• 제목/요약/키워드: Cardiac -specific gene

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A semi-automatic cell type annotation method for single-cell RNA sequencing dataset

  • Kim, Wan;Yoon, Sung Min;Kim, Sangsoo
    • Genomics & Informatics
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    • 제18권3호
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    • pp.26.1-26.6
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    • 2020
  • Single-cell RNA sequencing (scRNA-seq) has been widely applied to provide insights into the cell-by-cell expression difference in a given bulk sample. Accordingly, numerous analysis methods have been developed. As it involves simultaneous analyses of many cell and genes, efficiency of the methods is crucial. The conventional cell type annotation method is laborious and subjective. Here we propose a semi-automatic method that calculates a normalized score for each cell type based on user-supplied cell type-specific marker gene list. The method was applied to a publicly available scRNA-seq data of mouse cardiac non-myocyte cell pool. Annotating the 35 t-stochastic neighbor embedding clusters into 12 cell types was straightforward, and its accuracy was evaluated by constructing co-expression network for each cell type. Gene Ontology analysis was congruent with the annotated cell type and the corollary regulatory network analysis showed upstream transcription factors that have well supported literature evidences. The source code is available as an R script upon request.

Involvement of TGF-β1 Signaling in Cardiomyocyte Differentiation from P19CL6 Cells

  • Lim, Joong-Yeon;Kim, Won Ho;Kim, Joon;Park, Sang Ick
    • Molecules and Cells
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    • 제24권3호
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    • pp.431-436
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    • 2007
  • Stem cell-based therapy is being considered as an alternative treatment for cardiomyopathy. Hence understanding the basic molecular mechanisms of cardiomyocyte differentiation is important. Besides BMP or Wnt family proteins, $TGF-{\beta}$ family members are thought to play a role in cardiac development and differentiation. Although $TGF-{\beta}$ has been reported to induce cardiac differentiation in embryonic stem cells, the differential role of $TGF-{\beta}$ isoforms has not been elucidated. In this study, employing the DMSO-induced cardiomyocyte differentiation system using P19CL6 mouse embryonic teratocarcinoma stem cells, we investigated the $TGF-{\beta}$-induced signaling pathway in cardiomyocyte differentiation. $TGF-{\beta}1$, but not the other two isoforms of $TGF-{\beta}$, was induced at the mRNA and protein level at an early stage of differentiation, and Smad2 phosphorylation increased in parallel with $TGF-{\beta}1$ induction. Inhibition of $TGF-{\beta}1$ activity with $TGF-{\beta}1$-specific neutralizing antibody reduced cell cycle arrest as well as expression of the CDK inhibitor $p21^{WAF1}$. The antibody also inhibited induction of the cardiac transcription factor Nkx2.5. Taken together, these results suggest that $TGF-{\beta}1$ is involved in cardiomyocyte differentiation by regulating cell cycle progression and cardiac gene expression in an autocrine or paracrine manner.

Transfection of Mesenchymal Stem Cells with the FGF-2 Gene Improves Their Survival Under Hypoxic Conditions

  • Song, Heesang;Kwon, Kihwan;Lim, Soyeon;Kang, Seok-Min;Ko, Young-Guk;Xu, ZhengZhe;Chung, Ji Hyung;Kim, Byung-Soo;Lee, Hakbae;Joung, Boyoung;Park, Sungha;Choi, Donghoon;Jang, Yangsoo;Chung, Nam-Sik;Yoo, Kyung-Jong;Hwang, Ki-Chul
    • Molecules and Cells
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    • 제19권3호
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    • pp.402-407
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    • 2005
  • Bone marrow mesenchymal stem cells (MSCs) have shown potential for cardiac repair following myocardial injury, but this approach is limited by their poor viability after transplantation. To reduce cell loss after transplantation, we introduced the fibroblast growth factor-2 (FGF-2) gene ex vivo before transplantation. The isolated MSCs produced colonies with a fibroblast-like morphology in 2 weeks; over 95% expressed CD71, and 28% expressed the cardiomyocyte-specific transcription factor, Nkx2.5, as well as ${\alpha}$-skeletal actin, Nkx2.5, and GATA4. In hypoxic culture, the FGF-2-transfected MSCs (FGF-2-MSCs) secreted increased levels of FGF-2 and displayed a threefold increase in viability, as well as increased expression of the anti-apoptotic gene, Bcl2, and reduced DNA laddering. They had functional adrenergic receptors, like cardiomyocytes, and exposure to norepinephrine led to phosphorylation of ERK1/2. Viable cells persisted 4 weeks after implantation of $5.0{\times}10^5$ FGF-2-MSCs into infarcted myocardia. Expression of cardiac troponin T (CTn T) and a voltage-gated $Ca^{2+}$ channel (CaV2.1) increased, and new blood vessels formed. These data suggest that genetic modification of MSCs before transplantation could be useful for treating myocardial infarction and end-stage cardiac failure.

