Zehra Yildirim

All Publications

• Protocol to study electrophysiological properties of hPSC-derived 3D cardiac organoids using MEA and sharp electrode techniques. STAR protocols Venkateshappa, R., Yildirim, Z., Zhao, S. R., Wu, M. A., Vacante, F., Abilez, O. J., Wu, J. C. 2024; 5 (4): 103406

  Abstract

  Continuing advancements in human pluripotent stem cell (hPSC)-derived complex three-dimensional (3D) cardiac tissues require the development of novel technologies or adaptation of existing technologies to understand the physiology of the derived 3D cardiac tissues. In this protocol, we describe the use of multielectrode array (MEA) and sharp electrode electrophysiology techniques to investigate the electrical properties of 3D cardiac organoids. This protocol deciphers the electrical behavior of 3D cardiac organoids at both the single-cell level and tissue level.

  View details for DOI 10.1016/j.xpro.2024.103406

  View details for PubMedID 39514393

• Next-Gen Therapeutics: Pioneering Drug Discovery with iPSCs, Genomics, AI, and Clinical Trials in a Dish. Annual review of pharmacology and toxicology Yildirim, Z., Swanson, K., Wu, X., Zou, J., Wu, J. 2024

  Abstract

  In the high-stakes arena of drug discovery, the journey from bench to bedside is hindered by a daunting 92% failure rate, primarily due to unpredicted toxicities and inadequate therapeutic efficacy in clinical trials. The FDA Modernization Act 2.0 heralds a transformative approach, advocating for the integration of alternative methods to conventional animal testing, including cell-based assays that employ human induced pluripotent stem cell (iPSC)-derived organoids, and organ-on-a-chip technologies, in conjunction with sophisticated artificial intelligence (AI) methodologies. Our review explores the innovative capacity of iPSC-derived clinical trial in a dish models designed for cardiovascular disease research. We also highlight how integrating iPSC technology with AI can accelerate the identification of viable therapeutic candidates, streamline drug screening, and pave the way toward more personalized medicine. Through this, we provide a comprehensive overview of the current landscape and future implications of iPSC and AI applications being navigated by the research community and pharmaceutical industry.

  View details for DOI 10.1146/annurev-pharmtox-022724-095035

  View details for PubMedID 39284102

• Clinical trials in-a-dish for cardiovascular medicine. European heart journal Wu, X., Swanson, K., Yildirim, Z., Liu, W., Liao, R., Wu, J. C. 2024

  Abstract

  Cardiovascular diseases persist as a global health challenge that requires methodological innovation for effective drug development. Conventional pipelines relying on animal models suffer from high failure rates due to significant interspecies variation between humans and animal models. In response, the recently enacted Food and Drug Administration Modernization Act 2.0 encourages alternative approaches including induced pluripotent stem cells (iPSCs). Human iPSCs provide a patient-specific, precise, and screenable platform for drug testing, paving the way for cardiovascular precision medicine. This review discusses milestones in iPSC differentiation and their applications from disease modelling to drug discovery in cardiovascular medicine. It then explores challenges and emerging opportunities for the implementation of 'clinical trials in-a-dish'. Concluding, this review proposes a framework for future clinical trial design with strategic incorporations of iPSC technology, microphysiological systems, clinical pan-omics, and artificial intelligence to improve success rates and advance cardiovascular healthcare.

  View details for DOI 10.1093/eurheartj/ehae519

  View details for PubMedID 39270727

• Generation of two iPSC lines from long QT syndrome patients carrying SNTA1 variants. Stem cell research Jimenez-Tellez, N., Vera, C. D., Yildirim, Z., Vicente Guevara, J., Zhang, T., Wu, J. C. 2022; 66: 103003

  Abstract

  Long QT syndrome (LQTS) is an inherited cardiovascular disorder characterized by electrical conduction abnormalities leading to arrhythmia, fainting, seizures, and an increased risk of sudden death. There are over 15 genes involved in causing LQTS, including SNTA1. Here we generated two human-induced pluripotent stem cell (iPSC) lines from two LQT patients carrying a missense mutation in SNTA1 (c.1088A>C). Both lines showed normal morphological properties, expressed pluripotency markers, showed a normal karyotype profile, and had the ability to differentiate into the three germ layers, making them a valuable tool to model LQTS to investigate the pathological mechanisms related to this SNTA1 variant.

