Biology subjects

Keller, T.

Publications and source records attributed to Keller, T..

9 recordsLinked to original sources

bioRxiv2026

Amino Acid Stress Induces Non-AUG Initiation of c-myc Translation

Initiation of translation at non-AUG start codons can generate novel isoforms of important cellular regulators, with activities or localization distinct from their AUG-initiated counterparts. Ribosomes scanning the 5UTR upstream of canonical AUG starts recognize near-cognate starts inefficiently, however, and the mechanisms by which non-canonical starts might be regulated physiologically are poorly understood. We show here that the restriction of utilization of individual amino acid induces a switch in expression of c-myc from its AUG-initiated isoform, c-myc-2, to an upstream CUG-initiated isoform, c-myc-1. This switch is enhanced in cells lacking GCN2, the protein kinase linking amino acid stress to phosphorylation and inhibition of eif2. Induction of upstream CUG start site usage in c-myc by restriction of proline utilization depends on the proximity of proline codons downstream of the canonical AUG start site. These observations support a model in which the stalling of an elongating ribosome near a canonical start leads to the accumulation of a ribosome queue that facilitates initiation at an upstream non-canonical start site. We find similar effects associated with deprivation of amino acids other than proline, and isoform changes with ATF-3 as well as c-myc. These findings suggest a broad mechanism by which amino acid stress can regulate translation initiation site use to modify the N-terminal proteome.

cell biology↗

bioRxiv2026

Vascularized tumor organoids enable immunotherapy testing in tumor-remodeled stroma

Accurately predicting whether a new molecule will be safe and effective in humans remains a fundamental challenge in biomedical research, requiring models that can reliably inform clinical outcomes. In oncology, drug attrition rates remain disproportionately high compared to other therapeutic areas, largely due to the poor translatability of conventional preclinical models that fail to capture the complexity of human immune-tumor-stroma interactions (1, 2). Here, we describe human vascularized organoids (VascO), formed through self-assembly of an immune cell perfused capillary network and stromal compartment, interfacing with patient-derived colorectal cancer organoids that enable the combined safety and efficacy assessment of tumor-targeted immunotherapies. VascO generates functional and integrated vascular networks within tumor organoids that sustain organoid growth and recapitulate the morphology and functionality of tumor vasculature. Single-cell transcriptomics reveals that the tumor organoids-educated VascO niche reprograms otherwise healthy fibroblasts into canonical cancer-associated fibroblast states, adopting my-ofibroblastic or inflammatory signatures, and faithfully mirroring donor-specific tumor cues. In parallel, VascO tumor vessels display an expanded tip-cell program, aberrant morphology, and VEGF/ANG2-driven permeability, recapitulating defining hallmarks of tumor vasculature. Immune perfusion with a tumor-targeted T cell bispecific antibody induces dynamic immune trafficking, infiltration and engagement of effector cells with the tumor tissue, leading to its effective killing. A protease-activated variant restricts T cell activation to the tumor microenvironment, retaining potent tumoricidal activity while sparing donor-matched healthy colon organoids, and thereby improving the therapeutic index. VascO thus models a patient-specific, tumor-educated microenvironment that is amenable to assessing the combined safety and efficacy of new drug candidates and provides a scalable platform to improve the preclinical assessment of innovative cancer immunotherapies.

bioengineering↗

bioRxiv2025

Localized Reconstruction of Multimodal Distance Distribution from DEER Data of Biopolymers

Pulsed Dipolar ESR Spectroscopy (PDS) is a uniquely powerful technique to characterize the structural property of intrinsically disordered proteins (IDPs) and polymers and the conformational evolution of IDPs and polymers, e.g. during assembly, by offering the probability distribution of segment end-to-end distances. However, it is challenging to determine distance distribution P(r) of IDPs by PDS because of the uncertain and broad shape information that is intrinsic to the distance distribution of IDPs. We demonstrate here that the Srivastava-Freed Singular Value Decomposition (SF-SVD) point-wise mathematical inversion method along with wavelet denoising (WavPDS) can aid in obtaining reliable shapes for the distance distribution, P(r), for IDPs. We show that broad regions of P(r) as well as mixed narrow and broad features within the captured distance distribution range can be effectively resolved and differentiated without a priori knowledge. The advantage of SF-SVD and WavPDS is that the methods are transparent, requiring no adjustable parameters, the processing of the magnitude for the probability distribution is performed separately for each distance increment, and the outcome of the analysis is independent of the users judgement. We demonstrate the performance and present the application of WavPDS and SF-SVD on model ruler molecules, model polyethylene glycol polymers with end-to-end spin labeling, and IDPs with pairwise labeling spanning different segments of the protein tau to generate the transparent solutions to the P(r)s including their uncertainties and error analysis.

biophysics↗

bioRxiv2024

Functional dynamics and selectivity of two parallel corticocortical pathways from motor cortex to layer 5 circuits in somatosensory cortex