The end effector of circadian heart rate variation: the sinoatrial node pacemaker cell

  • Yaniv, Yael;Lakatta, Edward G.
    • BMB Reports
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    • 제48권12호
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    • pp.677-684
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    • 2015
  • Cardiovascular function is regulated by the rhythmicity of circadian, infradian and ultradian clocks. Specific time scales of different cell types drive their functions: circadian gene regulation at hours scale, activation-inactivation cycles of ion channels at millisecond scales, the heart's beating rate at hundreds of millisecond scales, and low frequency autonomic signaling at cycles of tens of seconds. Heart rate and rhythm are modulated by a hierarchical clock system: autonomic signaling from the brain releases neurotransmitters from the vagus and sympathetic nerves to the heart's pacemaker cells and activate receptors on the cell. These receptors activating ultradian clock functions embedded within pacemaker cells include sarcoplasmic reticulum rhythmic spontaneous Ca2+ cycling, rhythmic ion channel current activation and inactivation, and rhythmic oscillatory mitochondria ATP production. Here we summarize the evidence that intrinsic pacemaker cell mechanisms are the end effector of the hierarchical brain-heart circadian clock system.

Expression of the Novel Basic Helix-Loop-Helix Gene dHAND in Neural Crest Derivatives and Extraembryonic Membranes during Mouse Development

  • S.I Yun;Kim, S.K;Kim, S.K.;K.T Chang;B.H Hyun;D.S Son;Kim, M.K;D.S Suh
    • 한국동물번식학회:학술대회논문집
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    • 한국동물번식학회 2001년도 발생공학 국제심포지움 및 학술대회 발표자료집
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    • pp.53-54
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    • 2001
  • Expression of HAND genes in sympathetic adrenal lineage suggests that HAND genes may regulate Mash-I independent neuronal genes. HAND genes are also expressed in other cell types, e.g. Cardiac cells, trophoblasts, and decidua, suggesting that HAND genes are not cell fate determination factors. It is unclear how HAND genes function specifically in different types of cells. Combinational actions of HANDs with other cell-lineage specific transcription factor may determine each cell fate and differentiation processes. Identifying the transcription target genes of HANDs and Mash-I will be important to elucidate the function of these bHLH factors in SNS factors in SNS development. (omitted)

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Generation of Induced Pluripotent Stem Cells from Lymphoblastoid Cell Lines by Electroporation of Episomal Vectors

  • Myunghyun Kim;Junmyeong Park;Sujin Kim;Dong Wook Han;Borami Shin;Hans Robert Scholer;Johnny Kim;Kee-Pyo Kim
    • International Journal of Stem Cells
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    • 제16권1호
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    • pp.36-43
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    • 2023
  • Background and Objectives: Lymphoblastoid cell lines (LCLs) deposited from disease-affected individuals could be a valuable donor cell source for generating disease-specific induced pluripotent stem cells (iPSCs). However, generation of iPSCs from the LCLs is still challenging, as yet no effective gene delivery strategy has been developed. Methods and Results: Here, we reveal an effective gene delivery method specifically for LCLs. We found that LCLs appear to be refractory toward retroviral and lentiviral transduction. Consequently, lentiviral and retroviral transduction of OCT4, SOX2, KFL4 and c-MYC into LCLs does not elicit iPSC colony formation. Interestingly, however we found that transfection of oriP/EBNA-1-based episomal vectors by electroporation is an efficient gene delivery system into LCLs, enabling iPSC generation from LCLs. These iPSCs expressed pluripotency makers (OCT4, NANOG, SSEA4, SALL4) and could form embryoid bodies. Conclusions: Our data show that electroporation is an effective gene delivery method with which LCLs can be efficiently reprogrammed into iPSCs.

