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Pubblicazioni recenti - cardiac stem
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In vitro model of ischemic heart failure using human induced pluripotent stem cell-derived cardiomyocytes.
JCI Insight2021 Apr;():. doi: 10.1172/jci.insight.134368.
Davis Justin, Chouman Ahmad, Creech Jeffery, Monteiro da Rocha Andre, Ponce-Balbuena Daniela, Jimenez Vazquez Eric N, Nichols Ruthann, Lozhkin Andrey, Madamanchi Nageswara R, Campbell Katherine F, Herron Todd J,
Abstract
Human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) have been used extensively to model inherited heart diseases, but hiPSC-CM models of ischemic heart disease are lacking. Here our objective was to generate an hiPSC-CM model of ischemic heart disease. To this end, hiPSCs were differentiated to functional hiPSC-CMs and then purified using either a simulated ischemia media or by using magnetic antibody-based purification targeting the non-myocyte population for depletion from the cell population. Flow cytometry analysis confirmed that each purification approach generated hiPSC-CM cultures of >94% cTnT+ cells. Following purification hiPSC-CMs were re-plated as confluent syncytial monolayers for electrophysiological phenotype analysis and protein expression by Western blotting. Metabolic selected hiPSC-CM monolayers' phenotype recapitulated many of the functional and structural hallmarks of ischemic cardiomyocytes, including: elevated diastolic calcium, diminished calcium transient amplitude, prolonged action potential duration, depolarized resting membrane potential, hypersensitivity to chemotherapy induced cardiotoxicity, depolarized mitochondrial membrane potential, depressed SERCA2a expression, reduced maximal oxygen consumption rate and abnormal response to ?1-adrenergic receptor stimulation. These findings indicate that metabolic selection of hiPSC-CMs generates cell populations with phenotype like what is well known to occur in the setting of ischemic heart failure, and thus provides a novel opportunity for study of human ischemic heart disease.
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GPR182 is an endothelium-specific atypical chemokine receptor that maintains hematopoietic stem cell homeostasis.
Proc Natl Acad Sci U S A2021 Apr;118(17):. doi: e2021596118.
Le Mercier Alan, Bonnavion Remy, Yu Weijia, Alnouri Mohamad Wessam, Ramas Sophie, Zhang Yang, Jäger Yannick, Roquid Kenneth Anthony, Jeong Hyun-Woo, Sivaraj Kishor Kumar, Cho Haaglim, Chen Xinyi, Strilic Boris, Sijmonsma Tjeerd, Adams Ralf, Schroeder Timm, Rieger Michael A, Offermanns Stefan,
Abstract
G protein-coupled receptor 182 (GPR182) has been shown to be expressed in endothelial cells; however, its ligand and physiological role has remained elusive. We found GPR182 to be expressed in microvascular and lymphatic endothelial cells of most organs and to bind with nanomolar affinity the chemokines CXCL10, CXCL12, and CXCL13. In contrast to conventional chemokine receptors, binding of chemokines to GPR182 did not induce typical downstream signaling processes, including G- and G-mediated signaling or ?-arrestin recruitment. GPR182 showed relatively high constitutive activity in regard to ?-arrestin recruitment and rapidly internalized in a ligand-independent manner. In constitutive GPR182-deficient mice, as well as after induced endothelium-specific loss of GPR182, we found significant increases in the plasma levels of CXCL10, CXCL12, and CXCL13. Global and induced endothelium-specific GPR182-deficient mice showed a significant decrease in hematopoietic stem cells in the bone marrow as well as increased colony-forming units of hematopoietic progenitors in the blood and the spleen. Our data show that GPR182 is a new atypical chemokine receptor for CXCL10, CXCL12, and CXCL13, which is involved in the regulation of hematopoietic stem cell homeostasis.
Copyright © 2021 the Author(s). Published by PNAS.
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Engrafted Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Undergo Clonal Expansion In Vivo.
Circulation2021 Apr;143(16):1635-1638. doi: 10.1161/CIRCULATIONAHA.119.044974.
El-Nachef Danny, Bugg Darrian, Beussman Kevin M, Steczina Sonette, Martinson Amy M, Murry Charles E, Sniadecki Nathan J, Davis Jennifer,
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Cell Therapy in Patients with Heart Failure: A Comprehensive Review and Emerging Concepts.