In the rodent whisker system, active sensing and sensorimotor integration are mediated in part by the dynamic interactions between the motor cortex (M1) and somatosensory cortex (S1). However, understanding these dynamic interactions requires knowledge about the synapses and how specific neurons respond to their input. Here, we combined optogenetics, retrograde labeling, and electrophysiology to characterize the synaptic connections between M1 and layer 5 (L5) intratelencephalic (IT) and pyramidal tract (PT) neurons in S1 of mice (both sexes). We found that M1 synapses onto IT cells displayed modest short-term depression, whereas synapses onto PT neurons showed robust short-term facilitation. Despite M1 inputs to IT cells depressing, their slower kinetics resulted in summation and a response that increased during short trains. In contrast, summation was minimal in PT neurons due to the fast time course of their M1 responses. The functional consequences of this reduced summation, however, were outweighed by the strong facilitation at these M1 synapses, resulting in larger response amplitudes in PT neurons than IT cells during repetitive stimulation. To understand the impact of facilitating M1 inputs on PT output, we paired trains of inputs with single backpropagating action potentials, finding that repetitive M1 activation increased the probability of bursts in PT cells without impacting the time-dependence of this coupling. Thus, there are two parallel but dynamically distinct systems of M1 synaptic excitation in L5 of S1, each defined by the short-term dynamics of its synapses, the class of postsynaptic neurons, and how the neurons respond to those inputs. SIGNIFICANCE STATEMENTNormal sensorimotor integration depends in part on the dynamic interactions between the primary motor cortex and the somatosensory cortex, but the functional properties of the excitatory synapses interconnecting the motor cortex with the somatosensory cortex are poorly understood. Our results show that the short-term dynamics of excitatory motor cortex synapses and the nature of the postsynaptic response they generate onto layer 5 pyramidal neurons in the somatosensory cortex depend on the postsynaptic cell type and if their axons project to other cortical areas or subcortical regions. These two parallel but dynamically distinct channels of synaptic excitation constitute previously unknown synaptic circuits by which different temporal patterns of motor cortex activity can shape how signals propagate out of the somatosensory cortex.

neuroscience↗

bioRxiv2023

Quantifying stem cell derived islet graft volume and composition with FDOPA positron emission tomography

Stem cell derived islets (SC-islets) are being developed as a novel source of beta cells that would enable large scale cell replacement therapy for insulin dependent diabetes. Therapeutic use of SC-islets carries an inherent risk of unwanted growth; and multiple strategies are being explored for optimizing long-term SC-islet graft effectiveness. However, a method for noninvasive in vivo monitoring for SC-islet graft safety and efficacy is lacking, as current insulin secretion measurements are inadequate. Here, we demonstrate the potential of positron emission tomography (PET) for monitoring SC-islet grafts using two tracers: GLP1-receptor binding [18F]F-DBCO-exendin and dopamine precursor [18F]FDOPA. We could detect and longitudinally monitor human SC-islet grafts in calf muscles of immunocompromised mice. Importantly, graft volume quantified with PET strongly correlated with actual graft volume (r2=0.91 for [18F]F-DBCO-exendin). PET using [18F]F-DBCO-exendin allowed delineation of cystic structures and its uptake correlated with graft beta cell proportion, enabling study of SC-islet graft purity noninvasively. [18F]FDOPA performed similarly to [18F]F-DBCO-exendin, but with slightly weaker sensitivity. Uptake of neither tracer was biased in SC-islet grafts genetically rendered hyper- or hypoactive. Insulin secretion measurements under fasted, glucose-stimulated or hypoglycemic conditions did not correlate with graft volume. In conclusion, [18F]F-DBCO-exendin and [18F]FDOPA PET constitute powerful approaches to noninvasively assess SC-islet graft volume and composition regardless of their functionality. PET imaging could therefore be leveraged for optimizing safety and effectiveness of SC-islet grafts in patients with insulin dependent diabetes.

cell biology↗

bioRxiv2022

Vascular mimicry by VE-cadherin enables trophoblast endovascular invasion and spiral artery remodeling during placental development

During formation of the mammalian placenta trophoblasts invade the maternal decidua and remodel spiral arteries to bring maternal blood into the placenta. This process, known as endovascular invasion, is thought to involve the adoption of functional characteristics of vascular endothelial cells (ECs) by trophoblasts through a process termed vascular mimicry. The genetic and molecular basis of vascular mimicry remains poorly defined, however, and whether trophoblasts utilize specialized endothelial proteins in an analogous manner to create vascular channels remains untested. Vascular endothelial (VE-)cadherin is a homotypic adhesion protein that is expressed selectively by ECs in which it enables formation of tight vessels and regulation of EC junctions. VE-cadherin is also expressed in invasive trophoblasts and is a prime candidate for a molecular mechanism of vascular mimicry by those cells. Here, we show that the VE-cadherin is required for trophoblast migration and endovascular invasion into the maternal decidua in the mouse. VE-cadherin deficiency results in loss of spiral artery remodeling that leads to decreased flow of maternal blood into the placenta, fetal growth restriction, and death. These studies identify a non-endothelial role for VE-cadherin in trophoblasts during placental development and suggest that endothelial proteins may play functionally unique roles in trophoblasts that do not simply mimic those in ECs.