Mucopolysaccharidoses in Taiwan

  • Lin, Hsiang-Yu;Chuang, Chih-Kuang;Lin, Shuan-Pei
    • Journal of mucopolysaccharidosis and rare diseases
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    • 제4권1호
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    • pp.14-20
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    • 2018
  • Mucopolysaccharidoses (MPSs) are a group of rare inherited metabolic disorders caused by specific lysosomal enzyme deficiencies leading to the sequential degradation of glycosaminoglycans, causing substrate accumulation in various cells and tissues and progressive multiple organ dysfunction. The rare disease medical care team at Mackay Memorial Hospital in Taiwan has been dedicated to the study of MPSs for more than 20 years. Since 1999, more than 50 academic papers focusing on MPSs have been published in international medical journals. Topics of research include the following items regarding MPSs: incidence, natural history, clinical manifestations, gene mutation characteristics, cardiac function, bone mineral density, sleep studies, pulmonary function tests, hearing assessments, percutaneous endoscopic gastrostomy, anesthetic experience, imaging analysis, special biochemical tests, laboratory diagnostics, global expert consensus conferences, prenatal diagnosis, new drug clinical trials, newborn screening, and treatment outcomes. Of these published academic research papers, more than half were cross-domain, cross-industry, and international studies with results in cooperation with experts from European, American and other Asian countries. A cross-specialty collaboration platform was established based on high-risk population screening criteria with the acronym "BECARE" (Bone and joints, Eyes, Cardiac and central nervous system, Abdomen and appearance, Respiratory system, and Ear, nose, and throat involvement). Through this platform, orthopedic surgeons, rheumatologists, ophthalmologists, cardiologists, rehabilitation physicians, gastroenterologists, otorhinolaryngologists, and medical geneticists have been educated with regards to awareness of suspected cases of MPSs patients to allow for a further confirmative diagnosis of MPSs. Because of the progressive nature of the disease, an early diagnosis and early multidisciplinary therapeutic interventions including surgery, rehabilitation programs, symptom-based treatments, hematopoietic stem cell transplantation, and enzyme replacement therapy, are very important.

Apoptosis and remodeling in adriamycin-induced cardiomyopathy rat model

  • Hong, Young Mi;Lee, Hyeryon;Cho, Min-Sun;Kim, Kwan Chang
    • Clinical and Experimental Pediatrics
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    • 제60권11호
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    • pp.365-372
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    • 2017
  • Purpose: The mechanism for the pathogenesis of adriamycin (ADR)-induced cardiomyopathy is not yet known. Different hypotheses include the production of free radicals, an interaction between ADR and nuclear components, and a disruption in cardiac-specific gene expression. Apoptosis has also been proposed as being involved in cardiac dysfunction. The purpose of this study was to determine if apoptosis might play a role in ADR-induced cardiomyopathy. Methods: Male Sprague-Dawley rats were separated into 2 groups: the control group (C group) and the experimental group (ADR 5 mg/wk for 3 weeks through intraperitoneal injections; A group). Echocardiographic images were obtained at week 3. Changes in caspase-3, B-cell leukemia/lymphoma (Bcl)-2, Bcl-2-associated X (Bax), interleukin (IL)-6, tumor necrosis $factor-{\alpha}$, brain natriuretic peptide (BNP), troponin I, collagen 1, and collagen 3 protein expression from the left ventricle tissues of C and A group rats were determined by Western blot. Results: Ascites and heart failure as well as left ventricular hypertrophy were noted in the A group. Ejection fraction and shortening fraction were significantly lower in the A group by echocardiography. The expression of caspase-3, Bax, IL-6, BNP, collagen 1, and collagen 3 were significantly higher in the A group as compared with the C group. Protein expression of Bcl-2 decreased significantly in the A group compared with the C group. Conclusion: ADR induced an upregulation of caspase-3, Bax, IL-6, and collagen, as well as a depression in Bcl-2. Thus, apoptosis and fibrosis may play an important role in ADR-induced cardiomyopathy.

