Biology subjects

Schiller, D.

Publications and source records attributed to Schiller, D..

12 recordsLinked to original sources

bioRxiv2025

HM-DyadCap - Capture and Mapping of 5-Hydroxymethyl-cytosine/5-Methylcytosine CpG Dyads in Mammalian DNA

5-Methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) are the main epigenetic modifications of mammalian DNA, and play crucial roles in cell differentiation, development, and tumorigenesis. Both modifications co-exist with unmodified cytosine in palindromic CpG dyads in different symmetric and asymmetric combinations across the two DNA strands, each having unique regulatory potential. To facilitate investigating the individual functions of such dyad modifications, we report HM-DyadCap. This method employs an evolved methyl-CpG-binding domain (MECP2 HM) for the direct capture and sequencing of DNA fragments containing the CpG dyad hmC/mC. Binding studies reveal a high discrimination of MECP2 HM against off-target dinucleotides. We conduct comparative mapping experiments for mESC genomes with HM-DyadCap, standard MethylCap employing wild type MECP2, as well as MeDIP and hMeDIP protocols. We find that MECP2 HM is blocked by hmC glucosylation, and conduct control enrichments with glucosylated genomes that indicate highly selective enrichment of hmC/mC dyads by MECP2 HM. Metagene profiles correlate hmC/mC marks with actively transcribed genes, and reveal global enrichment in gene bodies as well as depletion at transcription start sites. We anticipate that HM-DyadCap will enable effective enrichment and mapping of hmC/mC marks with broad applicability for unravelling the function of this dyad in chromatin biology and cancer.

genomics↗

bioRxiv2024

Dissociable memory modulation mechanisms facilitate fear amnesia at different timescales

Memory reactivation renders consolidated memory fragile and thereby opens the window for memory updates, such as memory reconsolidation. However, whether memory retrieval facilitates update mechanisms other than memory reconsolidation remains unclear. We tested this hypothesis in three experiments with healthy human participants. First, we demonstrate that memory retrieval-extinction protocol prevents the return of fear expression shortly after extinction training and this short-term effect is memory reactivation dependent (Study 1, N = 57 adults). Furthermore, across different timescales, the memory retrieval-extinction paradigm triggers distinct types of fear amnesia in terms of cue-specificity and cognitive control dependence, suggesting that the short-term fear amnesia might be caused by different mechanisms from the cue-specific amnesia at a longer and separable timescale (Study 2, N = 79 adults). Finally, using continuous theta-burst stimulation (Study 3, N = 75 adults), we directly manipulated brain activity in the dorsolateral prefrontal cortex, and found that both memory reactivation and intact prefrontal cortex function were necessary for the short-term fear amnesia after the retrieval-extinction protocol. The differences in temporal scale, cue-specificity, and cognitive control ability dependence between the short- and long-term amnesia suggest that memory retrieval and extinction training trigger distinct underlying memory update mechanisms. These findings suggest the potential involvement of coordinated memory modulation processes upon memory retrieval and may inform clinical approaches for addressing persistent maladaptive memories.

neuroscience↗

bioRxiv2023

Neural Trajectories of Social Relationships on a Map-like Manifold

In a series of conceptually related episodes, meaning arises from the link between these events rather than from each event individually. How does the brain keep track of conceptually related sequences of events (i.e., conceptual trajectories)? In a particular kind of conceptual trajectory--a social relationship--meaning arises from a specific sequence of interactions. To test whether such abstract sequences are neurally tracked, we had participants complete a naturalistic narrative-based social interaction game, during functional magnetic resonance imaging. We modeled the simulated relationships as trajectories through an abstract affiliation and power space. Using two independent samples (n = 50), we found evidence of both the underlying social dimensions of affiliation and power and the evolving social relationships themselves as being tracked by the hippocampus. These results suggest that our evolving relationships with others, despite being composed of isolated events that occur independently across time and space (i.e., spatially and temporally non-consecutive events), but are nevertheless related conceptually, are represented in trajectory-like neural patterns in the human hippocampus.

