Biology subjects

Rios, A.

Publications and source records attributed to Rios, A..

6 recordsLinked to original sources

bioRxiv2024

Metabolic regulation of RNA methylation by the m6A-reader IGF2BP3

The interplay of RNA modifications - deposited by "writers", removed by "erasers" and identified by RNA binding proteins known as "readers" - forms the basis of the epitranscriptomic gene regulation hypothesis. Recent studies have identified the oncofetal RNA-binding protein IGF2BP3 as a "reader" of the N6-methyladenosine (m6A) modification and crucial for regulating gene expression. Yet, how its function as a reader overlaps with its critical oncogenic function in leukemia remains an open question. Here, we report the novel finding that the reader IGF2BP3 reprograms cellular metabolism, resulting in an altered ability of the "writers" to modify the epitranscriptome. In leukemia cells, IGF2BP3 supports increased glycolytic flux and one-carbon metabolism, leading to increased production of S-adenosyl methionine (SAM), a key substrate for methylation reactions within the cell. IGF2BP3 directly regulates the translation of MAT2B, the regulatory subunit of the methionine-adenosyltransferase complex, which is the final enzyme in a pathway leading to SAM production. This, in turn, results in increased m6A modifications on RNA, resulting in positive feedback regulation. This novel mechanism illustrates how metabolism mutually acts with epitranscriptomic modifications, underscoring the pervasive impact of IGF2BP3 in gene regulatory mechanisms governing a broad range of cancer-specific processes.

cancer biology↗

bioRxiv2024

BEHAV3D Tumor Profiler to map heterogeneous cancer cell behavior in the tumor microenvironment

Intravital microscopy (IVM) enables live imaging of animals at single-cell level, offering essential insights into cancer progression. This technique allows for the observation of single-cell behaviors within their natural 3D tissue environments, shedding light on how genetic and microenvironmental changes influence the complex dynamics of tumors. IVM generates highly complex datasets that often exceed the analytical capacity of traditional uni-parametric approaches, which can neglect single-cell heterogeneous in vivo behavior and limit insights into microenvironmental influences on cellular behavior. To overcome these limitations, we present BEHAV3D Tumor Profiler (BEHAV3D-TP), a computational framework that enables unbiased single-cell classification based on a range of morphological, environmental and dynamic single cell features. BEHAV3D-TP integrates with widely used 2D and 3D image processing pipelines, enabling researchers without advanced computational expertise to profile cancer and healthy cell dynamics in IVM data. Here, we apply BEHAV3D-TP to study diffuse midline glioma (DMG), a highly aggressive pediatric brain tumor characterized by invasive progression. By extending BEHAV3D-TP to incorporate tumor microenvironment (TME) data from IVM or fixed correlative imaging, we demonstrate that distinct migratory behaviors of DMG cells are associated with specific TME components, including tumor-associated macrophages and vasculature. BEHAV3D-TP enhances the accessibility of computational tools for analyzing the complex behaviors of cancer cells and their interactions with the TME in IVM data.

cancer biology↗

bioRxiv2024

Pro-inflammatory macrophage activation does not require inhibition of mitochondrial respiration

Pro-inflammatory macrophage activation is a hallmark example of how mitochondria serve as signaling organelles. Upon classical macrophage activation, oxidative phosphorylation sharply decreases and mitochondria are repurposed to accumulate signals that amplify effector function. However, evidence is conflicting as to whether this collapse in respiration is essential or largely dispensable. Here we systematically examine this question and show that reduced oxidative phosphorylation is not required for pro-inflammatory macrophage activation. Only stimuli that engage both MyD88- and TRIF-linked pathways decrease mitochondrial respiration, and different pro-inflammatory stimuli have varying effects on other bioenergetic parameters. Additionally, pharmacologic and genetic models of electron transport chain inhibition show no direct link between respiration and pro-inflammatory activation. Studies in mouse and human macrophages also reveal accumulation of the signaling metabolites succinate and itaconate can occur independently of characteristic breaks in the TCA cycle. Finally, in vivo activation of peritoneal macrophages further demonstrates that a pro-inflammatory response can be elicited without reductions to oxidative phosphorylation. Taken together, the results suggest the conventional model of mitochondrial reprogramming upon macrophage activation is incomplete.

immunology↗

bioRxiv2024

The metabolic cofactor Coenzyme A enhances alternative macrophage activation via MyD88-linked signaling

