scanned at preschool age (N=26), we show distributions of iron shift between timepoints. In infants, the pallidum had the least iron of the three regions but had the most by preschool age. Together, this provides evidence of distinct change for striatal subregions, a possible differentiation between motor and cognitive systems, identifying a mechanism that may impact future trajectories. HighlightsO_LINeonatal striatal tissue iron can be measured using the T2* signal from rsfMRI C_LIO_LInT2* changed with postnatal age in the pallidum and putamen but not in the caudate C_LIO_LInT2* did not change with gestational age in any of the three regions C_LIO_LIPatterns of iron deposition (nT2*) among regions shift from infancy to preschool C_LI

neuroscience↗

bioRxiv2023

Field cancerization impacts tumor development, T-cell exhaustion and clinical outcomes in bladder cancer

Bladder field cancerization may be associated with disease outcome in patients with bladder cancer. To investigate this, we analyzed biopsies from bladder urothelium and urine samples by genomics and proteomics analyses. Samples were procured from multiple timepoints from 134 patients with early stage bladder cancer and detailed long term follow-up. We measured the field cancerization in normal-appearing bladder biopsies and found that high levels were associated with high tumor mutational burden, high neoantigen load, and high tumor-associated CD8 T-cell exhaustion. Non-synonymous mutations in known bladder cancer driver genes such as KDM6A and TP53 were identified as early disease drivers in normal urothelium. High field cancerization was associated with worse outcome but not with response to BCG. The level of urinary tumor DNA (utDNA) reflected the bladder tumor burden and originated from both tumors and field cancerization. High utDNA levels after BCG were associated with worse clinical outcomes for the patients. Our results indicate that the level of field cancerization may affect clinical outcome, tumor development and immune responses. utDNA measurements have significant prognostic value and reflect the disease status of the bladder.

cancer biology↗

bioRxiv2022

LINE-1 retrotransposon activation intrinsic to interneuron development

Retrotransposons are a reservoir of cis-regulatory innovation1-3. Developmental programs that activate these elements could, in principle, manifest in lineage-specific retrotransposition. Somatic LINE-1 (L1) retrotransposon insertions have been detected in human and non-human primate neurons4-7. It is however unknown whether L1 is mobile in only some neuronal lineages, or therein regulates neurodevelopmental genes. Here, we report programmed L1 activation by SOX6, a transcription factor critical for parvalbumin (PV) interneuron development8-10. PV+ neurons permit L1 mobilization in vitro and in vivo, harbor unmethylated L1 promoters, and express full-length L1 mRNAs and proteins. Via nanopore long-read sequencing, we identify unmethylated L1 promoters proximal to PV+ neuron genes. One such L1, which promotes transcription of a novel CAPS2 gene isoform, significantly enhances neuron morphological complexity when phenotyped in vitro. These data highlight the contribution made by L1 cis-regulatory elements to PV+ neuron development and transcriptome diversity, uncovered due to L1 mobility in this milieu.

genomics↗

bioRxiv2021

Osteoblasts pattern endothelium and somatosensory axons during zebrafish caudal fin organogenesis

Skeletal elements frequently associate with vasculature and somatosensory nerves, which regulate bone development and homeostasis. However, the deep, internal location of bones in many vertebrates has limited in vivo exploration of the neurovascular-bone relationship. Here, we use the zebrafish caudal fin, an optically accessible organ formed of repeating bony ray skeletal units, to determine the cellular relationship between nerves, bones, and endothelium. In adults, we establish the presence of somatosensory axons running through the inside of the bony fin rays, juxtaposed with osteoblasts on the inner hemiray surface. During development, we show the caudal fin progresses through sequential stages of endothelial plexus formation, bony ray addition, ray innervation, and endothelial remodeling. Surprisingly, the initial stages of fin morphogenesis proceed normally in animals lacking either fin endothelium or somatosensory nerves. Instead, we find that sp7+ osteoblasts are required for endothelial remodeling and somatosensory axon innervation in the developing fin. Overall, this study demonstrates that the proximal neurovascular-bone relationship in the adult caudal fin is established during fin organogenesis and suggests that ray-associated osteoblasts pattern axons and endothelium. Summary statementAnalysis of cellular interdependence during caudal fin development reveals roles for osteoblasts in patterning endothelium and somatosensory axon innervation.

developmental biology↗

bioRxiv2021

Human genome integration of SARS-CoV-2 contradicted by long-read sequencing

A recent study proposed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hijacks the LINE-1 (L1) retrotransposition machinery to integrate into the DNA of infected cells. If confirmed, this finding could have significant clinical implications. Here, we applied deep (>50x) long-read Oxford Nanopore Technologies (ONT) sequencing to HEK293T cells infected with SARS-CoV-2, and did not find the virus integrated into the genome. By examining ONT data from separate HEK293T cultivars, we completely resolved 78 L1 insertions arising in vitro in the absence of L1 overexpression systems. ONT sequencing applied to hepatitis B virus (HBV) positive liver cancer tissues located a single HBV insertion. These experiments demonstrate reliable resolution of retrotransposon and exogenous virus insertions via ONT sequencing. That we found no evidence of SARS-CoV-2 integration suggests such events are, at most, extremely rare in vivo, and therefore are unlikely to drive oncogenesis or explain post-recovery detection of the virus.

genomics↗

bioRxiv2019

Co-occurrence of organic and inorganic N sources influences asparagine uptake and internal amino acid profiles in white clover

Direct plant uptake of organic nitrogen (N) is important for plant N nutrition, but we lack knowledge of how the concentration of external N forms (organic and inorganic) -influence organic N uptake and plant N status. We investigated the uptake of the amino acid asparagine (Asn) in white clover in the presence of different nitrate (NO3-), Asn, and total N concentrations. White clover seedlings were for one week exposed to combinations of NO3- (3-30 {micro}mol N kg-1 sand DW) and Asn (3-30 {micro}mol N kg-1 sand DW), where after the Asn uptake rate was determined by addition of 13C4-Asn. Shoot and root Asn content and amino acid profiles were also analyzed. Increasing external NO3- and total N concentrations decreased 13C4-Asn uptake rates and internal clover Asn content. Furthermore, total N affected clover amino acid profiles from non-essential amino acids at low N doses to the dominance of essential amino acids at increasing N doses. Asn uptake rate in white clover is reduced by increasing inorganic N, but not by increasing organic N concentrations. Furthermore, plant amino acid profiles are likely to be a more sensitive indicator of N supply and descriptor of the N status.

plant biology↗