Biology subjects

Gottlieb, J.

Publications and source records attributed to Gottlieb, J..

14 recordsLinked to original sources

bioRxiv2026

Single-cell and spatial transcriptomics resolve airway obliteration in bronchiolitis obliterans syndrome

Background: Chronic lung allograft dysfunction (CLAD) is the leading cause of death beyond the first year after lung transplantation, and its most frequent phenotype is bronchiolitis obliterans syndrome (BOS), a fibrotic small-airway disease. Mechanistic work has focused on the immune compartment, yet intensified immunosuppression does not alter established disease. Aim: To resolve which structural cell states populate the BOS graft and how they are spatially organized during airway obliteration. Methods: We profiled explanted lungs from 33 BOS patients undergoing re-transplantation and 33 controls, combining single-nucleus RNA sequencing (14 BOS, 13 controls) with targeted spatial transcriptomics of 108 regions (27 BOS, 24 controls) and multiplex immunofluorescence validation. Single-nucleus data were integrated with a published restrictive allograft syndrome (RAS) atlas. Results: Across 175,128 nuclei and 1.67 million spatially resolved cells, BOS lungs harbored a profibrotic circuit of Aberrant Basaloid cells and CTHRC1+ fibrotic fibroblasts previously described in fibrotic lung diseases, including RAS. Spatial mapping identified a CXCL14+TNC+ injury-associated basal cell state arising early in the obliterative cascade, identifying basal cells as their major reservoir. CTHRC1+ fibroblasts expanded subepithelially replacing resident peribronchial fibroblasts, alongside a peribronchial vascular shift toward systemic venous endothelium. The circuit extended beyond the airway wall to the alveolar interface, defining two convergent remodeling fronts. Conclusion: BOS engages structural-cell circuits largely shared with RAS and fibrotic lung diseases, but along an airway-centered rather than parenchyma-centered axis. CLAD thus emerges as a spatial rather than cellular spectrum, defined by anatomical distribution more than cell identity. Shared structural programs may therefore be targetable across CLAD phenotypes.

cell biology↗

bioRxiv2025

Single-Neuron Encoding of Learnability in the Dorsal Anterior Cingulate Cortex

In natural environments, associations that indicate true learnable regularities are intermixed with those that arise from random and ultimately unlearnable relationships between events. To efficiently allocate cognitive resources and avoid inferring spurious patterns, organisms must distinguish learnable from unlearnable associations, but the mechanisms underlying this ability are not understood. We recently showed that monkeys performing a transitive inference task, while discovering the true hidden order in learnable image sets, also behaved to varying degrees as if they inferred subjective order in objectively random (unlearnable) image sets. Here, we show that the ability to detect learnability is encoded by neurons in the dorsal anterior cingulate cortex (dACC, area 24c). dACC neurons responded strongly after a decision outcome as reported in previous studies and, additionally, signaled whether a trial was from a learnable vs unlearnable set before outcome delivery, and showed interactions whereby their selectivity for the outcome (reward vs lack of reward) was stronger for learnable versus unlearnable sets. Learnability and interaction responses were independent of sensory or reward cues (which were equated for learnable and unlearnable sets) but their strength correlated with the monkeys ability to avoid inferring false order in unlearnable sets. The findings suggest that the dACC is part of a network that monitors learnability and enables animals to appropriately focus learning on true patterns while avoiding false inferences about spurious and random associations.

neuroscience↗

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

Spatial transcriptomics uncovers hybrid, pro-inflammatory and pro-fibrotic cellular niches in pulmonary granuloma of patients with chronic sarcoidosis

BackgroundSarcoidosis is a disease of unknown etiology characterized by the formation of immune cell accumulation (granuloma) in the lung and other tissues. Chronic sarcoidosis may lead to pulmonary fibrosis. AimTo unravel cellular niches within pulmonary granuloma of chronic sarcoidosis patients using spatial transcriptomics. MethodsSpatial transcriptomics using the Visium platform (10x Genomics) was performed on nine granuloma-containing lung explants from sarcoidosis patients. Validation of gene expression was performed through immunohistofluorescence protein staining and RNA in situ hybridization. ResultsSpatial gene expression covered 30,587 gene expression spots and 173 granulomas. A CD68+ macrophage niche was localized in the center of the granuloma, with a CD3+ T and CD20+ B cell niche in close proximity, surrounded by a COL3A1+ fibroblast niche. In the central granuloma macrophage niche, expression of the pro-fibrotic macrophage genes SPP1, CHIT1 and CHI3L1 was observed, genes whose expression has recently been described for macrophages in idiopathic pulmonary fibrosis. Additionally, pro-inflammatory macrophage genes were expressed in the central granuloma niche: macrophages appear armed for lysosomal degradation and ready for phagocytosis. Inner granuloma niches showed high responsiveness to interferon gamma (IFN-{gamma}), expressing a multitude of IFN-{gamma}-induced genes. High collagen and CTHRC1 expression were observed in granuloma fibroblasts niches, characteristics of pro-fibrotic lung remodeling. Ligand-receptor analysis identified pro-inflammatory and pro-fibrotic interactions between granuloma niches. ConclusionTaken together, macrophages in the center of the sarcoidosis granuloma form an armed-and-ready, hybrid pro-inflammatory and pro-fibrotic niche, supporting granuloma persistence through continuous IFN-{gamma}-stimulation and fibrotic remodeling conducted by fibrotic fibroblasts surrounding the granuloma.