neuroscience↗

bioRxiv2023

cGAS/STING and NLRP3 cooperatively activate CD8+ T cell-mediated anti-tumor immunity in colorectal cancer

Colorectal cancer (CRC) is a highly prevalent and deadly disease that is largely refractory to immunotherapy. The only CRC subset that responds to these therapies is characterized by prevalent microsatellite instability (MSI), extensive CD8+ T cell infiltration and high expression of innate immune signaling pathways. Endogenous activation of the cGAS/STING pathway is essential for the CD8+ T cell antitumor response in MSI CRCs, suggesting that activating it in other CRCs could boost immunotherapy response rates. We show that cGAS/STING signaling can be enhanced by costimulation of the NLRP3 inflammasome and that dual stimulation increases CD8+ T cell-mediated antitumor immunity in both MSI and non-MSI CRCs. The ability of NLRP3 to boost cGAS/STING signaling was specific and did not occur with activation of other innate immune pathways such as AIM2 or TLRs. Cooperativity between cGAS/STING and NLRP3 proceeded via a positive feedback loop that was inflammasome-independent and required early crosstalk between the signaling mediators and regulation of their gene expression. Notably, increased cGAS/STING signaling enhanced CD8+ T cell activation when in conjunction with anti-PD1 immunotherapy, suggesting that signaling via NLRP3 could further boost this response and render otherwise resistant CRC susceptible to immunotherapy. SignificanceInnate immune signaling pathways cooperatively regulate CD8+ T cell-mediated antitumor immunity in both hot and cold tumors. In addition to serving as predictive biomarkers, these pathways can be therapeutically targeted to increase response rates to immunotherapy while minimizing undesirable adverse events.

cancer biology↗

bioRxiv2023

Hippocampal timestamp for goals

Our brain must manage multiple goals that differ in their temporal proximity. Some goals require immediate attention, while others have already been accomplished, or will be relevant later in time. Here, we examined how the hippocampus represents the temporal distance to different goals using a novel space-themed paradigm during 7T functional MRI (n=31). The hippocampus has an established role in mental time travel and a system in place to stratify information along its longitudinal axis on the basis of representational granularity. Previous work has documented a functional transformation from fine-grained, detail rich representations in the posterior hippocampus to coarse, gist-like representations in the anterior hippocampus. We tested whether the hippocampus uses this long axis system to dissociate goals based upon their temporal distance from the present. We hypothesized that the hippocampus would distinguish goals relevant for ones current needs from those that are removed in time along the long axis, with temporally removed past and future goals eliciting increasingly anterior activation. We sent participants on a mission to Mars where they had to track goals that differed in when they needed to be accomplished. We observed a long-axis dissociation, where temporally removed past and future goals activated the left anterior hippocampus and current goals activated the left posterior hippocampus. Altogether, this study demonstrates that the timestamp attached to a goal is a key driver in where the goal is represented in the hippocampus. This work extends the scope of the hippocampus long axis system to the goal-mapping domain.

neuroscience↗

bioRxiv2023

A generalizable computational mechanism underlying the interaction between momentary craving and decision-making

Substance craving and maladaptive choices are intertwined across addictive disorders. However, the computational mechanisms connecting craving and decision-making remain elusive. Here, we tested a hypothesis that momentary craving and value-based decision-making influence each other during substance-related reinforcement learning. We measured momentary craving as two groups of human participants (alcohol drinkers and cannabis users; total n=132) performed a reinforcement learning task in which they received group-specific addictive cue or monetary rewards. Using computational modeling, we found that, across both groups, momentary craving biased learning rate related to substance-associated prediction errors (RPEs), but not monetary RPEs. Additionally, expected values and RPEs jointly influenced elicited craving across reward types and participant groups. Alcohol and cannabis users also differed in the extent to which their craving and decision-making influenced each other, suggesting important computational divergence between the two groups. Finally, regressions incorporating model-derived parameters best predicted substance use severity in the alcohol, but not cannabis group, supporting the utility of using these model-based parameters in making clinical predictions for selective substance groups. Together, these findings provide a computational mechanism for the interaction between substance craving and maladaptive choices that is generalizable across addictive domains.