DNA Microarray 분석을 통한 한우 부위별 특이 마커 유전자의 발굴 (Identification of Cuts-specific Myogenic Marker Genes in Hanwoo by DNA Microarray)

  • 이은주;신유미;이현정;윤두학;전태훈;이용석;최인호
    • Journal of Animal Science and Technology
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    • 제52권4호
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    • pp.329-336
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    • 2010
  • 본 연구는 소의 부위별 근육에 특이하게 발현하는 유전자 마커를 발굴하여 소고기의 부위를 과학적으로 판명할 수 있는 기술을 개발하고자 실시하였다. 이러한 연구 목표 아래 먼저 사태(Beef shank), 등심(Longissimus dorsi), 양지(Deep pectoral), 홍두깨(Semitendinosus) 부위의 근육조직에서 MSC (myogenic satellite cell, 근육줄기세포)를 순수 분리하고 이를 MFC (myotube-formed cell; 근관이 형성된 세포)로 분화시키거나 ALC (adipocyte-like cell; 지방세포와 유사한 세포)로 이형분화 시킨 후 3가지의 세포로 부터 각각의 RNA를 추출하였다. 이렇게 추출한 RNA는 24,000개의 bovine oligo-nucelotide (70 mer)가 집적된 microarray를 이용해 4개의 조직 중 1개의 조직에서만 MSC의 분화(MFC) 또는 이형분화 과정에서 mRNA의 발현이 증감을 보이는 유전자 135개를 먼저 발굴하였다. 135개의 유전자에 대해 microarray 분석에 사용한 동일한 RNA를 이용하여 real-time PCR 기술로 검증한 결과 총 29개의 유전자가 microarray 분석 결과와 유사함을 보였다. 29개의 유전자를 다시 4개 부위의 생체 조직에서 추출한 RNA를 이용해 real-time PCR 방법으로 분석한 결과 TS (thymi- dlyate synthase), TE (tropoelastin), RAD52(similar RAD52 motifcontaining protein 1), unknown gene), MLC2 (myosin light 2, regulatory cardiac, slow), TXNIP (thioredoxin-interating protein) 6개의 유전자만이 다른 부위에 비해 사태 부위에서 현저한 발현의 차이를 나타냈다. 결론적으로 본 연구를 통해 소 부위별 근육을 구분할 수 있는 과학적 기술의 토대를 확립하였다.

자기공명(M.R.)진단법의 특징 및 그 영상기전의 이해 (Characteristics of Magnetic Resonance(M.R.) and Comprehension of its Imaging Mechanism)

  • 장재천;황미수;김선용
    • Journal of Yeungnam Medical Science
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    • 제4권1호
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    • pp.1-15
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    • 1987
  • Magnetic Resonance (M.R.) is rapidly emerging technique that provides high quality images and potentially provides much more diagnostic information than do conventional imaging modalities. M.R.I. is conceptually quite different from currently used imaging methods. The complex nature of M.R.I. allows a great deal of flexibility in image product ion and available information, and key points are as follows. 1. M.R.I. offers a non-invasive technique with which to gene rate in vivo human images without ionizing radiation and with no known adverse biological effects. 2. Imaging mechanism of M.R.I. is quite different from conventional imaging modality and for more accurate diagnostic application, It is necessary for physician to understand imaging mechanism of M.R.I. 3. M.R. makes available basic chemical parameters that may provide to be useful for diagnostic medical imaging and more specific pathophysiologic information which are not available by alternate techniques. 4. M.R. can be produced by number of different methods. This flexibility allows the imaging technique to be applicated for particular clinical purpose. Multiplanar and three dimensional imaging may extend the imaging process beyond the single section available with current CT. 5. Future directions include efforts to; a. Further development of hard ware b. More fasternning scan time c. Respiratory and cardiac gated imaging d. Imaging of additional nuclei except hydrogen e. Further development of contrast media f. M.R. in vivo spectroscopy g. Real time M.R. imaging.

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