molecular biology↗

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↗

bioRxiv2023

A Distinct Neural Code Supports Prospection of Future Probabilities During Instrumental Information-Seeking

To make adaptive decisions, we must actively demand information, but relatively little is known about the mechanisms of active information gathering. An open question is how the brain estimates expected information gains (EIG) when comparing the current decision uncertainty with the uncertainty that is expected after gathering information. We examined this question using fMRI in a task in which people placed bids to obtain information in conditions that varied independently by prior decision uncertainty, information diagnosticity, and the penalty for an erroneous choice. Consistent with value of information theory, bids were sensitive to EIG and its components of prior certainty and expected posterior certainty. Expected posterior certainty was decoded above chance from multivoxel activation patterns in the posterior parietal and extrastriate cortices. This representation was independent of instrumental rewards and overlapped with distinct representations of EIG and prior certainty. Thus, posterior parietal and extrastriate cortices are candidates for mediating the prospection of posterior probabilities as a key step to estimate EIG during active information gathering.

neuroscience↗

bioRxiv2022

Leveraging vision to understand curiosity

Humans are immensely curious and motivated to reduce uncertainty. Inspired by studies of sensory uncertainty, we hypothesized that visual areas provide multivariate representations of uncertainty, which are read out by higher-order areas that encode confidence and, ultimately, translated into curiosity. During fMRI, participants rated their confidence in identifying distorted images of animals and objects and their curiosity to see the clear image. We found that curiosity peaked at low confidence. To link sensory certainty and curiosity, we estimated "OTC Certainty" as the product of absolute and relative evidence for animals vs. object categories in occipitotemporal cortex (OTC) while participants viewed the distorted image. OTC Certainty negatively correlated with curiosity, while univariate activity in two frontal regions - vmPFC and ACC - positively correlated with confidence. The relationship between OTC certainty and curiosity was mediated by the vmPFC but not ACC. The results reveal neural mechanisms that generate curiosity from representations of uncertainty.

neuroscience↗

bioRxiv2022

Traveling waves in the monkey frontoparietal network predict recent reward memory

Brain function depends on neural communication, but the mechanisms of this communication are not well understood. Recent studies suggest that one form of neural communication is through traveling waves (TWs)--patterns of neural oscillations that propagate within and between areas. We show that TWs appear robustly in microarray recordings in monkey frontal and parietal cortex and encode memory for recent rewards. While making saccades to obtain probabilistic rewards, monkeys were sensitive to the (statistically irrelevant) prior reward, which is consistent with behavioral biases produced by reward history. TWs in frontal and parietal areas were stronger in trials following a prior reward versus a lack of reward and, in the frontal lobe, correlated with the monkeys sensitivity to the prior reward. The findings suggest that neural communication across fronto-parietal areas, reflected by TWs, maintains default reward memories, while communication within the frontal lobe mediates the read out of the memories for prospective expectations.

neuroscience↗

bioRxiv2021

A neural substrate for Bayesian integration in human parietal cortex

Making adaptive decisions often requires inferring unobservable states based on unreliable information. Bayesian logic prescribes that individuals form probabilistic beliefs about a state by integrating the likelihood of new evidence with their prior beliefs, but human neuroimaging studies on probability representations have not typically examined this integration process. We developed an inference fMRI task in which participants estimated the posterior probability of a hidden state while we parametrically modulated the prior probability of the state, the likelihood of the supporting evidence, and a monetary penalty for estimation inaccuracy. Consistent with a neural substrate for Bayesian integration, activation in left posterior parietal cortex tracked the estimated posterior probability of the solicited state and its components of prior probability and likelihood, all independently of expected value. This activation further reflected deviations in individual reports from objective probabilities. Thus, this region may provide a neural substrate for humans ability to approximate Bayesian inference.

neuroscience↗

bioRxiv2021

Learning of biased representations in LIP through interactions between recurrent connectivity and Hebbian plasticity