neuroscience↗

bioRxiv2022

A translational repression reporter assay for the analysis of RNA-binding protein consensus sites

RNA-binding proteins are essential regulators of RNA processing and function. Translational repression assays can be used to study how they interact with specific RNA sequences by insertion of such a consensus sequence into the 5 untranslated region of a reporter mRNA and measuring reporter protein translation. The straightforward set-up of these translational repression assays avoids the need for the isolation of the protein or the RNA providing speed, robustness, and a low-cost method. Here we report the optimization of the assay to function with linear RNA sequences instead of the previously reported hairpin type sequences to allow the study of a wider variety of RNA-binding proteins. Multiplication of a consensus sequence strongly improves the signal allowing analysis by both fluorescence intensity measurements and fluorescence activated cell sorting.

molecular biology↗

bioRxiv2022

Neural patterns differentiate traumatic from sad autobiographical memories in PTSD

For people with post-traumatic stress disorder (PTSD), recalling traumatic memories often displays as intrusions that differ profoundly from processing of regular negative memories. These mnemonic features fueled theories speculating a qualitative divergence in cognitive state linked with traumatic memories. Yet to date, little empirical evidence supports this view. Here, we examined neural activity of PTSD patients who were listening to narratives depicting their own memories. An inter-subject representational similarity analysis of cross-subject semantic content and neural patterns revealed a differentiation in hippocampal representation by narrative type: Semantically similar sad autobiographical memories elicited similar neural representations across participants. By contrast, within the same individuals, semantically thematically similar trauma memories were not represented similarly. Furthermore, we were able to decode memory type from hippocampal multivoxel patterns. Finally, individual symptom severity modulated semantic representation of the traumatic narratives in the posterior cingulate cortex. Taken together, these findings suggest that traumatic memories are a qualitatively divergent cognitive entity.

neuroscience↗

bioRxiv2022

Hippocampal Place-like Signal in Latent Social Space

During navigation, the hippocampus represents physical places like coordinates on a map; similar location-like signals have been seen in sensory and concept spaces. It is unclear just how general this hippocampal place code is, however: does it map places in wholly non-perceivable spaces, without locations being instructed or reinforced and during navigation-like behavior? To search for such a signal, we imaged participants brains while they played a naturalistic, narrativebased social interaction game, and modeled their relationships as a kind of navigation through social space. Two independent samples showed hippocampal place-like signals in both region-based and whole-brain representational similarity analyses, as well as decoding and average pattern similarity analyses; the effects were not explained by other measures of the behavior or task information. These results are the first demonstration of complete domain generality in hippocampal place representation. One-Sentence Summaryhippocampal place-like signal in non-perceivable and unreinforced space during naturalistic navigational behavior. Significance statementThe hippocampus is a brain structure known to encode maps of physical spaces; this study shows that it also maps fully abstract, latent and uninstructed spaces. People played a naturalistic social interaction game while their brains were scanned. Hippocampal brain activity correlated with the fictional characters locations in an abstract social space framed by axes of affiliation and power, despite the participants never being exposed to a perceivable spatial representation. This mapping was present across multiple analyses and two samples, demonstrating that the brain system responsible for spatial mapping maps our social interactions too.

neuroscience↗

bioRxiv2021

An interpretable connectivity-based decoding model for classification of chronic marijuana use

