Biology subjects

Gutierrez, J. A.

Publications and source records attributed to Gutierrez, J. A..

6 recordsLinked to original sources

bioRxiv2025

Topoisomerase II inhibitors CX-5461 and Doxorubicin differ in their cardiotoxicity profiles

CX-5461 (CX) is a chemotherapeutic drug currently under investigation for the treatment of late-stage cancers. While CX was first described as an RNA polymerase I inhibitor, it has recently been shown to primarily inhibit the beta isoform of topoisomerase II. This isoform is also inhibited by anthracycline drugs including Doxorubicin (DOX) and mediates the toxic effects of these drugs on the heart. It is unclear whether CX will similarly cause cardiotoxicity. We therefore designed a study to test the effects of CX compared to DOX on iPSC-derived cardiomyocytes from six individuals. While both CX and DOX induce cell death in cardiomyocytes, CX is 20-fold less cytotoxic than DOX. At sub-lethal doses, DOX induces DNA damage, while CX does not. Transcriptome profiling following treatment with two sub-micromolar concentrations of both drugs over time reveals that DOX induces thousands of gene expression changes compared to hundreds induced by CX. Comparison of gene expression trajectories across drugs reveals that genes that respond to CX also respond to DOX, while most DOX response genes are drug specific. Shared response genes correspond to pathways related to chromosome segregation and DNA replication. CX does not affect the expression of any of the genes in functionally-validated loci associated with DOX-induced cardiotoxicity. Our data demonstrate that CX treatment of cardiomyocytes induces gene expression changes that mirror a subset of those induced by DOX; however these changes do not coincide with the cardiotoxicity observed with DOX treatment.

genomics↗

bioRxiv2025

Anthracyclines induce global changes in cardiomyocyte chromatin accessibility that overlap with cardiovascular disease loci

Breast cancer drugs including anthracyclines (ACs) and Trastuzumab increase the risk for cardiovascular diseases (CVDs) such as atrial fibrillation (AF) and heart failure (HF) that ultimately affect the heart muscle. These CVDs are associated with hundreds of genetic variants in non- coding regions of the genome. However, how these drugs affect the regulatory potential of the non-coding genome of the heart and CVD risk loci is unknown. We therefore measured global chromatin accessibility across iPSC-derived cardiomyocytes from four individuals treated with the ACs, Doxorubicin, Epirubicin, and Daunorubicin, a related non-AC, Mitoxantrone, and the monoclonal antibody Trastuzumab, or a vehicle control for three and 24 hours. We identified 155,557 high-confidence regions of open chromatin across 48 samples where the major sources of variation are associated with drug type and time. Jointly modeling the data revealed three accessibility response signatures denoted as early-acute, early-sustained, and late that correspond to 67,329 regions that open or close in response to drug treatment. Sequences associated with drug-induced chromatin opening contain motifs for DNA damage-associated transcription factors including p53 and ZBTB14, and associate with increases in active histone acetylation and gene expression. 21 AF- and HF-associated SNPs directly overlap with regions associated with drug-induced opening. A shared intronic HF and AF SNP, rs3176326, that is also an eQTL for CDKN1A in heart tissue, associates with increased chromatin accessibility, histone acetylation, and CDKN1A expression in response to all ACs. Our results demonstrate large-scale changes in chromatin accessibility in cardiomyocytes treated with ACs, which correspond to several regions harboring CVD risk loci. Author summaryAnthracyclines are a widely used class of breast cancer drugs that are linked to cardiac toxicity and the development of heart disease in some women. There are hundreds of genetic variants that associate with risk for heart disease; however their role and mechanism of action in drug- induced toxicity is unclear given that most reside in the non-coding genome. We therefore tested the effects of five breast cancer drugs on genome-wide chromatin accessibility using induced pluripotent stem cell-derived cardiomyocytes. We found tens of thousands of chromatin regions that change in accessibility after drug treatment. Regions with increased accessibility contain sequences that have been shown to bind DNA damage-associated transcription factors, and associate with increases in nearby gene expression. We find 21 heart disease-associated genetic variants in regions that increase in chromatin accessibility following treatment. This suggests that cancer drugs have large effects on the non-coding genome of heart cells including at regions associated with heart disease. This research contributes to our understanding of how genetic variants associated with disease exert their effects.