Cardiovasc Res2021 Apr;():. doi: cvab135.
Bolli Roberto, Solankhi Mitesh, Tang Xiang-Liang, Kahlon Arunpreet,
Abstract
This review summarizes the results of clinical trials of cell therapy in patients with heart failure (HF). In contrast to acute myocardial infarction (where results have been consistently negative for more than a decade), in the setting of HF the results of Phase I-II trials are encouraging, both in ischemic and nonischemic cardiomyopathy. Several well-designed Phase II studies have met their primary endpoint and demonstrated an efficacy signal, which is remarkable considering that only one dose of cells was used. That an efficacy signal was seen 6-12 months after a single treatment provides a rationale for larger, rigorous trials. Importantly, no safety concerns have emerged. Amongst the various cell types tested, mesenchymal stromal cells (MSCs) derived from bone marrow, umbilical cord, or adipose tissue show the greatest promise. In contrast, embryonic stem cells are not likely to become a clinical therapy. Unfractionated bone marrow cells and cardiosphere-derived cells have been abandoned. The cell products used for HF will most likely be allogeneic. New approaches, such as repeated cell treatment and intravenous delivery, may revolutionize the field. As is the case for most new therapies, the development of cell therapies for HF has been slow, plagued by multifarious problems, and punctuated by many setbacks; at present, the utility of cell therapy in HF remains to be determined. What the field needs is rigorous, well-designed Phase III trials. The most important things to move forward are to keep an open mind, avoid preconceived notions, and let ourselves be guided by the evidence.
Published on behalf of the European Society of Cardiology. All rights reserved. © The Author(s) 2021. For permissions please email: journals.permissions@oup.com.
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Semaphorin3E-PlexinD1 signaling in coronary artery and lymphatic vessel development with clinical implications in myocardial recovery.
iScience2021 Apr;24(4):102305. doi: 10.1016/j.isci.2021.102305.
Maruyama Kazuaki, Naemura Kazuaki, Arima Yuichiro, Uchijima Yasunobu, Nagao Hiroaki, Yoshihara Kenji, Singh Manvendra K, Uemura Akiyoshi, Matsuzaki Fumio, Yoshida Yutaka, Kurihara Yukiko, Miyagawa-Tomita Sachiko, Kurihara Hiroki,
Abstract
Blood and lymphatic vessels surrounding the heart develop through orchestrated processes from cells of different origins. In particular, cells around the outflow tract which constitute a primordial transient vasculature, referred to as aortic subepicardial vessels, are crucial for the establishment of coronary artery stems and cardiac lymphatic vessels. Here, we revealed that the epicardium and pericardium-derived Semaphorin 3E (Sema3E) and its receptor, PlexinD1, play a role in the development of the coronary stem, as well as cardiac lymphatic vessels. analyses demonstrated that Sema3E may demarcate areas to repel PlexinD1-expressing lymphatic endothelial cells, resulting in proper coronary and lymphatic vessel formation. Furthermore, inactivation of Sema3E-PlexinD1 signaling improved the recovery of cardiac function by increasing reactive lymphangiogenesis in an adult mouse model of myocardial infarction. These findings may lead to therapeutic strategies that target Sema3E-PlexinD1 signaling in coronary artery diseases.
© 2021 The Author(s).
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Assessment of human bioengineered cardiac tissue function in hypoxic and re-oxygenized environments to understand functional recovery in heart failure.
Regen Ther2021 Dec;18():66-75. doi: 10.1016/j.reth.2021.03.007.
Yamasaki Yu, Matsuura Katsuhisa, Sasaki Daisuke, Shimizu Tatsuya,
Abstract
Introduction:
Myocardial recovery is one of the targets for heart failure treatment. A non-negligible number of heart failure with reduced ejection fraction (EF) patients experience myocardial recovery through treatment. Although myocardial hypoxia has been reported to contribute to the progression of heart failure even in non-ischemic cardiomyopathy, the relationship between contractile recovery and re-oxygenation and its underlying mechanisms remain unclear. The present study investigated the effects of hypoxia/re-oxygenation on bioengineered cardiac cell sheets-tissue function and the underlying mechanisms.