developmental biology↗

bioRxiv2019

REMI-seq: Development of methods and resources for functional genomics in Dictyostelium

Genomes can be sequenced with relative ease, but ascribing gene function remains a major challenge. Genetically tractable model systems are crucial to meet this challenge. One powerful model is the social amoeba Dictyostelium discoideum, a eukaryotic microbe widely used to study diverse questions in cell, developmental and evolutionary biology. However, its utility is hampered by the inefficiency with which sequence, transcriptome or proteome variation can be linked to phenotype. To address this, we have developed methods (REMI-seq) to (1) generate a near genome-wide resource of individual mutants (2) allow large-scale parallel phenotyping. We demonstrate that integrating these resources allows novel regulators of cell migration, phagocytosis and macropinocytosis to be rapidly identified. Therefore, these methods and resources provide a step change for high throughput gene discovery in a key model system, and the study of genes affecting traits associated with higher eukaryotes.

genomics↗

bioRxiv2018

Agricultural intensification reduces microbial network complexity and the abundance of keystone taxa in roots

Root-associated microbes play a key role in plant performance and productivity, making them important players in agroecosystems. So far, very few studies have assessed the impact of different farming systems on the root microbiota and it is still unclear whether agricultural intensification influences network complexity of microbial communities. We investigated the impact of conventional, no-till and organic farming on wheat root fungal communities using PacBio SMRT sequencing on samples collected from 60 farmlands in Switzerland. Organic farming harboured a much more complex fungal network than conventional and no-till farming systems. The abundance of keystone taxa was the highest under organic farming where agricultural intensification was the lowest. The occurrence of keystone taxa was best explained by soil phosphorus levels, bulk density, pH and mycorrhizal colonization. The majority of keystone taxa are known to form arbuscular mycorrhizal associations with plants and belong to the orders Glomerales, Paraglomerales, and Diversisporales. Supporting this, the abundance of mycorrhizal fungi in roots and soils was also significantly higher under organic farming. To our knowledge, this is the first study to report mycorrhizal keystone taxa for agroecosystems, and we demonstrate that agricultural intensification reduces network complexity and the abundance of keystone taxa in the root microbiota.

microbiology↗

bioRxiv2017

Extensive Tonotopic Mapping Across Auditory Cortex Is Recapitulated By Spectrally-Directed Attention, And Systematically Related To Cortical Myeloarchitecture

Auditory selective attention is vital in natural soundscapes. But, it is unclear how attentional focus on the primary dimension of auditory representation - acoustic frequency - might modulate basic auditory functional topography during active listening. In contrast to visual selective attention, which is supported by motor-mediated optimization of input across saccades and pupil dilation, the primate auditory system has fewer means of differentially sampling the world. This makes spectrally-directed endogenous attention a particularly crucial aspect of auditory attention. Using a novel functional paradigm combined with quantitative MRI, we establish that human frequency-band-selective attention drives activation in both myeloarchitectonically-estimated auditory core, and across the majority of tonotopically-mapped non-primary auditory cortex. The attentionally-driven best-frequency maps show strong concordance with sensory-driven maps in the same subjects across much of the temporal plane, with poor concordance in non-auditory areas. There is significantly greater activation across most of auditory cortex when best frequency is attended, versus ignored. Moreover, the single frequency bands that evoke the least activation and the frequency bands that elicit the least activation when attention is directed to them also correspond closely. Finally, the results demonstrate that there is spatial correspondence between the degree of myelination and the strength of the tonotopic signal across a number of regions in auditory cortex. Strong frequency preferences across tonotopically-mapped auditory cortex spatially correlate with R1-estimated myeloarchitecture, indicating shared functional and anatomical organization that may underlie intrinsic auditory regionalization.\n\nSignificancePerception is an active process especially sensitive to attentional state. Listeners direct auditory attention to track a violins melody within an ensemble performance, or to follow a voice in a crowded cafe. Although diverse pathologies reduce quality of life by impacting such spectrally-directed auditory attention, its neurobiological bases are unclear. We demonstrate that human primary and non-primary auditory cortical activation is modulated by spectrally-directed attention in a manner that recapitulates its tonotopic sensory organization. Further, the graded activation profiles evoked by single frequency bands are correlated with attentionally-driven activation when these bands are presented in complex soundscapes. Finally, we observe a strong concordance in the degree of cortical myelination and the strength of tonotopic activation across several auditory cortical regions.

neuroscience↗