Metabolites and metabolic co-factors can shape the innate immune response, though the pathways by which these molecules adjust inflammation remain incompletely understood. Here we show that the metabolic cofactor Coenzyme A (CoA) enhances IL-4 driven alternative macrophage activation [m(IL-4)] in vitro and in vivo. Unexpectedly, we found that perturbations in intracellular CoA metabolism did not influence m(IL-4) differentiation. Rather, we discovered that exogenous CoA provides a weak TLR4 signal which primes macrophages for increased receptivity to IL-4 signals and resolution of inflammation via MyD88. Mechanistic studies revealed MyD88-linked signals prime for IL-4 responsiveness, in part, by reshaping chromatin accessibility to enhance transcription of IL-4-linked genes. The results identify CoA as a host metabolic co-factor that influences macrophage function through an extrinsic TLR4-dependent mechanism, and suggests that damage-associated molecular patterns (DAMPs) can prime macrophages for alternative activation and resolution of inflammation.

immunology↗

bioRxiv2023

Highly multiplexed, image-based pooled screens in primary cells and tissues with PerturbView

Optical pooled screening (OPS) is a highly scalable method for linking image-based phenotypes with cellular perturbations. However, it has thus far been restricted to relatively low-plex phenotypic readouts in cancer cell lines in culture, due to limitations associated with in situ sequencing (ISS) of perturbation barcodes. Here, we developed PerturbView, an OPS technology that leverages in vitro transcription (IVT) to amplify barcodes prior to ISS, enabling screens with highly multiplexed phenotypic readouts across diverse systems, including primary cells and tissues. We demonstrate PerturbView in iPSC-derived neurons, primary immune cells, and tumor tissue sections from animal models. In a screen of immune signaling pathways in primary bone marrow-derived macrophages, PerturbView uncovered both known and novel regulators of NF{kappa}B signaling. Furthermore, we combined PerturbView with spatial transcriptomics in tissue sections from a mouse xenograft model, paving the way to in vivo screens with rich optical and transcriptomic phenotypes. PerturbView broadens the scope of OPS to a wide range of models and applications.

systems biology↗

bioRxiv2023

Sequential Optimal Experimental Design of Perturbation Screens Guided by Multi-modal Priors

Understanding a cells expression response to genetic perturbations helps to address important challenges in biology and medicine, including the function of gene circuits, discovery of therapeutic targets and cell reprogramming and engineering. In recent years, Perturb-seq, pooled genetic screens with single cell RNA-seq (scRNA-seq) readouts, has emerged as a common method to collect such data. However, irrespective of technological advances, because combinations of gene perturbations can have unpredictable, non-additive effects, the number of experimental configurations far exceeds experimental capacity, and for certain cases, the number of available cells. While recent machine learning models, trained on existing Perturb-seq data sets, can predict perturbation outcomes with some degree of accuracy, they are currently limited by sub-optimal training set selection and the small number of cell contexts of training data, leading to poor predictions for unexplored parts of perturbation space. As biologists deploy Perturb-seq across diverse biological systems, there is an enormous need for algorithms to guide iterative experiments while exploring the large space of possible perturbations and their combinations. Here, we propose a sequential approach for designing Perturb-seq experiments that uses the model to strategically select the most informative perturbations at each step for subsequent experiments. This enables a significantly more efficient exploration of the perturbation space, while predicting the effect of the rest of the unseen perturbations with high-fidelity. Analysis of a previous large-scale Perturb-seq experiment reveals that our setting is severely restricted by the number of examples and rounds, falling into a non-conventional active learning regime called "active learning on a budget". Motivated by this insight, we develop IO_SCPLOWTERC_SCPLOWPO_SCPLOWERTC_SCPLOW, a novel active learning method that exploits rich and multi-modal prior knowledge in order to efficiently guide the selection of subsequent perturbations. Using prior knowledge for this task is novel, and crucial for successful active learning on a budget. We validate IO_SCPLOWTERC_SCPLOWPO_SCPLOWERTC_SCPLOW using insilico benchmarking of active learning, constructed from a large-scale CRISPRi Perturb-seq data set. We find that IO_SCPLOWTERC_SCPLOWPO_SCPLOWERTC_SCPLOW outperforms other active learning strategies by reaching comparable accuracy at only a third of the number of perturbations profiled as the next best method. Overall, our results demonstrate the potential of sequentially designing perturbation screens through IO_SCPLOWTERC_SCPLOWPO_SCPLOWERTC_SCPLOW.

bioinformatics↗