  View details for DOI 10.1016/j.scr.2022.103003

  View details for PubMedID 36528013

• Generation of two induced pluripotent stem cell lines from dilated cardiomyopathy patients caused by heterozygous mutations in the HCN4 gene. Stem cell research Yildirim, Z., Kojic, A., Yan, C. D., Wu, M. A., Vagelos, R., Wu, J. C. 2022; 65: 102951

  Abstract

  Dilated cardiomyopathy (DCM) is a progressive heart muscle disease that can culminate with heart failure and death. Mutations in several genes can cause DCM, including hyperpolarization-activated cyclic nucleotide-gated channel (HCN4), which has a critical function in the autonomic control of the heart rate. Here, we generated two human induced pluripotent stem cell (iPSC) lines generated from two DCM patients carrying variants in the HCN4 gene (c.2587G > T and c.2846G > A). Both lines display normal karyotype, typical morphology of pluripotent stem cells, and differentiate into all three germ layers in vitro. These lines are valuable resources for studying the pathological mechanisms of DCM.

  View details for DOI 10.1016/j.scr.2022.102951

  View details for PubMedID 36332467

• ER Stress-Induced Sphingosine-1-Phosphate Lyase Phosphorylation Potentiates the Mitochondrial Unfolded Protein Response. Journal of lipid research Yildirim, A. D., Citir, M., Dogan, A. E., Veli, Z., Yildirim, Z., Tufanli, O., Traynor Kaplan, A., Schultz, C., Erbay, E. 2022: 100279

  Abstract

  The unfolded protein response (UPR) is an elaborate signaling network that evolved to maintain proteostasis in the endoplasmic reticulum (ER) and mitochondria (mt). These organelles are functionally and physically associated and consequently, their stress responses are often intertwined. It is unclear how these two adaptive stress responses are coordinated during ER stress. The inositol-requiring enzyme-1 (IRE1), a central ER stress sensor and proximal regulator of the UPRER, harbors dual kinase and endoribonuclease (RNase) activities. IRE1 RNase activity initiates the transcriptional layer of the UPRER, but IRE1's kinase substrate(s) and their functions are largely unknown. Here, we discovered that sphingosine 1-phosphate (S1P) lyase (SPL), the enzyme that degrades S1P, is a substrate for the mammalian IRE1 kinase. Our data show that IRE1-dependent SPL phosphorylation inhibits SPL's enzymatic activity, resulting in increased intracellular S1P levels. S1P has previously been shown to induce the activation of mitochondrial UPR (UPRmt) in nematodes. We determined that IRE1 kinase-dependent S1P induction during ER stress potentiates UPRmt signaling in mammalian cells. Phosphorylation of eukaryotic translation initiation factor 2alpha (eif2alpha) is recognized as a critical molecular event for UPRmt activation in mammalian cells. Our data further demonstrate that inhibition of the IRE1-SPL axis abrogates the activation of two eif2alpha kinases, namely double-stranded RNA-activated protein kinase (PKR) and PKR-like ER kinase (PERK) upon ER stress. These findings show that the IRE1-SPL axis plays a central role in coordinating the adaptive responses of both organelles to ER stress in mammalian cells.

  View details for DOI 10.1016/j.jlr.2022.100279

  View details for PubMedID 36100091

• PACT Establishes a Post-transcriptional Brake on Mitochondrial Biogenesis by Promoting the Maturation of miR-181c. The Journal of biological chemistry Dogan, A. E., Hamid, S. M., Yildirim, A. D., Yildirim, Z., Sen, G., Riera, C. E., Gottlieb, R. A., Erbay, E. 2022: 102050

  Abstract

  The double-stranded RNA-dependent protein kinase (PKR) activating protein (PACT), an RNA-binding protein (RNAbp) that is part of the RNA-induced silencing complex (RISC), plays a key role in microRNA (miR)-mediated translational repression. Previous studies showed that PACT regulates the expression of various miRs, selects the miR strand to be loaded onto RISC, and determines proper miR length. Apart from PACT's role in mediating the anti-viral response in immune cells, what PACT does in other cell types is unknown. Strikingly, it has also been shown that cold exposure leads to marked downregulation of PACT protein in mouse brown adipose tissue (BAT), where mitochondrial biogenesis and metabolism play a central role. Here, we show that PACT establishes a post-transcriptional brake on mitochondrial biogenesis (mitobiogenesis) by promoting the maturation of miR-181c, a key suppressor of mitobiogenesis that has been shown to target mitochondrial Complex IV subunit I (Mtco1) and Sirtuin 1 (Sirt1). Consistently, we found that a partial reduction in PACT expression is sufficient to enhance mitobiogenesis in brown adipocytes in culture as well as during BAT activation in mice. In conclusion, we demonstrate an unexpected role for PACT in the regulation of mitochondrial biogenesis and energetics in cells and BAT.

