Biology subjects

Kaminski, J.

Publications and source records attributed to Kaminski, J..

13 recordsLinked to original sources

bioRxiv2026

Temporal dynamics of grooming reciprocity in crested macaques: do social bonds affect exchange?

Primates maintain cooperative relationships largely through grooming reciprocity, yet studies disagree on the timescales over which grooming is returned. Part of this disagreement stems from statistical issues: inconsistent definitions of a reciprocation window, combined with the exclusion of unreciprocated grooming, leave the debate unresolved. We still do not know if primates exchange grooming within the short windows predicted by biological market theory or over much longer timescales. Whilst survival analysis can identify reciprocation windows objectively by retaining unreciprocated grooming as censored data, previous studies have applied it inconsistently. This inconsistency leaves the true time frames over which primates reciprocate grooming somewhat blurred. Here, we use a statistical approach that addresses these problems to examine grooming reciprocity in crested macaques (Macaca nigra), a socially tolerant macaque species. We applied survival analysis to identify each group's short-term reciprocation window without imposing arbitrary cut offs, and Bayesian survival models to test whether social bond strength and eigenvector centrality predicted reciprocation latency. Short-term reciprocation occurred rarely (29% of events in one group and 5% in the other); most reciprocation occurred over longer timescales than previous research commonly assumes. Stronger bonds predicted faster reciprocation; this finding suggests that crested macaques express social investment in valued partners through how promptly they return grooming, meaning that the timing of exchange carries information about relationship value. Eigenvector centrality showed no credible effect, though our small sample size and dense groups prevent us from interpreting this outcome more robustly. Substantial variation between dyads remained unexplained, pointing to partnerspecific properties we have yet to identify. These findings caution against assuming that reciprocity operates over short windows. They show that social predictors, such as bond strength, remain essential to understanding when primates return grooming. This work provides a baseline for testing whether grooming is exchanged for other social commodities, and for comparing reciprocation timescales across macaque species that differ in social tolerance.

animal behavior and cognition↗

bioRxiv2025

PTPN2-KO CAR-T Cells Demonstrate Enhanced Effector Function, CNS Infiltration, and Toxicity in a Non-Human Primate CAR-T Model

B-cell targeting CAR-T cell therapies achieve high remission rates, yet durable responses occur in fewer than 40% of patients. Deletion of negative T-cell regulators, such as PTPN2, a key inhibitor of TCR and cytokine signaling, represents a promising strategy to enhance the efficacy of CAR-T cells. While transfer of PTPN2 knockout (KO) T cells has demonstrated antitumor benefits in murine models, its impact on human-derived CAR-T cells and, importantly, the associated in vivo efficacy and toxicity remain unclear. Here, we demonstrate that PTPN2-KO human CD19 CAR-T cells exhibit enhanced cytokine production, cytotoxicity, TCR and CAR affinity and signaling, leading to superior in vitro elimination of leukemic cells with low CD19 expression. To assess in vivo efficacy and toxicity, we performed a dose-escalation study using a non-human primate (NHP) model of B-cell-targeting CD20 CAR-T cell therapy. We demonstrated that PTPN2-KO CD20 CAR-T cells exhibited superior in vivo expansion and B-cell depletion compared to WT CAR-T cells, in a dose-dependent manner. At the highest dose level, CAR-T expansion was associated with increased toxicities, particularly ICANS, compared to PTPN2 WT CD20 CAR-T cells driven by enhanced CNS-infiltration. Transcriptional profiling revealed a dominant effector and proliferative signature, with cytotoxic CNS-infiltrating CD8+ PTPN2-KO CAR-T cells implicated in ICANS pathogenesis. This study details the comprehensive evaluation of PTPN2-KO CAR-T cells in an immunocompetent model, demonstrating their enhanced on-target functionality, while highlighting increased toxicity risks, underscoring the need for rigorous preclinical assessment of potent genetic modifications in CAR-T therapy. Key pointsO_LIPTPN2-KO CAR-T cells exhibit enhanced effector function C_LIO_LIIn a dose escalation study in rhesus macaques, PTPN2-KO mediated enhanced proliferation and CNS infiltration was associated with increased ICANS C_LI

immunology↗

bioRxiv2025

Hippocampal stimulation reveals causal role of persistent neural activity in human working memory