Methods:
Bioengineered cardiac cell sheets-tissue was fabricated with human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CM) using temperature-responsive culture dishes. Cardiac tissue functions in the following conditions were evaluated with a contractile force measurement system: continuous normoxia (20% O) for 12 days; hypoxia (1% O) for 4 days followed by normoxia (20% O) for 8 days; or continuous hypoxia (1% O) for 8 days. Cell number, sarcomere structure, ATP levels, mRNA expressions and Ca transients of hiPSC-CM in those conditions were also assessed.
Results:
Hypoxia (4 days) elicited progressive decreases in contractile force, maximum contraction velocity, maximum relaxation velocity, Ca transient amplitude and ATP level, but sarcomere structure and cell number were not affected. Re-oxygenation (8 days) after hypoxia (4 days) was associated with progressive increases in contractile force, maximum contraction velocity and relaxation time to the similar extent levels of continuous normoxia group, while maximum relaxation velocity was still significantly low even after re-oxygenation. Ca transient magnitude, cell number, sarcomere structure and ATP level after re-oxygenation were similar to those in the continuous normoxia group. Hypoxia/re-oxygenation up-regulated mRNA expression of PLN.
Conclusions:
Hypoxia and re-oxygenation condition directly affected human bioengineered cardiac tissue function. Further understanding the molecular mechanisms of functional recovery of cardiac tissue after re-oxygenation might provide us the new insight on heart failure with recovered ejection fraction and preserved ejection fraction.
© 2021 The Japanese Society for Regenerative Medicine. Production and hosting by Elsevier B.V.
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Targeting of CAT and VCAM1 as Novel Therapeutic Targets for DMD Cardiomyopathy.
Front Cell Dev Biol2021 ;9():659177. doi: 10.3389/fcell.2021.659177.
Li Bin, Xiong Weiyao, Liang Wen-Miin, Chiou Jian-Shiun, Lin Ying-Ju, Chang Alex C Y,
Abstract
Duchenne muscular dystrophy (DMD) related cardiomyopathy is the leading cause of early mortality in DMD patients. There is an urgent need to gain a better understanding of the disease molecular pathogenesis and develop effective therapies to prevent the onset of heart failure. In the present study, we used DMD human induced pluripotent stem cells (DMD-hiPSCs) derived cardiomyocytes (CMs) as a platform to explore the active compounds in commonly used Chinese herbal medicine (CHM) herbs. Single CHM herb (DaH, ZK, and CQZ) reduced cell beating rate, decreased cellular ROS accumulation, and improved structure of DMD hiPSC-CMs. Cross-comparison of transcriptomic profiling data and active compound library identified nine active chemicals targeting ROS neutralizing Catalase (CAT) and structural protein vascular cell adhesion molecule 1 (VCAM1). Treatment with Quecetin, Kaempferol, and Vitamin C, targeting CAT, conferred ROS protection and improved contraction; treatment with Hesperidin and Allicin, targeting VCAM1, induced structure enhancement via induction of focal adhesion. Lastly, overexpression of CAT or VCAM1 in DMD hiPSC-CMs reconstituted efficacious effects and conferred increase in cardiomyocyte function. Together, our results provide a new insight in treating DMD cardiomyopathy via targeting of CAT and VCAM1, and serves as an example of translating Bed to Bench back to Bed using a muti-omics approach.
Copyright © 2021 Li, Xiong, Liang, Chiou, Lin and Chang.
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Human Pluripotent Stem Cell-Derived Cardiac Cells: Application in Disease Modeling, Cell Therapy, and Drug Discovery.
Front Cell Dev Biol2021 ;9():655161. doi: 10.3389/fcell.2021.655161.
Huang Juan, Feng Qi, Wang Li, Zhou Bingying,
Abstract
Cardiac diseases are the leading cause of deaths worldwide; however, to date, there has been limited progress in the development of therapeutic options for these conditions. Animal models have been the most extensively studied methods to recapitulate a wide variety of cardiac diseases, but these models exhibit species-specific differences in physiology, metabolism and genetics, which lead to inaccurate and unpredictable drug safety and efficacy results, resulting in drug attrition. The development of human pluripotent stem cell (hPSC) technology in theory guarantees an unlimited source of human cardiac cells. These hPSC-derived cells are not only well suited for traditional two-dimensional (2-D) monoculture, but also applicable to more complex systems, such as three-dimensional (3-D) organoids, tissue engineering and heart on-a-chip. In this review, we discuss the application of hPSCs in heart disease modeling, cell therapy, and next-generation drug discovery. While the hPSC-related technologies still require optimization, their advances hold promise for revolutionizing cell-based therapies and drug discovery.
