Biology subjects

Nelson, T. J.

Publications and source records attributed to Nelson, T. J..

7 recordsLinked to original sources

bioRxiv2026

Dual-acting Estrogen Receptor Modulator-Histone Lysine Demethylase Inhibitors

Epigenetic dysfunction and the malfunction of endocrine proteins such as estrogen receptor alpha (ER) are two key mechanisms for the sustenance of breast carcinoma. Agents that target ER signaling malfunctions are standard therapies for ER-dependent breast cancer (BCa) subtypes. Small molecule inhibitors of epigenetic modifiers, histone lysine demethylases (KDMs), have shown promise as therapeutic agents for several BCa subtypes. We demonstrated herein that the integration of ER antagonist (Tamoxifen) and agonist (17-ethinylestradiol) ligands with deferiprone (DFP)-derived KDM inhibitor moiety furnished dual-acting agents Tam-KDMi and EED-KDMi, respectively. These agents showed robust on-target effects and potent BCa cells-selective anti-proliferative activities. The Tam-KDMi are cytotoxic to both ER(+) and ER(-) BCa cells, while the lack of ER-signaling inhibition conferred an enhanced ER(-) cells cytotoxic to the EED-KDMi. Representative lead compounds Tam-KDMi DW-116 and EED-KDMi DW-088 and DW-95 significantly reduce tumor growth in murine xenograft models of ER(-) and ER(+) BCas with TGI as high as 70%. Collectively, our data showed that DW-116, DW-088 and DW-95 have a high potential as leads for the development of new agents for the treatment of BCa subtypes regardless of the tumor ER expression status.

cancer biology↗

bioRxiv2025

Transcriptomic Signature and PROTAC Strategy Revealed Histone Lysine Demethylase as a Target of Anticancer Activity of Deferiprone.

Deferiprone (DFP) is an iron chelator approved for treating iron overload in thalassemia patients. Recent observations have suggested that DFP has promising anticancer activities ascribed to several mechanisms including reduction of the intracellular free labile iron and zinc ion pools and inhibition of the activities of other intracellular targets, including ribonucleotide reductase (RNR). We previously reported that DFP inhibits the demethylase activities of several Fe(II)/- ketoglutarate dependent histone lysine demethylases (KDMs) at much lower concentrations at which it inhibits RNR activities and/or reduces the labile intracellular iron and zinc ion pools. In this study, we used RNA sequencing (RNA seq) and PROTACs strategies to validate and quantify the contribution of intracellular KDM inhibition to the antiproliferative activities of DFP. We report herein that DFP elicited gene expression signature that is largely similar to that of JIB-04, an established KDM inhibitor (KDMi), in two breast cancer (BCa) cells (MCF-7 and MDA-MD-231). Importantly, RNA seq revealed that DFP and JIB-04 downregulated the expression of hypoxia-inducible factor 1 (HIF-1), an oncogene whose expression is commonly modulated through histone demethylation mediated by KDMs and degraded by several KDMi. Moreover, DFP-derived PROTACs elicited enhanced cancer cell selective antiproliferative activities and intracellular on-target effects, downregulating several KDMs implicated in the etiology of BCa cells, including a strong degradation of KDMs 2A, 3A and 5B, and a moderate degradation of KDMs 4A-C, 5C, 6B. Collectively, our data supports KDM inhibition as a key mechanism of anticancer activity of DFP and identifies PROTAC is a viable strategy to obtain novel DFP analogs with improved potency and therapeutic index.

cancer biology↗

bioRxiv2021

Abnormal Differentiation and Proliferation of Coronary Arterial Endothelium in Hypoplastic Left Heart Syndrome