Working memory (WM) enables the temporary maintenance and manipulation of information, supporting flexible, goal-directed behavior. While converging evidence suggests that persistent activity in the hippocampus and other areas of the brain contributes to WM storage, this link has not been examined by manipulating neural activity experimentally. Here, we combined simultaneous intracranial single-neuron recordings with focal electrical stimulation in the human hippocampus to test the role of memoranda-selective persistent neural activity for WM. Thirty patients with implanted hybrid depth electrodes performed a WM task with images as memoranda. Electrical stimulation (2 s, 50 Hz, 1 mA) was delivered to the hippocampus during the maintenance period on a subset of trials. Behaviorally, stimulation impaired WM performance, increasing response times especially in low-load conditions. Neuronally, stimulation reduced memoranda-selective activity in hippocampus and ventral temporal cortex (VTC), thereby disrupting content-specific neural representations of WM content. The extent of stimulation-induced change in firing rate mediated trial-by-trial impaired WM-related behavior, linking disrupted neural selectivity to impaired WM. At the population level, stimulation shifted neural trajectories farther from attractor states, consistent with degraded mnemonic fidelity. Together, these data provide evidence that selective persistent activity of individual neurons in hippocampus and VTC supports WM maintenance in humans. Our results demonstrate that hippocampal stimulation disrupts both single-neuron coding and population-level attractor stability, linking cellular mechanisms to behavior and highlighting the contributions of persistent activity to WM maintenance.

neuroscience↗

bioRxiv2024

Persistent activity during working memory maintenance predicts long-term memory formation in the human hippocampus

Working Memory (WM) and Long-Term Memory (LTM) are often viewed as separate cognitive systems. Little is known about how these systems interact when forming memories. We recorded single neurons in the human medial temporal lobe while patients maintained novel items in WM and a subsequent recognition memory test for the same items. In the hippocampus but not the amygdala, the level of WM content-selective persist activity during WM maintenance was predictive of whether the item was later recognized with high confidence or forgotten. In contrast, visually evoked activity in the same cells was not predictive of LTM formation. During LTM retrieval, memory-selective neurons responded more strongly to familiar stimuli for which persistent activity was high while they were maintained in WM. Our study suggests that hippocampal persistent activity of the same cell supports both WM maintenance and LTM encoding, thereby revealing a common single-neuron component of these two memory systems.

neuroscience↗

bioRxiv2023

B cell directed CAR-T cell therapy results in activation of CD8+ cytotoxic CAR-negative bystander T cells in both non-human primates and patients

There is growing appreciation for the emergence of CARneg bystander T cells after CAR-T cell infusion. However, their phenotypic and transcriptomic hallmarks and mechanisms of activation remain uncertain. We performed single-cell RNA-Seq (scRNA-Seq) on non-human primate (NHP) and patient-derived T cells to interrogate CARneg T cells following B cell targeted CAR-T cell therapy. In a NHP model, we observed a distinct population of activated CD8+ CARneg T cells emerging during CAR-T cell expansion. These bystander CD8+ CARneg T cells exhibited a unique transcriptional signature with upregulation of NK-cell markers (KIR3DL2, CD160, KLRD1), chemokines and chemokine receptors (CCL5, XCL1, CCR9), and downregulation of naive T cell-associated genes (SELL, CD28). A transcriptionally similar population was identified in patients following Tisangelecleucel infusion. Mechanistic studies revealed that IL-2 and IL-15 exposure induced bystander-like CD8+ T cells. These T cells efficiently killed leukemic cells through a TCR-independent mechanism. Together, these data identify bystander CD8+ T cells as a novel mechanism by which CAR-T cell infusion can induce further anti-leukemic activity, measurable in both NHP and in patients. Statement of SignificanceWe have deeply interrogated CARneg bystander CD8+ T cells during CAR-T cell expansion in non{-}human primates and patients receiving Tisangelecleucel to identify the unique transcriptomic signature defining these cells, and to determine that IL-2-and IL-15-induced cytotoxic bystander T cells are capable of killing in a TCR-independent manner. These data highlight the potential of bystander T cells for leukemia control and provide a critical foundation for their future analysis.

immunology↗

bioRxiv2023

Control of working memory maintenance by theta-gamma phase amplitude coupling of human hippocampal neurons

Retaining information in working memory (WM) is a demanding process that relies on cognitive control to protect memoranda-specific persistent activity from interference. How cognitive control regulates WM storage, however, remains unknown. We hypothesized that interactions of frontal control and hippocampal persistent activity are coordinated by theta-gamma phase amplitude coupling (TG-PAC). We recorded single neurons in the human medial temporal and frontal lobe while patients maintained multiple items in WM. In the hippocampus, TG-PAC was indicative of WM load and quality. We identified cells that selectively spiked during nonlinear interactions of theta phase and gamma amplitude. These PAC neurons were more strongly coordinated with frontal theta activity when cognitive control demand was high, and they introduced information-enhancing and behaviorally relevant noise correlations with persistently active neurons in the hippocampus. We show that TG-PAC integrates cognitive control and WM storage to improve the fidelity of WM representations and facilitate behavior.

neuroscience↗

bioRxiv2021

Identification and tracking of alloreactive T cell clones in Rhesus Macaques through the RM-scTCR-Seq platform.