Copyright © 2021 Huang, Feng, Wang and Zhou.
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The cause of cardiac dysfunction.
Nat Rev Mater -
Rain Evaporation, Snow Melt, and Entrainment at the Heart of Water Vapor Isotopic Variations in the Tropical Troposphere, According to Large-Eddy Simulations and a Two-Column Model.
J Adv Model Earth Syst2021 Apr;13(4):e2020MS002381. doi: 10.1029/2020MS002381.
Risi Camille, Muller Caroline, Blossey Peter,
Abstract
We aim at developing a simple model as an interpretative framework for the water vapor isotopic variations in the tropical troposphere over the ocean. We use large-eddy simulations of disorganized convection in radiative-convective equilibrium to justify the underlying assumptions of this simple model, to constrain its input parameters and to evaluate its results. We also aim at interpreting the depletion of the water vapor isotopic composition in the lower and midtroposphere as precipitation increases, which is a salient feature in tropical oceanic observations. This feature constitutes a stringent test on the relevance of our interpretative framework. Previous studies, based on observations or on models with parameterized convection, have highlighted the roles of deep convective and mesoscale downdrafts, rain evaporation, rain-vapor diffusive exchanges, and mixing processes. The interpretative framework that we develop, valid in case of disorganized convection, is a two-column model representing the net ascent in clouds and the net descent in the environment. We show that the mechanisms for depleting the troposphere as the precipitation rate increases all stem from the higher tropospheric relative humidity. First, when the relative humidity is larger, less snow sublimates before melting and a smaller fraction of rain evaporates. Both effects lead to more depleted rain evaporation and eventually more depleted water vapor. This mechanism dominates in regimes of large-scale ascent. Second, the entrainment of dry air into clouds reduces the vertical isotopic gradient and limits the depletion of tropospheric water vapor. This mechanism dominates in regimes of large-scale descent.
© 2021. The Authors.
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Targeting HIF-? for robust prevascularization of human cardiac organoids.
J Tissue Eng Regen Med2021 Feb;15(2):189-202. doi: 10.1002/term.3165.
Coyle Robert C, Barrs Ryan W, Richards Dylan J, Ladd Emma P, Menick Donald R, Mei Ying,
Abstract
Prevascularized 3D microtissues have been shown to be an effective cell delivery vehicle for cardiac repair. To this end, our lab has explored the development of self-organizing, prevascularized human cardiac organoids by co-seeding human cardiomyocytes with cardiac fibroblasts, endothelial cells, and stromal cells into agarose microwells. We hypothesized that this prevascularization process is facilitated by the endogenous upregulation of hypoxia-inducible factor (HIF) pathway in the avascular 3D microtissues. In this study, we used Molidustat, a selective PHD (prolyl hydroxylase domain enzymes) inhibitor that stabilizes HIF-?, to treat human cardiac organoids, which resulted in 150 ± 61% improvement in endothelial expression (CD31) and 220 ± 20% improvement in the number of lumens per organoids. We hypothesized that the improved endothelial expression seen in Molidustat treated human cardiac organoids was dependent upon upregulation of VEGF, a well-known downstream target of HIF pathway. Through the use of immunofluorescent staining and ELISA assays, we determined that Molidustat treatment improved VEGF expression of non-endothelial cells and resulted in improved co-localization of supporting cell types and endothelial structures. We further demonstrated that Molidustat treated human cardiac organoids maintain cardiac functionality. Lastly, we showed that Molidustat treatment improves survival of cardiac organoids when exposed to both hypoxic and ischemic conditions . For the first time, we demonstrate that targeted HIF-? stabilization provides a robust strategy to improve endothelial expression and lumen formation in cardiac microtissues, which will provide a powerful framework for prevascularization of various microtissues in developing successful cell transplantation therapies.
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Sympathetic hyperactivity, hypertension, and tachycardia induced by stimulation of the ponto-medullary junction in humans.
Clin Neurophysiol2021 Mar;():. doi: S1388-2457(21)00473-9.
Hamasaki Tadashi, Yamakawa Toshitaka, Fujiwara Koichi, Harashima Haruki, Nakamura Kota, Ikuta Yoshihiro, Yamamoto Tatsuo, Hasegawa Yu, Takezaki Tatsuya, Mukasa Akitake,
Abstract
OBJECTIVE:
The purpose of this study is to investigate changes in autonomic activities and systemic circulation generated by surgical manipulation or electrical stimulation to the human brain stem.