Hypoplastic left heart syndrome (HLHS) is a severe form of single ventricle congenital heart disease characterized by the underdevelopment of the left ventricle. Early serial postmortem examinations revealed high rate of coronary artery abnormalities in HLHS fetal hearts, such as thickened wall, kinking arteries and ventriculo-coronary arterial connection. However, it is unclear if there is an intrinsic defect in the HLHS coronary vessels and what the underlying molecular mechanism is. Here, we profiled both human fetal heart with an underdeveloped left ventricle (ULV) and ECs differentiated from induced pluripotent stem cells (iPSCs) derived from HLHS patients at single cell resolution. CD144+/NPR3-vascular ECs were selected and further classified as venous, arterial and late arterial subclusters. To study the arterial EC phenotype, we specifically generated iPSC-arterial ECs (AECs, CD34+CDH5+CXCR4+NT5E-/low) derived from three HLHS patients and three age-matched healthy controls. Gene ontology analysis revealed that ULV late arterial EC subcluster showed specific defects in endothelial development, proliferation, and Notch signaling compared to control. Consistently, HLHS iPSCs exhibited impaired AEC differentiation shown as the reduced CXCR4+NT5E-/low AEC progenitor population. Mature HLHS iPSC-AECs also exhibited increased G0/G1 cell cycle arrest with decreased expression of cell cycle related genes (e.g., Ki67, CCND1/2). Additionally, NOTCH targeted genes (e.g., DLL4, HEY1, GJA5) were found suppressed in both ULV AECs and HLHS iPSC-AECs compared to control. We also found the HLHS de novo mutation gene KMT2D directly regulated the transcription of NOTCH targeted genes participating in arterial differentiation and cell proliferation, contributing to the HLHS AEC dysfunctionalities. Intriguingly, the treatment of NOTCH ligand JAG1 improved cell proliferation of HLHS AECs and upregulated G1/S transition genes downstream of NOTCH pathway. In summary, our results revealed that KMT2D directly regulated transcription activity of NOTCH signaling, contributing to the poor differentiation and low proliferation of HLHS coronary AECs.

developmental biology↗

bioRxiv2019

Patient-specific functional genomics and disease modeling suggest a role for LRP2 in Hypoplastic Left Heart Syndrome

Congenital heart diseases (CHD), such as hypoplastic left heart syndrome (HLHS), are considered to have complex genetic underpinnings that are poorly understood. Here, an integrated multi-disciplinary approach was applied to identify novel genes and underlying mechanisms associated with HLHS. A family-based strategy was employed that coupled whole genome sequencing (WGS) with RNA sequencing of patient-derived induced pluripotent stem cells (iPSCs) from a sporadic HLHS proband-parent trio to identify, prioritize and functionally evaluate candidate genes in model systems. Consistent with the hypoplastic phenotype, the probands iPSCs had reduced proliferation capacity. Filtering WGS for rare de novo, recessive, and loss-of-function variants revealed 10 candidate genes with recessive variants and altered expression compared to the parents iPSCs. siRNA/RNAi-mediated knockdown in generic human iPSC-derived cardiac progenitors and in the in vivo Drosophila heart model revealed that LDL receptor related protein LRP2 and apolipoprotein APOB are required for robust hiPSC-derived cardiomyocyte proliferation and normal hear structure and function, possibly involving an oligogenic mechanism via growth-promoting WNT and SHH signaling. LRP2 was further validated as a CHD gene in a zebrafish heart model and rare variant burden testing in an HLHS cohort. Collectively, this cross-functional genetic approach to complex congenital heart disease revealed LRP2 dysfunction as a likely novel genetic driver of HLHS, and hereby established a scalable approach to decipher the oligogenic underpinnings of maladaptive left heart development. One sentence summaryWhole genome sequencing and a multi-model system candidate gene validation - human iPSC-derived cardiomyocytes and Drosophila and zebrafish hearts - identified lipoprotein LRP2 as a new potential driver in congenital heart disease and suggests a deficit in proliferation as a hallmark of hypoplastic left heart syndrome.

genetics↗

bioRxiv2019

Single-Cell RNA-Seq Reveals Endocardial Defect in Hypoplastic Left Heart Syndrome