T cell receptor clonotype tracking is a powerful tool for interrogating T cell mediated immune processes. New methods to pair a single cells transcriptional program with its T cell receptor (TCR) identity allow monitoring of T cell clonotype-specific transcriptional dynamics. While these technologies have been available for human and mouse T cells studies, they have not been developed for Rhesus Macaques, a critical translational organism for autoimmune diseases, vaccine development and transplantation. We describe a new pipeline, RM-scTCR-Seq, which, for the first time, enables RM specific single cell TCR amplification, reconstitution and pairing of RM TCRs with their transcriptional profiles. We apply this method to a RM model of GVHD, and identify and track in vitro detected alloreactive clonotypes in GVHD target organs and explore their GVHD driven cytotoxic T cell signature. This novel, state-of-the-art platform fundamentally advances the utility of RM to study protective and pathogenic T cell responses.

immunology↗

bioRxiv2021

T cell self-reactivity during thymic development dictates the timing of positive selection

Functional tuning of T cells based on their degree of self-reactivity is established during positive selection in the thymus, although how positive selection differs for thymocytes with relatively low versus high self-reactivity is unclear. In addition, preselection thymocytes are highly sensitive to low-affinity ligands, but the mechanism underlying their enhanced TCR sensitivity is not fully understood. Here we show that murine thymocytes with low self-reactivity experience briefer TCR signals and complete positive selection more slowly than those with high self-reactivity. Additionally, we provide evidence that cells with low self-reactivity retain a preselection gene expression signature as they mature, including genes previously implicated in modulating TCR sensitivity and a novel group of ion channel genes. Our results imply that thymocytes with low self-reactivity down-regulate TCR sensitivity more slowly during positive selection, and suggest that modulation of membrane ion channel function may play a role in regulating TCR tuning throughout development. Impact StatementDeveloping T cells whose TCRs have relatively low reactivity experience very brief TCR signaling events, delayed positive selection, and do not fully down regulate their TCR sensitivity as they mature.

developmental biology↗

bioRxiv2021

Batf-mediated Epigenetic Control of Effector CD8+ T Cell Differentiation

The response of cytotoxic T cells to their cognate antigen involves rapid and broad changes in gene expression that are coupled with extensive chromatin remodeling. Here, we study the mechanisms by which the basic leucine zipper ATF-like transcription factor Batf helps regulate this process. Through genome-scale profiling, we observe critical roles for Batf in inducing transcriptional changes in stimulated naive cells, while affecting the chromatin at several levels, namely binding of key transcription factors, accessibility, and long range contacts. We identify a critical network of transcription factors that cooperate with Batf, including its binding partner Irf4, as well as Runx3 and T-bet, and demonstrate its synergistic activity in initiating aspects of the effector T cells transcriptional and epigenetic program in ectopically-induced fibroblasts. Our results provide a comprehensive resource for studying the epigenomic and transcriptomic landscape of effector differentiation of cytotoxic T cells.

immunology↗

bioRxiv2020

Spatiotemporal single-cell profiling of gastrointestinal GVHD reveals invasive and resident memory T cell states.

One of the central challenges in the field of allo-immunity is deciphering the mechanisms driving T cells to infiltrate and subsequently occupy target organs to cause disease. The act of CD8-dominated T cell infiltration is critical to acute graft-versus-host disease (aGVHD), wherein donor T cells become activated, tissue-infiltrating and highly cytotoxic, causing wide-spread tissue damage after allogeneic hematopoietic stem cell transplant (allo-HCT). However, in human and non-human primate studies, deconvolving the transcriptional programs of newly recruited relative to resident memory T cells in the gastrointestinal (GI) tract has remained a challenge. In this study, we combined the novel technique of Serial Intravascular Staining (SIVS) with single-cell RNA-Seq (scRNA-seq) to enable detailed dissection of the tightly connected processes by which T cells first infiltrate tissues and then establish a pathogenic tissue residency program after allo-HCT in non-human primates. Our results have enabled the creation of a spatiotemporal map of the transcriptional drivers of CD8 T cell infiltration into the primary aGVHD target-organ, the GI tract. We identify the large and small intestines as the only two sites demonstrating allo-specific, rather than lymphdepletion-driven T cell infiltration. The donor CD8 T cells that infiltrate the GI tract demonstrate a highly activated, cytotoxic phenotype while simultaneously rapidly developing canonical tissue-resident memory (TRM) protein expression and transcriptional signatures, driven by IL-15/IL-21 signaling. Moreover, by combining SIVS and transcriptomic analysis, we have been able to work backwards from this pathogenic TRM programing, and, for the first time, identify a cluster of genes directly associated with tissue invasiveness, prominently including specific chemokines and adhesion molecules and their receptors, as well as a central cytoskeletal transcriptional node. The clinical relevance of this new tissue invasion signature was validated by its ability to discriminate the CD8 T cell transcriptome of patients with GI aGVHD. These results provide new insights into the mechanisms controlling tissue infiltration and pathogenic CD8 TRM transcriptional programing, uncovering critical transitions in allo-immune tissue invasion and destruction. One sentence summaryFlow cytometric and transcriptomic analysis reveals coordinated tissue-infiltration and tissue-residency programs driving gastrointestinal aGVHD.