METHODS:
We constructed a system that simultaneously recorded microsurgical field videos and heart rate variability (HRV) that represent autonomic activities. In 20 brain stem surgeries recorded, HRV features and sites of surgical manipulation were analyzed in 19 hypertensive epochs, defined as the periods with transient increases in the blood pressure. We analyzed the period during electrical stimulation to the ponto-medullary junction, performed for the purpose of monitoring a cranial nerve function.
RESULTS:
In the hypertensive epoch, HRV analysis showed that sympathetic activity predominated over the parasympathetic activity. The hypertensive epoch was more associated with surgical manipulation of the area in the caudal pons or the rostral medulla oblongata compared to controls. During the period of electrical stimulation, there were significant increases in blood pressures and heart rates, accompanied by sympathetic overdrive.
CONCLUSIONS:
Our results provide physiological evidence that there is an important autonomic center located adjacent to the ponto-medullary junction.
SIGNIFICANCE:
A large study would reveal a candidate target of neuromodulation for disorders with autonomic imbalances such as drug-resistant hypertension.
Copyright © 2021 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.
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Therapeutic potential of mesenchymal stem cells in multiple organs affected by COVID-19.
Life Sci2021 Apr;():119510. doi: S0024-3205(21)00495-1.
Paris Gustavo C, de A Azevedo Aline, Ferreira Adriana L, de A Azevedo Yanca M, Rainho Mateus A, de Oliveira Genilza P, Silv Karina R, Cortez Erika A C, Stumbo Ana C, Carvalho Simone N, de Carvalho Lais, Thole Alessandra A,
Abstract
Currently, the world has been devastated by an unprecedented pandemic in this century. The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the agent of coronavirus disease 2019 (COVID-19), has been causing disorders, dysfunction and morphophysiological alterations in multiple organs as the disease evolves. There is a great scientific community effort to obtain a therapy capable of reaching the multiple affected organs in order to contribute for tissue repair and regeneration. In this regard, mesenchymal stem cells (MSCs) have emerged as potential candidates concerning the promotion of beneficial actions at different stages of COVID-19. MSCs are promising due to the observed therapeutic effects in respiratory preclinical models, as well as in cardiac, vascular, renal and nervous system models. Their immunomodulatory properties and secretion of paracrine mediators, such as cytokines, chemokines, growth factors and extracellular vesicles allow for long range tissue modulation and, particularly, blood-brain barrier crossing. This review focuses on SARS-CoV-2 impact to lungs, kidneys, heart, vasculature and central nervous system while discussing promising MSC's therapeutic mechanisms in each tissue. In addition, MSC's therapeutic effects in high-risk groups for COVID-19, such as obese, diabetic and hypertensive patients are also explored.
Copyright © 2018. Published by Elsevier Inc.
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High-mobility group box 1 serves as an inflammation driver of cardiovascular disease.
Biomed Pharmacother2021 Apr;139():111555. doi: S0753-3322(21)00340-1.
Wahid Abdul, Chen Wei, Wang Xuewen, Tang Xiaohong,
Abstract
Cardiovascular disease (CVD) is the most deadly disease, which can cause sudden death, in which inflammation is a key factor in its occurrence and development. High-mobility group box 1 (HMGB1) is a novel nuclear DNA-binding protein that activates innate immunity to induce inflammation in CVD. HMGB1 exists in the cytoplasm and nucleus of different cell types, including those in the heart. By binding to its receptors, HMGB1 triggers a variety of signaling cascades, leading to inflammation and CVD. To help develop HMGB1-targeted therapies, here we discuss HMGB1 and its biological functions, receptors, signaling pathways, and pathophysiology related to inflammation and CVD, including cardiac remodeling, cardiac hypertrophy, myocardial infarction, heart failure, pulmonary hypertension, atherosclerosis, and cardiomyopathy.
Copyright © 2021. Published by Elsevier Masson SAS.
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Cardiac Differentiation of Mesenchymal Stem Cells: Impact of Biological and Chemical Inducers.
Stem Cell Rev Rep2021 Apr;():. doi: 10.1007/s12015-021-10165-3.