Hypoplastic left heart syndrome (HLHS) is one of the most challenging forms of congenital heart diseases. Previous studies were mainly focused on intrinsic defects in myocardium. However, this does not sufficiently explain the abnormal development of the cardiac valve, septum, and vasculature, known to originate from the endocardium. Here, using single-cell RNA profiling, induced pluripotent stem cells, and human fetal heart tissue with an underdeveloped left ventricle, we identified a developmentally impaired endocardial population in HLHS. The intrinsic endocardial deficits contributed to abnormal endothelial to mesenchymal transition, NOTCH signaling, and extracellular matrix organization, all of which are key factors in valve formation. Consequently, endocardial abnormalities conferred reduced proliferation and maturation of cardiomyocytes through a disrupted fibronectin-integrin interaction. Several recently described HLHS de novo mutations were associated with abnormal endocardial gene and FN1 regulation and expression. Our studies provide a rationale for considering endocardial function in future regenerative strategies for HLHS.

developmental biology↗

bioRxiv2019

Mitochondrial dysfunction impairs human neuronal development and reduces neuronal network activity and synchronicity

Epilepsy, intellectual and cortical sensory deficits and psychiatric manifestations are among the most frequent manifestations of mitochondrial diseases. Yet, how mitochondrial dysfunction affects neural structure and function remains largely elusive. This is mostly due to the lack of a proper in vitro translational neuronal model system(s) with impaired energy metabolism. Leveraging the induced pluripotent stem cell technology, from a cohort of patients with the common pathogenic m.3243A>G variant of mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS), we differentiated excitatory cortical neurons (iNeurons) with normal (low heteroplasmy) and impaired (high heteroplasmy) mitochondrial function on an isogenic nuclear DNA background. iNeurons with high levels of heteroplasmy exhibited mitochondrial dysfunction, delayed neural maturation, reduced dendritic complexity and fewer functional excitatory synapses. Micro-electrode array recordings of neuronal networks with high heteroplasmy displayed reduced network activity and decreased synchronous network bursting. The impaired neural energy metabolism of iNeurons compromising the structural and functional integrity of neurons and neural networks, could be the primary driver of increased susceptibility to neuropsychiatric manifestations of mitochondrial disease.

neuroscience↗

bioRxiv2018

Engineering targeted deletions in the mitochondrial genome

Summary ParagraphMitochondria are a network of critical intracellular organelles with diverse functions ranging from energy production to cell signaling. The mitochondrial genome (mtDNA) consists of 37 genes that support oxidative phosphorylation and are prone to dysfunction that can lead to currently untreatable diseases. Further characterization of mtDNA gene function and creation of more accurate models of human disease will require the ability to engineer precise genomic sequence modifications. To date, mtDNA has been inaccessible to direct modification using traditional genome engineering tools due to unique DNA repair contexts in mitochondria1. Here, we report a new DNA modification process using sequence-specific transcription activator-like effector (TALE) proteins to manipulate mtDNA in vivo and in vitro for reverse genetics applications. First, we show mtDNA deletions can be induced in Danio rerio (zebrafish) using site-directed mitoTALE-nickases (mito-nickases). Using this approach, the protein-encoding mtDNA gene nd4 was deleted in injected zebrafish embryos. Furthermore, this DNA engineering system recreated a large deletion spanning from nd5 to atp8, which is commonly found in human diseases like Kearns-Sayre syndrome (KSS) and Pearson syndrome. Enrichment of mtDNA-deleted genomes was achieved using targeted mitoTALE-nucleases (mitoTALENs) by co-delivering both mito-nickases and mitoTALENs into zebrafish embryos. This combined approach yielded deletions in over 90% of injected animals, which were maintained through adulthood in various tissues. Subsequently, we confirmed that large, targeted deletions could be induced with this approach in human cells. In addition, we show that, when provided with a single nick on the mtDNA light strand, the binding of a terminal TALE protein alone at the intended recombination site is sufficient for deletion induction. This \"block and nick\" approach yielded engineered mitochondrial molecules with single nucleotide precision using two different targeted deletion sites. This precise seeding method to engineer mtDNA variants is a critical step for the exploration of mtDNA function and for creating new cellular and animal models of mitochondrial disease.

molecular biology↗