genomics↗

bioRxiv2024

deadtrees.earth - An Open-Access and Interactive Database for Centimeter-Scale Aerial Imagery to Uncover Global Tree Mortality Dynamics

Excessive tree mortality is a global concern and remains poorly understood as it is a complex phenomenon. We lack global and temporally continuous coverage on tree mortality data. Ground-based observations on tree mortality, e.g., derived from national inventories, are very sparse, not standardized and not spatially explicit. Earth observation data, combined with supervised machine learning, offer a promising approach to map tree mortality over time. However, global-scale machine learning requires broad training data covering a wide range of environmental settings and forest types. Drones provide a cost-effective source of training data by capturing high-resolution orthophotos of tree mortality events at sub-centimeter resolution. Here, we introduce deadtrees.earth, an open-access platform hosting more than a thousand centimeter-resolution orthophotos, covering already more than 300,000 ha, of which more than 58,000 ha are fully annotated. This community-sourced and rigorously curated dataset shall serve as a foundation for a global initiative to gather comprehensive reference data. In concert with Earth observation data and machine learning it will serve to uncover tree mortality patterns from local to global scales. This will provide the foundation to attribute tree mortality patterns to environmental changes or project tree mortality dynamics to the future. Thus, the open and interactive nature of deadtrees.earth together with the collective effort of the community is meant to continuously increase our capacity to uncover and understand tree mortality patterns.

ecology↗

bioRxiv2024

DNA damage-associated protein co-expression network in cardiomyocytes informs on tolerance to genetic variation and disease

Cardiovascular disease (CVD) is associated with both genetic variants and environmental factors. One unifying consequence of the molecular risk factors in CVD is DNA damage, which must be repaired by DNA damage response proteins. However, the impact of DNA damage on global cardiomyocyte protein abundance, and its relationship to CVD risk remains unclear. We therefore treated induced pluripotent stem cell-derived cardiomyocytes with the DNA-damaging agent Doxorubicin (DOX) and a vehicle control, and identified 4,178 proteins that contribute to a network comprising 12 co-expressed modules and 403 hub proteins with high intramodular connectivity. Five modules correlate with DOX and represent distinct biological processes including RNA processing, chromatin regulation and metabolism. DOX-correlated hub proteins are depleted for proteins that vary in expression across individuals due to genetic variation but are enriched for proteins encoded by loss-of-function intolerant genes. While proteins associated with genetic risk for CVD, such as arrhythmia are enriched in specific DOX-correlated modules, DOX-correlated hub proteins are not enriched for known CVD risk proteins. Instead, they are enriched among proteins that physically interact with CVD risk proteins. Our data demonstrate that DNA damage in cardiomyocytes induces diverse effects on biological processes through protein co-expression modules that are relevant for CVD, and that the level of protein connectivity in DNA damage-associated modules influences the tolerance to genetic variation.

genetics↗

bioRxiv2023

Anthracycline-induced cardiotoxicity associates with a shared gene expression response signature to TOP2-inhibiting breast cancer drugs in cardiomyocytes