Ramesh Saravanan, Govarthanan Kavitha, Ostrovidov Serge, Zhang Haiguang, Hu Qingxi, Camci-Unal Gulden, Verma Rama S, Ramalingam Murugan,
Abstract
Cardiovascular disorders (CVDs) are the leading cause of global death, widely occurs due to irreparable loss of the functional cardiomyocytes. Stem cell-based therapeutic approaches, particularly the use of Mesenchymal Stem Cells (MSCs) is an emerging strategy to regenerate myocardium and thereby improving the cardiac function after myocardial infarction (MI). Most of the current approaches often employ the use of various biological and chemical factors as cues to trigger and modulate the differentiation of MSCs into the cardiac lineage. However, the recent advanced methods of using specific epigenetic modifiers and exosomes to manipulate the epigenome and molecular pathways of MSCs to modify the cardiac gene expression yield better profiled cardiomyocyte like cells in vitro. Hitherto, the role of cardiac specific inducers triggering cardiac differentiation at the cellular and molecular level is not well understood. Therefore, the current review highlights the impact and recent trends in employing biological and chemical inducers on cardiac differentiation of MSCs. Thereby, deciphering the interactions between the cellular microenvironment and the cardiac inducers will help us to understand cardiomyogenesis of MSCs. Additionally, the review also provides an insight on skeptical roles of the cell free biological factors and extracellular scaffold assisted mode for manipulation of native and transplanted stem cells towards translational cardiac research.
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A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency.
Genome Biol2021 Apr;22(1):111. doi: 10.1186/s13059-021-02316-z.
Jones Wendell, Gong Binsheng, Novoradovskaya Natalia, Li Dan, Kusko Rebecca, Richmond Todd A, Johann Donald J, Bisgin Halil, Sahraeian Sayed Mohammad Ebrahim, Bushel Pierre R, Pirooznia Mehdi, Wilkins Katherine, Chierici Marco, Bao Wenjun, Basehore Lee Scott, Lucas Anne Bergstrom, Burgess Daniel, Butler Daniel J, Cawley Simon, Chang Chia-Jung, Chen Guangchun, Chen Tao, Chen Yun-Ching, Craig Daniel J, Del Pozo Angela, Foox Jonathan, Francescatto Margherita, Fu Yutao, Furlanello Cesare, Giorda Kristina, Grist Kira P, Guan Meijian, Hao Yingyi, Happe Scott, Hariani Gunjan, Haseley Nathan, Jasper Jeff, Jurman Giuseppe, Kreil David Philip, ?abaj Pawe?, Lai Kevin, Li Jianying, Li Quan-Zhen, Li Yulong, Li Zhiguang, Liu Zhichao, López Mario Solís, Miclaus Kelci, Miller Raymond, Mittal Vinay K, Mohiyuddin Marghoob, Pabón-Peña Carlos, Parsons Barbara L, Qiu Fujun, Scherer Andreas, Shi Tieliu, Stiegelmeyer Suzy, Suo Chen, Tom Nikola, Wang Dong, Wen Zhining, Wu Leihong, Xiao Wenzhong, Xu Chang, Yu Ying, Zhang Jiyang, Zhang Yifan, Zhang Zhihong, Zheng Yuanting, Mason Christopher E, Willey James C, Tong Weida, Shi Leming, Xu Joshua,
Abstract
BACKGROUND:
Oncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a suitably large number of pre-identified variants for properly assessing oncopanel assay analytical quality and performance. The FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually and their pool, termed Sample A, to develop a reference sample with suitably large numbers of coding positions with known (variant) positives and negatives for properly evaluating oncopanel analytical performance.
RESULTS:
In reference Sample A, we identify more than 40,000 variants down to 1% allele frequency with more than 25,000 variants having less than 20% allele frequency with 1653 variants in COSMIC-related genes. This is 5-100× more than existing commercially available samples. We also identify an unprecedented number of negative positions in coding regions, allowing statistical rigor in assessing limit-of-detection, sensitivity, and precision. Over 300 loci are randomly selected and independently verified via droplet digital PCR with 100% concordance. Agilent normal reference Sample B can be admixed with Sample A to create new samples with a similar number of known variants at much lower allele frequency than what exists in Sample A natively, including known variants having allele frequency of 0.02%, a range suitable for assessing liquid biopsy panels.