  View details for DOI 10.1016/j.jbc.2022.102050

  View details for PubMedID 35598827

• Intercepting IRE1 kinase-FMRP signaling prevents atherosclerosis progression EMBO MOLECULAR MEDICINE Yildirim, Z., Baboo, S., Hamid, S. M., Dogan, A. E., Tufanli, O., Robichaud, S., Emerton, C., Diedrich, J. K., Vatandaslar, H., Nikolos, F., Gu, Y., Iwawaki, T., Tarling, E., Ouimet, M., Nelson, D. L., Yates, J. R., Walter, P., Erbay, E. 2022: e15344

  Abstract

  Fragile X Mental Retardation protein (FMRP), widely known for its role in hereditary intellectual disability, is an RNA-binding protein (RBP) that controls translation of select mRNAs. We discovered that endoplasmic reticulum (ER) stress induces phosphorylation of FMRP on a site that is known to enhance translation inhibition of FMRP-bound mRNAs. We show ER stress-induced activation of Inositol requiring enzyme-1 (IRE1), an ER-resident stress-sensing kinase/endoribonuclease, leads to FMRP phosphorylation and to suppression of macrophage cholesterol efflux and apoptotic cell clearance (efferocytosis). Conversely, FMRP deficiency and pharmacological inhibition of IRE1 kinase activity enhances cholesterol efflux and efferocytosis, reducing atherosclerosis in mice. Our results provide mechanistic insights into how ER stress-induced IRE1 kinase activity contributes to macrophage cholesterol homeostasis and suggests IRE1 inhibition as a promising new way to counteract atherosclerosis.

  View details for DOI 10.15252/emmm.202115344

  View details for Web of Science ID 000758718600001

  View details for PubMedID 35191199

• S-Adenosylmethionine Inhibits La Ribonucleoprotein Domain Family Member 1 in Murine Liver and Human Liver Cancer Cells. Hepatology (Baltimore, Md.) Ramani, K., Robinson, A. E., Berlind, J., Fan, W., Abeynayake, A., Binek, A., Barbier-Torres, L., Noureddin, M., Nissen, N. N., Yildirim, Z., Erbay, E., Mato, J. M., Van Eyk, J. E., Lu, S. C. 2021

  Abstract

  BACKGROUND & AIMS: Methionine adenosyltransferase 1A (MAT1A) is responsible for S-adenosylmethionine (SAMe) biosynthesis in the liver. Mice lacking Mat1a have hepatic SAMe depletion, develop non-alcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC) spontaneously. Several kinases are activated in Mat1a knockout (KO) mice livers. However, the phosphos-proteome has not been characterized and whether they contribute to liver pathology is largely unknown. Our study aimed to fill this gap.APPROACH & RESULTS: We performed phospho-proteomics in Mat1a KO mice livers with and without SAMe treatment to identify SAMe-dependent changes that may contribute to liver pathology. Our studies used Mat1a KO mice at different ages treated with and without SAMe, cell lines, in vitro translation and kinase assays, and human liver specimens. We found the most striking change was hyperphosphorylation and increased content of La-Related Protein 1 (LARP1), which in the unphosphorylated form negatively regulates translation of 5'-terminal oligopyrimidine (TOP)-containing mRNAs. Consistently, multiple TOP proteins are induced in the KO livers. The translation of TOP mRNAs RPS3 and RPL18 was enhanced by LARP1 overexpression in liver cancer cells. We identified LARP1-T449 as a novel, SAMe-sensitive phospho-site of cyclin-dependent kinase 2 (CDK2). Knocking down CDK2 lowered LARP1 phosphorylation and prevented LARP1 overexpression mediated increase in translation. LARP1-T449 phosphorylation induced global translation, cell growth, migration, invasion, and expression of oncogenic TOP-ribosomal proteins in HCC cells. LARP1 expression is increased in human NASH and HCC.CONCLUSION: Our results reveal a novel SAMe-sensitive mechanism of LARP1 phosphorylation that may be involved in the progression of NASH to HCC.