immunology↗

bioRxiv2020

Evidence for an Active Role of Inferior Frontal Cortex in Conscious Experience

2In the search for the neural correlates of consciousness, it has remained controversial whether prefrontal cortex determines what is consciously experienced or, alternatively, serves only complementary functions such as introspection or action. Here, we provide converging evidence from computational modeling and two functional magnetic resonance imaging experiments for a key role of inferior frontal cortex in detecting perceptual conflicts that emerge from ambiguous sensory information. Crucially, the detection of perceptual conflicts by prefrontal cortex turned out to be critical in the process of transforming ambiguous sensory information into unambiguous conscious experiences: In a third experiment, disruption of neural activity in inferior frontal cortex through transcranial magnetic stimulation slowed down the updating of conscious experience that occurs in response to perceptual conflicts. These findings show that inferior frontal cortex actively contributes to the resolution of perceptual ambiguities. Prefrontal cortex is thus causally involved in determining the contents of conscious experience. 3 One-sentence SummaryInferior frontal cortex detects and resolves perceptual conflict during bistable perception.

neuroscience↗

bioRxiv2017

Overestimating environmental volatility increases switching behavior and is linked to activation of dorsolateral prefrontal cortex in schizophrenia

BackgroundReward-based decision-making is impaired in patients with schizophrenia (PSZ) as reflected by increased choice switching. The underlying cognitive and motivational processes as well as associated neural signatures remain unknown. Reinforcement Learning (RL) and hierarchical Bayesian learning account for choice switching in different ways. We hypothesized that enhanced choice switching, as seen in PSZ during reward-based decision-making, relates to higher-order beliefs about environmental volatility and examined the associated neural activity.\n\nMethods46 medicated PSZ and 43 healthy controls (HC) performed a reward-based decision-making task requiring flexible responses to changing action-outcome contingencies during functional Magnetic Resonance Imaging (fMRI). Detailed computational modeling of choice data was performed, including RL and the hierarchical Gaussian filter (HGF). Trajectories of learning from computational modeling informed the analysis of fMRI data.\n\nResultsA three-level HGF accounted best for the observed choice data. This model revealed a heightened initial belief about environmental volatility and a stronger influence of volatility on lower-level learning of action-outcome contingencies in PSZ as compared to HC. This was replicated in an independent sample of non-medicated PSZ. Beliefs about environmental volatility were reflected by higher activity in dorsolateral prefrontal cortex of PSZ as compared to HC.\n\nConclusionsOur study suggests that PSZ inferred the environment as overly volatile, which may explain increased choice switching. In PSZ, activity in dorsolateral prefrontal cortex was more strongly related to beliefs about environmental volatility. Our computational phenotyping approach may provide useful information to dissect clinical heterogeneity and could improve prediction of outcome.

neuroscience↗

bioRxiv2017

GWAS meta-analysis (N=279,930) identifies new genes and functional links to intelligence

Intelligence is highly heritable1 and a major determinant of human health and well-being2. Recent genome-wide meta-analyses have identified 24 genomic loci linked to intelligence3-7, but much about its genetic underpinnings remains to be discovered. Here, we present the largest genetic association study of intelligence to date (N=279,930), identifying 206 genomic loci (191 novel) and implicating 1,041 genes (963 novel) via positional mapping, expression quantitative trait locus (eQTL) mapping, chromatin interaction mapping, and gene-based association analysis. We find enrichment of genetic effects in conserved and coding regions and identify 89 nonsynonymous exonic variants. Associated genes are strongly expressed in the brain and specifically in striatal medium spiny neurons and cortical and hippocampal pyramidal neurons. Gene-set analyses implicate pathways related to neurogenesis, neuron differentiation and synaptic structure. We confirm previous strong genetic correlations with several neuropsychiatric disorders, and Mendelian Randomization results suggest protective effects of intelligence for Alzheimers dementia and ADHD, and bidirectional causation with strong pleiotropy for schizophrenia. These results are a major step forward in understanding the neurobiology of intelligence as well as genetically associated neuropsychiatric traits.

genetics↗