CONCLUSION:
These new reference samples and their admixtures provide superior capability for performing oncopanel quality control, analytical accuracy, and validation for small to large oncopanels and liquid biopsy assays.
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Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions.
Genome Biol2021 Apr;22(1):109. doi: 10.1186/s13059-021-02315-0.
Gong Binsheng, Li Dan, Kusko Rebecca, Novoradovskaya Natalia, Zhang Yifan, Wang Shangzi, Pabón-Peña Carlos, Zhang Zhihong, Lai Kevin, Cai Wanshi, LoCoco Jennifer S, Lader Eric, Richmond Todd A, Mittal Vinay K, Liu Liang-Chun, Johann Donald J, Willey James C, Bushel Pierre R, Yu Ying, Xu Chang, Chen Guangchun, Burgess Daniel, Cawley Simon, Giorda Kristina, Haseley Nathan, Qiu Fujun, Wilkins Katherine, Arib Hanane, Attwooll Claire, Babson Kevin, Bao Longlong, Bao Wenjun, Lucas Anne Bergstrom, Best Hunter, Bhandari Ambica, Bisgin Halil, Blackburn James, Blomquist Thomas M, Boardman Lisa, Burgher Blake, Butler Daniel J, Chang Chia-Jung, Chaubey Alka, Chen Tao, Chierici Marco, Chin Christopher R, Close Devin, Conroy Jeffrey, Coleman Jessica Cooley, Craig Daniel J, Crawford Erin, Del Pozo Angela, Deveson Ira W, Duncan Daniel, Eterovic Agda Karina, Fan Xiaohui, Foox Jonathan, Furlanello Cesare, Ghosal Abhisek, Glenn Sean, Guan Meijian, Haag Christine, Hang Xinyi, Happe Scott, Hennigan Brittany, Hipp Jennifer, Hong Huixiao, Horvath Kyle, Hu Jianhong, Hung Li-Yuan, Jarosz Mirna, Kerkhof Jennifer, Kipp Benjamin, Kreil David Philip, ?abaj Pawe?, Lapunzina Pablo, Li Peng, Li Quan-Zhen, Li Weihua, Li Zhiguang, Liang Yu, Liu Shaoqing, Liu Zhichao, Ma Charles, Marella Narasimha, Martín-Arenas Rubén, Megherbi Dalila B, Meng Qingchang, Mieczkowski Piotr A, Morrison Tom, Muzny Donna, Ning Baitang, Parsons Barbara L, Paweletz Cloud P, Pirooznia Mehdi, Qu Wubin, Raymond Amelia, Rindler Paul, Ringler Rebecca, Sadikovic Bekim, Scherer Andreas, Schulze Egbert, Sebra Robert, Shaknovich Rita, Shi Qiang, Shi Tieliu, Silla-Castro Juan Carlos, Smith Melissa, López Mario Solís, Song Ping, Stetson Daniel, Strahl Maya, Stuart Alan, Supplee Julianna, Szankasi Philippe, Tan Haowen, Tang Lin-Ya, Tao Yonghui, Thakkar Shraddha, Thierry-Mieg Danielle, Thierry-Mieg Jean, Thodima Venkat J, Thomas David, Tichý Boris, Tom Nikola, Garcia Elena Vallespin, Verma Suman, Walker Kimbley, Wang Charles, Wang Junwen, Wang Yexun, Wen Zhining, Wirta Valtteri, Wu Leihong, Xiao Chunlin, Xiao Wenzhong, Xu Shibei, Yang Mary, Ying Jianming, Yip Shun H, Zhang Guangliang, Zhang Sa, Zhao Meiru, Zheng Yuanting, Zhou Xiaoyan, Mason Christopher E, Mercer Timothy, Tong Weida, Shi Leming, Jones Wendell, Xu Joshua,
Abstract
BACKGROUND:
Targeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing.
RESULTS:
All panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden.
CONCLUSION:
This comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.
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Cues from human atrial extracellular matrix enrich the atrial differentiation of human induced pluripotent stem cell-derived cardiomyocytes.
Biomater Sci2021 Apr;():. doi: 10.1039/d0bm01686a.