  View details for DOI 10.1002/hep.32130

  View details for PubMedID 34449924

• Inositol-requiring enzyme-1 regulates phosphoinositide signaling lipids and macrophage growth EMBO REPORTS Hamid, S., Citir, M., Terzi, E., Cimen, I., Yildirim, Z., Dogan, A., Kocaturk, B., Onat, U., Arditi, M., Weber, C., Traynor-Kaplan, A., Schultz, C., Erbay, E. 2020; 21 (12): e51462

  Abstract

  The ER-bound kinase/endoribonuclease (RNase), inositol-requiring enzyme-1 (IRE1), regulates the phylogenetically most conserved arm of the unfolded protein response (UPR). However, the complex biology and pathology regulated by mammalian IRE1 cannot be fully explained by IRE1's one known, specific RNA target, X box-binding protein-1 (XBP1) or the RNA substrates of IRE1-dependent RNA degradation (RIDD) activity. Investigating other specific substrates of IRE1 kinase and RNase activities may illuminate how it performs these diverse functions in mammalian cells. We report that macrophage IRE1 plays an unprecedented role in regulating phosphatidylinositide-derived signaling lipid metabolites and has profound impact on the downstream signaling mediated by the mammalian target of rapamycin (mTOR). This cross-talk between UPR and mTOR pathways occurs through the unconventional maturation of microRNA (miR) 2137 by IRE1's RNase activity. Furthermore, phosphatidylinositol (3,4,5) phosphate (PI(3,4,5)P3 ) 5-phosphatase-2 (INPPL1) is a direct target of miR-2137, which controls PI(3,4,5)P3 levels in macrophages. The modulation of cellular PI(3,4,5)P3 /PIP2 ratio and anabolic mTOR signaling by the IRE1-induced miR-2137 demonstrates how the ER can provide a critical input into cell growth decisions.

  View details for DOI 10.15252/embr.202051462

  View details for Web of Science ID 000583773600001

  View details for PubMedID 33140520

  View details for PubMedCentralID PMC7726810

• Double bond configuration of palmitoleate is critical for atheroprotection MOLECULAR METABOLISM Cimen, I., Yildirim, Z., Dogan, A., Yildirim, A., Tufanli, O., Onat, U., UyenThao Nguyen, Watkins, S. M., Weber, C., Erbay, E. 2019; 28: 58-72

  Abstract

  Saturated and trans fat consumption is associated with increased cardiovascular disease (CVD) risk. Current dietary guidelines recommend low fat and significantly reduced trans fat intake. Full fat dairy can worsen dyslipidemia, but recent epidemiological studies show full-fat dairy consumption may reduce diabetes and CVD risk. This dairy paradox prompted a reassessment of the dietary guidelines. The beneficial metabolic effects in dairy have been claimed for a ruminant-derived, trans fatty acid, trans-C16:1n-7 or trans-palmitoleate (trans-PAO). A close relative, cis-PAO, is produced by de novo lipogenesis and mediates inter-organ crosstalk, improving insulin-sensitivity and alleviating atherosclerosis in mice. These findings suggest trans-PAO may be a useful substitute for full fat dairy, but a metabolic function for trans-PAO has not been shown to date.Using lipidomics, we directly investigated trans-PAO's impact on plasma and tissue lipid profiles in a hypercholesterolemic atherosclerosis mouse model. Furthermore, we investigated trans-PAO's impact on hyperlipidemia-induced inflammation and atherosclerosis progression in these mice.Oral trans-PAO supplementation led to significant incorporation of trans-PAO into major lipid species in plasma and tissues. Unlike cis-PAO, however, trans-PAO did not prevent organelle stress and inflammation in macrophages or atherosclerosis progression in mice.A significant, inverse correlation between circulating trans-PAO levels and diabetes incidence and cardiovascular mortality has been reported. Our findings show that trans-PAO can incorporate efficiently into the same pools that its cis counterpart is known to incorporate into. However, we found trans-PAO's anti-inflammatory and anti-atherosclerotic effects are muted due to its different structure from cis-PAO.

  View details for DOI 10.1016/j.molmet.2019.08.004

  View details for Web of Science ID 000487684000006

  View details for PubMedID 31422082

  View details for PubMedCentralID PMC6822256

• Periplasmic and extracellular production of cellulase from recombinant Escherichia coli cells JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY Yildirim, Z., Celik, E. 2017; 92 (2): 319-324

  View details for DOI 10.1002/jctb.5008

  View details for Web of Science ID 000396893400008