BackgroundPsychiatric neuroimaging typically proceeds with one of two approaches: encoding models, which aim to model neural mechanisms, or decoding models, which aim to predict behavioral or clinical characteristics from brain imaging data. In this study, we seek to combine these aims by developing interpretable decoding models that offer both accurate prediction and novel neural insights. We demonstrate the effectiveness of this combined approach in a case study of chronic marijuana use. MethodsChronic marijuana (MJ) users (n=195) and non-using healthy controls (n=128) completed a cue-elicited craving task during functional magnetic resonance imaging. Linear machine learning methods were used to classify individuals into chronic MJ users and non-users based on task-evoked, whole-brain functional connectivity. We then used graph theoretic analyses to identify predictive functional connectivities among brain regions that contributed most substantially to the classification of chronic marijuana use. ResultsWe obtained high (~80% out-of-sample) accuracy across four different classification models, demonstrating that task-evoked, whole-brain functional connectivity can successfully differentiate chronic marijuana users from non-users. Subsequent network analyses revealed key predictive regions (e.g., anterior cingulate cortex, dorsolateral prefrontal cortex, and precuneus) that are often implicated in neuroimaging studies of substance use disorders, as well as some key exceptions. We also identified a core set of networks of brain regions that contributed to successful classification, comprised of many of the same predictive regions. ConclusionsOur dual aims of accurate prediction and interpretability were successful, producing a predictive model that also provides interpretability at the neural level. This novel approach may complement other predictive-exploratory approaches for a more complete understanding of neural mechanisms in drug use and other neuropsychiatric disorders.

neuroscience↗

bioRxiv2020

Antitumor immunity in dMMR colorectal cancers requires interferon-induced CCL5 and CXCL10

Colorectal cancers (CRCs) deficient in DNA mismatch repair (dMMR) are heavily infiltrated by CD8+ tumor infiltrating lymphocytes (TILs) and are associated with a better prognosis than the majority of CRCs. The immunogenicity of dMMR CRCs is commonly attributed to abundant neoantigen generation due to their extreme genomic instability. However, lack of neoantigenic overlap between these and other CRCs necessitates study of antigen-independent mechanisms of immune activation by dMMR CRCs in order identify therapeutic strategies for treating MMR proficient CRCs. We show here using organoid cocultures and orthotopic models that a critical component of dMMR CRCs immunogenicity is the activation and recruitment of systemic CD8+ T cells into the tumor epithelium by overexpression of the chemokines CCL5 and CXCL10. This is dependent on endogenous activation of the cGAS/STING and IFN signaling pathways by the damaged DNA in dMMR CRCs. These signaling pathways remain sensitive to exogenous stimulation in other CRCs, identifying an attractive therapeutic avenue for increasing TIL infiltration into normally immune resistant CRC subtypes. We have thus identified a key neoantigen-independent mechanism that underlies the ability for dMMR CRCs to recruit TILs into the tumor epithelium. Given that TIL recruitment is a prerequisite for effective tumor killing either by the endogenous immune system or in the context of immunotherapies, treatments that activate IFN-induced chemokine-production by tumor cells promise to improve the prognosis of patients with many different CRC subsets. Statement of SignificanceA critical component of antitumor immunity in dMMR CRCs is their ability to recruit T cells into the tumor epithelium as a prerequisite to tumor cell killing. This occurs because their extensive genomic instability leads to endogenous activation of cGAS/STING and overexpression of CCL5 and CXCL10.

cancer biology↗

bioRxiv2018

Affective flexibility without perceptual awareness

In an ever-changing environment, survival depends on learning which stimuli represent threat, and also on updating such associations when circumstances shift. Humans can acquire physiological responses to threat-associated stimuli even when they are unaware of them, but the role of awareness in updating threat contingencies remains unknown. This complex process - generating novel responses while simultaneously suppressing learned ones - relies on distinct neural mechanisms from initial learning, and has only been shown with awareness. Can it occur unconsciously? Here we show that it can. Participants underwent classical threat conditioning to visual stimuli that were suppressed from their awareness. One of two images was paired with an electric shock; halfway through the experiment, contingencies were reversed and the shock was paired with the other image. We found that physiological responses reflected changes in stimulus-threat pairings independently of stimulus awareness, demonstrating the sophistication of unconscious affective flexibility.

neuroscience↗