Mesquita Fernanda C P, Morrissey Jacquelynn, Lee Po-Feng, Monnerat Gustavo, Xi Yutao, Andersson Helen, Nogueira Fabio C S, Domont Gilberto B, Sampaio Luiz C, Hochman-Mendez Camila, Taylor Doris A,
Abstract
New robust and reproducible differentiation approaches are needed to generate induced pluripotent stem cell (iPSC)-derived cardiomyocytes of specific subtypes in predictable quantities for tissue-specific disease modeling, tissue engineering, and eventual clinical translation. Here, we assessed whether powdered decellularized extracellular matrix (dECM) particles contained chamber-specific cues that could direct the cardiac differentiation of human iPSCs toward an atrial phenotype. Human hearts were dissected and the left ventricle (LV) and left atria (LA) were isolated, minced, and decellularized using an adapted submersion decellularization technique to generate chamber-specific powdered dECM. Comparative proteomic analyses showed chamber-specific dECM segregation, with atrial- and ventricle-specific proteins uniquely present in powdered dECM-hA and dECM-hV, respectively. Cell populations differentiated in the presence of dECM-hA showed upregulated atrial molecular markers and a two-fold increase in the number of atrial-like cells as compared with cells differentiated with dECM-hV or no dECM (control). Finally, electrophysiological data showed an increase in action potentials characteristic of atrial-like cells in the dECM-hA group. These findings support the hypothesis that dECM powder derived from human atria retained endogenous cues to drive cardiac differentiation toward an atrial fate.
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Targeting Adenosine Receptors in Neurological Diseases.
Cell Reprogram2021 Apr;23(2):57-72. doi: 10.1089/cell.2020.0087.
Atif Muhmmad, Alsrhani Abdullah, Naz Farrah, Imran Muhammad, Imran Muhammad, Ullah Muhammad Ikram, Alameen Ayman A M, Gondal Tanweer Aslam, Raza Qaisar,
Abstract
Adenosine plays a significant role in neurotransmission process by controlling the blood pressure, while adenosine triphosphate (ATP) acts as a neuromodulator and neurotransmitter and by activation of P2 receptors, regulates the contractility of the heart. Adenosine signaling is essential in the process of regeneration by regulating proliferation, differentiation, and apoptosis of stem cells. In this review, we have selected neurological disorders (Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, multiple sclerosis, and epilepsy) with clinical trials using antagonists and epigenetic tools targeting adenosine receptor as a therapeutic approach in the treatment of these disorders. Promising results have been reported from many clinical trials. It has been found that higher expression levels of A2A and P2X7 receptors in neurological disorders further complicate the disease condition. Therefore, modulations of these receptors by using antagonists of these receptors or SAM (S-adenosylmethionine) therapy as an epigenetic tool could be useful in reversing the complications of these disorders. Finally, we suggest that modulation of adenosine receptors in neurological disorders can increase the regenerative phase by increasing the rate of proliferation and differentiation in the damaged tissues.
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Clonal haematopoiesis of indeterminate potential: intersections between inflammation, vascular disease and heart failure.
Clin Sci (Lond)2021 Apr;135(7):991-1007. doi: 10.1042/CS20200306.
Mooney Leanne, Goodyear Carl S, Chandra Tamir, Kirschner Kristina, Copland Mhairi, Petrie Mark C, Lang Ninian N,
Abstract
Ageing is a major risk factor for the development of cardiovascular disease (CVD) and cancer. Whilst the cumulative effect of exposure to conventional cardiovascular risk factors is important, recent evidence highlights clonal haematopoiesis of indeterminant potential (CHIP) as a further key risk factor. CHIP reflects the accumulation of somatic, potentially pro-leukaemic gene mutations within haematopoietic stem cells over time. The most common mutations associated with CHIP and CVD occur in genes that also play central roles in the regulation of inflammation. While CHIP carriers have a low risk of haematological malignant transformation (<1% per year), their relative risk of mortality is increased by 40% and this reflects an excess of cardiovascular events. Evidence linking CHIP, inflammation and atherosclerotic disease has recently become better defined. However, there is a paucity of information about the role of CHIP in the development and progression of heart failure, particularly heart failure with preserved ejection fraction (HFpEF). While systemic inflammation plays a role in the pathophysiology of both heart failure with reduced and preserved ejection fraction (EF), it may be of greater relevance in the pathophysiology of HFpEF, which is also strongly associated with ageing. This review describes CHIP and its pathogenetic links with ageing, inflammation and CVD, while providing insight into its putative role in HFpEF.
© 2021 The Author(s).
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