When monkeys learn to group visual stimuli into arbitrary categories, lateral intraparietal area (LIP) neurons become category-selective. Surprisingly, the representations of learned categories are overwhelmingly biased: nearly all LIP neurons in a given animal prefer the same category over other behaviorally equivalent categories. We propose a model where such biased representations develop through the interplay between Hebbian plasticity and the recurrent connectivity of LIP. In this model, two separable processes of positive feedback unfold in parallel: in one, category selectivity emerges from competition between prefrontal inputs; in the other, bias develops due to lateral interactions among LIP neurons. This model reproduces the levels of category selectivity and bias observed under a variety of conditions, as well as the redevelopment of bias after monkeys learn redefined categories. It predicts that LIP receptive fields would spatially cluster by preferred category, which we experimentally confirm. In summary, our model reveals a mechanism by which LIP learns abstract representations and assigns meaning to sensory inputs.

neuroscience↗

bioRxiv2021

Uncertainty modulates visual maps during non-instrumental information demand

Animals are intrinsically motivated to resolve uncertainty and predict future events. This motivation is encoded in cortical and subcortical structures, but a key open question is how it generates concrete policies for attending to informative stimuli. We examined this question using neural recordings in the monkey lateral intraparietal area (LIP), a visual area implicated in attention and gaze, during non-instrumental information demand. We show that the uncertainty that was resolved by a visual cue enhanced visuo-spatial responses of LIP cells independently of reward probability. This enhancement was independent of immediate saccade plans but correlated with the sensitivity to uncertainty in eye movement behavior on longer time scales (across sessions/days). The findings suggest that topographic visual maps receive motivational signals of uncertainty, which enhance the priority of informative stimuli and the likelihood that animals will orient to the stimuli to reduce uncertainty.

neuroscience↗

bioRxiv2021

A Reinforcement Meta-Learning Framework of Executive Function and Information Demand

Gathering information is crucial for maximizing fitness, but requires diverting resources from searching directly for primary rewards to actively exploring the environment. Optimal decision-making thus maximizes information while reducing effort costs, but little is known about the neural implementation of these tradeoffs. We present a Reinforcement Meta-Learning (RML) computational mechanism that solves the trade-offs between the value and costs of gathering information. We implement the RML in a biologically plausible architecture that links catecholaminergic neuromodulators, the medial prefrontal cortex and topographically organized visual maps and show that it accounts for neural and behavioral findings on information demand motivated by instrumental incentives and intrinsic utility. Moreover, the utility function used by the RML, encoded by dopamine, is an approximation of free-energy. Thus, the RML presents a biologically plausible mechanism through which coordinated motivational, executive and sensory systems generate visual information gathering policies that minimize free energy.

neuroscience↗

bioRxiv2019

Distinct signatures of reward value and variance on spiking activity and functional interactions in monkey fronto-parietal areas

Theories of executive function propose that controlled information processing is costly and is allocated according to the behavioral benefits it brings. Computational theories predict that the benefits of new information depend on prior uncertainty, but the cellular effects of uncertainty on the executive network are incompletely understood. Using simultaneous recordings in monkeys, we reveal several mechanisms by which the fronto-parietal network reacts to uncertainty independently of average reward gains. We show that the variance of expected rewards, independently of the value of the rewards, was represented in single neuron and population spiking activity and local field potential (LFP) oscillations. Moreover, uncertainty asymmetrically affected the coherence between spikes and LFPs, selectively suppressing information transmission from the frontal to the parietal lobe but enhancing transmission from the parietal to the frontal lobe, consistent with Bayesian principles of optimal inference under uncertainty.

neuroscience↗

bioRxiv2019

Frontal and parietal neurons encode reward prediction errors in multiple reference frames

Computing expectancy violations is essential for decision making and cognitive functions, but its neural mechanisms are incompletely understood. We describe a novel mechanism by which prefrontal and posterior parietal neurons encode reward prediction errors (RPEs) in their population but not single-neuron activity. Simultaneous recordings of neural populations showed that both areas co-activated information about experienced and expected rewards in a precise opponent organization. Neurons encoding expected rewards with positive (negative) scaling were reactivated simultaneously with those encoding experienced rewards with negative (positive) scaling. This opponent organization was mirrored in polarity-dependent noise correlations. Moreover, it extended to two types of expectancy information - based on task-relevant visual cues and statistically irrelevant reward history - allowing decoding of signed and unsigned RPE in two reference frames. Frontal and parietal areas implement canonical computations that facilitate contextual comparisons and the readout of multiple types of expectancy violations to flexibly serve behavioral goals.

neuroscience↗