TOP2 inhibitors (TOP2i) are effective drugs for breast cancer treatment. However, they can cause cardiotoxicity in some women. The most widely used TOP2i include anthracyclines (AC) Doxorubicin (DOX), Daunorubicin (DNR), Epirubicin (EPI), and the anthraquinone Mitoxantrone (MTX). It is unclear whether women would experience the same adverse effects from all drugs in this class, or if specific drugs would be preferable for certain individuals based on their cardiotoxicity risk profile. To investigate this, we studied the effects of treatment of DOX, DNR, EPI, MTX, and an unrelated monoclonal antibody Trastuzumab (TRZ) on iPSC-derived cardiomyocytes (iPSC-CMs) from six healthy females. All TOP2i induce cell death at concentrations observed in cancer patient serum, while TRZ does not. A sub-lethal dose of all TOP2i induces limited cellular stress but affects calcium handling, a function critical for cardiomyocyte contraction. TOP2i induce thousands of gene expression changes over time, giving rise to four distinct gene expression response signatures, denoted as TOP2i early-acute, early-sustained, and late response genes, and non-response genes. TOP2i early response genes are enriched in chromatin regulators, which mediate AC sensitivity across breast cancer patients. However, there is increased transcriptional variability between individuals following AC treatments. To investigate potential genetic effects on response variability, we first identified a reported set of expression quantitative trait loci (eQTLs) uncovered following DOX treatment in iPSC-CMs. Indeed, DOX response eQTLs are enriched in genes that respond to all TOP2i. Next, we identified eight genes in loci associated with AC toxicity by GWAS or TWAS. All eight genes, including RARG and SLC28A3, respond to at least two ACs, and their expression correlates with the release of cardiotoxicity markers. Our data demonstrate that TOP2i induce thousands of shared gene expression changes in cardiomyocytes, including genes near SNPs associated with inter-individual variation in response to DOX treatment and AC-induced cardiotoxicity. Author summaryAnthracycline drugs such as Doxorubicin are effective treatments for breast cancer; however, they can cause cardiotoxicity in some women. It is unclear whether women would experience the same toxicity for all drugs in this class, or whether specific drugs would be better tolerated in specific individuals. We used an in vitro system of induced pluripotent stem cell-derived cardiomyocytes from six healthy females to test the effects of five breast cancer drugs on cell heath and global gene expression. We identified a strong shared cellular and gene expression response to drugs from the same class. However, there is more variation in gene expression levels between individuals following treatment with each anthracycline compared to untreated cells. We found that genes in regions previously associated with Doxorubicin-induced cardiotoxicity in cancer patients, respond to at least two drugs in the class. This suggests that drugs in the same class induce similar effects on an individuals heart. This work contributes to our understanding of how drug response, in the context of off-target effects, varies across individuals.

genomics↗

bioRxiv2023

SHIP1 modulation and proteome characterization of microglia

Microglia, the resident macrophage in brain, has gained significant attention due to their involvement in neurodegenerative diseases. Disease associated microglia (DAM) have been identified at sites of amyloid-beta plaques and neurodegeneration. Understanding microglial states in the aging brain has become crucial, especially with the discovery of numerous Alzheimers disease (AD) risk and protective variants in genes such as TREM2, CD33, APOE, ABCA7, PLCG2, and INPP5D, which are essential to microglia function1. Here we present a thorough examination of microglia-like cell lines and primary mouse microglia at the proteomic and transcriptomic levels to help illuminate the roles these genes and the proteins they encode play in various cell states. This analysis serves as a guide to the exploration of potential therapeutic targets in the context of neurodegeneration. INPP5D, which encodes the SHIP1 protein, is essential for microglia function. SHIP1 has emerged as a target of interest having been nominated as a therapeutic target by three teams within the Accelerating Medicines Partnership for Alzheimers Disease (AMP-AD)2. In this study, we compared the proteomic profiles of wildtype, SHIP1 heterozygous knockout, and homozygous knockout primary microglia. Our findings revealed significant proteomic alterations only in the homozygous knockout of the SHIP1 gene, revealing its impact on the microglial proteome. Additionally, we compared the proteomic and transcriptomic profiles of BV2 and HMC3 cells with primary mouse microglia because these cell lines are often used as microglial cellular models. Our results demonstrated a substantial similarity between the proteome of BV2 cells and mouse primary cells, while notable differences were observed between BV2 and human HMC3 cells, with some shared characteristics. Since SHIP1 functions as a lipid phosphatase that modulates phosphatidylinositol (PI) species, we conducted lipidomic analysis to quantify different phosphatidylinositols (PIs), phosphatidylinositol monophosphate (PIPs), and polyphosphoinositides (PPIs) in the HMC3 and BV2 cells. Under basal conditions, PI(3,4,5)P3 and PI(3,4)P2 species were detected at extremely low levels, making confident quantification challenging; however, PIP species within the overall pool were significantly changed upon SHIP1 overexpression in HMC3. This in-depth proteomic analysis of both mouse and human microglia, complemented by targeted lipidomic studies, enhances our understanding of these cellular models. The similarities between primary mouse microglia and the BV2 cell line is especially encouraging, supporting the use of this model for further investigations into the role that SHIP1 and other potential drug targets may play in the regulation of microglial states.

neuroscience↗